Expanding Characterized Diversity and the Pool of Complete Genome Sequences of Methylococcus Species, the Bacteria of High Environmental and Biotechnological Relevance

Abstract

The bacterial genus Methylococcus, which comprises aerobic thermotolerant methanotrophic cocci, was described half-a-century ago. Over the years, a member of this genus, Methylococcus capsulatus Bath, has become a major model organism to study genomic and metabolic basis of obligate methanotrophy. High biotechnological potential of fast-growing Methylococcus species, mainly as a promising source of feed protein, has also been recognized. Despite this big research attention, the currently cultured Methylococcus diversity is represented by members of the two species, M. capsulatus and M. geothermalis, while finished genome sequences are available only for two strains of these methanotrophs. This study extends the pool of phenotypically characterized Methylococcus strains with good-quality genome sequences by contributing four novel isolates of these bacteria from activated sludge, landfill cover soil, and freshwater sediments. The determined genome sizes of novel isolates varied between 3.2 and 4.0Mb. As revealed by the phylogenomic analysis, strains IO1, BH, and KN2 affiliate with M. capsulatus, while strain Mc7 may potentially represent a novel species. Highest temperature optima (45–50°C) and highest growth rates in bioreactor cultures (up to 0.3h−1) were recorded for strains obtained from activated sludge. The comparative analysis of all complete genomes of Methylococcus species revealed 4,485 gene clusters. Of these, pan-genome core comprised 2,331 genes (on average 51.9% of each genome), with the accessory genome containing 846 and 1,308 genes in the shell and the cloud, respectively. Independently of the isolation source, all strains of M. capsulatus displayed surprisingly high genome synteny and a striking similarity in gene content. Strain Mc7 from a landfill cover soil differed from other isolates by the high content of mobile genetic elements in the genome and a number of genome-encoded features missing in M. capsulatus, such as sucrose biosynthesis and the ability to scavenge phosphorus and sulfur from the environment.

Complete Genome Sequence of Methylococcus capsulatus MIR, a Methanotroph Capable of Growth on Methanol

“…The species Methylococcus capsulatus represents aerobic thermotolerant methanotrophic bacteria that are widely distributed in various habitats ( 1 , 2 ) and possess high biotechnological potential. With very few exceptions, characterized strains of this species display only trace growth on methanol ( 3 ). Here, we report the complete genome sequence of a new M. capsulatus isolate, strain MIR, which is capable of growth on methanol in the range of concentrations of 0.05 to 3.5% (vol/vol) in a mineral medium ( 3 ) during incubation at 42°C ( Fig.…”

“…With very few exceptions, characterized strains of this species display only trace growth on methanol ( 3 ). Here, we report the complete genome sequence of a new M. capsulatus isolate, strain MIR, which is capable of growth on methanol in the range of concentrations of 0.05 to 3.5% (vol/vol) in a mineral medium ( 3 ) during incubation at 42°C ( Fig. 1 ).…”

“…1 ). Strain MIR was isolated from the upper oxic layer of activated sludge from the Irkutsk municipal wastewater treatment plant using a mineral medium with 20% (vol/vol) methane and the previously described isolation procedure ( 3 ). Genomic DNA was extracted from a liquid culture of strain MIR grown with methane ( 3 ) using the standard cetyltrimethyl ammonium bromide (CTAB) and phenol-chloroform protocol ( 4 ).…”

“…Strain MIR was isolated from the upper oxic layer of activated sludge from the Irkutsk municipal wastewater treatment plant using a mineral medium with 20% (vol/vol) methane and the previously described isolation procedure ( 3 ). Genomic DNA was extracted from a liquid culture of strain MIR grown with methane ( 3 ) using the standard cetyltrimethyl ammonium bromide (CTAB) and phenol-chloroform protocol ( 4 ). The 16S rRNA gene of strain MIR was PCR amplified using the primers 9f and 1492r ( 5 ) and displayed greatest similarity (99.93%) to that of M. capsulatus Bath (GenBank accession number AE017282.2 ).…”

“…Both MxaFI and XoxF methanol dehydrogenases ( 12 ), as well as three different isozymes of formate dehydrogenase, are also encoded. Since C 1 assimilation pathways are common among all Methylococcus species ( 2 , 3 ), strain MIR may serve as a model organism for studying the metabolic basis of methanol tolerance.…”