Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil
Identifieur interne : 000376 ( Istex/Corpus ); précédent : 000375; suivant : 000377Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil
Auteurs : Alexandre De Menezes ; Nicholas Clipson ; Evelyn DoyleSource :
- Environmental Microbiology [ 1462-2912 ] ; 2012-09.
Abstract
Soil microbial community response to phenanthrene was evaluated by metatranscriptomics. A marked increase in transcripts involved in aromatic compound metabolism, respiration and stress responses, and concurrent decreases in virulence, carbohydrate, DNA metabolism and phosphorus metabolism transcripts was revealed. Phenanthrene addition led to a 1.8‐fold to 33‐fold increase in the abundance of dioxygenase, stress response and detoxification transcripts, whereas those of general metabolism were little affected. Heavy metal P‐type ATPases and thioredoxin transcripts were more abundant in the phenanthrene‐amended soil, and this is the first time these proteins have been associated with polycyclic aromatic hydrocarbon (PAH) stress in microorganisms. Annotation with custom databases constructed with bacterial or fungal PAH metabolism protein sequences showed that increases in PAH‐degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed widespread changes in the bacteria, archaea and fungi, and the actinobacteria were responsible for most of the de novo expression of transcripts associated with dioxygenases, stress response and detoxification genes. This is the first report of an experimental metatranscriptomic study detailing microbial community responses to a pollutant in soil, and offers information on novel in situ effects of PAHs on soil microbes that can be explored further.
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DOI: 10.1111/j.1462-2920.2012.02781.x
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<front><div type="abstract" xml:lang="en">Soil microbial community response to phenanthrene was evaluated by metatranscriptomics. A marked increase in transcripts involved in aromatic compound metabolism, respiration and stress responses, and concurrent decreases in virulence, carbohydrate, DNA metabolism and phosphorus metabolism transcripts was revealed. Phenanthrene addition led to a 1.8‐fold to 33‐fold increase in the abundance of dioxygenase, stress response and detoxification transcripts, whereas those of general metabolism were little affected. Heavy metal P‐type ATPases and thioredoxin transcripts were more abundant in the phenanthrene‐amended soil, and this is the first time these proteins have been associated with polycyclic aromatic hydrocarbon (PAH) stress in microorganisms. Annotation with custom databases constructed with bacterial or fungal PAH metabolism protein sequences showed that increases in PAH‐degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed widespread changes in the bacteria, archaea and fungi, and the actinobacteria were responsible for most of the de novo expression of transcripts associated with dioxygenases, stress response and detoxification genes. This is the first report of an experimental metatranscriptomic study detailing microbial community responses to a pollutant in soil, and offers information on novel in situ effects of PAHs on soil microbes that can be explored further.</div>
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<supportingInformation><p><b>Table S1A.</b>
Protein sequence GenBank accessions for sequences used in the bacterial custom database.</p>
<p><b>Table S1B.</b>
References for PAH metabolism protein sequences used in the bacterial custom database.</p>
<p><b>Table S2A.</b>
GenBank accessions of protein sequences used to construct fungal custom database.</p>
<p><b>Table S2B.</b>
References for fungal PAH metabolism protein sequences used in the bacterial custom database.</p>
<p><b>Table S3.</b>
Absolute numbers of non‐rRNA sequences classified to bacterial, archaeal and fungal classes determined by BLASTn and MEGAN analysis. Presented here are the absolute numbers of reads (non‐normalized).</p>
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<p>Soil microbial community response to phenanthrene was evaluated by metatranscriptomics. A marked increase in transcripts involved in aromatic compound metabolism, respiration and stress responses, and concurrent decreases in virulence, carbohydrate, DNA metabolism and phosphorus metabolism transcripts was revealed. Phenanthrene addition led to a 1.8‐fold to 33‐fold increase in the abundance of dioxygenase, stress response and detoxification transcripts, whereas those of general metabolism were little affected. Heavy metal P‐type ATPases and thioredoxin transcripts were more abundant in the phenanthrene‐amended soil, and this is the first time these proteins have been associated with polycyclic aromatic hydrocarbon (PAH) stress in microorganisms. Annotation with custom databases constructed with bacterial or fungal PAH metabolism protein sequences showed that increases in PAH‐degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed widespread changes in the bacteria, archaea and fungi, and the actinobacteria were responsible for most of the <i>de novo</i>
expression of transcripts associated with dioxygenases, stress response and detoxification genes. This is the first report of an experimental metatranscriptomic study detailing microbial community responses to a pollutant in soil, and offers information on novel <i>in situ</i>
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<abstract lang="en">Soil microbial community response to phenanthrene was evaluated by metatranscriptomics. A marked increase in transcripts involved in aromatic compound metabolism, respiration and stress responses, and concurrent decreases in virulence, carbohydrate, DNA metabolism and phosphorus metabolism transcripts was revealed. Phenanthrene addition led to a 1.8‐fold to 33‐fold increase in the abundance of dioxygenase, stress response and detoxification transcripts, whereas those of general metabolism were little affected. Heavy metal P‐type ATPases and thioredoxin transcripts were more abundant in the phenanthrene‐amended soil, and this is the first time these proteins have been associated with polycyclic aromatic hydrocarbon (PAH) stress in microorganisms. Annotation with custom databases constructed with bacterial or fungal PAH metabolism protein sequences showed that increases in PAH‐degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed widespread changes in the bacteria, archaea and fungi, and the actinobacteria were responsible for most of the de novo expression of transcripts associated with dioxygenases, stress response and detoxification genes. This is the first report of an experimental metatranscriptomic study detailing microbial community responses to a pollutant in soil, and offers information on novel in situ effects of PAHs on soil microbes that can be explored further.</abstract>
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<note type="content"> Table S1A. Protein sequence GenBank accessions for sequences used in the bacterial custom database. Table S1B. References for PAH metabolism protein sequences used in the bacterial custom database. Table S2A. GenBank accessions of protein sequences used to construct fungal custom database. Table S2B. References for fungal PAH metabolism protein sequences used in the bacterial custom database. Table S3. Absolute numbers of non‐rRNA sequences classified to bacterial, archaeal and fungal classes determined by BLASTn and MEGAN analysis. Presented here are the absolute numbers of reads (non‐normalized). Table S1A. Protein sequence GenBank accessions for sequences used in the bacterial custom database. Table S1B. References for PAH metabolism protein sequences used in the bacterial custom database. Table S2A. GenBank accessions of protein sequences used to construct fungal custom database. Table S2B. References for fungal PAH metabolism protein sequences used in the bacterial custom database. Table S3. Absolute numbers of non‐rRNA sequences classified to bacterial, archaeal and fungal classes determined by BLASTn and MEGAN analysis. Presented here are the absolute numbers of reads (non‐normalized). Table S1A. Protein sequence GenBank accessions for sequences used in the bacterial custom database. Table S1B. References for PAH metabolism protein sequences used in the bacterial custom database. Table S2A. GenBank accessions of protein sequences used to construct fungal custom database. Table S2B. References for fungal PAH metabolism protein sequences used in the bacterial custom database. Table S3. Absolute numbers of non‐rRNA sequences classified to bacterial, archaeal and fungal classes determined by BLASTn and MEGAN analysis. Presented here are the absolute numbers of reads (non‐normalized). Table S1A. Protein sequence GenBank accessions for sequences used in the bacterial custom database. Table S1B. References for PAH metabolism protein sequences used in the bacterial custom database. Table S2A. GenBank accessions of protein sequences used to construct fungal custom database. Table S2B. References for fungal PAH metabolism protein sequences used in the bacterial custom database. Table S3. Absolute numbers of non‐rRNA sequences classified to bacterial, archaeal and fungal classes determined by BLASTn and MEGAN analysis. Presented here are the absolute numbers of reads (non‐normalized). Table S1A. Protein sequence GenBank accessions for sequences used in the bacterial custom database. Table S1B. References for PAH metabolism protein sequences used in the bacterial custom database. Table S2A. GenBank accessions of protein sequences used to construct fungal custom database. Table S2B. References for fungal PAH metabolism protein sequences used in the bacterial custom database. Table S3. Absolute numbers of non‐rRNA sequences classified to bacterial, archaeal and fungal classes determined by BLASTn and MEGAN analysis. Presented here are the absolute numbers of reads (non‐normalized).Supporting Info Item: Supporting info item - </note>
<identifier type="ISSN">1462-2912</identifier>
<identifier type="eISSN">1462-2920</identifier>
<identifier type="DOI">10.1111/(ISSN)1462-2920</identifier>
<identifier type="PublisherID">EMI</identifier>
<part><date>2012</date>
<detail type="title"><title>Microbial Communities ‐ Structure, Behaviour, Evolution</title>
</detail>
<detail type="volume"><caption>vol.</caption>
<number>14</number>
</detail>
<detail type="issue"><caption>no.</caption>
<number>9</number>
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<extent unit="pages"><start>2577</start>
<end>2588</end>
<total>12</total>
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<identifier type="DOI">10.1111/j.1462-2920.2012.02781.x</identifier>
<identifier type="ArticleID">EMI2781</identifier>
<accessCondition type="use and reproduction" contentType="copyright">© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd</accessCondition>
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