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Background    Methylocystis  sp. strain SC2 can adapt to a wide range of methane concentrations. This is due to the presence of two isozymes of particulate methane monooxygenase exhibiting different methane oxidation kinetics. To gain insight into the underlying genetic information, its genome was sequenced and found to comprise a 3.77 Mb chromosome and two large plasmids.    Principal Findings  We report important features of the strain SC2 genome. Its sequence is compared with those of seven other methanotroph genomes, comprising members of the  Alphaproteobacteria ,  Gammaproteobacteria , and  Verrucomicrobia . While the pan-genome of all eight methanotroph genomes totals 19,358 CDS, only 154 CDS are shared. The number of core genes increased with phylogenetic relatedness: 328 CDS for proteobacterial methanotrophs and 1,853 CDS for the three alphaproteobacterial  Methylocystaceae  members,  Methylocystis  sp. strain SC2 and strain Rockwell, and  Methylosinus trichosporium  OB3b. The comparative study was coupled with physiological experiments to verify that strain SC2 has diverse nitrogen metabolism capabilities. In correspondence to a full complement of 34 genes involved in N 2  fixation, strain SC2 was found to grow with atmospheric N 2  as the sole nitrogen source, preferably at low oxygen concentrations. Denitrification-mediated accumulation of 0.7 nmol  30 N 2 /hr/mg dry weight of cells under anoxic conditions was detected by tracer analysis. N 2  production is related to the activities of plasmid-borne nitric oxide and nitrous oxide reductases.    Conclusions/Perspectives  Presence of a complete denitrification pathway in strain SC2, including the plasmid-encoded  nosRZDFYX  operon, is unique among known methanotrophs. However, the exact ecophysiological role of this pathway still needs to be elucidated. Detoxification of toxic nitrogen compounds and energy conservation under oxygen-limiting conditions are among the possible roles. Relevant features that may stimulate further research are, for example, absence of CRISPR/Cas systems in strain SC2, high number of iron acquisition systems in strain OB3b, and large number of transposases in strain Rockwell.

Genome Analysis Coupled with Physiological Studies Reveals a Diverse Nitrogen Metabolism in Methylocystis sp. Strain SC2