Evaluation and update of cutoff values for methanotrophic pmoA gene sequences.
The functional pmoA gene is frequently used to probe the diversity and phylogeny of methane-oxidizing bacteria (MOB) in various environments. Here, we compared the similarities between the pmoA gene and the corresponding 16S rRNA gene sequences of 77 described species covering gamma- and alphaproteobacterial methanotrophs (type I and type II MOB, respectively) as well as methanotrophs from the phylum Verrucomicrobia. We updated and established the weighted mean pmoA gene cutoff values on the nucleotide level at 86, 82, and 71 % corresponding to the 97, 95, and 90 % similarity of the 16S rRNA gene. Based on these cutoffs, the functional gene fragments can be entirely processed at the nucleotide level throughout software platforms such as Mothur or QIIME which provide a user-friendly and command-based alternative to amino acid-based pipelines. Type II methanotrophs are less divergent than type I both with regard to ribosomal and functional gene sequence similarity and GC content. We suggest that this agrees with the theory of different life strategies proposed for type I and type II MOB.
Helmholtz Center Potsdam, GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Telegrafenberg, 14473, Potsdam, Germany.|College of Electrical Engineering, Northwest University for Nationalities, Lanzhou, 730030, China.
Xi
X
Wen
Helmholtz Center Potsdam, GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Telegrafenberg, 14473, Potsdam, Germany. syang@gfz-potsdam.de.|State Key Laboratory of Frozen Soils Engineering, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, China. syang@gfz-potsdam.de.
Sizhong
S
Yang
Helmholtz Center Potsdam, GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Telegrafenberg, 14473, Potsdam, Germany.
Susanne
S
Liebner
D001482:Base Composition; D001483:Base Sequence; D008697:Methane / Q000378:metabolism*; D008772:Methylococcaceae / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D010084:Oxidation-Reduction; D010105:Oxygenases / Q000235:genetics*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D061327:Verrucomicrobia / Q000145:classification / Q000235:genetics* / Q000378:metabolism
D012336:RNA, Ribosomal, 16S; D010105:Oxygenases; D008697:Methane
Cutoff; GC content; Methanotrophs; Mothur; pmoA gene