structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis
To identify the bacterial and archaeal composition in a mesophilic biogas digester treating pig manure and to compare the consistency of two 16S rDNA-based methods to investigate the microbial structure. Sixty-nine bacterial operational taxonomic units (OTU) and 25 archaeal OTU were identified by se...
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creator | Liu, F.H Wang, S.B Zhang, J.S Zhang, J Yan, X Zhou, H.K Zhao, G.P Zhou, Z.H |
description | To identify the bacterial and archaeal composition in a mesophilic biogas digester treating pig manure and to compare the consistency of two 16S rDNA-based methods to investigate the microbial structure. Sixty-nine bacterial operational taxonomic units (OTU) and 25 archaeal OTU were identified by sequencing two 16S rDNA clone libraries. Most bacterial OTU were identified as phyla of Firmicutes (47·2% of total clones), Bacteroides (35·4%) and Spirochaetes (13·2%). Methanoculleus bourgensis (29·0%), Methanosarcina barkeri (27·4%) and Methanospirillum hungatei (10·8%) were the dominant methanogens. Only 9% of bacterial and 20% of archaeal OTU matched cultured isolates at a similarity index of greater-than-or-equal97%. About 78% of the dominant bacterial (with abundance >3%) and 83% of archaeal OTU were recovered from the denaturing gradient gel electrophoresis (DGGE) bands of V3 regions in 16S rDNAs. In the digester, most bacterial and archaeal species were uncultured; bacteria belonging to Firmicutes, Bacteroides and Spirochaetes seem to take charge of cellulolysis, proteolysis, acidogenesis, sulfur-reducing and homoacetogenesis; the most methanogens were typical hydrogenotrophic or hydrogenotrophic/aceticlastic; DGGE profiles reflected the dominant microbiota. This study gave a first insight of the overall microbial structure in a rural biogas digester and also indicated DGGE was useful in displaying its dominant microbiota. |
doi_str_mv | 10.1111/j.1365-2672.2008.04064.x |
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Sixty-nine bacterial operational taxonomic units (OTU) and 25 archaeal OTU were identified by sequencing two 16S rDNA clone libraries. Most bacterial OTU were identified as phyla of Firmicutes (47·2% of total clones), Bacteroides (35·4%) and Spirochaetes (13·2%). Methanoculleus bourgensis (29·0%), Methanosarcina barkeri (27·4%) and Methanospirillum hungatei (10·8%) were the dominant methanogens. Only 9% of bacterial and 20% of archaeal OTU matched cultured isolates at a similarity index of greater-than-or-equal97%. About 78% of the dominant bacterial (with abundance >3%) and 83% of archaeal OTU were recovered from the denaturing gradient gel electrophoresis (DGGE) bands of V3 regions in 16S rDNAs. In the digester, most bacterial and archaeal species were uncultured; bacteria belonging to Firmicutes, Bacteroides and Spirochaetes seem to take charge of cellulolysis, proteolysis, acidogenesis, sulfur-reducing and homoacetogenesis; the most methanogens were typical hydrogenotrophic or hydrogenotrophic/aceticlastic; DGGE profiles reflected the dominant microbiota. This study gave a first insight of the overall microbial structure in a rural biogas digester and also indicated DGGE was useful in displaying its dominant microbiota.</description><identifier>ISSN: 1364-5072</identifier><identifier>EISSN: 1365-2672</identifier><identifier>DOI: 10.1111/j.1365-2672.2008.04064.x</identifier><identifier>PMID: 19187154</identifier><language>eng</language><publisher>Oxford, UK: Oxford, UK : Blackwell Publishing Ltd</publisher><subject>16S rDNA ; anaerobic digestion ; Animals ; Archaea - classification ; Archaea - genetics ; Archaea - isolation & purification ; Bacteria ; Bacteria - classification ; Bacteria - genetics ; Bacteria - isolation & purification ; Bacteroides ; Biodegradation, Environmental ; biogas digester ; Biological and medical sciences ; Bioreactors ; denaturing gradient gel electrophoresis (DGGE) ; DNA, Ribosomal - genetics ; Electrophoresis - methods ; Firmicutes ; Fundamental and applied biological sciences. Psychology ; Gene Library ; Genes, Archaeal ; Genes, Bacterial ; Genome, Archaeal ; Genome, Bacterial ; Manure - microbiology ; Methanoculleus bourgensis ; Methanosarcina barkeri ; Methanospirillum hungatei ; microbial community ; Microbiology ; Molecular Sequence Data ; pig manure ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S - genetics ; Sequence Analysis, DNA ; Swine</subject><ispartof>Journal of applied microbiology, 2009-03, Vol.106 (3), p.952-966</ispartof><rights>2009 The Authors. Journal compilation © 2009 The Society for Applied Microbiology</rights><rights>2009 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5504-3a33cdaf1ef26902417f60a2b867587ffaf523238ff59a96b92d25c8c8e6fe8f3</citedby><cites>FETCH-LOGICAL-c5504-3a33cdaf1ef26902417f60a2b867587ffaf523238ff59a96b92d25c8c8e6fe8f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1365-2672.2008.04064.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1365-2672.2008.04064.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=21145424$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19187154$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Liu, F.H</creatorcontrib><creatorcontrib>Wang, S.B</creatorcontrib><creatorcontrib>Zhang, J.S</creatorcontrib><creatorcontrib>Zhang, J</creatorcontrib><creatorcontrib>Yan, X</creatorcontrib><creatorcontrib>Zhou, H.K</creatorcontrib><creatorcontrib>Zhao, G.P</creatorcontrib><creatorcontrib>Zhou, Z.H</creatorcontrib><title>structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis</title><title>Journal of applied microbiology</title><addtitle>J Appl Microbiol</addtitle><description>To identify the bacterial and archaeal composition in a mesophilic biogas digester treating pig manure and to compare the consistency of two 16S rDNA-based methods to investigate the microbial structure. Sixty-nine bacterial operational taxonomic units (OTU) and 25 archaeal OTU were identified by sequencing two 16S rDNA clone libraries. Most bacterial OTU were identified as phyla of Firmicutes (47·2% of total clones), Bacteroides (35·4%) and Spirochaetes (13·2%). Methanoculleus bourgensis (29·0%), Methanosarcina barkeri (27·4%) and Methanospirillum hungatei (10·8%) were the dominant methanogens. Only 9% of bacterial and 20% of archaeal OTU matched cultured isolates at a similarity index of greater-than-or-equal97%. About 78% of the dominant bacterial (with abundance >3%) and 83% of archaeal OTU were recovered from the denaturing gradient gel electrophoresis (DGGE) bands of V3 regions in 16S rDNAs. In the digester, most bacterial and archaeal species were uncultured; bacteria belonging to Firmicutes, Bacteroides and Spirochaetes seem to take charge of cellulolysis, proteolysis, acidogenesis, sulfur-reducing and homoacetogenesis; the most methanogens were typical hydrogenotrophic or hydrogenotrophic/aceticlastic; DGGE profiles reflected the dominant microbiota. This study gave a first insight of the overall microbial structure in a rural biogas digester and also indicated DGGE was useful in displaying its dominant microbiota.</description><subject>16S rDNA</subject><subject>anaerobic digestion</subject><subject>Animals</subject><subject>Archaea - classification</subject><subject>Archaea - genetics</subject><subject>Archaea - isolation & purification</subject><subject>Bacteria</subject><subject>Bacteria - classification</subject><subject>Bacteria - genetics</subject><subject>Bacteria - isolation & purification</subject><subject>Bacteroides</subject><subject>Biodegradation, Environmental</subject><subject>biogas digester</subject><subject>Biological and medical sciences</subject><subject>Bioreactors</subject><subject>denaturing gradient gel electrophoresis (DGGE)</subject><subject>DNA, Ribosomal - genetics</subject><subject>Electrophoresis - methods</subject><subject>Firmicutes</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Library</subject><subject>Genes, Archaeal</subject><subject>Genes, Bacterial</subject><subject>Genome, Archaeal</subject><subject>Genome, Bacterial</subject><subject>Manure - microbiology</subject><subject>Methanoculleus bourgensis</subject><subject>Methanosarcina barkeri</subject><subject>Methanospirillum hungatei</subject><subject>microbial community</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>pig manure</subject><subject>Polymerase Chain Reaction</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Sequence Analysis, DNA</subject><subject>Swine</subject><issn>1364-5072</issn><issn>1365-2672</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNksuO1DAQRSMEYoaBXwBvgFUHP2LHWbBoDW8NsBhmbVWcctqtPBo7gemf4VtxulvDDvDGZfncuiVfZxlhNGdpvdrmTCi54qrkOadU57Sgqshv72Xndxf3D3WxkrTkZ9mjGLeUMkGlepidsYrpksniPPsVpzDbaQ5IRkemDZIa7ITBQ0dgaAgEuwFMBzv2_Tz4aU_8QIDUfmwhksa3GBNOUh3wRwKxIfWeNDhAauqHlrQBGo_DRFrsCHZopzDuNmPA6OPBgqlrEt58WZOI32cc7CKCAbp9Ah5nDxx0EZ-c9ovs5t3bb5cfVldf33-8XF-trJS0WAkQwjbgGDquKsoLVjpFgddalVKXzoGTXHChnZMVVKqueMOl1VajcqiduMheHvvuwpiGiJPpfbTYdTDgOEdTCpHknFWJfPFXkjNWUFHof4OUqkqWLIH6CNowxhjQmV3wPYS9YdQscZutWVI1S6qLTJtD3OY2SZ-ePOa6x-aP8JRvAp6fAIgWOhcgvW-845ZhZcEX7vWR--k73P_3AObT-vNSJf2zo97BaKANyePmmi__jcmKy4KJ37va0M0</recordid><startdate>200903</startdate><enddate>200903</enddate><creator>Liu, F.H</creator><creator>Wang, S.B</creator><creator>Zhang, J.S</creator><creator>Zhang, J</creator><creator>Yan, X</creator><creator>Zhou, H.K</creator><creator>Zhao, G.P</creator><creator>Zhou, Z.H</creator><general>Oxford, UK : Blackwell Publishing Ltd</general><general>Blackwell Publishing Ltd</general><general>Blackwell</general><scope>FBQ</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7T7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>7QL</scope><scope>7QO</scope><scope>7TM</scope><scope>7X8</scope></search><sort><creationdate>200903</creationdate><title>structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis</title><author>Liu, F.H ; Wang, S.B ; Zhang, J.S ; Zhang, J ; Yan, X ; Zhou, H.K ; Zhao, G.P ; Zhou, Z.H</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5504-3a33cdaf1ef26902417f60a2b867587ffaf523238ff59a96b92d25c8c8e6fe8f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>16S rDNA</topic><topic>anaerobic digestion</topic><topic>Animals</topic><topic>Archaea - classification</topic><topic>Archaea - genetics</topic><topic>Archaea - isolation & purification</topic><topic>Bacteria</topic><topic>Bacteria - classification</topic><topic>Bacteria - genetics</topic><topic>Bacteria - isolation & purification</topic><topic>Bacteroides</topic><topic>Biodegradation, Environmental</topic><topic>biogas digester</topic><topic>Biological and medical sciences</topic><topic>Bioreactors</topic><topic>denaturing gradient gel electrophoresis (DGGE)</topic><topic>DNA, Ribosomal - genetics</topic><topic>Electrophoresis - methods</topic><topic>Firmicutes</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Library</topic><topic>Genes, Archaeal</topic><topic>Genes, Bacterial</topic><topic>Genome, Archaeal</topic><topic>Genome, Bacterial</topic><topic>Manure - microbiology</topic><topic>Methanoculleus bourgensis</topic><topic>Methanosarcina barkeri</topic><topic>Methanospirillum hungatei</topic><topic>microbial community</topic><topic>Microbiology</topic><topic>Molecular Sequence Data</topic><topic>pig manure</topic><topic>Polymerase Chain Reaction</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Sequence Analysis, DNA</topic><topic>Swine</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Liu, F.H</creatorcontrib><creatorcontrib>Wang, S.B</creatorcontrib><creatorcontrib>Zhang, J.S</creatorcontrib><creatorcontrib>Zhang, J</creatorcontrib><creatorcontrib>Yan, X</creatorcontrib><creatorcontrib>Zhou, H.K</creatorcontrib><creatorcontrib>Zhao, G.P</creatorcontrib><creatorcontrib>Zhou, Z.H</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of applied microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Liu, F.H</au><au>Wang, S.B</au><au>Zhang, J.S</au><au>Zhang, J</au><au>Yan, X</au><au>Zhou, H.K</au><au>Zhao, G.P</au><au>Zhou, Z.H</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis</atitle><jtitle>Journal of applied microbiology</jtitle><addtitle>J Appl Microbiol</addtitle><date>2009-03</date><risdate>2009</risdate><volume>106</volume><issue>3</issue><spage>952</spage><epage>966</epage><pages>952-966</pages><issn>1364-5072</issn><eissn>1365-2672</eissn><abstract>To identify the bacterial and archaeal composition in a mesophilic biogas digester treating pig manure and to compare the consistency of two 16S rDNA-based methods to investigate the microbial structure. Sixty-nine bacterial operational taxonomic units (OTU) and 25 archaeal OTU were identified by sequencing two 16S rDNA clone libraries. Most bacterial OTU were identified as phyla of Firmicutes (47·2% of total clones), Bacteroides (35·4%) and Spirochaetes (13·2%). Methanoculleus bourgensis (29·0%), Methanosarcina barkeri (27·4%) and Methanospirillum hungatei (10·8%) were the dominant methanogens. Only 9% of bacterial and 20% of archaeal OTU matched cultured isolates at a similarity index of greater-than-or-equal97%. About 78% of the dominant bacterial (with abundance >3%) and 83% of archaeal OTU were recovered from the denaturing gradient gel electrophoresis (DGGE) bands of V3 regions in 16S rDNAs. In the digester, most bacterial and archaeal species were uncultured; bacteria belonging to Firmicutes, Bacteroides and Spirochaetes seem to take charge of cellulolysis, proteolysis, acidogenesis, sulfur-reducing and homoacetogenesis; the most methanogens were typical hydrogenotrophic or hydrogenotrophic/aceticlastic; DGGE profiles reflected the dominant microbiota. This study gave a first insight of the overall microbial structure in a rural biogas digester and also indicated DGGE was useful in displaying its dominant microbiota.</abstract><cop>Oxford, UK</cop><pub>Oxford, UK : Blackwell Publishing Ltd</pub><pmid>19187154</pmid><doi>10.1111/j.1365-2672.2008.04064.x</doi><tpages>15</tpages></addata></record> |
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subjects | 16S rDNA anaerobic digestion Animals Archaea - classification Archaea - genetics Archaea - isolation & purification Bacteria Bacteria - classification Bacteria - genetics Bacteria - isolation & purification Bacteroides Biodegradation, Environmental biogas digester Biological and medical sciences Bioreactors denaturing gradient gel electrophoresis (DGGE) DNA, Ribosomal - genetics Electrophoresis - methods Firmicutes Fundamental and applied biological sciences. Psychology Gene Library Genes, Archaeal Genes, Bacterial Genome, Archaeal Genome, Bacterial Manure - microbiology Methanoculleus bourgensis Methanosarcina barkeri Methanospirillum hungatei microbial community Microbiology Molecular Sequence Data pig manure Polymerase Chain Reaction RNA, Ribosomal, 16S - genetics Sequence Analysis, DNA Swine |
title | structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis |
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