CheneBelgiqueV2, Pmc, Corpus, bibRecord, 000231

Fungi Unearthed: Transcripts Encoding Lignocellulolytic and Chitinolytic Enzymes in Forest Soil

Identifieur interne : 000231 ( Pmc/Corpus ); précédent : 000230; suivant : 000232

Fungi Unearthed: Transcripts Encoding Lignocellulolytic and Chitinolytic Enzymes in Forest Soil

Auteurs : Harald Kellner ; Micheline Vandenbol

Source :

PLoS ONE [ 1932-6203 ] ; 2010.

RBID : PMC:2881045

Abstract

Background

Fungi are the main organisms responsible for the degradation of biopolymers such as lignin, cellulose, hemicellulose, and chitin in forest ecosystems. Soil surveys largely target fungal diversity, paying less attention to fungal activity.

Methodology/Principal Findings

Here we have focused on the organic horizon of a hardwood forest dominated by sugar maple that spreads widely across Eastern North America. The sampling site included three plots receiving normal atmospheric nitrogen deposition and three that received an extra 3 g nitrogen m⁻² y⁻¹ in form of sodium nitrate pellets since 1994, which led to increased accumulation of organic matter in the soil. Our aim was to assess, in samples taken from all six plots, transcript-level expression of fungal genes encoding lignocellulolytic and chitinolytic enzymes. For this we collected RNA from the forest soil, reverse-transcribed it, and amplified cDNAs of interest, using both published primer pairs as well as 23 newly developed ones. We thus detected transcript-level expression of 234 genes putatively encoding 26 different groups of fungal enzymes, notably major ligninolytic and diverse aromatic-oxidizing enzymes, various cellulose- and hemicellulose-degrading glycoside hydrolases and carbohydrate esterases, enzymes involved in chitin breakdown, N-acetylglucosamine metabolism, and cell wall degradation. Among the genes identified, 125 are homologous to known ascomycete genes and 105 to basidiomycete genes. Transcripts corresponding to all 26 enzyme groups were detected in both control and nitrogen-supplemented plots.

Conclusions/Significance

Many of these enzyme groups are known to be important in soil turnover processes, but the contribution of some is probably underestimated. Our data highlight the importance of ascomycetes, as well as basidiomycetes, in important biogeochemical cycles. In the nitrogen-supplemented plots, we have detected no transcript-level gap likely to explain the observed increased carbon storage, which is more likely due to community changes and perhaps transcriptional and/or post-transcriptional down-regulation of relevant genes.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881045

DOI: 10.1371/journal.pone.0010971
PubMed: 20532045
PubMed Central: 2881045

Links to Exploration step

PMC:2881045

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Fungi Unearthed: Transcripts Encoding Lignocellulolytic and Chitinolytic Enzymes in Forest Soil</title>
<author><name sortKey="Kellner, Harald" sort="Kellner, Harald" uniqKey="Kellner H" first="Harald" last="Kellner">Harald Kellner</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Vandenbol, Micheline" sort="Vandenbol, Micheline" uniqKey="Vandenbol M" first="Micheline" last="Vandenbol">Micheline Vandenbol</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">20532045</idno>
<idno type="pmc">2881045</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881045</idno>
<idno type="RBID">PMC:2881045</idno>
<idno type="doi">10.1371/journal.pone.0010971</idno>
<date when="2010">2010</date>
<idno type="wicri:Area/Pmc/Corpus">000231</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000231</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Fungi Unearthed: Transcripts Encoding Lignocellulolytic and Chitinolytic Enzymes in Forest Soil</title>
<author><name sortKey="Kellner, Harald" sort="Kellner, Harald" uniqKey="Kellner H" first="Harald" last="Kellner">Harald Kellner</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Vandenbol, Micheline" sort="Vandenbol, Micheline" uniqKey="Vandenbol M" first="Micheline" last="Vandenbol">Micheline Vandenbol</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">PLoS ONE</title>
<idno type="eISSN">1932-6203</idno>
<imprint><date when="2010">2010</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Fungi are the main organisms responsible for the degradation of biopolymers such as lignin, cellulose, hemicellulose, and chitin in forest ecosystems. Soil surveys largely target fungal diversity, paying less attention to fungal activity.</p>
</sec>
<sec><title>Methodology/Principal Findings</title>
<p>Here we have focused on the organic horizon of a hardwood forest dominated by sugar maple that spreads widely across Eastern North America. The sampling site included three plots receiving normal atmospheric nitrogen deposition and three that received an extra 3 g nitrogen m<sup>−2</sup>
 y<sup>−1</sup>
 in form of sodium nitrate pellets since 1994, which led to increased accumulation of organic matter in the soil. Our aim was to assess, in samples taken from all six plots, transcript-level expression of fungal genes encoding lignocellulolytic and chitinolytic enzymes. For this we collected RNA from the forest soil, reverse-transcribed it, and amplified cDNAs of interest, using both published primer pairs as well as 23 newly developed ones. We thus detected transcript-level expression of 234 genes putatively encoding 26 different groups of fungal enzymes, notably major ligninolytic and diverse aromatic-oxidizing enzymes, various cellulose- and hemicellulose-degrading glycoside hydrolases and carbohydrate esterases, enzymes involved in chitin breakdown, <italic>N</italic>
-acetylglucosamine metabolism, and cell wall degradation. Among the genes identified, 125 are homologous to known ascomycete genes and 105 to basidiomycete genes. Transcripts corresponding to all 26 enzyme groups were detected in both control and nitrogen-supplemented plots.</p>
</sec>
<sec><title>Conclusions/Significance</title>
<p>Many of these enzyme groups are known to be important in soil turnover processes, but the contribution of some is probably underestimated. Our data highlight the importance of ascomycetes, as well as basidiomycetes, in important biogeochemical cycles. In the nitrogen-supplemented plots, we have detected no transcript-level gap likely to explain the observed increased carbon storage, which is more likely due to community changes and perhaps transcriptional and/or post-transcriptional down-regulation of relevant genes.</p>
</sec>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Dighton, J" uniqKey="Dighton J">J Dighton</name>
</author>
<author><name sortKey="White, Jf" uniqKey="White J">JF White</name>
</author>
<author><name sortKey="Oudemans, P" uniqKey="Oudemans P">P Oudemans</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Deacon, J" uniqKey="Deacon J">J Deacon</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Buee, M" uniqKey="Buee M">M Buée</name>
</author>
<author><name sortKey="Reich, M" uniqKey="Reich M">M Reich</name>
</author>
<author><name sortKey="Murat, C" uniqKey="Murat C">C Murat</name>
</author>
<author><name sortKey="Morin, E" uniqKey="Morin E">E Morin</name>
</author>
<author><name sortKey="Nilsson, Rh" uniqKey="Nilsson R">RH Nilsson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lindahl, Bd" uniqKey="Lindahl B">BD Lindahl</name>
</author>
<author><name sortKey="Ihrmark, K" uniqKey="Ihrmark K">K Ihrmark</name>
</author>
<author><name sortKey="Boberg, J" uniqKey="Boberg J">J Boberg</name>
</author>
<author><name sortKey="Trumbore, Se" uniqKey="Trumbore S">SE Trumbore</name>
</author>
<author><name sortKey="Hogberg, P" uniqKey="Hogberg P">P Högberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="O Brien, He" uniqKey="O Brien H">HE O'Brien</name>
</author>
<author><name sortKey="Parrent, Jl" uniqKey="Parrent J">JL Parrent</name>
</author>
<author><name sortKey="Jackson, Ja" uniqKey="Jackson J">JA Jackson</name>
</author>
<author><name sortKey="Moncalvo, Jm" uniqKey="Moncalvo J">JM Moncalvo</name>
</author>
<author><name sortKey="Vilgalys, R" uniqKey="Vilgalys R">R Vilgalys</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Edwards, Ip" uniqKey="Edwards I">IP Edwards</name>
</author>
<author><name sortKey="Upchurch, Ra" uniqKey="Upchurch R">RA Upchurch</name>
</author>
<author><name sortKey="Zak, Dr" uniqKey="Zak D">DR Zak</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Luis, P" uniqKey="Luis P">P Luis</name>
</author>
<author><name sortKey="Walther, G" uniqKey="Walther G">G Walther</name>
</author>
<author><name sortKey="Kellner, H" uniqKey="Kellner H">H Kellner</name>
</author>
<author><name sortKey="Martin, F" uniqKey="Martin F">F Martin</name>
</author>
<author><name sortKey="Buscot, F" uniqKey="Buscot F">F Buscot</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Luis, P" uniqKey="Luis P">P Luis</name>
</author>
<author><name sortKey="Kellner, H" uniqKey="Kellner H">H Kellner</name>
</author>
<author><name sortKey="Zimdars, B" uniqKey="Zimdars B">B Zimdars</name>
</author>
<author><name sortKey="Langer, U" uniqKey="Langer U">U Langer</name>
</author>
<author><name sortKey="Martin, F" uniqKey="Martin F">F Martin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lyons, Ji" uniqKey="Lyons J">JI Lyons</name>
</author>
<author><name sortKey="Newell, Sy" uniqKey="Newell S">SY Newell</name>
</author>
<author><name sortKey="Buchan, A" uniqKey="Buchan A">A Buchan</name>
</author>
<author><name sortKey="Moran, Ma" uniqKey="Moran M">MA Moran</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Courty, Pe" uniqKey="Courty P">PE Courty</name>
</author>
<author><name sortKey="Poletto, M" uniqKey="Poletto M">M Poletto</name>
</author>
<author><name sortKey="Duchaussoy, F" uniqKey="Duchaussoy F">F Duchaussoy</name>
</author>
<author><name sortKey="Buee, M" uniqKey="Buee M">M Buée</name>
</author>
<author><name sortKey="Garbaye, J" uniqKey="Garbaye J">J Garbaye</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kellner, H" uniqKey="Kellner H">H Kellner</name>
</author>
<author><name sortKey="Luis, P" uniqKey="Luis P">P Luis</name>
</author>
<author><name sortKey="Schlitt, B" uniqKey="Schlitt B">B Schlitt</name>
</author>
<author><name sortKey="Buscot, F" uniqKey="Buscot F">F Buscot</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kellner, H" uniqKey="Kellner H">H Kellner</name>
</author>
<author><name sortKey="Zak, Dr" uniqKey="Zak D">DR Zak</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Luis, P" uniqKey="Luis P">P Luis</name>
</author>
<author><name sortKey="Kellner, H" uniqKey="Kellner H">H Kellner</name>
</author>
<author><name sortKey="Martin, F" uniqKey="Martin F">F Martin</name>
</author>
<author><name sortKey="Buscot, F" uniqKey="Buscot F">F Buscot</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bailly, J" uniqKey="Bailly J">J Bailly</name>
</author>
<author><name sortKey="Fraissinet Tachet, L" uniqKey="Fraissinet Tachet L">L Fraissinet-Tachet</name>
</author>
<author><name sortKey="Verner, Mc" uniqKey="Verner M">MC Verner</name>
</author>
<author><name sortKey="Debaud, Jc" uniqKey="Debaud J">JC Debaud</name>
</author>
<author><name sortKey="Lemaire, M" uniqKey="Lemaire M">M Lemaire</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Berg, B" uniqKey="Berg B">B Berg</name>
</author>
<author><name sortKey="Matzner, E" uniqKey="Matzner E">E Matzner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Goodale, Cl" uniqKey="Goodale C">CL Goodale</name>
</author>
<author><name sortKey="Apps, Mj" uniqKey="Apps M">MJ Apps</name>
</author>
<author><name sortKey="Birdsey, Ra" uniqKey="Birdsey R">RA Birdsey</name>
</author>
<author><name sortKey="Field, Cb" uniqKey="Field C">CB Field</name>
</author>
<author><name sortKey="Heath, Ls" uniqKey="Heath L">LS Heath</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pregitzer, Ks" uniqKey="Pregitzer K">KS Pregitzer</name>
</author>
<author><name sortKey="Burton, Aj" uniqKey="Burton A">AJ Burton</name>
</author>
<author><name sortKey="Zak, Dr" uniqKey="Zak D">DR Zak</name>
</author>
<author><name sortKey="Talhelm, Af" uniqKey="Talhelm A">AF Talhelm</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zak, Dr" uniqKey="Zak D">DR Zak</name>
</author>
<author><name sortKey="Holmes, We" uniqKey="Holmes W">WE Holmes</name>
</author>
<author><name sortKey="Burton, Aj" uniqKey="Burton A">AJ Burton</name>
</author>
<author><name sortKey="Pregitzer, Ks" uniqKey="Pregitzer K">KS Pregitzer</name>
</author>
<author><name sortKey="Talhelm, Af" uniqKey="Talhelm A">AF Talhelm</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Deforest, Jl" uniqKey="Deforest J">JL DeForest</name>
</author>
<author><name sortKey="Zak, Dr" uniqKey="Zak D">DR Zak</name>
</author>
<author><name sortKey="Pregitzer, Ks" uniqKey="Pregitzer K">KS Pregitzer</name>
</author>
<author><name sortKey="Burton, Aj" uniqKey="Burton A">AJ Burton</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kues, U" uniqKey="Kues U">U Kües</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bodeker, Itm" uniqKey="Bodeker I">ITM Bödeker</name>
</author>
<author><name sortKey="Nygren, Cmr" uniqKey="Nygren C">CMR Nygren</name>
</author>
<author><name sortKey="Taylor, Afs" uniqKey="Taylor A">AFS Taylor</name>
</author>
<author><name sortKey="Olson, A" uniqKey="Olson A">A Olson</name>
</author>
<author><name sortKey="Lindahl, Bd" uniqKey="Lindahl B">BD Lindahl</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kogel Knabner, I" uniqKey="Kogel Knabner I">I Kögel-Knabner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hofrichter, M" uniqKey="Hofrichter M">M Hofrichter</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Baldrian, P" uniqKey="Baldrian P">P Baldrian</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Baldrian, P" uniqKey="Baldrian P">P Baldrian</name>
</author>
<author><name sortKey="Valaskova, V" uniqKey="Valaskova V">V Valášková</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Levasseur, A" uniqKey="Levasseur A">A Levasseur</name>
</author>
<author><name sortKey="Piumi, F" uniqKey="Piumi F">F Piumi</name>
</author>
<author><name sortKey="Coutinho, Pm" uniqKey="Coutinho P">PM Coutinho</name>
</author>
<author><name sortKey="Rancurel, C" uniqKey="Rancurel C">C Rancurel</name>
</author>
<author><name sortKey="Asther, M" uniqKey="Asther M">M Asther</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pecyna, Mj" uniqKey="Pecyna M">MJ Pecyna</name>
</author>
<author><name sortKey="Ullrich, R" uniqKey="Ullrich R">R Ullrich</name>
</author>
<author><name sortKey="Bittner, B" uniqKey="Bittner B">B Bittner</name>
</author>
<author><name sortKey="Clemens, A" uniqKey="Clemens A">A Clemens</name>
</author>
<author><name sortKey="Scheibner, K" uniqKey="Scheibner K">K Scheibner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Morris, Dr" uniqKey="Morris D">DR Morris</name>
</author>
<author><name sortKey="Hager, Lp" uniqKey="Hager L">LP Hager</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ullrich, R" uniqKey="Ullrich R">R Ullrich</name>
</author>
<author><name sortKey="Hofrichter, M" uniqKey="Hofrichter M">M Hofrichter</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Halaouli, S" uniqKey="Halaouli S">S Halaouli</name>
</author>
<author><name sortKey="Asther, M" uniqKey="Asther M">M Asther</name>
</author>
<author><name sortKey="Sigoillot, J C" uniqKey="Sigoillot J">J-C Sigoillot</name>
</author>
<author><name sortKey="Hamdi, M" uniqKey="Hamdi M">M Hamdi</name>
</author>
<author><name sortKey="Lomascolo, A" uniqKey="Lomascolo A">A Lomascolo</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Burke, Rm" uniqKey="Burke R">RM Burke</name>
</author>
<author><name sortKey="Cairney, Jwg" uniqKey="Cairney J">JWG Cairney</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sinsabaugh, Rl" uniqKey="Sinsabaugh R">RL Sinsabaugh</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rieble, S" uniqKey="Rieble S">S Rieble</name>
</author>
<author><name sortKey="Joshi, Dk" uniqKey="Joshi D">DK Joshi</name>
</author>
<author><name sortKey="Gold, Mh" uniqKey="Gold M">MH Gold</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Svedruzi, D" uniqKey="Svedruzi D">D Svedružić</name>
</author>
<author><name sortKey="J Nsson, S" uniqKey="J Nsson S">S Jónsson</name>
</author>
<author><name sortKey="Toyota, Cg" uniqKey="Toyota C">CG Toyota</name>
</author>
<author><name sortKey="Reinhardt, La" uniqKey="Reinhardt L">LA Reinhardt</name>
</author>
<author><name sortKey="Ricagno, S" uniqKey="Ricagno S">S Ricagno</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Coutinho, Pm" uniqKey="Coutinho P">PM Coutinho</name>
</author>
<author><name sortKey="Henrissat, B" uniqKey="Henrissat B">B Henrissat</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Henrissat, B" uniqKey="Henrissat B">B Henrissat</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Cantarel, Bl" uniqKey="Cantarel B">BL Cantarel</name>
</author>
<author><name sortKey="Coutinho, Pm" uniqKey="Coutinho P">PM Coutinho</name>
</author>
<author><name sortKey="Rancurel, C" uniqKey="Rancurel C">C Rancurel</name>
</author>
<author><name sortKey="Bernard, T" uniqKey="Bernard T">T Bernard</name>
</author>
<author><name sortKey="Lombard, V" uniqKey="Lombard V">V Lombard</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jacobsen, J" uniqKey="Jacobsen J">J Jacobsen</name>
</author>
<author><name sortKey="Lydolph, M" uniqKey="Lydolph M">M Lydolph</name>
</author>
<author><name sortKey="Lange, L" uniqKey="Lange L">L Lange</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Tian, Xj" uniqKey="Tian X">XJ Tian</name>
</author>
<author><name sortKey="Takeda, H" uniqKey="Takeda H">H Takeda</name>
</author>
<author><name sortKey="Azuma, J" uniqKey="Azuma J">J Azuma</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hoegger, Pj" uniqKey="Hoegger P">PJ Hoegger</name>
</author>
<author><name sortKey="Majcherczyk, A" uniqKey="Majcherczyk A">A Majcherczyk</name>
</author>
<author><name sortKey="Dwivedi, Rc" uniqKey="Dwivedi R">RC Dwivedi</name>
</author>
<author><name sortKey="Svobodova, K" uniqKey="Svobodova K">K Svobodová</name>
</author>
<author><name sortKey="Kilaru, S" uniqKey="Kilaru S">S Kilaru</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Schulze, Wx" uniqKey="Schulze W">WX Schulze</name>
</author>
<author><name sortKey="Gleixner, G" uniqKey="Gleixner G">G Gleixner</name>
</author>
<author><name sortKey="Kaiser, K" uniqKey="Kaiser K">K Kaiser</name>
</author>
<author><name sortKey="Guggenberger, G" uniqKey="Guggenberger G">G Guggenberger</name>
</author>
<author><name sortKey="Mann, M" uniqKey="Mann M">M Mann</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Urich, T" uniqKey="Urich T">T Urich</name>
</author>
<author><name sortKey="Lanzen, A" uniqKey="Lanzen A">A Lanzén</name>
</author>
<author><name sortKey="Qi, J" uniqKey="Qi J">J Qi</name>
</author>
<author><name sortKey="Huson, Dh" uniqKey="Huson D">DH Huson</name>
</author>
<author><name sortKey="Schleper, C" uniqKey="Schleper C">C Schleper</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Baldrian, P" uniqKey="Baldrian P">P Baldrian</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Baldrian, P" uniqKey="Baldrian P">P Baldrian</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Cullings, K" uniqKey="Cullings K">K Cullings</name>
</author>
<author><name sortKey="Courty, P E" uniqKey="Courty P">P-E Courty</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Devries, Rp" uniqKey="Devries R">RP deVries</name>
</author>
<author><name sortKey="Visser, J" uniqKey="Visser J">J Visser</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Devries, W" uniqKey="Devries W">W deVries</name>
</author>
<author><name sortKey="Solberg, S" uniqKey="Solberg S">S Solberg</name>
</author>
<author><name sortKey="Dobbertin, M" uniqKey="Dobbertin M">M Dobbertin</name>
</author>
<author><name sortKey="Sterba, H" uniqKey="Sterba H">H Sterba</name>
</author>
<author><name sortKey="Laubhahn, D" uniqKey="Laubhahn D">D Laubhahn</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Magnani, F" uniqKey="Magnani F">F Magnani</name>
</author>
<author><name sortKey="Mencuccini, M" uniqKey="Mencuccini M">M Mencuccini</name>
</author>
<author><name sortKey="Borghetti, M" uniqKey="Borghetti M">M Borghetti</name>
</author>
<author><name sortKey="Berbigier, P" uniqKey="Berbigier P">P Berbigier</name>
</author>
<author><name sortKey="Berninger, F" uniqKey="Berninger F">F Berninger</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sutton, Ma" uniqKey="Sutton M">MA Sutton</name>
</author>
<author><name sortKey="Simpson, D" uniqKey="Simpson D">D Simpson</name>
</author>
<author><name sortKey="Levy, Pe" uniqKey="Levy P">PE Levy</name>
</author>
<author><name sortKey="Smith, Ri" uniqKey="Smith R">RI Smith</name>
</author>
<author><name sortKey="Reis, S" uniqKey="Reis S">S Reis</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Nadelhoffer, Kj" uniqKey="Nadelhoffer K">KJ Nadelhoffer</name>
</author>
<author><name sortKey="Emmett, Ba" uniqKey="Emmett B">BA Emmett</name>
</author>
<author><name sortKey="Gundersen, P" uniqKey="Gundersen P">P Gundersen</name>
</author>
<author><name sortKey="Kj Naas, Oj" uniqKey="Kj Naas O">OJ Kjønaas</name>
</author>
<author><name sortKey="Koopmans, Cj" uniqKey="Koopmans C">CJ Koopmans</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Reay, Ds" uniqKey="Reay D">DS Reay</name>
</author>
<author><name sortKey="Dentener, F" uniqKey="Dentener F">F Dentener</name>
</author>
<author><name sortKey="Smith, P" uniqKey="Smith P">P Smith</name>
</author>
<author><name sortKey="Grace, J" uniqKey="Grace J">J Grace</name>
</author>
<author><name sortKey="Feely, Ra" uniqKey="Feely R">RA Feely</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Galloway, Jn" uniqKey="Galloway J">JN Galloway</name>
</author>
<author><name sortKey="Dentener, Fj" uniqKey="Dentener F">FJ Dentener</name>
</author>
<author><name sortKey="Capone, Dg" uniqKey="Capone D">DG Capone</name>
</author>
<author><name sortKey="Boyer, Ew" uniqKey="Boyer E">EW Boyer</name>
</author>
<author><name sortKey="Howarth, Rw" uniqKey="Howarth R">RW Howarth</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Boominathan, K" uniqKey="Boominathan K">K Boominathan</name>
</author>
<author><name sortKey="Dass, Sb" uniqKey="Dass S">SB Dass</name>
</author>
<author><name sortKey="Randall, Ta" uniqKey="Randall T">TA Randall</name>
</author>
<author><name sortKey="Reddy, Ca" uniqKey="Reddy C">CA Reddy</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Vanderwoude, Mw" uniqKey="Vanderwoude M">MW Vanderwoude</name>
</author>
<author><name sortKey="Boominathan, K" uniqKey="Boominathan K">K Boominathan</name>
</author>
<author><name sortKey="Reddy, Ca" uniqKey="Reddy C">CA Reddy</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hall, Ta" uniqKey="Hall T">TA Hall</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">PLoS One</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
<journal-title-group><journal-title>PLoS ONE</journal-title>
</journal-title-group>
<issn pub-type="epub">1932-6203</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">20532045</article-id>
<article-id pub-id-type="pmc">2881045</article-id>
<article-id pub-id-type="publisher-id">10-PONE-RA-16545R2</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0010971</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline"><subject>Microbiology</subject>
<subject>Ecology/Ecosystem Ecology</subject>
<subject>Ecology/Environmental Microbiology</subject>
<subject>Microbiology/Applied Microbiology</subject>
</subj-group>
</article-categories>
<title-group><article-title>Fungi Unearthed: Transcripts Encoding Lignocellulolytic and Chitinolytic Enzymes in Forest Soil</article-title>
<alt-title alt-title-type="running-head">Fungal Gene Expression in Soil</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Kellner</surname>
<given-names>Harald</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
<xref ref-type="corresp" rid="cor1"><sup>*</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Vandenbol</surname>
<given-names>Micheline</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
</contrib-group>
<aff id="aff1"><addr-line>Unité de Biologie Animale et Microbienne, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Wang</surname>
<given-names>Ping</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1">Research Institute for Children and the Louisiana State University Health Sciences Center, United States of America</aff>
<author-notes><corresp id="cor1">* E-mail: <email>mail@haraldkellner.com</email>
</corresp>
<fn fn-type="con"><p>Conceived and designed the experiments: HK MV. Performed the experiments: HK. Analyzed the data: HK MV. Contributed reagents/materials/analysis tools: HK MV. Wrote the paper: HK MV.</p>
</fn>
</author-notes>
<pub-date pub-type="collection"><year>2010</year>
</pub-date>
<pub-date pub-type="epub"><day>4</day>
<month>6</month>
<year>2010</year>
</pub-date>
<volume>5</volume>
<issue>6</issue>
<elocation-id>e10971</elocation-id>
<history><date date-type="received"><day>24</day>
<month>2</month>
<year>2010</year>
</date>
<date date-type="accepted"><day>14</day>
<month>5</month>
<year>2010</year>
</date>
</history>
<permissions><copyright-statement>Kellner, Vandenbol. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</copyright-statement>
</permissions>
<abstract><sec><title>Background</title>
<p>Fungi are the main organisms responsible for the degradation of biopolymers such as lignin, cellulose, hemicellulose, and chitin in forest ecosystems. Soil surveys largely target fungal diversity, paying less attention to fungal activity.</p>
</sec>
<sec><title>Methodology/Principal Findings</title>
<p>Here we have focused on the organic horizon of a hardwood forest dominated by sugar maple that spreads widely across Eastern North America. The sampling site included three plots receiving normal atmospheric nitrogen deposition and three that received an extra 3 g nitrogen m<sup>−2</sup>
 y<sup>−1</sup>
 in form of sodium nitrate pellets since 1994, which led to increased accumulation of organic matter in the soil. Our aim was to assess, in samples taken from all six plots, transcript-level expression of fungal genes encoding lignocellulolytic and chitinolytic enzymes. For this we collected RNA from the forest soil, reverse-transcribed it, and amplified cDNAs of interest, using both published primer pairs as well as 23 newly developed ones. We thus detected transcript-level expression of 234 genes putatively encoding 26 different groups of fungal enzymes, notably major ligninolytic and diverse aromatic-oxidizing enzymes, various cellulose- and hemicellulose-degrading glycoside hydrolases and carbohydrate esterases, enzymes involved in chitin breakdown, <italic>N</italic>
-acetylglucosamine metabolism, and cell wall degradation. Among the genes identified, 125 are homologous to known ascomycete genes and 105 to basidiomycete genes. Transcripts corresponding to all 26 enzyme groups were detected in both control and nitrogen-supplemented plots.</p>
</sec>
<sec><title>Conclusions/Significance</title>
<p>Many of these enzyme groups are known to be important in soil turnover processes, but the contribution of some is probably underestimated. Our data highlight the importance of ascomycetes, as well as basidiomycetes, in important biogeochemical cycles. In the nitrogen-supplemented plots, we have detected no transcript-level gap likely to explain the observed increased carbon storage, which is more likely due to community changes and perhaps transcriptional and/or post-transcriptional down-regulation of relevant genes.</p>
</sec>
</abstract>
<counts><page-count count="7"></page-count>
</counts>
</article-meta>
</front>
<body><sec id="s1"><title>Introduction</title>
<p>Fungi are an important and diverse component of soil microbial communities. They provide essential ecosystem services, such as decomposing organic matter, nutrient cycling, and in the case of mycorrhizal species, also nutrient transfer to plants <xref ref-type="bibr" rid="pone.0010971-Dighton1">[1]</xref>
. In forest ecosystems they are largely responsible for breakdown of the abundant large biopolymers cellulose, hemicellulose, lignin, and chitin <xref ref-type="bibr" rid="pone.0010971-Deacon1">[2]</xref>
. Activities of single fungal species or groups are difficult to access in soils. Methods commonly applied in soil surveys, such as determination of enzyme activities or soil respiration rates, phospholipid fatty acid analysis, or isolation of fungi, do not reveal which fungi in particular are responsible for diverse soil or ecosystem processes. In fact, they often only distinguish between prokaryotes and eukaryotes. A molecular approach is to use DNA extracted from soil to investigate fungal diversity, mainly <italic>via</italic>
 either the amplification of partial ribosomal genes <xref ref-type="bibr" rid="pone.0010971-Bue1">[3]</xref>
–<xref ref-type="bibr" rid="pone.0010971-OBrien1">[5]</xref>
, or the deduction of putative soil functions from protein-encoding fungal genes of single species or communities <xref ref-type="bibr" rid="pone.0010971-Edwards1">[6]</xref>
–<xref ref-type="bibr" rid="pone.0010971-Lyons1">[9]</xref>
. Only recently has it become possible to detect fungal activity on the basis of transcript-level gene expression. Used in studies focusing on single genes such as laccase, polyketide synthase, etc. <xref ref-type="bibr" rid="pone.0010971-Courty1">[10]</xref>
–<xref ref-type="bibr" rid="pone.0010971-Luis3">[13]</xref>
, or on multiple genes expressed in parallel within communities <xref ref-type="bibr" rid="pone.0010971-Courty1">[10]</xref>
, <xref ref-type="bibr" rid="pone.0010971-Bailly1">[14]</xref>
, this approach has revealed in forest environments the presence of ascomycetes and basidiomycetes with diverse ecological behaviors.</p>
<p>To elucidate the roles that fungi play in carbon sequestration and ecosystem functioning, there remains much to be learned about their contribution to biopolymer degradation and biogeochemical cycling. A problem that received considerable attention is the link between carbon cycling and nitrogen availability. Additional nitrogen can stimulate early-stage decomposition of plant litter and soil organic matter, but it suppresses this activity at later stages, when humus and lignin are abundant <xref ref-type="bibr" rid="pone.0010971-Berg1">[15]</xref>
. Northern-hemisphere temperate and boreal forest ecosystems cover large areas, representing huge terrestrial carbon stocks and acting as a substantial carbon sink (0.6–0.7 pg carbon yr<sup>−1</sup>
) <xref ref-type="bibr" rid="pone.0010971-Goodale1">[16]</xref>
. In a previous ecosystem study it was demonstrated that a decade of simulated additional atmospheric nitrogen deposition, at a rate expected by 2050 (additional 3 g nitrogen m<sup>−2</sup>
 y<sup>−1</sup>
 to ambient deposition), slowed the decay of plant detritus, thereby significantly increasing soil carbon storage in a temperate forest dominated by sugar maple (<italic>Acer saccharum</italic>
 Marsh.), that spreads widely across Eastern North America <xref ref-type="bibr" rid="pone.0010971-Pregitzer1">[17]</xref>
, <xref ref-type="bibr" rid="pone.0010971-Zak1">[18]</xref>
. Over the same period a decline in lignocellulolytic enzyme activity was observed in the forest floor <xref ref-type="bibr" rid="pone.0010971-DeForest1">[19]</xref>
.</p>
<p>One cause of this nitrogen-supplementation-induced slowing of plant detritus decomposition might be that single biodegradation steps involving important lignocellulolytic enzymes are “switched off”, leaving gaps in the degradative carbon cycle. Accumulating intermediates might then participate in negative feedback loops affecting other genes. It is known, for instance, that the expression of fungal genes required for cellulose biodegradation is subject to regulations such as catabolic repression <xref ref-type="bibr" rid="pone.0010971-Kes1">[20]</xref>
. Alternatively, increased nitrogen deposition might gradually down-regulate the expression of fungal genes encoding biopolymer-degrading enzymes, or the fungal community might change in response to additional nitrogen.</p>
<p>Here we have focused on this same sugar-maple-dominated forest site, with the intention of identifying transcriptionally expressed fungal genes encoding key lignocellulolytic, chitinolytic, and related enzymes. For this, we have isolated total RNA from the forest soil, reverse-transcribed it, and synthesized cDNAs using long-distance PCR (LD PCR), thus providing templates for subsequent detection of relevant transcripts by PCR. As few primers are available for accessing such genes, our first goal was to develop molecular tools for detecting transcripts encoding a wide range of fungal enzymes (phenol oxidases, peroxidases, cellulases, hemicellulases, esterases and chitinases…) that are both ecologically interesting and potentially useful in biotechnology <xref ref-type="bibr" rid="pone.0010971-Kes1">[20]</xref>
. Having developed these tools, we then addressed the following questions: i) Are transcripts of the targeted genes detectable in these soils? ii) Which fungi or fungal groups, i.e. ascomycetes or basidiomycetes, deploy them? iii) How does nitrogen supplementation affect the presence of transcript-level expression of the targeted genes and thereby the carbon balance of this ecosystem?</p>
</sec>
<sec id="s2"><title>Results and Discussion</title>
<sec id="s2a"><title>Transcript-level expression of ligninolytic, cellulolytic, chitinolytic, and related fungal enzymes</title>
<p>Twenty-three degenerate primer pairs were developed for PCR-based detection of transcripts related to biopolymer degradation in the organic horizon of the above-mentioned forest site (Supplementary <xref ref-type="supplementary-material" rid="pone.0010971.s001">Table S1</xref>
). Published primers were also used: primers for fungal laccase and cellobiohydrolase genes, which were used in several soil surveys to gain first insights into molecular fungal diversity and putative activity in soils <xref ref-type="bibr" rid="pone.0010971-Edwards1">[6]</xref>
–<xref ref-type="bibr" rid="pone.0010971-Luis2">[8]</xref>
, <xref ref-type="bibr" rid="pone.0010971-Kellner1">[11]</xref>
, and recently published primer pairs for Class II fungal secretory heme peroxidase genes <xref ref-type="bibr" rid="pone.0010971-Bdeker1">[21]</xref>
. Some of the newly developed primer pairs appeared quite specific, others less so. Future improvements might include decreased primer degeneracy, a search for other conserved protein stretches useful for primer design, and adapting the PCR conditions. All primer pairs, however, proved useful in achieving our research goals.</p>
<p>A total of 234 partial genes were amplified from six forest soil cDNAs, corresponding to 26 different fungal enzyme groups involved in biopolymer degradation (<xref ref-type="table" rid="pone-0010971-t001">Table 1</xref>
, Supplementary <xref ref-type="supplementary-material" rid="pone.0010971.s002">Table S2</xref>
). Twenty-three of these enzyme groups were accessed thanks to our newly developed primer pairs for fungal phyla or groups (<xref ref-type="supplementary-material" rid="pone.0010971.s001">Table S1</xref>
).</p>
<p>Among the enzyme groups highlighted, 7 are involved directly or indirectly in the breakdown or conversion of lignin or in the oxidation of aromatic derivatives. Lignin has a complex three-dimensional structure based on phenyl propane units, and provides structural rigidity in woody plants <xref ref-type="bibr" rid="pone.0010971-KgelKnabner1">[22]</xref>
 and protects energy-rich cellulose from degradation. Fungi are the main agents responsible for the decomposition of lignin, and transcripts were detected for manganese peroxidases <xref ref-type="bibr" rid="pone.0010971-Hofrichter1">[23]</xref>
, laccases <xref ref-type="bibr" rid="pone.0010971-Baldrian1">[24]</xref>
, and cellobiose dehydrogenases (important in both lignin and cellulose degradation - see <xref ref-type="table" rid="pone-0010971-t001">Table 1</xref>
 and <xref ref-type="bibr" rid="pone.0010971-Baldrian2">[25]</xref>
). These enzyme groups are viewed as the three major ones acting on lignin <xref ref-type="bibr" rid="pone.0010971-Levasseur1">[26]</xref>
 (FOLy database: LO1 – LO3, <ext-link ext-link-type="uri" xlink:href="http://foly.esil.univ-mrs.fr/">http://foly.esil.univ-mrs.fr/</ext-link>
). We further detected transcripts of aromatic-oxidizing enzymes, including aromatic peroxygenases <xref ref-type="bibr" rid="pone.0010971-Pecyna1">[27]</xref>
 and chloroperoxidases <xref ref-type="bibr" rid="pone.0010971-Morris1">[28]</xref>
, which are members of a newly discovered group of heme-thiolate haloperoxidases displaying a broad range of extracellular enzymatic activities (see <xref ref-type="table" rid="pone-0010971-t001">Table 1</xref>
 and <xref ref-type="bibr" rid="pone.0010971-Ullrich1">[29]</xref>
). The involvement of this enzyme group in soil turnover processes has received relatively little attention, but their versatility is likely to make them an important focus of future studies. Another underestimated but relevant enzyme for which transcripts were found in our soil samples is fungal tyrosinase, which oxidizes monophenolic compounds <xref ref-type="bibr" rid="pone.0010971-Halaouli1">[30]</xref>
. Although this type of enzyme may contribute to the soil phenoloxidase activity measured with substrates such as L-3,4-dihydroxyphenylalanine <xref ref-type="bibr" rid="pone.0010971-Burke1">[31]</xref>
, <xref ref-type="bibr" rid="pone.0010971-Sinsabaugh1">[32]</xref>
, there is a tendency to underestimate its contribution.</p>
<p>Fungal tyrosinases probably act mostly intracellularly, e.g. in pigmentation or detoxification processes, however there remains a need to investigate their contribution to extracellular phenol or lignin conversions in soils. Interestingly, the expression of a specific fungal tyrosinase was recently monitored in a forest soil, suggesting its potential importance <xref ref-type="bibr" rid="pone.0010971-Courty1">[10]</xref>
. Fungi need detoxifying enzymes to destroy potentially cytotoxic intermediates of, or participants in, lignin degradation. Laccases, tyrosinases, and also various peroxidases are thus suggested to have detoxifying effects <xref ref-type="bibr" rid="pone.0010971-Baldrian1">[24]</xref>
, <xref ref-type="bibr" rid="pone.0010971-Sinsabaugh1">[32]</xref>
. Another potentially detoxifying mechanism is ring cleavage of catecholate derivatives into citric acid intermediates by intradiol ring cleavage dioxygenases (IRDC) such as catechol 1,2-dioxygenase, also highlighted in this soil RNA study. Few fungal IRDCs have been characterized, but a 1,2,4-trihydroxybenzene 1,2-dioxygenase of <italic>Phanerochaete chrysosporium</italic>
, that catalyzes key steps in the degradation pathway of vanillate, an intermediate in general lignin breakdown, suggests a contribution to soil turnover processes involving fungi <xref ref-type="bibr" rid="pone.0010971-Rieble1">[33]</xref>
. The seventh type of lignolysis-related enzyme highlighted in this study is oxalate decarboxylase, an enzyme required by fungi to degrade oxalic acid, which is useful in lignin degradation as a chelator of Mn<sup>3+</sup>
 ions <xref ref-type="bibr" rid="pone.0010971-Svedrui1">[34]</xref>
 but cytotoxic when present in excess.</p>
<p>Enzymes related to the degradation of cellulose and hemicellulose, the most abundant biopolymers in terrestrial ecosystems <xref ref-type="bibr" rid="pone.0010971-KgelKnabner1">[22]</xref>
, were also identified on the basis of the cDNAs amplified.</p>
<p>Cellulose, a linear polymer consisting of D-glucose monomers linked by β-1,4-glycosidic bonds, is the major structural component of cell walls in woody plants. To degrade cellulose and hemicellulose, fungi use a panoply of glycoside hydrolases (GH) and carbohydrate esterases (CE) <xref ref-type="bibr" rid="pone.0010971-Baldrian2">[25]</xref>
, <xref ref-type="bibr" rid="pone.0010971-Coutinho1">[35]</xref>
, <xref ref-type="bibr" rid="pone.0010971-Henrissat1">[36]</xref>
. Our work brought to light no less than twelve different glycoside hydrolase families and one type of carbohydrate esterase (<xref ref-type="table" rid="pone-0010971-t001">Table 1</xref>
, <ext-link ext-link-type="uri" xlink:href="http://www.cazy.org">http://www.cazy.org</ext-link>
 <xref ref-type="bibr" rid="pone.0010971-Cantarel1">[37]</xref>
). Among these families, the enzymes endoglucanase, cellobiohydrolase, and β-glucosidase cover all essential steps of cellulose degradation down to monomeric glucose units <xref ref-type="bibr" rid="pone.0010971-Baldrian2">[25]</xref>
. Previous studies have revealed sequences corresponding to fungal endoglucanase and cellobiohydrolase in DNA extracted from decaying plant material and soil samples, thus highlighting their potential ecosystem importance <xref ref-type="bibr" rid="pone.0010971-Edwards1">[6]</xref>
, <xref ref-type="bibr" rid="pone.0010971-Jacobsen1">[38]</xref>
. As for cellobiose dehydrogenase, mentioned above in relation to lignin degradation, its role in cellulose breakdown may be to control the quantity of the breakdown intermediate cellobiose, which in excess can repress cellobiohydrolase expression <xref ref-type="bibr" rid="pone.0010971-Baldrian2">[25]</xref>
. Furthermore, the generated hydroxyl radicals may act directly on cellulose polymers <xref ref-type="bibr" rid="pone.0010971-Baldrian2">[25]</xref>
.</p>
<p>Hemicellulose, another major component of forest soil inputs from wood and leaves, is a frequently branching polymer with a heterogeneous composition. Its building blocks are mainly pentoses, hexoses, hexuronic acids, and deoxyhexoses <xref ref-type="bibr" rid="pone.0010971-KgelKnabner1">[22]</xref>
. Decaying leaf litter, for example, consists of 6.5–6.6% arabinose, 3.3–3.9% galactose, 1.2–4.9% mannose, 0.4–1.7% rhamnose, and 3.6–6.7% xylose <xref ref-type="bibr" rid="pone.0010971-Tian1">[39]</xref>
. Given this complexity, fungi deploy a distinct set of hydrolytic enzymes for hemicellulose decomposition <xref ref-type="bibr" rid="pone.0010971-Hoegger1">[40]</xref>
. In our study (<xref ref-type="table" rid="pone-0010971-t001">Table 1</xref>
) we detected putative transcripts of enzymes decomposing the xylan backbone and enzymes preferentially hydrolyzing xylan sidechains consisting of arabinan or glucuronic acid. Also identified was acetylxylan esterase involved in hydrolysis of acetyl groups of polymeric xylan and acetylated xylose. Putative transcripts for enzymes involved in the decomposition of mannan were also identified, as were transcripts for α-glucosidase, involved in starch hydrolysis.</p>
<p>Lastly, our study highlighted six groups of chitinolytic or related enzymes (<xref ref-type="table" rid="pone-0010971-t001">Table 1</xref>
). Chitin, the most abundant aminopolysaccharide in nature, is composed of <italic>N</italic>
-acetyl-D-glucosamine monomers linked <italic>via</italic>
 β-1,4-glycosidic bonds <xref ref-type="bibr" rid="pone.0010971-KgelKnabner1">[22]</xref>
. In soils, chitin polymers are derived mainly from fungal sources but also from arthropods. They provide a considerable pool of nitrogen for other organisms. Several soil microorganisms, especially fungi use mainly hydrolytic enzymes to degrade chitin. It is unknown whether fungi preferentially use chitinase and related enzymes to attack other chitin-containing organisms, to recycle their own chitin structures, or both. The transcripts we registered (<xref ref-type="table" rid="pone-0010971-t001">Table 1</xref>
) concerned the chitinolytic enzymes chitinase and β-<italic>N</italic>
-acetylhexosaminidase (expression of a specific fungal β-<italic>N</italic>
-acetylhexosaminidase was recently monitored in a forest soil, indicating its relevance to soil processes and fungal nutrient acquisition <xref ref-type="bibr" rid="pone.0010971-Courty1">[10]</xref>
), fungal enzymes involved in other cell wall degradation or attack mechanisms (putative endo-α-1,4-polygalactosaminidase, degrading polygalactosamine polymers, and putative glucan endo-1,6-β-glucosidase, probably involved in microbial degradation of glucans that do not necessarily contain nitrogen), and also enzymes likely to be involved in <italic>N</italic>
-acetyl-D-glucosamine metabolism in fungi (amidohydrolase or putative <italic>N</italic>
-acetylglucosamine-6-phosphate deacetylase). Interestingly, we also amplified cDNA corresponding to the hydrolysis of nitrogen-rich <italic>S</italic>
-formylglutathione.</p>
<p>In this study we have looked only at transcript-level gene expression in the soil horizon, so our data can tell us nothing about post-transcriptional regulation. It should be stressed, however, that many of the enzyme activities highlighted here have been detected with various classical enzymatic substrates in soil extracts from the organic horizon of this research site <xref ref-type="bibr" rid="pone.0010971-DeForest1">[19]</xref>
. We thus feel confident that our transcript-level data provide a good picture of corresponding soil enzymatic activities. Final evidence might be provided by metaproteomic studies accessing all the enzymes present in soils and matching them with species or groups in databases <xref ref-type="bibr" rid="pone.0010971-Schulze1">[41]</xref>
. To link community structure with transcript-level expression, it might be interesting to use high-throughput approaches which access the total soil metatranscriptome <xref ref-type="bibr" rid="pone.0010971-Urich1">[42]</xref>
.</p>
</sec>
<sec id="s2b"><title>Ascomycetes <italic>vs.</italic>
 basidiomycetes</title>
<p>How different kinds of fungi contribute to soil turnover processes is a major question in forest soil ecology. Basidiomycetes are regarded as major degraders of wood resources and are characterized as white-rot fungi decaying preferentially lignin components or brown-rot fungi decaying primarily cellulose <xref ref-type="bibr" rid="pone.0010971-Baldrian3">[43]</xref>
. Forest floor and soil horizons are much more heterogeneous than solid wood. They harbor different and ecologically more diverse fungal populations, notably comprising mycorrhizal, saprotrophic, and pathogenic/parasitic fungi. A current debate centers on the respective contributions of saprotrophic fungi <italic>vs</italic>
. ectomycorrhizal basidiomycetes to decomposition and soil cycling in forest soils <xref ref-type="bibr" rid="pone.0010971-Baldrian4">[44]</xref>
, <xref ref-type="bibr" rid="pone.0010971-Cullings1">[45]</xref>
. Recent molecular biological data highlight the presence of varying proportions of ascomycetes in soils <xref ref-type="bibr" rid="pone.0010971-Bue1">[3]</xref>
–<xref ref-type="bibr" rid="pone.0010971-OBrien1">[5]</xref>
, but their actual activities remain largely unknown. In our survey, 125 of the highlighted genes are homologous to known ascomycete genes, 105 to putative basidiomycete genes, and a few to zygomycete or animal genes (<xref ref-type="supplementary-material" rid="pone.0010971.s002">Table S2</xref>
). As this identification is based on a blastp search with sometimes low identity rates (<xref ref-type="supplementary-material" rid="pone.0010971.s002">Table S2</xref>
), our results might change slightly with increasing support from database references and potentially higher identities. Furthermore, our primers do not necessarily target all fungal phyla (e.g. our cellobiose dehydrogenase primers are basidiomycete-specific, the β-glucosidase primers are ascomycete-specific, etc., see <xref ref-type="supplementary-material" rid="pone.0010971.s001">Table S1</xref>
). Nevertheless, the high number of biogeochemical relevant ascomycete transcripts is new and noteworthy, as ligninolytic enzymes, such as laccase, tyrosinase, intradiol-ring cleavage dioxygenase, and potentially heme-thiolate haloperoxidase (<xref ref-type="table" rid="pone-0010971-t001">Table 1</xref>
, <xref ref-type="supplementary-material" rid="pone.0010971.s002">S2</xref>
), are traditionally viewed as characteristic of basidiomycetes. The expression of ascomycete laccase or laccase-like multicopper oxidase has been reported for a beech forest organic horizon <xref ref-type="bibr" rid="pone.0010971-Kellner1">[11]</xref>
, and the presence of diverse ascomycete laccase genes has been found in decaying leaf samples from a salt marsh <xref ref-type="bibr" rid="pone.0010971-Lyons1">[9]</xref>
. However, the full extent of the contribution of ascomycete laccases to lignin decomposition remains unclear, notably because these enzymes exert both polymerizing and depolymerizing activities. On the other hand, the involvement of ascomycetes in the decomposition of cellulose, hemicellulose, and chitin is well documented <xref ref-type="bibr" rid="pone.0010971-deVries1">[46]</xref>
, and corresponds with our present findings (<xref ref-type="supplementary-material" rid="pone.0010971.s002">Table S2</xref>
). Taken together, our data thus provide fundamental information on the expression of both ascomycete and basidiomycete genes encoding enzymes involved in the biogeochemical important processes of lignin, cellulose, hemicellulose, and chitin decomposition. As the number of annotated fungal genes in databases like GenBank increases, it should become possible to determine which fungi or ecological groups (e.g. ectomycorrhizal <italic>vs</italic>
. saprotrophic basidiomycetes <italic>vs</italic>
. saprotrophic ascomycetes) are most important in soil cycling processes.</p>
</sec>
<sec id="s2c"><title>Fungal biogeochemical cycling under increased nitrogen deposition</title>
<p>Much debate centers on the mechanisms governing carbon sequestration in the globally important carbon sink constituted by the forests of the northern hemisphere <xref ref-type="bibr" rid="pone.0010971-deVries2">[47]</xref>
–<xref ref-type="bibr" rid="pone.0010971-Sutton1">[49]</xref>
. The effect of anthropogenic nitrogen deposition from the atmosphere is variably believed to be strong or negligible <xref ref-type="bibr" rid="pone.0010971-Pregitzer1">[17]</xref>
, <xref ref-type="bibr" rid="pone.0010971-Nadelhoffer1">[50]</xref>
, <xref ref-type="bibr" rid="pone.0010971-Reay1">[51]</xref>
, as depositions increase continuously over these forests <xref ref-type="bibr" rid="pone.0010971-Galloway1">[52]</xref>
. The present research is part of a large-scale field experiment that has demonstrated a significant slowing of plant detritus decay in response to simulated atmospheric nitrogen deposition at a rate expected by 2050 in this region (additional 3 g nitrogen m<sup>−2</sup>
 y<sup>−1</sup>
 to ambient deposition). This means increased carbon storage in the soil of a temperate forest spreading widely across Eastern North America <xref ref-type="bibr" rid="pone.0010971-Pregitzer1">[17]</xref>
, <xref ref-type="bibr" rid="pone.0010971-Zak1">[18]</xref>
. In parallel, a decline in ligninolytic and cellulolytic enzyme activities has been observed in the forest floor <xref ref-type="bibr" rid="pone.0010971-DeForest1">[19]</xref>
. Under laboratory conditions, high inorganic nitrogen concentrations can repress transcription of lignocellulolytic genes <xref ref-type="bibr" rid="pone.0010971-Boominathan1">[53]</xref>
, <xref ref-type="bibr" rid="pone.0010971-Vanderwoude1">[54]</xref>
. This raises the question: might anthropogenic nitrogen deposition elicit a similar effect?</p>
<p>In the above-mentioned field-based experiment, replicate plots continuously received either ambient or simulated increased atmospheric nitrogen deposition over a 14-yr period beginning in 1994. The simulated deposition treatment consisted of 3 g sodium nitrate m<sup>−2</sup>
 y<sup>−1</sup>
 applied to the forest floor in equal increments over the growing season <xref ref-type="bibr" rid="pone.0010971-Zak1">[18]</xref>
. PCR amplification was performed on cDNA from each plot, but cloning and sequencing of PCR products was performed only on pooled samples (<xref ref-type="supplementary-material" rid="pone.0010971.s001">Table S1</xref>
).</p>
<p>As transcripts corresponding to all 26 enzyme groups highlighted here were found in both nitrogen-supplemented and control soils (<xref ref-type="table" rid="pone-0010971-t001">Table 1</xref>
, <xref ref-type="supplementary-material" rid="pone.0010971.s002">Table S2</xref>
), our data provide no evidence of a total transcriptional “switch-off” in response to increased nitrogen deposition. Transcriptional down-regulation of relevant fungal genes cannot be excluded, but to assess its contribution would require large-scale application of real-time PCR as used for single specific genes from a forest soil <xref ref-type="bibr" rid="pone.0010971-Courty1">[10]</xref>
. We do provide evidence suggesting that increased nitrogen deposition induced changes in the composition of the fungal community: only 22 of the 234 detected transcripts were found in both nitrogen-supplemented and control plots, the remainder being potentially unique to one or the other. This finding is interesting, but it must be stressed that our sampling setup did not allow an in-depth community analysis. Our data may provide a starting point for an ulterior exhaustive analysis of the biopolymer-degrading fungal community. It should also be mentioned that our data represent only one sampling site of the large-scale field experiment. To draw reliable conclusions, one should use multiple data from all sites. Nevertheless, the results presented here provide the first molecular evidence of major fungal involvement in biogeochemical cycling, i.e. lignocellulose and chitin decomposition, even in a manipulated ecosystem.</p>
</sec>
<sec id="s2d"><title>Conclusion</title>
<p>Fungi provide essential ecosystem services, even in a changing environment. Future research should aim to understand molecular regulatory mechanisms in soils in order to draw conclusions about effects on ecosystems. Some of the tools provided here may help to establish links between fungal communities, their enzymatic activities in soils, and the consequences for ecosystems. Many of the fungal enzymes highlighted in this work receive much attention in applied biotechnological research, and the molecular tools developed here may find further use in both basic and applied research.</p>
</sec>
</sec>
<sec id="s3" sec-type="materials|methods"><title>Materials and Methods</title>
<sec id="s3a"><title>Study site and soil sampling</title>
<p>Soil samples were taken from a long-term study site in Oceana County, Michigan, USA (43° 40′ N, 86° 09′ W), a northern hardwood forest dominated by <italic>Acer saccharum</italic>
 Marsh. This is the southernmost site of a zone involved in a long-term, 500-km climatic and nitrogen-deposition gradient study begun in 1994 <xref ref-type="bibr" rid="pone.0010971-Pregitzer1">[17]</xref>
, including four sites with varying amounts of ambient atmospheric nitrogen (N) deposition (0.68–1.17 g N m<sup>−2</sup>
 yr<sup>−1</sup>
, lowest amount in the northernmost site, highest in the southernmost site). At the Oceana site, three 30-m×30-m plots receive ambient atmospheric nitrogen deposition and three 30-m×30-m plots receive simulated increased atmospheric nitrogen deposition. The simulated atmospheric nitrogen deposition treatment (an additional 3 g N m<sup>−2</sup>
 y<sup>−1</sup>
) was initiated in 1994 and consists of six equal applications of sodium nitrate (NaNO<sub>3</sub>
) delivered as dry pellets to the forest floor over the growing season. The soil is sandy, mixed, a mesic Entic Haplorthod. Soil sampling was done in November 2007 after leaf senescence. In each of the six plots, 10 random 0.1 m×0.1 m litter samples (intermediately decomposed organic horizon O<sub>e</sub>
 and highly decomposed O<sub>a</sub>
 horizon; together up to 2 cm thick) were collected, composited, and homogenized (by cutting the litter in 1–2 cm<sup>2</sup>
 pieces and mixing them in a plastic container), in order to ensure plot coverage and representation of all overstory tree species. The homogenized samples were immediately transferred to liquid nitrogen for RNA extraction.</p>
</sec>
<sec id="s3b"><title>RNA extraction and cDNA construction</title>
<p>A previously published protocol <xref ref-type="bibr" rid="pone.0010971-Luis3">[13]</xref>
 was used to extract total RNA from the six composite forest floor samples obtained from the Oceana research site. Briefly, the RNA of one gram of forest floor was extracted with glass beads and a phenol-based solution. The sample was disrupted with the FastPrep FP120A instrument (MP Biomedicals, Solon, USA) for 30 s at a speed of 6.5. The RNA of this crude mix was then centrifuged, precipitated with ethanol, and separated with the RNA/DNA Midi kit (10) (Qiagen, Hilden, Germany) as recommended by the manufacturer. Before further purification of the RNA with the RNeasy Plant Mini kit (Qiagen), an extra DNAse step (Qiagen) was carried out as recommended by the manufacturer. Three microliters of purified DNA-free RNA was used as template for reverse transcription, after which the six cDNAs were amplified <italic>via</italic>
 17 cycles of a long-distance PCR (LD-PCR) using the SMART™ PCR cDNA Synthesis Kit (Clontech, Mountain View, USA).</p>
</sec>
<sec id="s3c"><title>Primers, PCR conditions, cloning, and sequencing</title>
<p>Degenerate primer pairs for amplifying coding sequences corresponding to fungal ligninolytic, cellulolytic, hemicellulolytic, and chitinolytic enzymes were developed on the basis of reference protein sequences from curated databases like CAZy (<ext-link ext-link-type="uri" xlink:href="http://www.cazy.org">http://www.cazy.org</ext-link>
 <xref ref-type="bibr" rid="pone.0010971-Cantarel1">[37]</xref>
, see also <ext-link ext-link-type="uri" xlink:href="http://www.cazypedia.org">http://www.cazypedia.org</ext-link>
) or FOLy (<ext-link ext-link-type="uri" xlink:href="http://foly.esil.univ-mrs.fr/">http://foly.esil.univ-mrs.fr/</ext-link>
 <xref ref-type="bibr" rid="pone.0010971-Levasseur1">[26]</xref>
), or GenBank. The reference sequences were compared against the NCBI database standard protein-protein BLAST (blastp) (<xref ref-type="supplementary-material" rid="pone.0010971.s001">Table S1</xref>
), and the distance tree option implemented in the NCBI result page was used to display the phylogenetic relationship of each protein of interest among different fungal groups. Then the implemented multiple alignment function for distinct clades was used to find conserved protein sequences of the selected candidates (<xref ref-type="supplementary-material" rid="pone.0010971.s001">Table S1</xref>
). Using this procedure, degenerate primer pairs were developed for conserved protein regions of each enzyme group, and are able to amplify either from broad fungal groups in general, or fungal subsets for example ascomycetes or basidiomycetes, or members of fungal family level (<xref ref-type="supplementary-material" rid="pone.0010971.s001">Table S1</xref>
). For PCR amplification, in a 25 µl PCR reaction using DreamTaq Green PCR Master Mix (Fermentas, Burlington, Canada), 0.25 µl of forward and reverse primer (100 mM, Eurogentec, Liege, Belgium) and 0.5 µl cDNA template were added. The following program on a PT-200 thermocycler (MJ Research, Watertown, USA) was used for amplification: initial denaturation for 5 min at 94°C, 35 cycles of denaturation (45 s at 94°C), annealing (45 s at 50°C), and elongation (1 min 40 s at 72°C), followed by a final elongation step for 10 min at 72°C. PCR products of expected sizes (<xref ref-type="supplementary-material" rid="pone.0010971.s001">Table S1</xref>
) were gel purified, composited among three ambient and simulated increased nitrogen receiving plots, and cloned into the pCR4-TOPO vector using the TOPO TA Cloning kit for sequencing (Invitrogen Life Technology, Karlsruhe, Germany). About 10 positive clones for each expressed enzyme group and per treatment were sequenced at GATC Biotech AG (Konstanz, Germany). Obtained nucleotide sequences were edited with BioEdit 7 <xref ref-type="bibr" rid="pone.0010971-Hall1">[55]</xref>
, translated to protein sequences, and identified with blastp (<xref ref-type="supplementary-material" rid="pone.0010971.s001">Table S1</xref>
). Protein sequences were aligned and phylogenetically compared with references obtained from NCBI. They are accessible on request (<ext-link ext-link-type="uri" xlink:href="http://www.haraldkellner.com/oceanastudy/welcome.html">http://www.haraldkellner.com/oceanastudy/welcome.html</ext-link>
). All sequences were submitted to GenBank and are available under accession numbers FJ040216-FJ040219, FJ040222-FJ040225, GU734340-GU734565.</p>
<table-wrap id="pone-0010971-t001" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0010971.t001</object-id>
<label>Table 1</label>
<caption><title>Expressed genes encoding putative lignocellulolytic and chitinolytic fungal enzymes found in ambient and simulated increased nitrogen litter samples.</title>
</caption>
<alternatives><graphic id="pone-0010971-t001-1" xlink:href="pone.0010971.t001"></graphic>
<table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col>
<col align="center" span="1"></col>
<col align="center" span="1"></col>
<col align="center" span="1"></col>
</colgroup>
<thead><tr><td align="left" rowspan="1" colspan="1">Enzyme (EC number)</td>
<td align="left" rowspan="1" colspan="1">Putative enzyme function</td>
<td align="left" rowspan="1" colspan="1">Total number of transcribed gene types (ambient, nitrogen plot)</td>
<td align="left" rowspan="1" colspan="1">Detected fungal phyla<xref ref-type="table-fn" rid="nt101">#</xref>
</td>
</tr>
</thead>
<tbody><tr><td align="left" rowspan="1" colspan="1"><bold><italic>Ligninolytic enzymes and related</italic>
</bold>
</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">Manganese peroxidase (EC 1.11.1.13), Class II of the non-animal heme peroxidase superfamily</td>
<td align="left" rowspan="1" colspan="1">Extracellular lignin oxidation and breakdown <italic>via</italic>
 Mn<sup>3+</sup>
</td>
<td align="left" rowspan="1" colspan="1">4 (1, 3)</td>
<td align="left" rowspan="1" colspan="1">B</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">Laccase (EC 1.10.3.2)</td>
<td align="left" rowspan="1" colspan="1">Extracelluar oxidation of phenolics and lignin</td>
<td align="left" rowspan="1" colspan="1">9 (8, 6)</td>
<td align="left" rowspan="1" colspan="1">A, B</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">Cellobiose dehydrogenase (EC 1.1.99.18)</td>
<td align="left" rowspan="1" colspan="1">Extracellular; putative lignin oxidation <italic>via</italic>
 Fenton reaction (generation of hydroxyl-radicals)</td>
<td align="left" rowspan="1" colspan="1">4 (2, 3)</td>
<td align="left" rowspan="1" colspan="1">B</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">Oxalate decarboxylase (EC 4.1.1.2)</td>
<td align="left" rowspan="1" colspan="1">Oxalate breakdown</td>
<td align="left" rowspan="1" colspan="1">17 (6, 11)</td>
<td align="left" rowspan="1" colspan="1">A, B</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1"><bold><italic>Enzymes oxidizing aromatics</italic>
</bold>
</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">Heme-thiolate peroxidases; i.e. aromatic peroxygenase (EC 1.11.2.-), chloroperoxidase (EC 1.11.1.10)</td>
<td align="left" rowspan="1" colspan="1">Extracellular oxygenations (<italic>O</italic>
-dealkylation, hydroxylation, epoxidation, sulfoxidation, <italic>N</italic>
-oxidation, etc.); unspecific halogenation</td>
<td align="left" rowspan="1" colspan="1">11 (9, 3)</td>
<td align="left" rowspan="1" colspan="1">A, B</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">Tyrosinase (EC 1.14.18.1)</td>
<td align="left" rowspan="1" colspan="1">Intracellular and cell-wall-associated oxidation of phenols, pigmentation</td>
<td align="left" rowspan="1" colspan="1">5 (3, 2)</td>
<td align="left" rowspan="1" colspan="1">A, B</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">Intradiol ring cleavage dioxygenase, putative catechol 1,2-dioxygenase (EC 1.13.11.1) or hydroxyquinol 1,2-dioxygenase (EC 1.13.11.37)</td>
<td align="left" rowspan="1" colspan="1">Intracellular cleavage of aromatic rings</td>
<td align="left" rowspan="1" colspan="1">7 (5, 3)</td>
<td align="left" rowspan="1" colspan="1">A</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1"><bold><italic>Cellulolytic, hemicellulolytic and related enzymes (all extracellular)</italic>
</bold>
<xref ref-type="table-fn" rid="nt102">§</xref>
</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">GH3: putative β-glucosidase (EC 3.2.1.21) or xylan 1,4-β-xylosidase (EC 3.2.1.37)</td>
<td align="left" rowspan="1" colspan="1">Cellulose and xylan backbone degradation</td>
<td align="left" rowspan="1" colspan="1">25 (22, 4)</td>
<td align="left" rowspan="1" colspan="1">A</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">GH5: putative mannan endo-1,4-β-mannosidase (EC 3.2.1.78) or endoglucanase (EC 3.2.1.4)</td>
<td align="left" rowspan="1" colspan="1">Mannan & cellulose degradation</td>
<td align="left" rowspan="1" colspan="1">9 (4, 5)</td>
<td align="left" rowspan="1" colspan="1">A, B</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">GH6: cellulose 1,4-β-cellobiosidase, i.e. cellobiohydrolase II (EC 3.2.1.91)</td>
<td align="left" rowspan="1" colspan="1">Cellulose degradation</td>
<td align="left" rowspan="1" colspan="1">3 (2, 1)</td>
<td align="left" rowspan="1" colspan="1">A, B</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">GH7: cellobiohydrolase I (EC 3.2.1.-) or endoglucanase (EC 3.2.1.4)</td>
<td align="left" rowspan="1" colspan="1">Cellulose degradation</td>
<td align="left" rowspan="1" colspan="1">11 (5, 6)</td>
<td align="left" rowspan="1" colspan="1">A, B</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">GH10: endo-1,4-β-xylanase (EC 3.2.1.8)</td>
<td align="left" rowspan="1" colspan="1">Xylan backbone degradation</td>
<td align="left" rowspan="1" colspan="1">3 (2, 1)</td>
<td align="left" rowspan="1" colspan="1">A, B</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">GH11: endo-1,4-β-xylanase (EC 3.2.1.8)</td>
<td align="left" rowspan="1" colspan="1">Xylan backbone degradation</td>
<td align="left" rowspan="1" colspan="1">14 (10, 8)</td>
<td align="left" rowspan="1" colspan="1">A, B</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">GH31: α-glucosidase (EC 3.2.1.20)</td>
<td align="left" rowspan="1" colspan="1">Starch degradation</td>
<td align="left" rowspan="1" colspan="1">10 (4, 6)</td>
<td align="left" rowspan="1" colspan="1">A</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">GH45: endoglucanase (EC 3.2.1.4)</td>
<td align="left" rowspan="1" colspan="1">Cellulose degradation</td>
<td align="left" rowspan="1" colspan="1">11 (7, 7)</td>
<td align="left" rowspan="1" colspan="1">A, Z</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">GH51: α-L-arabinofuranosidase (EC 3.2.1.55)</td>
<td align="left" rowspan="1" colspan="1">Xylan sidechain (arabinan) degradation</td>
<td align="left" rowspan="1" colspan="1">9 (5, 4)</td>
<td align="left" rowspan="1" colspan="1">B</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">GH67: α-glucuronidase (EC 3.2.1.139) or xylan α-1,2-glucuronosidase (EC 3.2.1.131)</td>
<td align="left" rowspan="1" colspan="1">Xylan sidechain (glucuronic acid) degradation</td>
<td align="left" rowspan="1" colspan="1">8 (5, 3)</td>
<td align="left" rowspan="1" colspan="1">A</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">GH74: endoglucanase (EC 3.2.1.4) or putative xyloglucan-specific endo-β-1,4-glucanase (EC 3.2.1.151)</td>
<td align="left" rowspan="1" colspan="1">Cellulose degradation</td>
<td align="left" rowspan="1" colspan="1">4 (2, 2)</td>
<td align="left" rowspan="1" colspan="1">A, B</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">GH92: putative α-1,2-mannosidase (EC 3.2.1.-)</td>
<td align="left" rowspan="1" colspan="1">Mannan sidechain degradation</td>
<td align="left" rowspan="1" colspan="1">9 (2, 8)</td>
<td align="left" rowspan="1" colspan="1">A</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">CE1: acetylxylan esterase (EC 3.1.1.72)</td>
<td align="left" rowspan="1" colspan="1">Xylan sidechain degradation</td>
<td align="left" rowspan="1" colspan="1">5 (2, 3)</td>
<td align="left" rowspan="1" colspan="1">A</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">Cellobiose dehydrogenase (EC 1.1.99.18)</td>
<td align="left" rowspan="1" colspan="1">Cellobiose decomposition; generation of hydroxyl radicals putatively acting on cellulose</td>
<td align="left" rowspan="1" colspan="1">4 (2, 3)</td>
<td align="left" rowspan="1" colspan="1">B</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1"><bold><italic>Enzymes related to chitinolysis and aminosugar metabolism</italic>
</bold>
</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">GH18: chitinase (EC 3.2.1.14)</td>
<td align="left" rowspan="1" colspan="1">Chitin degradation</td>
<td align="left" rowspan="1" colspan="1">12 (4, 9)</td>
<td align="left" rowspan="1" colspan="1">A, B</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">GH20: β-<italic>N</italic>
-acetylhexosaminidase (EC 3.2.1.52)</td>
<td align="left" rowspan="1" colspan="1">Chitobiose hydrolysis</td>
<td align="left" rowspan="1" colspan="1">15 (9, 8)</td>
<td align="left" rowspan="1" colspan="1">A, B</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">GH30: putative glucan endo-1,6-β-glucosidase (EC 3.2.1.75)</td>
<td align="left" rowspan="1" colspan="1">Microbial glucan degradation (e.g. fungal cell walls)</td>
<td align="left" rowspan="1" colspan="1">2 (1, 1)</td>
<td align="left" rowspan="1" colspan="1">A</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">GH114: putative endo-α-1,4-polygalactosaminidase (EC 3.2.1.109)</td>
<td align="left" rowspan="1" colspan="1">Glucan degradation (e.g. fungal cell walls)</td>
<td align="left" rowspan="1" colspan="1">10 (6, 4)</td>
<td align="left" rowspan="1" colspan="1">A</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">CE1: <italic>S</italic>
-formylglutathione hydrolase (EC 3.1.2.12)</td>
<td align="left" rowspan="1" colspan="1">Methane cycle (or nitrogen cycle)</td>
<td align="left" rowspan="1" colspan="1">8 (4, 5)</td>
<td align="left" rowspan="1" colspan="1">A</td>
</tr>
<tr><td align="left" rowspan="1" colspan="1">CE9: amidohydrolase (EC 3.5.-.-) or putative <italic>N</italic>
-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25)</td>
<td align="left" rowspan="1" colspan="1">Internal aminosugar metabolism, nitrogen cycle</td>
<td align="left" rowspan="1" colspan="1">9 (7, 3)</td>
<td align="left" rowspan="1" colspan="1">B</td>
</tr>
</tbody>
</table>
</alternatives>
<table-wrap-foot><fn id="nt101"><label></label>
<p>#Fungal phyla: A – ascomycetes, B – basidiomycetes, Z – zygomycetes.</p>
</fn>
<fn id="nt102"><label></label>
<p>§GH – glycoside hydrolase family and CE – carbohydrate esterase family according to <ext-link ext-link-type="uri" xlink:href="http://www.cazy.org">www.cazy.org</ext-link>
 <xref ref-type="bibr" rid="pone.0010971-Cantarel1">[37]</xref>
.</p>
</fn>
</table-wrap-foot>
</table-wrap>
</sec>
</sec>
<sec sec-type="supplementary-material" id="s4"><title>Supporting Information</title>
<supplementary-material content-type="local-data" id="pone.0010971.s001"><label>Table S1</label>
<caption><p>Developed degenerate primer pairs for different fungal enzyme groups.</p>
<p>(0.12 MB RTF)</p>
</caption>
<media xlink:href="pone.0010971.s001.rtf" mimetype="application" mime-subtype="rtf"><caption><p>Click here for additional data file.</p>
</caption>
</media>
</supplementary-material>
<supplementary-material content-type="local-data" id="pone.0010971.s002"><label>Table S2</label>
<caption><p>Transcribed genes giving a blastp match, putative fungal phylum (A - ascomycetes, B - basidiomycetes, Z - zygomycetes), derived ambient (A) or nitrogen-amended (N) plots, and accession number.</p>
<p>(0.50 MB RTF)</p>
</caption>
<media xlink:href="pone.0010971.s002.rtf" mimetype="application" mime-subtype="rtf"><caption><p>Click here for additional data file.</p>
</caption>
</media>
</supplementary-material>
</sec>
</body>
<back><ack><p>The authors wish to thank D.R. Zak and his soil ecology group for access to the research site and for use of laboratory capacities for soil RNA extraction. We also wish to thank M. Hofrichter and R.R.E. Artz for reading the manuscript and giving precious advice.</p>
</ack>
<fn-group><fn fn-type="conflict"><p><bold>Competing Interests: </bold>
The authors have declared that no competing interests exist.</p>
</fn>
<fn fn-type="financial-disclosure"><p><bold>Funding: </bold>
Grant was received from the Belgian Research Foundation (FNRS, <ext-link ext-link-type="uri" xlink:href="http://www2.frs-fnrs.be/">http://www2.frs-fnrs.be/</ext-link>
, grant no. 2.4503.08). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</p>
</fn>
</fn-group>
<ref-list><title>References</title>
<ref id="pone.0010971-Dighton1"><label>1</label>
<mixed-citation publication-type="other"><person-group person-group-type="author"><name><surname>Dighton</surname>
<given-names>J</given-names>
</name>
<name><surname>White</surname>
<given-names>JF</given-names>
</name>
<name><surname>Oudemans</surname>
<given-names>P</given-names>
</name>
</person-group>
<year>2005</year>
<article-title>The Fungal community: its organization and role in the ecosystem.</article-title>
<size units="page"></size>
<comment>Taylor and Francis, Boca Raton, USA</comment>
</mixed-citation>
</ref>
<ref id="pone.0010971-Deacon1"><label>2</label>
<mixed-citation publication-type="other"><person-group person-group-type="author"><name><surname>Deacon</surname>
<given-names>J</given-names>
</name>
</person-group>
<year>2005</year>
<article-title>Fungal biology.</article-title>
<size units="page"></size>
<comment>Blackwell Publishing, Oxford, UK</comment>
</mixed-citation>
</ref>
<ref id="pone.0010971-Bue1"><label>3</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Buée</surname>
<given-names>M</given-names>
</name>
<name><surname>Reich</surname>
<given-names>M</given-names>
</name>
<name><surname>Murat</surname>
<given-names>C</given-names>
</name>
<name><surname>Morin</surname>
<given-names>E</given-names>
</name>
<name><surname>Nilsson</surname>
<given-names>RH</given-names>
</name>
<etal></etal>
</person-group>
<year>2009</year>
<article-title>454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity.</article-title>
<source>New Phytol</source>
<volume>184</volume>
<fpage>449</fpage>
<lpage>456</lpage>
<pub-id pub-id-type="pmid">19703112</pub-id>
</mixed-citation>
</ref>
<ref id="pone.0010971-Lindahl1"><label>4</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lindahl</surname>
<given-names>BD</given-names>
</name>
<name><surname>Ihrmark</surname>
<given-names>K</given-names>
</name>
<name><surname>Boberg</surname>
<given-names>J</given-names>
</name>
<name><surname>Trumbore</surname>
<given-names>SE</given-names>
</name>
<name><surname>Högberg</surname>
<given-names>P</given-names>
</name>
<etal></etal>
</person-group>
<year>2007</year>
<article-title>Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest.</article-title>
<source>New Phytol</source>
<volume>173</volume>
<fpage>611</fpage>
<lpage>620</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-OBrien1"><label>5</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>O'Brien</surname>
<given-names>HE</given-names>
</name>
<name><surname>Parrent</surname>
<given-names>JL</given-names>
</name>
<name><surname>Jackson</surname>
<given-names>JA</given-names>
</name>
<name><surname>Moncalvo</surname>
<given-names>JM</given-names>
</name>
<name><surname>Vilgalys</surname>
<given-names>R</given-names>
</name>
</person-group>
<year>2005</year>
<article-title>Fungal community analysis by large-scale sequencing of environmental samples.</article-title>
<source>Appl Environ Microbiol</source>
<volume>71</volume>
<fpage>5544</fpage>
<lpage>5550</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Edwards1"><label>6</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Edwards</surname>
<given-names>IP</given-names>
</name>
<name><surname>Upchurch</surname>
<given-names>RA</given-names>
</name>
<name><surname>Zak</surname>
<given-names>DR</given-names>
</name>
</person-group>
<year>2008</year>
<article-title>Isolation of fungal Cellobiohydrolase I genes from sporocarps and forest soils by PCR.</article-title>
<source>Appl Environ Microbiol</source>
<volume>74</volume>
<fpage>3481</fpage>
<lpage>3489</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Luis1"><label>7</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Luis</surname>
<given-names>P</given-names>
</name>
<name><surname>Walther</surname>
<given-names>G</given-names>
</name>
<name><surname>Kellner</surname>
<given-names>H</given-names>
</name>
<name><surname>Martin</surname>
<given-names>F</given-names>
</name>
<name><surname>Buscot</surname>
<given-names>F</given-names>
</name>
</person-group>
<year>2004</year>
<article-title>Diversity of laccase genes from basidiomycetes in a forest soil.</article-title>
<source>Soil Biol Biochem</source>
<volume>36</volume>
<fpage>1025</fpage>
<lpage>1036</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Luis2"><label>8</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Luis</surname>
<given-names>P</given-names>
</name>
<name><surname>Kellner</surname>
<given-names>H</given-names>
</name>
<name><surname>Zimdars</surname>
<given-names>B</given-names>
</name>
<name><surname>Langer</surname>
<given-names>U</given-names>
</name>
<name><surname>Martin</surname>
<given-names>F</given-names>
</name>
<etal></etal>
</person-group>
<year>2005</year>
<article-title>Patchiness and spatial distribution of laccase genes of ectomycorrhizal, saprotrophic and unknown basidiomycetes in the upper horizons of a mixed forest Cambisol.</article-title>
<source>Microb Ecol</source>
<volume>50</volume>
<fpage>570</fpage>
<lpage>579</lpage>
<pub-id pub-id-type="pmid">16341831</pub-id>
</mixed-citation>
</ref>
<ref id="pone.0010971-Lyons1"><label>9</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lyons</surname>
<given-names>JI</given-names>
</name>
<name><surname>Newell</surname>
<given-names>SY</given-names>
</name>
<name><surname>Buchan</surname>
<given-names>A</given-names>
</name>
<name><surname>Moran</surname>
<given-names>MA</given-names>
</name>
</person-group>
<year>2003</year>
<article-title>Diversity of ascomycete laccase gene sequences in a Southeastern US salt marsh.</article-title>
<source>Microb Ecol</source>
<volume>45</volume>
<fpage>270</fpage>
<lpage>281</lpage>
<pub-id pub-id-type="pmid">12632211</pub-id>
</mixed-citation>
</ref>
<ref id="pone.0010971-Courty1"><label>10</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Courty</surname>
<given-names>PE</given-names>
</name>
<name><surname>Poletto</surname>
<given-names>M</given-names>
</name>
<name><surname>Duchaussoy</surname>
<given-names>F</given-names>
</name>
<name><surname>Buée</surname>
<given-names>M</given-names>
</name>
<name><surname>Garbaye</surname>
<given-names>J</given-names>
</name>
<etal></etal>
</person-group>
<year>2008</year>
<article-title>Gene transcription in <italic>Lactarius quietus</italic>
-<italic>Quercus petraea</italic>
 ectomycorrhizas from a forest soil.</article-title>
<source>Appl Environ Microbiol</source>
<volume>74</volume>
<fpage>6598</fpage>
<lpage>6605</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Kellner1"><label>11</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kellner</surname>
<given-names>H</given-names>
</name>
<name><surname>Luis</surname>
<given-names>P</given-names>
</name>
<name><surname>Schlitt</surname>
<given-names>B</given-names>
</name>
<name><surname>Buscot</surname>
<given-names>F</given-names>
</name>
</person-group>
<year>2009</year>
<article-title>Temporal changes in diversity and expression patterns of fungal laccase genes within the organic horizon of a brown forest soil.</article-title>
<source>Soil Biol Biochem</source>
<volume>41</volume>
<fpage>1380</fpage>
<lpage>1389</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Kellner2"><label>12</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kellner</surname>
<given-names>H</given-names>
</name>
<name><surname>Zak</surname>
<given-names>DR</given-names>
</name>
</person-group>
<year>2009</year>
<article-title>Detection of expressed fungal type I polyketide synthase genes in a forest soil.</article-title>
<source>Soil Biol Biochem</source>
<volume>41</volume>
<fpage>1344</fpage>
<lpage>1347</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Luis3"><label>13</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Luis</surname>
<given-names>P</given-names>
</name>
<name><surname>Kellner</surname>
<given-names>H</given-names>
</name>
<name><surname>Martin</surname>
<given-names>F</given-names>
</name>
<name><surname>Buscot</surname>
<given-names>F</given-names>
</name>
</person-group>
<year>2005</year>
<article-title>A molecular method to evaluate basidiomycete laccase gene expression in forest soils.</article-title>
<source>Geoderma</source>
<volume>128</volume>
<fpage>18</fpage>
<lpage>27</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Bailly1"><label>14</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bailly</surname>
<given-names>J</given-names>
</name>
<name><surname>Fraissinet-Tachet</surname>
<given-names>L</given-names>
</name>
<name><surname>Verner</surname>
<given-names>MC</given-names>
</name>
<name><surname>Debaud</surname>
<given-names>JC</given-names>
</name>
<name><surname>Lemaire</surname>
<given-names>M</given-names>
</name>
<etal></etal>
</person-group>
<year>2007</year>
<article-title>Soil eukaryotic functional diversity, a metatranscriptomic approach.</article-title>
<source>ISME J</source>
<volume>1</volume>
<fpage>632</fpage>
<lpage>642</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Berg1"><label>15</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Berg</surname>
<given-names>B</given-names>
</name>
<name><surname>Matzner</surname>
<given-names>E</given-names>
</name>
</person-group>
<year>1997</year>
<article-title>Effect of N deposition on decomposition of plant litter and soil organic matter in forest systems.</article-title>
<source>Environ Rev</source>
<volume>5</volume>
<fpage>1</fpage>
<lpage>25</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Goodale1"><label>16</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Goodale</surname>
<given-names>CL</given-names>
</name>
<name><surname>Apps</surname>
<given-names>MJ</given-names>
</name>
<name><surname>Birdsey</surname>
<given-names>RA</given-names>
</name>
<name><surname>Field</surname>
<given-names>CB</given-names>
</name>
<name><surname>Heath</surname>
<given-names>LS</given-names>
</name>
<etal></etal>
</person-group>
<year>2002</year>
<article-title>Forest carbon sinks in the Northern Hemisphere.</article-title>
<source>Ecol Appl</source>
<volume>12</volume>
<fpage>891</fpage>
<lpage>899</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Pregitzer1"><label>17</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pregitzer</surname>
<given-names>KS</given-names>
</name>
<name><surname>Burton</surname>
<given-names>AJ</given-names>
</name>
<name><surname>Zak</surname>
<given-names>DR</given-names>
</name>
<name><surname>Talhelm</surname>
<given-names>AF</given-names>
</name>
</person-group>
<year>2008</year>
<article-title>Simulated chronic nitrogen deposition increases carbon storage in Northern Temperate forests.</article-title>
<source>Glob Chang Biol</source>
<volume>14</volume>
<fpage>142</fpage>
<lpage>153</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Zak1"><label>18</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zak</surname>
<given-names>DR</given-names>
</name>
<name><surname>Holmes</surname>
<given-names>WE</given-names>
</name>
<name><surname>Burton</surname>
<given-names>AJ</given-names>
</name>
<name><surname>Pregitzer</surname>
<given-names>KS</given-names>
</name>
<name><surname>Talhelm</surname>
<given-names>AF</given-names>
</name>
</person-group>
<year>2008</year>
<article-title>Simulated atmospheric NO<sub>3</sub>
− deposition increases soil organic matter by slowing decomposition.</article-title>
<source>Ecol Appl</source>
<volume>18</volume>
<fpage>2016</fpage>
<lpage>2027</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-DeForest1"><label>19</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>DeForest</surname>
<given-names>JL</given-names>
</name>
<name><surname>Zak</surname>
<given-names>DR</given-names>
</name>
<name><surname>Pregitzer</surname>
<given-names>KS</given-names>
</name>
<name><surname>Burton</surname>
<given-names>AJ</given-names>
</name>
</person-group>
<year>2004</year>
<article-title>Atmospheric nitrate deposition, microbial community composition, and enzyme activity in Northern Hardwood forests.</article-title>
<source>Soil Sci Soc Am J</source>
<volume>68</volume>
<fpage>132</fpage>
<lpage>138</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Kes1"><label>20</label>
<mixed-citation publication-type="other"><person-group person-group-type="author"><name><surname>Kües</surname>
<given-names>U</given-names>
</name>
</person-group>
<year>2007</year>
<article-title>Wood production, wood technology, and biotechnological impacts.</article-title>
<size units="page"></size>
<comment>Universitätsverlag Göttingen, Germany</comment>
</mixed-citation>
</ref>
<ref id="pone.0010971-Bdeker1"><label>21</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bödeker</surname>
<given-names>ITM</given-names>
</name>
<name><surname>Nygren</surname>
<given-names>CMR</given-names>
</name>
<name><surname>Taylor</surname>
<given-names>AFS</given-names>
</name>
<name><surname>Olson</surname>
<given-names>A</given-names>
</name>
<name><surname>Lindahl</surname>
<given-names>BD</given-names>
</name>
</person-group>
<year>2009</year>
<article-title>ClassII peroxidase-encoding genes are present in a phylogenetically wide range of ectomycorrhizal fungi.</article-title>
<source>ISME J</source>
<volume>3</volume>
<fpage>1387</fpage>
<lpage>1395</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-KgelKnabner1"><label>22</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kögel-Knabner</surname>
<given-names>I</given-names>
</name>
</person-group>
<year>2002</year>
<article-title>The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter.</article-title>
<source>Soil Biol Biochem</source>
<volume>34</volume>
<fpage>139</fpage>
<lpage>162</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Hofrichter1"><label>23</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hofrichter</surname>
<given-names>M</given-names>
</name>
</person-group>
<year>2002</year>
<article-title>Review: lignin conversion by manganese peroxidase (MnP).</article-title>
<source>Enzyme Microb Technol</source>
<volume>30</volume>
<fpage>454</fpage>
<lpage>466</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Baldrian1"><label>24</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Baldrian</surname>
<given-names>P</given-names>
</name>
</person-group>
<year>2006</year>
<article-title>Fungal laccases: occurrence and properties.</article-title>
<source>FEMS Microbiol Rev</source>
<volume>30</volume>
<fpage>215</fpage>
<lpage>242</lpage>
<pub-id pub-id-type="pmid">16472305</pub-id>
</mixed-citation>
</ref>
<ref id="pone.0010971-Baldrian2"><label>25</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Baldrian</surname>
<given-names>P</given-names>
</name>
<name><surname>Valášková</surname>
<given-names>V</given-names>
</name>
</person-group>
<year>2008</year>
<article-title>Degradation of cellulose by basidiomycetous fungi.</article-title>
<source>FEMS Microbiol Rev</source>
<volume>32</volume>
<fpage>501</fpage>
<lpage>521</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Levasseur1"><label>26</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Levasseur</surname>
<given-names>A</given-names>
</name>
<name><surname>Piumi</surname>
<given-names>F</given-names>
</name>
<name><surname>Coutinho</surname>
<given-names>PM</given-names>
</name>
<name><surname>Rancurel</surname>
<given-names>C</given-names>
</name>
<name><surname>Asther</surname>
<given-names>M</given-names>
</name>
<etal></etal>
</person-group>
<year>2008</year>
<article-title>FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds.</article-title>
<source>Fungal Genet Biol</source>
<volume>45</volume>
<fpage>638</fpage>
<lpage>645</lpage>
<pub-id pub-id-type="pmid">18308593</pub-id>
</mixed-citation>
</ref>
<ref id="pone.0010971-Pecyna1"><label>27</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pecyna</surname>
<given-names>MJ</given-names>
</name>
<name><surname>Ullrich</surname>
<given-names>R</given-names>
</name>
<name><surname>Bittner</surname>
<given-names>B</given-names>
</name>
<name><surname>Clemens</surname>
<given-names>A</given-names>
</name>
<name><surname>Scheibner</surname>
<given-names>K</given-names>
</name>
<etal></etal>
</person-group>
<year>2009</year>
<article-title>Molecular characterization of aromatic peroxygenase from <italic>Agrocybe aegerita</italic>
.</article-title>
<source>Appl Microbiol Biotechnol</source>
<volume>84</volume>
<fpage>885</fpage>
<lpage>897</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Morris1"><label>28</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Morris</surname>
<given-names>DR</given-names>
</name>
<name><surname>Hager</surname>
<given-names>LP</given-names>
</name>
</person-group>
<year>1966</year>
<article-title>Chloroperoxidase. I. Isolation and properties of the crystalline glycoprotein.</article-title>
<source>J Biol Chem</source>
<volume>241</volume>
<fpage>1763</fpage>
<lpage>1768</lpage>
<pub-id pub-id-type="pmid">5949836</pub-id>
</mixed-citation>
</ref>
<ref id="pone.0010971-Ullrich1"><label>29</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ullrich</surname>
<given-names>R</given-names>
</name>
<name><surname>Hofrichter</surname>
<given-names>M</given-names>
</name>
</person-group>
<year>2005</year>
<article-title>The haloperoxidase of the agaric fungus <italic>Agrocybe aegerita</italic>
 hydroxylates toluene and naphthalene.</article-title>
<source>FEBS Lett</source>
<volume>579</volume>
<fpage>6247</fpage>
<lpage>6250</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Halaouli1"><label>30</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Halaouli</surname>
<given-names>S</given-names>
</name>
<name><surname>Asther</surname>
<given-names>M</given-names>
</name>
<name><surname>Sigoillot</surname>
<given-names>J-C</given-names>
</name>
<name><surname>Hamdi</surname>
<given-names>M</given-names>
</name>
<name><surname>Lomascolo</surname>
<given-names>A</given-names>
</name>
</person-group>
<year>2006</year>
<article-title>Fungal tyrosinases: new prospects in molecular characteristics, bioengineering and biotechnological applications.</article-title>
<source>J Appl Microbiol</source>
<volume>100</volume>
<fpage>219</fpage>
<lpage>232</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Burke1"><label>31</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Burke</surname>
<given-names>RM</given-names>
</name>
<name><surname>Cairney</surname>
<given-names>JWG</given-names>
</name>
</person-group>
<year>2002</year>
<article-title>Laccases and other polyphenol oxidases in ecto- and ericoid mycorrhizal fungi.</article-title>
<source>Mycorrhiza</source>
<volume>12</volume>
<fpage>105</fpage>
<lpage>116</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Sinsabaugh1"><label>32</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sinsabaugh</surname>
<given-names>RL</given-names>
</name>
</person-group>
<year>2010</year>
<article-title>Phenol oxidase, peroxidase and organic matter dynamics of soil.</article-title>
<source>Soil Biol Biochem</source>
<volume>42</volume>
<fpage>391</fpage>
<lpage>404</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Rieble1"><label>33</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rieble</surname>
<given-names>S</given-names>
</name>
<name><surname>Joshi</surname>
<given-names>DK</given-names>
</name>
<name><surname>Gold</surname>
<given-names>MH</given-names>
</name>
</person-group>
<year>1994</year>
<article-title>Purification and characterization of a 1,2,4-trihydroxybenzene 1,2-dioxygenase from the basidiomycete <italic>Phanerochaete chrysosporium</italic>
.</article-title>
<source>J Bacteriol</source>
<volume>176</volume>
<fpage>4838</fpage>
<lpage>4844</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Svedrui1"><label>34</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Svedružić</surname>
<given-names>D</given-names>
</name>
<name><surname>Jónsson</surname>
<given-names>S</given-names>
</name>
<name><surname>Toyota</surname>
<given-names>CG</given-names>
</name>
<name><surname>Reinhardt</surname>
<given-names>LA</given-names>
</name>
<name><surname>Ricagno</surname>
<given-names>S</given-names>
</name>
<etal></etal>
</person-group>
<year>2005</year>
<article-title>The enzymes of oxalate metabolism: unexpected structures and mechanisms.</article-title>
<source>Arch Biochem Biophys</source>
<volume>433</volume>
<fpage>176</fpage>
<lpage>192</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Coutinho1"><label>35</label>
<mixed-citation publication-type="other"><person-group person-group-type="author"><name><surname>Coutinho</surname>
<given-names>PM</given-names>
</name>
<name><surname>Henrissat</surname>
<given-names>B</given-names>
</name>
</person-group>
<year>1999</year>
<article-title>Carbohydrate-active enzymes: an integrated database approach.</article-title>
<person-group person-group-type="editor"><name><surname>Gilbert</surname>
<given-names>HJ</given-names>
</name>
<name><surname>Davies</surname>
<given-names>G</given-names>
</name>
<name><surname>Henrissat</surname>
<given-names>B</given-names>
</name>
<name><surname>Svensson</surname>
<given-names>B</given-names>
</name>
</person-group>
<source>Recent Advances in Carbohydrate Bioengineering</source>
<fpage>3</fpage>
<lpage>12</lpage>
<comment>The Royal Society of Chemistry, Cambridge</comment>
</mixed-citation>
</ref>
<ref id="pone.0010971-Henrissat1"><label>36</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Henrissat</surname>
<given-names>B</given-names>
</name>
</person-group>
<year>1991</year>
<article-title>A classification of glycosyl hydrolases based on amino-acid sequence similarities.</article-title>
<source>Biochem J</source>
<volume>280</volume>
<fpage>309</fpage>
<lpage>316</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Cantarel1"><label>37</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cantarel</surname>
<given-names>BL</given-names>
</name>
<name><surname>Coutinho</surname>
<given-names>PM</given-names>
</name>
<name><surname>Rancurel</surname>
<given-names>C</given-names>
</name>
<name><surname>Bernard</surname>
<given-names>T</given-names>
</name>
<name><surname>Lombard</surname>
<given-names>V</given-names>
</name>
<etal></etal>
</person-group>
<year>2009</year>
<article-title>The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics.</article-title>
<source>Nucleic Acids Res</source>
<volume>37</volume>
<fpage>D233</fpage>
<lpage>238</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Jacobsen1"><label>38</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jacobsen</surname>
<given-names>J</given-names>
</name>
<name><surname>Lydolph</surname>
<given-names>M</given-names>
</name>
<name><surname>Lange</surname>
<given-names>L</given-names>
</name>
</person-group>
<year>2005</year>
<article-title>Culture independent PCR: an alternative enzyme discovery strategy.</article-title>
<source>J Microbiol Methods</source>
<volume>60</volume>
<fpage>63</fpage>
<lpage>71</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Tian1"><label>39</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Tian</surname>
<given-names>XJ</given-names>
</name>
<name><surname>Takeda</surname>
<given-names>H</given-names>
</name>
<name><surname>Azuma</surname>
<given-names>J</given-names>
</name>
</person-group>
<year>2000</year>
<article-title>Dynamics of organic-chemical components in leaf litters during a 3.5-year decomposition.</article-title>
<source>Eur J Soil Biol</source>
<volume>36</volume>
<fpage>81</fpage>
<lpage>89</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Hoegger1"><label>40</label>
<mixed-citation publication-type="other"><person-group person-group-type="author"><name><surname>Hoegger</surname>
<given-names>PJ</given-names>
</name>
<name><surname>Majcherczyk</surname>
<given-names>A</given-names>
</name>
<name><surname>Dwivedi</surname>
<given-names>RC</given-names>
</name>
<name><surname>Svobodová</surname>
<given-names>K</given-names>
</name>
<name><surname>Kilaru</surname>
<given-names>S</given-names>
</name>
<etal></etal>
</person-group>
<year>2007</year>
<article-title>Enzymes in wood degradation.</article-title>
<person-group person-group-type="editor"><name><surname>Kües</surname>
<given-names>U</given-names>
</name>
</person-group>
<source>Wood production, wood technology, and biotechnological impacts</source>
<fpage>383</fpage>
<lpage>432</lpage>
<comment>Universitätsverlag Göttingen, Germany</comment>
</mixed-citation>
</ref>
<ref id="pone.0010971-Schulze1"><label>41</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Schulze</surname>
<given-names>WX</given-names>
</name>
<name><surname>Gleixner</surname>
<given-names>G</given-names>
</name>
<name><surname>Kaiser</surname>
<given-names>K</given-names>
</name>
<name><surname>Guggenberger</surname>
<given-names>G</given-names>
</name>
<name><surname>Mann</surname>
<given-names>M</given-names>
</name>
<etal></etal>
</person-group>
<year>2005</year>
<article-title>A proteomic fingerprint of dissolved organic carbon and of soil particles.</article-title>
<source>Oecologia</source>
<volume>142</volume>
<fpage>335</fpage>
<lpage>343</lpage>
<pub-id pub-id-type="pmid">15449171</pub-id>
</mixed-citation>
</ref>
<ref id="pone.0010971-Urich1"><label>42</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Urich</surname>
<given-names>T</given-names>
</name>
<name><surname>Lanzén</surname>
<given-names>A</given-names>
</name>
<name><surname>Qi</surname>
<given-names>J</given-names>
</name>
<name><surname>Huson</surname>
<given-names>DH</given-names>
</name>
<name><surname>Schleper</surname>
<given-names>C</given-names>
</name>
<etal></etal>
</person-group>
<year>2008</year>
<article-title>Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome.</article-title>
<source>PLoS ONE</source>
<volume>3(6)</volume>
<fpage>e2527</fpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Baldrian3"><label>43</label>
<mixed-citation publication-type="other"><person-group person-group-type="author"><name><surname>Baldrian</surname>
<given-names>P</given-names>
</name>
</person-group>
<year>2008</year>
<article-title>Enzymes of Saprotrophic Basidiomycetes.</article-title>
<person-group person-group-type="editor"><name><surname>Boddy</surname>
<given-names>L</given-names>
</name>
<name><surname>Frankland</surname>
<given-names>J</given-names>
</name>
<name><surname>vanWest</surname>
<given-names>P</given-names>
</name>
</person-group>
<source>Ecology of Saprotrophic Basidiomycetes</source>
<fpage>19</fpage>
<lpage>41</lpage>
<comment>Academic Press, New York</comment>
</mixed-citation>
</ref>
<ref id="pone.0010971-Baldrian4"><label>44</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Baldrian</surname>
<given-names>P</given-names>
</name>
</person-group>
<year>2009</year>
<article-title>Ectomycorrhizal fungi and their enzymes in soils: is there enough evidence for their role as facultative soil saprotrophs?</article-title>
<source>Oecologia</source>
<volume>161</volume>
<fpage>657</fpage>
<lpage>660</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Cullings1"><label>45</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cullings</surname>
<given-names>K</given-names>
</name>
<name><surname>Courty</surname>
<given-names>P-E</given-names>
</name>
</person-group>
<year>2009</year>
<article-title>Saprotrophic capabilities as functional traits to study functional diversity and resilience of ectomycorrhizal community Oecologia</article-title>
<volume>161</volume>
<fpage>661</fpage>
<lpage>664</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-deVries1"><label>46</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>deVries</surname>
<given-names>RP</given-names>
</name>
<name><surname>Visser</surname>
<given-names>J</given-names>
</name>
</person-group>
<year>2001</year>
<article-title><italic>Aspergillus</italic>
 enzymes involved in degradation of plant cell wall polysaccharides.</article-title>
<source>Microbiol Mol Biol Rev</source>
<volume>65</volume>
<fpage>497</fpage>
<lpage>522</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-deVries2"><label>47</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>deVries</surname>
<given-names>W</given-names>
</name>
<name><surname>Solberg</surname>
<given-names>S</given-names>
</name>
<name><surname>Dobbertin</surname>
<given-names>M</given-names>
</name>
<name><surname>Sterba</surname>
<given-names>H</given-names>
</name>
<name><surname>Laubhahn</surname>
<given-names>D</given-names>
</name>
<etal></etal>
</person-group>
<year>2008</year>
<article-title>Ecologically implausible carbon response?</article-title>
<source>Nature</source>
<volume>451</volume>
<fpage>E1</fpage>
<lpage>E3</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Magnani1"><label>48</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Magnani</surname>
<given-names>F</given-names>
</name>
<name><surname>Mencuccini</surname>
<given-names>M</given-names>
</name>
<name><surname>Borghetti</surname>
<given-names>M</given-names>
</name>
<name><surname>Berbigier</surname>
<given-names>P</given-names>
</name>
<name><surname>Berninger</surname>
<given-names>F</given-names>
</name>
<etal></etal>
</person-group>
<year>2007</year>
<article-title>The human footprint in the carbon cycle of temperate and boreal forests.</article-title>
<source>Nature</source>
<volume>447</volume>
<fpage>849</fpage>
<lpage>851</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Sutton1"><label>49</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sutton</surname>
<given-names>MA</given-names>
</name>
<name><surname>Simpson</surname>
<given-names>D</given-names>
</name>
<name><surname>Levy</surname>
<given-names>PE</given-names>
</name>
<name><surname>Smith</surname>
<given-names>RI</given-names>
</name>
<name><surname>Reis</surname>
<given-names>S</given-names>
</name>
<etal></etal>
</person-group>
<year>2008</year>
<article-title>Uncertainties in the relationship between atmospheric nitrogen deposition and forest carbon sequestration.</article-title>
<source>Glob Chang Biol</source>
<volume>14</volume>
<fpage>2057</fpage>
<lpage>2063</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Nadelhoffer1"><label>50</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nadelhoffer</surname>
<given-names>KJ</given-names>
</name>
<name><surname>Emmett</surname>
<given-names>BA</given-names>
</name>
<name><surname>Gundersen</surname>
<given-names>P</given-names>
</name>
<name><surname>Kjønaas</surname>
<given-names>OJ</given-names>
</name>
<name><surname>Koopmans</surname>
<given-names>CJ</given-names>
</name>
<etal></etal>
</person-group>
<year>1999</year>
<article-title>Nitrogen deposition makes a minor contribution to carbon sequestration in temperate forests.</article-title>
<source>Nature</source>
<volume>398</volume>
<fpage>145</fpage>
<lpage>148</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Reay1"><label>51</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Reay</surname>
<given-names>DS</given-names>
</name>
<name><surname>Dentener</surname>
<given-names>F</given-names>
</name>
<name><surname>Smith</surname>
<given-names>P</given-names>
</name>
<name><surname>Grace</surname>
<given-names>J</given-names>
</name>
<name><surname>Feely</surname>
<given-names>RA</given-names>
</name>
</person-group>
<year>2008</year>
<article-title>Global nitrogen deposition and carbon sinks.</article-title>
<source>Nat Geosci</source>
<volume>1</volume>
<fpage>430</fpage>
<lpage>437</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Galloway1"><label>52</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Galloway</surname>
<given-names>JN</given-names>
</name>
<name><surname>Dentener</surname>
<given-names>FJ</given-names>
</name>
<name><surname>Capone</surname>
<given-names>DG</given-names>
</name>
<name><surname>Boyer</surname>
<given-names>EW</given-names>
</name>
<name><surname>Howarth</surname>
<given-names>RW</given-names>
</name>
<etal></etal>
</person-group>
<year>2004</year>
<article-title>Nitrogen cycles: past, present, and future.</article-title>
<source>Biogeochemistry</source>
<volume>70</volume>
<fpage>153</fpage>
<lpage>226</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Boominathan1"><label>53</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Boominathan</surname>
<given-names>K</given-names>
</name>
<name><surname>Dass</surname>
<given-names>SB</given-names>
</name>
<name><surname>Randall</surname>
<given-names>TA</given-names>
</name>
<name><surname>Reddy</surname>
<given-names>CA</given-names>
</name>
</person-group>
<year>1990</year>
<article-title>Nitrogen-deregulated mutants of <italic>Phanerochaete chrysosporium</italic>
 – a lignin-degrading basidiomycete.</article-title>
<source>Arch Microbiol</source>
<volume>153</volume>
<fpage>521</fpage>
<lpage>527</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Vanderwoude1"><label>54</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Vanderwoude</surname>
<given-names>MW</given-names>
</name>
<name><surname>Boominathan</surname>
<given-names>K</given-names>
</name>
<name><surname>Reddy</surname>
<given-names>CA</given-names>
</name>
</person-group>
<year>1993</year>
<article-title>Nitrogen regulation of lignin peroxidase and manganese-dependent peroxidase production is independent of carbon and manganese regulation in <italic>Phanerochaete chrysosporium</italic>
.</article-title>
<source>Arch Microbiol</source>
<volume>160</volume>
<fpage>1</fpage>
<lpage>4</lpage>
</mixed-citation>
</ref>
<ref id="pone.0010971-Hall1"><label>55</label>
<mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hall</surname>
<given-names>TA</given-names>
</name>
</person-group>
<year>1999</year>
<article-title>BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows95/98/NT.</article-title>
<source>Nucleic Acids Symp Ser</source>
<volume>41</volume>
<fpage>95</fpage>
<lpage>98</lpage>
</mixed-citation>
</ref>
</ref-list>
</back>
</pmc>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Wicri/Bois/explor/CheneBelgiqueV2/Data/Pmc/Corpus

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000231 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Pmc/Corpus/biblio.hfd -nk 000231 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Wicri/Bois
   |area=    CheneBelgiqueV2
   |flux=    Pmc
   |étape=   Corpus
   |type=    RBID
   |clé=     PMC:2881045
   |texte=   Fungi Unearthed: Transcripts Encoding Lignocellulolytic and Chitinolytic Enzymes in Forest Soil
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Corpus/RBID.i   -Sk "pubmed:20532045" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Corpus/biblio.hfd   \
       | NlmPubMed2Wicri -a CheneBelgiqueV2

This area was generated with Dilib version V0.6.27.
Data generation: Wed Mar 22 20:06:11 2017. Site generation: Wed Mar 6 16:09:04 2024

	Serveur d'exploration sur le chêne en Belgique
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.

Serveur d'exploration sur le chêne en Belgique

Fungi Unearthed: Transcripts Encoding Lignocellulolytic and Chitinolytic Enzymes in Forest Soil

Fungi Unearthed: Transcripts Encoding Lignocellulolytic and Chitinolytic Enzymes in Forest Soil

Source :

Abstract

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki