Metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system
Identifieur interne : 000397 ( Pmc/Checkpoint ); précédent : 000396; suivant : 000398Metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system
Auteurs : Vicente Gomez-Alvarez [États-Unis] ; Randy P. Revetta [États-Unis] ; Jorge W Santo Domingo [États-Unis]Source :
- BMC Microbiology [ 1471-2180 ] ; 2012.
Abstract
Concrete corrosion of wastewater collection systems is a significant cause of deterioration and premature collapse. Failure to adequately address the deteriorating infrastructure networks threatens our environment, public health, and safety. Analysis of whole-metagenome pyrosequencing data and 16S rRNA gene clone libraries was used to determine microbial composition and functional genes associated with biomass harvested from crown (top) and invert (bottom) sections of a corroded wastewater pipe.
Taxonomic and functional analysis demonstrated that approximately 90% of the total diversity was associated with the phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The top (TP) and bottom pipe (BP) communities were different in composition, with some of the differences attributed to the abundance of sulfide-oxidizing and sulfate-reducing bacteria. Additionally, human fecal bacteria were more abundant in the BP communities. Among the functional categories, proteins involved in sulfur and nitrogen metabolism showed the most significant differences between biofilms. There was also an enrichment of genes associated with heavy metal resistance, virulence (protein secretion systems) and stress response in the TP biofilm, while a higher number of genes related to motility and chemotaxis were identified in the BP biofilm. Both biofilms contain a high number of genes associated with resistance to antibiotics and toxic compounds subsystems.
The function potential of wastewater biofilms was highly diverse with level of COG diversity similar to that described for soil. On the basis of the metagenomic data, some factors that may contribute to niche differentiation were pH, aerobic conditions and availability of substrate, such as nitrogen and sulfur. The results from this study will help us better understand the genetic network and functional capability of microbial members of wastewater concrete biofilms.
Url:
DOI: 10.1186/1471-2180-12-122
PubMed: 22727216
PubMed Central: 3409016
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system</title><author><name sortKey="Gomez Alvarez, Vicente" sort="Gomez Alvarez, Vicente" uniqKey="Gomez Alvarez V" first="Vicente" last="Gomez-Alvarez">Vicente Gomez-Alvarez</name><affiliation wicri:level="1"><nlm:aff id="I1">U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268</wicri:regionArea><wicri:noRegion>45268</wicri:noRegion></affiliation></author><author><name sortKey="Revetta, Randy P" sort="Revetta, Randy P" uniqKey="Revetta R" first="Randy P" last="Revetta">Randy P. Revetta</name><affiliation wicri:level="1"><nlm:aff id="I1">U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268</wicri:regionArea><wicri:noRegion>45268</wicri:noRegion></affiliation></author><author><name sortKey="Domingo, Jorge W Santo" sort="Domingo, Jorge W Santo" uniqKey="Domingo J" first="Jorge W Santo" last="Domingo">Jorge W Santo Domingo</name><affiliation wicri:level="1"><nlm:aff id="I1">U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268</wicri:regionArea><wicri:noRegion>45268</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22727216</idno><idno type="pmc">3409016</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3409016</idno><idno type="RBID">PMC:3409016</idno><idno type="doi">10.1186/1471-2180-12-122</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000333</idno><idno type="wicri:Area/Pmc/Curation">000333</idno><idno type="wicri:Area/Pmc/Checkpoint">000397</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system</title><author><name sortKey="Gomez Alvarez, Vicente" sort="Gomez Alvarez, Vicente" uniqKey="Gomez Alvarez V" first="Vicente" last="Gomez-Alvarez">Vicente Gomez-Alvarez</name><affiliation wicri:level="1"><nlm:aff id="I1">U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268</wicri:regionArea><wicri:noRegion>45268</wicri:noRegion></affiliation></author><author><name sortKey="Revetta, Randy P" sort="Revetta, Randy P" uniqKey="Revetta R" first="Randy P" last="Revetta">Randy P. Revetta</name><affiliation wicri:level="1"><nlm:aff id="I1">U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268</wicri:regionArea><wicri:noRegion>45268</wicri:noRegion></affiliation></author><author><name sortKey="Domingo, Jorge W Santo" sort="Domingo, Jorge W Santo" uniqKey="Domingo J" first="Jorge W Santo" last="Domingo">Jorge W Santo Domingo</name><affiliation wicri:level="1"><nlm:aff id="I1">U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268</wicri:regionArea><wicri:noRegion>45268</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Microbiology</title><idno type="eISSN">1471-2180</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Concrete corrosion of wastewater collection systems is a significant cause of deterioration and premature collapse. Failure to adequately address the deteriorating infrastructure networks threatens our environment, public health, and safety. Analysis of whole-metagenome pyrosequencing data and 16S rRNA gene clone libraries was used to determine microbial composition and functional genes associated with biomass harvested from crown (top) and invert (bottom) sections of a corroded wastewater pipe.</p></sec><sec><title>Results</title><p>Taxonomic and functional analysis demonstrated that approximately 90% of the total diversity was associated with the phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The top (TP) and bottom pipe (BP) communities were different in composition, with some of the differences attributed to the abundance of sulfide-oxidizing and sulfate-reducing bacteria. Additionally, human fecal bacteria were more abundant in the BP communities. Among the functional categories, proteins involved in sulfur and nitrogen metabolism showed the most significant differences between biofilms. There was also an enrichment of genes associated with heavy metal resistance, virulence (protein secretion systems) and stress response in the TP biofilm, while a higher number of genes related to motility and chemotaxis were identified in the BP biofilm. Both biofilms contain a high number of genes associated with resistance to antibiotics and toxic compounds subsystems.</p></sec><sec><title>Conclusions</title><p>The function potential of wastewater biofilms was highly diverse with level of COG diversity similar to that described for soil. On the basis of the metagenomic data, some factors that may contribute to niche differentiation were pH, aerobic conditions and availability of substrate, such as nitrogen and sulfur. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Microbiol</journal-id><journal-id journal-id-type="iso-abbrev">BMC Microbiol</journal-id><journal-title-group><journal-title>BMC Microbiology</journal-title></journal-title-group><issn pub-type="epub">1471-2180</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22727216</article-id><article-id pub-id-type="pmc">3409016</article-id><article-id pub-id-type="publisher-id">1471-2180-12-122</article-id><article-id pub-id-type="doi">10.1186/1471-2180-12-122</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system</article-title></title-group><contrib-group><contrib contrib-type="author" id="A1"><name><surname>Gomez-Alvarez</surname><given-names>Vicente</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>Gomez-Alvarez.Vicente@epa.gov</email></contrib><contrib contrib-type="author" id="A2"><name><surname>Revetta</surname><given-names>Randy P</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>Revetta.Randy@epa.gov</email></contrib><contrib contrib-type="author" corresp="yes" id="A3"><name><surname>Domingo</surname><given-names>Jorge W Santo</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>Santodomingo.Jorge@epa.gov</email></contrib></contrib-group><aff id="I1"><label>1</label>U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, USA</aff><pub-date pub-type="collection"><year>2012</year></pub-date><pub-date pub-type="epub"><day>22</day><month>6</month><year>2012</year></pub-date><volume>12</volume><fpage>122</fpage><lpage>122</lpage><history><date date-type="received"><day>19</day><month>12</month><year>2011</year></date><date date-type="accepted"><day>22</day><month>6</month><year>2012</year></date></history><permissions><copyright-statement>Copyright ©2012 Gomez-Alvarez et al.; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2012</copyright-year><copyright-holder>Gomez-Alvarez et al.; licensee BioMed Central Ltd.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri xlink:href="http://www.biomedcentral.com/1471-2180/12/122"></self-uri><abstract><sec><title>Background</title><p>Concrete corrosion of wastewater collection systems is a significant cause of deterioration and premature collapse. Failure to adequately address the deteriorating infrastructure networks threatens our environment, public health, and safety. Analysis of whole-metagenome pyrosequencing data and 16S rRNA gene clone libraries was used to determine microbial composition and functional genes associated with biomass harvested from crown (top) and invert (bottom) sections of a corroded wastewater pipe.</p></sec><sec><title>Results</title><p>Taxonomic and functional analysis demonstrated that approximately 90% of the total diversity was associated with the phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The top (TP) and bottom pipe (BP) communities were different in composition, with some of the differences attributed to the abundance of sulfide-oxidizing and sulfate-reducing bacteria. Additionally, human fecal bacteria were more abundant in the BP communities. Among the functional categories, proteins involved in sulfur and nitrogen metabolism showed the most significant differences between biofilms. There was also an enrichment of genes associated with heavy metal resistance, virulence (protein secretion systems) and stress response in the TP biofilm, while a higher number of genes related to motility and chemotaxis were identified in the BP biofilm. Both biofilms contain a high number of genes associated with resistance to antibiotics and toxic compounds subsystems.</p></sec><sec><title>Conclusions</title><p>The function potential of wastewater biofilms was highly diverse with level of COG diversity similar to that described for soil. On the basis of the metagenomic data, some factors that may contribute to niche differentiation were pH, aerobic conditions and availability of substrate, such as nitrogen and sulfur. The results from this study will help us better understand the genetic network and functional capability of microbial members of wastewater concrete biofilms.</p></sec></abstract></article-meta></front></pmc><affiliations><list><country><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Gomez Alvarez, Vicente" sort="Gomez Alvarez, Vicente" uniqKey="Gomez Alvarez V" first="Vicente" last="Gomez-Alvarez">Vicente Gomez-Alvarez</name></noRegion><name sortKey="Domingo, Jorge W Santo" sort="Domingo, Jorge W Santo" uniqKey="Domingo J" first="Jorge W Santo" last="Domingo">Jorge W Santo Domingo</name><name sortKey="Revetta, Randy P" sort="Revetta, Randy P" uniqKey="Revetta R" first="Randy P" last="Revetta">Randy P. Revetta</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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