Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing.
Identifieur interne : 000927 ( Main/Corpus ); précédent : 000926; suivant : 000928Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing.
Auteurs : Loreen Sommermann ; Joerg Geistlinger ; Daniel Wibberg ; Annette Deubel ; Jessica Zwanzig ; Doreen Babin ; Andreas Schlüter ; Ingo SchellenbergSource :
- PloS one [ 1932-6203 ] ; 2018.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Soil.
- methods : Agriculture, Crop Production.
- microbiology : Crops, Agricultural.
- physiology : Mycorrhizae.
- Farms, Fungi, Germany, Soil Microbiology.
Abstract
Fungal communities in agricultural soils are assumed to be affected by soil and crop management. Our intention was to investigate the impact of different tillage and fertilization practices on fungal communities in a long-term crop rotation field trial established in 1992 in Central Germany. Two winter wheat fields in replicated strip-tillage design, comprising conventional vs. conservation tillage, intensive vs. extensive fertilization and different pre-crops (maize vs. rapeseed) were analyzed by a metabarcoding approach applying Illumina paired-end sequencing of amplicons generated by two recently developed primer pairs targeting the two fungal Internal Transcribed Spacer regions (ITS1, ITS2). Analysis of 5.1 million high-quality sequence reads uncovered a diverse fungal community in the two fields, composed of 296 fungal genera including 3,398 Operational Taxonomic Units (OTUs) at the 97% sequence similarity threshold. Both primer pairs detected the same fungal phyla (Basidio-, Asco-, Zygo-, Glomero- and Chytridiomycota), but in different relative abundances. OTU richness was higher in the ITS1 dataset, while ITS2 data were more diverse and of higher evenness. Effects of farming practice on fungal community structures were revealed. Almost two-thirds of the fungal genera were represented in all different soil treatments, whereas the remaining genera clearly responded to farming practice. Principal Component Analysis revealed four distinct clusters according to tillage practice and pre-crop. Analysis of Variance (ANOVA) substantiated the results and proved significant influences of tillage and pre-crop, while fertilization had the smallest and non-significant effect. In-depth analysis of putative phytopathogenic and plant beneficial fungal groups indicated distinct responses; for example Fusarium was significantly enriched in the intensively fertilized conservation tillage variants with the pre-crop maize, while Phoma displayed significant association with conventional tillage and pre-crop rapeseed. Many putative plant beneficial fungi also reacted differentially to farming practice with the most distinct responders identified among the Glomeromycota (arbuscular mycorrhizal fungi, AMF).
DOI: 10.1371/journal.pone.0195345
PubMed: 29621291
PubMed Central: PMC5886558
Links to Exploration step
pubmed:29621291Le document en format XML
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Bernburg, Saxony-Anhalt, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Geistlinger, Joerg" sort="Geistlinger, Joerg" uniqKey="Geistlinger J" first="Joerg" last="Geistlinger">Joerg Geistlinger</name><affiliation><nlm:affiliation>Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Wibberg, Daniel" sort="Wibberg, Daniel" uniqKey="Wibberg D" first="Daniel" last="Wibberg">Daniel Wibberg</name><affiliation><nlm:affiliation>Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms (GRIM), Bielefeld University, Bielefeld, North Rhine-Westphalia, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Deubel, Annette" sort="Deubel, Annette" uniqKey="Deubel A" first="Annette" last="Deubel">Annette Deubel</name><affiliation><nlm:affiliation>Department of Agriculture, Ecotrophology and Landscape Development, Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Zwanzig, Jessica" sort="Zwanzig, Jessica" uniqKey="Zwanzig J" first="Jessica" last="Zwanzig">Jessica Zwanzig</name><affiliation><nlm:affiliation>Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Babin, Doreen" sort="Babin, Doreen" uniqKey="Babin D" first="Doreen" last="Babin">Doreen Babin</name><affiliation><nlm:affiliation>Institute for Epidemiology and Pathogen Diagnostics, Julius-Kühn-Institut-Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Lower Saxony, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Schluter, Andreas" sort="Schluter, Andreas" uniqKey="Schluter A" first="Andreas" last="Schlüter">Andreas Schlüter</name><affiliation><nlm:affiliation>Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms (GRIM), Bielefeld University, Bielefeld, North Rhine-Westphalia, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Schellenberg, Ingo" sort="Schellenberg, Ingo" uniqKey="Schellenberg I" first="Ingo" last="Schellenberg">Ingo Schellenberg</name><affiliation><nlm:affiliation>Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany.</nlm:affiliation></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Agriculture (methods)</term><term>Crop Production (methods)</term><term>Crops, Agricultural (microbiology)</term><term>Farms (MeSH)</term><term>Fungi (MeSH)</term><term>Germany (MeSH)</term><term>Mycorrhizae (physiology)</term><term>Soil (chemistry)</term><term>Soil Microbiology (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Soil</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Agriculture</term><term>Crop Production</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Crops, Agricultural</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Mycorrhizae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Farms</term><term>Fungi</term><term>Germany</term><term>Soil Microbiology</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Fungal communities in agricultural soils are assumed to be affected by soil and crop management. Our intention was to investigate the impact of different tillage and fertilization practices on fungal communities in a long-term crop rotation field trial established in 1992 in Central Germany. Two winter wheat fields in replicated strip-tillage design, comprising conventional vs. conservation tillage, intensive vs. extensive fertilization and different pre-crops (maize vs. rapeseed) were analyzed by a metabarcoding approach applying Illumina paired-end sequencing of amplicons generated by two recently developed primer pairs targeting the two fungal Internal Transcribed Spacer regions (ITS1, ITS2). Analysis of 5.1 million high-quality sequence reads uncovered a diverse fungal community in the two fields, composed of 296 fungal genera including 3,398 Operational Taxonomic Units (OTUs) at the 97% sequence similarity threshold. Both primer pairs detected the same fungal phyla (Basidio-, Asco-, Zygo-, Glomero- and Chytridiomycota), but in different relative abundances. OTU richness was higher in the ITS1 dataset, while ITS2 data were more diverse and of higher evenness. Effects of farming practice on fungal community structures were revealed. Almost two-thirds of the fungal genera were represented in all different soil treatments, whereas the remaining genera clearly responded to farming practice. Principal Component Analysis revealed four distinct clusters according to tillage practice and pre-crop. Analysis of Variance (ANOVA) substantiated the results and proved significant influences of tillage and pre-crop, while fertilization had the smallest and non-significant effect. In-depth analysis of putative phytopathogenic and plant beneficial fungal groups indicated distinct responses; for example Fusarium was significantly enriched in the intensively fertilized conservation tillage variants with the pre-crop maize, while Phoma displayed significant association with conventional tillage and pre-crop rapeseed. Many putative plant beneficial fungi also reacted differentially to farming practice with the most distinct responders identified among the Glomeromycota (arbuscular mycorrhizal fungi, AMF).</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29621291</PMID><DateCompleted><Year>2018</Year><Month>08</Month><Day>06</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>14</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>13</Volume><Issue>4</Issue><PubDate><Year>2018</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing.</ArticleTitle><Pagination><MedlinePgn>e0195345</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0195345</ELocationID><Abstract><AbstractText>Fungal communities in agricultural soils are assumed to be affected by soil and crop management. Our intention was to investigate the impact of different tillage and fertilization practices on fungal communities in a long-term crop rotation field trial established in 1992 in Central Germany. Two winter wheat fields in replicated strip-tillage design, comprising conventional vs. conservation tillage, intensive vs. extensive fertilization and different pre-crops (maize vs. rapeseed) were analyzed by a metabarcoding approach applying Illumina paired-end sequencing of amplicons generated by two recently developed primer pairs targeting the two fungal Internal Transcribed Spacer regions (ITS1, ITS2). Analysis of 5.1 million high-quality sequence reads uncovered a diverse fungal community in the two fields, composed of 296 fungal genera including 3,398 Operational Taxonomic Units (OTUs) at the 97% sequence similarity threshold. Both primer pairs detected the same fungal phyla (Basidio-, Asco-, Zygo-, Glomero- and Chytridiomycota), but in different relative abundances. OTU richness was higher in the ITS1 dataset, while ITS2 data were more diverse and of higher evenness. Effects of farming practice on fungal community structures were revealed. Almost two-thirds of the fungal genera were represented in all different soil treatments, whereas the remaining genera clearly responded to farming practice. Principal Component Analysis revealed four distinct clusters according to tillage practice and pre-crop. Analysis of Variance (ANOVA) substantiated the results and proved significant influences of tillage and pre-crop, while fertilization had the smallest and non-significant effect. In-depth analysis of putative phytopathogenic and plant beneficial fungal groups indicated distinct responses; for example Fusarium was significantly enriched in the intensively fertilized conservation tillage variants with the pre-crop maize, while Phoma displayed significant association with conventional tillage and pre-crop rapeseed. Many putative plant beneficial fungi also reacted differentially to farming practice with the most distinct responders identified among the Glomeromycota (arbuscular mycorrhizal fungi, AMF).</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sommermann</LastName><ForeName>Loreen</ForeName><Initials>L</Initials><Identifier Source="ORCID">0000-0002-6293-877X</Identifier><AffiliationInfo><Affiliation>Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Geistlinger</LastName><ForeName>Joerg</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wibberg</LastName><ForeName>Daniel</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms (GRIM), Bielefeld University, Bielefeld, North Rhine-Westphalia, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Deubel</LastName><ForeName>Annette</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Agriculture, Ecotrophology and Landscape Development, Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zwanzig</LastName><ForeName>Jessica</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Babin</LastName><ForeName>Doreen</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Institute for Epidemiology and Pathogen Diagnostics, Julius-Kühn-Institut-Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Lower Saxony, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schlüter</LastName><ForeName>Andreas</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms (GRIM), Bielefeld University, Bielefeld, North Rhine-Westphalia, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schellenberg</LastName><ForeName>Ingo</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>04</Month><Day>05</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012987">Soil</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000383" MajorTopicYN="N">Agriculture</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000069599" MajorTopicYN="N">Crop 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HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Corpus/RBID.i -Sk "pubmed:29621291" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Corpus/biblio.hfd \
| NlmPubMed2Wicri -a MycorrhizaeV1
| This area was generated with Dilib version V0.6.37. |  |