Secondary successional trajectories of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid poplar.
Identifieur interne : 001E60 ( Main/Corpus ); précédent : 001E59; suivant : 001E61Secondary successional trajectories of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid poplar.
Auteurs : Shinjini Mukherjee ; Timo Sipil ; Pertti Pulkkinen ; Kim Yrj LSource :
- Molecular ecology [ 1365-294X ] ; 2015.
English descriptors
- KwdEn :
- Bacteria (classification), Bacteria (genetics), Biodegradation, Environmental (MeSH), Biodiversity (MeSH), Cytochrome P-450 CYP4A (genetics), DNA, Bacterial (genetics), Microbial Consortia (MeSH), Oxygenases (genetics), Petroleum Pollution (MeSH), Phylogeny (MeSH), Populus (MeSH), RNA, Ribosomal, 16S (genetics), Rhizosphere (MeSH), Sequence Analysis, DNA (MeSH), Soil Microbiology (MeSH), Soil Pollutants (MeSH).
- MESH :
- chemical , genetics : Cytochrome P-450 CYP4A, DNA, Bacterial, Oxygenases, RNA, Ribosomal, 16S.
- classification : Bacteria.
- genetics : Bacteria.
- Biodegradation, Environmental, Biodiversity, Microbial Consortia, Petroleum Pollution, Phylogeny, Populus, Rhizosphere, Sequence Analysis, DNA, Soil Microbiology, Soil Pollutants.
Abstract
Poplars have widely been used for rhizoremediation of a broad range of organic contaminants for the past two decades. Still, there is a knowledge gap regarding the rhizosphere-associated bacterial communities of poplars and their dynamics during the remediation process. It is envisaged that a detailed understanding of rhizosphere-associated microbial populations will greatly contribute to a better design and implementation of rhizoremediation. To investigate the long-term succession of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula × Populus tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at seven different time points during the course of 2 years and sampling time points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing, whereas catabolic diversity was monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late-phase communities. Sphingomonas type extradiol dioxygenases and alkane hydroxylase homologs of Rhodococcus clearly dominated the early-phase communities. The high-dominance/low-diversity functional gene communities underwent a transition to low-dominance/high-diversity communities in the late phase. These results pointed towards increased catabolic capacities and a change from specialist to generalist strategy of bacterial communities during the course of secondary succession.
DOI: 10.1111/mec.13053
PubMed: 25545194
Links to Exploration step
pubmed:25545194Le document en format XML
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Still, there is a knowledge gap regarding the rhizosphere-associated bacterial communities of poplars and their dynamics during the remediation process. It is envisaged that a detailed understanding of rhizosphere-associated microbial populations will greatly contribute to a better design and implementation of rhizoremediation. To investigate the long-term succession of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula × Populus tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at seven different time points during the course of 2 years and sampling time points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing, whereas catabolic diversity was monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late-phase communities. Sphingomonas type extradiol dioxygenases and alkane hydroxylase homologs of Rhodococcus clearly dominated the early-phase communities. The high-dominance/low-diversity functional gene communities underwent a transition to low-dominance/high-diversity communities in the late phase. These results pointed towards increased catabolic capacities and a change from specialist to generalist strategy of bacterial communities during the course of secondary succession.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25545194</PMID><DateCompleted><Year>2015</Year><Month>08</Month><Day>20</Day></DateCompleted><DateRevised><Year>2018</Year><Month>08</Month><Day>08</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1365-294X</ISSN><JournalIssue CitedMedium="Internet"><Volume>24</Volume><Issue>3</Issue><PubDate><Year>2015</Year><Month>Feb</Month></PubDate></JournalIssue><Title>Molecular ecology</Title><ISOAbbreviation>Mol Ecol</ISOAbbreviation></Journal><ArticleTitle>Secondary successional trajectories of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid poplar.</ArticleTitle><Pagination><MedlinePgn>628-42</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/mec.13053</ELocationID><Abstract><AbstractText>Poplars have widely been used for rhizoremediation of a broad range of organic contaminants for the past two decades. Still, there is a knowledge gap regarding the rhizosphere-associated bacterial communities of poplars and their dynamics during the remediation process. It is envisaged that a detailed understanding of rhizosphere-associated microbial populations will greatly contribute to a better design and implementation of rhizoremediation. To investigate the long-term succession of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula × Populus tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at seven different time points during the course of 2 years and sampling time points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing, whereas catabolic diversity was monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late-phase communities. Sphingomonas type extradiol dioxygenases and alkane hydroxylase homologs of Rhodococcus clearly dominated the early-phase communities. The high-dominance/low-diversity functional gene communities underwent a transition to low-dominance/high-diversity communities in the late phase. These results pointed towards increased catabolic capacities and a change from specialist to generalist strategy of bacterial communities during the course of secondary succession.</AbstractText><CopyrightInformation>© 2014 John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Mukherjee</LastName><ForeName>Shinjini</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Biosciences, MEM-Group, University of Helsinki, PO Box 56, FI-00014, Helsinki, Finland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sipilä</LastName><ForeName>Timo</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Pulkkinen</LastName><ForeName>Pertti</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Yrjälä</LastName><ForeName>Kim</ForeName><Initials>K</Initials></Author></AuthorList><Language>eng</Language><DataBankList 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Pollutants</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 1.13.-</RegistryNumber><NameOfSubstance UI="D010105">Oxygenases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 1.14.15.3</RegistryNumber><NameOfSubstance UI="D042926">Cytochrome P-450 CYP4A</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 1.14.99.-</RegistryNumber><NameOfSubstance UI="C439587">extradiol dioxygenase</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></MeshHeading><MeshHeading><DescriptorName UI="D001673" MajorTopicYN="N">Biodegradation, Environmental</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D044822" MajorTopicYN="Y">Biodiversity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D042926" MajorTopicYN="N">Cytochrome P-450 CYP4A</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004269" MajorTopicYN="N">DNA, Bacterial</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059013" MajorTopicYN="N">Microbial Consortia</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010105" MajorTopicYN="N">Oxygenases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059392" MajorTopicYN="Y">Petroleum Pollution</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="Y">Populus</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012336" MajorTopicYN="N">RNA, Ribosomal, 16S</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D058441" MajorTopicYN="N">Rhizosphere</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012988" MajorTopicYN="Y">Soil Microbiology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012989" MajorTopicYN="Y">Soil Pollutants</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Populus</Keyword><Keyword MajorTopicYN="N">alkane monooxygenase</Keyword><Keyword MajorTopicYN="N">extradiol dioxygenase</Keyword><Keyword MajorTopicYN="N">field study</Keyword><Keyword MajorTopicYN="N">petroleum hydrocarbons</Keyword><Keyword MajorTopicYN="N">pyrosequencing</Keyword><Keyword MajorTopicYN="N">secondary succession</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>06</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2014</Year><Month>12</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>12</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>12</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>12</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>8</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25545194</ArticleId><ArticleId IdType="doi">10.1111/mec.13053</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce 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