Fungi Unearthed: Transcripts Encoding Lignocellulolytic and Chitinolytic Enzymes in Forest Soil
Identifieur interne : 000228 ( Pmc/Checkpoint ); précédent : 000227; suivant : 000229Fungi Unearthed: Transcripts Encoding Lignocellulolytic and Chitinolytic Enzymes in Forest Soil
Auteurs : Harald Kellner ; Micheline VandenbolSource :
- PLoS ONE [ 1932-6203 ] ; 2010.
Abstract
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.
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,
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:
DOI: 10.1371/journal.pone.0010971
PubMed: 20532045
PubMed Central: 2881045
Affiliations:
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<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><idno type="wicri:Area/Pmc/Curation">000231</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000231</idno><idno type="wicri:Area/Pmc/Checkpoint">000228</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000228</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 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<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></pmc><affiliations><list></list><tree><noCountry><name sortKey="Kellner, Harald" sort="Kellner, Harald" uniqKey="Kellner H" first="Harald" last="Kellner">Harald Kellner</name><name sortKey="Vandenbol, Micheline" sort="Vandenbol, Micheline" uniqKey="Vandenbol M" first="Micheline" last="Vandenbol">Micheline Vandenbol</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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