Microbial expression profiles in the rhizosphere of willows depend on soil contamination.
Identifieur interne : 001219 ( Main/Corpus ); précédent : 001218; suivant : 001220Microbial expression profiles in the rhizosphere of willows depend on soil contamination.
Auteurs : Etienne Yergeau ; Sylvie Sanschagrin ; Christine Maynard ; Marc St-Arnaud ; Charles W. GreerSource :
- The ISME journal [ 1751-7370 ] ; 2014.
English descriptors
- KwdEn :
- Amino Acids (metabolism), Biodegradation, Environmental (MeSH), Carbon (metabolism), Gene Expression Profiling (MeSH), Gene Expression Regulation (drug effects), Hydrocarbons (metabolism), Nitrogen Cycle (genetics), Plant Roots (microbiology), RNA, Ribosomal, 16S (genetics), Rhizosphere (MeSH), Salix (microbiology), Salix (physiology), Soil (chemistry), Soil Microbiology (MeSH), Soil Pollutants (metabolism), Soil Pollutants (pharmacology).
- MESH :
- chemical , chemistry : Soil.
- chemical , genetics : RNA, Ribosomal, 16S.
- chemical , metabolism : Amino Acids, Carbon, Hydrocarbons, Soil Pollutants.
- drug effects : Gene Expression Regulation.
- genetics : Nitrogen Cycle.
- microbiology : Plant Roots, Salix.
- chemical , pharmacology : Soil Pollutants.
- physiology : Salix.
- Biodegradation, Environmental, Gene Expression Profiling, Rhizosphere, Soil Microbiology.
Abstract
The goal of phytoremediation is to use plants to immobilize, extract or degrade organic and inorganic pollutants. In the case of organic contaminants, plants essentially act indirectly through the stimulation of rhizosphere microorganisms. A detailed understanding of the effect plants have on the activities of rhizosphere microorganisms could help optimize phytoremediation systems and enhance their use. In this study, willows were planted in contaminated and non-contaminated soils in a greenhouse, and the active microbial communities and the expression of functional genes in the rhizosphere and bulk soil were compared. Ion Torrent sequencing of 16S rRNA and Illumina sequencing of mRNA were performed. Genes related to carbon and amino-acid uptake and utilization were upregulated in the willow rhizosphere, providing indirect evidence of the compositional content of the root exudates. Related to this increased nutrient input, several microbial taxa showed a significant increase in activity in the rhizosphere. The extent of the rhizosphere stimulation varied markedly with soil contamination levels. The combined selective pressure of contaminants and rhizosphere resulted in higher expression of genes related to competition (antibiotic resistance and biofilm formation) in the contaminated rhizosphere. Genes related to hydrocarbon degradation were generally more expressed in contaminated soils, but the exact complement of genes induced was different for bulk and rhizosphere soils. Together, these results provide an unprecedented view of microbial gene expression in the plant rhizosphere during phytoremediation.
DOI: 10.1038/ismej.2013.163
PubMed: 24067257
PubMed Central: PMC3906822
Links to Exploration step
pubmed:24067257Le document en format XML
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Greer</name><affiliation><nlm:affiliation>National Research Council Canada, Energy, Mining and Environment, Montreal, Quebec, Canada.</nlm:affiliation></affiliation></author></analytic><series><title level="j">The ISME journal</title><idno type="eISSN">1751-7370</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acids (metabolism)</term><term>Biodegradation, Environmental (MeSH)</term><term>Carbon (metabolism)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation (drug effects)</term><term>Hydrocarbons (metabolism)</term><term>Nitrogen Cycle (genetics)</term><term>Plant Roots (microbiology)</term><term>RNA, Ribosomal, 16S (genetics)</term><term>Rhizosphere (MeSH)</term><term>Salix (microbiology)</term><term>Salix (physiology)</term><term>Soil (chemistry)</term><term>Soil Microbiology (MeSH)</term><term>Soil Pollutants (metabolism)</term><term>Soil Pollutants (pharmacology)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Soil</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Ribosomal, 16S</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Amino Acids</term><term>Carbon</term><term>Hydrocarbons</term><term>Soil Pollutants</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>Gene Expression Regulation</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Nitrogen Cycle</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Roots</term><term>Salix</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Soil Pollutants</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Salix</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biodegradation, Environmental</term><term>Gene Expression Profiling</term><term>Rhizosphere</term><term>Soil Microbiology</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The goal of phytoremediation is to use plants to immobilize, extract or degrade organic and inorganic pollutants. In the case of organic contaminants, plants essentially act indirectly through the stimulation of rhizosphere microorganisms. A detailed understanding of the effect plants have on the activities of rhizosphere microorganisms could help optimize phytoremediation systems and enhance their use. In this study, willows were planted in contaminated and non-contaminated soils in a greenhouse, and the active microbial communities and the expression of functional genes in the rhizosphere and bulk soil were compared. Ion Torrent sequencing of 16S rRNA and Illumina sequencing of mRNA were performed. Genes related to carbon and amino-acid uptake and utilization were upregulated in the willow rhizosphere, providing indirect evidence of the compositional content of the root exudates. Related to this increased nutrient input, several microbial taxa showed a significant increase in activity in the rhizosphere. The extent of the rhizosphere stimulation varied markedly with soil contamination levels. The combined selective pressure of contaminants and rhizosphere resulted in higher expression of genes related to competition (antibiotic resistance and biofilm formation) in the contaminated rhizosphere. Genes related to hydrocarbon degradation were generally more expressed in contaminated soils, but the exact complement of genes induced was different for bulk and rhizosphere soils. Together, these results provide an unprecedented view of microbial gene expression in the plant rhizosphere during phytoremediation. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">24067257</PMID><DateCompleted><Year>2014</Year><Month>04</Month><Day>03</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>05</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1751-7370</ISSN><JournalIssue CitedMedium="Internet"><Volume>8</Volume><Issue>2</Issue><PubDate><Year>2014</Year><Month>Feb</Month></PubDate></JournalIssue><Title>The ISME journal</Title><ISOAbbreviation>ISME J</ISOAbbreviation></Journal><ArticleTitle>Microbial expression profiles in the rhizosphere of willows depend on soil contamination.</ArticleTitle><Pagination><MedlinePgn>344-58</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/ismej.2013.163</ELocationID><Abstract><AbstractText>The goal of phytoremediation is to use plants to immobilize, extract or degrade organic and inorganic pollutants. In the case of organic contaminants, plants essentially act indirectly through the stimulation of rhizosphere microorganisms. A detailed understanding of the effect plants have on the activities of rhizosphere microorganisms could help optimize phytoremediation systems and enhance their use. In this study, willows were planted in contaminated and non-contaminated soils in a greenhouse, and the active microbial communities and the expression of functional genes in the rhizosphere and bulk soil were compared. Ion Torrent sequencing of 16S rRNA and Illumina sequencing of mRNA were performed. Genes related to carbon and amino-acid uptake and utilization were upregulated in the willow rhizosphere, providing indirect evidence of the compositional content of the root exudates. Related to this increased nutrient input, several microbial taxa showed a significant increase in activity in the rhizosphere. The extent of the rhizosphere stimulation varied markedly with soil contamination levels. The combined selective pressure of contaminants and rhizosphere resulted in higher expression of genes related to competition (antibiotic resistance and biofilm formation) in the contaminated rhizosphere. Genes related to hydrocarbon degradation were generally more expressed in contaminated soils, but the exact complement of genes induced was different for bulk and rhizosphere soils. 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