{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T01:49:15Z","timestamp":1792201755900,"version":"4.4.0"},"reference-count":51,"publisher":"American Society for Microbiology","issue":"4","license":[{"start":{"date-parts":[[2005,4,1]],"date-time":"2005-04-01T00:00:00Z","timestamp":1112313600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2005,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title><jats:p>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<jats:italic>pmoA<\/jats:italic>gene of the MMO particulate form and the<jats:italic>amoA<\/jats:italic>gene of ammonia monooxygenase; A189-mb661, which specifically targets the<jats:italic>pmoA<\/jats:italic>gene; and mmoXA-mmoXB, which amplifies the<jats:italic>mmoX<\/jats:italic>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<jats:italic>Methylocystis<\/jats:italic>. A small subset of type I sequences found only in free-living communities possessed oxygenase genes that grouped nearest to<jats:italic>Methylobacter<\/jats:italic>and<jats:italic>Methylomonas<\/jats:italic>spp. Sequences similar to that of the<jats:italic>amoA<\/jats:italic>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<jats:italic>Methylocystis<\/jats:italic>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.<\/jats:p>","DOI":"10.1128\/aem.71.4.2016-2025.2005","type":"journal-article","created":{"date-parts":[[2005,4,6]],"date-time":"2005-04-06T13:23:15Z","timestamp":1112793795000},"page":"2016-2025","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":64,"title":["Diversity of Oxygenase Genes from Methane- and Ammonia-Oxidizing Bacteria in the Eastern Snake River Plain Aquifer"],"prefix":"10.1128","volume":"71","author":[{"given":"Daniel P.","family":"Erwin","sequence":"first","affiliation":[{"name":"Environmental Biotechnology Institute"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Issac K.","family":"Erickson","sequence":"additional","affiliation":[{"name":"Biology Department, University of Idaho, Moscow"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark E.","family":"Delwiche","sequence":"additional","affiliation":[{"name":"Idaho National Engineering and Environmental Laboratory, Idaho Falls, Idaho"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frederick S.","family":"Colwell","sequence":"additional","affiliation":[{"name":"Idaho National Engineering and Environmental Laboratory, Idaho Falls, Idaho"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janice L.","family":"Strap","sequence":"additional","affiliation":[{"name":"Environmental Biotechnology Institute"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ronald L.","family":"Crawford","sequence":"additional","affiliation":[{"name":"Environmental Biotechnology Institute"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.58.6.1886-1893.1992"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1023\/A:1012075322466"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.63.2.687-693.1997"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1023\/A:1012089908518"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1462-2920.2002.00323.x"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.66.12.5259-5266.2000"},{"key":"e_1_3_2_8_2","unstructured":"Barnes J. M. C. Rae V. S. Thompson M. R. Walton D. T. Maiers and K. S. Sorenson. 2000. Aerobic biodegradation laboratory studies at Test Area North Operable Unit 1-07B (INEEL\/EXT-99-00736). U.S. Department of Energy Idaho Operations Office Idaho Falls Idaho."},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0021-9258(18)81883-X"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00117048"},{"key":"e_1_3_2_11_2","first-page":"3327","volume":"130","year":"1984","unstructured":"Burrows, K. J., A. Cornish, D. Scott, and I. J. Higgins. 1984. Substrate specificities of the soluble and particulate methane monooxygenases of Methylosinus trichosporium OB3b. J. Gen. Microbiol.130:3327-3333.","journal-title":"J. Gen. Microbiol."},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.65.11.5066-5074.1999"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.082089499"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.282.5387.281"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0021-9258(18)53833-3"},{"key":"e_1_3_2_16_2","first-page":"48184","volume":"54","year":"1989","unstructured":"Federal Register. 1989. National primary and secondary drinking water regulations. Fed. Regist.54:48184-48189.","journal-title":"Fed. Regist."},{"key":"e_1_3_2_17_2","first-page":"22062","volume":"54","year":"1989","unstructured":"Federal Register. 1989. National primary and secondary drinking water regulations. Fed. Regist.54:22062-22160.","journal-title":"Fed. Regist."},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/mr.60.2.439-471.1996"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.58.9.3020-3026.1992"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.1995.tb07834.x"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.67.9.4177-4185.2001"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.816903"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.61.4.1480-1487.1995"},{"key":"e_1_3_2_24_2","unstructured":"Idaho National Engineering and Environmental Laboratory. 2001. Fiscal year 2000 groundwater monitoring annual report Test Area North Operable Unit 1-07B. Idaho National Engineering and Environmental Laboratory Idaho Falls Idaho."},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.59.4.960-967.1993"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.377203"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tibtech.2003.09.010"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.67.6.2799-2809.2001"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.68.4.1569-1575.2002"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1080\/01490450490275848"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0536703100"},{"key":"e_1_3_2_32_2","first-page":"951","volume":"45","year":"1988","unstructured":"Little, C. K., A. V. Palumbo, S. E. Herbes, M. E. Lidstrom, R. L. Tyndall, and P. J. Gilmer. 1988. Trichloroethylene biodegradation by a methane-oxidizing bacterium. Appl. Environ. Microbiol.45:951-956.","journal-title":"Appl. Environ. Microbiol."},{"key":"e_1_3_2_33_2","first-page":"33","year":"1988","unstructured":"Maltoni, C., G. Lefemine, C. Cotti, and G. Perino. 1988. Long-term carcinogenicity bioassays on trichloroethylene administered by inhalation to Sprague Dawley rats and Swiss and B6C3F1 mice, p. 33-36. In C. Maltoni and I. J. Selikoff (ed.), Living in a chemical world. New York Academy of Science, New York.","journal-title":"Living in a chemical world."},{"key":"e_1_3_2_34_2","first-page":"315","volume":"150","year":"1999","unstructured":"Marion, M. J., and S. Boivin-Angele. 1999. Vinyl chloride-specific mutations in humans and animals. IARC Sci. Publ.150:315-324.","journal-title":"IARC Sci. Publ."},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.61.1.116-121.1995"},{"key":"e_1_3_2_36_2","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1111\/j.1749-6632.2002.tb04932.x","volume":"982","year":"2002","unstructured":"Melnick, R. L. 2002. Carcinogenicity and mechanistic insights on the behavior of epoxides and epoxide-forming chemicals. Ann. N. Y. Acad. Sci.982:177-189.","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1007\/s002489900004"},{"key":"e_1_3_2_38_2","first-page":"1145","volume":"43","year":"1983","unstructured":"Miller, R. E., and F. P. Guengerich. 1983. Metabolism of trichloroethylene in isolated hepatocytes, microsomes and reconstituted enzyme systems containing cytochrome P-450. Cancer Res.43:1145-1152.","journal-title":"Cancer Res."},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1080\/10635150390235494"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1007\/s002030000158"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.femsec.2004.02.001"},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.273.14.7957"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.55.11.2819-2826.1989"},{"key":"e_1_3_2_44_2","first-page":"357","volume":"12","year":"1996","unstructured":"Page, R. D. 1996. TreeView: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci.12:357-358.","journal-title":"Comput. Appl. Biosci."},{"key":"e_1_3_2_45_2","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/0162-0134(94)00056-G","volume":"58","year":"1995","unstructured":"Semrau, J. D., D. Zolandz, M. E. Lidstrom, and S. I. Chan. 1995. The role of copper in the pMMO of Methylococcus capsulatus bath: a structural vs. catalytic function. J. Inorg. Biochem.58:235-244.","journal-title":"J. Inorg. Biochem."},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.65.12.5198-5206.1999"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.1021\/es011162d"},{"key":"e_1_3_2_48_2","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1080\/10889860091114293","volume":"4","year":"2000","unstructured":"Sorenson, K. S., L. N. Peterson, R. E. Hinchee, and R. L. Ely. 2000. An evaluation of aerobic trichloroethene attenuation using first-order rate estimation. Bioremediat. J.4:337-357.","journal-title":"Bioremediat. J."},{"key":"e_1_3_2_49_2","first-page":"11","volume":"65","year":"1987","unstructured":"Storck, W. 1987. Chlorinated solvent use hurt by federal rules. Chem. Eng. News65:11.","journal-title":"Chem. Eng. News"},{"key":"e_1_3_2_50_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.55.12.3155-3161.1989"},{"key":"e_1_3_2_51_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.58.3.953-960.1992"},{"key":"e_1_3_2_52_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2003.10.014"}],"container-title":["Applied and Environmental Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/AEM.71.4.2016-2025.2005","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/AEM.71.4.2016-2025.2005","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,24]],"date-time":"2024-01-24T16:25:02Z","timestamp":1706113502000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/AEM.71.4.2016-2025.2005"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,4]]},"references-count":51,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2005,4]]}},"alternative-id":["10.1128\/AEM.71.4.2016-2025.2005"],"URL":"https:\/\/doi.org\/10.1128\/aem.71.4.2016-2025.2005","relation":{},"ISSN":["0099-2240","1098-5336"],"issn-type":[{"value":"0099-2240","type":"print"},{"value":"1098-5336","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,4]]},"assertion":[{"value":"2004-07-30","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2004-11-10","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2005-04-01","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}