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

Igor Y Oshkin,Valentina N Khmelenina,Nikolai V Pimenov,Kirill K Miroshnikov,Olga V Danilova,Svetlana N Dedysh,Ruslan Z Suleimanov,Sergey Y But,Nikolai N Kuznetsov,Ekaterina N Tikhonova,Svetlana E Belova

doi:10.3389/fmicb.2021.756830

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.

Highlights

The genus Methylococcus was described in 1966 by Foster and Davis, who isolated a culture of coccus-shaped bacteria capable of growth in a mineral medium with methane (CH4) as the only carbon source from a sludge sample of the Austin municipal sewage plant, Texas (Foster and Davis, 1966)
One novel isolate from a landfill cover soil possessed 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
The set of selected colonies was subjected to several additional serial dilution steps in a liquid modified AMS medium (mAMS) medium at 42°C until isolates of methanotrophic bacteria were obtained

Summary

INTRODUCTION

The genus Methylococcus was described in 1966 by Foster and Davis, who isolated a culture of coccus-shaped bacteria capable of growth in a mineral medium with methane (CH4) as the only carbon source from a sludge sample of the Austin municipal sewage plant, Texas (Foster and Davis, 1966). As suggested by culture-independent studies, Methylococcus-like methanotrophs can be detected in landfill cover soils (Gebert et al, 2009), geothermal soils (Gagliano et al, 2014), and hot springs (Kizilova et al, 2014; Houghton and Stewart, 2020) Cells of these bacteria possess both known types of methane monooxygenase (MMO), which catalyzes the oxidation of methane to methanol, i.e., particulate (pMMO) and soluble (sMMO) forms of this enzyme. Despite the big research interest in methanotrophs of the genus Methylococcus, the number of currently available goodquality genome assemblies of Methylococcus species is limited to those of M. capulatus Bath and M. geothermalis IM1T. One novel isolate from a landfill cover soil possessed 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 This isolate may potentially represent a novel species of the genus Methylococcus

Isolation Procedures

RESULTS AND DISCUSSION

DATA AVAILABILITY STATEMENT