Impact of flooding on soil bacterial communities associated with poplar (Populus sp.) trees.
Identifieur interne : 004016 ( Main/Exploration ); précédent : 004015; suivant : 004017Impact of flooding on soil bacterial communities associated with poplar (Populus sp.) trees.
Auteurs : Andrea Graff [Allemagne] ; Ralf ConradSource :
- FEMS microbiology ecology [ 0168-6496 ] ; 2005.
Descripteurs français
- KwdFr :
- ADN bactérien (analyse), ADN bactérien (génétique), ARN ribosomique 16S (génétique), Analyse de séquence d'ADN (MeSH), Bactéries (classification), Bactéries (génétique), Bactéries (isolement et purification), Catastrophes (MeSH), Fréquence d'allèle (MeSH), Gènes d'ARN ribosomique (MeSH), Microbiologie du sol (MeSH), Phylogenèse (MeSH), Polymorphisme de restriction (MeSH), Populus (microbiologie), Racines de plante (microbiologie).
- MESH :
- analyse : ADN bactérien.
- génétique : ADN bactérien, ARN ribosomique 16S, Bactéries.
- isolement et purification : Bactéries.
- microbiologie : Populus, Racines de plante.
- classification : Analyse de séquence d'ADN, Bactéries, Catastrophes, Fréquence d'allèle, Gènes d'ARN ribosomique, Microbiologie du sol, Phylogenèse, Polymorphisme de restriction.
English descriptors
- KwdEn :
- Bacteria (classification), Bacteria (genetics), Bacteria (isolation & purification), DNA, Bacterial (analysis), DNA, Bacterial (genetics), Disasters (MeSH), Gene Frequency (MeSH), Genes, rRNA (MeSH), Phylogeny (MeSH), Plant Roots (microbiology), Polymorphism, Restriction Fragment Length (MeSH), Populus (microbiology), RNA, Ribosomal, 16S (genetics), Sequence Analysis, DNA (MeSH), Soil Microbiology (MeSH).
- MESH :
- chemical , analysis : DNA, Bacterial.
- classification : Bacteria.
- genetics : Bacteria, DNA, Bacterial, RNA, Ribosomal, 16S.
- isolation & purification : Bacteria.
- microbiology : Plant Roots, Populus.
- Disasters, Gene Frequency, Genes, rRNA, Phylogeny, Polymorphism, Restriction Fragment Length, Sequence Analysis, DNA, Soil Microbiology.
Abstract
Soil bacterial communities were analyzed in different habitats (bulk soil, rhizosphere, rhizoplane) of poplar tree microcosms (Populus tremulaxP. alba) using cultivation-independent methods. The roots of poplar trees regularly experience flooded and anoxic conditions. Therefore, we also determined the effect of flooding on microbial communities in microcosm experiments. Total community DNA was extracted and bacterial 16S rRNA genes were amplified by PCR and analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis, cloning and sequencing. Clone libraries were created from all three habitats under both unflooded and flooded conditions resulting in a total of 281 sequences. Numbers of different sequences (<97% similarity) in the different habitats represented 16-55% of total bacterial species richness determined from the nonparametric richness estimator Chao1. According to the number of different terminal restriction fragments (T-RFs), all of the different habitats contained approximately 20 different operational taxonomic units (OTUs), except the flooded rhizoplane habitat whose community contained less OTUs. Results of cloning and T-RFLP analysis generally supported each other. Correspondence analysis of T-RFLP patterns showed that the bacterial communities were different in bulk soil, rhizosphere and rhizoplane and changed upon flooding. For example OTUs representing Bacillus sp. were highest in the unflooded bulk soil and rhizosphere. Sequences related to Aquaspirillum, in contrast, were predominant on the poplar roots and in the rhizosphere of flooded microcosms but were rarely found in the other habitats.
DOI: 10.1016/j.femsec.2005.01.009
PubMed: 16329959
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Impact of flooding on soil bacterial communities associated with poplar (Populus sp.) trees.</title><author><name sortKey="Graff, Andrea" sort="Graff, Andrea" uniqKey="Graff A" first="Andrea" last="Graff">Andrea Graff</name><affiliation wicri:level="3"><nlm:affiliation>Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043 Marburg, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043 Marburg</wicri:regionArea><placeName><region type="land" nuts="1">Hesse (Land)</region><region type="district" nuts="2">District de Giessen</region><settlement type="city">Marbourg</settlement></placeName></affiliation></author><author><name sortKey="Conrad, Ralf" sort="Conrad, Ralf" uniqKey="Conrad R" first="Ralf" last="Conrad">Ralf Conrad</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2005">2005</date><idno type="RBID">pubmed:16329959</idno><idno type="pmid">16329959</idno><idno type="doi">10.1016/j.femsec.2005.01.009</idno><idno type="wicri:Area/Main/Corpus">003F15</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003F15</idno><idno type="wicri:Area/Main/Curation">003F15</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003F15</idno><idno type="wicri:Area/Main/Exploration">003F15</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Impact of flooding on soil bacterial communities associated with poplar (Populus sp.) trees.</title><author><name sortKey="Graff, Andrea" sort="Graff, Andrea" uniqKey="Graff A" first="Andrea" last="Graff">Andrea Graff</name><affiliation wicri:level="3"><nlm:affiliation>Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043 Marburg, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043 Marburg</wicri:regionArea><placeName><region type="land" nuts="1">Hesse (Land)</region><region type="district" nuts="2">District de Giessen</region><settlement type="city">Marbourg</settlement></placeName></affiliation></author><author><name sortKey="Conrad, Ralf" sort="Conrad, Ralf" uniqKey="Conrad R" first="Ralf" last="Conrad">Ralf Conrad</name></author></analytic><series><title level="j">FEMS microbiology ecology</title><idno type="ISSN">0168-6496</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacteria (classification)</term><term>Bacteria (genetics)</term><term>Bacteria (isolation & purification)</term><term>DNA, Bacterial (analysis)</term><term>DNA, Bacterial (genetics)</term><term>Disasters (MeSH)</term><term>Gene Frequency (MeSH)</term><term>Genes, rRNA (MeSH)</term><term>Phylogeny (MeSH)</term><term>Plant Roots (microbiology)</term><term>Polymorphism, Restriction Fragment Length (MeSH)</term><term>Populus (microbiology)</term><term>RNA, Ribosomal, 16S (genetics)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Soil Microbiology (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN bactérien (analyse)</term><term>ADN bactérien (génétique)</term><term>ARN ribosomique 16S (génétique)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Bactéries (classification)</term><term>Bactéries (génétique)</term><term>Bactéries (isolement et purification)</term><term>Catastrophes (MeSH)</term><term>Fréquence d'allèle (MeSH)</term><term>Gènes d'ARN ribosomique (MeSH)</term><term>Microbiologie du sol (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Polymorphisme de restriction (MeSH)</term><term>Populus (microbiologie)</term><term>Racines de plante (microbiologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>DNA, Bacterial</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>ADN bactérien</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteria</term><term>DNA, Bacterial</term><term>RNA, Ribosomal, 16S</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN bactérien</term><term>ARN ribosomique 16S</term><term>Bactéries</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Bactéries</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Populus</term><term>Racines de plante</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Roots</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Disasters</term><term>Gene Frequency</term><term>Genes, rRNA</term><term>Phylogeny</term><term>Polymorphism, Restriction Fragment Length</term><term>Sequence Analysis, DNA</term><term>Soil Microbiology</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Bactéries</term><term>Catastrophes</term><term>Fréquence d'allèle</term><term>Gènes d'ARN ribosomique</term><term>Microbiologie du sol</term><term>Phylogenèse</term><term>Polymorphisme de restriction</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Soil bacterial communities were analyzed in different habitats (bulk soil, rhizosphere, rhizoplane) of poplar tree microcosms (Populus tremulaxP. alba) using cultivation-independent methods. The roots of poplar trees regularly experience flooded and anoxic conditions. Therefore, we also determined the effect of flooding on microbial communities in microcosm experiments. Total community DNA was extracted and bacterial 16S rRNA genes were amplified by PCR and analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis, cloning and sequencing. Clone libraries were created from all three habitats under both unflooded and flooded conditions resulting in a total of 281 sequences. Numbers of different sequences (<97% similarity) in the different habitats represented 16-55% of total bacterial species richness determined from the nonparametric richness estimator Chao1. According to the number of different terminal restriction fragments (T-RFs), all of the different habitats contained approximately 20 different operational taxonomic units (OTUs), except the flooded rhizoplane habitat whose community contained less OTUs. Results of cloning and T-RFLP analysis generally supported each other. Correspondence analysis of T-RFLP patterns showed that the bacterial communities were different in bulk soil, rhizosphere and rhizoplane and changed upon flooding. For example OTUs representing Bacillus sp. were highest in the unflooded bulk soil and rhizosphere. Sequences related to Aquaspirillum, in contrast, were predominant on the poplar roots and in the rhizosphere of flooded microcosms but were rarely found in the other habitats.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16329959</PMID><DateCompleted><Year>2006</Year><Month>06</Month><Day>01</Day></DateCompleted><DateRevised><Year>2008</Year><Month>11</Month><Day>21</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0168-6496</ISSN><JournalIssue CitedMedium="Print"><Volume>53</Volume><Issue>3</Issue><PubDate><Year>2005</Year><Month>Aug</Month><Day>01</Day></PubDate></JournalIssue><Title>FEMS microbiology ecology</Title><ISOAbbreviation>FEMS Microbiol Ecol</ISOAbbreviation></Journal><ArticleTitle>Impact of flooding on soil bacterial communities associated with poplar (Populus sp.) trees.</ArticleTitle><Pagination><MedlinePgn>401-15</MedlinePgn></Pagination><Abstract><AbstractText>Soil bacterial communities were analyzed in different habitats (bulk soil, rhizosphere, rhizoplane) of poplar tree microcosms (Populus tremulaxP. alba) using cultivation-independent methods. The roots of poplar trees regularly experience flooded and anoxic conditions. Therefore, we also determined the effect of flooding on microbial communities in microcosm experiments. Total community DNA was extracted and bacterial 16S rRNA genes were amplified by PCR and analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis, cloning and sequencing. Clone libraries were created from all three habitats under both unflooded and flooded conditions resulting in a total of 281 sequences. Numbers of different sequences (<97% similarity) in the different habitats represented 16-55% of total bacterial species richness determined from the nonparametric richness estimator Chao1. According to the number of different terminal restriction fragments (T-RFs), all of the different habitats contained approximately 20 different operational taxonomic units (OTUs), except the flooded rhizoplane habitat whose community contained less OTUs. Results of cloning and T-RFLP analysis generally supported each other. Correspondence analysis of T-RFLP patterns showed that the bacterial communities were different in bulk soil, rhizosphere and rhizoplane and changed upon flooding. For example OTUs representing Bacillus sp. were highest in the unflooded bulk soil and rhizosphere. Sequences related to Aquaspirillum, in contrast, were predominant on the poplar roots and in the rhizosphere of flooded microcosms but were rarely found in the other habitats.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Graff</LastName><ForeName>Andrea</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043 Marburg, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Conrad</LastName><ForeName>Ralf</ForeName><Initials>R</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>FEMS Microbiol Ecol</MedlineTA><NlmUniqueID>8901229</NlmUniqueID><ISSNLinking>0168-6496</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004269">DNA, Bacterial</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012336">RNA, Ribosomal, 16S</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001419" MajorTopicYN="N">Bacteria</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004269" MajorTopicYN="N">DNA, Bacterial</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="N">analysis</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004190" MajorTopicYN="Y">Disasters</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005787" MajorTopicYN="N">Gene Frequency</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020459" MajorTopicYN="N">Genes, rRNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012150" MajorTopicYN="N">Polymorphism, Restriction Fragment Length</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012336" MajorTopicYN="N">RNA, Ribosomal, 16S</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012988" MajorTopicYN="Y">Soil Microbiology</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2004</Year><Month>10</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2005</Year><Month>01</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2005</Year><Month>01</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2005</Year><Month>12</Month><Day>7</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2006</Year><Month>6</Month><Day>2</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2005</Year><Month>12</Month><Day>7</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16329959</ArticleId><ArticleId IdType="pii">S0168-6496(05)00034-6</ArticleId><ArticleId IdType="doi">10.1016/j.femsec.2005.01.009</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Allemagne</li></country><region><li>District de Giessen</li><li>Hesse (Land)</li></region><settlement><li>Marbourg</li></settlement></list><tree><noCountry><name sortKey="Conrad, Ralf" sort="Conrad, Ralf" uniqKey="Conrad R" first="Ralf" last="Conrad">Ralf Conrad</name></noCountry><country name="Allemagne"><region name="Hesse (Land)"><name sortKey="Graff, Andrea" sort="Graff, Andrea" uniqKey="Graff A" first="Andrea" last="Graff">Andrea Graff</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PoplarV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 004016 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 004016 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PoplarV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:16329959
|texte= Impact of flooding on soil bacterial communities associated with poplar (Populus sp.) trees.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:16329959" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |