The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics
Identifieur interne : 002C29 ( Istex/Corpus ); précédent : 002C28; suivant : 002C30The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics
Auteurs : Timothy J. Williams ; David Wilkins ; Emilie Long ; Flavia Evans ; Mathew Z. Demaere ; Mark J. Raftery ; Ricardo CavicchioliSource :
- Environmental Microbiology [ 1462-2912 ] ; 2013-05.
English descriptors
- KwdEn :
- Abell, Acid metabolism, Algal, Alphaproteobacteria, Alteromonadales, Amino, Amino acids, Antarctic, Antarctic peninsula, Antarctic surface waters, Antarctica, Antcomb, Appl, Appl environ microbiol, Archaea, Archaeal, Arctic ocean, Austral summer, Bacterioplankton, Bacteroidetes, Biosynthesis, Blackwell publishing, Bowman, Burtonii, Carbohydrate, Chlorophyll, Clade, Class alphaproteobacteria, Class flavobacteria, Community composition, Database, Dehydrogenase, Delong, Diatom, East antarctica, Ecol, Environ, Environ microbiol, Environmental microbiology, Eukaryotic phytoplankton, Fems, Fems microbiol ecol, Flavobacteria, Fosmid libraries, Gaas, Gaas analysis, Gammaproteobacteria, Genome, Giovannoni, Grzymski, Heterotroph, Highest sequence identity, Isme, Kirchman, Labile, Labile solutes, Limnol oceanogr, Marine antarctic flavobacteria, Metabolism, Metagenome, Metagenome data, Metagenomic, Metaproteome, Metaproteomic, Metaproteomics, Microbial, Microbiol, Microbiology, Newcomb, Nutrient, Ocean surface, Oceanospirillales, Oceanospirillales alteromonadales, Organic matter, Otus, Outer membrane proteins, Pathway, Pelagibacter ubique, Phylogenetic, Phylogenetic assignment, Phytoplankton, Phytoplankton blooms, Pinhassi, Polaribacter, Primary production, Proc natl acad, Relative abundance, Relative abundances, Rhodobacterales, Roseobacter, Roseobacter clade, Seawater, Solute, Southern ocean, Southern ocean metagenome data, Southern ocean metagenomes, Sowell, Subunit, Surface waters, Synthetase, Teeling, Transport system, Transporter, Trna biosynthesis, Unique peptides, Uorescence, Water column depth.
- Teeft :
- Abell, Acid metabolism, Algal, Alphaproteobacteria, Alteromonadales, Amino, Amino acids, Antarctic, Antarctic peninsula, Antarctic surface waters, Antarctica, Antcomb, Appl, Appl environ microbiol, Archaea, Archaeal, Arctic ocean, Austral summer, Bacterioplankton, Bacteroidetes, Biosynthesis, Blackwell publishing, Bowman, Burtonii, Carbohydrate, Chlorophyll, Clade, Class alphaproteobacteria, Class flavobacteria, Community composition, Database, Dehydrogenase, Delong, Diatom, East antarctica, Ecol, Environ, Environ microbiol, Environmental microbiology, Eukaryotic phytoplankton, Fems, Fems microbiol ecol, Flavobacteria, Fosmid libraries, Gaas, Gaas analysis, Gammaproteobacteria, Genome, Giovannoni, Grzymski, Heterotroph, Highest sequence identity, Isme, Kirchman, Labile, Labile solutes, Limnol oceanogr, Marine antarctic flavobacteria, Metabolism, Metagenome, Metagenome data, Metagenomic, Metaproteome, Metaproteomic, Metaproteomics, Microbial, Microbiol, Microbiology, Newcomb, Nutrient, Ocean surface, Oceanospirillales, Oceanospirillales alteromonadales, Organic matter, Otus, Outer membrane proteins, Pathway, Pelagibacter ubique, Phylogenetic, Phylogenetic assignment, Phytoplankton, Phytoplankton blooms, Pinhassi, Polaribacter, Primary production, Proc natl acad, Relative abundance, Relative abundances, Rhodobacterales, Roseobacter, Roseobacter clade, Seawater, Solute, Southern ocean, Southern ocean metagenome data, Southern ocean metagenomes, Sowell, Subunit, Surface waters, Synthetase, Teeling, Transport system, Transporter, Trna biosynthesis, Unique peptides, Uorescence, Water column depth.
Abstract
Heterotrophic marine bacteria play key roles in remineralizing organic matter generated from primary production. However, far more is known about which groups are dominant than about the cellular processes they perform in order to become dominant. In the Southern Ocean, eukaryotic phytoplankton are the dominant primary producers. In this study we used metagenomics and metaproteomics to determine how the dominant bacterial and archaeal plankton processed bloom material. We examined the microbial community composition in 14 metagenomes and found that the relative abundance of Flavobacteria (dominated by Polaribacter) was positively correlated with chlorophyll a fluorescence, and the relative abundance of SAR11 was inversely correlated with both fluorescence and Flavobacteria abundance. By performing metaproteomics on the sample with the highest relative abundance of Flavobacteria (Newcomb Bay, East Antarctica) we defined how Flavobacteria attach to and degrade diverse complex organic material, how they make labile compounds available to Alphaproteobacteria (especially SAR11) and Gammaproteobacteria, and how these heterotrophic Proteobacteria target and utilize these nutrients. The presence of methylotrophic proteins for archaea and bacteria also indicated the importance of metabolic specialists. Overall, the study provides functional data for the microbial mechanisms of nutrient cycling at the surface of the coastal Southern Ocean.
Url:
DOI: 10.1111/1462-2920.12017
Links to Exploration step
ISTEX:EAE38D4D3AF96C645B4652BE6941D6A4E1EFF53ELe document en format XML
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Williams</name><affiliation><mods:affiliation>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney, Australia</mods:affiliation></affiliation></author><author><name sortKey="Wilkins, David" sort="Wilkins, David" uniqKey="Wilkins D" first="David" last="Wilkins">David Wilkins</name><affiliation><mods:affiliation>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney, Australia</mods:affiliation></affiliation></author><author><name sortKey="Long, Emilie" sort="Long, Emilie" uniqKey="Long E" first="Emilie" last="Long">Emilie Long</name><affiliation><mods:affiliation>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, 2052, Sydney, New South Wales, Australia</mods:affiliation></affiliation><affiliation><mods:affiliation>UFR 927, Université Pierre et Marie Curie (UPMC) Paris VI, 4 place Jussieu, 75532, Paris, France</mods:affiliation></affiliation></author><author><name sortKey="Evans, Flavia" sort="Evans, Flavia" uniqKey="Evans F" first="Flavia" last="Evans">Flavia Evans</name><affiliation><mods:affiliation>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney, Australia</mods:affiliation></affiliation></author><author><name sortKey="Demaere, Mathew Z" sort="Demaere, Mathew Z" uniqKey="Demaere M" first="Mathew Z." last="Demaere">Mathew Z. Demaere</name><affiliation><mods:affiliation>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney, Australia</mods:affiliation></affiliation></author><author><name sortKey="Raftery, Mark J" sort="Raftery, Mark J" uniqKey="Raftery M" first="Mark J." last="Raftery">Mark J. Raftery</name><affiliation><mods:affiliation>Bioanalytical Mass Spectrometry Facility, The University of New South Wales, New South Wales, 2052, Sydney, Australia</mods:affiliation></affiliation></author><author><name sortKey="Cavicchioli, Ricardo" sort="Cavicchioli, Ricardo" uniqKey="Cavicchioli R" first="Ricardo" last="Cavicchioli">Ricardo Cavicchioli</name><affiliation><mods:affiliation>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney, Australia</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: r.cavicchioli@unsw.edu.au</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Environmental Microbiology</title><title level="j" type="sub">Marine Microbial Ecophysiology and Metagenomics</title><title level="j" type="alt">ENVIRONMENTAL MICROBIOLOGY</title><idno type="ISSN">1462-2912</idno><idno type="eISSN">1462-2920</idno><imprint><biblScope unit="vol">15</biblScope><biblScope unit="issue">5</biblScope><biblScope unit="page" from="1302">1302</biblScope><biblScope unit="page" to="1317">1317</biblScope><biblScope unit="page-count">16</biblScope><date type="published" when="2013-05">2013-05</date></imprint><idno type="ISSN">1462-2912</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1462-2912</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Abell</term><term>Acid metabolism</term><term>Algal</term><term>Alphaproteobacteria</term><term>Alteromonadales</term><term>Amino</term><term>Amino acids</term><term>Antarctic</term><term>Antarctic peninsula</term><term>Antarctic surface waters</term><term>Antarctica</term><term>Antcomb</term><term>Appl</term><term>Appl environ microbiol</term><term>Archaea</term><term>Archaeal</term><term>Arctic ocean</term><term>Austral summer</term><term>Bacterioplankton</term><term>Bacteroidetes</term><term>Biosynthesis</term><term>Blackwell publishing</term><term>Bowman</term><term>Burtonii</term><term>Carbohydrate</term><term>Chlorophyll</term><term>Clade</term><term>Class alphaproteobacteria</term><term>Class flavobacteria</term><term>Community composition</term><term>Database</term><term>Dehydrogenase</term><term>Delong</term><term>Diatom</term><term>East antarctica</term><term>Ecol</term><term>Environ</term><term>Environ microbiol</term><term>Environmental microbiology</term><term>Eukaryotic phytoplankton</term><term>Fems</term><term>Fems microbiol ecol</term><term>Flavobacteria</term><term>Fosmid libraries</term><term>Gaas</term><term>Gaas analysis</term><term>Gammaproteobacteria</term><term>Genome</term><term>Giovannoni</term><term>Grzymski</term><term>Heterotroph</term><term>Highest sequence identity</term><term>Isme</term><term>Kirchman</term><term>Labile</term><term>Labile solutes</term><term>Limnol oceanogr</term><term>Marine antarctic flavobacteria</term><term>Metabolism</term><term>Metagenome</term><term>Metagenome data</term><term>Metagenomic</term><term>Metaproteome</term><term>Metaproteomic</term><term>Metaproteomics</term><term>Microbial</term><term>Microbiol</term><term>Microbiology</term><term>Newcomb</term><term>Nutrient</term><term>Ocean surface</term><term>Oceanospirillales</term><term>Oceanospirillales alteromonadales</term><term>Organic matter</term><term>Otus</term><term>Outer membrane proteins</term><term>Pathway</term><term>Pelagibacter ubique</term><term>Phylogenetic</term><term>Phylogenetic assignment</term><term>Phytoplankton</term><term>Phytoplankton blooms</term><term>Pinhassi</term><term>Polaribacter</term><term>Primary production</term><term>Proc natl acad</term><term>Relative abundance</term><term>Relative abundances</term><term>Rhodobacterales</term><term>Roseobacter</term><term>Roseobacter clade</term><term>Seawater</term><term>Solute</term><term>Southern ocean</term><term>Southern ocean metagenome data</term><term>Southern ocean metagenomes</term><term>Sowell</term><term>Subunit</term><term>Surface waters</term><term>Synthetase</term><term>Teeling</term><term>Transport system</term><term>Transporter</term><term>Trna biosynthesis</term><term>Unique peptides</term><term>Uorescence</term><term>Water column depth</term></keywords><keywords scheme="Teeft" xml:lang="en"><term>Abell</term><term>Acid metabolism</term><term>Algal</term><term>Alphaproteobacteria</term><term>Alteromonadales</term><term>Amino</term><term>Amino acids</term><term>Antarctic</term><term>Antarctic peninsula</term><term>Antarctic surface waters</term><term>Antarctica</term><term>Antcomb</term><term>Appl</term><term>Appl environ microbiol</term><term>Archaea</term><term>Archaeal</term><term>Arctic ocean</term><term>Austral summer</term><term>Bacterioplankton</term><term>Bacteroidetes</term><term>Biosynthesis</term><term>Blackwell publishing</term><term>Bowman</term><term>Burtonii</term><term>Carbohydrate</term><term>Chlorophyll</term><term>Clade</term><term>Class alphaproteobacteria</term><term>Class flavobacteria</term><term>Community composition</term><term>Database</term><term>Dehydrogenase</term><term>Delong</term><term>Diatom</term><term>East antarctica</term><term>Ecol</term><term>Environ</term><term>Environ microbiol</term><term>Environmental microbiology</term><term>Eukaryotic phytoplankton</term><term>Fems</term><term>Fems microbiol ecol</term><term>Flavobacteria</term><term>Fosmid libraries</term><term>Gaas</term><term>Gaas analysis</term><term>Gammaproteobacteria</term><term>Genome</term><term>Giovannoni</term><term>Grzymski</term><term>Heterotroph</term><term>Highest sequence identity</term><term>Isme</term><term>Kirchman</term><term>Labile</term><term>Labile solutes</term><term>Limnol oceanogr</term><term>Marine antarctic flavobacteria</term><term>Metabolism</term><term>Metagenome</term><term>Metagenome data</term><term>Metagenomic</term><term>Metaproteome</term><term>Metaproteomic</term><term>Metaproteomics</term><term>Microbial</term><term>Microbiol</term><term>Microbiology</term><term>Newcomb</term><term>Nutrient</term><term>Ocean surface</term><term>Oceanospirillales</term><term>Oceanospirillales alteromonadales</term><term>Organic matter</term><term>Otus</term><term>Outer membrane proteins</term><term>Pathway</term><term>Pelagibacter ubique</term><term>Phylogenetic</term><term>Phylogenetic assignment</term><term>Phytoplankton</term><term>Phytoplankton blooms</term><term>Pinhassi</term><term>Polaribacter</term><term>Primary production</term><term>Proc natl acad</term><term>Relative abundance</term><term>Relative abundances</term><term>Rhodobacterales</term><term>Roseobacter</term><term>Roseobacter clade</term><term>Seawater</term><term>Solute</term><term>Southern ocean</term><term>Southern ocean metagenome data</term><term>Southern ocean metagenomes</term><term>Sowell</term><term>Subunit</term><term>Surface waters</term><term>Synthetase</term><term>Teeling</term><term>Transport system</term><term>Transporter</term><term>Trna biosynthesis</term><term>Unique peptides</term><term>Uorescence</term><term>Water column depth</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract">Heterotrophic marine bacteria play key roles in remineralizing organic matter generated from primary production. However, far more is known about which groups are dominant than about the cellular processes they perform in order to become dominant. In the Southern Ocean, eukaryotic phytoplankton are the dominant primary producers. In this study we used metagenomics and metaproteomics to determine how the dominant bacterial and archaeal plankton processed bloom material. We examined the microbial community composition in 14 metagenomes and found that the relative abundance of Flavobacteria (dominated by Polaribacter) was positively correlated with chlorophyll a fluorescence, and the relative abundance of SAR11 was inversely correlated with both fluorescence and Flavobacteria abundance. By performing metaproteomics on the sample with the highest relative abundance of Flavobacteria (Newcomb Bay, East Antarctica) we defined how Flavobacteria attach to and degrade diverse complex organic material, how they make labile compounds available to Alphaproteobacteria (especially SAR11) and Gammaproteobacteria, and how these heterotrophic Proteobacteria target and utilize these nutrients. The presence of methylotrophic proteins for archaea and bacteria also indicated the importance of metabolic specialists. Overall, the study provides functional data for the microbial mechanisms of nutrient cycling at the surface of the coastal Southern Ocean.</div></front></TEI><istex><corpusName>wiley</corpusName><keywords><teeft><json:string>flavobacteria</json:string><json:string>antarctic</json:string><json:string>metagenome</json:string><json:string>microbiology</json:string><json:string>metaproteome</json:string><json:string>microbiol</json:string><json:string>newcomb</json:string><json:string>clade</json:string><json:string>phytoplankton</json:string><json:string>gammaproteobacteria</json:string><json:string>southern ocean</json:string><json:string>database</json:string><json:string>otus</json:string><json:string>bacteroidetes</json:string><json:string>teeling</json:string><json:string>bacterioplankton</json:string><json:string>alphaproteobacteria</json:string><json:string>blackwell publishing</json:string><json:string>environ</json:string><json:string>genome</json:string><json:string>environmental microbiology</json:string><json:string>grzymski</json:string><json:string>kirchman</json:string><json:string>transporter</json:string><json:string>chlorophyll</json:string><json:string>uorescence</json:string><json:string>metaproteomics</json:string><json:string>alteromonadales</json:string><json:string>oceanospirillales</json:string><json:string>relative abundance</json:string><json:string>phylogenetic</json:string><json:string>surface waters</json:string><json:string>dehydrogenase</json:string><json:string>archaea</json:string><json:string>polaribacter</json:string><json:string>subunit</json:string><json:string>rhodobacterales</json:string><json:string>appl</json:string><json:string>appl environ microbiol</json:string><json:string>algal</json:string><json:string>ecol</json:string><json:string>isme</json:string><json:string>fems</json:string><json:string>biosynthesis</json:string><json:string>giovannoni</json:string><json:string>gaas</json:string><json:string>archaeal</json:string><json:string>roseobacter</json:string><json:string>burtonii</json:string><json:string>solute</json:string><json:string>diatom</json:string><json:string>pathway</json:string><json:string>relative abundances</json:string><json:string>delong</json:string><json:string>transport system</json:string><json:string>metagenomic</json:string><json:string>pinhassi</json:string><json:string>seawater</json:string><json:string>metaproteomic</json:string><json:string>oceanospirillales alteromonadales</json:string><json:string>amino acids</json:string><json:string>synthetase</json:string><json:string>sowell</json:string><json:string>organic matter</json:string><json:string>heterotroph</json:string><json:string>antcomb</json:string><json:string>amino</json:string><json:string>marine antarctic flavobacteria</json:string><json:string>environ microbiol</json:string><json:string>antarctic peninsula</json:string><json:string>fems microbiol ecol</json:string><json:string>trna biosynthesis</json:string><json:string>antarctica</json:string><json:string>primary production</json:string><json:string>acid metabolism</json:string><json:string>proc natl acad</json:string><json:string>east antarctica</json:string><json:string>metabolism</json:string><json:string>microbial</json:string><json:string>abell</json:string><json:string>roseobacter clade</json:string><json:string>fosmid libraries</json:string><json:string>water column depth</json:string><json:string>labile solutes</json:string><json:string>austral summer</json:string><json:string>labile</json:string><json:string>carbohydrate</json:string><json:string>outer membrane proteins</json:string><json:string>highest sequence identity</json:string><json:string>pelagibacter ubique</json:string><json:string>class alphaproteobacteria</json:string><json:string>metagenome data</json:string><json:string>community composition</json:string><json:string>phytoplankton blooms</json:string><json:string>gaas analysis</json:string><json:string>class flavobacteria</json:string><json:string>phylogenetic assignment</json:string><json:string>unique peptides</json:string><json:string>southern ocean metagenome data</json:string><json:string>southern ocean metagenomes</json:string><json:string>limnol oceanogr</json:string><json:string>ocean surface</json:string><json:string>eukaryotic phytoplankton</json:string><json:string>arctic ocean</json:string><json:string>antarctic surface waters</json:string><json:string>nutrient</json:string><json:string>bowman</json:string></teeft></keywords><author><json:item><name>Timothy J. Williams</name><affiliations><json:string>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney, Australia</json:string></affiliations></json:item><json:item><name>David Wilkins</name><affiliations><json:string>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney, Australia</json:string></affiliations></json:item><json:item><name>Emilie Long</name><affiliations><json:string>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, 2052, Sydney, New South Wales, Australia</json:string><json:string>UFR 927, Université Pierre et Marie Curie (UPMC) Paris VI, 4 place Jussieu, 75532, Paris, France</json:string></affiliations></json:item><json:item><name>Flavia Evans</name><affiliations><json:string>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney, Australia</json:string></affiliations></json:item><json:item><name>Mathew Z. DeMaere</name><affiliations><json:string>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney, Australia</json:string></affiliations></json:item><json:item><name>Mark J. Raftery</name><affiliations><json:string>Bioanalytical Mass Spectrometry Facility, The University of New South Wales, New South Wales, 2052, Sydney, Australia</json:string></affiliations></json:item><json:item><name>Ricardo Cavicchioli</name><affiliations><json:string>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney, Australia</json:string><json:string>E-mail: r.cavicchioli@unsw.edu.au</json:string></affiliations></json:item></author><articleId><json:string>EMI12017</json:string></articleId><arkIstex>ark:/67375/WNG-M54VD9WS-G</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>article</json:string></originalGenre><abstract>Heterotrophic marine bacteria play key roles in remineralizing organic matter generated from primary production. However, far more is known about which groups are dominant than about the cellular processes they perform in order to become dominant. In the Southern Ocean, eukaryotic phytoplankton are the dominant primary producers. In this study we used metagenomics and metaproteomics to determine how the dominant bacterial and archaeal plankton processed bloom material. We examined the microbial community composition in 14 metagenomes and found that the relative abundance of Flavobacteria (dominated by Polaribacter) was positively correlated with chlorophyll a fluorescence, and the relative abundance of SAR11 was inversely correlated with both fluorescence and Flavobacteria abundance. By performing metaproteomics on the sample with the highest relative abundance of Flavobacteria (Newcomb Bay, East Antarctica) we defined how Flavobacteria attach to and degrade diverse complex organic material, how they make labile compounds available to Alphaproteobacteria (especially SAR11) and Gammaproteobacteria, and how these heterotrophic Proteobacteria target and utilize these nutrients. The presence of methylotrophic proteins for archaea and bacteria also indicated the importance of metabolic specialists. Overall, the study provides functional data for the microbial mechanisms of nutrient cycling at the surface of the coastal Southern Ocean.</abstract><qualityIndicators><refBibsNative>true</refBibsNative><abstractWordCount>197</abstractWordCount><abstractCharCount>1453</abstractCharCount><keywordCount>0</keywordCount><score>9.364</score><pdfWordCount>8777</pdfWordCount><pdfCharCount>62936</pdfCharCount><pdfVersion>1.3</pdfVersion><pdfPageCount>16</pdfPageCount><pdfPageSize>595.276 x 782.333 pts</pdfPageSize></qualityIndicators><title>The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics</title><pmid><json:string>23126454</json:string></pmid><genre><json:string>article</json:string></genre><host><title>Environmental Microbiology</title><language><json:string>unknown</json:string></language><doi><json:string>10.1111/(ISSN)1462-2920</json:string></doi><issn><json:string>1462-2912</json:string></issn><eissn><json:string>1462-2920</json:string></eissn><publisherId><json:string>EMI</json:string></publisherId><volume>15</volume><issue>5</issue><pages><first>1302</first><last>1317</last><total>16</total></pages><genre><json:string>journal</json:string></genre><subject><json:item><value>Research Article</value></json:item></subject></host><namedEntities><unitex><date><json:string>2007</json:string><json:string>16S</json:string><json:string>2008</json:string><json:string>1310</json:string><json:string>2012-10-16</json:string></date><geogName><json:string>Kerguelen Island</json:string><json:string>Ocean Flavobacteria</json:string><json:string>North Sea</json:string><json:string>Newcomb</json:string></geogName><orgName><json:string>University of New South Wales</json:string><json:string>Environmental Microbiology</json:string><json:string>Society for Applied Microbiology</json:string><json:string>Blackwell Publishing Ltd</json:string></orgName><orgName_funder></orgName_funder><orgName_provider></orgName_provider><persName><json:string>Ricardo Cavicchioli</json:string><json:string>David Wilkins</json:string><json:string>Mark J. Raftery</json:string><json:string>Mathew Z. DeMaere</json:string><json:string>B. Location</json:string><json:string>Bacteroidetes</json:string><json:string>Flavia Evans</json:string><json:string>Marie Curie</json:string><json:string>Aurora Australis</json:string><json:string>Flavobacteria</json:string><json:string>Marine Gammaproteobacteria</json:string><json:string>C. Photograph</json:string><json:string>Southern</json:string></persName><placeName><json:string>Paris</json:string><json:string>Australia</json:string><json:string>OR</json:string><json:string>Portland</json:string><json:string>USA</json:string><json:string>France</json:string></placeName><ref_url><json:string>ftp://ftp.theseed.org/subsystems/subsystems.complex</json:string><json:string>ftp://ftp.ncbi.nih.gov/refseq/release/</json:string></ref_url><ref_bibl><json:string>Giovannoni et al., 2008</json:string><json:string>Béjà et al., 2000</json:string><json:string>Glöckner et al., 1999</json:string><json:string>Morris et al., 2002</json:string><json:string>Williams et al., 2012</json:string><json:string>Bowman et al., 1997</json:string><json:string>Kuwahara et al., 2011</json:string><json:string>Abell and Bowman, 2005a</json:string><json:string>Cottrell and Kirchman, 2000</json:string><json:string>Galand et al., 2009</json:string><json:string>T. J. 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2012</json:string><json:string>McBride, 2001</json:string><json:string>Pinhassi et al., 1999</json:string><json:string>González et al., 2008</json:string><json:string>Marshall and Morris, 2012</json:string><json:string>Rusch et al., 2007</json:string><json:string>Brinkhoff et al., 2008</json:string><json:string>Murray and Grzymski, 2007</json:string><json:string>Sowell et al., 2011</json:string><json:string>West et al., 2008</json:string><json:string>Ye and Doak, 2009</json:string></ref_bibl><bibl></bibl></unitex></namedEntities><ark><json:string>ark:/67375/WNG-M54VD9WS-G</json:string></ark><categories><wos><json:string>1 - science</json:string><json:string>2 - microbiology</json:string></wos><scienceMetrix><json:string>1 - health sciences</json:string><json:string>2 - biomedical research</json:string><json:string>3 - microbiology</json:string></scienceMetrix><scopus><json:string>1 - Life Sciences</json:string><json:string>2 - Agricultural and Biological Sciences</json:string><json:string>3 - Ecology, Evolution, Behavior and Systematics</json:string><json:string>1 - Life Sciences</json:string><json:string>2 - Immunology and Microbiology</json:string><json:string>3 - Microbiology</json:string></scopus></categories><publicationDate>2013</publicationDate><copyrightDate>2013</copyrightDate><doi><json:string>10.1111/1462-2920.12017</json:string></doi><id>EAE38D4D3AF96C645B4652BE6941D6A4E1EFF53E</id><score>1</score><fulltext><json:item><extension>pdf</extension><original>true</original><mimetype>application/pdf</mimetype><uri>https://api.istex.fr/document/EAE38D4D3AF96C645B4652BE6941D6A4E1EFF53E/fulltext/pdf</uri></json:item><json:item><extension>zip</extension><original>false</original><mimetype>application/zip</mimetype><uri>https://api.istex.fr/document/EAE38D4D3AF96C645B4652BE6941D6A4E1EFF53E/fulltext/zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/document/EAE38D4D3AF96C645B4652BE6941D6A4E1EFF53E/fulltext/tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main">The role of planktonic <hi rend="italic"><hi rend="fc">F</hi>lavobacteria</hi> in processing algal organic matter in coastal <hi rend="fc">E</hi>ast <hi rend="fc">A</hi>ntarctica revealed using metagenomics and metaproteomics</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher>Wiley Publishing Ltd</publisher><availability><licence>© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd</licence></availability><date type="published" when="2013-05"></date></publicationStmt><notesStmt><note type="content-type" subtype="article" source="article" scheme="https://content-type.data.istex.fr/ark:/67375/XTP-6N5SZHKN-D">article</note><note type="publication-type" subtype="journal" scheme="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</note></notesStmt><sourceDesc><biblStruct type="article"><analytic><title level="a" type="main">The role of planktonic <hi rend="italic"><hi rend="fc">F</hi>lavobacteria</hi> in processing algal organic matter in coastal <hi rend="fc">E</hi>ast <hi rend="fc">A</hi>ntarctica revealed using metagenomics and metaproteomics</title><title level="a" type="short">Metaproteomics of marine Antarctic Flavobacteria</title><author xml:id="author-0000"><persName><forename type="first">Timothy J.</forename><surname>Williams</surname></persName><affiliation><orgName>School of Biotechnology and Biomolecular Sciences</orgName><orgName>The University of New South Wales</orgName><address><settlement type="city">Sydney</settlement><postCode>2052</postCode><region>New South Wales</region><country key="AU">Australia</country></address></affiliation></author><author xml:id="author-0001"><persName><forename type="first">David</forename><surname>Wilkins</surname></persName><affiliation><orgName>School of Biotechnology and Biomolecular Sciences</orgName><orgName>The University of New South Wales</orgName><address><settlement type="city">Sydney</settlement><postCode>2052</postCode><region>New South Wales</region><country key="AU">Australia</country></address></affiliation></author><author xml:id="author-0002"><persName><forename type="first">Emilie</forename><surname>Long</surname></persName><affiliation><orgName>School of Biotechnology and Biomolecular Sciences</orgName><orgName>The University of New South Wales</orgName><address><settlement type="city">Sydney</settlement><postCode>2052</postCode><region>New South Wales</region><country key="AU">Australia</country></address></affiliation><affiliation><orgName>UFR 927</orgName><orgName>Université Pierre et Marie Curie (UPMC) Paris VI</orgName><address><street>4 place Jussieu</street><settlement type="city">Paris</settlement><postCode>75532</postCode><country key="FR">France</country></address></affiliation></author><author xml:id="author-0003"><persName><forename type="first">Flavia</forename><surname>Evans</surname></persName><affiliation><orgName>School of Biotechnology and Biomolecular Sciences</orgName><orgName>The University of New South Wales</orgName><address><settlement type="city">Sydney</settlement><postCode>2052</postCode><region>New South Wales</region><country key="AU">Australia</country></address></affiliation></author><author xml:id="author-0004"><persName><forename type="first">Mathew Z.</forename><surname>DeMaere</surname></persName><affiliation><orgName>School of Biotechnology and Biomolecular Sciences</orgName><orgName>The University of New South Wales</orgName><address><settlement type="city">Sydney</settlement><postCode>2052</postCode><region>New South Wales</region><country key="AU">Australia</country></address></affiliation></author><author xml:id="author-0005"><persName><forename type="first">Mark J.</forename><surname>Raftery</surname></persName><affiliation><orgName>Bioanalytical Mass Spectrometry Facility</orgName><orgName>The University of New South Wales</orgName><address><settlement type="city">Sydney</settlement><postCode>2052</postCode><region>New South Wales</region><country key="AU">Australia</country></address></affiliation></author><author xml:id="author-0006" role="corresp"><persName><forename type="first">Ricardo</forename><surname>Cavicchioli</surname></persName><affiliation><orgName>School of Biotechnology and Biomolecular Sciences</orgName><orgName>The University of New South Wales</orgName><address><settlement type="city">Sydney</settlement><postCode>2052</postCode><region>New South Wales</region><country key="AU">Australia</country></address></affiliation><affiliation>For correspondence. E‐mail r.cavicchioli@unsw.edu.au; Tel. (+61) 2 9385 3516; Fax (+61) 2 9385 2742.</affiliation></author><idno type="istex">EAE38D4D3AF96C645B4652BE6941D6A4E1EFF53E</idno><idno type="ark">ark:/67375/WNG-M54VD9WS-G</idno><idno type="DOI">10.1111/1462-2920.12017</idno><idno type="unit">EMI12017</idno><idno type="toTypesetVersion">file:EMI.EMI12017.pdf</idno></analytic><monogr><title level="j" type="main">Environmental Microbiology</title><title level="j" type="sub">Marine Microbial Ecophysiology and Metagenomics</title><title level="j" type="alt">ENVIRONMENTAL MICROBIOLOGY</title><idno type="pISSN">1462-2912</idno><idno type="eISSN">1462-2920</idno><idno type="book-DOI">10.1111/(ISSN)1462-2920</idno><idno type="book-part-DOI">10.1111/emi.2013.15.issue-5</idno><idno type="product">EMI</idno><imprint><biblScope unit="vol">15</biblScope><biblScope unit="issue">5</biblScope><biblScope unit="page" from="1302">1302</biblScope><biblScope unit="page" to="1317">1317</biblScope><biblScope unit="page-count">16</biblScope><date type="published" when="2013-05"></date></imprint></monogr></biblStruct></sourceDesc></fileDesc><profileDesc><abstract style="main"><head>Summary</head><p>Heterotrophic marine bacteria play key roles in remineralizing organic matter generated from primary production. However, far more is known about which groups are dominant than about the cellular processes they perform in order to become dominant. In the <hi rend="fc">S</hi>outhern <hi rend="fc">O</hi>cean, eukaryotic phytoplankton are the dominant primary producers. In this study we used metagenomics and metaproteomics to determine how the dominant bacterial and archaeal plankton processed bloom material. We examined the microbial community composition in 14 metagenomes and found that the relative abundance of <hi rend="italic"><hi rend="fc">F</hi>lavobacteria</hi> (dominated by <hi rend="italic"><hi rend="fc">P</hi>olaribacter</hi>) was positively correlated with chlorophyll <hi rend="italic">a</hi> fluorescence, and the relative abundance of <hi rend="fc">SAR</hi>11 was inversely correlated with both fluorescence and <hi rend="italic"><hi rend="fc">F</hi>lavobacteria</hi> abundance. By performing metaproteomics on the sample with the highest relative abundance of <hi rend="italic"><hi rend="fc">F</hi>lavobacteria</hi> (<hi rend="fc">N</hi>ewcomb <hi rend="fc">B</hi>ay, <hi rend="fc">E</hi>ast <hi rend="fc">A</hi>ntarctica) we defined how <hi rend="italic"><hi rend="fc">F</hi>lavobacteria</hi> attach to and degrade diverse complex organic material, how they make labile compounds available to <hi rend="italic"><hi rend="fc">A</hi>lphaproteobacteria</hi> (especially <hi rend="fc">SAR</hi>11) and <hi rend="italic"><hi rend="fc">G</hi>ammaproteobacteria</hi>, and how these heterotrophic <hi rend="italic">Proteobacteria</hi> target and utilize these nutrients. The presence of methylotrophic proteins for archaea and bacteria also indicated the importance of metabolic specialists. Overall, the study provides functional data for the microbial mechanisms of nutrient cycling at the surface of the coastal <hi rend="fc">S</hi>outhern <hi rend="fc">O</hi>cean.</p></abstract><textClass><keywords rend="tocHeading1"><term>Research articles</term></keywords><keywords rend="articleCategory"><term>Research Article</term></keywords></textClass><langUsage><language ident="en"></language></langUsage></profileDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/document/EAE38D4D3AF96C645B4652BE6941D6A4E1EFF53E/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component type="serialArticle" version="2.0" xml:id="emi12017" xml:lang="en"><header><publicationMeta level="product"><doi origin="wiley">10.1111/(ISSN)1462-2920</doi><issn type="print">1462-2912</issn><issn type="electronic">1462-2920</issn><idGroup><id type="product" value="EMI"></id></idGroup><titleGroup><title sort="ENVIRONMENTAL MICROBIOLOGY" type="main">Environmental Microbiology</title><title type="short">Environ Microbiol</title></titleGroup></publicationMeta><publicationMeta level="part" position="05105"><doi>10.1111/emi.2013.15.issue-5</doi><titleGroup><title type="specialIssueTitle">Marine Microbial Ecophysiology and Metagenomics</title></titleGroup><copyright ownership="joint">Copyright © 2013 Society for Applied Microbiology and Blackwell Publishing Ltd</copyright><numberingGroup><numbering number="15" type="journalVolume">15</numbering><numbering type="journalIssue">5</numbering></numberingGroup><coverDate startDate="2013-05">May 2013</coverDate></publicationMeta><publicationMeta level="unit" position="60" status="forIssue" type="article"><doi>10.1111/1462-2920.12017</doi><idGroup><id type="unit" value="EMI12017"></id></idGroup><countGroup><count number="16" type="pageTotal"></count></countGroup><titleGroup><title type="tocHeading1">Research articles</title><title type="articleCategory">Research Article</title></titleGroup><copyright ownership="joint">© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd</copyright><eventGroup><event agent="bestset" date="2012-10-16" type="xmlCreated"></event><event date="2012-07-03" type="manuscriptReceived"></event><event date="2012-09-20" type="manuscriptRevised"></event><event date="2012-09-26" type="manuscriptAccepted"></event><event type="publishedOnlineAccepted" date="2012-10-10"></event><event type="publishedOnlineEarlyUnpaginated" date="2012-11-06"></event><event type="firstOnline" date="2012-11-06"></event><event type="publishedOnlineFinalForm" date="2013-04-18"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:3.8.8" date="2014-01-24"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.6.4 mode:FullText" date="2015-10-02"></event></eventGroup><numberingGroup><numbering type="pageFirst">1302</numbering><numbering type="pageLast">1317</numbering></numberingGroup><correspondenceTo>For correspondence. E‐mail <email>r.cavicchioli@unsw.edu.au</email>; Tel. (+61) 2 9385 3516; Fax (+61) 2 9385 2742.</correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:EMI.EMI12017.pdf"></link></linkGroup></publicationMeta><contentMeta><titleGroup><title type="short">Metaproteomics of marine Antarctic <i><fc>F</fc>lavobacteria</i></title><title type="shortAuthors">T. <fc>J</fc>. <fc>W</fc>illiams <i>et al</i>.</title><title type="main">The role of planktonic <i><fc>F</fc>lavobacteria</i> in processing algal organic matter in coastal <fc>E</fc>ast <fc>A</fc>ntarctica revealed using metagenomics and metaproteomics</title></titleGroup><creators><creator affiliationRef="#emi12017-aff-0001" creatorRole="author" xml:id="emi12017-cr-0001"><personName><givenNames>Timothy J.</givenNames><familyName>Williams</familyName></personName></creator><creator affiliationRef="#emi12017-aff-0001" creatorRole="author" xml:id="emi12017-cr-0002"><personName><givenNames>David</givenNames><familyName>Wilkins</familyName></personName></creator><creator affiliationRef="#emi12017-aff-0001 #emi12017-aff-0003" creatorRole="author" xml:id="emi12017-cr-0003"><personName><givenNames>Emilie</givenNames><familyName>Long</familyName></personName></creator><creator affiliationRef="#emi12017-aff-0001" creatorRole="author" xml:id="emi12017-cr-0004"><personName><givenNames>Flavia</givenNames><familyName>Evans</familyName></personName></creator><creator affiliationRef="#emi12017-aff-0001" creatorRole="author" xml:id="emi12017-cr-0005"><personName><givenNames>Mathew Z.</givenNames><familyName>DeMaere</familyName></personName></creator><creator affiliationRef="#emi12017-aff-0002" creatorRole="author" xml:id="emi12017-cr-0006"><personName><givenNames>Mark J.</givenNames><familyName>Raftery</familyName></personName></creator><creator affiliationRef="#emi12017-aff-0001" corresponding="yes" creatorRole="author" xml:id="emi12017-cr-0007"><personName><givenNames>Ricardo</givenNames><familyName>Cavicchioli</familyName></personName></creator></creators><affiliationGroup><affiliation countryCode="AU" xml:id="emi12017-aff-0001"><orgDiv>School of Biotechnology and Biomolecular Sciences</orgDiv><orgName>The University of New South Wales</orgName><address><city>Sydney</city><countryPart>New South Wales</countryPart><postCode>2052</postCode><country>Australia</country></address></affiliation><affiliation countryCode="AU" xml:id="emi12017-aff-0002"><orgDiv>Bioanalytical Mass Spectrometry Facility</orgDiv><orgName>The University of New South Wales</orgName><address><city>Sydney</city><countryPart>New South Wales</countryPart><postCode>2052</postCode><country>Australia</country></address></affiliation><affiliation countryCode="FR" xml:id="emi12017-aff-0003"><orgDiv>UFR 927</orgDiv><orgName>Université Pierre et Marie Curie (UPMC) Paris VI</orgName><address><street>4 place Jussieu</street><postCode>75532</postCode><city>Paris</city><country>France</country></address></affiliation></affiliationGroup><fundingInfo><fundingAgency>Australian Research Council</fundingAgency></fundingInfo><fundingInfo><fundingAgency>Australian Antarctic Division</fundingAgency></fundingInfo><fundingInfo><fundingAgency>Bioanalytical Mass Spectrometry Facility within the Analytical Centre of the University of New South Wales</fundingAgency></fundingInfo><fundingInfo><fundingAgency>NSW Government co‐investment in the National Collaborative Research Infrastructure Scheme</fundingAgency></fundingInfo><fundingInfo><fundingAgency>J. Craig Venter Institute</fundingAgency></fundingInfo><fundingInfo><fundingAgency>Gordon and Betty Moore Foundation</fundingAgency></fundingInfo><supportingInformation><supportingInfoItem><mediaResource alt="doc" href="urn-x:wiley:14622912:media:emi12017:emi12017-sup-0001-si"></mediaResource><caption><p><b>Table S1.</b> Complete list of bacterial and archaeal proteins identified in the NB metaproteome.</p></caption></supportingInfoItem><supportingInfoItem><mediaResource alt="docx" href="urn-x:wiley:14622912:media:emi12017:emi12017-sup-0002-si"></mediaResource><caption><p><b>Table S2.</b> Counts for unique peptides and assigned spectra for proteins identified using the NR database, and a customized Antarctic database ‘AntComb’, which was constructed from fosmid libraries and Southern Ocean metagenome data.</p></caption></supportingInfoItem><supportingInfoItem><mediaResource alt="xlsx" href="urn-x:wiley:14622912:media:emi12017:emi12017-sup-0003-si"></mediaResource><caption><p><b>Table S3.</b> All genes identified in the NB metagenome (Excel file).</p></caption></supportingInfoItem></supportingInformation><abstractGroup><abstract type="main"><title type="main">Summary</title><p>Heterotrophic marine bacteria play key roles in remineralizing organic matter generated from primary production. However, far more is known about which groups are dominant than about the cellular processes they perform in order to become dominant. In the <fc>S</fc>outhern <fc>O</fc>cean, eukaryotic phytoplankton are the dominant primary producers. In this study we used metagenomics and metaproteomics to determine how the dominant bacterial and archaeal plankton processed bloom material. We examined the microbial community composition in 14 metagenomes and found that the relative abundance of <i><fc>F</fc>lavobacteria</i> (dominated by <i><fc>P</fc>olaribacter</i>) was positively correlated with chlorophyll <i>a</i> fluorescence, and the relative abundance of <fc>SAR</fc>11 was inversely correlated with both fluorescence and <i><fc>F</fc>lavobacteria</i> abundance. By performing metaproteomics on the sample with the highest relative abundance of <i><fc>F</fc>lavobacteria</i> (<fc>N</fc>ewcomb <fc>B</fc>ay, <fc>E</fc>ast <fc>A</fc>ntarctica) we defined how <i><fc>F</fc>lavobacteria</i> attach to and degrade diverse complex organic material, how they make labile compounds available to <i><fc>A</fc>lphaproteobacteria</i> (especially <fc>SAR</fc>11) and <i><fc>G</fc>ammaproteobacteria</i>, and how these heterotrophic <i>Proteobacteria</i> target and utilize these nutrients. The presence of methylotrophic proteins for archaea and bacteria also indicated the importance of metabolic specialists. Overall, the study provides functional data for the microbial mechanisms of nutrient cycling at the surface of the coastal <fc>S</fc>outhern <fc>O</fc>cean.</p></abstract></abstractGroup> </contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>Metaproteomics of marine Antarctic Flavobacteria</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics</title></titleInfo><name type="personal"><namePart type="given">Timothy J.</namePart><namePart type="family">Williams</namePart><affiliation>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney, Australia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">David</namePart><namePart type="family">Wilkins</namePart><affiliation>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney, Australia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Emilie</namePart><namePart type="family">Long</namePart><affiliation>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, 2052, Sydney, New South Wales, Australia</affiliation><affiliation>UFR 927, Université Pierre et Marie Curie (UPMC) Paris VI, 4 place Jussieu, 75532, Paris, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Flavia</namePart><namePart type="family">Evans</namePart><affiliation>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney, Australia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Mathew Z.</namePart><namePart type="family">DeMaere</namePart><affiliation>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney, Australia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Mark J.</namePart><namePart type="family">Raftery</namePart><affiliation>Bioanalytical Mass Spectrometry Facility, The University of New South Wales, New South Wales, 2052, Sydney, Australia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Ricardo</namePart><namePart type="family">Cavicchioli</namePart><affiliation>School of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales, 2052, Sydney, Australia</affiliation><affiliation>E-mail: r.cavicchioli@unsw.edu.au</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-6N5SZHKN-D">article</genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><dateIssued encoding="w3cdtf">2013-05</dateIssued><dateCreated encoding="w3cdtf">2012-10-16</dateCreated><dateCaptured encoding="w3cdtf">2012-07-03</dateCaptured><dateValid encoding="w3cdtf">2012-09-26</dateValid><copyrightDate encoding="w3cdtf">2013</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><abstract>Heterotrophic marine bacteria play key roles in remineralizing organic matter generated from primary production. However, far more is known about which groups are dominant than about the cellular processes they perform in order to become dominant. In the Southern Ocean, eukaryotic phytoplankton are the dominant primary producers. In this study we used metagenomics and metaproteomics to determine how the dominant bacterial and archaeal plankton processed bloom material. We examined the microbial community composition in 14 metagenomes and found that the relative abundance of Flavobacteria (dominated by Polaribacter) was positively correlated with chlorophyll a fluorescence, and the relative abundance of SAR11 was inversely correlated with both fluorescence and Flavobacteria abundance. By performing metaproteomics on the sample with the highest relative abundance of Flavobacteria (Newcomb Bay, East Antarctica) we defined how Flavobacteria attach to and degrade diverse complex organic material, how they make labile compounds available to Alphaproteobacteria (especially SAR11) and Gammaproteobacteria, and how these heterotrophic Proteobacteria target and utilize these nutrients. The presence of methylotrophic proteins for archaea and bacteria also indicated the importance of metabolic specialists. Overall, the study provides functional data for the microbial mechanisms of nutrient cycling at the surface of the coastal Southern Ocean.</abstract><note type="additional physical form">Table S1. Complete list of bacterial and archaeal proteins identified in the NB metaproteome.Table S2. Counts for unique peptides and assigned spectra for proteins identified using the NR database, and a customized Antarctic database ‘AntComb’, which was constructed from fosmid libraries and Southern Ocean metagenome data.Table S3. All genes identified in the NB metagenome (Excel file).</note><note type="funding">Australian Research Council</note><note type="funding">Australian Antarctic Division</note><note type="funding">Bioanalytical Mass Spectrometry Facility within the Analytical Centre of the University of New South Wales</note><note type="funding">NSW Government co‐investment in the National Collaborative Research Infrastructure Scheme</note><note type="funding">J. Craig Venter Institute</note><note type="funding">Gordon and Betty Moore Foundation</note><relatedItem type="host"><titleInfo><title>Environmental Microbiology</title></titleInfo><titleInfo type="abbreviated"><title>Environ Microbiol</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><subject><genre>article-category</genre><topic>Research Article</topic></subject><identifier type="ISSN">1462-2912</identifier><identifier type="eISSN">1462-2920</identifier><identifier type="DOI">10.1111/(ISSN)1462-2920</identifier><identifier type="PublisherID">EMI</identifier><part><date>2013</date><detail type="title"><title>Marine Microbial Ecophysiology and Metagenomics</title></detail><detail type="volume"><caption>vol.</caption><number>15</number></detail><detail type="issue"><caption>no.</caption><number>5</number></detail><extent unit="pages"><start>1302</start><end>1317</end><total>16</total></extent></part></relatedItem><identifier type="istex">EAE38D4D3AF96C645B4652BE6941D6A4E1EFF53E</identifier><identifier type="ark">ark:/67375/WNG-M54VD9WS-G</identifier><identifier type="DOI">10.1111/1462-2920.12017</identifier><identifier type="ArticleID">EMI12017</identifier><accessCondition type="use and reproduction" contentType="copyright">Copyright © 2013 Society for Applied Microbiology and Blackwell Publishing Ltd© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-L0C46X92-X">wiley</recordContentSource></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/document/EAE38D4D3AF96C645B4652BE6941D6A4E1EFF53E/metadata/json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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