Members of the genus Methylococcus are thermotolerant or moderately thermophilic methanotrophs utilizing methane as the sole carbon and energy source (Bowman, 2015). They possess both particulate methane monooxygenase (pMMO) and soluble methane monooxygenase (sMMO) (Bowman, 2015). They are typically found in environments such as sewage, freshwaters, geothermal fields, and landfills (Malashenko et al., 1975; Bowman et al., 1993). Members of this genus have numerous biotechnological applications, including bioremediation of pollutants and conversion of methane into commercially valuable products (Semrau, 2011; Semrau and DiSpirito, 2019). Here, we report the complete genome sequence of a recently described member of this genus, Methylococcus geothermalis IM1^T (Awala et al., 2020).

Strain IM1^T was grown in a low salt mineral (LSM) medium with methane as the sole carbon and energy source under constant agitation (200 rpm) at 42°C. High molecular-weight genomic DNA was extracted from this culture using a previously described modified CTAB method (Hurt et al., 2001). Whole-genome sequencing was performed using the PacBio RS II and Illumina HiSeq (2 × 150 bp) platforms at Macrogen. Long-read sequencing from the PacBio RS II platform was used for de novo assembly with HGAP assembler (v3.0) (Chin et al., 2013). Error correction of the assembled genome was performed with Pilon (v1.23; default settings with three iterations) (Walker et al., 2014) using the HiSeq reads. Annotation of the assembled genome was performed using the NCBI Prokaryotic Genome Annotation Pipeline v5.3 (Tatusova et al., 2016).

Strain IM1^T has a circular chromosome of 3,371,031 bp in size and a G + C content of 63.25%. Other genomic features are presented in Table 1. Genes required for methanotrophic traits were found in strain IM1^T genome. These include two nearly identical copies of the pmoCAB operon and a single pmoC paralog encoding the pMMO. A gene cluster (mmoRSQG-hypothetical protein-mmoCDZBYX) containing components of the sMMO was also detected. Methanol from methane oxidation is oxidized to formaldehyde using the pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenases. Gene clusters for PQQ biosynthesis (pqqABCDE), calcium-(mxaEYFJGIRSACKLD), and lanthanide-(xoxFJ and xoxG) dependent methanol dehydrogenases were found.

Table 1

Feature type	Value
Size (bp)	3,371,031
Contigs	1
Circular chromosome	Yes
G + C content (%)	63.25
Contig N50	3,371,031
Genes (total)	3,147
CDS (total)	3,090
CDS (with protein)	2,985
rRNAs (5S, 16S, 23S)	2, 2, 2
tRNAs	47
ncRNAs	3
GenBank Accession	CP046565

Genes for formaldehyde oxidation to CO₂ via formate, and biomass generation via the serine, ribulose monophosphate (RuMP), and Calvin-Benson-Bassham (CBB) cycles were found. These include (1) genes for the tetrahydromethanopterin-(fae, fhcCDAB, mch, mptG, mtdB) and tetrahydrofolate-(fch, fhs, and mtdA) dependent formaldehyde oxidation, (2) genes encoding different orthologs of formate dehydrogenase, and (3) key genes of the serine (sgaA, hpr, and gck), RuMP (phi and hps), and CBB (cbbSL) cycles.

Nitrogen-metabolism genes were also present in the genome. A gene cluster containing an assimilatory nitrate reductase (nasA), nitrite reductase (nirBD), and nitrate transporter was present. Strain IM1^T also possessed genes encoding hydroxylamine oxidoreductase (haoAB), nitric oxide reductase (norBC), and nitrogenase (nifHDK and nifENX).

Nucleotide sequence accession number

The whole-genome sequence accession number for Methylococcus geothermalis IM1^T in GenBank is CP046565. The strain accession numbers at the Korean Collection for Type Cultures and Japan Collection of Microorganisms are KCTC 72677 and JCM 33941, respectively.

한국의 온천에서 분리한 Methylococcus 속의 고온성 호기성 메탄산화균의 유전체를 분석하였다. 이 세균은 메탄의 산화에 관여하는 핵심 유전자(pMMO 와 sMMO)를 포함하여 전체 메탄 산화 과정에 관여하는 다양한 유전자를 보유하고 있다. 또한, 탄소 고정을 위한 대사(ribulose monophosphate, serine, 그리고 Calvin-Benson-Bassham cycle)를 포함하여 다양한 질소 대사 과정(질산 및 질소 동화; hydroxylamine 무독화)에 관여하는 유전자를 보유하고 있다.

This work was financially supported by the Research Year of Chungbuk National University in 2019 and the National Institute of Agricultural Science, Ministry of Rural Development Administration, Republic of Korea (research project PJ01700703).

The authors declare no notable conflict of interest.