The Methanol Dehydrogenase Gene, mxaF, as a Functional and Phylogenetic Marker for Proteobacterial Methanotrophs in Natural Environments Journal Article


Authors: Lau, Evan; Fisher, Meredith C.; Steudler, Paul A.; Cavanaugh, Colleen M.
Article Title: The Methanol Dehydrogenase Gene, mxaF, as a Functional and Phylogenetic Marker for Proteobacterial Methanotrophs in Natural Environments
Abstract: The mxaF gene, coding for the large (a) subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the Alpha-, Beta- and Gammaproteobacteria. It is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoA and mmoX genes, which are absent in some methanotrophic proteobacterial genera. This study examined the potential for using the mxaF gene as a functional and phylogenetic marker for methanotrophs. mxaF and 16S rRNA gene phylogenies were constructed based on over 100 database sequences of known proteobacterial methanotrophs and other methylotrophs to assess their evolutionary histories. Topology tests revealed that mxaF and 16S rDNA genes of methanotrophs do not show congruent evolutionary histories, with incongruencies in methanotrophic taxa in the Methylococcaceae, Methylocystaceae, and Beijerinckiacea. However, known methanotrophs generally formed coherent clades based on mxaF gene sequences, allowing for phylogenetic discrimination of major taxa. This feature highlights the mxaF gene#39;s usefulness as a biomarker in studying the molecular diversity of proteobacterial methanotrophs in nature. To verify this, PCR-directed assays targeting this gene were used to detect novel methanotrophs from diverse environments including soil, peatland, hydrothermal vent mussel tissues, and methanotroph isolates. The placement of the majority of environmental mxaF gene sequences in distinct methanotroph-specific clades (Methylocystaceae and Methylococcaceae) detected in this study supports the use of mxaF as a biomarker for methanotrophic proteobacteria.
Keywords: MID-ATLANTIC RIDGE; OXIDATION; ATMOSPHERIC METHANE; Hydrothermal vents; PHYLUM; COMPLETE GENOME SEQUENCE; ANAEROBIC; SP NOV.; ACIDOPHILIC BACTERIUM; Verrucomicrobia; CANDIDATUS METHYLOMIRABILIS OXYFERA; THIOTROPHIC ENDOSYMBIONTS
Journal Title: PLoS One
Volume: 8
Issue: 2
ISSN: 1932-6203
Publisher: Public Library of Science  
Publication Place: SAN FRANCISCO; 1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA
Date Published: 2013
Start Page: e56993
End Page: e56993
DOI/URL:
Notes: PT: J; TC: 0; UT: WOS:000316658800060