Family- and genus-level 16S rRNA-targeted oligonucleotide probes for ecological studies of methanotrophic bacteria
Steudler, Paul A.
Pomerantz, William J.
Cavanaugh, Colleen M.
MetadataShow full item record
Methanotrophic bacteria play a major role in the global carbon cycle, degrade xenobiotic pollutants, and have the potential for a variety of biotechnological applications. To facilitate ecological studies of these important organisms, we developed a suite of oligonucleotide probes for quantitative analysis of methanotroph-specific 16S rRNA from environmental samples. Two probes target methanotrophs in the family Methylocystaceae (type II methanotrophs) as a group. No oligonucleotide signatures that distinguish between the two genera in this family, Methylocystis and Methylosinus, were identified. Two other probes target, as a single group, a majority of the known methanotrophs belonging to the family Methylococcaceae (type I/X methanotrophs). The remaining probes target members of individual genera of the Methylococcaceae, including Methylobacter, Methylomonas, Methylomicrobium, Methylococcus, and Methylocaldum. One of the family-level probes also covers all methanotrophic endosymbionts of marine mollusks for which 16S rRNA sequences have been published. The two known species of the newly described genus Methylosarcina gen. nov. are covered by a probe that otherwise targets only members of the closely related genus Methylomicrobium. None of the probes covers strains of the newly proposed genera Methylocella and "Methylothermus," which are polyphyletic with respect to the recognized methanotrophic families. Empirically determined midpoint dissociation temperatures were 49 to 57°C for all probes. In dot blot screening against RNA from positive- and negative-control strains, the probes were specific to their intended targets. The broad coverage and high degree of specificity of this new suite of probes will provide more detailed, quantitative information about the community structure of methanotrophs in environmental samples than was previously available.
Author Posting. © American Society for Microbiology, 2001. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 67 (2001): 4726-4733, doi:10.1128/AEM.67.10.4726-4733.2001.
Showing items related by title, author, creator and subject.
Doherty, Mary; Yager, Patricia L.; Moran, Mary Ann; Coles, Victoria J.; Fortunato, Caroline S.; Krusche, Alex V.; Medeiros, Patricia M.; Payet, Jérôme P.; Richey, Jeffrey E.; Satinsky, Brandon; Sawakuchi, Henrique O.; Ward, Nicholas D.; Crump, Byron C. (Frontiers Media, 2017-05-23)Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ∼675 km of the lower Amazon River mainstem, in the Tapajós River tributary, and in the plume and coastal ...
Gradients in dimethylsulfide, dimethylsulfoniopropionate, dimethylsulfoxide, and bacteria near the sea surface Zemmelink, Hendrik J.; Houghton, Leah A.; Sievert, Stefan M.; Frew, Nelson M.; Dacey, John W. H. (Inter-Research, 2005-06-23)Gradients of dimethylsulfide (DMS), dimethylsulfoniopropionate (DMSP), dimethylsulfoxide (DMSO), and bacterial numbers and diversity from the surface microlayer to 500 cm depth were assessed in coastal waters surrounding ...
Krey, Whitney B. (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2008-06)An increased understanding of heterotrophic bacterial strategies for acquiring nutrients and trace elements is critical for elucidating their impact on biogeochemical cycling in the ocean. It is estimated that iron is a ...