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Applied and Environmental Microbiology, April 2005, p. 2016-2025, Vol. 71, No. 4
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.4.2016-2025.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Diversity of Oxygenase Genes from Methane- and Ammonia-Oxidizing Bacteria in the Eastern Snake River Plain Aquifer

Daniel P. Erwin,1 Issac K. Erickson,2 Mark E. Delwiche,3 Frederick S. Colwell,3 Janice L. Strap,1 and Ronald L. Crawford1*

Environmental Biotechnology Institute,1 Biology Department, University of Idaho, Moscow,2 Idaho National Engineering and Environmental Laboratory, Idaho Falls, Idaho3

Received 30 July 2004/ Accepted 10 November 2004

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.

* Corresponding author. Mailing address: University of Idaho, Environmental Biotechnology Institute, Food Research Center 204, Moscow, ID 83844-1052. Phone: (208) 885-6580. Fax: (208) 885-5741. E-mail: crawford{at}uidaho.edu.

Applied and Environmental Microbiology, April 2005, p. 2016-2025, Vol. 71, No. 4
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.4.2016-2025.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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  • Kalyuzhnaya, M. G., Zabinsky, R., Bowerman, S., Baker, D. R., Lidstrom, M. E., Chistoserdova, L. (2006). Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations.. Appl. Environ. Microbiol. 72: 4293-4301 [Abstract] [Full Text]  


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