Diversity of Oxygenase Genes from Methane- and Ammonia-Oxidizing Bacteria in the Eastern Snake River Plain Aquifer
PCR amplification, restriction fragment length polymorphism, and phylogenetic analysis of oxygenase genes were used for the characterization of in situ methane- and ammonia-oxidizing bacteria from free-living and attached communities in the Eastern Snake River Plain aquifer. The following three meth...
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| Veröffentlicht in: | Applied and Environmental Microbiology 2005-04, Vol.71 (4), p.2016-2025 |
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| creator | Erwin, Daniel P Erickson, Issac K Delwiche, Mark E Colwell, Frederick S Strap, Janice L Crawford, Ronald L |
| description | PCR amplification, restriction fragment length polymorphism, and phylogenetic analysis of oxygenase genes were used for the characterization of in situ methane- and ammonia-oxidizing bacteria from free-living and attached communities in the Eastern Snake River Plain aquifer. The following three methane monooxygenase (MMO) PCR primer sets were used: A189-A682, which amplifies an internal region of both the pmoA gene of the MMO particulate form and the amoA gene of ammonia monooxygenase; A189-mb661, which specifically targets the pmoA gene; and mmoXA-mmoXB, which amplifies the mmoX gene of the MMO soluble form (sMMO). Whole-genome amplification (WGA) was used to amplify metagenomic DNA from each community to assess its applicability for generating unbiased metagenomic template DNA. The majority of sequences in each archive were related to oxygenases of type II-like methanotrophs of the genus METHYLOCYSTIS: A small subset of type I sequences found only in free-living communities possessed oxygenase genes that grouped nearest to Methylobacter and Methylomonas spp. Sequences similar to that of the amoA gene associated with ammonia-oxidizing bacteria (AOB) most closely matched a sequence from the uncultured bacterium BS870 but showed no substantial alignment to known cultured AOB. Based on these functional gene analyses, bacteria related to the type II methanotroph Methylocystis sp. were found to dominate both free-living and attached communities. Metagenomic DNA amplified by WGA showed characteristics similar to those of unamplified samples. Overall, numerous sMMO-like gene sequences that have been previously associated with high rates of trichloroethylene cometabolism were observed in both free-living and attached communities in this basaltic aquifer. |
| doi_str_mv | 10.1128/aem.71.4.2016-2025.2005 |
| format | Article |
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The following three methane monooxygenase (MMO) PCR primer sets were used: A189-A682, which amplifies an internal region of both the pmoA gene of the MMO particulate form and the amoA gene of ammonia monooxygenase; A189-mb661, which specifically targets the pmoA gene; and mmoXA-mmoXB, which amplifies the mmoX gene of the MMO soluble form (sMMO). Whole-genome amplification (WGA) was used to amplify metagenomic DNA from each community to assess its applicability for generating unbiased metagenomic template DNA. The majority of sequences in each archive were related to oxygenases of type II-like methanotrophs of the genus METHYLOCYSTIS: A small subset of type I sequences found only in free-living communities possessed oxygenase genes that grouped nearest to Methylobacter and Methylomonas spp. Sequences similar to that of the amoA gene associated with ammonia-oxidizing bacteria (AOB) most closely matched a sequence from the uncultured bacterium BS870 but showed no substantial alignment to known cultured AOB. Based on these functional gene analyses, bacteria related to the type II methanotroph Methylocystis sp. were found to dominate both free-living and attached communities. Metagenomic DNA amplified by WGA showed characteristics similar to those of unamplified samples. Overall, numerous sMMO-like gene sequences that have been previously associated with high rates of trichloroethylene cometabolism were observed in both free-living and attached communities in this basaltic aquifer.</description><identifier>ISSN: 0099-2240</identifier><identifier>EISSN: 1098-5336</identifier><identifier>DOI: 10.1128/aem.71.4.2016-2025.2005</identifier><identifier>PMID: 15812034</identifier><identifier>CODEN: AEMIDF</identifier><language>eng</language><publisher>United States: American Society for Microbiology</publisher><subject>Ammonia ; Ammonia - metabolism ; ammonia monooxygenase ; amoA gene ; Aquifers ; Bacteria ; DNA, Bacterial - analysis ; Freshwater ; genes ; Genetic diversity ; Genetic Variation ; Idaho ; Methane ; Methane - metabolism ; methane monooxygenase ; methanotrophs ; Methylococcaceae - classification ; Methylococcaceae - enzymology ; Methylococcaceae - genetics ; Methylocystaceae - classification ; Methylocystaceae - enzymology ; Methylocystaceae - genetics ; Microbial Ecology ; mmoX gene ; molecular sequenc data ; Nitrosomonadaceae ; nucleotide sequences ; Oxidation ; Oxidation-Reduction ; Oxidoreductases - genetics ; Oxidoreductases - metabolism ; oxygenases ; Oxygenases - genetics ; Oxygenases - metabolism ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Quantitative genetics ; restriction fragment length polymorphism ; Rivers - microbiology ; Sequence Analysis, DNA ; Water Supply</subject><ispartof>Applied and Environmental Microbiology, 2005-04, Vol.71 (4), p.2016-2025</ispartof><rights>Copyright American Society for Microbiology Apr 2005</rights><rights>Copyright © 2005, American Society for Microbiology 2005</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5045-a15dc8386f61c7d5660905dc3173ea49b151c18a4b99999fb13a93fbcf1a28f73</citedby><cites>FETCH-LOGICAL-c5045-a15dc8386f61c7d5660905dc3173ea49b151c18a4b99999fb13a93fbcf1a28f73</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1082543/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1082543/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,723,776,780,881,3175,3176,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15812034$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Erwin, Daniel P</creatorcontrib><creatorcontrib>Erickson, Issac K</creatorcontrib><creatorcontrib>Delwiche, Mark E</creatorcontrib><creatorcontrib>Colwell, Frederick S</creatorcontrib><creatorcontrib>Strap, Janice L</creatorcontrib><creatorcontrib>Crawford, Ronald L</creatorcontrib><title>Diversity of Oxygenase Genes from Methane- and Ammonia-Oxidizing Bacteria in the Eastern Snake River Plain Aquifer</title><title>Applied and Environmental Microbiology</title><addtitle>Appl Environ Microbiol</addtitle><description>PCR amplification, restriction fragment length polymorphism, and phylogenetic analysis of oxygenase genes were used for the characterization of in situ methane- and ammonia-oxidizing bacteria from free-living and attached communities in the Eastern Snake River Plain aquifer. The following three methane monooxygenase (MMO) PCR primer sets were used: A189-A682, which amplifies an internal region of both the pmoA gene of the MMO particulate form and the amoA gene of ammonia monooxygenase; A189-mb661, which specifically targets the pmoA gene; and mmoXA-mmoXB, which amplifies the mmoX gene of the MMO soluble form (sMMO). Whole-genome amplification (WGA) was used to amplify metagenomic DNA from each community to assess its applicability for generating unbiased metagenomic template DNA. The majority of sequences in each archive were related to oxygenases of type II-like methanotrophs of the genus METHYLOCYSTIS: A small subset of type I sequences found only in free-living communities possessed oxygenase genes that grouped nearest to Methylobacter and Methylomonas spp. Sequences similar to that of the amoA gene associated with ammonia-oxidizing bacteria (AOB) most closely matched a sequence from the uncultured bacterium BS870 but showed no substantial alignment to known cultured AOB. Based on these functional gene analyses, bacteria related to the type II methanotroph Methylocystis sp. were found to dominate both free-living and attached communities. Metagenomic DNA amplified by WGA showed characteristics similar to those of unamplified samples. Overall, numerous sMMO-like gene sequences that have been previously associated with high rates of trichloroethylene cometabolism were observed in both free-living and attached communities in this basaltic aquifer.</description><subject>Ammonia</subject><subject>Ammonia - metabolism</subject><subject>ammonia monooxygenase</subject><subject>amoA gene</subject><subject>Aquifers</subject><subject>Bacteria</subject><subject>DNA, Bacterial - analysis</subject><subject>Freshwater</subject><subject>genes</subject><subject>Genetic diversity</subject><subject>Genetic Variation</subject><subject>Idaho</subject><subject>Methane</subject><subject>Methane - metabolism</subject><subject>methane monooxygenase</subject><subject>methanotrophs</subject><subject>Methylococcaceae - classification</subject><subject>Methylococcaceae - enzymology</subject><subject>Methylococcaceae - genetics</subject><subject>Methylocystaceae - classification</subject><subject>Methylocystaceae - enzymology</subject><subject>Methylocystaceae - genetics</subject><subject>Microbial Ecology</subject><subject>mmoX gene</subject><subject>molecular sequenc data</subject><subject>Nitrosomonadaceae</subject><subject>nucleotide sequences</subject><subject>Oxidation</subject><subject>Oxidation-Reduction</subject><subject>Oxidoreductases - genetics</subject><subject>Oxidoreductases - metabolism</subject><subject>oxygenases</subject><subject>Oxygenases - genetics</subject><subject>Oxygenases - metabolism</subject><subject>Phylogeny</subject><subject>Polymerase Chain Reaction</subject><subject>Polymorphism, Restriction Fragment Length</subject><subject>Quantitative genetics</subject><subject>restriction fragment length polymorphism</subject><subject>Rivers - microbiology</subject><subject>Sequence Analysis, DNA</subject><subject>Water Supply</subject><issn>0099-2240</issn><issn>1098-5336</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkk1vEzEQhlcIREPhL1DDgduG8ed6L0ihhILUKojSszW7sROXrLe1N6Xh1-NVIgpc8MUezzOv7HmnKE4oTCll-i3ablrRqZgyoKpkwGQ-gXxUTCjUupScq8fFBKCuS8YEHBXPUroGAAFKPy2OqNSUAReTIn7wdzYmP-xI78jifreyAZMlZzbYRFzsO3JhhzUGWxIMSzLruj54LBf3ful_-rAi77EdbPRIfCDD2pI5phwHchnwuyVfR3nyZYM5O7vdemfj8-KJw02yLw77cXH1cf7t9FN5vjj7fDo7L1sJQpZI5bLVXCunaFstpVJQQ77itOIWRd1QSVuqUTT1uFxDOdbcNa2jyLSr-HHxbq97s206u2xtGCJuzE30Hcad6dGbvzPBr82qvzMUNJOCZ4E3B4HY325tGkznU2s3m9yNfpuMqiqoOfs_SCvFhdIqg6__Aa_7bQy5C4aBrBUwLTJU7aE29ilF634_mYIZ3Tez-YWpqBFmdN-M7pvR_Vz58s8fP9Qd7M7Aqz2w9qv1Dx-twdSZPEwPcpk52TMOe4Or6JO5uswZnqdJ1wCc_wLWBr_4</recordid><startdate>200504</startdate><enddate>200504</enddate><creator>Erwin, Daniel P</creator><creator>Erickson, Issac K</creator><creator>Delwiche, Mark E</creator><creator>Colwell, Frederick S</creator><creator>Strap, Janice L</creator><creator>Crawford, Ronald L</creator><general>American Society for Microbiology</general><scope>FBQ</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>7QL</scope><scope>7QO</scope><scope>7SN</scope><scope>7SS</scope><scope>7ST</scope><scope>7T7</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>SOI</scope><scope>7UA</scope><scope>F1W</scope><scope>H95</scope><scope>L.G</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>200504</creationdate><title>Diversity of Oxygenase Genes from Methane- and Ammonia-Oxidizing Bacteria in the Eastern Snake River Plain Aquifer</title><author>Erwin, Daniel P ; 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The following three methane monooxygenase (MMO) PCR primer sets were used: A189-A682, which amplifies an internal region of both the pmoA gene of the MMO particulate form and the amoA gene of ammonia monooxygenase; A189-mb661, which specifically targets the pmoA gene; and mmoXA-mmoXB, which amplifies the mmoX gene of the MMO soluble form (sMMO). Whole-genome amplification (WGA) was used to amplify metagenomic DNA from each community to assess its applicability for generating unbiased metagenomic template DNA. The majority of sequences in each archive were related to oxygenases of type II-like methanotrophs of the genus METHYLOCYSTIS: A small subset of type I sequences found only in free-living communities possessed oxygenase genes that grouped nearest to Methylobacter and Methylomonas spp. Sequences similar to that of the amoA gene associated with ammonia-oxidizing bacteria (AOB) most closely matched a sequence from the uncultured bacterium BS870 but showed no substantial alignment to known cultured AOB. Based on these functional gene analyses, bacteria related to the type II methanotroph Methylocystis sp. were found to dominate both free-living and attached communities. Metagenomic DNA amplified by WGA showed characteristics similar to those of unamplified samples. Overall, numerous sMMO-like gene sequences that have been previously associated with high rates of trichloroethylene cometabolism were observed in both free-living and attached communities in this basaltic aquifer.</abstract><cop>United States</cop><pub>American Society for Microbiology</pub><pmid>15812034</pmid><doi>10.1128/aem.71.4.2016-2025.2005</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Ammonia Ammonia - metabolism ammonia monooxygenase amoA gene Aquifers Bacteria DNA, Bacterial - analysis Freshwater genes Genetic diversity Genetic Variation Idaho Methane Methane - metabolism methane monooxygenase methanotrophs Methylococcaceae - classification Methylococcaceae - enzymology Methylococcaceae - genetics Methylocystaceae - classification Methylocystaceae - enzymology Methylocystaceae - genetics Microbial Ecology mmoX gene molecular sequenc data Nitrosomonadaceae nucleotide sequences Oxidation Oxidation-Reduction Oxidoreductases - genetics Oxidoreductases - metabolism oxygenases Oxygenases - genetics Oxygenases - metabolism Phylogeny Polymerase Chain Reaction Polymorphism, Restriction Fragment Length Quantitative genetics restriction fragment length polymorphism Rivers - microbiology Sequence Analysis, DNA Water Supply |
| title | Diversity of Oxygenase Genes from Methane- and Ammonia-Oxidizing Bacteria in the Eastern Snake River Plain Aquifer |
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