Transcriptional Changes Underlying Elemental Stoichiometry Shifts in a Marine Heterotrophic Bacterium
Identifieur interne : 000529 ( Pmc/Corpus ); précédent : 000528; suivant : 000530Transcriptional Changes Underlying Elemental Stoichiometry Shifts in a Marine Heterotrophic Bacterium
Auteurs : Leong-Keat Chan ; Ryan J. Newton ; Shalabh Sharma ; Christa B. Smith ; Pratibha Rayapati ; Alexander J. Limardo ; Christof Meile ; Mary Ann MoranSource :
- Frontiers in Microbiology [ 1664-302X ] ; 2012.
Abstract
Marine bacteria drive the biogeochemical processing of oceanic dissolved organic carbon (DOC), a 750-Tg C reservoir that is a critical component of the global C cycle. Catabolism of DOC is thought to be regulated by the biomass composition of heterotrophic bacteria, as cells maintain a C:N:P ratio of ∼50:10:1 during DOC processing. Yet a complicating factor in stoichiometry-based analyses is that bacteria can change the C:N:P ratio of their biomass in response to resource composition. We investigated the physiological mechanisms of resource-driven shifts in biomass stoichiometry in continuous cultures of the marine heterotrophic bacterium
Url:
DOI: 10.3389/fmicb.2012.00159
PubMed: 22783226
PubMed Central: 3390766
Links to Exploration step
PMC:3390766Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Transcriptional Changes Underlying Elemental Stoichiometry Shifts in a Marine Heterotrophic Bacterium</title><author><name sortKey="Chan, Leong Keat" sort="Chan, Leong Keat" uniqKey="Chan L" first="Leong-Keat" last="Chan">Leong-Keat Chan</name><affiliation><nlm:aff id="aff1"><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff></affiliation></author><author><name sortKey="Newton, Ryan J" sort="Newton, Ryan J" uniqKey="Newton R" first="Ryan J." last="Newton">Ryan J. Newton</name><affiliation><nlm:aff id="aff1"><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff2"><institution>Great Lakes WATER Institute, University of Wisconsin-Milwaukee</institution><country>Milwaukee, WI, USA</country></nlm:aff></affiliation></author><author><name sortKey="Sharma, Shalabh" sort="Sharma, Shalabh" uniqKey="Sharma S" first="Shalabh" last="Sharma">Shalabh Sharma</name><affiliation><nlm:aff id="aff1"><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff></affiliation></author><author><name sortKey="Smith, Christa B" sort="Smith, Christa B" uniqKey="Smith C" first="Christa B." last="Smith">Christa B. Smith</name><affiliation><nlm:aff id="aff1"><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff></affiliation></author><author><name sortKey="Rayapati, Pratibha" sort="Rayapati, Pratibha" uniqKey="Rayapati P" first="Pratibha" last="Rayapati">Pratibha Rayapati</name><affiliation><nlm:aff id="aff1"><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff></affiliation></author><author><name sortKey="Limardo, Alexander J" sort="Limardo, Alexander J" uniqKey="Limardo A" first="Alexander J." last="Limardo">Alexander J. Limardo</name><affiliation><nlm:aff id="aff1"><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff></affiliation></author><author><name sortKey="Meile, Christof" sort="Meile, Christof" uniqKey="Meile C" first="Christof" last="Meile">Christof Meile</name><affiliation><nlm:aff id="aff1"><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff></affiliation></author><author><name sortKey="Moran, Mary Ann" sort="Moran, Mary Ann" uniqKey="Moran M" first="Mary Ann" last="Moran">Mary Ann Moran</name><affiliation><nlm:aff id="aff1"><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22783226</idno><idno type="pmc">3390766</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390766</idno><idno type="RBID">PMC:3390766</idno><idno type="doi">10.3389/fmicb.2012.00159</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000529</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Transcriptional Changes Underlying Elemental Stoichiometry Shifts in a Marine Heterotrophic Bacterium</title><author><name sortKey="Chan, Leong Keat" sort="Chan, Leong Keat" uniqKey="Chan L" first="Leong-Keat" last="Chan">Leong-Keat Chan</name><affiliation><nlm:aff id="aff1"><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff></affiliation></author><author><name sortKey="Newton, Ryan J" sort="Newton, Ryan J" uniqKey="Newton R" first="Ryan J." last="Newton">Ryan J. Newton</name><affiliation><nlm:aff id="aff1"><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff2"><institution>Great Lakes WATER Institute, University of Wisconsin-Milwaukee</institution><country>Milwaukee, WI, USA</country></nlm:aff></affiliation></author><author><name sortKey="Sharma, Shalabh" sort="Sharma, Shalabh" uniqKey="Sharma S" first="Shalabh" last="Sharma">Shalabh Sharma</name><affiliation><nlm:aff id="aff1"><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff></affiliation></author><author><name sortKey="Smith, Christa B" sort="Smith, Christa B" uniqKey="Smith C" first="Christa B." last="Smith">Christa B. Smith</name><affiliation><nlm:aff id="aff1"><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff></affiliation></author><author><name sortKey="Rayapati, Pratibha" sort="Rayapati, Pratibha" uniqKey="Rayapati P" first="Pratibha" last="Rayapati">Pratibha Rayapati</name><affiliation><nlm:aff id="aff1"><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff></affiliation></author><author><name sortKey="Limardo, Alexander J" sort="Limardo, Alexander J" uniqKey="Limardo A" first="Alexander J." last="Limardo">Alexander J. Limardo</name><affiliation><nlm:aff id="aff1"><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff></affiliation></author><author><name sortKey="Meile, Christof" sort="Meile, Christof" uniqKey="Meile C" first="Christof" last="Meile">Christof Meile</name><affiliation><nlm:aff id="aff1"><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff></affiliation></author><author><name sortKey="Moran, Mary Ann" sort="Moran, Mary Ann" uniqKey="Moran M" first="Mary Ann" last="Moran">Mary Ann Moran</name><affiliation><nlm:aff id="aff1"><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff></affiliation></author></analytic><series><title level="j">Frontiers in Microbiology</title><idno type="eISSN">1664-302X</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Marine bacteria drive the biogeochemical processing of oceanic dissolved organic carbon (DOC), a 750-Tg C reservoir that is a critical component of the global C cycle. Catabolism of DOC is thought to be regulated by the biomass composition of heterotrophic bacteria, as cells maintain a C:N:P ratio of ∼50:10:1 during DOC processing. Yet a complicating factor in stoichiometry-based analyses is that bacteria can change the C:N:P ratio of their biomass in response to resource composition. We investigated the physiological mechanisms of resource-driven shifts in biomass stoichiometry in continuous cultures of the marine heterotrophic bacterium <italic>Ruegeria pomeroyi</italic> (a member of the <italic>Roseobacter</italic> clade) under four element limitation regimes (C, N, P, and S). Microarray analysis indicated that the bacterium scavenged for alternate sources of the scarce element when cells were C-, N-, or P-limited; reworked the ratios of biomolecules when C- and P- limited; and exerted tighter control over import/export and cytoplasmic pools when N-limited. Under S limitation, a scenario not existing naturally for surface ocean microbes, stress responses dominated transcriptional changes. Resource-driven changes in C:N ratios of up to 2.5-fold and in C:P ratios of up to sixfold were measured in <italic>R. pomeroyi</italic> biomass. These changes were best explained if the C and P content of the cells was flexible in the face of shifting resources but N content was not, achieved through the net balance of different transcriptional strategies. The cellular-level metabolic trade-offs that govern biomass stoichiometry in <italic>R. pomeroyi</italic> may have implications for global carbon cycling if extendable to other heterotrophic bacteria. Strong homeostatic responses to N limitation by marine bacteria would intensify competition with autotrophs. Modification of cellular inventories in C- and P-limited heterotrophs would vary the elemental ratio of particulate organic matter sequestered in the deep ocean.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Anderson, A J" uniqKey="Anderson A">A. J. Anderson</name></author><author><name sortKey="Dawes, E A" uniqKey="Dawes E">E. A. Dawes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Azam, F" uniqKey="Azam F">F. Azam</name></author><author><name sortKey="Fenchel, T" uniqKey="Fenchel T">T. Fenchel</name></author><author><name sortKey="Field, J G" uniqKey="Field J">J. G. Field</name></author><author><name sortKey="Gray, J S" uniqKey="Gray J">J. S. Gray</name></author><author><name sortKey="Meyer Reil, L A" uniqKey="Meyer Reil L">L. A. Meyer-Reil</name></author><author><name sortKey="Thingstad, F" uniqKey="Thingstad F">F. Thingstad</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bradford, M M" uniqKey="Bradford M">M. M. Bradford</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brazma, A" uniqKey="Brazma A">A. Brazma</name></author><author><name sortKey="Hingamp, P" uniqKey="Hingamp P">P. Hingamp</name></author><author><name sortKey="Quackenbush, J" uniqKey="Quackenbush J">J. Quackenbush</name></author><author><name sortKey="Sherlock, G" uniqKey="Sherlock G">G. Sherlock</name></author><author><name sortKey="Spellman, P" uniqKey="Spellman P">P. Spellman</name></author><author><name sortKey="Stoeckert, C" uniqKey="Stoeckert C">C. Stoeckert</name></author><author><name sortKey="Aach, J" uniqKey="Aach J">J. Aach</name></author><author><name sortKey="Ansorge, W" uniqKey="Ansorge W">W. Ansorge</name></author><author><name sortKey="Ball, C A" uniqKey="Ball C">C. A. Ball</name></author><author><name sortKey="Causton, H C" uniqKey="Causton H">H. C. Causton</name></author><author><name sortKey="Gaasterland, T" uniqKey="Gaasterland T">T. Gaasterland</name></author><author><name sortKey="Glenisson, P" uniqKey="Glenisson P">P. Glenisson</name></author><author><name sortKey="Holstege, F C" uniqKey="Holstege F">F. C. Holstege</name></author><author><name sortKey="Kim, I F" uniqKey="Kim I">I. F. Kim</name></author><author><name sortKey="Markowitz, V" uniqKey="Markowitz V">V. Markowitz</name></author><author><name sortKey="Matese, J C" uniqKey="Matese J">J. C. Matese</name></author><author><name sortKey="Parkinson, H" uniqKey="Parkinson H">H. Parkinson</name></author><author><name sortKey="Robinson, A" uniqKey="Robinson A">A. Robinson</name></author><author><name sortKey="Sarkans, U" uniqKey="Sarkans U">U. Sarkans</name></author><author><name sortKey="Schulze Kremer, S" uniqKey="Schulze Kremer S">S. Schulze-Kremer</name></author><author><name sortKey="Stewart, J" uniqKey="Stewart J">J. Stewart</name></author><author><name sortKey="Taylor, R" uniqKey="Taylor R">R. Taylor</name></author><author><name sortKey="Vilo, J" uniqKey="Vilo J">J. Vilo</name></author><author><name sortKey="Vingron, M" uniqKey="Vingron M">M. Vingron</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brown, M R" uniqKey="Brown M">M. R. Brown</name></author><author><name sortKey="Kornberg, A" uniqKey="Kornberg A">A. Kornberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Burgmann, H" uniqKey="Burgmann H">H. Bürgmann</name></author><author><name sortKey="Howard, E C" uniqKey="Howard E">E. C. Howard</name></author><author><name sortKey="Ye, W" uniqKey="Ye W">W. Ye</name></author><author><name sortKey="Sun, F" uniqKey="Sun F">F. Sun</name></author><author><name sortKey="Sun, S" uniqKey="Sun S">S. Sun</name></author><author><name sortKey="Napierala, S" uniqKey="Napierala S">S. Napierala</name></author><author><name sortKey="Moran, M A" uniqKey="Moran M">M. A. Moran</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cherrier, J" uniqKey="Cherrier J">J. Cherrier</name></author><author><name sortKey="Bauer, J E" uniqKey="Bauer J">J. E. Bauer</name></author><author><name sortKey="Druffel, E R M" uniqKey="Druffel E">E. R. M. Druffel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cotner, J B" uniqKey="Cotner J">J. B. Cotner</name></author><author><name sortKey="Ammerman, J W" uniqKey="Ammerman J">J. W. Ammerman</name></author><author><name sortKey="Peele, E R" uniqKey="Peele E">E. R. Peele</name></author><author><name sortKey="Bentzen, E" uniqKey="Bentzen E">E. Bentzen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cotner, J B" uniqKey="Cotner J">J. B. Cotner</name></author><author><name sortKey="Hall, E K" uniqKey="Hall E">E. K. Hall</name></author><author><name sortKey="Scott, J T" uniqKey="Scott J">J. T. Scott</name></author><author><name sortKey="Heldal, M" uniqKey="Heldal M">M. Heldal</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dawes, E A" uniqKey="Dawes E">E. A. Dawes</name></author><author><name sortKey="Senior, P J" uniqKey="Senior P">P. J. Senior</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Del Giorgio, P A" uniqKey="Del Giorgio P">P. A. del Giorgio</name></author><author><name sortKey="Cole, J J" uniqKey="Cole J">J. J. Cole</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ducklow, H W" uniqKey="Ducklow H">H. W. Ducklow</name></author><author><name sortKey="Hill, S M" uniqKey="Hill S">S. M. Hill</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Elser, J J" uniqKey="Elser J">J. J. Elser</name></author><author><name sortKey="Dobberfuhl, D R" uniqKey="Dobberfuhl D">D. R. Dobberfuhl</name></author><author><name sortKey="Mackay, N A" uniqKey="Mackay N">N. A. MacKay</name></author><author><name sortKey="Schampel, J H" uniqKey="Schampel J">J. H. Schampel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Elser, J J" uniqKey="Elser J">J. J. Elser</name></author><author><name sortKey="Stabler, L B" uniqKey="Stabler L">L. B. Stabler</name></author><author><name sortKey="Hassett, R P" uniqKey="Hassett R">R. P. Hassett</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fagerbakke, K M" uniqKey="Fagerbakke K">K. M. Fagerbakke</name></author><author><name sortKey="Heldal, M" uniqKey="Heldal M">M. Heldal</name></author><author><name sortKey="Norland, S" uniqKey="Norland S">S. Norland</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ferenci, T" uniqKey="Ferenci T">T. Ferenci</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Franklin, O" uniqKey="Franklin O">O. Franklin</name></author><author><name sortKey="Hall, E K" uniqKey="Hall E">E. K. Hall</name></author><author><name sortKey="Kaiser, C" uniqKey="Kaiser C">C. Kaiser</name></author><author><name sortKey="Richter, A" uniqKey="Richter A">A. Richter</name></author><author><name sortKey="Battin, T" uniqKey="Battin T">T. Battin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fuser, G" uniqKey="Fuser G">G. Füser</name></author><author><name sortKey="Steinbuchel, A" uniqKey="Steinbuchel A">A. Steinbüchel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gangaiah, D" uniqKey="Gangaiah D">D. Gangaiah</name></author><author><name sortKey="Liu, Z" uniqKey="Liu Z">Z. Liu</name></author><author><name sortKey="Arcos, J" uniqKey="Arcos J">J. Arcos</name></author><author><name sortKey="Kassem, I I" uniqKey="Kassem I">I. I. Kassem</name></author><author><name sortKey="Sanad, Y" uniqKey="Sanad Y">Y. Sanad</name></author><author><name sortKey="Torrelles, J B" uniqKey="Torrelles J">J. B. Torrelles</name></author><author><name sortKey="Rajashekara, G" uniqKey="Rajashekara G">G. Rajashekara</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gao, J L" uniqKey="Gao J">J. L. Gao</name></author><author><name sortKey="Weissenmayer, B" uniqKey="Weissenmayer B">B. Weissenmayer</name></author><author><name sortKey="Taylor, A M" uniqKey="Taylor A">A. M. Taylor</name></author><author><name sortKey="Thomas Oates, J" uniqKey="Thomas Oates J">J. Thomas-Oates</name></author><author><name sortKey="L Pez Lara, I M" uniqKey="L Pez Lara I">I. M. López-Lara</name></author><author><name sortKey="Geiger, O" uniqKey="Geiger O">O. Geiger</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Geider, R J" uniqKey="Geider R">R. J. Geider</name></author><author><name sortKey="La Roche, J" uniqKey="La Roche J">J. La Roche</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goldman, J C" uniqKey="Goldman J">J. C. Goldman</name></author><author><name sortKey="Caron, D A" uniqKey="Caron D">D. A. Caron</name></author><author><name sortKey="Dennett, M R" uniqKey="Dennett M">M. R. Dennett</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gonzalez, J M" uniqKey="Gonzalez J">J. M. González</name></author><author><name sortKey="Covert, J S" uniqKey="Covert J">J. S. Covert</name></author><author><name sortKey="Whitman, W B" uniqKey="Whitman W">W. B. Whitman</name></author><author><name sortKey="Henriksen, J R" uniqKey="Henriksen J">J. R. Henriksen</name></author><author><name sortKey="Mayer, F" uniqKey="Mayer F">F. Mayer</name></author><author><name sortKey="Scharf, B" uniqKey="Scharf B">B. Scharf</name></author><author><name sortKey="Schmitt, R" uniqKey="Schmitt R">R. Schmitt</name></author><author><name sortKey="Buchan, A" uniqKey="Buchan A">A. Buchan</name></author><author><name sortKey="Fuhrman, J A" uniqKey="Fuhrman J">J. A. Fuhrman</name></author><author><name sortKey="Kiene, R P" uniqKey="Kiene R">R. P. Kiene</name></author><author><name sortKey="Moran, M A" uniqKey="Moran M">M. A. Moran</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goyal, S" uniqKey="Goyal S">S. Goyal</name></author><author><name sortKey="Yuan, J" uniqKey="Yuan J">J. Yuan</name></author><author><name sortKey="Chen, T" uniqKey="Chen T">T. Chen</name></author><author><name sortKey="Rabinowitz, J D" uniqKey="Rabinowitz J">J. D. Rabinowitz</name></author><author><name sortKey="Wingreen, N S" uniqKey="Wingreen N">N. S. Wingreen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gundersen, K" uniqKey="Gundersen K">K. Gundersen</name></author><author><name sortKey="Heldal, M" uniqKey="Heldal M">M. Heldal</name></author><author><name sortKey="Purdie, D A" uniqKey="Purdie D">D. A. Purdie</name></author><author><name sortKey="Knap, A H" uniqKey="Knap A">A. H. Knap</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gyaneshwar, P" uniqKey="Gyaneshwar P">P. Gyaneshwar</name></author><author><name sortKey="Paliy, O" uniqKey="Paliy O">O. Paliy</name></author><author><name sortKey="Mcauliffe, J" uniqKey="Mcauliffe J">J. McAuliffe</name></author><author><name sortKey="Popham, D L" uniqKey="Popham D">D. L. Popham</name></author><author><name sortKey="Jordan, M I" uniqKey="Jordan M">M. I. Jordan</name></author><author><name sortKey="Kustu, S" uniqKey="Kustu S">S. Kustu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hall, E K" uniqKey="Hall E">E. K. Hall</name></author><author><name sortKey="Maixner, F" uniqKey="Maixner F">F. Maixner</name></author><author><name sortKey="Franklin, O" uniqKey="Franklin O">O. Franklin</name></author><author><name sortKey="Daims, H" uniqKey="Daims H">H. Daims</name></author><author><name sortKey="Richter, A" uniqKey="Richter A">A. Richter</name></author><author><name sortKey="Battin, T" uniqKey="Battin T">T. Battin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Harder, W" uniqKey="Harder W">W. Harder</name></author><author><name sortKey="Dijkhuizen, L" uniqKey="Dijkhuizen L">L. Dijkhuizen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hendrickson, E L" uniqKey="Hendrickson E">E. L. Hendrickson</name></author><author><name sortKey="Liu, Y" uniqKey="Liu Y">Y. Liu</name></author><author><name sortKey="Rosas Sandoval, G" uniqKey="Rosas Sandoval G">G. Rosas-Sandoval</name></author><author><name sortKey="Porat, I" uniqKey="Porat I">I. Porat</name></author><author><name sortKey="Soll, D" uniqKey="Soll D">D. Söll</name></author><author><name sortKey="Whitman, W B" uniqKey="Whitman W">W. B. Whitman</name></author><author><name sortKey="Leigh, J A" uniqKey="Leigh J">J. A. Leigh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Henriksen, J R" uniqKey="Henriksen J">J. R. Henriksen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hessen, D O" uniqKey="Hessen D">D. O. Hessen</name></author><author><name sortKey="Agren, G I" uniqKey="Agren G">G. I. Agren</name></author><author><name sortKey="Anderson, T R" uniqKey="Anderson T">T. R. Anderson</name></author><author><name sortKey="Elser, J J" uniqKey="Elser J">J. J. Elser</name></author><author><name sortKey="De Ruiter, P C" uniqKey="De Ruiter P">P. C. De Ruiter</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ikeda, T P" uniqKey="Ikeda T">T. P. Ikeda</name></author><author><name sortKey="Shauger, A E" uniqKey="Shauger A">A. E. Shauger</name></author><author><name sortKey="Kustu, S" uniqKey="Kustu S">S. Kustu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ishige, K" uniqKey="Ishige K">K. Ishige</name></author><author><name sortKey="Noguchi, T" uniqKey="Noguchi T">T. Noguchi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kirchman, D" uniqKey="Kirchman D">D. Kirchman</name></author><author><name sortKey="Rich, J" uniqKey="Rich J">J. Rich</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kirchman, D L" uniqKey="Kirchman D">D. L. Kirchman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kornberg, A" uniqKey="Kornberg A">A. Kornberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kranz, R G" uniqKey="Kranz R">R. G. Kranz</name></author><author><name sortKey="Gabbert, K K" uniqKey="Gabbert K">K. K. Gabbert</name></author><author><name sortKey="Locke, T A" uniqKey="Locke T">T. A. Locke</name></author><author><name sortKey="Madigan, M T" uniqKey="Madigan M">M. T. Madigan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kulaev, I S" uniqKey="Kulaev I">I. S. Kulaev</name></author><author><name sortKey="Bobyk, M A" uniqKey="Bobyk M">M. A. Bobyk</name></author><author><name sortKey="Nikolaev, N N" uniqKey="Nikolaev N">N. N. Nikolaev</name></author><author><name sortKey="Sergeev, N S" uniqKey="Sergeev N">N. S. Sergeev</name></author><author><name sortKey="Uryson, S O" uniqKey="Uryson S">S. O. Uryson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Loladze, I" uniqKey="Loladze I">I. Loladze</name></author><author><name sortKey="Elser, J J" uniqKey="Elser J">J. J. Elser</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Martinussen, I" uniqKey="Martinussen I">I. Martinussen</name></author><author><name sortKey="Thingstad, T F" uniqKey="Thingstad T">T. F. Thingstad</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Matsen, F A" uniqKey="Matsen F">F. A. Matsen</name></author><author><name sortKey="Kodner, R B" uniqKey="Kodner R">R. B. Kodner</name></author><author><name sortKey="Armbrust, E V" uniqKey="Armbrust E">E. V. Armbrust</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Metcalf, W W" uniqKey="Metcalf W">W. W. Metcalf</name></author><author><name sortKey="Wanner, B L" uniqKey="Wanner B">B. L. Wanner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Moran, M A" uniqKey="Moran M">M. A. Moran</name></author><author><name sortKey="Buchan, A" uniqKey="Buchan A">A. Buchan</name></author><author><name sortKey="Gonzalez, J M" uniqKey="Gonzalez J">J. M. González</name></author><author><name sortKey="Heidelberg, J F" uniqKey="Heidelberg J">J. F. Heidelberg</name></author><author><name sortKey="Whitman, W B" uniqKey="Whitman W">W. B. Whitman</name></author><author><name sortKey="Kiene, R P" uniqKey="Kiene R">R. P. Kiene</name></author><author><name sortKey="Henriksen, J R" uniqKey="Henriksen J">J. R. Henriksen</name></author><author><name sortKey="King, G M" uniqKey="King G">G. M. King</name></author><author><name sortKey="Belas, R" uniqKey="Belas R">R. Belas</name></author><author><name sortKey="Fuqua, C" uniqKey="Fuqua C">C. Fuqua</name></author><author><name sortKey="Brinkac, L" uniqKey="Brinkac L">L. Brinkac</name></author><author><name sortKey="Lewis, M" uniqKey="Lewis M">M. Lewis</name></author><author><name sortKey="Johri, S" uniqKey="Johri S">S. Johri</name></author><author><name sortKey="Weaver, B" uniqKey="Weaver B">B. Weaver</name></author><author><name sortKey="Pai, G" uniqKey="Pai G">G. Pai</name></author><author><name sortKey="Eisen, J A" uniqKey="Eisen J">J. A. Eisen</name></author><author><name sortKey="Rahe, E" uniqKey="Rahe E">E. Rahe</name></author><author><name sortKey="Sheldon, W M" uniqKey="Sheldon W">W. M. Sheldon</name></author><author><name sortKey="Ye, W" uniqKey="Ye W">W. Ye</name></author><author><name sortKey="Miller, T R" uniqKey="Miller T">T. R. Miller</name></author><author><name sortKey="Carlton, J" uniqKey="Carlton J">J. Carlton</name></author><author><name sortKey="Rasko, D A" uniqKey="Rasko D">D. A. Rasko</name></author><author><name sortKey="Paulsen, I T" uniqKey="Paulsen I">I. T. Paulsen</name></author><author><name sortKey="Ren, Q" uniqKey="Ren Q">Q. Ren</name></author><author><name sortKey="Daugherty, S C" uniqKey="Daugherty S">S. C. Daugherty</name></author><author><name sortKey="Deboy, R T" uniqKey="Deboy R">R. T. Deboy</name></author><author><name sortKey="Dodson, R J" uniqKey="Dodson R">R. J. Dodson</name></author><author><name sortKey="Durkin, A S" uniqKey="Durkin A">A. S. Durkin</name></author><author><name sortKey="Madupu, R" uniqKey="Madupu R">R. Madupu</name></author><author><name sortKey="Nelson, W C" uniqKey="Nelson W">W. C. Nelson</name></author><author><name sortKey="Sullivan, S A" uniqKey="Sullivan S">S. A. Sullivan</name></author><author><name sortKey="Rosovitz, M J" uniqKey="Rosovitz M">M. J. Rosovitz</name></author><author><name sortKey="Haft, D H" uniqKey="Haft D">D. H. Haft</name></author><author><name sortKey="Selengut, J" uniqKey="Selengut J">J. Selengut</name></author><author><name sortKey="Ward, N" uniqKey="Ward N">N. Ward</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Moran, M A" uniqKey="Moran M">M. A. Moran</name></author><author><name sortKey="Reisch, C R" uniqKey="Reisch C">C. R. Reisch</name></author><author><name sortKey="Kiene, R P" uniqKey="Kiene R">R. P. Kiene</name></author><author><name sortKey="Whitman, W B" uniqKey="Whitman W">W. B. Whitman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nahalka, J" uniqKey="Nahalka J">J. Nahálka</name></author><author><name sortKey="P Toprst, V" uniqKey="P Toprst V">V. Pätoprstý</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Newton, R J" uniqKey="Newton R">R. J. Newton</name></author><author><name sortKey="Griffin, L E" uniqKey="Griffin L">L. E. Griffin</name></author><author><name sortKey="Bowles, K M" uniqKey="Bowles K">K. M. Bowles</name></author><author><name sortKey="Meile, C" uniqKey="Meile C">C. Meile</name></author><author><name sortKey="Gifford, S" uniqKey="Gifford S">S. Gifford</name></author><author><name sortKey="Givens, C E" uniqKey="Givens C">C. E. Givens</name></author><author><name sortKey="Howard, E C" uniqKey="Howard E">E. C. Howard</name></author><author><name sortKey="King, E" uniqKey="King E">E. King</name></author><author><name sortKey="Oakley, C A" uniqKey="Oakley C">C. A. Oakley</name></author><author><name sortKey="Reisch, C R" uniqKey="Reisch C">C. R. Reisch</name></author><author><name sortKey="Rinta Kanto, J M" uniqKey="Rinta Kanto J">J. M. Rinta-Kanto</name></author><author><name sortKey="Sharma, S" uniqKey="Sharma S">S. Sharma</name></author><author><name sortKey="Sun, S" uniqKey="Sun S">S. Sun</name></author><author><name sortKey="Varaljay, V" uniqKey="Varaljay V">V. Varaljay</name></author><author><name sortKey="Vila Costa, M" uniqKey="Vila Costa M">M. Vila-Costa</name></author><author><name sortKey="Westrich, J R" uniqKey="Westrich J">J. R. Westrich</name></author><author><name sortKey="Moran, M A" uniqKey="Moran M">M. A. Moran</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Obernosterer, I" uniqKey="Obernosterer I">I. Obernosterer</name></author><author><name sortKey="Kawasaki, N" uniqKey="Kawasaki N">N. Kawasaki</name></author><author><name sortKey="Benner, R" uniqKey="Benner R">R. Benner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Parker, G F" uniqKey="Parker G">G. F. Parker</name></author><author><name sortKey="Higgins, T P" uniqKey="Higgins T">T. P. Higgins</name></author><author><name sortKey="Hawkes, T" uniqKey="Hawkes T">T. Hawkes</name></author><author><name sortKey="Robson, R L" uniqKey="Robson R">R. L. Robson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pomeroy, L R" uniqKey="Pomeroy L">L. R. Pomeroy</name></author><author><name sortKey="Sheldon, J E" uniqKey="Sheldon J">J. E. Sheldon</name></author><author><name sortKey="Sheldon, W M J" uniqKey="Sheldon W">W. M. J. Sheldon</name></author><author><name sortKey="Peters, F" uniqKey="Peters F">F. Peters</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Poretsky, R S" uniqKey="Poretsky R">R. S. Poretsky</name></author><author><name sortKey="Gifford, S M" uniqKey="Gifford S">S. M. Gifford</name></author><author><name sortKey="Rinta Kanto, J M" uniqKey="Rinta Kanto J">J. M. Rinta-Kanto</name></author><author><name sortKey="Vila Costa, M" uniqKey="Vila Costa M">M. Vila-Costa</name></author><author><name sortKey="Moran, M A" uniqKey="Moran M">M. A. Moran</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Redfield, A C" uniqKey="Redfield A">A. C. Redfield</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rinta Kanto, J M" uniqKey="Rinta Kanto J">J. M. Rinta-Kanto</name></author><author><name sortKey="Burgmann, H" uniqKey="Burgmann H">H. Bürgmann</name></author><author><name sortKey="Gifford, S M" uniqKey="Gifford S">S. M. Gifford</name></author><author><name sortKey="Sun, S" uniqKey="Sun S">S. Sun</name></author><author><name sortKey="Sharma, S" uniqKey="Sharma S">S. Sharma</name></author><author><name sortKey="Del Valle, D A" uniqKey="Del Valle D">D. A. del Valle</name></author><author><name sortKey="Kiene, R P" uniqKey="Kiene R">R. P. Kiene</name></author><author><name sortKey="Moran, M A" uniqKey="Moran M">M. A. Moran</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rivkin, R B" uniqKey="Rivkin R">R. B. Rivkin</name></author><author><name sortKey="Anderson, M R" uniqKey="Anderson M">M. R. Anderson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rusch, D B" uniqKey="Rusch D">D. B. Rusch</name></author><author><name sortKey="Halpern, A L" uniqKey="Halpern A">A. L. Halpern</name></author><author><name sortKey="Sutton, G" uniqKey="Sutton G">G. Sutton</name></author><author><name sortKey="Heidelberg, K B" uniqKey="Heidelberg K">K. B. Heidelberg</name></author><author><name sortKey="Williamson, S" uniqKey="Williamson S">S. Williamson</name></author><author><name sortKey="Yooseph, S" uniqKey="Yooseph S">S. Yooseph</name></author><author><name sortKey="Wu, D" uniqKey="Wu D">D. Wu</name></author><author><name sortKey="Eisen, J A" uniqKey="Eisen J">J. A. Eisen</name></author><author><name sortKey="Hoffman, J M" uniqKey="Hoffman J">J. M. Hoffman</name></author><author><name sortKey="Remington, K" uniqKey="Remington K">K. Remington</name></author><author><name sortKey="Beeson, K" uniqKey="Beeson K">K. Beeson</name></author><author><name sortKey="Tran, B" uniqKey="Tran B">B. Tran</name></author><author><name sortKey="Smith, H" uniqKey="Smith H">H. Smith</name></author><author><name sortKey="Baden Tillson, H" uniqKey="Baden Tillson H">H. Baden-Tillson</name></author><author><name sortKey="Stewart, C" uniqKey="Stewart C">C. Stewart</name></author><author><name sortKey="Thorpe, J" uniqKey="Thorpe J">J. Thorpe</name></author><author><name sortKey="Freeman, J" uniqKey="Freeman J">J. Freeman</name></author><author><name sortKey="Andrews Pfannkoch, C" uniqKey="Andrews Pfannkoch C">C. Andrews-Pfannkoch</name></author><author><name sortKey="Venter, J E" uniqKey="Venter J">J. E. Venter</name></author><author><name sortKey="Li, K" uniqKey="Li K">K. Li</name></author><author><name sortKey="Kravitz, S" uniqKey="Kravitz S">S. Kravitz</name></author><author><name sortKey="Heidelberg, J F" uniqKey="Heidelberg J">J. F. Heidelberg</name></author><author><name sortKey="Utterback, T" uniqKey="Utterback T">T. Utterback</name></author><author><name sortKey="Rogers, Y H" uniqKey="Rogers Y">Y. H. Rogers</name></author><author><name sortKey="Falc N, L I" uniqKey="Falc N L">L. I. Falcón</name></author><author><name sortKey="Souza, V" uniqKey="Souza V">V. Souza</name></author><author><name sortKey="Bonilla Rosso, G" uniqKey="Bonilla Rosso G">G. Bonilla-Rosso</name></author><author><name sortKey="Eguiarte, L E" uniqKey="Eguiarte L">L. E. Eguiarte</name></author><author><name sortKey="Karl, D M" uniqKey="Karl D">D. M. Karl</name></author><author><name sortKey="Sathyendranath, S" uniqKey="Sathyendranath S">S. Sathyendranath</name></author><author><name sortKey="Platt, T" uniqKey="Platt T">T. Platt</name></author><author><name sortKey="Bermingham, E" uniqKey="Bermingham E">E. Bermingham</name></author><author><name sortKey="Gallardo, V" uniqKey="Gallardo V">V. Gallardo</name></author><author><name sortKey="Tamayo Castillo, G" uniqKey="Tamayo Castillo G">G. Tamayo-Castillo</name></author><author><name sortKey="Ferrari, M R" uniqKey="Ferrari M">M. R. Ferrari</name></author><author><name sortKey="Strausberg, R L" uniqKey="Strausberg R">R. L. Strausberg</name></author><author><name sortKey="Nealson, K" uniqKey="Nealson K">K. Nealson</name></author><author><name sortKey="Friedman, R" uniqKey="Friedman R">R. Friedman</name></author><author><name sortKey="Frazier, M" uniqKey="Frazier M">M. Frazier</name></author><author><name sortKey="Venter, J C" uniqKey="Venter J">J. C. Venter</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Saeed, A I" uniqKey="Saeed A">A. I. Saeed</name></author><author><name sortKey="Bhagabati, N K" uniqKey="Bhagabati N">N. K. Bhagabati</name></author><author><name sortKey="Braisted, J C" uniqKey="Braisted J">J. C. Braisted</name></author><author><name sortKey="Liang, W" uniqKey="Liang W">W. Liang</name></author><author><name sortKey="Sharov, V" uniqKey="Sharov V">V. Sharov</name></author><author><name sortKey="Howe, E A" uniqKey="Howe E">E. A. Howe</name></author><author><name sortKey="Li, J" uniqKey="Li J">J. Li</name></author><author><name sortKey="Thiagarajan, M" uniqKey="Thiagarajan M">M. Thiagarajan</name></author><author><name sortKey="White, J A" uniqKey="White J">J. A. White</name></author><author><name sortKey="Quackenbush, J" uniqKey="Quackenbush J">J. Quackenbush</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Scott, J T" uniqKey="Scott J">J. T. Scott</name></author><author><name sortKey="Cotner, J B" uniqKey="Cotner J">J. B. Cotner</name></author><author><name sortKey="Lapara, T M" uniqKey="Lapara T">T. M. LaPara</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sebastian, M" uniqKey="Sebastian M">M. Sebastian</name></author><author><name sortKey="Ammerman, J W" uniqKey="Ammerman J">J. W. Ammerman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Solorzano, L" uniqKey="Solorzano L">L. Solorzano</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sterner, R W" uniqKey="Sterner R">R. W. Sterner</name></author><author><name sortKey="Andersen, T" uniqKey="Andersen T">T. Andersen</name></author><author><name sortKey="Elser, J J" uniqKey="Elser J">J. J. Elser</name></author><author><name sortKey="Hessen, D O" uniqKey="Hessen D">D. O. Hessen</name></author><author><name sortKey="Hood, J M" uniqKey="Hood J">J. M. Hood</name></author><author><name sortKey="Mccauley, E" uniqKey="Mccauley E">E. McCauley</name></author><author><name sortKey="Urabe, J" uniqKey="Urabe J">J. Urabe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Strickland, J D H" uniqKey="Strickland J">J. D. H. Strickland</name></author><author><name sortKey="Parsons, T R" uniqKey="Parsons T">T. R. Parsons</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tezuka, Y" uniqKey="Tezuka Y">Y. Tezuka</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thingstad, T F" uniqKey="Thingstad T">T. F. Thingstad</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thingstad, T F" uniqKey="Thingstad T">T. F. Thingstad</name></author><author><name sortKey="Bellerby, R G" uniqKey="Bellerby R">R. G. Bellerby</name></author><author><name sortKey="Bratbak, G" uniqKey="Bratbak G">G. Bratbak</name></author><author><name sortKey="B Rsheim, K Y" uniqKey="B Rsheim K">K. Y. Børsheim</name></author><author><name sortKey="Egge, J K" uniqKey="Egge J">J. K. Egge</name></author><author><name sortKey="Heldal, M" uniqKey="Heldal M">M. Heldal</name></author><author><name sortKey="Larsen, A" uniqKey="Larsen A">A. Larsen</name></author><author><name sortKey="Neill, C" uniqKey="Neill C">C. Neill</name></author><author><name sortKey="Nejstgaard, J" uniqKey="Nejstgaard J">J. Nejstgaard</name></author><author><name sortKey="Norland, S" uniqKey="Norland S">S. Norland</name></author><author><name sortKey="Sandaa, R A" uniqKey="Sandaa R">R.-A. Sandaa</name></author><author><name sortKey="Skjoldal, E F" uniqKey="Skjoldal E">E. F. Skjoldal</name></author><author><name sortKey="Tanaka, T" uniqKey="Tanaka T">T. Tanaka</name></author><author><name sortKey="Thyrhaug, R" uniqKey="Thyrhaug R">R. Thyrhaug</name></author><author><name sortKey="Topper, B" uniqKey="Topper B">B. Töpper</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thingstad, T F" uniqKey="Thingstad T">T. F. Thingstad</name></author><author><name sortKey="Krom, M D" uniqKey="Krom M">M. D. Krom</name></author><author><name sortKey="Mantoura, R F" uniqKey="Mantoura R">R. F. Mantoura</name></author><author><name sortKey="Flaten, G A" uniqKey="Flaten G">G. A. Flaten</name></author><author><name sortKey="Groom, S" uniqKey="Groom S">S. Groom</name></author><author><name sortKey="Herut, B" uniqKey="Herut B">B. Herut</name></author><author><name sortKey="Kress, N" uniqKey="Kress N">N. Kress</name></author><author><name sortKey="Law, C S" uniqKey="Law C">C. S. Law</name></author><author><name sortKey="Pasternak, A" uniqKey="Pasternak A">A. Pasternak</name></author><author><name sortKey="Pitta, P" uniqKey="Pitta P">P. Pitta</name></author><author><name sortKey="Psarra, S" uniqKey="Psarra S">S. Psarra</name></author><author><name sortKey="Rassoulzadegan, F" uniqKey="Rassoulzadegan F">F. Rassoulzadegan</name></author><author><name sortKey="Tanaka, T" uniqKey="Tanaka T">T. Tanaka</name></author><author><name sortKey="Tselepides, A" uniqKey="Tselepides A">A. Tselepides</name></author><author><name sortKey="Wassmann, P" uniqKey="Wassmann P">P. Wassmann</name></author><author><name sortKey="Woodward, E M S" uniqKey="Woodward E">E. M. S. Woodward</name></author><author><name sortKey="Wexels Riser, C" uniqKey="Wexels Riser C">C. Wexels Riser</name></author><author><name sortKey="Zodiatis, G" uniqKey="Zodiatis G">G. Zodiatis</name></author><author><name sortKey="Zohary, T" uniqKey="Zohary T">T. Zohary</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Torreton, J P" uniqKey="Torreton J">J. P. Torréton</name></author><author><name sortKey="Talbot, V" uniqKey="Talbot V">V. Talbot</name></author><author><name sortKey="Garcia, N" uniqKey="Garcia N">N. Garcia</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tusher, V G" uniqKey="Tusher V">V. G. Tusher</name></author><author><name sortKey="Tibshirani, R" uniqKey="Tibshirani R">R. Tibshirani</name></author><author><name sortKey="Chu, G" uniqKey="Chu G">G. Chu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Mooy, B A" uniqKey="Van Mooy B">B. A. Van Mooy</name></author><author><name sortKey="Fredricks, H F" uniqKey="Fredricks H">H. F. Fredricks</name></author><author><name sortKey="Pedler, B E" uniqKey="Pedler B">B. E. Pedler</name></author><author><name sortKey="Dyhrman, S T" uniqKey="Dyhrman S">S. T. Dyhrman</name></author><author><name sortKey="Karl, D M" uniqKey="Karl D">D. M. Karl</name></author><author><name sortKey="Koblizek, M" uniqKey="Koblizek M">M. Koblizek</name></author><author><name sortKey="Lomas, M W" uniqKey="Lomas M">M. W. Lomas</name></author><author><name sortKey="Mincer, T J" uniqKey="Mincer T">T. J. Mincer</name></author><author><name sortKey="Moore, L R" uniqKey="Moore L">L. R. Moore</name></author><author><name sortKey="Moutin, T" uniqKey="Moutin T">T. Moutin</name></author><author><name sortKey="Rappe, M S" uniqKey="Rappe M">M. S. Rappé</name></author><author><name sortKey="Webb, E A" uniqKey="Webb E">E. A. Webb</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Wambeke, F" uniqKey="Van Wambeke F">F. Van Wambeke</name></author><author><name sortKey="Christaki, U" uniqKey="Christaki U">U. Christaki</name></author><author><name sortKey="Giannakourou, A" uniqKey="Giannakourou A">A. Giannakourou</name></author><author><name sortKey="Moutin, T" uniqKey="Moutin T">T. Moutin</name></author><author><name sortKey="Souvemerzoglou, K" uniqKey="Souvemerzoglou K">K. Souvemerzoglou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vrede, K" uniqKey="Vrede K">K. Vrede</name></author><author><name sortKey="Heldal, M" uniqKey="Heldal M">M. Heldal</name></author><author><name sortKey="Norland, S" uniqKey="Norland S">S. Norland</name></author><author><name sortKey="Bratbak, G" uniqKey="Bratbak G">G. Bratbak</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vrljic, M" uniqKey="Vrljic M">M. Vrljic</name></author><author><name sortKey="Garg, J" uniqKey="Garg J">J. Garg</name></author><author><name sortKey="Bellmann, A" uniqKey="Bellmann A">A. Bellmann</name></author><author><name sortKey="Wachi, S" uniqKey="Wachi S">S. Wachi</name></author><author><name sortKey="Freudl, R" uniqKey="Freudl R">R. Freudl</name></author><author><name sortKey="Malecki, M J" uniqKey="Malecki M">M. J. Malecki</name></author><author><name sortKey="Sahm, H" uniqKey="Sahm H">H. Sahm</name></author><author><name sortKey="Kozina, V J" uniqKey="Kozina V">V. J. Kozina</name></author><author><name sortKey="Eggeling, L" uniqKey="Eggeling L">L. Eggeling</name></author><author><name sortKey="Saier, M H" uniqKey="Saier M">M. H. Saier</name></author><author><name sortKey="Eggeling, L" uniqKey="Eggeling L">L. Eggeling</name></author><author><name sortKey="Saier, M H" uniqKey="Saier M">M. H. Saier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wachi, M" uniqKey="Wachi M">M. Wachi</name></author><author><name sortKey="Doi, M" uniqKey="Doi M">M. Doi</name></author><author><name sortKey="Okada, Y" uniqKey="Okada Y">Y. Okada</name></author><author><name sortKey="Matsuhashi, M" uniqKey="Matsuhashi M">M. Matsuhashi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Walter, B" uniqKey="Walter B">B. Walter</name></author><author><name sortKey="H Nssler, E" uniqKey="H Nssler E">E. Hänssler</name></author><author><name sortKey="Kalinowski, J" uniqKey="Kalinowski J">J. Kalinowski</name></author><author><name sortKey="Burkovski, A" uniqKey="Burkovski A">A. Burkovski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Weber, T S" uniqKey="Weber T">T. S. Weber</name></author><author><name sortKey="Deutsch, C" uniqKey="Deutsch C">C. Deutsch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Weissenmayer, B" uniqKey="Weissenmayer B">B. Weissenmayer</name></author><author><name sortKey="Gao, J L" uniqKey="Gao J">J. L. Gao</name></author><author><name sortKey="L Pez Lara, I M" uniqKey="L Pez Lara I">I. M. López-Lara</name></author><author><name sortKey="Geiger, O" uniqKey="Geiger O">O. Geiger</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Whitman, W B" uniqKey="Whitman W">W. B. Whitman</name></author><author><name sortKey="Coleman, D C" uniqKey="Coleman D">D. C. Coleman</name></author><author><name sortKey="Wiebe, W J" uniqKey="Wiebe W">W. J. Wiebe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yooseph, S" uniqKey="Yooseph S">S. Yooseph</name></author><author><name sortKey="Sutton, G" uniqKey="Sutton G">G. Sutton</name></author><author><name sortKey="Rusch, D B" uniqKey="Rusch D">D. B. Rusch</name></author><author><name sortKey="Halpern, A L" uniqKey="Halpern A">A. L. Halpern</name></author><author><name sortKey="Williamson, S J" uniqKey="Williamson S">S. J. Williamson</name></author><author><name sortKey="Remington, K" uniqKey="Remington K">K. Remington</name></author><author><name sortKey="Eisen, J A" uniqKey="Eisen J">J. A. Eisen</name></author><author><name sortKey="Heidelberg, K B" uniqKey="Heidelberg K">K. B. Heidelberg</name></author><author><name sortKey="Manning, G" uniqKey="Manning G">G. Manning</name></author><author><name sortKey="Li, W" uniqKey="Li W">W. Li</name></author><author><name sortKey="Jaroszewski, L" uniqKey="Jaroszewski L">L. Jaroszewski</name></author><author><name sortKey="Cieplak, P" uniqKey="Cieplak P">P. Cieplak</name></author><author><name sortKey="Miller, C S" uniqKey="Miller C">C. S. Miller</name></author><author><name sortKey="Li, H" uniqKey="Li H">H. Li</name></author><author><name sortKey="Mashiyama, S T" uniqKey="Mashiyama S">S. T. Mashiyama</name></author><author><name sortKey="Joachimiak, M P" uniqKey="Joachimiak M">M. P. Joachimiak</name></author><author><name sortKey="Van Belle, C" uniqKey="Van Belle C">C. van Belle</name></author><author><name sortKey="Chandonia, J M" uniqKey="Chandonia J">J. M. Chandonia</name></author><author><name sortKey="Soergel, D A" uniqKey="Soergel D">D. A. Soergel</name></author><author><name sortKey="Zhai, Y" uniqKey="Zhai Y">Y. Zhai</name></author><author><name sortKey="Natarajan, K" uniqKey="Natarajan K">K. Natarajan</name></author><author><name sortKey="Lee, S" uniqKey="Lee S">S. Lee</name></author><author><name sortKey="Raphael, B J" uniqKey="Raphael B">B. J. Raphael</name></author><author><name sortKey="Bafna, V" uniqKey="Bafna V">V. Bafna</name></author><author><name sortKey="Friedman, R" uniqKey="Friedman R">R. Friedman</name></author><author><name sortKey="Brenner, S E" uniqKey="Brenner S">S. E. Brenner</name></author><author><name sortKey="Godzik, A" uniqKey="Godzik A">A. Godzik</name></author><author><name sortKey="Eisenberg, D" uniqKey="Eisenberg D">D. Eisenberg</name></author><author><name sortKey="Dixon, J E" uniqKey="Dixon J">J. E. Dixon</name></author><author><name sortKey="Taylor, S S" uniqKey="Taylor S">S. S. Taylor</name></author><author><name sortKey="Strausberg, R L" uniqKey="Strausberg R">R. L. Strausberg</name></author><author><name sortKey="Frazier, M" uniqKey="Frazier M">M. Frazier</name></author><author><name sortKey="Venter, J C" uniqKey="Venter J">J. C. Venter</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yuan, Z C" uniqKey="Yuan Z">Z. C. Yuan</name></author><author><name sortKey="Zaheer, R" uniqKey="Zaheer R">R. Zaheer</name></author><author><name sortKey="Finan, T M" uniqKey="Finan T">T. M. Finan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yurkov, V V" uniqKey="Yurkov V">V. V. Yurkov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zimmer, D P" uniqKey="Zimmer D">D. P. Zimmer</name></author><author><name sortKey="Soupene, E" uniqKey="Soupene E">E. Soupene</name></author><author><name sortKey="Lee, H L" uniqKey="Lee H">H. L. Lee</name></author><author><name sortKey="Wendisch, V F" uniqKey="Wendisch V">V. F. Wendisch</name></author><author><name sortKey="Khodursky, A B" uniqKey="Khodursky A">A. B. Khodursky</name></author><author><name sortKey="Peter, B J" uniqKey="Peter B">B. J. Peter</name></author><author><name sortKey="Bender, R A" uniqKey="Bender R">R. A. Bender</name></author><author><name sortKey="Kustu, S" uniqKey="Kustu S">S. Kustu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zohary, T" uniqKey="Zohary T">T. Zohary</name></author><author><name sortKey="Robarts, R D" uniqKey="Robarts R">R. D. Robarts</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Microbiol</journal-id><journal-id journal-id-type="iso-abbrev">Front Microbiol</journal-id><journal-id journal-id-type="publisher-id">Front. Microbio.</journal-id><journal-title-group><journal-title>Frontiers in Microbiology</journal-title></journal-title-group><issn pub-type="epub">1664-302X</issn><publisher><publisher-name>Frontiers Research Foundation</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22783226</article-id><article-id pub-id-type="pmc">3390766</article-id><article-id pub-id-type="doi">10.3389/fmicb.2012.00159</article-id><article-categories><subj-group subj-group-type="heading"><subject>Microbiology</subject><subj-group><subject>Original Research</subject></subj-group></subj-group></article-categories><title-group><article-title>Transcriptional Changes Underlying Elemental Stoichiometry Shifts in a Marine Heterotrophic Bacterium</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Chan</surname><given-names>Leong-Keat</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn002"><sup>†</sup></xref><xref ref-type="author-notes" rid="fn003"><sup>‡</sup></xref></contrib><contrib contrib-type="author"><name><surname>Newton</surname><given-names>Ryan J.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="author-notes" rid="fn003"><sup>‡</sup></xref></contrib><contrib contrib-type="author"><name><surname>Sharma</surname><given-names>Shalabh</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Smith</surname><given-names>Christa B.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Rayapati</surname><given-names>Pratibha</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn002"><sup>†</sup></xref></contrib><contrib contrib-type="author"><name><surname>Limardo</surname><given-names>Alexander J.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Meile</surname><given-names>Christof</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Moran</surname><given-names>Mary Ann</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn001">*</xref></contrib></contrib-group><aff id="aff1"><sup>1</sup><institution>Department of Marine Sciences, University of Georgia</institution><country>Athens, GA, USA</country></aff><aff id="aff2"><sup>2</sup><institution>Great Lakes WATER Institute, University of Wisconsin-Milwaukee</institution><country>Milwaukee, WI, USA</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: James Cotner, University of Minnesota, USA</p></fn><fn fn-type="edited-by"><p>Reviewed by: Katherine McMahon, University of Wisconsin-Madison, USA; Edward Hall, United States Geological Survey, USA</p></fn><corresp id="fn001">*Correspondence: Mary Ann Moran, Department of Marine Sciences, University of Georgia, Athens, GA 30602-3636, USA. e-mail: <email>mmoran@uga.edu</email></corresp><fn fn-type="present-address" id="fn002"><p><sup>†</sup>Present address: Leong-Keat Chan, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, USA; Pratibha Rayapati, Georgia Health Sciences University, Augusta, GA, USA.</p></fn><fn fn-type="other" id="fn003"><p><sup>‡</sup>Leong-Keat Chan and Ryan J. Newton have contributed equally to this work.</p></fn><fn fn-type="other" id="fn004"><p>This article was submitted to Frontiers in Aquatic Microbiology, a specialty of Frontiers in Microbiology.</p></fn></author-notes><pub-date pub-type="epub"><day>16</day><month>5</month><year>2012</year></pub-date><pub-date pub-type="collection"><year>2012</year></pub-date><volume>3</volume><elocation-id>159</elocation-id><history><date date-type="received"><day>31</day><month>12</month><year>2011</year></date><date date-type="accepted"><day>09</day><month>4</month><year>2012</year></date></history><permissions><copyright-statement>Copyright © 2012 Chan, Newton, Sharma, Smith, Rayapati, Limardo, Meile and Moran.</copyright-statement><copyright-year>2012</copyright-year><license license-type="open-access" xlink:href="http://www.frontiersin.org/licenseagreement"><license-p>This is an open-access article distributed under the terms of the <uri xlink:type="simple" xlink:href="http://creativecommons.org/licenses/by-nc/3.0/">Creative Commons Attribution Non Commercial License</uri>, which permits non-commercial use, distribution, and reproduction in other forums, provided the original authors and source are credited.</license-p></license></permissions><abstract><p>Marine bacteria drive the biogeochemical processing of oceanic dissolved organic carbon (DOC), a 750-Tg C reservoir that is a critical component of the global C cycle. Catabolism of DOC is thought to be regulated by the biomass composition of heterotrophic bacteria, as cells maintain a C:N:P ratio of ∼50:10:1 during DOC processing. Yet a complicating factor in stoichiometry-based analyses is that bacteria can change the C:N:P ratio of their biomass in response to resource composition. We investigated the physiological mechanisms of resource-driven shifts in biomass stoichiometry in continuous cultures of the marine heterotrophic bacterium <italic>Ruegeria pomeroyi</italic> (a member of the <italic>Roseobacter</italic> clade) under four element limitation regimes (C, N, P, and S). Microarray analysis indicated that the bacterium scavenged for alternate sources of the scarce element when cells were C-, N-, or P-limited; reworked the ratios of biomolecules when C- and P- limited; and exerted tighter control over import/export and cytoplasmic pools when N-limited. Under S limitation, a scenario not existing naturally for surface ocean microbes, stress responses dominated transcriptional changes. Resource-driven changes in C:N ratios of up to 2.5-fold and in C:P ratios of up to sixfold were measured in <italic>R. pomeroyi</italic> biomass. These changes were best explained if the C and P content of the cells was flexible in the face of shifting resources but N content was not, achieved through the net balance of different transcriptional strategies. The cellular-level metabolic trade-offs that govern biomass stoichiometry in <italic>R. pomeroyi</italic> may have implications for global carbon cycling if extendable to other heterotrophic bacteria. Strong homeostatic responses to N limitation by marine bacteria would intensify competition with autotrophs. Modification of cellular inventories in C- and P-limited heterotrophs would vary the elemental ratio of particulate organic matter sequestered in the deep ocean.</p></abstract><kwd-group><kwd>elemental stoichiometry</kwd><kwd>element limitation</kwd><kwd>microarray</kwd><kwd>chemostat</kwd><kwd><italic>Ruegeria pomeroyi</italic> DSS-3</kwd></kwd-group><counts><fig-count count="6"></fig-count><table-count count="9"></table-count><equation-count count="1"></equation-count><ref-count count="81"></ref-count><page-count count="24"></page-count><word-count count="12180"></word-count></counts></article-meta></front><body><sec><title>Introduction</title><p>Bacterioplankton control the flux of dissolved organic carbon (DOC) into the microbial food web and influence the release of carbon to atmospheric, offshore, and deep sea reservoirs. Many studies suggest that catabolism of DOC is regulated by the biomass stoichiometry of heterotrophic bacteria with respect to N and other nutrients (del Giorgio and Cole, <xref ref-type="bibr" rid="B11">1998</xref>). Thus bacteria incorporate a higher percentage of metabolized DOC into biomass when C is the limiting element and a lower percentage when other elements (typically N or P) limit growth, resulting in decreased growth efficiency as the substrate C:N ratio increases (Goldman et al., <xref ref-type="bibr" rid="B22">1987</xref>). While the molar stoichiometry of C:N:P in marine seston averages ∼106:16:1 (the Redfield ratio; Redfield, <xref ref-type="bibr" rid="B51">1934</xref>), bacteria from a variety of freshwater and marine environments have higher N and P requirements relative to C and typically must attain a biomass stoichiometry closer to 50:10:1 during DOC processing (Fagerbakke et al., <xref ref-type="bibr" rid="B15">1996</xref>; Cotner et al., <xref ref-type="bibr" rid="B9">2010</xref>).</p><p>A confounding factor in stoichiometry-based analyses is that heterotrophic bacteria can change the C:N:P ratio of their biomass in response to the substrate composition (Martinussen and Thingstad, <xref ref-type="bibr" rid="B40">1987</xref>; Tezuka, <xref ref-type="bibr" rid="B61">1990</xref>; Fagerbakke et al., <xref ref-type="bibr" rid="B15">1996</xref>; Gundersen et al., <xref ref-type="bibr" rid="B25">2002</xref>). This plasticity occurs either by uncoupling catabolism and anabolism to overproduce metabolites rich in the excess element (which can be stored or excreted), or by reducing the requirement for the limiting element. Resource-driven shifts in C:N:P ratios of bacterial biomass can affect the efficiency of DOC transformation, modify C flux through the marine food web (Elser et al., <xref ref-type="bibr" rid="B14">1995</xref>), buffer mismatches between bacterial requirements and ecosystem resource availability, and alter the composition of particulate organic matter sequestered in the deep ocean (Thingstad et al., <xref ref-type="bibr" rid="B63">2008</xref>).</p><p>While it is clear that any modifications in elemental stoichiometry must occur within the basic macromolecular constraints of a functioning heterotrophic bacterial cell, there is yet only rudimentary knowledge of the physiological mechanisms that might allow C:N:P ratio variability in marine bacteria. Proposed avenues for changes in stoichiometry include alteration of the cellular inventory of P-rich rRNA (Elser et al., <xref ref-type="bibr" rid="B13">1996</xref>), trade-offs in macromolecular composition to maximize growth (Franklin et al., <xref ref-type="bibr" rid="B17">2011</xref>), substitution of S for P in bacterial membrane lipids (Van Mooy et al., <xref ref-type="bibr" rid="B67">2009</xref>), depletion of P reserves stored in the form of polyphosphate (Kornberg, <xref ref-type="bibr" rid="B36">1999</xref>), depletion of C reserves stored in the form of polyhydroxybutyrate (Dawes and Senior, <xref ref-type="bibr" rid="B10">1973</xref>), and reduction of the cell quota of the limiting element (i.e., the required cell concentration; Harder and Dijkhuizen, <xref ref-type="bibr" rid="B28">1983</xref>; Rivkin and Anderson, <xref ref-type="bibr" rid="B53">1997</xref>).</p><p>Here we investigate the global transcriptional response underlying resource-driven shifts in biomass stoichiometry in the marine heterotrophic bacterium <italic>Ruegeria pomeroyi</italic> DSS-3, a member of the ubiquitous <italic>Roseobacter</italic> clade, under four different element limitation regimes (C, N, P, and S). Our experimental approach equalized growth rates across treatments using continuous cultures (Ferenci, <xref ref-type="bibr" rid="B16">2008</xref>), thereby disentangling effects of the limiting element from any growth rate-driven differences in cell composition (Elser et al., <xref ref-type="bibr" rid="B14">1995</xref>). <italic>R. pomeroyi</italic> exhibited significant flexibility in biomass content of some elements but not others, and gene transcription patterns deduced from whole-genome microarrays revealed element-specific metabolic strategies underlying the stoichiometric shifts.</p></sec><sec sec-type="materials|methods" id="s1"><title>Materials and Methods</title><sec><title>Cell growth conditions</title><p><italic>Ruegeria pomeroyi</italic> DSS-3 was grown in 320 ml custom-made chemostats with a culture volume of 200 ml. Steady-state biomass was limited either by carbon (glucose, 1 mmol l<sup>−1</sup>), nitrogen (NH<sub>4</sub>Cl, 0.26 mmol l<sup>−1</sup>), phosphorus (KH<sub>2</sub>PO<sub>4</sub>, 9.2 μmol l<sup>−1</sup>), or sulfur (Na<sub>2</sub>SO<sub>4</sub>, 25 μmol l<sup>−1</sup>). The appropriate concentrations of limiting nutrients needed to produce similar biomass were initially approximated from batch culture experiments that measured growth yields of <italic>R. pomeroyi</italic> under a range of concentrations. The range was then narrowed in test runs of the chemostats. Once the correct element concentration was determined, six independent chemostat cultures for each macroelement limitation run at two different times were used for elemental analysis and triplicate RNA sampling.</p><p>Chemostat culture medium (Table <xref ref-type="table" rid="TA1">A1</xref> in Appendix) modified from Henriksen (<xref ref-type="bibr" rid="B30">2008</xref>) was buffered with 10 mmol l<sup>−1</sup> 1,3-bis(tris(hydroxymethyl)methyl amino)propane (Bis–tris propane), a C- and N-containing compound; batch cultures of <italic>R. pomeroyi</italic> did not grow with 10 mmol l<sup>−1</sup> Bis–tris propane when it was added as the sole N or C source. Vitamins and trace metals were added to the culture medium (Table <xref ref-type="table" rid="TA1">A1</xref> in Appendix). The feed medium was added to each chemostat at a rate of 8.4 ml h<sup>−1</sup>, equivalent to a dilution rate of 0.042 h<sup>−1</sup>, chosen to approach the rate of marine bacterial growth <italic>in situ</italic> (∼1–2 day<sup>−1</sup>; Ducklow and Hill, <xref ref-type="bibr" rid="B12">1985</xref>) while maintaining sufficient cell yield for biological and chemical analysis. During the incubation, cell cultures were mixed by constant stirring, and temperature was maintained at 30°C using a circulating water bath. Air was bubbled into the culture at a flow rate of 2 ml min<sup>−1</sup>. Salinity was constant at 25 and pH ranged from 6.6 to 7.0 during all growth regimes. Cell cultures were considered to be at steady-state when the change in OD600 was ≤10% between two successive measurements. At steady-state, the feed medium dilution rate equals cell growth rate, which was equivalent to a 16.5-h doubling time for <italic>R. pomeroyi</italic> DSS-3. All cultures reached steady-state after three volume exchanges, and cells were harvested after five volume exchanges</p><p>Inoculum for the chemostat cultures was from a frozen glycerol stock of <italic>R. pomeroyi</italic> DSS-3, revived by streaking onto 1/2 strength YTSS agar (yeast extract, 4 g l<sup>−1</sup>; tryptone, 2.5 g l<sup>−1</sup>; sea salts, 20 g l<sup>−1</sup>; agar, 20 g l<sup>−1</sup>; González et al., <xref ref-type="bibr" rid="B23">2003</xref>; pH adjusted to 6.8), and incubating at 30°C in the dark. After colonies appeared (∼3 days after streaking), a patch of cells was transferred into 1/2 YTSS liquid medium and grown at 30°C with shaking at 150 rpm. After an overnight incubation, cells were washed two times and resuspended in fresh medium lacking glucose, ammonium, phosphate, and sulfate (Table <xref ref-type="table" rid="TA1">A1</xref> in Appendix). Cells were inoculated into 200 ml chemostat medium to an OD600 of 0.05 (∼7 × 10<sup>6</sup> cells ml<sup>−1</sup>), and cultured initially with the outflow pump turned off. After ∼16 h, the flow carrying the feed medium was started and the medium supply was maintained at a constant rate during the chemostat run.</p></sec><sec><title>Cell counts and protein measurements</title><p>Chemostat cultures were routinely monitored for OD600, cell counts, and cell protein concentration. For cell counts, aliquots taken from the chemostats were fixed with glutaraldehyde (2% vol/vol, final concentration), incubated at room temperature for 10 min, and frozen at −20°C. One freeze–thaw cycle did not cause a change in the cell count (data not shown). Thawed cells were stained with SYBR Green II (Molecular Probes/Invitrogen, Carlsbad, CA, USA), incubated in the dark for 10 min, and analyzed with a Beckman Colter Cyan Flow Cytometer. Bacterial cells were quantified using a combination of forward light scatter and fluorescence detection. To reduce the contribution of background fluorescence, cells were quantified within a gate encompassing ≥94% of total fluorescence. Light scatter values provided an index of cell size. The cell protein concentration was measured from cells flash-frozen in a dry ice–ethanol bath according to the method of Bradford (<xref ref-type="bibr" rid="B3">1976</xref>) using Bovine Serum Albumin as a standard.</p></sec><sec><title>Spent medium analysis</title><p>For each treatment regime, concentrations of glucose, <inline-formula><mml:math id="M1"><mml:mrow><mml:msubsup><mml:mrow><mml:mstyle class="text"><mml:mtext>NH</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>4</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mo class="MathClass-bin">+</mml:mo></mml:mrow></mml:msubsup><mml:mo class="MathClass-punc">,</mml:mo></mml:mrow></mml:math></inline-formula><inline-formula><mml:math id="M2"><mml:mrow><mml:msubsup><mml:mrow><mml:mstyle class="text"><mml:mtext>PO</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>4</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>3</mml:mtext></mml:mstyle><mml:mo class="MathClass-bin">-</mml:mo></mml:mrow></mml:msubsup><mml:mo class="MathClass-punc">,</mml:mo></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M3"><mml:mrow><mml:msubsup><mml:mrow><mml:mstyle class="text"><mml:mtext>SO</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>4</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>2</mml:mtext></mml:mstyle><mml:mo class="MathClass-bin">-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula> were measured in one sample (one or two technical duplicates) of cell-free spent medium pooled from three independent chemostat cultures. Cells were pelleted by centrifugation at 16,250 × <italic>g</italic>. The supernatant from three replicates was combined and passed through a 0.22-μm pore-size cellulose acetate filter to remove remaining cells and stored at −20°C until analysis. An estimate of ammonium in the supernatant was obtained by assaying the spent medium using the Ammonia Assay Kit (BioVision, Mountain View, CA, USA; detection limit of 20 μmol l<sup>−1</sup>) according to the manufacturer’s instructions and correcting for the interference from pyruvate based on a control prepared in parallel with the sample. Attempts to measure ammonium with the more sensitive phenol–hypochlorite method (Solorzano, <xref ref-type="bibr" rid="B58">1969</xref>) failed due to inhibiting agents in the culture medium. Glucose concentration was measured with the Glucose Assay Kit (Sigma, St. Louis, MO, USA; detection limit of 50 μmol l<sup>−1</sup>), and control samples were prepared in parallel with the supplied glucose standard. The concentration of <inline-formula><mml:math id="M4"><mml:mrow><mml:msubsup><mml:mrow><mml:mstyle class="text"><mml:mtext>PO</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>4</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>3</mml:mtext></mml:mstyle><mml:mo class="MathClass-bin">-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula> was determined with a Shimadzu UV-1601 spectrophotometer using the molybdenum blue reaction (Strickland and Parsons, <xref ref-type="bibr" rid="B60">1972</xref>) and the concentration of <inline-formula><mml:math id="M5"><mml:mrow><mml:msubsup><mml:mrow><mml:mstyle class="text"><mml:mtext>SO</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>4</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>2</mml:mtext></mml:mstyle><mml:mo class="MathClass-bin">-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula> was determined with a DIONEX ICS-2000 ion chromatography system. Internal standards were used in <inline-formula><mml:math id="M6"><mml:mrow><mml:msubsup><mml:mrow><mml:mstyle class="text"><mml:mtext>PO</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>4</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>3</mml:mtext></mml:mstyle><mml:mo class="MathClass-bin">-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M7"><mml:mrow><mml:msubsup><mml:mrow><mml:mstyle class="text"><mml:mtext>SO</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>4</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>2</mml:mtext></mml:mstyle><mml:mo class="MathClass-bin">-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula> measurements.</p></sec><sec><title>Growth efficiency calculations</title><p>Carbon assimilatory efficiency was calculated as C<sub>b</sub>/C<sub>ipt</sub>, where C<sub>b</sub> is the C present in cell biomass per chemostat volume (200 ml), calculated as 3,072, 1,007, 2,928, and 511 μg C for the C-, N-, P-, and S-limited conditions, respectively, based on measures of biomass %C and dry weight; and C<sub>ipt</sub> is the C input to the chemostat per cell doubling minus any C remaining in the spent medium, calculated as 9,988 μg C for C-limited conditions (8.4 ml h<sup>−1</sup> of a 1-mmol l<sup>−1</sup> solution) and 44,946 μg C minus spent medium C for N-, P-, and S-limited conditions (8.4 ml h<sup>−1</sup> of a 4.5-mmol l<sup>−1</sup> solution).</p></sec><sec><title>Cell elemental analysis</title><p><italic>Ruegeria pomeroyi</italic> DSS-3 cells from 240 ml of culture, pooled from three independent chemostat replicates (80 ml per replicate), were pelleted by centrifugation at 16,250 × <italic>g</italic>, washed twice in fresh medium without glucose, ammonium, phosphate, and sulfate (Table <xref ref-type="table" rid="TA1">A1</xref> in Appendix), immediately frozen in a dry ice–ethanol bath, and stored at −70°C. Frozen cell samples were lyophilized for dry weight measurements and then used in elemental analysis with a Perkin-Elmer 2400 CHN analyzer (C and N) and an inductively coupled plasma mass spectrometer (P).</p></sec><sec><title>Free amino acid analysis</title><p>Cells from 180 ml of culture pooled from three independent chemostat replicates (60 ml per replicate) were washed and pelleted as described above. A portion was saved for cell counts by flow cytometry. To the remainder, 9.7 nmol of β-amino isobutyric acid was added as an internal standard (Hendrickson et al., <xref ref-type="bibr" rid="B29">2008</xref>) and cells were rapidly frozen in a dry ice–ethanol bath and stored at −80°C until analysis. Frozen cell pellets were sent to the Molecular Structure Facility at the University of California Davis for assay with a Hitachi L-8900 Amino Acid Analyzer according to the facility’s protocol. Briefly, cell pellets were lysed with acetonitrile (50% vol/vol) and formic acid (5% vol/vol), and amino-ethyl cysteine was added as an internal standard for quality control. The final amount of amino acids was corrected for the standard and converted to units of pmoles (mg dry weight)<sup>−1</sup>.</p></sec><sec><title>Microarray hybridization</title><p>Cell culture from each replicate chemostat (45 ml) was rapidly fixed with 5 ml of phenol–ethanol solution (5% vol/vol). Cells were collected by centrifugation at 4,500 × g, the supernatant was removed, and the loose cell pellets were frozen at −70°C. Total RNA was purified using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to procedures described previously (Poretsky et al., <xref ref-type="bibr" rid="B50">2009</xref>). DNA was removed by the TURBO DNA-free kit (Applied Biosystems/Ambion, Austin, TX, USA), ribosomal RNA was removed with the MicrobeExpress kit (Applied Biosystems/Ambion), and mRNA-enriched RNA was amplified with the MessageAmp II-Bacteria Kit (Applied Biosystems/Ambion).</p><p>A non-competitive, single-color hybridization strategy was used to hybridize the mRNA samples to microarray slides. Amplified mRNA was labeled with AlexaFluor 647 dye (Invitrogen), with modifications to the manufacturer’s protocol as described previously (Bürgmann et al., <xref ref-type="bibr" rid="B6">2007</xref>). Amplified and labeled mRNA was purified with the MEGAclear kit (Applied Biosystems/Ambion) and concentrated by ethanol precipitation. Samples were hybridized to a whole-genome microarray manufactured by Combimatrix (Mukilteo, WA, USA) and imaged according to the procedures described in the manufacturer’s protocol. The CustomArray 12 K microarray slides for <italic>R. pomeroyi</italic> DSS-3 used in this study were described in detail by Bürgmann et al. (<xref ref-type="bibr" rid="B6">2007</xref>). A total of 8,143 probes, each present up to three times, were represented on the array (Bürgmann et al., <xref ref-type="bibr" rid="B6">2007</xref>). Hybridized slides were stripped according to Combimatrix’s protocol and re-used up to three times. Arrays were re-imaged after each stripping, and re-stripped as needed until minimal fluorescence signal remained.</p></sec><sec><title>Microarray data analysis</title><p>Quality control of microarray hybridizations was performed as described previously (Bürgmann et al., <xref ref-type="bibr" rid="B6">2007</xref>). Each hybridized spot was manually examined in GenePix Pro 6.0 Software (Molecular Devices, Sunnyvale, CA, USA), and the background fluorescence was subtracted (i.e., fluorescence values of the five closest empty spots). Spots were flagged as bad with Acuity 4.0 (Molecular Devices) when they were unevenly hybridized (determined manually by checking the hybridization circularity), when the detected fluorescence minus the background fluorescence was less than 2 SDs of the background fluorescence [F635–B635 < 2 SD (B635)], or when the signal to noise ratio was <3. Probes were removed when the flagged spots were present in >25% of arrays. For the remaining probes with good hybridization signal, those targeting 5S rRNA, 16S rRNA, 23S rRNA, mismatch probes, and manufacturer’s control probes were removed. Each gene was represented by up to two probes and each probe was spotted up to three times on the array (Bürgmann et al., <xref ref-type="bibr" rid="B6">2007</xref>). After probe removal, 5,145 probes (covering 3,324 genes out of the total 4,252 genes in the <italic>R. pomeroyi</italic> DSS-3 genome) remained for analysis. The complete microarray dataset, reported according to the Minimum Information About a Microarray Experiment guidelines (Brazma et al., <xref ref-type="bibr" rid="B4">2001</xref>), was appended to the Gene Expression Omnibus<xref ref-type="fn" rid="fn1"><sup>1</sup></xref> (GEO; The National Center for Biotechnology Information), platform GPL4067, under series accession number GSE27032.</p><p>Florescence values from 14 microarray hybridizations (three biological replicates from each macroelement-limited condition and one technical replicate each for the N and S limitations) were normalized globally, as in Rinta-Kanto et al. (<xref ref-type="bibr" rid="B52">2010</xref>). Data for the technical replicates were averaged and combined (Figure <xref ref-type="fig" rid="FA1">A1</xref> in Appendix). Spearman rank correlation coefficients between replicate arrays ranged between 0.82 and 0.96, while those between arrays from different treatments were ≤0.80 (Table <xref ref-type="table" rid="TA2">A2</xref> in Appendix). The exception was between P and S limitation arrays, for which the correlation coefficients ranged between 0.71 and 0.85 (Table <xref ref-type="table" rid="TA2">A2</xref> in Appendix). Statistical analysis was performed in MultiExperiment Viewer<xref ref-type="fn" rid="fn2"><sup>2</sup></xref> (MeV, Dana-Farber Cancer Institute, Boston, MA, USA; Saeed et al., <xref ref-type="bibr" rid="B55">2006</xref>). Significance analysis of microarray (SAM; Tusher et al., <xref ref-type="bibr" rid="B66">2001</xref>), available through the MeV interface, was used for statistical analysis. Pairwise comparisons were made between treatments, with the following settings: two-class unpaired, 5,000 permutations, and false discovery rate (FDR; Tusher et al., <xref ref-type="bibr" rid="B66">2001</xref>) ≤2%. Pairwise SAM analyses were performed as follows: C limitation compared to C excess conditions (where N, P, or S was limiting); N limitation compared to N excess conditions (where C, P, or S was limiting); P limitation compared to P excess conditions (where N, C, or S was limiting); and S limitation compared to S excess conditions (where N, C, or P were limiting; Figure <xref ref-type="fig" rid="FA1">A1</xref> in Appendix).</p><p>Transcriptionally responsive genes were identified as those with a ≥3-fold enrichment in all three pairwise comparisons across treatments (Figure <xref ref-type="fig" rid="FA1">A1</xref> in Appendix). Four genes (SPO0968, SPO1031, SPO1795, and SPO3300) were transcriptionally enriched under one treatment but transcriptionally depleted under another, due to different responses of two probes for a single gene; these were not considered further. Designation of enriched or depleted genes was conservative. In many cases genes had significant responses in two out of three pairwise comparisons or had a ≥2-fold (but ≤3-fold) transcriptional change, but they were not considered further.</p></sec><sec><title>Gene annotation and metabolic pathway construction</title><p><italic>Ruegeria pomeroyi</italic> DSS-3 gene products were generally assigned according to the annotations in GenBank (Accession number NC_003911.11) with updated gene calls as appropriate (SPO0781, <italic>phnD</italic>; SPO1948, <italic>pstS</italic>; SPO1979, OlsA-like protein; SPO1980, OlsB-like protein; SPO0372 and SPO2287, LuxI-type proteins). Operons were as predicted in Roseobase<xref ref-type="fn" rid="fn3"><sup>3</sup></xref>, and metabolic pathways were constructed manually from BioCyc<xref ref-type="fn" rid="fn4"><sup>4</sup></xref> (SRI International, Menlo Park, CA, USA). For analysis of the global ocean sampling (GOS) metagenome (Rusch et al., <xref ref-type="bibr" rid="B54">2007</xref>; Yooseph et al., <xref ref-type="bibr" rid="B76">2007</xref>; data obtained from Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis<xref ref-type="fn" rid="fn5"><sup>5</sup></xref>), BLASTp was used to identify homologous sequences using an <italic>E</italic>-value of <10<sup>−5</sup>. The percent of bacterioplankton cells in GOS samples (as of May 2011; Sargasso Sea, northwest Atlantic, Pacific, and Indian Ocean sequences; Rusch et al., <xref ref-type="bibr" rid="B54">2007</xref>; Yooseph et al., <xref ref-type="bibr" rid="B76">2007</xref>) harboring a homolog was calculated as (number of homologs × 100)/number of <italic>recA</italic>, assuming only one homolog and one <italic>recA</italic> per genome and 10,196 <italic>recA</italic> homologs in the analyzed portion of the GOS dataset (Moran et al., <xref ref-type="bibr" rid="B44">2011</xref>). For analysis of other microbial genomes, BLASTp was used to identify homologs using an <italic>E</italic>-value < 10<sup>−30</sup>. In both cases, candidate homologs were subjected to phylogenetic analysis using pplacer (Matsen et al., <xref ref-type="bibr" rid="B41">2010</xref>) to confirm homology with genes of known function.</p></sec><sec><title>Cell stoichiometry</title><p>The stoichiometry rules that best reproduced observed C:N:P ratios under elemental limitation were explored. A simple model that assumed limitation shifted the concentration of the limiting element away from the concentration found under balanced growth (when all elements are available in non-limiting conditions) by a factor α, while the other two (non-limiting) elements were unaffected by the limitation gave the best fit to the observed C:N:P ratios. Thus the C:N:P ratio for <italic>R. pomeroyi</italic> under balanced growth conditions was approximated as:</p><disp-formula id="E1"><mml:math id="M11"><mml:msub><mml:mrow><mml:mi>α</mml:mi></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>c</mml:mtext></mml:mstyle></mml:mrow></mml:msub><mml:msub><mml:mrow><mml:mstyle class="text"><mml:mtext>C</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>c</mml:mtext></mml:mstyle></mml:mrow></mml:msub><mml:mo class="MathClass-punc">:</mml:mo><mml:msub><mml:mrow><mml:mstyle class="text"><mml:mtext>N</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>c</mml:mtext></mml:mstyle></mml:mrow></mml:msub><mml:mo class="MathClass-punc">:</mml:mo><mml:msub><mml:mrow><mml:mstyle class="text"><mml:mtext>P</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>c</mml:mtext></mml:mstyle></mml:mrow></mml:msub><mml:mo class="MathClass-rel">≈</mml:mo><mml:msub><mml:mrow><mml:mstyle class="text"><mml:mtext>C</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>N</mml:mtext></mml:mstyle></mml:mrow></mml:msub><mml:mo class="MathClass-punc">:</mml:mo><mml:msub><mml:mrow><mml:mi>α</mml:mi></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>N</mml:mtext></mml:mstyle></mml:mrow></mml:msub><mml:msub><mml:mrow><mml:mstyle class="text"><mml:mtext>N</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>N</mml:mtext></mml:mstyle></mml:mrow></mml:msub><mml:mo class="MathClass-punc">:</mml:mo><mml:msub><mml:mrow><mml:mstyle class="text"><mml:mtext>P</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>N</mml:mtext></mml:mstyle></mml:mrow></mml:msub><mml:mo class="MathClass-rel">≈</mml:mo><mml:msub><mml:mrow><mml:mstyle class="text"><mml:mtext>C</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>P</mml:mtext></mml:mstyle></mml:mrow></mml:msub><mml:mo class="MathClass-punc">:</mml:mo><mml:msub><mml:mrow><mml:mstyle class="text"><mml:mtext>N</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>P</mml:mtext></mml:mstyle></mml:mrow></mml:msub><mml:mo class="MathClass-punc">:</mml:mo><mml:msub><mml:mrow><mml:mi>α</mml:mi></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>p</mml:mtext></mml:mstyle></mml:mrow></mml:msub><mml:msub><mml:mrow><mml:mstyle class="text"><mml:mtext>P</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>p</mml:mtext></mml:mstyle></mml:mrow></mml:msub></mml:math></disp-formula><p>where α<sub>X</sub> is the factor by which element <sc>x</sc> changes when it is limiting, and C<sub><sc>x</sc></sub>, N<sub><sc>x</sc></sub>, and P<sub><sc>x</sc></sub> are the C, N, and P content, respectively, under limiting element <sc>x</sc>.</p></sec></sec><sec><title>Results and Discussion</title><sec><title>Attributes of steady-state cultures</title><p>Measurements of cell-free spent media indicated that limiting elements were below the detection limit while non-limiting elements were in excess for chemostat-grown <italic>R. pomeroyi</italic> DSS-3 (Table <xref ref-type="table" rid="T1">1</xref>). Cell dry weights for the C, N, and S treatments averaged 486 fg cell<sup>−1</sup>, similar to those reported for heterotrophic marine bacteria during exponential growth (322–512 fg cell<sup>−1</sup>, Vrede et al., <xref ref-type="bibr" rid="B69">2002</xref>; Table <xref ref-type="table" rid="TA3">A3</xref> in Appendix), but P-limited cells had an unusually high dry weight (1,388 fg cell<sup>−1</sup>). C-limited cells were smaller and had higher growth efficiency (i.e., amount of new bacterial biomass produced per unit of organic C assimilated) than N-, P-, or S- limited cells (31 versus 1–8%; Table <xref ref-type="table" rid="T1">1</xref>). By way of comparison, del Giorgio and Cole (<xref ref-type="bibr" rid="B11">1998</xref>) report 9–47% bacterial growth efficiencies (interquartile range) for heterotrophic bacteria in oceans and estuaries. The protein: dry weight ratio of S-limited cells was atypically high, likely reflecting an unnatural condition for marine bacterioplankton. Molar C:N ratios in biomass varied up to 2.5-fold and C:P ratios varied up to sixfold among the different limiting element regimes (Table <xref ref-type="table" rid="T1">1</xref>).</p><table-wrap id="T1" position="float"><label>Table 1</label><caption><p><bold>Biological and chemical status of <italic>R. pomeroy</italic><italic>i</italic> DSS-3 chemostat cultures</bold>.</p></caption><table frame="hsides" rules="groups"><thead><tr><th valign="top" align="left" rowspan="1" colspan="1">Limitation</th><th valign="top" colspan="4" align="center" rowspan="1">Spent medium (mmol l<sup>−1</sup>)<hr></hr></th><th valign="top" colspan="8" align="center" rowspan="1">Steady-state culture<hr></hr></th></tr><tr><th valign="top" align="left" rowspan="1" colspan="1"></th><th valign="top" align="left" rowspan="1" colspan="1">Glucose<xref ref-type="table-fn" rid="tfn1"><sup>a</sup></xref></th><th valign="top" align="left" rowspan="1" colspan="1"><inline-formula><mml:math id="M8"><mml:mrow><mml:msubsup><mml:mrow><mml:mstyle class="text"><mml:mtext>NH</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>4</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mo class="MathClass-bin">+</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula><xref ref-type="table-fn" rid="tfn1"><sup>a</sup></xref></th><th valign="top" align="left" rowspan="1" colspan="1"><inline-formula><mml:math id="M9"><mml:mrow><mml:msubsup><mml:mrow><mml:mstyle class="text"><mml:mtext>PO</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>4</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>3</mml:mtext></mml:mstyle><mml:mo class="MathClass-bin">-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula><xref ref-type="table-fn" rid="tfn2"><sup>b</sup></xref></th><th valign="top" align="left" rowspan="1" colspan="1"><inline-formula><mml:math id="M10"><mml:mrow><mml:msubsup><mml:mrow><mml:mstyle class="text"><mml:mtext>SO</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>4</mml:mtext></mml:mstyle></mml:mrow><mml:mrow><mml:mstyle class="text"><mml:mtext>2</mml:mtext></mml:mstyle><mml:mo class="MathClass-bin">-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula><xref ref-type="table-fn" rid="tfn2"><sup>b</sup></xref></th><th valign="top" align="left" rowspan="1" colspan="1">Protein (fg cell<sup>−1</sup>)<xref ref-type="table-fn" rid="tfn3"><sup>c</sup></xref></th><th valign="top" align="left" rowspan="1" colspan="1">Dry weight (fg cell<sup>−1</sup>)<xref ref-type="table-fn" rid="tfn2"><sup>b</sup></xref></th><th valign="top" align="left" rowspan="1" colspan="1">Protein: dry weight (%)</th><th valign="top" align="left" rowspan="1" colspan="1">Flow scatter (mode)<xref ref-type="table-fn" rid="tfn3"><sup>c</sup></xref></th><th valign="top" align="left" rowspan="1" colspan="1">C growth efficiency</th><th valign="top" colspan="3" align="center" rowspan="1">Molar ratio<xref ref-type="table-fn" rid="tfn2"><sup>b</sup></xref><hr></hr></th></tr><tr><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1">C:N</th><th align="left" rowspan="1" colspan="1">C:P</th><th align="left" rowspan="1" colspan="1">N:P</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">C</td><td align="left" rowspan="1" colspan="1">BD<xref ref-type="table-fn" rid="tfn4"><sup>d</sup></xref></td><td align="left" rowspan="1" colspan="1">1.02</td><td align="left" rowspan="1" colspan="1">0.40</td><td align="left" rowspan="1" colspan="1">1.76</td><td align="left" rowspan="1" colspan="1">140.8</td><td align="left" rowspan="1" colspan="1">454.0</td><td align="left" rowspan="1" colspan="1">31.0</td><td align="left" rowspan="1" colspan="1">1,792</td><td align="left" rowspan="1" colspan="1">30.8</td><td align="right" rowspan="1" colspan="1">4.4</td><td align="right" rowspan="1" colspan="1">55.6</td><td align="right" rowspan="1" colspan="1">12.7</td></tr><tr><td align="left" rowspan="1" colspan="1">N</td><td align="left" rowspan="1" colspan="1">0.72</td><td align="left" rowspan="1" colspan="1">BD</td><td align="left" rowspan="1" colspan="1">0.46</td><td align="left" rowspan="1" colspan="1">1.52</td><td align="left" rowspan="1" colspan="1">353.9</td><td align="left" rowspan="1" colspan="1">757.9</td><td align="left" rowspan="1" colspan="1">46.7</td><td align="left" rowspan="1" colspan="1">2,048</td><td align="left" rowspan="1" colspan="1">2.7</td><td align="right" rowspan="1" colspan="1">11.2</td><td align="right" rowspan="1" colspan="1">166.7</td><td align="right" rowspan="1" colspan="1">14.8</td></tr><tr><td align="left" rowspan="1" colspan="1">P</td><td align="left" rowspan="1" colspan="1">0.67</td><td align="left" rowspan="1" colspan="1">0.54</td><td align="left" rowspan="1" colspan="1">BD</td><td align="left" rowspan="1" colspan="1">1.81</td><td align="left" rowspan="1" colspan="1">371.5</td><td align="left" rowspan="1" colspan="1">1388.4</td><td align="left" rowspan="1" colspan="1">26.8</td><td align="left" rowspan="1" colspan="1">2,048</td><td align="left" rowspan="1" colspan="1">7.7</td><td align="right" rowspan="1" colspan="1">9.5</td><td align="right" rowspan="1" colspan="1">333.3</td><td align="right" rowspan="1" colspan="1">35.0</td></tr><tr><td align="left" rowspan="1" colspan="1">S</td><td align="left" rowspan="1" colspan="1">0.66</td><td align="left" rowspan="1" colspan="1">ND<xref ref-type="table-fn" rid="tfn5"><sup>e</sup></xref></td><td align="left" rowspan="1" colspan="1">0.43</td><td align="left" rowspan="1" colspan="1">0.01</td><td align="left" rowspan="1" colspan="1">234.6</td><td align="left" rowspan="1" colspan="1">245.8</td><td align="left" rowspan="1" colspan="1">95.4</td><td align="left" rowspan="1" colspan="1">2,099 ± 280</td><td align="left" rowspan="1" colspan="1">1.3</td><td align="right" rowspan="1" colspan="1">4.9</td><td align="right" rowspan="1" colspan="1">62.5</td><td align="right" rowspan="1" colspan="1">12.7</td></tr></tbody></table><table-wrap-foot><fn id="tfn1"><p><italic><sup>a</sup>Average of two technical replicates from pooled triplicate chemostat cultures</italic>.</p></fn><fn id="tfn2"><p><italic><sup>b</sup>Value for one sample from pooled triplicate chemostat cultures</italic>.</p></fn><fn id="tfn3"><p><italic><sup>c</sup>Average of triplicate chemostat cultures; ±SD is specified if >10% of the mean</italic>.</p></fn><fn id="tfn4"><p><italic><sup>d</sup>Below detection of the assay (see <xref ref-type="sec" rid="s1">Materials and Methods</xref>)</italic>.</p></fn><fn id="tfn5"><p><italic><sup>e</sup>Not determined</italic>.</p></fn></table-wrap-foot></table-wrap><p>Transcripts for 190 genes (4.5% of the 4,252 genes in the <italic>R. pomeroyi</italic> DSS-3 genome) were responsive exclusively to C, N, P, or S limitation, with 134 genes enriched (3.2%) and 56 genes depleted (1.3%; Figure <xref ref-type="fig" rid="FA1">A1</xref> in Appendix; see Tables <xref ref-type="table" rid="TA4">A4</xref> and <xref ref-type="table" rid="TA5">A5</xref> in Appendix for a complete list of significantly enriched and depleted genes).</p></sec><sec><title>Transcriptional response to C limitation</title><p>The C-limited transcriptome was enriched in transporters for dicarboxylic acids, peptides, branched-chain amino acids, sugars, and glycine betaine/proline (Table <xref ref-type="table" rid="T2">2</xref>), indicating increased investment in substrate acquisition. Several cell division transcripts were also present in higher proportion, including those for a chromosome initiation replication protein (<italic>dnaA</italic>), DNA helicase (<italic>recQ</italic>), DNA polymerase, and a purine biosynthesis enzyme (<italic>hisF</italic>; Table <xref ref-type="table" rid="T2">2</xref>), coinciding with the smaller and more numerous cells observed under C limitation (Table <xref ref-type="table" rid="T1">1</xref>). Transcripts for the rod shape-determining <italic>mreD</italic>, a mutated version of which causes <italic>Escherichia coli</italic> cells to take on a spherical shape (Wachi et al., <xref ref-type="bibr" rid="B71">1989</xref>), were depleted (Table <xref ref-type="table" rid="T2">2</xref>). Spherical shape and small cell size are characteristic of marine bacterioplankton in oligotrophic conditions, and are hypothesized to afford a more favorable surface-to-volume ratio to compete for scarce substrates (Azam et al., <xref ref-type="bibr" rid="B2">1983</xref>). Relative increases in transcripts for three proteins involved in flagellum synthesis indicated increased motility of C-limited cells. Together, these changes represent a strong C scavenging response by C-limited <italic>R. pomeroyi</italic> cells.</p><table-wrap id="T2" position="float"><label>Table 2</label><caption><p><bold>Selected <italic>R. pomeroyi</italic> DSS-3 genes responding uniquely to a C-, N-, P-, or S-limited regime</bold>.</p></caption><table frame="hsides" rules="groups"><thead><tr><th valign="top" align="left" rowspan="1" colspan="1">Locus tag</th><th valign="top" align="left" rowspan="1" colspan="1">Product (gene name, if available)</th><th valign="top" colspan="2" align="center" rowspan="1">Fold-change ratio<sup>a</sup><hr></hr></th><th valign="top" colspan="3" align="center" rowspan="1">Response strategy<hr></hr></th></tr><tr><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1">Probe 1</th><th align="left" rowspan="1" colspan="1">Probe 2</th><th align="left" rowspan="1" colspan="1">Scavenging</th><th align="left" rowspan="1" colspan="1">Quota Change</th><th align="left" rowspan="1" colspan="1">Gate-keeping</th></tr></thead><tbody><tr><td style="background-color:#B2B2B2" colspan="7" align="left" rowspan="1"><bold>C-LIMITED</bold></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0107</td><td align="left" rowspan="1" colspan="1">ATP-dependent DNA helicase (<italic>recQ</italic>)</td><td align="left" rowspan="1" colspan="1">1.0</td><td align="left" rowspan="1" colspan="1">6.3</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0149</td><td align="left" rowspan="1" colspan="1">Chromosomal replication initiation protein (<italic>dnaA</italic>)</td><td align="left" rowspan="1" colspan="1">16.5</td><td align="left" rowspan="1" colspan="1">1.2</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0171</td><td align="left" rowspan="1" colspan="1">Flagellar biosynthetic protein</td><td align="left" rowspan="1" colspan="1">1.3</td><td align="left" rowspan="1" colspan="1">6.7</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0183</td><td align="left" rowspan="1" colspan="1">H<sup>+</sup>-transporting two-sector ATPase, flagellum-specific</td><td align="left" rowspan="1" colspan="1">6.3</td><td align="left" rowspan="1" colspan="1">1.0</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0590</td><td align="left" rowspan="1" colspan="1">LacI family transcriptional regulator (carbon catabolite repression domain-containing)</td><td align="left" rowspan="1" colspan="1">14.5</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0970</td><td align="left" rowspan="1" colspan="1">Aquaporin Z (<italic>apqZ</italic>)</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">1.3</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1132</td><td align="left" rowspan="1" colspan="1">Glycine betaine/proline ABC transporter, ATP-binding protein</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">3.0</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1156</td><td align="left" rowspan="1" colspan="1">Imidazole glycerol phosphate synthase subunit (<italic>hisF</italic>)</td><td align="left" rowspan="1" colspan="1">3.0</td><td align="left" rowspan="1" colspan="1">3.5</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1463</td><td align="left" rowspan="1" colspan="1">TRAP dicarboxylate transporter, DctM subunit</td><td align="left" rowspan="1" colspan="1">8.3</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1645</td><td align="left" rowspan="1" colspan="1">Oligopeptide/dipeptide ABC transporter, permease protein</td><td align="left" rowspan="1" colspan="1">4.6</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1807</td><td align="left" rowspan="1" colspan="1">DNA polymerase III epsilon subunit family exonuclease</td><td align="left" rowspan="1" colspan="1">3.7</td><td align="left" rowspan="1" colspan="1">1.0</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2370</td><td align="left" rowspan="1" colspan="1">Sodium:alanine symporter family protein</td><td align="left" rowspan="1" colspan="1">3.4</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3291</td><td align="left" rowspan="1" colspan="1">Branched-chain amino acid ABC transporter, periplasmic binding protein, putative</td><td align="left" rowspan="1" colspan="1">5.5</td><td align="left" rowspan="1" colspan="1">4.0</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3461</td><td align="left" rowspan="1" colspan="1">Flagellar protein FlgJ, putative</td><td align="left" rowspan="1" colspan="1">8.5</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3783</td><td align="left" rowspan="1" colspan="1">Sugar ABC transporter, ATP-binding protein</td><td align="left" rowspan="1" colspan="1">8.0</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPOA0097</td><td align="left" rowspan="1" colspan="1">Branched-chain amino acid ABC transporter, permease protein</td><td align="left" rowspan="1" colspan="1">3.6</td><td align="left" rowspan="1" colspan="1">1.4</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPOA0160</td><td align="left" rowspan="1" colspan="1">TRAP dicarboxylate transporter, DctM subunit</td><td align="left" rowspan="1" colspan="1">8.7</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPOA0299</td><td align="left" rowspan="1" colspan="1">Branched-chain amino acid ABC transporter, permease protein</td><td align="left" rowspan="1" colspan="1">0.9</td><td align="left" rowspan="1" colspan="1">3.7</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0416</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Rod-shaped determining protein (<italic>mreD</italic>)</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">•</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1293</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Phasin (<italic>phaP</italic>)</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.1</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.1</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">•</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1756</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Polysaccharide biosynthesis/export protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.7</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">•</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td></tr><tr><td style="background-color:#B2B2B2" colspan="7" align="left" rowspan="1"><bold>N-LIMITED</bold></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0860</td><td align="left" rowspan="1" colspan="1">Xylose repressor, putative</td><td align="left" rowspan="1" colspan="1">3.2</td><td align="left" rowspan="1" colspan="1">3.2</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">•</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1707</td><td align="left" rowspan="1" colspan="1">Urea transporter, ATP-binding protein (<italic>urtE</italic>)</td><td align="left" rowspan="1" colspan="1">3.8</td><td align="left" rowspan="1" colspan="1">3.0</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPOA0447</td><td align="left" rowspan="1" colspan="1">Urea transporter, ATP-binding protein (<italic>urtD</italic>)</td><td align="left" rowspan="1" colspan="1">5.5</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1708</td><td align="left" rowspan="1" colspan="1">Urea transporter, permease protein (<italic>urtC</italic>)</td><td align="left" rowspan="1" colspan="1">11.6</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2087</td><td align="left" rowspan="1" colspan="1">Nitrogen regulation protein (<italic>ntrC</italic>)</td><td align="left" rowspan="1" colspan="1">1.1</td><td align="left" rowspan="1" colspan="1">4.3</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2294</td><td align="left" rowspan="1" colspan="1">Nitrogen regulatory protein P<sub>II</sub> (<italic>glnB-1</italic>)</td><td align="left" rowspan="1" colspan="1">9.0</td><td align="left" rowspan="1" colspan="1">6.6</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2295</td><td align="left" rowspan="1" colspan="1">Glutamine synthetase, type I (<italic>glnA</italic>)</td><td align="left" rowspan="1" colspan="1">4.7</td><td align="left" rowspan="1" colspan="1">5.1</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2364</td><td align="left" rowspan="1" colspan="1">Amino acid ABC transporter, periplasmic binding protein</td><td align="left" rowspan="1" colspan="1">1.3</td><td align="left" rowspan="1" colspan="1">4.1</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3723</td><td align="left" rowspan="1" colspan="1">Ammonium transporter (<italic>amt-2</italic>)</td><td align="left" rowspan="1" colspan="1">28.0</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3724</td><td align="left" rowspan="1" colspan="1">Nitrogen regulatory protein P<sub>II</sub> (<italic>glnB-2</italic>)</td><td align="left" rowspan="1" colspan="1">124.3</td><td align="left" rowspan="1" colspan="1">39.1</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPOA0300</td><td align="left" rowspan="1" colspan="1">Branched-chain amino acid ABC transporter, periplasmic binding protein</td><td align="left" rowspan="1" colspan="1">6.6</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0862</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Xylose ABC transporter, permease protein (<italic>xylH</italic>)</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">•</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1079</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Lysine exporter, putative</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.1</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">2.0</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">•</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1743</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Glutamate dehydrogenase</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">•</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO3156</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><sc>l</sc>-threonine aldolase, low-specificity, putative</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">1.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO3712</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Aspartate-semialdehyde dehydrogenase (<italic>asd</italic>)</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">•</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO3720</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Aromatic amino acid aminotransferase (<italic>tyrB</italic>)</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.9</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">•</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPOA0011</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>S</italic>-adenosylmethionine synthetase (<italic>metK</italic>)</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.4</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">•</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPOA0057</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Glycine cleavage system T protein (<italic>gcvT</italic>)</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">•</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPOA0215</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Nitric oxide reductase Q protein (<italic>norQ</italic>)</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">2.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.1</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">•</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPOA0220</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Cytochrome cd1 nitrite reductase (<italic>nirS</italic>)</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">•</td></tr><tr><td style="background-color:#B2B2B2" colspan="7" align="left" rowspan="1"><bold>P-LIMITED</bold></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0147</td><td align="left" rowspan="1" colspan="1">Enoyl-CoA hydratase</td><td align="left" rowspan="1" colspan="1">4.3</td><td align="left" rowspan="1" colspan="1">3.0</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0304</td><td align="left" rowspan="1" colspan="1">Lipoprotein, putative</td><td align="left" rowspan="1" colspan="1">7.0</td><td align="left" rowspan="1" colspan="1">5.4</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0468</td><td align="left" rowspan="1" colspan="1">Alkylphosphonate utilization protein (<italic>phnG</italic>)</td><td align="left" rowspan="1" colspan="1">5.2</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0472</td><td align="left" rowspan="1" colspan="1">Phosphonate C-P lyase system protein (<italic>phnK</italic>)</td><td align="left" rowspan="1" colspan="1">10.9</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0781</td><td align="left" rowspan="1" colspan="1">Phosphonate ABC transporter, periplasmic phosphonate-binding (<italic>phnD</italic>)</td><td align="left" rowspan="1" colspan="1">103.5</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1860</td><td align="left" rowspan="1" colspan="1">Alkaline phosphatase (<italic>phoX</italic>)</td><td align="left" rowspan="1" colspan="1">7.4</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1948</td><td align="left" rowspan="1" colspan="1">Phosphate ABC transporter, periplasmic binding protein (<italic>pstS</italic>)</td><td align="left" rowspan="1" colspan="1">47.9</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1949</td><td align="left" rowspan="1" colspan="1">Phosphate ABC transporter, permease protein (<italic>pstC</italic>)</td><td align="left" rowspan="1" colspan="1">4.7</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1951</td><td align="left" rowspan="1" colspan="1">Phosphate transporter ATP-binding protein (<italic>pstB</italic>)</td><td align="left" rowspan="1" colspan="1">7.4</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1953</td><td align="left" rowspan="1" colspan="1">Phosphate regulon transcriptional regulatory protein (<italic>phoB</italic>)</td><td align="left" rowspan="1" colspan="1">10.7</td><td align="left" rowspan="1" colspan="1">26.1</td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPOA0294</td><td align="left" rowspan="1" colspan="1">Phosphatidylethanolamine <italic>N</italic>-methyltransferase (<italic>pmtA</italic>)</td><td align="left" rowspan="1" colspan="1">3.6</td><td align="left" rowspan="1" colspan="1">1.2</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">•</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td style="background-color:#B2B2B2" colspan="7" align="left" rowspan="1"><bold>S-LIMITED</bold></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1256</td><td align="left" rowspan="1" colspan="1">Polyphosphate kinase 2 (<italic>ppk2</italic>)</td><td align="left" rowspan="1" colspan="1">5.0</td><td align="left" rowspan="1" colspan="1">4.0</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1409</td><td align="left" rowspan="1" colspan="1">RNA polymerase factor sigma-32 (<italic>rpoH-2</italic>)</td><td align="left" rowspan="1" colspan="1">12.5</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2596</td><td align="left" rowspan="1" colspan="1">5-amino-levulinate synthase (<italic>hemA-1</italic>)</td><td align="left" rowspan="1" colspan="1">1.8</td><td align="left" rowspan="1" colspan="1">4.6</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2632</td><td align="left" rowspan="1" colspan="1">Uroporphyrinogen-III <italic>C</italic>-methyltransferase (<italic>cobA-1</italic>)</td><td align="left" rowspan="1" colspan="1">3.4</td><td align="left" rowspan="1" colspan="1">5.9</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2634</td><td align="left" rowspan="1" colspan="1">Sulfite reductase, putative</td><td align="left" rowspan="1" colspan="1">5.7</td><td align="left" rowspan="1" colspan="1">5.3</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3383</td><td align="left" rowspan="1" colspan="1">Thiol-specific antioxidant protein</td><td align="left" rowspan="1" colspan="1">4.9</td><td align="left" rowspan="1" colspan="1">4.5</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3527</td><td align="left" rowspan="1" colspan="1">Universal stress protein family protein</td><td align="left" rowspan="1" colspan="1">3.7</td><td align="left" rowspan="1" colspan="1">5.3</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3532</td><td align="left" rowspan="1" colspan="1">Coproporphyrinogen III oxidase (<italic>hemN</italic>)</td><td align="left" rowspan="1" colspan="1">7.3</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0371</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Autoinducer-binding transcriptional regulator (<italic>luxR-1</italic>)</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.0</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1679</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">DNA-binding response regulator (<italic>ctrA</italic>)</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"></td></tr></tbody></table><table-wrap-foot><p><italic>The enriched genes included here (unshaded rows) represent 36% of all enriched genes (Table <xref ref-type="table" rid="TA4">A4</xref> in Appendix); the depleted genes (gray-shaded rows) represent 27% of all depleted genes (Table <xref ref-type="table" rid="TA5">A5</xref> in Appendix)</italic>.</p><p><italic><sup>a</sup>Calculated as the median value for limitation-to-excess pairwise comparisons</italic>.</p><p><italic>Black dots indicate response strategy assignment</italic>.</p></table-wrap-foot></table-wrap><p>In the C-limited cultures, the <italic>R. pomeroyi</italic> transcriptome was depleted in transcripts encoding the synthesis and export of high C-content surface-associated polysaccharides, a strategy that would lower the cellular C quota (Table <xref ref-type="table" rid="T2">2</xref>). Transcripts for phasin (<italic>phaP</italic>), a protein that binds to the surface of C storage inclusions composed of polyhydroxyalkanoate (PHA; Anderson and Dawes, <xref ref-type="bibr" rid="B1">1990</xref>), were depleted (Table <xref ref-type="table" rid="T2">2</xref>), indicating degradation of internal C reservoirs. Other genes involved in PHA metabolism (<italic>phbA</italic>, <italic>phbB</italic>, <italic>phaZ</italic>, <italic>phaR</italic>) did not have altered transcription levels (Figure <xref ref-type="fig" rid="FA2">A2</xref> in Appendix), but this is consistent with data from the related alphaproteobacterium <italic>Rhodobacter capsulatus</italic> showing PHA synthesis genes to be constitutively expressed, with control occurring post-translationally (Kranz et al., <xref ref-type="bibr" rid="B37">1997</xref>). Since PHA storage molecules have been observed in <italic>R. pomeroyi</italic> cells (González et al., <xref ref-type="bibr" rid="B23">2003</xref>) and can occupy 40–50% of cell volume in some C-replete bacteria (Yurkov, <xref ref-type="bibr" rid="B78">2006</xref>), this finding coincides with the smaller cell size observed under C limitation (Table <xref ref-type="table" rid="T1">1</xref>). Together, this set of transcriptional changes comprise strategies for a reduced cell quota for C.</p></sec><sec><title>Transcriptional response to N limitation</title><p>N limitation induced a strong scavenging response for acquiring available N compounds mediated through a conserved bacterial regulatory system involving P<sub>II</sub> regulators (<italic>glnB-1</italic> and <italic>glnB-2</italic>) and the N response regulator NtrC (Ikeda et al., <xref ref-type="bibr" rid="B32">1996</xref>; Gyaneshwar et al., <xref ref-type="bibr" rid="B26">2005</xref>; Walter et al., <xref ref-type="bibr" rid="B72">2007</xref>; Table <xref ref-type="table" rid="T2">2</xref>). Two genes previously found to be controlled by these regulators in <italic>E. coli</italic> (Zimmer et al., <xref ref-type="bibr" rid="B79">2000</xref>; Gyaneshwar et al., <xref ref-type="bibr" rid="B26">2005</xref>) were also part of the <italic>R. pomeroyi</italic> scavenging response: an ammonium transporter (<italic>amt-2</italic>, located adjacent to <italic>glnB-2</italic>) and a glutamine synthetase (<italic>glnA</italic>, mediating ammonium incorporation; located adjacent to <italic>glnB-1</italic>). Two other N scavenging activities included enrichment of transcripts for urea transport and amino acid transport (Table <xref ref-type="table" rid="T2">2</xref>).</p><p>There was no evidence of a role for N storage compounds in the <italic>R. pomeroyi</italic> response to N limitation. The genome does not contain homologs to the genes required for synthesis of cyanophycin granule polypeptide (CGP), the only known bacterial mechanism for N storage (Füser and Steinbüchel, <xref ref-type="bibr" rid="B18">2007</xref>). Instead, transcriptional responses focused on tightening of the import/export balance of N through better “gate-keeping.” In one response, depletion of a xylose ABC transporter (<italic>xylH</italic>) and enrichment of a putative xylose uptake repressor (Table <xref ref-type="table" rid="T2">2</xref>) would work to decrease the import of high C:N content carbohydrates. In another, depletion of transcripts for a putative lysine exporter (Table <xref ref-type="table" rid="T2">2</xref>) involved in cytoplasmic amino acid regulation (Vrljic et al., <xref ref-type="bibr" rid="B70">1999</xref>) would suppress the export of low C:N content amino acids. Two genes mediating dissimilatory nitrite reduction (<italic>norQ</italic> and <italic>nirS</italic>, which are part of a partial denitrification pathway; Moran et al., <xref ref-type="bibr" rid="B43">2004</xref>) were also depleted (Table <xref ref-type="table" rid="T2">2</xref>), suggesting another mechanism for N retention through a decrease in N-based respiration. The underrepresentation of transcripts for amino acid metabolism, including glutamate dehydrogenase, threonine aldolase, <italic>asd</italic> (aspartate-semialdehyde dehydrogenase), <italic>metK</italic> (<italic>S</italic>-adenosylmethionine synthetase), <italic>tyrB</italic> (aromatic amino acid aminotransferase), and <italic>gcvT</italic> (glycine cleavage system T protein; Table <xref ref-type="table" rid="T2">2</xref>) was consistent with the substantial change in free amino acid concentrations observed under N-limited conditions (0.5% of cell N content compared to 1.3 and 4.2% under C and P limitation; Table <xref ref-type="table" rid="TA6">A6</xref> in Appendix), suggesting a reallocation of cytoplasmic N. Collectively, the transcriptional data support strong N homeostasis as the major response to N limitation, enabled through intense scavenging and tighter controls over N import/export and cytoplasmic pools.</p></sec><sec><title>Transcriptional response to P limitation</title><p>A <italic>phoB</italic>-mediated response involving scavenging for inorganic and organic sources of P dominated the P-limited transcriptome (Table <xref ref-type="table" rid="T2">2</xref>). Transcripts were enriched for transport or utilization of phosphate (<italic>pstB</italic>, -<italic>C</italic>, -<italic>S;</italic> Yuan et al., <xref ref-type="bibr" rid="B77">2006</xref>), phosphonate (<italic>phnD</italic>, -<italic>G</italic>, and -<italic>K</italic>; Metcalf and Wanner, <xref ref-type="bibr" rid="B42">1991</xref>; Parker et al., <xref ref-type="bibr" rid="B48">1999</xref>), and phosphate esters (<italic>phoX</italic>; Sebastian and Ammerman, <xref ref-type="bibr" rid="B57">2011</xref>; Table <xref ref-type="table" rid="T2">2</xref>). While inorganic P storage is common among bacteria, <italic>R. pomeroyi</italic> does not have a close homolog to the widespread P storage enzyme polyphosphate kinase I (<italic>ppk1</italic>; Newton et al., <xref ref-type="bibr" rid="B46">2010</xref>) or to 1,3-diphosphoglycerate-polyphosphate phosphotransferase or polyphosphate:AMP-phosphotransferase (Kulaev et al., <xref ref-type="bibr" rid="B38">1971</xref>; Ishige and Noguchi, <xref ref-type="bibr" rid="B33">2000</xref>). It has been suggested that SPO0224 functions as a <italic>ppk1</italic> in <italic>R. pomeroyi</italic> (Nahálka and Pätoprstý, <xref ref-type="bibr" rid="B45">2009</xref>), but neither that gene nor the two <italic>ppk2</italic> genes purported to degrade polyphosphates (SPOP1256 and SPO1727; Nahálka and Pätoprstý, <xref ref-type="bibr" rid="B45">2009</xref>) were transcriptionally modified under P limitation. Instead, there was evidence for lowering the P cell quota by reworking of membrane phospholipids, including enrichment of transcripts for an enoyl-CoA hydratase mediating fatty acid degradation, a phosphatidyl ethanolamine <italic>N</italic>-methyltransferase (<italic>pmtA</italic>), and a lipoprotein likely representing a membrane-bound degradative enzyme or stress sensor (Table <xref ref-type="table" rid="T2">2</xref>; Figure <xref ref-type="fig" rid="FA3">A3</xref> in Appendix). <italic>R. pomeroyi</italic> possesses genes for the synthesis of ornithine-containing lipids (<italic>olsAB-</italic>like genes), which incorporate N rather than P into lipid membranes. The transcription of <italic>olsB</italic> was highest under P limitation (Figure <xref ref-type="fig" rid="FA3">A3</xref> in Appendix), although the probes did not meet the significance cut off of ≥3-fold. These genes are important under P limitation in closely related Alphaproteobacteria (Weissenmayer et al., <xref ref-type="bibr" rid="B74">2002</xref>; Gao et al., <xref ref-type="bibr" rid="B20">2004</xref>) and in marine bacterioplankton communities (Van Mooy et al., <xref ref-type="bibr" rid="B67">2009</xref>), and we leave open the possibility that this pathway is involved in P content reworking in <italic>R. pomeroyi</italic>.</p></sec><sec><title>Transcriptional response to S limitation</title><p>Unlike responses to C, N, and P limitation, none of the 21 transcriptionally responsive genes to S limitation were indicative of scavenging (Tables <xref ref-type="table" rid="TA4">A4</xref> and <xref ref-type="table" rid="TA5">A5</xref> in Appendix). Instead, response took the form of increased relative expression of enzymes requiring S-containing substrates or cofactors (Figure <xref ref-type="fig" rid="FA4">A4</xref> in Appendix). Changes in transcript abundance for the synthesis of 5-amino-levulinate (<italic>hemA-1</italic>), protoporphyrinogen IX (<italic>hemN</italic>), sirohydrochlorin (<italic>cobA-1</italic>), and the quorum sensor regulator <italic>luxR-1</italic> (Table <xref ref-type="table" rid="T2">2</xref>; Figure <xref ref-type="fig" rid="FA4">A4</xref> in Appendix) may all be linked to a depleted pool of <italic>S</italic>-adenosyl-methionine (Figure <xref ref-type="fig" rid="FA4">A4</xref> in Appendix). Evidence for a cellular stress response was strongest under S limitation, and this included enrichment of transcripts for a thiol-containing antioxidant protein, a universal stress protein, and a σ<sup>32</sup> factor (<italic>rpoH-2</italic>), along with the gene <italic>ppk2</italic> (Table <xref ref-type="table" rid="TA4">A4</xref> in Appendix), which degrades polyphosphate to GTP and is implicated in bacterial stress responses (Brown and Kornberg, <xref ref-type="bibr" rid="B5">2008</xref>; Gangaiah et al., <xref ref-type="bibr" rid="B19">2010</xref>).</p><p>The S-limited transcriptome provided a useful perspective on transcriptional responses to limitation by an element that is not naturally limiting in the ocean (seawater SO<sub>4</sub> concentrations are ∼28 mmol l<sup>−1</sup>) and therefore for which there is little selective pressure to evolve responses to scarcity. The biasing of the S-limited transcriptome toward biosynthetic pathways with depleted end products, while a successful strategy for addressing metabolic imbalances in bacteria (Goyal et al., <xref ref-type="bibr" rid="B24">2010</xref>), cannot solve a cell-wide elemental deficit. In <italic>E. coli</italic>, scavenging responses occur through the CysB system that upregulates transporters for sulfate, cysteine, and alternate sources of S (Gyaneshwar et al., <xref ref-type="bibr" rid="B26">2005</xref>). However, the <italic>R. pomeroyi</italic> DSS-3 genome does not contain a CysB ortholog.</p><p>The fact that S limitation was the only condition that did not invoke a scavenging response for obtaining more of the limiting element indicates that transcriptional regulation in <italic>R. pomeroyi</italic> is not evolutionarily attuned for S limitation. By analogy, the absence of an N storage response may indicate that conditions under which excess N is available for transport and storage by bacterioplankton are rare in the ocean. Indeed, a search of the marine bacterioplankton genes captured in the Global Ocean Sampling (GOS) dataset (Rusch et al., <xref ref-type="bibr" rid="B54">2007</xref>; Yooseph et al., <xref ref-type="bibr" rid="B76">2007</xref>) indicated that fewer than 3% of surface ocean bacterioplankton have homologs for <italic>cysB</italic>. Similarly, fewer than 1% of bacterioplankton carry homologs for either of the two genes required for N storage (CPG synthetase and cyanophycinase; Table <xref ref-type="table" rid="TA7">A7</xref> in Appendix). Transcriptional responses of <italic>R. pomeroyi</italic> may therefore provide insights into the role of seawater chemistry in molding the evolution of marine bacterioplankton genome content.</p></sec><sec><title>Explaining cell stoichiometry changes</title><p>To link transcriptional responses to cell stoichiometry under different element limitations, we estimated the composition of <italic>R. pomeroyi</italic> biomass under balanced growth (i.e., when all elements are available in excess and the C:N:P ratio is optimal); this is the conceptual starting point from which the cells’ transcriptional responses produced the observed element-limited ratios (Table <xref ref-type="table" rid="T1">1</xref>). The simplest model, one in which C:N:P ratios under element limitation are reached through a proportional change in only the limiting element, fit our data well. This does not necessarily require that C, N, and P are unlinked in the cell, but rather that the net result of resource limitation is a decrease in only the limiting element, where α<sub>X</sub> is the factor by which element <sc>x (c, n</sc>, or <sc>p)</sc> changes when it is limiting. The best solution to the elemental ratio data emerged with a C:N:P of ∼154:15:1 under balanced growth (Figure <xref ref-type="fig" rid="F1">1</xref>). From this initial ratio, C-limited cells (56:13:1; Table <xref ref-type="table" rid="T1">1</xref>) would have undergone a relative C decrease to 38% of balanced growth levels (αC = 1/0.38), P-limited cells (333:35:1) would have undergone a relative P decrease to 40% of balanced growth (αP = 1/0.4), but N-limited cells (167:15:1) would have undergone almost no change in N content (αN = 1/1.0; Figure <xref ref-type="fig" rid="F1">1</xref>).</p><fig id="F1" position="float"><label>Figure 1</label><caption><p><bold>Modeled C:P and N:P atomic ratios of <italic>R. pomeroyi</italic> DSS-3 cells over a range of depletion factors (α) for the limiting element (see <xref ref-type="sec" rid="s1">Materials and Methods</xref>)</bold>. The model assumes that limitation decreases the concentration of the limiting element relative to its value under balanced growth by a factor α, but the non-limiting elements are not affected. Measured C:N:P ratios in the element-limited chemostats are shown as symbols with bold borders, and modeled balanced growth ratios assuming different values of α are shown as solid lines. Dotted lines show elemental ratios if one of the non-limiting elements also changes during limitation, but by a factor 10-fold less than for the limiting element. The region where the three lines intersect (yellow shading) indicates the simultaneous solution for the C:N:P ratio (∼154:15:1). Other plotted C:P and N:P ratios are as follows: gray circle with black border, S-limited <italic>R. pomeroyi</italic> DSS-3 cells; purple X, Redfield ratio (Redfield, <xref ref-type="bibr" rid="B51">1934</xref>); orange X, marine bacteria (Cotner et al., <xref ref-type="bibr" rid="B8">1997</xref>); brown X, aquatic bacteria (Fagerbakke et al., <xref ref-type="bibr" rid="B15">1996</xref>); blue X, freshwater bacteria (Cotner et al., <xref ref-type="bibr" rid="B9">2010</xref>).</p></caption><graphic xlink:href="fmicb-03-00159-g001"></graphic></fig><p>The transcriptional changes in <italic>R. pomeroyi</italic> strongly support this model. Only the C- and P-limited cells exhibited reworking strategies to decrease cell quotas (degradation of stored reserves, decreases in production or secretion of extracellular products, restructuring of membranes; Table <xref ref-type="table" rid="T2">2</xref>). Only the N-limited cells showed a substantial gate-keeping response and tightening of control over cytoplasmic pools (Table <xref ref-type="table" rid="T2">2</xref>). It is not yet evident whether strong N homeostasis compared to C and P is a feature that can be generalized to other heterotrophic marine bacterioplankton, although <italic>R. pomeroyi</italic> represents a ubiquitous bacterial taxon in surface ocean waters (Moran et al., <xref ref-type="bibr" rid="B43">2004</xref>) and its growth rate in the continuous cultures was within the range measured for marine bacterioplankton <italic>in situ</italic> (Ducklow and Hill, <xref ref-type="bibr" rid="B12">1985</xref>; Whitman et al., <xref ref-type="bibr" rid="B75">1998</xref>). Four unidentified marine bacterial isolates studied by Vrede et al. (<xref ref-type="bibr" rid="B69">2002</xref>) did not show a similar N homeostasis (Figure <xref ref-type="fig" rid="FA5">A5</xref> in Appendix), although they were not grown in continuous culture. Elemental ratios measured for natural bacterioplankton typically do not fall within the balanced growth region for <italic>R. pomeroyi</italic> (Figure <xref ref-type="fig" rid="F1">1</xref>) and are a better match to the ratios found under C limitation, suggesting that marine bacteria may be most often C-limited in the ocean.</p><p>A central concept in stoichiometric ecology is that growth rate changes drive differences in biomass elemental composition through shifts in the content of P-rich RNA (Sterner et al., <xref ref-type="bibr" rid="B59">2008</xref>). For marine microbes, this growth rate hypothesis (GRH) will be most relevant when bacterioplankton are growing at different rates, such as during phytoplankton blooms or mixing events relative to non-bloom conditions or dormancy. By comparison, <italic>R. pomeroyi</italic> was studied under constant growth rate but differing stoichiometry of external resources, a scenario more relevant when the element limiting heterotrophic growth varies over time or space (e.g., Thingstad, <xref ref-type="bibr" rid="B62">1987</xref>; Kirchman, <xref ref-type="bibr" rid="B35">1990</xref>; Pomeroy et al., <xref ref-type="bibr" rid="B49">1995</xref>; Cherrier et al., <xref ref-type="bibr" rid="B7">1996</xref>; Cotner et al., <xref ref-type="bibr" rid="B8">1997</xref>; Kirchman and Rich, <xref ref-type="bibr" rid="B34">1997</xref>; Zohary and Robarts, <xref ref-type="bibr" rid="B80">1998</xref>; Torréton et al., <xref ref-type="bibr" rid="B65">2000</xref>; Van Wambeke et al., <xref ref-type="bibr" rid="B68">2002</xref>; Obernosterer et al., <xref ref-type="bibr" rid="B47">2003</xref>; Thingstad et al., <xref ref-type="bibr" rid="B64">2005</xref>). In exploring stoichiometric changes predicted under the GRH, Loladze and Elser (<xref ref-type="bibr" rid="B39">2011</xref>) calculated a microbial protein:rRNA ratio of 3 under optimal growth conditions (cellular N:P ratio = 16). Our balanced growth-stoichiometry calculation for <italic>R. pomeroyi</italic> agrees with this (N:P ratio = 15; Figure <xref ref-type="fig" rid="F1">1</xref>). Under non-optimal conditions however, which are commonplace in the ocean, transcriptional responses of heterotrophic bacteria can drive biomass C:N:P ratios from this ideal value through physiological mechanisms that store certain elements when available in excess and strongly retain others when scarce. The consistency of transcriptional reactions among the diverse taxa that make up marine bacterial assemblages will determine the aggregate community response to element limitation in the ocean (Hall et al., <xref ref-type="bibr" rid="B27">2011</xref>; Scott et al., <xref ref-type="bibr" rid="B56">2012</xref>).</p></sec></sec><sec><title>Conclusion</title><p>Bacterioplankton transcriptional changes reveal the cellular basis for biomass stoichiometry outcomes whose effects are manifested at the ecosystem level. Flexible biomass ratios provide a buffer in the development of nutrient limitation (Thingstad et al., <xref ref-type="bibr" rid="B63">2008</xref>) and, at least in the short term, delay intensification of bacterial–phytoplankton competition. Stoichiometric flexibility also broadens the range of C:N:P ratios in bacterial biomass produced in ocean surface waters, with consequences for basin-scale differences in particulate material and sequestration of organic matter deviating from Redfield proportions (Geider and La Roche, <xref ref-type="bibr" rid="B21">2002</xref>; Hessen et al., <xref ref-type="bibr" rid="B31">2004</xref>; Sterner et al., <xref ref-type="bibr" rid="B59">2008</xref>; Weber and Deutsch, <xref ref-type="bibr" rid="B73">2010</xref>). For model marine heterotrophic bacterium <italic>R. pomeroyi</italic>, cellular biomass ratios reflect a net transcriptional balance between element scavenging responses, gate-keeping activities, and cell quota changes, with the balance between these expression responses dictated by which element is limiting its growth.</p></sec><sec><title>Conflict of Interest Statement</title><p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p></sec></body><back><ack><p>This work was supported by a grant from the Gordon and Betty Moore Foundation and the National Science Foundation (OCE-0724017). We thank J. Rinta-Kanto for advice on microarray analysis, C. Reisch and W. Whitman for guidance on chemostat setup, Y. Liu for advice on amino acid analysis, and C. English for graphics assistance.</p></ack><fn-group><fn id="fn1"><p><sup>1</sup><uri xlink:type="simple" xlink:href="http://www.ncbi.nlm.nih.gov/geo/">http://www.ncbi.nlm.nih.gov/geo/</uri></p></fn><fn id="fn2"><p><sup>2</sup><uri xlink:type="simple" xlink:href="http://www.tm4.org/mev/">http://www.tm4.org/mev/</uri></p></fn><fn id="fn3"><p><sup>3</sup><uri xlink:type="simple" xlink:href="http://www.roseobase.org/">http://www.roseobase.org/</uri></p></fn><fn id="fn4"><p><sup>4</sup><uri xlink:type="simple" xlink:href="http://biocyc.org/">http://biocyc.org/</uri></p></fn><fn id="fn5"><p><sup>5</sup><uri xlink:type="simple" xlink:href="http://camera.calit2.net/">http://camera.calit2.net/</uri></p></fn></fn-group><app-group><app id="A1"><title>Appendix</title><table-wrap id="TA1" position="anchor"><label>Table A1</label><caption><p><bold>Chemostat culture medium</bold>.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">Compound</th><th align="left" rowspan="1" colspan="1">Concentration</th></tr></thead><tbody><tr><td style="background-color:#B2B2B2" colspan="2" align="left" rowspan="1"><bold>MACRONUTRIENT<xref ref-type="table-fn" rid="tfn6"><sup>a</sup></xref></bold></td></tr><tr><td align="left" rowspan="1" colspan="1">Glucose (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>)</td><td align="left" rowspan="1" colspan="1">4.50 mmol l<sup>−1</sup> (1.00 mmol l<sup>−1</sup>)</td></tr><tr><td align="left" rowspan="1" colspan="1">Phosphate (KH<sub>2</sub>PO<sub>4</sub>)</td><td align="left" rowspan="1" colspan="1">0.50 mmol l<sup>−1</sup> (9.20 μmol l<sup>−1</sup>)</td></tr><tr><td align="left" rowspan="1" colspan="1">Ammonium (NH<sub>4</sub>Cl)</td><td align="left" rowspan="1" colspan="1">2.80 mmol l<sup>−1</sup> (0.26 mmol l<sup>−1</sup>)</td></tr><tr><td align="left" rowspan="1" colspan="1">Sulfate (Na<sub>2</sub>SO<sub>4</sub>)</td><td align="left" rowspan="1" colspan="1">2.50 mmol l<sup>−1</sup> (25.00 μmol l<sup>−1</sup>)</td></tr><tr><td style="background-color:#B2B2B2" colspan="2" align="left" rowspan="1"><bold>BUFFER, IRON, AND SALT<xref ref-type="table-fn" rid="tfn7"><sup>b</sup></xref></bold></td></tr><tr><td align="left" rowspan="1" colspan="1">Bis–tris propane (C<sub>11</sub>H<sub>26</sub>N<sub>2</sub>O<sub>6</sub>)<xref ref-type="table-fn" rid="tfn8"><sup>c</sup></xref></td><td align="left" rowspan="1" colspan="1">9.91 mmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">CaCl<sub>2</sub>·2H<sub>2</sub>O</td><td align="left" rowspan="1" colspan="1">7.42 mmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">MgCl<sub>2</sub></td><td align="left" rowspan="1" colspan="1">106.21 mmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">Iron-EDTA (C<sub>10</sub>H<sub>12</sub>FeN<sub>2</sub>NaO<sub>8</sub>)<xref ref-type="table-fn" rid="tfn9"><sup>d</sup></xref></td><td align="left" rowspan="1" colspan="1">67.52 μmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">KCl</td><td align="left" rowspan="1" colspan="1">10.64 mmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">NaCl</td><td align="left" rowspan="1" colspan="1">198.49 mmol l<sup>−1</sup></td></tr><tr><td style="background-color:#B2B2B2" colspan="2" align="left" rowspan="1"><bold>TRACE ELEMENT</bold></td></tr><tr><td align="left" rowspan="1" colspan="1">C<sub>6</sub>H<sub>9</sub>NO<sub>6</sub></td><td align="left" rowspan="1" colspan="1">12.95 μmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">CoCl<sub>2</sub>·6H<sub>2</sub>O</td><td align="left" rowspan="1" colspan="1">0.80 μmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">Na<sub>2</sub>SeO<sub>3</sub></td><td align="left" rowspan="1" colspan="1">1.87 μmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">Na<sub>2</sub>WO<sub>4</sub>·2H<sub>2</sub>O</td><td align="left" rowspan="1" colspan="1">0.55 μmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">BaCl<sub>2</sub>·2H<sub>2</sub>O</td><td align="left" rowspan="1" colspan="1">0.49 μmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">CuSO<sub>4</sub></td><td align="left" rowspan="1" colspan="1">55.57 nmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">MnSO<sub>4</sub>·H<sub>2</sub>O</td><td align="left" rowspan="1" colspan="1">0.77 μmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">ZnSO<sub>4</sub>·7H<sub>2</sub>O</td><td align="left" rowspan="1" colspan="1">0.54 μmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">Na<sub>2</sub>MoO<sub>4</sub>·2H<sub>2</sub>O</td><td align="left" rowspan="1" colspan="1">0.57 μmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">Na<sub>2</sub>SiO<sub>3</sub>·9H<sub>2</sub>O</td><td align="left" rowspan="1" colspan="1">0.45 μmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">SrCl<sub>2</sub>·6H<sub>2</sub>O</td><td align="left" rowspan="1" colspan="1">0.19 mmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">NiCl<sub>2</sub>·6H<sub>2</sub>O</td><td align="left" rowspan="1" colspan="1">96.32 nmol l<sup>−1</sup></td></tr><tr><td style="background-color:#B2B2B2" colspan="2" align="left" rowspan="1"><bold>VITAMIN</bold></td></tr><tr><td align="left" rowspan="1" colspan="1">Thiamine (B1)</td><td align="left" rowspan="1" colspan="1">0.15 μmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">Nicotinic acid (B3)</td><td align="left" rowspan="1" colspan="1">0.40 μmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">Pyridoxine-HCl (B6)</td><td align="left" rowspan="1" colspan="1">0.48 μmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">Folic acid (B9)</td><td align="left" rowspan="1" colspan="1">44.86 nmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">Cyanocobalamin (B12)</td><td align="left" rowspan="1" colspan="1">7.30 nmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">Riboflavin (B2)</td><td align="left" rowspan="1" colspan="1">0.13 μmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">Pantothenic acid (B5)</td><td align="left" rowspan="1" colspan="1">0.23 μmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1">Biotin (B7)</td><td align="left" rowspan="1" colspan="1">81.05 nmol l<sup>−1</sup></td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>p</italic>-aminobenzoic acid (B10)</td><td align="left" rowspan="1" colspan="1">0.36 μmol l<sup>−1</sup></td></tr></tbody></table><table-wrap-foot><fn id="tfn6"><p><italic><sup>a</sup>Limiting macronutrient in parenthesis</italic>.</p></fn><fn id="tfn7"><p><italic><sup>b</sup>Final salts concentration is 23.6 g l<sup>−1</sup> (salinity of ∼25)</italic>.</p></fn><fn id="tfn8"><p><italic><sup>c</sup>Bis–tris propane, 1,3-bis(tris(hydroxymethyl)methylamino)propane</italic>.</p></fn><fn id="tfn9"><p><italic><sup>d</sup>Iron-EDTA, ethylenediaminetetraacetic acid iron (III) sodium salts</italic>.</p></fn></table-wrap-foot></table-wrap><table-wrap id="TA2" position="anchor"><label>Table A2</label><caption><p><bold>Spearman’s rank correlation coefficients of the normalized fluorescence values in 5,145 probes between replicate arrays</bold>.</p></caption><table frame="hsides" rules="groups"><thead><tr><th colspan="2" align="left" rowspan="1">C-limited</th><th colspan="3" align="left" rowspan="1">N-limited<xref ref-type="table-fn" rid="tfn10"><sup>a</sup></xref></th><th colspan="3" align="left" rowspan="1">P-limited</th><th colspan="3" align="left" rowspan="1">S-limited<xref ref-type="table-fn" rid="tfn10"><sup>a</sup></xref></th><th align="left" rowspan="1" colspan="1"></th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">0.91</td><td align="left" rowspan="1" colspan="1">0.92</td><td align="left" rowspan="1" colspan="1">0.80</td><td align="left" rowspan="1" colspan="1">0.78</td><td align="left" rowspan="1" colspan="1">0.79</td><td align="left" rowspan="1" colspan="1">0.74</td><td align="left" rowspan="1" colspan="1">0.77</td><td align="left" rowspan="1" colspan="1">0.70</td><td align="left" rowspan="1" colspan="1">0.76</td><td align="left" rowspan="1" colspan="1">0.76</td><td align="left" rowspan="1" colspan="1">0.74</td><td align="left" rowspan="1" colspan="1"><bold>C-limited</bold></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.96</td><td align="left" rowspan="1" colspan="1">0.70</td><td align="left" rowspan="1" colspan="1">0.75</td><td align="left" rowspan="1" colspan="1">0.74</td><td align="left" rowspan="1" colspan="1">0.67</td><td align="left" rowspan="1" colspan="1">0.66</td><td align="left" rowspan="1" colspan="1">0.64</td><td align="left" rowspan="1" colspan="1">0.73</td><td align="left" rowspan="1" colspan="1">0.69</td><td align="left" rowspan="1" colspan="1">0.69</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.72</td><td align="left" rowspan="1" colspan="1">0.78</td><td align="left" rowspan="1" colspan="1">0.79</td><td align="left" rowspan="1" colspan="1">0.66</td><td align="left" rowspan="1" colspan="1">0.69</td><td align="left" rowspan="1" colspan="1">0.63</td><td align="left" rowspan="1" colspan="1">0.71</td><td align="left" rowspan="1" colspan="1">0.71</td><td align="left" rowspan="1" colspan="1">0.69</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.91</td><td align="left" rowspan="1" colspan="1">0.88</td><td align="left" rowspan="1" colspan="1">0.76</td><td align="left" rowspan="1" colspan="1">0.77</td><td align="left" rowspan="1" colspan="1">0.69</td><td align="left" rowspan="1" colspan="1">0.67</td><td align="left" rowspan="1" colspan="1">0.69</td><td align="left" rowspan="1" colspan="1">0.73</td><td align="left" rowspan="1" colspan="1"><bold>N-limited<xref ref-type="table-fn" rid="tfn10"><sup>a</sup></xref></bold></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.92</td><td align="left" rowspan="1" colspan="1">0.75</td><td align="left" rowspan="1" colspan="1">0.75</td><td align="left" rowspan="1" colspan="1">0.69</td><td align="left" rowspan="1" colspan="1">0.63</td><td align="left" rowspan="1" colspan="1">0.69</td><td align="left" rowspan="1" colspan="1">0.70</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.68</td><td align="left" rowspan="1" colspan="1">0.75</td><td align="left" rowspan="1" colspan="1">0.60</td><td align="left" rowspan="1" colspan="1">0.58</td><td align="left" rowspan="1" colspan="1">0.69</td><td align="left" rowspan="1" colspan="1">0.63</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.91</td><td align="left" rowspan="1" colspan="1">0.96</td><td align="left" rowspan="1" colspan="1">0.75</td><td align="left" rowspan="1" colspan="1">0.81</td><td align="left" rowspan="1" colspan="1">0.82</td><td align="left" rowspan="1" colspan="1"><bold>P-limited</bold></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.89</td><td align="left" rowspan="1" colspan="1">0.71</td><td align="left" rowspan="1" colspan="1">0.85</td><td align="left" rowspan="1" colspan="1">0.79</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.76</td><td align="left" rowspan="1" colspan="1">0.81</td><td align="left" rowspan="1" colspan="1">0.84</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.82</td><td align="left" rowspan="1" colspan="1">0.90</td><td align="left" rowspan="1" colspan="1"><bold>S-limited<xref ref-type="table-fn" rid="tfn10"><sup>a</sup></xref></bold></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.87</td><td align="left" rowspan="1" colspan="1"></td></tr></tbody></table><table-wrap-foot><fn id="tfn10"><p><italic><sup>a</sup>The coefficient of correlation between the two technical replicate N limitation arrays is 0.89; for the two S limitation arrays is 0.96</italic>.</p></fn></table-wrap-foot></table-wrap><table-wrap id="TA3" position="anchor"><label>Table A3</label><caption><p><bold>Bacterial dry weights</bold>.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">Organism</th><th align="left" rowspan="1" colspan="1">Growth conditions<xref ref-type="table-fn" rid="tfn11"><sup>a</sup></xref></th><th align="left" rowspan="1" colspan="1">Dry weight (fg cell<sup>−1</sup>)</th><th align="left" rowspan="1" colspan="1">Reference</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"><italic>Ruegeria pomeroyi</italic></td><td align="left" rowspan="1" colspan="1">Steady-state culture, C-limited (dt = 16.5 h)</td><td align="left" rowspan="1" colspan="1">454</td><td align="left" rowspan="1" colspan="1">This study</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Steady-state culture, N-limited (dt = 16.5 h)</td><td align="left" rowspan="1" colspan="1">758</td><td align="left" rowspan="1" colspan="1">This study</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Steady-state culture, P-limited (dt = 16.5 h)</td><td align="left" rowspan="1" colspan="1">1388</td><td align="left" rowspan="1" colspan="1">This study</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Steady-state culture, S-limited (dt = 16.5 h)</td><td align="left" rowspan="1" colspan="1">246</td><td align="left" rowspan="1" colspan="1">This study</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Escherichia coli</italic></td><td align="left" rowspan="1" colspan="1">Batch culture in low potassium medium (growing)</td><td align="left" rowspan="1" colspan="1">710<xref ref-type="table-fn" rid="tfn12"><sup>b</sup></xref></td><td align="left" rowspan="1" colspan="1">Fagerbakke et al. (<xref ref-type="bibr" rid="B15">1996</xref>)</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Batch culture in low potassium medium (stationary)</td><td align="left" rowspan="1" colspan="1">180<xref ref-type="table-fn" rid="tfn12"><sup>b</sup></xref></td><td align="left" rowspan="1" colspan="1">Fagerbakke et al. (<xref ref-type="bibr" rid="B15">1996</xref>)</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Batch culture in glucose minimal medium (dt = 40 min)</td><td align="left" rowspan="1" colspan="1">280<xref ref-type="table-fn" rid="tfn13"><sup>c</sup></xref></td><td align="left" rowspan="1" colspan="1">Neidhardt et al. (<xref ref-type="bibr" rid="B81">1996</xref>)</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Vibrio natriegens</italic></td><td align="left" rowspan="1" colspan="1">Batch culture in brain heart infusion medium (growing)</td><td align="left" rowspan="1" colspan="1">850<xref ref-type="table-fn" rid="tfn12"><sup>b</sup></xref></td><td align="left" rowspan="1" colspan="1">Fagerbakke et al. (<xref ref-type="bibr" rid="B15">1996</xref>)</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Batch culture in brain heart infusion medium (stationary)</td><td align="left" rowspan="1" colspan="1">145<xref ref-type="table-fn" rid="tfn12"><sup>b</sup></xref></td><td align="left" rowspan="1" colspan="1">Fagerbakke et al. (<xref ref-type="bibr" rid="B15">1996</xref>)</td></tr><tr><td align="left" rowspan="1" colspan="1">Natural marine bacterioplankton isolate</td><td align="left" rowspan="1" colspan="1">Batch culture (exponential)</td><td align="left" rowspan="1" colspan="1">427<xref ref-type="table-fn" rid="tfn14"><sup>d</sup></xref></td><td align="left" rowspan="1" colspan="1">Vrede et al. (<xref ref-type="bibr" rid="B69">2002</xref>)</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Batch culture, C-limited (stationary)</td><td align="left" rowspan="1" colspan="1">110<xref ref-type="table-fn" rid="tfn14"><sup>d</sup></xref></td><td align="left" rowspan="1" colspan="1">Vrede et al. (<xref ref-type="bibr" rid="B69">2002</xref>)</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Batch culture, N-limited (stationary)</td><td align="left" rowspan="1" colspan="1">276<xref ref-type="table-fn" rid="tfn14"><sup>d</sup></xref></td><td align="left" rowspan="1" colspan="1">Vrede et al. (<xref ref-type="bibr" rid="B69">2002</xref>)</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Batch culture, P-limited (stationary)</td><td align="left" rowspan="1" colspan="1">270<xref ref-type="table-fn" rid="tfn14"><sup>d</sup></xref></td><td align="left" rowspan="1" colspan="1">Vrede et al. (<xref ref-type="bibr" rid="B69">2002</xref>)</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Native isolates from various aquatic environments</td><td align="left" rowspan="1" colspan="1">21–60<xref ref-type="table-fn" rid="tfn15"><sup>e</sup></xref></td><td align="left" rowspan="1" colspan="1">Fagerbakke et al. (<xref ref-type="bibr" rid="B15">1996</xref>)</td></tr></tbody></table><table-wrap-foot><fn id="tfn11"><p><italic><sup>a</sup>dt = doubling time (specified if available)</italic>.</p></fn><fn id="tfn12"><p><italic><sup>b</sup>Data from Table 1 (Fagerbakke et al., <xref ref-type="bibr" rid="B15">1996</xref>)</italic>.</p></fn><fn id="tfn13"><p><italic><sup>c</sup>Calculated with data in page 14 (Neidhardt et al., <xref ref-type="bibr" rid="B81">1996</xref>) with an assumption that 70% of cytoplasm is water</italic>.</p></fn><fn id="tfn14"><p><italic><sup>d</sup>Data from Table 3 (Vrede et al., <xref ref-type="bibr" rid="B69">2002</xref>). Average of four isolates (exponential and C-limited cultures), three isolates (N-limited cultures), or two isolates (P-limited cultures)</italic>.</p></fn><fn id="tfn15"><p><italic><sup>e</sup>Native bacteria were from aquatic environments in Norway, Finland, and Denmark (see Table 1 in Fagerbakke et al., <xref ref-type="bibr" rid="B15">1996</xref>)</italic>.</p></fn></table-wrap-foot></table-wrap><table-wrap id="TA4" position="anchor"><label>Table A4</label><caption><p><bold>Transcriptionally enriched <italic>R. pomeroy</italic><italic>i</italic> DSS-3 genes</bold>.</p></caption><table frame="hsides" rules="groups"><thead><tr><th valign="top" align="left" rowspan="1" colspan="1">Locus tag</th><th valign="top" align="left" rowspan="1" colspan="1">Gene</th><th valign="top" align="left" rowspan="1" colspan="1">Product</th><th valign="top" colspan="2" align="center" rowspan="1">Fold-change ratio<xref ref-type="table-fn" rid="tfn16"><sup>a</sup></xref><hr></hr></th></tr><tr><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1">Probe 1</th><th align="left" rowspan="1" colspan="1">Probe 2</th></tr></thead><tbody><tr><td style="background-color:#B2B2B2" colspan="5" align="left" rowspan="1"><bold>C-LIMITED (68 GENES)</bold></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0090</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">5.3</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0107</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>recQ</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">ATP-dependent DNA helicase</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">1.0</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">6.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0120</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">3.9</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0149</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>dnaA</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Chromosomal replication initiation protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">16.5</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">1.2</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0171</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>fliR</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Flagellar biosynthetic protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">1.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">6.7</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0183</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>fliI</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">H<sup>+</sup>-transporting two-sector ATPase, flagellum-specific</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">6.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">1.0</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0265</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Auxin efflux carrier family protein</td><td align="left" rowspan="1" colspan="1">2.1</td><td align="left" rowspan="1" colspan="1">4.4</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0276</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">LuxR family transcriptional regulator</td><td align="left" rowspan="1" colspan="1">0.8</td><td align="left" rowspan="1" colspan="1">3.0</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0590</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">LacI family transcription regulator (carbon catabolite repression domain-containing)</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">14.5</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0875</td><td align="left" rowspan="1" colspan="1"><italic>gap-2</italic></td><td align="left" rowspan="1" colspan="1">Glyceraldehyde-3-phosphate dehydrogenase, type I</td><td align="left" rowspan="1" colspan="1">8.4</td><td align="left" rowspan="1" colspan="1">1.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0911</td><td align="left" rowspan="1" colspan="1"><italic>proC</italic></td><td align="left" rowspan="1" colspan="1">Pyrroline-5-carboxylate reductase</td><td align="left" rowspan="1" colspan="1">3.2</td><td align="left" rowspan="1" colspan="1">3.2</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0939</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">M48 family peptidase</td><td align="left" rowspan="1" colspan="1">1.1</td><td align="left" rowspan="1" colspan="1">8.5</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0940</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">3.4</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0970</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>apqZ</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Aquaporin Z</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.1</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">1.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0988</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">YeeE/YedE family protein</td><td align="left" rowspan="1" colspan="1">1.1</td><td align="left" rowspan="1" colspan="1">3.0</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0999</td><td align="left" rowspan="1" colspan="1"><italic>soxD</italic></td><td align="left" rowspan="1" colspan="1">Diheme cytochrome c</td><td align="left" rowspan="1" colspan="1">1.4</td><td align="left" rowspan="1" colspan="1">3.8</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1001</td><td align="left" rowspan="1" colspan="1"><italic>soxF</italic></td><td align="left" rowspan="1" colspan="1">Sulfur oxidation F protein</td><td align="left" rowspan="1" colspan="1">3.2</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1063</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">1.2</td><td align="left" rowspan="1" colspan="1">3.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1092</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">LysR family transcriptional regulator</td><td align="left" rowspan="1" colspan="1">3.0</td><td align="left" rowspan="1" colspan="1">1.8</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1132</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Glycine betaine/proline ABC transporter, ATP-binding protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.1</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.0</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1138</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">AsnC family transcriptional regulator</td><td align="left" rowspan="1" colspan="1">6.2</td><td align="left" rowspan="1" colspan="1">4.7</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1156</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>hisF</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Imidazole glycerol phosphate synthase subunit</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.0</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.5</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1337</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">3.9</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1446</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Cyclase, putative</td><td align="left" rowspan="1" colspan="1">3.8</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1463</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">TRAP dicarboxylate transporter, DctM subunit</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">8.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1499</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Alpha/beta fold family hydrolase</td><td align="left" rowspan="1" colspan="1">5.2</td><td align="left" rowspan="1" colspan="1">1.4</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1592</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Aminomethyl transferase family protein</td><td align="left" rowspan="1" colspan="1">2.3</td><td align="left" rowspan="1" colspan="1">3.4</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1645</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Oligopeptide/dipeptide ABC transporter, permease protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">4.6</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1702</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">3.6</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1774</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">3-hydroxyanthranilate 3,4-dioxygenase</td><td align="left" rowspan="1" colspan="1">3.3</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1796</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Formate dehydrogenase, alpha subunit, putative</td><td align="left" rowspan="1" colspan="1">3.4</td><td align="left" rowspan="1" colspan="1">4.7</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1807</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">DNA polymerase III epsilon subunit family exonuclease</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.7</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">1.0</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2029</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Glutamine amidotransferase class-II</td><td align="left" rowspan="1" colspan="1">3.4</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2166</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Putative lipoprotein</td><td align="left" rowspan="1" colspan="1">0.6</td><td align="left" rowspan="1" colspan="1">3.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2205</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">ErfK/YbiS/YcfS/YnhG family protein</td><td align="left" rowspan="1" colspan="1">7.2</td><td align="left" rowspan="1" colspan="1">0.5</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2301</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">OsmC-like family protein</td><td align="left" rowspan="1" colspan="1">5.2</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2306</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">3.4</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2325</td><td align="left" rowspan="1" colspan="1"><italic>serS</italic></td><td align="left" rowspan="1" colspan="1">Seryl-tRNA synthetase</td><td align="left" rowspan="1" colspan="1">3.2</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO2370</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Sodium:alanine symporter family protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.4</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2371</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Universal stress protein family protein</td><td align="left" rowspan="1" colspan="1">4.4</td><td align="left" rowspan="1" colspan="1">1.8</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2422</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1"><sc>d</sc>-isomer specific 2-hydroxyacid dehydrogenase family protein</td><td align="left" rowspan="1" colspan="1">6.4</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2644</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">VWA domain CoxE-like family protein</td><td align="left" rowspan="1" colspan="1">11.3</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2647</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">3.0</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2668</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">LysR family transcriptional regulator</td><td align="left" rowspan="1" colspan="1">3.2</td><td align="left" rowspan="1" colspan="1">1.1</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2747</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Diguanylate cyclase, putative</td><td align="left" rowspan="1" colspan="1">3.7</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2845</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">3.8</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2881</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Xanthine dehydrogenase family protein, large subunit</td><td align="left" rowspan="1" colspan="1">5.0</td><td align="left" rowspan="1" colspan="1">1.0</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2989</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Cytochrome b562</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">1.4</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3121</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">MATE efflux family protein</td><td align="left" rowspan="1" colspan="1">4.3</td><td align="left" rowspan="1" colspan="1">0.9</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO3291</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Branched-chain amino acid ABC transporter, periplasmic</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">5.5</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">4.0</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3407</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">1.7</td><td align="left" rowspan="1" colspan="1">5.7</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO3461</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Flagellar protein FlgJ, putative</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">8.5</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3552</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Oxidoreductase, FAD-binding</td><td align="left" rowspan="1" colspan="1">3.2</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3562</td><td align="left" rowspan="1" colspan="1"><italic>tauR</italic></td><td align="left" rowspan="1" colspan="1">Transcriptional regulator</td><td align="left" rowspan="1" colspan="1">5.2</td><td align="left" rowspan="1" colspan="1">1.5</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3577</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">3.8</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3589</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">3.0</td><td align="left" rowspan="1" colspan="1">0.8</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3641</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">ABC transporter, permease protein</td><td align="left" rowspan="1" colspan="1">1.2</td><td align="left" rowspan="1" colspan="1">3.7</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3734</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">MerR family transcriptional regulator</td><td align="left" rowspan="1" colspan="1">4.2</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3735</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Major facilitator family protein</td><td align="left" rowspan="1" colspan="1">1.4</td><td align="left" rowspan="1" colspan="1">6.2</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3737</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Pyridine nucleotide-disulfide oxidoreductase family protein</td><td align="left" rowspan="1" colspan="1">4.4</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3764</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Glutathione <italic>S</italic>-transferase family protein</td><td align="left" rowspan="1" colspan="1">1.2</td><td align="left" rowspan="1" colspan="1">6.8</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO3783</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Sugar ABC transporter, ATP-binding protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">8.0</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPOA0097</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Branched-chain amino acid ABC transporter, permease protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.6</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">1.4</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPOA0160</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">TRAP dicarboxylate transporter, DctM subunit</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">8.7</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPOA0247</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">3.0</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPOA0289</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">AraC family transcriptional regulator</td><td align="left" rowspan="1" colspan="1">4.1</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPOA0299</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Branched-chain amino acid ABC transporter, permease protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.9</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.7</td></tr><tr><td align="left" rowspan="1" colspan="1">SPOA0317</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">AsnC family transcriptional regulator</td><td align="left" rowspan="1" colspan="1">10.1</td><td align="left" rowspan="1" colspan="1">3.0</td></tr><tr><td style="background-color:#B2B2B2" colspan="5" align="left" rowspan="1"><bold>N-LIMITED (35 GENES)</bold></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0021</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hpt domain-containing protein</td><td align="left" rowspan="1" colspan="1">3.3</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0161</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">LuxR family DNA-binding response regulator</td><td align="left" rowspan="1" colspan="1">3.1</td><td align="left" rowspan="1" colspan="1">0.8</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0296</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">4.6</td><td align="left" rowspan="1" colspan="1">3.0</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0322</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">3.9</td><td align="left" rowspan="1" colspan="1">6.5</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0327</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">EAL domain-containing protein</td><td align="left" rowspan="1" colspan="1">0.4</td><td align="left" rowspan="1" colspan="1">4.9</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0438</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">ErfK/YbiS/YcfS/YnhG family protein</td><td align="left" rowspan="1" colspan="1">1.5</td><td align="left" rowspan="1" colspan="1">3.0</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0804</td><td align="left" rowspan="1" colspan="1"><italic>ihfB</italic></td><td align="left" rowspan="1" colspan="1">Integration host factor subunit beta</td><td align="left" rowspan="1" colspan="1">3.0</td><td align="left" rowspan="1" colspan="1">1.4</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0860</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Xylose repressor, putative</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.2</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0919</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">MarR family transcriptional regulator</td><td align="left" rowspan="1" colspan="1">3.3</td><td align="left" rowspan="1" colspan="1">2.8</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1078</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Chromosome replication initiation inhibitor protein</td><td align="left" rowspan="1" colspan="1">3.0</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1275</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Cold shock family protein</td><td align="left" rowspan="1" colspan="1">2.5</td><td align="left" rowspan="1" colspan="1">3.5</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1286</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">0.5</td><td align="left" rowspan="1" colspan="1">3.7</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1384</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">MarR family transcriptional regulator</td><td align="left" rowspan="1" colspan="1">4.4</td><td align="left" rowspan="1" colspan="1">1.4</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1707</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Urea transporter, ATP-binding protein (<italic>urtE</italic>)</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.8</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.0</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPOA0447<xref ref-type="table-fn" rid="tfn17"><sup>b</sup></xref></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Urea transporter, ATP-binding protein (<italic>urtD</italic>)</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">5.5</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1708</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Urea transporter, permease protein (<italic>urtC</italic>)</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">11.6</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1808</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">4.6</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1853</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">TetR family transcriptional regulator</td><td align="left" rowspan="1" colspan="1">3.0</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1872</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">LysR family transcriptional regulator</td><td align="left" rowspan="1" colspan="1">6.2</td><td align="left" rowspan="1" colspan="1">2.1</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1911</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">1.1</td><td align="left" rowspan="1" colspan="1">4.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2067</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">6.5</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO2087</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>ntrC</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Nitrogen regulation protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">1.1</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">4.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2224</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">2.2</td><td align="left" rowspan="1" colspan="1">4.1</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO2294</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>glnB-1</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Nitrogen regulatory protein P<sub>II</sub></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">9.0</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">6.6</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO2295</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>glnA</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Glutamine synthetase, type I</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">4.7</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">5.1</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO2364</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Amino acid ABC transporter, periplasmic binding protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">1.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">4.1</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2602</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">RpiR family transcriptional regulator</td><td align="left" rowspan="1" colspan="1">5.1</td><td align="left" rowspan="1" colspan="1">2.2</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2778</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">3.0</td><td align="left" rowspan="1" colspan="1">1.5</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2818</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">4.9</td><td align="left" rowspan="1" colspan="1">3.0</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3607</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">4.6</td><td align="left" rowspan="1" colspan="1">0.6</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO3723</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>amt-2</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Ammonium transporter</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">28.0</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO3724</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>glnB-2</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Nitrogen regulatory protein P<sub>II</sub></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">124.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">39.1</td></tr><tr><td align="left" rowspan="1" colspan="1">SPOA0280</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">TRAP dicarboxylate transporter, DctP subunit, putative</td><td align="left" rowspan="1" colspan="1">7.9</td><td align="left" rowspan="1" colspan="1">4.5</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPOA0300</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Branched-chain amino acid ABC transporter, periplasmic binding protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">6.6</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPOA0399</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">R body protein RebB-like protein</td><td align="left" rowspan="1" colspan="1">5.6</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#B2B2B2" colspan="5" align="left" rowspan="1"><bold>P-LIMITED (20 GENES)</bold></td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0147</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Enoyl-CoA hydratase</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">4.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.0</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0304</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Putative lipoprotein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">7.0</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">5.4</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0468</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>phnG</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Alkylphosphonate utilization protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">5.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0472</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>phnK</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Phosphonate C-P lyase system protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">10.9</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0505</td><td align="left" rowspan="1" colspan="1"><italic>rplO</italic></td><td align="left" rowspan="1" colspan="1">Ribosomal protein L15</td><td align="left" rowspan="1" colspan="1">3.2</td><td align="left" rowspan="1" colspan="1">5.7</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0781</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>phnD</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Phosphonate ABC transporter, periplasmic binding protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">103.5</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1227</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">3.2</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1504</td><td align="left" rowspan="1" colspan="1"><italic>pqqA</italic></td><td align="left" rowspan="1" colspan="1">Coenzyme PQQ biosynthesis protein A</td><td align="left" rowspan="1" colspan="1">5.1</td><td align="left" rowspan="1" colspan="1">4.7</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1860</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Twin-arginine translocation pathway signal sequence domain-containing protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">7.4</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1928</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Tat pathway signal sequence domain-containing protein</td><td align="left" rowspan="1" colspan="1">3.5</td><td align="left" rowspan="1" colspan="1">0.7</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1948</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>pstS</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Phosphate ABC transporter, periplasmic binding protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">47.9</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1949</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>pstC</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Phosphate ABC transporter, permease protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">4.7</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1951</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>pstB</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Phosphate transporter ATP-binding protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">7.4</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1953</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>phoB</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Phosphate regulon transcriptional regulatory protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">10.7</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">26.1</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2626</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">TRAP transporter, DctM subunit</td><td align="left" rowspan="1" colspan="1">1.8</td><td align="left" rowspan="1" colspan="1">4.2</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2627</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">TRAP transporter, DctQ subunit</td><td align="left" rowspan="1" colspan="1">3.3</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3198</td><td align="left" rowspan="1" colspan="1"><italic>rnc</italic></td><td align="left" rowspan="1" colspan="1">Ribonuclease III</td><td align="left" rowspan="1" colspan="1">4.1</td><td align="left" rowspan="1" colspan="1">1.6</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3625</td><td align="left" rowspan="1" colspan="1"><italic>cspA</italic></td><td align="left" rowspan="1" colspan="1">Cold shock protein</td><td align="left" rowspan="1" colspan="1">2.6</td><td align="left" rowspan="1" colspan="1">4.2</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3868</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">1.6</td><td align="left" rowspan="1" colspan="1">3.6</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPOA0294</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>pmtA</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Phosphatidylethanolamine <italic>N</italic>-methyltransferase</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.6</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">1.2</td></tr><tr><td style="background-color:#B2B2B2" colspan="5" align="left" rowspan="1"><bold>S-LIMITED (11 GENES)</bold></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0412</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">13.2</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0636</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">EF hand domain-containing protein</td><td align="left" rowspan="1" colspan="1">3.9</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1256</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>ppk2</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Polyphosphate kinase 2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">5.0</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">4.0</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1330</td><td align="left" rowspan="1" colspan="1"><italic>hflC</italic></td><td align="left" rowspan="1" colspan="1">HflC protein</td><td align="left" rowspan="1" colspan="1">4.0</td><td align="left" rowspan="1" colspan="1">3.5</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1409</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>rpoH-2</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">RNA polymerase factor sigma-32</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">12.5</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO2596</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>hemA-1</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">5-amino-levulinate synthase</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">1.8</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">4.6</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO2632</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>cobA-1</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Uroporphyrin-III <italic>C</italic>-methyltransferase</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.4</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">5.9</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO2634</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Sulfite reductase, putative</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">5.7</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">5.3</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO3383</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Thiol-specific antioxidant protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">4.9</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">4.5</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO3527</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Universal stress protein family protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">3.7</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">5.3</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO3532</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>hemN</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Coproporphyrinogen III oxidase</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">7.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr></tbody></table><table-wrap-foot><fn id="tfn16"><p><italic><sup>a</sup>As the median value between limitation-to-excess pairwise comparisons</italic>.</p></fn><fn id="tfn17"><p><italic><sup>b</sup>SPOA0047 is a chromosomal gene</italic>.</p></fn><p><italic>Light gray shading indicates genes included in Table 2</italic>.</p></table-wrap-foot></table-wrap><table-wrap id="TA5" position="anchor"><label>Table A5</label><caption><p><bold>Transcriptionally depleted <italic>R. pomeroy</italic><italic>i</italic> DSS-3 genes</bold>.</p></caption><table frame="hsides" rules="groups"><thead><tr><th valign="top" align="left" rowspan="1" colspan="1">Locus tag</th><th valign="top" align="left" rowspan="1" colspan="1">Gene</th><th valign="top" align="left" rowspan="1" colspan="1">Product</th><th valign="top" colspan="2" align="center" rowspan="1">Fold-change ratio<xref ref-type="table-fn" rid="tfn18"><sup>a</sup></xref><hr></hr></th></tr><tr><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1">Probe 1</th><th align="left" rowspan="1" colspan="1">Probe 2</th></tr></thead><tbody><tr><td style="background-color:#B2B2B2" colspan="5" align="left" rowspan="1"><bold>C-LIMITED (12 GENES)</bold></td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0416</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>mreD</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Rod shape-determining protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0956</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">0.3</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1244</td><td align="left" rowspan="1" colspan="1"><italic>efp</italic></td><td align="left" rowspan="1" colspan="1">Elongation factor P</td><td align="left" rowspan="1" colspan="1">0.3</td><td align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1293</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>phaP</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Phasin</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.1</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.1</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1756</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Polysaccharide biosynthesis/export protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.7</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1868</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Glutaredoxin-related protein</td><td align="left" rowspan="1" colspan="1">0.4</td><td align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2135</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">0.3</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3022</td><td align="left" rowspan="1" colspan="1"><italic>valS</italic></td><td align="left" rowspan="1" colspan="1">Valyl-tRNA synthetase</td><td align="left" rowspan="1" colspan="1">0.3</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3253</td><td align="left" rowspan="1" colspan="1"><italic>rpsP</italic></td><td align="left" rowspan="1" colspan="1">30S ribosomal protein S16</td><td align="left" rowspan="1" colspan="1">2.0</td><td align="left" rowspan="1" colspan="1">0.2</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3658</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1"><sc>d</sc>-alanyl-<sc>d</sc>-alanine carboxypeptidase family protein</td><td align="left" rowspan="1" colspan="1">0.4</td><td align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3840</td><td align="left" rowspan="1" colspan="1"><italic>rpsO</italic></td><td align="left" rowspan="1" colspan="1">30S ribosomal protein S15</td><td align="left" rowspan="1" colspan="1">0.2</td><td align="left" rowspan="1" colspan="1">0.2</td></tr><tr><td align="left" rowspan="1" colspan="1">SPOA0031</td><td align="left" rowspan="1" colspan="1"><italic>nqrD</italic></td><td align="left" rowspan="1" colspan="1">Na<sup>+</sup>-translocating NADH-quinone reductase subunit D</td><td align="left" rowspan="1" colspan="1">0.5</td><td align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td style="background-color:#B2B2B2" colspan="5" align="left" rowspan="1"><bold>N-LIMITED (34 GENES)</bold></td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0227</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">PaxA, putative</td><td align="left" rowspan="1" colspan="1">0.3</td><td align="left" rowspan="1" colspan="1">0.2</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0406</td><td align="left" rowspan="1" colspan="1"><italic>rpoH-2</italic></td><td align="left" rowspan="1" colspan="1">RNA polymerase factor sigma-32</td><td align="left" rowspan="1" colspan="1">0.6</td><td align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0862</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>xylH</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Xylose ABC transporter, permease protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1060</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">0.1</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1079</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Lysine exporter, putative</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.1</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">2.0</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1308</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">0.3</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1336</td><td align="left" rowspan="1" colspan="1"><italic>ispZ</italic></td><td align="left" rowspan="1" colspan="1">Intracellular septation protein A</td><td align="left" rowspan="1" colspan="1">0.6</td><td align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1685</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">tRNA synthetase, class I family protein</td><td align="left" rowspan="1" colspan="1">0.1</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1743</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Glutamate dehydrogenase</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1747</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Sarcosine oxidase gamma subunit family protein</td><td align="left" rowspan="1" colspan="1">1.2</td><td align="left" rowspan="1" colspan="1">0.2</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1954</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">LysR family transcriptional regulator</td><td align="left" rowspan="1" colspan="1">1.7</td><td align="left" rowspan="1" colspan="1">0.2</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2071</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Bcr/CflA subfamily drug resistance transporter</td><td align="left" rowspan="1" colspan="1">0.3</td><td align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2271</td><td align="left" rowspan="1" colspan="1"><italic>fabF</italic></td><td align="left" rowspan="1" colspan="1">3-oxoacyl-(acyl carrier protein) synthase II</td><td align="left" rowspan="1" colspan="1">0.5</td><td align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2373</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">0.1</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2414</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Mandelate racemase/muconate lactonizing enzyme family protein</td><td align="left" rowspan="1" colspan="1">0.3</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2556</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Allantoate amidohydrolase</td><td align="left" rowspan="1" colspan="1">0.2</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2592</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Beta-lactamase, putative</td><td align="left" rowspan="1" colspan="1">1.0</td><td align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2616</td><td align="left" rowspan="1" colspan="1"><italic>tgt</italic></td><td align="left" rowspan="1" colspan="1">Queuine tRNA-ribosyltransferase</td><td align="left" rowspan="1" colspan="1">0.7</td><td align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3012</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Inositol-1-monophosphatase, putative</td><td align="left" rowspan="1" colspan="1">0.1</td><td align="left" rowspan="1" colspan="1">0.2</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO3156</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><sc>l</sc>-threonine aldolase, low-specificity, putative</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">1.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3419</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">UbiH/UbiF/VisC/COQ6 family ubiquinone biosynthesis hydroxylase</td><td align="left" rowspan="1" colspan="1">1.9</td><td align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3437</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Mechanosensitive ion channel family protein</td><td align="left" rowspan="1" colspan="1">0.2</td><td align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3484</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">HSP20 family protein</td><td align="left" rowspan="1" colspan="1">0.5</td><td align="left" rowspan="1" colspan="1">0.2</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO3712</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>asd</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Aspartate-semialdehyde dehydrogenase</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO3720</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>tyrB</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Aromatic amino acid aminotransferase</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.3</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.9</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3731</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Glycerophosphoryl diester phosphodiesterase, putative</td><td align="left" rowspan="1" colspan="1">0.3</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3752</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Radical SAM domain-containing protein</td><td align="left" rowspan="1" colspan="1">0.2</td><td align="left" rowspan="1" colspan="1">0.7</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPOA0011</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>metK</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>S</italic>-adenosylmethionine synthetase</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.4</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPOA0057</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>gcvT</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Glycine cleavage system T protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPOA0094</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">0.2</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPOA0099</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Branched-chain amino acid ABC transporter, ATP-binding protein</td><td align="left" rowspan="1" colspan="1">0.1</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPOA0115</td><td align="left" rowspan="1" colspan="1"><italic>gtdA-2</italic></td><td align="left" rowspan="1" colspan="1">Gentisate 1,2-dioxygenase</td><td align="left" rowspan="1" colspan="1">0.8</td><td align="left" rowspan="1" colspan="1">0.1</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPOA0215</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>norQ</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Nitric oxide reductase Q protein</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">2.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.1</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPOA0220</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>nirS</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Cytochrome cd1 nitrite reductase</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#B2B2B2" colspan="5" align="left" rowspan="1"><bold>P-LIMITED (NO GENES)</bold></td></tr><tr><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td style="background-color:#B2B2B2" colspan="5" align="left" rowspan="1"><bold>S-LIMITED (10 GENES)</bold></td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO0371</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>luxR-1</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">Autoinducer-binding transcriptional regulator</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.0</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0490</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Calcium-binding domain–containing protein</td><td align="left" rowspan="1" colspan="1">0.3</td><td align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO0491</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">0.2</td><td align="left" rowspan="1" colspan="1">0.7</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1054</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">0.3</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO1221</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">0.1</td><td align="left" rowspan="1" colspan="1">0.3</td></tr><tr><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">SPO1679</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1"><italic>ctrA</italic></td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">DNA-binding response regulator</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td><td style="background-color:#CCCCCC" align="left" rowspan="1" colspan="1">0.2</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO2580</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">0.1</td><td align="left" rowspan="1" colspan="1">0.1</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3223</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Response regulator</td><td align="left" rowspan="1" colspan="1">0.3</td><td align="left" rowspan="1" colspan="1">0.2</td></tr><tr><td align="left" rowspan="1" colspan="1">SPO3673</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Type I secretion target repeat-containing protein</td><td align="left" rowspan="1" colspan="1">0.3</td><td align="left" rowspan="1" colspan="1">0.2</td></tr><tr><td align="left" rowspan="1" colspan="1">SPOA0337</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">0.1</td><td align="left" rowspan="1" colspan="1">–</td></tr></tbody></table><table-wrap-foot><fn id="tfn18"><p><italic><sup>a</sup>Calculated as the median value for limitation-to-excess pairwise comparisons</italic>.</p></fn><p><italic>Light gray shading indicates genes included in Table 2</italic>.</p></table-wrap-foot></table-wrap><table-wrap id="TA6" position="anchor"><label>Table A6</label><caption><p><bold>N content in free amino acids measured in steady-state <italic>R. pomeroy</italic><italic>i</italic> DSS-3 cells</bold>.</p></caption><table frame="hsides" rules="groups"><thead><tr><th valign="top" align="left" rowspan="1" colspan="1">Amino acid<xref ref-type="table-fn" rid="tfn19"><sup>a</sup></xref></th><th valign="top" colspan="4" align="center" rowspan="1">N (ng) in free amino acid (mg dry weight)<sup>−1</sup><hr></hr></th></tr><tr><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1">C-limited</th><th align="left" rowspan="1" colspan="1">N-limited</th><th align="left" rowspan="1" colspan="1">P-limited</th><th align="left" rowspan="1" colspan="1">S-limited</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">Alanine</td><td align="left" rowspan="1" colspan="1">17.1</td><td align="left" rowspan="1" colspan="1">34.5</td><td align="left" rowspan="1" colspan="1">53.6</td><td align="left" rowspan="1" colspan="1">665.6</td></tr><tr><td align="left" rowspan="1" colspan="1">Arginine</td><td align="left" rowspan="1" colspan="1">0.0</td><td align="left" rowspan="1" colspan="1">0.0</td><td align="left" rowspan="1" colspan="1">52.0</td><td align="left" rowspan="1" colspan="1">550.3</td></tr><tr><td align="left" rowspan="1" colspan="1">Glutamate</td><td align="left" rowspan="1" colspan="1">1405.6</td><td align="left" rowspan="1" colspan="1">123.3</td><td align="left" rowspan="1" colspan="1">2310.3</td><td align="left" rowspan="1" colspan="1">18142.8</td></tr><tr><td align="left" rowspan="1" colspan="1">Glycine</td><td align="left" rowspan="1" colspan="1">46.7</td><td align="left" rowspan="1" colspan="1">29.2</td><td align="left" rowspan="1" colspan="1">57.7</td><td align="left" rowspan="1" colspan="1">1196.5</td></tr><tr><td align="left" rowspan="1" colspan="1">Isoleucine</td><td align="left" rowspan="1" colspan="1">0.0</td><td align="left" rowspan="1" colspan="1">11.7</td><td align="left" rowspan="1" colspan="1">0.0</td><td align="left" rowspan="1" colspan="1">425.4</td></tr><tr><td align="left" rowspan="1" colspan="1">Leucine</td><td align="left" rowspan="1" colspan="1">5.0</td><td align="left" rowspan="1" colspan="1">13.1</td><td align="left" rowspan="1" colspan="1">22.7</td><td align="left" rowspan="1" colspan="1">219.4</td></tr><tr><td align="left" rowspan="1" colspan="1">Lysine</td><td align="left" rowspan="1" colspan="1">10.6</td><td align="left" rowspan="1" colspan="1">28.5</td><td align="left" rowspan="1" colspan="1">37.2</td><td align="left" rowspan="1" colspan="1">391.2</td></tr><tr><td align="left" rowspan="1" colspan="1">Phenylalanine</td><td align="left" rowspan="1" colspan="1">4.7</td><td align="left" rowspan="1" colspan="1">12.0</td><td align="left" rowspan="1" colspan="1">0.0</td><td align="left" rowspan="1" colspan="1">111.5</td></tr><tr><td align="left" rowspan="1" colspan="1">Serine</td><td align="left" rowspan="1" colspan="1">0.0</td><td align="left" rowspan="1" colspan="1">0.0</td><td align="left" rowspan="1" colspan="1">24.8</td><td align="left" rowspan="1" colspan="1">204.5</td></tr><tr><td align="left" rowspan="1" colspan="1">Threonine</td><td align="left" rowspan="1" colspan="1">3.2</td><td align="left" rowspan="1" colspan="1">14.9</td><td align="left" rowspan="1" colspan="1">17.7</td><td align="left" rowspan="1" colspan="1">686.4</td></tr><tr><td align="left" rowspan="1" colspan="1">Valine</td><td align="left" rowspan="1" colspan="1">4.5</td><td align="left" rowspan="1" colspan="1">14.1</td><td align="left" rowspan="1" colspan="1">19.6</td><td align="left" rowspan="1" colspan="1">395.6</td></tr><tr><td align="left" rowspan="1" colspan="1">Sum</td><td align="left" rowspan="1" colspan="1">1497.4</td><td align="left" rowspan="1" colspan="1">281.3</td><td align="left" rowspan="1" colspan="1">2595.7</td><td align="left" rowspan="1" colspan="1">22989.2</td></tr><tr><td align="left" rowspan="1" colspan="1">%N<xref ref-type="table-fn" rid="tfn20"><sup>b</sup></xref></td><td align="left" rowspan="1" colspan="1">1.3</td><td align="left" rowspan="1" colspan="1">0.5</td><td align="left" rowspan="1" colspan="1">4.2</td><td align="left" rowspan="1" colspan="1">25.5</td></tr></tbody></table><table-wrap-foot><fn id="tfn19"><p><italic><sup>a</sup>Amino acids not listed were below the confidence of detection (verified by manually examining the chromatograms)</italic>.</p></fn><fn id="tfn20"><p><italic><sup>b</sup>As the N content in free amino acids divided by whole cell N content (%)</italic>.</p></fn></table-wrap-foot></table-wrap><table-wrap id="TA7" position="anchor"><label>Table A7</label><caption><p><bold>Abundance of homologs for <italic>cysB</italic> and N storage genes in the unassembled Global Ocean Sampling (GOS) metagenomic data set (through the April 2008 release)</bold>.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">Gene function</th><th align="left" rowspan="1" colspan="1">Gene name</th><th align="left" rowspan="1" colspan="1">Number of homologs<xref ref-type="table-fn" rid="tfn21"><sup>a</sup></xref></th><th align="left" rowspan="1" colspan="1">Cells with gene<xref ref-type="table-fn" rid="tfn22"><sup>b</sup></xref> (%)</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">S regulation</td><td align="left" rowspan="1" colspan="1"><italic>cysB</italic></td><td align="left" rowspan="1" colspan="1">281</td><td align="left" rowspan="1" colspan="1">2.8</td></tr><tr><td align="left" rowspan="1" colspan="1">Cyanophycin granule synthesis</td><td align="left" rowspan="1" colspan="1">CPG synthetase</td><td align="left" rowspan="1" colspan="1">53</td><td align="left" rowspan="1" colspan="1">0.5</td></tr><tr><td align="left" rowspan="1" colspan="1">Cyanophycin granule synthesis</td><td align="left" rowspan="1" colspan="1">Cyanophycinase</td><td align="left" rowspan="1" colspan="1">24</td><td align="left" rowspan="1" colspan="1">0.2</td></tr></tbody></table><table-wrap-foot><fn id="tfn21"><p><italic><sup>a</sup>BLASTp analysis was conducted against the GOS peptide database with an <italic>E</italic>-value ≤ 10 <sup>-30</sup> using an experimentally confirmed gene sequence as the query. Candidate homologs were then subjected to phylogenetic analysis using pplacer (Matsen et al., <xref ref-type="bibr" rid="B41">2010</xref>) to confirm homology with genes of known function</italic>.</p></fn><fn id="tfn22"><p><italic><sup>b</sup>See <xref ref-type="sec" rid="s1">Materials and Methods</xref></italic>.</p></fn></table-wrap-foot></table-wrap><fig id="FA1" position="anchor"><label>Figure A1</label><caption><p><bold>Schematic of microarray data analysis</bold>. Probe counts are shown in italicized font and gene counts are in bold font. <bold>(A)</bold> Significant Analysis of Microarray (SAM) was used to analyze the microarray data (pairwise SAM comparisons with 5,000 permutations and a false discovery rate ≤ 2%). From these results, probes significantly different in all three comparisons to the other treatments (that is, falling into the three-way overlap region of each Venn diagram) were selected for further analyses. <bold>(B)</bold> From the normalized fluorescence values, the fold-change for each probe was calculated as the median value between all limitation-to-excess pairwise comparisons and genes whose fold-change was ≥ 3 were retained.</p></caption><graphic xlink:href="fmicb-03-00159-a001"></graphic></fig><fig id="FA2" position="anchor"><label>Figure A2</label><caption><p><bold>Biosynthesis of polyhydroxyalkanoate (PHA) in <italic>R. pomeroyi</italic> DSS-3</bold>. <bold>(A)</bold> Pathway inferred from BioCyc; <bold>(B)</bold> arrangement of genes for PHA synthesis (<italic>phbAB</italic>, <italic>phaC</italic>), degradation (<italic>phaZ</italic>), and regulation (<italic>phaR</italic>) on <italic>R. pomeroyi</italic> DSS-3 chromosome; <bold>(C)</bold> transcriptional ratios for relevant genes; values are shown for genes listed in the pathway (solid red box) and genes that are not in the pathway, but are located proximal to PHA synthesis genes (dotted red box). Genes in the same operon are identically color-coded. *, transcriptional change is significant (≥3-fold, all limitation-to-excess pairwise comparisons).</p></caption><graphic xlink:href="fmicb-03-00159-a002"></graphic></fig><fig id="FA3" position="anchor"><label>Figure A3</label><caption><p><bold>Biosynthesis of phospholipid and ornithine lipid in <italic>R. pomeroyi</italic> DSS-3</bold>. Strain DSS-3 does not encode genes to synthesize other bacterial P-free lipids (betaine lipid, <italic>btaAB</italic>; glycolipid/sulfolipid, <italic>sqdBCDX</italic>). <bold>(A)</bold> Pathway inferred from BioCyc; <bold>(B)</bold> arrangement of lipid synthesis genes on the chromosome; <bold>(C)</bold> transcription ratios for relevant genes; values shown for genes listed in <bold>(A,B)</bold> (solid red box). Genes in the same operon are identically color-coded. Symbols for ornithine lipid synthesis genes (yellow and orange) are bordered in black. *, transcriptional change is significant (≥3-fold, all limitation-to-excess pairwise comparisons). Abbreviation in <bold>(A,B)</bold> as follows: G3P, glyceraldehyde 3-phosphate.</p></caption><graphic xlink:href="fmicb-03-00159-a003"></graphic></fig><fig id="FA4" position="anchor"><label>Figure A4</label><caption><p><bold>Relevant S-genes in <italic>R. pomeroyi</italic> DSS-3</bold>. <bold>(A)</bold> Pathway inferred from BioCyc; <bold>(B)</bold> arrangement of relevant genes on the chromosome; <bold>(C)</bold> transcriptional ratios for relevant genes; ratios are shown for genes listed in the pathway <bold>(A)</bold> (solid red box) and genes that are not in the pathway, but are located in proximity to relevant S-genes [dotted red box in <bold>(B)</bold>]. Genes located in the same operon are identically color-coded. Two sets of orthologous LuxR–LuxI-type proteins are boxed in <bold>(B)</bold>. Symbols for autoinducer-binding or synthesis genes (yellow, orange, brown) are bordered in black in <bold>(C)</bold>. *Transcriptional change is significant (≥3-fold, all limitation-to-excess pairwise comparisons). Abbreviations in <bold>(A)</bold> as follows: THF, tetrahydrofolate; 5-mthglu, 5-methyltetrahydropteroyltri-<sc>l</sc>-glutamate; thglu, tetrahydropteroyltri-<sc>l</sc>-glutamate.</p></caption><graphic xlink:href="fmicb-03-00159-a004a"></graphic><graphic xlink:href="fmicb-03-00159-a004b"></graphic></fig><fig id="FA5" position="anchor"><label>Figure A5</label><caption><p><bold>C:N:P ratios from various studies</bold>. Black symbols, steady-state <italic>R. pomeroyi</italic> DSS-3; the unlimited C:N:P ratio was modeled as ∼154:15:1 (this study); blue, batch-cultured marine bacterioplankton (Vrede et al., <xref ref-type="bibr" rid="B69">2002</xref>); purple, Redfield ratio, marine seston (Redfield, <xref ref-type="bibr" rid="B51">1934</xref>); brown, natural bacteria (Fagerbakke et al., <xref ref-type="bibr" rid="B15">1996</xref>); orange, natural bacteria (Cotner et al., <xref ref-type="bibr" rid="B8">1997</xref>).</p></caption><graphic xlink:href="fmicb-03-00159-a005"></graphic></fig><ref-list><ref id="B81"><mixed-citation publication-type="book"><person-group person-group-type="editor"><name><surname>Neidhardt</surname><given-names>F. C.</given-names></name><name><surname>Curtiss</surname><given-names>R.</given-names></name><name><surname>Ingraham</surname><given-names>J. L.</given-names></name><name><surname>Lin</surname><given-names>E. C. C.</given-names></name><name><surname>Low</surname><given-names>K. B.</given-names></name><name><surname>Magasanik</surname><given-names>B.</given-names></name><name><surname>Reznikoff</surname><given-names>W. S.</given-names></name><name><surname>Riley</surname><given-names>M.</given-names></name><name><surname>Schaechter</surname><given-names>M.</given-names></name><name><surname>Umbarger</surname><given-names>H. E.</given-names></name></person-group> (eds). (<year>1996</year>). <source>Escherichia coli and Salmonella: Cellular and Molecular Biology</source>, <edition>2nd Edn.</edition><publisher-loc>Washington, DC</publisher-loc>: <publisher-name>ASM Press</publisher-name></mixed-citation></ref></ref-list></app></app-group><ref-list><title>References</title><ref id="B1"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Anderson</surname><given-names>A. J.</given-names></name><name><surname>Dawes</surname><given-names>E. A.</given-names></name></person-group> (<year>1990</year>). <article-title>Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates</article-title>. <source>Microbiol. Rev.</source><volume>54</volume>, <fpage>450</fpage>–<lpage>472</lpage><pub-id pub-id-type="pmid">2087222</pub-id></mixed-citation></ref><ref id="B2"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Azam</surname><given-names>F.</given-names></name><name><surname>Fenchel</surname><given-names>T.</given-names></name><name><surname>Field</surname><given-names>J. G.</given-names></name><name><surname>Gray</surname><given-names>J. S.</given-names></name><name><surname>Meyer-Reil</surname><given-names>L. A.</given-names></name><name><surname>Thingstad</surname><given-names>F.</given-names></name></person-group> (<year>1983</year>). <article-title>The ecological role of water-column microbes in the sea</article-title>. <source>Mar. Ecol. Prog. Ser.</source><volume>10</volume>, <fpage>257</fpage>–<lpage>263</lpage><pub-id pub-id-type="doi">10.3354/meps010257</pub-id></mixed-citation></ref><ref id="B3"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bradford</surname><given-names>M. M.</given-names></name></person-group> (<year>1976</year>). <article-title>A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding</article-title>. <source>Anal. Biochem.</source><volume>72</volume>, <fpage>248</fpage>–<lpage>254</lpage><pub-id pub-id-type="doi">10.1016/0003-2697(76)90527-3</pub-id><pub-id pub-id-type="pmid">942051</pub-id></mixed-citation></ref><ref id="B4"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Brazma</surname><given-names>A.</given-names></name><name><surname>Hingamp</surname><given-names>P.</given-names></name><name><surname>Quackenbush</surname><given-names>J.</given-names></name><name><surname>Sherlock</surname><given-names>G.</given-names></name><name><surname>Spellman</surname><given-names>P.</given-names></name><name><surname>Stoeckert</surname><given-names>C.</given-names></name><name><surname>Aach</surname><given-names>J.</given-names></name><name><surname>Ansorge</surname><given-names>W.</given-names></name><name><surname>Ball</surname><given-names>C. A.</given-names></name><name><surname>Causton</surname><given-names>H. C.</given-names></name><name><surname>Gaasterland</surname><given-names>T.</given-names></name><name><surname>Glenisson</surname><given-names>P.</given-names></name><name><surname>Holstege</surname><given-names>F. C.</given-names></name><name><surname>Kim</surname><given-names>I. F.</given-names></name><name><surname>Markowitz</surname><given-names>V.</given-names></name><name><surname>Matese</surname><given-names>J. C.</given-names></name><name><surname>Parkinson</surname><given-names>H.</given-names></name><name><surname>Robinson</surname><given-names>A.</given-names></name><name><surname>Sarkans</surname><given-names>U.</given-names></name><name><surname>Schulze-Kremer</surname><given-names>S.</given-names></name><name><surname>Stewart</surname><given-names>J.</given-names></name><name><surname>Taylor</surname><given-names>R.</given-names></name><name><surname>Vilo</surname><given-names>J.</given-names></name><name><surname>Vingron</surname><given-names>M.</given-names></name></person-group> (<year>2001</year>). <article-title>Minimum information about a microarray experiment (MIAME)-toward standards for microarray data</article-title>. <source>Nat. Genet.</source><volume>29</volume>, <fpage>365</fpage>–<lpage>371</lpage><pub-id pub-id-type="doi">10.1038/ng1201-365</pub-id><pub-id pub-id-type="pmid">11726920</pub-id></mixed-citation></ref><ref id="B5"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Brown</surname><given-names>M. R.</given-names></name><name><surname>Kornberg</surname><given-names>A.</given-names></name></person-group> (<year>2008</year>). <article-title>The long and short of it- polyphosphate, PPK and bacterial survival</article-title>. <source>Trends Biochem. Sci.</source><volume>33</volume>, <fpage>284</fpage>–<lpage>290</lpage><pub-id pub-id-type="doi">10.1016/j.tibs.2008.04.009</pub-id><pub-id pub-id-type="pmid">18487048</pub-id></mixed-citation></ref><ref id="B6"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bürgmann</surname><given-names>H.</given-names></name><name><surname>Howard</surname><given-names>E. C.</given-names></name><name><surname>Ye</surname><given-names>W.</given-names></name><name><surname>Sun</surname><given-names>F.</given-names></name><name><surname>Sun</surname><given-names>S.</given-names></name><name><surname>Napierala</surname><given-names>S.</given-names></name><name><surname>Moran</surname><given-names>M. A.</given-names></name></person-group> (<year>2007</year>). <article-title>Transcriptional response of <italic>Silicibacter pomeroyi</italic> DSS-3 to dimethylsulfoniopropionate (DMSP)</article-title>. <source>Environ. Microbiol.</source><volume>9</volume>, <fpage>2742</fpage>–<lpage>2755</lpage><pub-id pub-id-type="doi">10.1111/j.1462-2920.2007.01386.x</pub-id><pub-id pub-id-type="pmid">17922758</pub-id></mixed-citation></ref><ref id="B7"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cherrier</surname><given-names>J.</given-names></name><name><surname>Bauer</surname><given-names>J. E.</given-names></name><name><surname>Druffel</surname><given-names>E. R. M.</given-names></name></person-group> (<year>1996</year>). <article-title>Utilization and turnover of labile dissolved organic matter by bacterial heterotrophs in eastern north Pacific surface waters</article-title>. <source>Mar. Ecol. Prog. Ser.</source><volume>139</volume>, <fpage>267</fpage>–<lpage>279</lpage><pub-id pub-id-type="doi">10.3354/meps139267</pub-id></mixed-citation></ref><ref id="B8"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cotner</surname><given-names>J. B.</given-names></name><name><surname>Ammerman</surname><given-names>J. W.</given-names></name><name><surname>Peele</surname><given-names>E. R.</given-names></name><name><surname>Bentzen</surname><given-names>E.</given-names></name></person-group> (<year>1997</year>). <article-title>Phosphorus-limited bacterioplankton growth in the Sargasso Sea</article-title>. <source>Aquat. Microb. Ecol.</source><volume>13</volume>, <fpage>141</fpage>–<lpage>149</lpage><pub-id pub-id-type="doi">10.3354/ame013141</pub-id></mixed-citation></ref><ref id="B9"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cotner</surname><given-names>J. B.</given-names></name><name><surname>Hall</surname><given-names>E. K.</given-names></name><name><surname>Scott</surname><given-names>J. T.</given-names></name><name><surname>Heldal</surname><given-names>M.</given-names></name></person-group> (<year>2010</year>). <article-title>Freshwater bacteria are stoichiometrically flexible with a nutrient composition similar to seston</article-title>. <source>Front. Microbiol.</source><volume>1</volume>:<fpage>132</fpage><pub-id pub-id-type="doi">10.3389/fmicb.2010.00132</pub-id><pub-id pub-id-type="pmid">21687767</pub-id></mixed-citation></ref><ref id="B10"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dawes</surname><given-names>E. A.</given-names></name><name><surname>Senior</surname><given-names>P. J.</given-names></name></person-group> (<year>1973</year>). <article-title>The role and regulation of energy reserve polymers in micro-organisms</article-title>. <source>Adv. Microb. Physiol.</source><volume>10</volume>, <fpage>135</fpage>–<lpage>266</lpage><pub-id pub-id-type="doi">10.1016/S0065-2911(08)60088-0</pub-id><pub-id pub-id-type="pmid">4594739</pub-id></mixed-citation></ref><ref id="B11"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>del Giorgio</surname><given-names>P. A.</given-names></name><name><surname>Cole</surname><given-names>J. J.</given-names></name></person-group> (<year>1998</year>). <article-title>Bacterial growth efficiency in natural aquatic systems</article-title>. <source>Annu. Rev. Ecol. Syst.</source><volume>29</volume>, <fpage>503</fpage>–<lpage>541</lpage><pub-id pub-id-type="doi">10.1146/annurev.ecolsys.29.1.503</pub-id></mixed-citation></ref><ref id="B12"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ducklow</surname><given-names>H. W.</given-names></name><name><surname>Hill</surname><given-names>S. M.</given-names></name></person-group> (<year>1985</year>). <article-title>The growth of heterotrophic bacteria in the surface waters of warm core rings</article-title>. <source>Limnol. Oceanogr.</source><volume>30</volume>, <fpage>239</fpage>–<lpage>259</lpage><pub-id pub-id-type="doi">10.4319/lo.1985.30.2.0260</pub-id></mixed-citation></ref><ref id="B13"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Elser</surname><given-names>J. J.</given-names></name><name><surname>Dobberfuhl</surname><given-names>D. R.</given-names></name><name><surname>MacKay</surname><given-names>N. A.</given-names></name><name><surname>Schampel</surname><given-names>J. H.</given-names></name></person-group> (<year>1996</year>). <article-title>Organism size, life history, and N:P stoichiometry</article-title>. <source>Bioscience</source><volume>46</volume>, <fpage>674</fpage>–<lpage>684</lpage><pub-id pub-id-type="doi">10.2307/1312897</pub-id></mixed-citation></ref><ref id="B14"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Elser</surname><given-names>J. J.</given-names></name><name><surname>Stabler</surname><given-names>L. B.</given-names></name><name><surname>Hassett</surname><given-names>R. P.</given-names></name></person-group> (<year>1995</year>). <article-title>Nutrient limitation of bacterial-growth and rates of bacterivory in lakes and oceans: a comparative study</article-title>. <source>Aquat. Microb. Ecol.</source><volume>9</volume>, <fpage>105</fpage>–<lpage>110</lpage><pub-id pub-id-type="doi">10.3354/ame009105</pub-id></mixed-citation></ref><ref id="B15"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Fagerbakke</surname><given-names>K. M.</given-names></name><name><surname>Heldal</surname><given-names>M.</given-names></name><name><surname>Norland</surname><given-names>S.</given-names></name></person-group> (<year>1996</year>). <article-title>Content of carbon, nitrogen, oxygen, sulfur and phosphorus in native aquatic and cultured bacteria</article-title>. <source>Aquat. Microb. Ecol.</source><volume>10</volume>, <fpage>15</fpage>–<lpage>27</lpage><pub-id pub-id-type="doi">10.3354/ame010015</pub-id></mixed-citation></ref><ref id="B16"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ferenci</surname><given-names>T.</given-names></name></person-group> (<year>2008</year>). <article-title>Bacterial physiology, regulation and mutational adaptation in a chemostat environment</article-title>. <source>Adv. Microb. Physiol.</source><volume>53</volume>, <fpage>169</fpage>–<lpage>229</lpage><pub-id pub-id-type="doi">10.1016/S0065-2911(07)53003-1</pub-id><pub-id pub-id-type="pmid">17707145</pub-id></mixed-citation></ref><ref id="B17"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Franklin</surname><given-names>O.</given-names></name><name><surname>Hall</surname><given-names>E. K.</given-names></name><name><surname>Kaiser</surname><given-names>C.</given-names></name><name><surname>Richter</surname><given-names>A.</given-names></name><name><surname>Battin</surname><given-names>T.</given-names></name></person-group> (<year>2011</year>). <article-title>Optimization of biomass composition explains microbial growth-stoichiometry relationships</article-title>. <source>Am. Nat.</source><volume>177</volume>, <fpage>E29</fpage>–<lpage>E42</lpage><pub-id pub-id-type="doi">10.1086/657684</pub-id><pub-id pub-id-type="pmid">21460549</pub-id></mixed-citation></ref><ref id="B18"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Füser</surname><given-names>G.</given-names></name><name><surname>Steinbüchel</surname><given-names>A.</given-names></name></person-group> (<year>2007</year>). <article-title>Analysis of genome sequences for genes of cyanophycin metabolism: identifying putative cyanophycin metabolizing prokaryotes</article-title>. <source>Macromol. Biosci.</source><volume>7</volume>, <fpage>278</fpage>–<lpage>296</lpage><pub-id pub-id-type="doi">10.1002/mabi.200600207</pub-id><pub-id pub-id-type="pmid">17390395</pub-id></mixed-citation></ref><ref id="B19"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gangaiah</surname><given-names>D.</given-names></name><name><surname>Liu</surname><given-names>Z.</given-names></name><name><surname>Arcos</surname><given-names>J.</given-names></name><name><surname>Kassem</surname><given-names>I. I.</given-names></name><name><surname>Sanad</surname><given-names>Y.</given-names></name><name><surname>Torrelles</surname><given-names>J. B.</given-names></name><name><surname>Rajashekara</surname><given-names>G.</given-names></name></person-group> (<year>2010</year>). <article-title>Polyphosphate kinase 2: a novel determinant of stress responses and pathogenesis in <italic>Campylobacter jejuni</italic></article-title>. <source>PLoS ONE</source><volume>5</volume>, <fpage>e12142</fpage><pub-id pub-id-type="doi">10.1371/journal.pone.0012142</pub-id><pub-id pub-id-type="pmid">20808906</pub-id></mixed-citation></ref><ref id="B20"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gao</surname><given-names>J. L.</given-names></name><name><surname>Weissenmayer</surname><given-names>B.</given-names></name><name><surname>Taylor</surname><given-names>A. M.</given-names></name><name><surname>Thomas-Oates</surname><given-names>J.</given-names></name><name><surname>López-Lara</surname><given-names>I. M.</given-names></name><name><surname>Geiger</surname><given-names>O.</given-names></name></person-group> (<year>2004</year>). <article-title>Identification of a gene required for the formation of lyso-ornithine lipid, an intermediate in the biosynthesis of ornithine-containing lipids</article-title>. <source>Mol. Microbiol.</source><volume>53</volume>, <fpage>1757</fpage>–<lpage>1770</lpage><pub-id pub-id-type="doi">10.1111/j.1365-2958.2004.04261.x</pub-id><pub-id pub-id-type="pmid">15341653</pub-id></mixed-citation></ref><ref id="B21"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Geider</surname><given-names>R. J.</given-names></name><name><surname>La Roche</surname><given-names>J.</given-names></name></person-group> (<year>2002</year>). <article-title>Redfield revisited: variability of C:N:P in marine microalgae and its biochemical basis</article-title>. <source>Eur. J. Phycol.</source><volume>37</volume>, <fpage>1</fpage>–<lpage>17</lpage><pub-id pub-id-type="doi">10.1017/S0967026201003456</pub-id></mixed-citation></ref><ref id="B22"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Goldman</surname><given-names>J. C.</given-names></name><name><surname>Caron</surname><given-names>D. A.</given-names></name><name><surname>Dennett</surname><given-names>M. R.</given-names></name></person-group> (<year>1987</year>). <article-title>Regulation of gross growth efficiency and ammonium regeneration in bacteria by substrate C:N ratio</article-title>. <source>Limnol. Oceanogr.</source><volume>32</volume>, <fpage>1239</fpage>–<lpage>1252</lpage><pub-id pub-id-type="doi">10.4319/lo.1987.32.6.1239</pub-id></mixed-citation></ref><ref id="B23"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>González</surname><given-names>J. M.</given-names></name><name><surname>Covert</surname><given-names>J. S.</given-names></name><name><surname>Whitman</surname><given-names>W. B.</given-names></name><name><surname>Henriksen</surname><given-names>J. R.</given-names></name><name><surname>Mayer</surname><given-names>F.</given-names></name><name><surname>Scharf</surname><given-names>B.</given-names></name><name><surname>Schmitt</surname><given-names>R.</given-names></name><name><surname>Buchan</surname><given-names>A.</given-names></name><name><surname>Fuhrman</surname><given-names>J. A.</given-names></name><name><surname>Kiene</surname><given-names>R. P.</given-names></name><name><surname>Moran</surname><given-names>M. A.</given-names></name></person-group> (<year>2003</year>). <article-title><italic>Silicibacter pomeroyi</italic> sp. nov. and <italic>Roseovarius nubinhibens</italic> sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments</article-title>. <source>Int. J. Syst. Evol. Microbiol.</source><volume>53</volume>, <fpage>1261</fpage>–<lpage>1269</lpage><pub-id pub-id-type="doi">10.1099/ijs.0.02491-0</pub-id><pub-id pub-id-type="pmid">13130004</pub-id></mixed-citation></ref><ref id="B24"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Goyal</surname><given-names>S.</given-names></name><name><surname>Yuan</surname><given-names>J.</given-names></name><name><surname>Chen</surname><given-names>T.</given-names></name><name><surname>Rabinowitz</surname><given-names>J. D.</given-names></name><name><surname>Wingreen</surname><given-names>N. S.</given-names></name></person-group> (<year>2010</year>). <article-title>Achieving optimal growth through product feedback inhibition in metabolism</article-title>. <source>PLoS Comput. Biol.</source><volume>6</volume>, <fpage>e1000802</fpage><pub-id pub-id-type="doi">10.1371/journal.pcbi.1000802</pub-id><pub-id pub-id-type="pmid">20532205</pub-id></mixed-citation></ref><ref id="B25"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gundersen</surname><given-names>K.</given-names></name><name><surname>Heldal</surname><given-names>M.</given-names></name><name><surname>Purdie</surname><given-names>D. A.</given-names></name><name><surname>Knap</surname><given-names>A. H.</given-names></name></person-group> (<year>2002</year>). <article-title>Elemental C, N, and P cell content of individual bacteria collected at the Bermuda Atlantic Time-series Study (BATS) site</article-title>. <source>Limnol. Oceanogr.</source><volume>47</volume>, <fpage>1525</fpage>–<lpage>1530</lpage><pub-id pub-id-type="doi">10.4319/lo.2002.47.5.1525</pub-id></mixed-citation></ref><ref id="B26"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gyaneshwar</surname><given-names>P.</given-names></name><name><surname>Paliy</surname><given-names>O.</given-names></name><name><surname>McAuliffe</surname><given-names>J.</given-names></name><name><surname>Popham</surname><given-names>D. L.</given-names></name><name><surname>Jordan</surname><given-names>M. I.</given-names></name><name><surname>Kustu</surname><given-names>S.</given-names></name></person-group> (<year>2005</year>). <article-title>Sulfur and nitrogen limitation in <italic>Escherichia coli</italic> K-12: specific homeostatic responses</article-title>. <source>J. Bacteriol.</source><volume>187</volume>, <fpage>1074</fpage>–<lpage>1090</lpage><pub-id pub-id-type="doi">10.1128/JB.187.3.1074-1090.2005</pub-id><pub-id pub-id-type="pmid">15659685</pub-id></mixed-citation></ref><ref id="B27"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hall</surname><given-names>E. K.</given-names></name><name><surname>Maixner</surname><given-names>F.</given-names></name><name><surname>Franklin</surname><given-names>O.</given-names></name><name><surname>Daims</surname><given-names>H.</given-names></name><name><surname>Richter</surname><given-names>A.</given-names></name><name><surname>Battin</surname><given-names>T.</given-names></name></person-group> (<year>2011</year>). <article-title>Linking microbial and ecosystem ecology using ecological stoichiometry: a synthesis of conceptual and empirical approaches</article-title>. <source>Ecosystems</source><volume>14</volume>, <fpage>261</fpage>–<lpage>273</lpage><pub-id pub-id-type="doi">10.1007/s10021-010-9408-4</pub-id></mixed-citation></ref><ref id="B28"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Harder</surname><given-names>W.</given-names></name><name><surname>Dijkhuizen</surname><given-names>L.</given-names></name></person-group> (<year>1983</year>). <article-title>Physiological responses to nutrient limitation</article-title>. <source>Annu. Rev. Microbiol.</source><volume>37</volume>, <fpage>1</fpage>–<lpage>23</lpage><pub-id pub-id-type="doi">10.1146/annurev.mi.37.100183.000245</pub-id><pub-id pub-id-type="pmid">6357049</pub-id></mixed-citation></ref><ref id="B29"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hendrickson</surname><given-names>E. L.</given-names></name><name><surname>Liu</surname><given-names>Y.</given-names></name><name><surname>Rosas-Sandoval</surname><given-names>G.</given-names></name><name><surname>Porat</surname><given-names>I.</given-names></name><name><surname>Söll</surname><given-names>D.</given-names></name><name><surname>Whitman</surname><given-names>W. B.</given-names></name><name><surname>Leigh</surname><given-names>J. A.</given-names></name></person-group> (<year>2008</year>). <article-title>Global responses of <italic>Methanococcus maripaludis</italic> to specific nutrient limitations and growth rate</article-title>. <source>J. Bacteriol.</source><volume>190</volume>, <fpage>2198</fpage>–<lpage>2205</lpage><pub-id pub-id-type="doi">10.1128/JB.01805-07</pub-id><pub-id pub-id-type="pmid">18203827</pub-id></mixed-citation></ref><ref id="B30"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Henriksen</surname><given-names>J. R.</given-names></name></person-group> (<year>2008</year>). <source>Physiology of Dimethylsulfoniopropionate Metabolism in a Model Marine Roseobacter, Silicibacter pomeroyi</source>. Ph.D. thesis, <publisher-name>University of Georgia</publisher-name>, <publisher-loc>Athens, GA, USA</publisher-loc></mixed-citation></ref><ref id="B31"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hessen</surname><given-names>D. O.</given-names></name><name><surname>Agren</surname><given-names>G. I.</given-names></name><name><surname>Anderson</surname><given-names>T. R.</given-names></name><name><surname>Elser</surname><given-names>J. J.</given-names></name><name><surname>De Ruiter</surname><given-names>P. C.</given-names></name></person-group> (<year>2004</year>). <article-title>Carbon sequestration in ecosystems: the role of stoichiometry</article-title>. <source>Ecology</source><volume>85</volume>, <fpage>1179</fpage>–<lpage>1192</lpage><pub-id pub-id-type="doi">10.1890/02-0251</pub-id></mixed-citation></ref><ref id="B32"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ikeda</surname><given-names>T. P.</given-names></name><name><surname>Shauger</surname><given-names>A. E.</given-names></name><name><surname>Kustu</surname><given-names>S.</given-names></name></person-group> (<year>1996</year>). <article-title><italic>Salmonella typhimurium</italic> apparently perceives external nitrogen limitation as internal glutamine limitation</article-title>. <source>J. Mol. Biol.</source><volume>259</volume>, <fpage>589</fpage>–<lpage>607</lpage><pub-id pub-id-type="doi">10.1006/jmbi.1996.0349</pub-id><pub-id pub-id-type="pmid">8683567</pub-id></mixed-citation></ref><ref id="B33"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ishige</surname><given-names>K.</given-names></name><name><surname>Noguchi</surname><given-names>T.</given-names></name></person-group> (<year>2000</year>). <article-title>Inorganic polyphosphate kinase and adenylate kinase participate in the polyphosphate:AMP phosphotransferase activity of <italic>Escherichia coli</italic></article-title>. <source>Proc. Natl. Acad. Sci. U.S.A.</source><volume>97</volume>, <fpage>14168</fpage>–<lpage>14171</lpage><pub-id pub-id-type="doi">10.1073/pnas.011518098</pub-id><pub-id pub-id-type="pmid">11106368</pub-id></mixed-citation></ref><ref id="B34"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kirchman</surname><given-names>D.</given-names></name><name><surname>Rich</surname><given-names>J.</given-names></name></person-group> (<year>1997</year>). <article-title>Regulation of bacterial growth rates by dissolved organic carbon and temperature in the Equatorial Pacific Ocean</article-title>. <source>Microb. Ecol.</source><volume>33</volume>, <fpage>11</fpage>–<lpage>20</lpage><pub-id pub-id-type="doi">10.1007/s002489900003</pub-id><pub-id pub-id-type="pmid">9039761</pub-id></mixed-citation></ref><ref id="B35"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kirchman</surname><given-names>D. L.</given-names></name></person-group> (<year>1990</year>). <article-title>Limitation of bacterial growth by dissolved organic matter in the subartic Pacific</article-title>. <source>Mar. Ecol. Prog. Ser.</source><volume>62</volume>, <fpage>47</fpage>–<lpage>54</lpage><pub-id pub-id-type="doi">10.3354/meps062047</pub-id></mixed-citation></ref><ref id="B36"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kornberg</surname><given-names>A.</given-names></name></person-group> (<year>1999</year>). <article-title>Inorganic polyphosphate: a molecule of many functions</article-title>. <source>Prog. Mol. Subcell. Biol.</source><volume>23</volume>, <fpage>1</fpage>–<lpage>18</lpage><pub-id pub-id-type="doi">10.1007/978-3-642-58444-2_1</pub-id><pub-id pub-id-type="pmid">10448669</pub-id></mixed-citation></ref><ref id="B37"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kranz</surname><given-names>R. G.</given-names></name><name><surname>Gabbert</surname><given-names>K. K.</given-names></name><name><surname>Locke</surname><given-names>T. A.</given-names></name><name><surname>Madigan</surname><given-names>M. T.</given-names></name></person-group> (<year>1997</year>). <article-title>Polyhydroxyalkanoate production in <italic>Rhodobacter capsulatus</italic>: genes, mutants, expression, and physiology</article-title>. <source>Appl. Environ. Microbiol.</source><volume>63</volume>, <fpage>3003</fpage>–<lpage>3009</lpage><pub-id pub-id-type="pmid">9251189</pub-id></mixed-citation></ref><ref id="B38"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kulaev</surname><given-names>I. S.</given-names></name><name><surname>Bobyk</surname><given-names>M. A.</given-names></name><name><surname>Nikolaev</surname><given-names>N. N.</given-names></name><name><surname>Sergeev</surname><given-names>N. S.</given-names></name><name><surname>Uryson</surname><given-names>S. O.</given-names></name></person-group> (<year>1971</year>). <article-title>Polyphosphate synthesizing enzymes in some fungi and bacteria</article-title>. <source>Biochemistry</source><volume>36</volume>, <fpage>791</fpage>–<lpage>796</lpage></mixed-citation></ref><ref id="B39"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Loladze</surname><given-names>I.</given-names></name><name><surname>Elser</surname><given-names>J. J.</given-names></name></person-group> (<year>2011</year>). <article-title>The origins of the Redfield nitrogen-to-phosphorus ratio are in a homoeostatic protein-to-rRNA ratio</article-title>. <source>Ecol. Lett.</source><volume>14</volume>, <fpage>244</fpage>–<lpage>250</lpage><pub-id pub-id-type="doi">10.1111/j.1461-0248.2010.01577.x</pub-id><pub-id pub-id-type="pmid">21244593</pub-id></mixed-citation></ref><ref id="B40"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Martinussen</surname><given-names>I.</given-names></name><name><surname>Thingstad</surname><given-names>T. F.</given-names></name></person-group> (<year>1987</year>). <article-title>Utilization of organic N, organic P and organic C by heterotrophic bacteria. 2. Comparison of experiments and a mathematical model</article-title>. <source>Mar. Ecol. Prog. Ser.</source><volume>37</volume>, <fpage>285</fpage>–<lpage>293</lpage><pub-id pub-id-type="doi">10.3354/meps037285</pub-id></mixed-citation></ref><ref id="B41"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Matsen</surname><given-names>F. A.</given-names></name><name><surname>Kodner</surname><given-names>R. B.</given-names></name><name><surname>Armbrust</surname><given-names>E. V.</given-names></name></person-group> (<year>2010</year>). <article-title>Pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree</article-title>. <source>BMC Bioinformatics</source><volume>11</volume>, <fpage>538</fpage><pub-id pub-id-type="doi">10.1186/1471-2105-11-538</pub-id><pub-id pub-id-type="pmid">21034504</pub-id></mixed-citation></ref><ref id="B42"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Metcalf</surname><given-names>W. W.</given-names></name><name><surname>Wanner</surname><given-names>B. L.</given-names></name></person-group> (<year>1991</year>). <article-title>Involvement of the <italic>Escherichia coli phn</italic> (<italic>psiD</italic>) gene cluster in assimilation of phosphorus in the form of phosphonates, phosphite, P<sub>i</sub> esters, and P<sub>i</sub></article-title>. <source>J. Bacteriol.</source><volume>173</volume>, <fpage>587</fpage>–<lpage>600</lpage><pub-id pub-id-type="pmid">1846145</pub-id></mixed-citation></ref><ref id="B43"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Moran</surname><given-names>M. A.</given-names></name><name><surname>Buchan</surname><given-names>A.</given-names></name><name><surname>González</surname><given-names>J. M.</given-names></name><name><surname>Heidelberg</surname><given-names>J. F.</given-names></name><name><surname>Whitman</surname><given-names>W. B.</given-names></name><name><surname>Kiene</surname><given-names>R. P.</given-names></name><name><surname>Henriksen</surname><given-names>J. R.</given-names></name><name><surname>King</surname><given-names>G. M.</given-names></name><name><surname>Belas</surname><given-names>R.</given-names></name><name><surname>Fuqua</surname><given-names>C.</given-names></name><name><surname>Brinkac</surname><given-names>L.</given-names></name><name><surname>Lewis</surname><given-names>M.</given-names></name><name><surname>Johri</surname><given-names>S.</given-names></name><name><surname>Weaver</surname><given-names>B.</given-names></name><name><surname>Pai</surname><given-names>G.</given-names></name><name><surname>Eisen</surname><given-names>J. A.</given-names></name><name><surname>Rahe</surname><given-names>E.</given-names></name><name><surname>Sheldon</surname><given-names>W. M.</given-names></name><name><surname>Ye</surname><given-names>W.</given-names></name><name><surname>Miller</surname><given-names>T. R.</given-names></name><name><surname>Carlton</surname><given-names>J.</given-names></name><name><surname>Rasko</surname><given-names>D. A.</given-names></name><name><surname>Paulsen</surname><given-names>I. T.</given-names></name><name><surname>Ren</surname><given-names>Q.</given-names></name><name><surname>Daugherty</surname><given-names>S. C.</given-names></name><name><surname>Deboy</surname><given-names>R. T.</given-names></name><name><surname>Dodson</surname><given-names>R. J.</given-names></name><name><surname>Durkin</surname><given-names>A. S.</given-names></name><name><surname>Madupu</surname><given-names>R.</given-names></name><name><surname>Nelson</surname><given-names>W. C.</given-names></name><name><surname>Sullivan</surname><given-names>S. A.</given-names></name><name><surname>Rosovitz</surname><given-names>M. J.</given-names></name><name><surname>Haft</surname><given-names>D. H.</given-names></name><name><surname>Selengut</surname><given-names>J.</given-names></name><name><surname>Ward</surname><given-names>N.</given-names></name></person-group> (<year>2004</year>). <article-title>Genome sequence of <italic>Silicibacter pomeroyi</italic> reveals adaptations to the marine environment</article-title>. <source>Nature</source><volume>432</volume>, <fpage>910</fpage>–<lpage>913</lpage><pub-id pub-id-type="doi">10.1038/nature03170</pub-id><pub-id pub-id-type="pmid">15602564</pub-id></mixed-citation></ref><ref id="B44"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Moran</surname><given-names>M. A.</given-names></name><name><surname>Reisch</surname><given-names>C. R.</given-names></name><name><surname>Kiene</surname><given-names>R. P.</given-names></name><name><surname>Whitman</surname><given-names>W. B.</given-names></name></person-group> (<year>2011</year>). <article-title>Genomic insights into bacterial DMSP transformations</article-title>. <source>Ann. Rev. Mar. Sci.</source><volume>4</volume>, <fpage>523</fpage>–<lpage>542</lpage><pub-id pub-id-type="doi">10.1146/annurev-marine-120710-100827</pub-id></mixed-citation></ref><ref id="B45"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nahálka</surname><given-names>J.</given-names></name><name><surname>Pätoprstý</surname><given-names>V.</given-names></name></person-group> (<year>2009</year>). <article-title>Enzymatic synthesis of sialylation substrates powered by a novel polyphosphate kinase (PPK3)</article-title>. <source>Org. Biomol. Chem.</source><volume>7</volume>, <fpage>1778</fpage>–<lpage>1780</lpage><pub-id pub-id-type="doi">10.1039/b822549b</pub-id><pub-id pub-id-type="pmid">19590770</pub-id></mixed-citation></ref><ref id="B46"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Newton</surname><given-names>R. J.</given-names></name><name><surname>Griffin</surname><given-names>L. E.</given-names></name><name><surname>Bowles</surname><given-names>K. M.</given-names></name><name><surname>Meile</surname><given-names>C.</given-names></name><name><surname>Gifford</surname><given-names>S.</given-names></name><name><surname>Givens</surname><given-names>C. E.</given-names></name><name><surname>Howard</surname><given-names>E. C.</given-names></name><name><surname>King</surname><given-names>E.</given-names></name><name><surname>Oakley</surname><given-names>C. A.</given-names></name><name><surname>Reisch</surname><given-names>C. R.</given-names></name><name><surname>Rinta-Kanto</surname><given-names>J. M.</given-names></name><name><surname>Sharma</surname><given-names>S.</given-names></name><name><surname>Sun</surname><given-names>S.</given-names></name><name><surname>Varaljay</surname><given-names>V.</given-names></name><name><surname>Vila-Costa</surname><given-names>M.</given-names></name><name><surname>Westrich</surname><given-names>J. R.</given-names></name><name><surname>Moran</surname><given-names>M. A.</given-names></name></person-group> (<year>2010</year>). <article-title>Genome characteristics of a generalist marine bacterial lineage</article-title>. <source>ISME J.</source><volume>4</volume>, <fpage>784</fpage>–<lpage>798</lpage><pub-id pub-id-type="doi">10.1038/ismej.2009.150</pub-id><pub-id pub-id-type="pmid">20072162</pub-id></mixed-citation></ref><ref id="B47"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Obernosterer</surname><given-names>I.</given-names></name><name><surname>Kawasaki</surname><given-names>N.</given-names></name><name><surname>Benner</surname><given-names>R.</given-names></name></person-group> (<year>2003</year>). <article-title>P-limitation of respiration in the Sargasso Sea and uncoupling of bacteria from P-regeneration in size-fractionation</article-title>. <source>Aquat. Microb. Ecol.</source><volume>32</volume>, <fpage>229</fpage>–<lpage>237</lpage><pub-id pub-id-type="doi">10.3354/ame032229</pub-id></mixed-citation></ref><ref id="B48"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Parker</surname><given-names>G. F.</given-names></name><name><surname>Higgins</surname><given-names>T. P.</given-names></name><name><surname>Hawkes</surname><given-names>T.</given-names></name><name><surname>Robson</surname><given-names>R. L.</given-names></name></person-group> (<year>1999</year>). <article-title><italic>Rhizobium</italic> (<italic>Sinorhizobium</italic>) <italic>meliloti phn</italic> genes: characterization and identification of their protein products</article-title>. <source>J. Bacteriol.</source><volume>181</volume>, <fpage>389</fpage>–<lpage>395</lpage><pub-id pub-id-type="pmid">9882650</pub-id></mixed-citation></ref><ref id="B49"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pomeroy</surname><given-names>L. R.</given-names></name><name><surname>Sheldon</surname><given-names>J. E.</given-names></name><name><surname>Sheldon</surname><given-names>W. M. J.</given-names></name><name><surname>Peters</surname><given-names>F.</given-names></name></person-group> (<year>1995</year>). <article-title>Limits to growth and respiration of bacterioplankton in the Gulf of Mexico</article-title>. <source>Mar. Ecol. Prog. Ser.</source><volume>117</volume>, <fpage>259</fpage>–<lpage>268</lpage><pub-id pub-id-type="doi">10.3354/meps117259</pub-id></mixed-citation></ref><ref id="B50"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Poretsky</surname><given-names>R. S.</given-names></name><name><surname>Gifford</surname><given-names>S. M.</given-names></name><name><surname>Rinta-Kanto</surname><given-names>J. M.</given-names></name><name><surname>Vila-Costa</surname><given-names>M.</given-names></name><name><surname>Moran</surname><given-names>M. A.</given-names></name></person-group> (<year>2009</year>). <article-title>Analyzing gene expression from marine microbial communities using environmental transcriptomics</article-title>. <source>J. Vis. Exp.</source><volume>24</volume>: <fpage>e1086</fpage><pub-id pub-id-type="doi">10.3791/1086</pub-id></mixed-citation></ref><ref id="B51"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Redfield</surname><given-names>A. C.</given-names></name></person-group> (<year>1934</year>). <article-title>“On the proportions of organic derivations in seawater and their relation to the composition of plankton,”</article-title> in <source>James Johnstone Memorial Volume</source>, ed. <person-group person-group-type="editor"><name><surname>Daniel</surname></name></person-group> (<publisher-loc>Liverpool</publisher-loc>: <publisher-name>University Press</publisher-name>), <fpage>177</fpage>–<lpage>192</lpage></mixed-citation></ref><ref id="B52"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rinta-Kanto</surname><given-names>J. M.</given-names></name><name><surname>Bürgmann</surname><given-names>H.</given-names></name><name><surname>Gifford</surname><given-names>S. M.</given-names></name><name><surname>Sun</surname><given-names>S.</given-names></name><name><surname>Sharma</surname><given-names>S.</given-names></name><name><surname>del Valle</surname><given-names>D. A.</given-names></name><name><surname>Kiene</surname><given-names>R. P.</given-names></name><name><surname>Moran</surname><given-names>M. A.</given-names></name></person-group> (<year>2010</year>). <article-title>Analysis of sulfur-related transcription by <italic>Roseobacter</italic> communities using a taxon-specific functional gene microarray</article-title>. <source>Environ. Microbiol.</source><volume>13</volume>, <fpage>453</fpage>–<lpage>467</lpage><pub-id pub-id-type="doi">10.1111/j.1462-2920.2010.02350.x</pub-id><pub-id pub-id-type="pmid">20880331</pub-id></mixed-citation></ref><ref id="B53"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rivkin</surname><given-names>R. B.</given-names></name><name><surname>Anderson</surname><given-names>M. R.</given-names></name></person-group> (<year>1997</year>). <article-title>Inorganic nutrient limitation of oceanic bacterioplankton</article-title>. <source>Limnol. Oceanogr.</source><volume>42</volume>, <fpage>730</fpage>–<lpage>740</lpage><pub-id pub-id-type="doi">10.4319/lo.1997.42.4.0730</pub-id></mixed-citation></ref><ref id="B54"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rusch</surname><given-names>D. B.</given-names></name><name><surname>Halpern</surname><given-names>A. L.</given-names></name><name><surname>Sutton</surname><given-names>G.</given-names></name><name><surname>Heidelberg</surname><given-names>K. B.</given-names></name><name><surname>Williamson</surname><given-names>S.</given-names></name><name><surname>Yooseph</surname><given-names>S.</given-names></name><name><surname>Wu</surname><given-names>D.</given-names></name><name><surname>Eisen</surname><given-names>J. A.</given-names></name><name><surname>Hoffman</surname><given-names>J. M.</given-names></name><name><surname>Remington</surname><given-names>K.</given-names></name><name><surname>Beeson</surname><given-names>K.</given-names></name><name><surname>Tran</surname><given-names>B.</given-names></name><name><surname>Smith</surname><given-names>H.</given-names></name><name><surname>Baden-Tillson</surname><given-names>H.</given-names></name><name><surname>Stewart</surname><given-names>C.</given-names></name><name><surname>Thorpe</surname><given-names>J.</given-names></name><name><surname>Freeman</surname><given-names>J.</given-names></name><name><surname>Andrews-Pfannkoch</surname><given-names>C.</given-names></name><name><surname>Venter</surname><given-names>J. E.</given-names></name><name><surname>Li</surname><given-names>K.</given-names></name><name><surname>Kravitz</surname><given-names>S.</given-names></name><name><surname>Heidelberg</surname><given-names>J. F.</given-names></name><name><surname>Utterback</surname><given-names>T.</given-names></name><name><surname>Rogers</surname><given-names>Y. H.</given-names></name><name><surname>Falcón</surname><given-names>L. I.</given-names></name><name><surname>Souza</surname><given-names>V.</given-names></name><name><surname>Bonilla-Rosso</surname><given-names>G.</given-names></name><name><surname>Eguiarte</surname><given-names>L. E.</given-names></name><name><surname>Karl</surname><given-names>D. M.</given-names></name><name><surname>Sathyendranath</surname><given-names>S.</given-names></name><name><surname>Platt</surname><given-names>T.</given-names></name><name><surname>Bermingham</surname><given-names>E.</given-names></name><name><surname>Gallardo</surname><given-names>V.</given-names></name><name><surname>Tamayo-Castillo</surname><given-names>G.</given-names></name><name><surname>Ferrari</surname><given-names>M. R.</given-names></name><name><surname>Strausberg</surname><given-names>R. L.</given-names></name><name><surname>Nealson</surname><given-names>K.</given-names></name><name><surname>Friedman</surname><given-names>R.</given-names></name><name><surname>Frazier</surname><given-names>M.</given-names></name><name><surname>Venter</surname><given-names>J. C.</given-names></name></person-group> (<year>2007</year>). <article-title>The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through Eastern Tropical Pacific</article-title>. <source>PLoS Biol.</source><volume>5</volume>, <fpage>77</fpage><pub-id pub-id-type="doi">10.1371/journal.pbio.0050077</pub-id></mixed-citation></ref><ref id="B55"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Saeed</surname><given-names>A. I.</given-names></name><name><surname>Bhagabati</surname><given-names>N. K.</given-names></name><name><surname>Braisted</surname><given-names>J. C.</given-names></name><name><surname>Liang</surname><given-names>W.</given-names></name><name><surname>Sharov</surname><given-names>V.</given-names></name><name><surname>Howe</surname><given-names>E. A.</given-names></name><name><surname>Li</surname><given-names>J.</given-names></name><name><surname>Thiagarajan</surname><given-names>M.</given-names></name><name><surname>White</surname><given-names>J. A.</given-names></name><name><surname>Quackenbush</surname><given-names>J.</given-names></name></person-group> (<year>2006</year>). <article-title>TM4 microarray software suite</article-title>. <source>Meth. Enzymol.</source><volume>411</volume>, <fpage>134</fpage>–<lpage>193</lpage><pub-id pub-id-type="doi">10.1016/S0076-6879(06)11009-5</pub-id><pub-id pub-id-type="pmid">16939790</pub-id></mixed-citation></ref><ref id="B56"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Scott</surname><given-names>J. T.</given-names></name><name><surname>Cotner</surname><given-names>J. B.</given-names></name><name><surname>LaPara</surname><given-names>T. M.</given-names></name></person-group> (<year>2012</year>). <article-title>Variable stoichiometry and homeostatic regulation of bacterial biomass elemental composition</article-title>. <source>Front. Microbiol.</source><volume>3</volume>:<fpage>42</fpage><pub-id pub-id-type="doi">10.3389/fmicb.2012.00042</pub-id><pub-id pub-id-type="pmid">22371708</pub-id></mixed-citation></ref><ref id="B57"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sebastian</surname><given-names>M.</given-names></name><name><surname>Ammerman</surname><given-names>J. W.</given-names></name></person-group> (<year>2011</year>). <article-title>Role of the phosphatase PhoX in the phosphorus metabolism of the marine bacterium <italic>Ruegeria pomeroyi</italic> DSS-3</article-title>. <source>Environ. Microbiol. Rep.</source><volume>3</volume>, <fpage>535</fpage>–<lpage>542</lpage><pub-id pub-id-type="doi">10.1111/j.1758-2229.2011.00253.x</pub-id></mixed-citation></ref><ref id="B58"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Solorzano</surname><given-names>L.</given-names></name></person-group> (<year>1969</year>). <article-title>Determination of ammonia in natural waters by the phenolhypochlorite method</article-title>. <source>Limnol. Oceanogr.</source><volume>14</volume>, <fpage>799</fpage>–<lpage>801</lpage><pub-id pub-id-type="doi">10.4319/lo.1969.14.5.0799</pub-id></mixed-citation></ref><ref id="B59"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sterner</surname><given-names>R. W.</given-names></name><name><surname>Andersen</surname><given-names>T.</given-names></name><name><surname>Elser</surname><given-names>J. J.</given-names></name><name><surname>Hessen</surname><given-names>D. O.</given-names></name><name><surname>Hood</surname><given-names>J. M.</given-names></name><name><surname>McCauley</surname><given-names>E.</given-names></name><name><surname>Urabe</surname><given-names>J.</given-names></name></person-group> (<year>2008</year>). <article-title>Scale-dependent carbon: nitrogen: phosphorus seston stoichiometry in marine and freshwaters</article-title>. <source>Limnol. Oceanogr.</source><volume>53</volume>, <fpage>1169</fpage>–<lpage>1180</lpage><pub-id pub-id-type="doi">10.4319/lo.2008.53.3.1169</pub-id></mixed-citation></ref><ref id="B60"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Strickland</surname><given-names>J. D. H.</given-names></name><name><surname>Parsons</surname><given-names>T. R.</given-names></name></person-group> (<year>1972</year>). <source>A Practical Handbook of Seawater Analysis</source>, <edition>2nd Edn.</edition><publisher-loc>Ottawa</publisher-loc>: <publisher-name>Fish Res Board Can</publisher-name></mixed-citation></ref><ref id="B61"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Tezuka</surname><given-names>Y.</given-names></name></person-group> (<year>1990</year>). <article-title>Bacterial regeneration of ammonium and phosphate as affected by the carbon:nitrogen:phosphorus ratio of organic substrates</article-title>. <source>Microb. Ecol.</source><volume>19</volume>, <fpage>227</fpage>–<lpage>238</lpage><pub-id pub-id-type="doi">10.1007/BF02017167</pub-id></mixed-citation></ref><ref id="B62"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Thingstad</surname><given-names>T. F.</given-names></name></person-group> (<year>1987</year>). <article-title>Utilization of N, P, and organic C by heterotrophic bacteria. 1. Outline of a chemostat theory with a consistent concept of maintenance metabolism</article-title>. <source>Mar. Ecol. Prog. Ser.</source><volume>35</volume>, <fpage>99</fpage>–<lpage>109</lpage><pub-id pub-id-type="doi">10.3354/meps035099</pub-id></mixed-citation></ref><ref id="B63"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Thingstad</surname><given-names>T. F.</given-names></name><name><surname>Bellerby</surname><given-names>R. G.</given-names></name><name><surname>Bratbak</surname><given-names>G.</given-names></name><name><surname>Børsheim</surname><given-names>K. Y.</given-names></name><name><surname>Egge</surname><given-names>J. K.</given-names></name><name><surname>Heldal</surname><given-names>M.</given-names></name><name><surname>Larsen</surname><given-names>A.</given-names></name><name><surname>Neill</surname><given-names>C.</given-names></name><name><surname>Nejstgaard</surname><given-names>J.</given-names></name><name><surname>Norland</surname><given-names>S.</given-names></name><name><surname>Sandaa</surname><given-names>R.-A.</given-names></name><name><surname>Skjoldal</surname><given-names>E. F.</given-names></name><name><surname>Tanaka</surname><given-names>T.</given-names></name><name><surname>Thyrhaug</surname><given-names>R.</given-names></name><name><surname>Töpper</surname><given-names>B.</given-names></name></person-group> (<year>2008</year>). <article-title>Counterintuitive carbon-to-nutrient coupling in an Arctic pelagic ecosystem</article-title>. <source>Nature</source><volume>455</volume>, <fpage>387</fpage>–<lpage>390</lpage><pub-id pub-id-type="doi">10.1038/nature07235</pub-id><pub-id pub-id-type="pmid">18716617</pub-id></mixed-citation></ref><ref id="B64"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Thingstad</surname><given-names>T. F.</given-names></name><name><surname>Krom</surname><given-names>M. D.</given-names></name><name><surname>Mantoura</surname><given-names>R. F.</given-names></name><name><surname>Flaten</surname><given-names>G. A.</given-names></name><name><surname>Groom</surname><given-names>S.</given-names></name><name><surname>Herut</surname><given-names>B.</given-names></name><name><surname>Kress</surname><given-names>N.</given-names></name><name><surname>Law</surname><given-names>C. S.</given-names></name><name><surname>Pasternak</surname><given-names>A.</given-names></name><name><surname>Pitta</surname><given-names>P.</given-names></name><name><surname>Psarra</surname><given-names>S.</given-names></name><name><surname>Rassoulzadegan</surname><given-names>F.</given-names></name><name><surname>Tanaka</surname><given-names>T.</given-names></name><name><surname>Tselepides</surname><given-names>A.</given-names></name><name><surname>Wassmann</surname><given-names>P.</given-names></name><name><surname>Woodward</surname><given-names>E. M. S.</given-names></name><name><surname>Wexels Riser</surname><given-names>C.</given-names></name><name><surname>Zodiatis</surname><given-names>G.</given-names></name><name><surname>Zohary</surname><given-names>T.</given-names></name></person-group> (<year>2005</year>). <article-title>Nature of phosphorus limitation in the ultraoligotrophic eastern Mediterranean</article-title>. <source>Science</source><volume>309</volume>, <fpage>1068</fpage>–<lpage>1071</lpage><pub-id pub-id-type="doi">10.1126/science.1112632</pub-id><pub-id pub-id-type="pmid">16099984</pub-id></mixed-citation></ref><ref id="B65"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Torréton</surname><given-names>J. P.</given-names></name><name><surname>Talbot</surname><given-names>V.</given-names></name><name><surname>Garcia</surname><given-names>N.</given-names></name></person-group> (<year>2000</year>). <article-title>Nutrient stimulation of bacterioplankton growth in Tuamotu atoll lagoons</article-title>. <source>Aquat. Microb. Ecol.</source><volume>21</volume>, <fpage>125</fpage>–<lpage>137</lpage><pub-id pub-id-type="doi">10.3354/ame021125</pub-id></mixed-citation></ref><ref id="B66"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Tusher</surname><given-names>V. G.</given-names></name><name><surname>Tibshirani</surname><given-names>R.</given-names></name><name><surname>Chu</surname><given-names>G.</given-names></name></person-group> (<year>2001</year>). <article-title>Significance analysis of microarrays applied to the ionizing radiation response</article-title>. <source>Proc. Natl. Acad. Sci. U.S.A.</source><volume>98</volume>, <fpage>5116</fpage>–<lpage>5121</lpage><pub-id pub-id-type="doi">10.1073/pnas.091062498</pub-id><pub-id pub-id-type="pmid">11309499</pub-id></mixed-citation></ref><ref id="B67"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Van Mooy</surname><given-names>B. A.</given-names></name><name><surname>Fredricks</surname><given-names>H. F.</given-names></name><name><surname>Pedler</surname><given-names>B. E.</given-names></name><name><surname>Dyhrman</surname><given-names>S. T.</given-names></name><name><surname>Karl</surname><given-names>D. M.</given-names></name><name><surname>Koblizek</surname><given-names>M.</given-names></name><name><surname>Lomas</surname><given-names>M. W.</given-names></name><name><surname>Mincer</surname><given-names>T. J.</given-names></name><name><surname>Moore</surname><given-names>L. R.</given-names></name><name><surname>Moutin</surname><given-names>T.</given-names></name><name><surname>Rappé</surname><given-names>M. S.</given-names></name><name><surname>Webb</surname><given-names>E. A.</given-names></name></person-group> (<year>2009</year>). <article-title>Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity</article-title>. <source>Nature</source><volume>458</volume>, <fpage>69</fpage>–<lpage>72</lpage><pub-id pub-id-type="doi">10.1038/nature07659</pub-id><pub-id pub-id-type="pmid">19182781</pub-id></mixed-citation></ref><ref id="B68"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Van Wambeke</surname><given-names>F.</given-names></name><name><surname>Christaki</surname><given-names>U.</given-names></name><name><surname>Giannakourou</surname><given-names>A.</given-names></name><name><surname>Moutin</surname><given-names>T.</given-names></name><name><surname>Souvemerzoglou</surname><given-names>K.</given-names></name></person-group> (<year>2002</year>). <article-title>Longitudinal and vertical trends of bacterial limitation by phosphorus and carbon in the Mediterranean Sea</article-title>. <source>Microb. Ecol.</source><volume>43</volume>, <fpage>119</fpage>–<lpage>133</lpage><pub-id pub-id-type="doi">10.1007/s00248-001-0038-4</pub-id><pub-id pub-id-type="pmid">11984634</pub-id></mixed-citation></ref><ref id="B69"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Vrede</surname><given-names>K.</given-names></name><name><surname>Heldal</surname><given-names>M.</given-names></name><name><surname>Norland</surname><given-names>S.</given-names></name><name><surname>Bratbak</surname><given-names>G.</given-names></name></person-group> (<year>2002</year>). <article-title>Elemental composition (C, N, P) and cell volume of exponentially growing and nutrient-limited bacterioplankton</article-title>. <source>Appl. Environ. Microbiol.</source><volume>68</volume>, <fpage>2965</fpage>–<lpage>2971</lpage><pub-id pub-id-type="doi">10.1128/AEM.68.6.2965-2971.2002</pub-id><pub-id pub-id-type="pmid">12039756</pub-id></mixed-citation></ref><ref id="B70"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Vrljic</surname><given-names>M.</given-names></name><name><surname>Garg</surname><given-names>J.</given-names></name><name><surname>Bellmann</surname><given-names>A.</given-names></name><name><surname>Wachi</surname><given-names>S.</given-names></name><name><surname>Freudl</surname><given-names>R.</given-names></name><name><surname>Malecki</surname><given-names>M. J.</given-names></name><name><surname>Sahm</surname><given-names>H.</given-names></name><name><surname>Kozina</surname><given-names>V. J.</given-names></name><name><surname>Eggeling</surname><given-names>L.</given-names></name><name><surname>Saier</surname><given-names>M. H.</given-names><suffix>Jr.</suffix></name><name><surname>Eggeling</surname><given-names>L.</given-names></name><name><surname>Saier</surname><given-names>M. H.</given-names><suffix>Jr.</suffix></name></person-group> (<year>1999</year>). <article-title>The LysE superfamily: topology of the lysine exporter LysE of <italic>Corynebacterium glutamicum</italic>, a paradigm for a novel superfamily of transmembrane solute translocators</article-title>. <source>J. Mol. Microbiol. Biotechnol.</source><volume>1</volume>, <fpage>327</fpage>–<lpage>336</lpage><pub-id pub-id-type="pmid">10943564</pub-id></mixed-citation></ref><ref id="B71"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wachi</surname><given-names>M.</given-names></name><name><surname>Doi</surname><given-names>M.</given-names></name><name><surname>Okada</surname><given-names>Y.</given-names></name><name><surname>Matsuhashi</surname><given-names>M.</given-names></name></person-group> (<year>1989</year>). <article-title>New <italic>mre</italic> genes <italic>mreC</italic> and <italic>mreD</italic>, responsible for formation of the rod shape of <italic>Escherichia coli</italic> cells</article-title>. <source>J. Bacteriol.</source><volume>171</volume>, <fpage>6511</fpage>–<lpage>6516</lpage><pub-id pub-id-type="pmid">2687239</pub-id></mixed-citation></ref><ref id="B72"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Walter</surname><given-names>B.</given-names></name><name><surname>Hänssler</surname><given-names>E.</given-names></name><name><surname>Kalinowski</surname><given-names>J.</given-names></name><name><surname>Burkovski</surname><given-names>A.</given-names></name></person-group> (<year>2007</year>). <article-title>Nitrogen metabolism and nitrogen control in corynebacteria: variations of a common theme</article-title>. <source>J. Mol. Microbiol. Biotechnol.</source><volume>12</volume>, <fpage>131</fpage>–<lpage>138</lpage><pub-id pub-id-type="doi">10.1159/000096468</pub-id><pub-id pub-id-type="pmid">17183220</pub-id></mixed-citation></ref><ref id="B73"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Weber</surname><given-names>T. S.</given-names></name><name><surname>Deutsch</surname><given-names>C.</given-names></name></person-group> (<year>2010</year>). <article-title>Ocean nutrient ratios governed by plankton biogeography</article-title>. <source>Nature</source><volume>467</volume>, <fpage>550</fpage>–<lpage>554</lpage><pub-id pub-id-type="doi">10.1038/nature09403</pub-id><pub-id pub-id-type="pmid">20882009</pub-id></mixed-citation></ref><ref id="B74"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Weissenmayer</surname><given-names>B.</given-names></name><name><surname>Gao</surname><given-names>J. L.</given-names></name><name><surname>López-Lara</surname><given-names>I. M.</given-names></name><name><surname>Geiger</surname><given-names>O.</given-names></name></person-group> (<year>2002</year>). <article-title>Identification of a gene required for the biosynthesis of ornithine-derived lipids</article-title>. <source>Mol. Microbiol.</source><volume>45</volume>, <fpage>721</fpage>–<lpage>733</lpage><pub-id pub-id-type="doi">10.1046/j.1365-2958.2002.03043.x</pub-id><pub-id pub-id-type="pmid">12139618</pub-id></mixed-citation></ref><ref id="B75"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Whitman</surname><given-names>W. B.</given-names></name><name><surname>Coleman</surname><given-names>D. C.</given-names></name><name><surname>Wiebe</surname><given-names>W. J.</given-names></name></person-group> (<year>1998</year>). <article-title>Prokaryotes: the unseen majority</article-title>. <source>Proc. Natl. Acad. Sci. U.S.A.</source><volume>95</volume>, <fpage>6578</fpage>–<lpage>6583</lpage><pub-id pub-id-type="doi">10.1073/pnas.95.12.6578</pub-id><pub-id pub-id-type="pmid">9618454</pub-id></mixed-citation></ref><ref id="B76"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yooseph</surname><given-names>S.</given-names></name><name><surname>Sutton</surname><given-names>G.</given-names></name><name><surname>Rusch</surname><given-names>D. B.</given-names></name><name><surname>Halpern</surname><given-names>A. L.</given-names></name><name><surname>Williamson</surname><given-names>S. J.</given-names></name><name><surname>Remington</surname><given-names>K.</given-names></name><name><surname>Eisen</surname><given-names>J. A.</given-names></name><name><surname>Heidelberg</surname><given-names>K. B.</given-names></name><name><surname>Manning</surname><given-names>G.</given-names></name><name><surname>Li</surname><given-names>W.</given-names></name><name><surname>Jaroszewski</surname><given-names>L.</given-names></name><name><surname>Cieplak</surname><given-names>P.</given-names></name><name><surname>Miller</surname><given-names>C. S.</given-names></name><name><surname>Li</surname><given-names>H.</given-names></name><name><surname>Mashiyama</surname><given-names>S. T.</given-names></name><name><surname>Joachimiak</surname><given-names>M. P.</given-names></name><name><surname>van Belle</surname><given-names>C.</given-names></name><name><surname>Chandonia</surname><given-names>J. M.</given-names></name><name><surname>Soergel</surname><given-names>D. A.</given-names></name><name><surname>Zhai</surname><given-names>Y.</given-names></name><name><surname>Natarajan</surname><given-names>K.</given-names></name><name><surname>Lee</surname><given-names>S.</given-names></name><name><surname>Raphael</surname><given-names>B. J.</given-names></name><name><surname>Bafna</surname><given-names>V.</given-names></name><name><surname>Friedman</surname><given-names>R.</given-names></name><name><surname>Brenner</surname><given-names>S. E.</given-names></name><name><surname>Godzik</surname><given-names>A.</given-names></name><name><surname>Eisenberg</surname><given-names>D.</given-names></name><name><surname>Dixon</surname><given-names>J. E.</given-names></name><name><surname>Taylor</surname><given-names>S. S.</given-names></name><name><surname>Strausberg</surname><given-names>R. L.</given-names></name><name><surname>Frazier</surname><given-names>M.</given-names></name><name><surname>Venter</surname><given-names>J. C.</given-names></name></person-group> (<year>2007</year>). <article-title>The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families</article-title>. <source>PLoS Biol.</source><volume>5</volume>, <fpage>e16</fpage><pub-id pub-id-type="doi">10.1371/journal.pbio.0050016</pub-id><pub-id pub-id-type="pmid">17355171</pub-id></mixed-citation></ref><ref id="B77"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yuan</surname><given-names>Z. C.</given-names></name><name><surname>Zaheer</surname><given-names>R.</given-names></name><name><surname>Finan</surname><given-names>T. M.</given-names></name></person-group> (<year>2006</year>). <article-title>Regulation and properties of PstSCAB, a high-affinity, high-velocity phosphate transport system of <italic>Sinorhizobium meliloti</italic></article-title>. <source>J. Bacteriol.</source><volume>188</volume>, <fpage>1089</fpage>–<lpage>1102</lpage><pub-id pub-id-type="doi">10.1128/JB.188.3.1089-1102.2006</pub-id><pub-id pub-id-type="pmid">16428413</pub-id></mixed-citation></ref><ref id="B78"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Yurkov</surname><given-names>V. V.</given-names></name></person-group> (<year>2006</year>). <article-title>“Aerobic phototrophic proteobacteria,”</article-title> in <source>The Prokaryotes</source>, <edition>3rd Edn</edition>, eds <person-group person-group-type="editor"><name><surname>Dworkin</surname><given-names>M.</given-names></name><name><surname>Falkow</surname><given-names>S.</given-names></name><name><surname>Rosenberg</surname><given-names>E.</given-names></name><name><surname>Schleifer</surname><given-names>K.-H.</given-names></name><name><surname>Stachebrandt</surname><given-names>E.</given-names></name></person-group> (<publisher-loc>Singapore</publisher-loc>: <publisher-name>Springer Science and Business Media, LLC</publisher-name>), <fpage>562</fpage>–<lpage>584</lpage></mixed-citation></ref><ref id="B79"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zimmer</surname><given-names>D. P.</given-names></name><name><surname>Soupene</surname><given-names>E.</given-names></name><name><surname>Lee</surname><given-names>H. L.</given-names></name><name><surname>Wendisch</surname><given-names>V. F.</given-names></name><name><surname>Khodursky</surname><given-names>A. B.</given-names></name><name><surname>Peter</surname><given-names>B. J.</given-names></name><name><surname>Bender</surname><given-names>R. A.</given-names></name><name><surname>Kustu</surname><given-names>S.</given-names></name></person-group> (<year>2000</year>). <article-title>Nitrogen regulatory protein C-controlled genes of <italic>Escherichia coli</italic>: scavenging as a defense against nitrogen limitation</article-title>. <source>Proc. Natl. Acad. Sci. U.S.A.</source><volume>97</volume>, <fpage>14674</fpage>–<lpage>14679</lpage><pub-id pub-id-type="doi">10.1073/pnas.97.26.14674</pub-id><pub-id pub-id-type="pmid">11121068</pub-id></mixed-citation></ref><ref id="B80"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zohary</surname><given-names>T.</given-names></name><name><surname>Robarts</surname><given-names>R. D.</given-names></name></person-group> (<year>1998</year>). <article-title>Experimental study of microbial P limitation in the eastern Mediterranean</article-title>. <source>Limnol. Oceanogr.</source><volume>43</volume>, <fpage>387</fpage>–<lpage>395</lpage><pub-id pub-id-type="doi">10.4319/lo.1998.43.2.0175</pub-id></mixed-citation></ref></ref-list></back></pmc></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Pmc/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000529 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Corpus/biblio.hfd -nk 000529 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Ticri/CIDE
|area= CyberinfraV1
|flux= Pmc
|étape= Corpus
|type= RBID
|clé= PMC:3390766
|texte= Transcriptional Changes Underlying Elemental Stoichiometry Shifts in a Marine Heterotrophic Bacterium
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Corpus/RBID.i -Sk "pubmed:22783226" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Corpus/biblio.hfd \
| NlmPubMed2Wicri -a CyberinfraV1
| This area was generated with Dilib version V0.6.25. |  |