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Complete genome sequence of Methylococcus geothermalis IM1T isolated from a geothermal field
Korean J. Microbiol. 2022;58(2):88-90
Published online June 30, 2022
© 2022 The Microbiological Society of Korea.

Samuel Imisi Awala, Joo-Han Gwak, Yong-Man Kim, Chanmee Seo, and Sung-Keun Rhee*

Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
Correspondence to: *E-mail:; Tel.: +82-43-261-2300; Fax: +82-43-264-9600
Received April 27, 2022; Revised May 20, 2022; Accepted May 21, 2022.
The genome of Methylococcus geothermalis strain IM1T, a moderately thermophilic aerobic methanotroph isolated from a geothermal field in South Korea, was sequenced. This bacterium possesses genes encoding the particulate and soluble membrane monooxygenase necessary for methane oxidation, and enzymes required for the following reaction steps converting methanol to CO2. Genes for carbon assimilation pathways including the ribulose monophosphate, serine, and Calvin-Benson-Bassham cycles, assimilation of various nitrogen compounds, and detoxification of reactive nitrogen species such as hydroxylamine oxidoreductase were also found.
Keywords : Methylococcus, genome, methane, methanotroph

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 IM1T (Awala et al., 2020).

Strain IM1T 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 IM1T 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 IM1T 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.

Genomic features of <italic>M. geothermalis</italic> IM1<sup>T</sup>
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 IM1T 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 IM1T 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.

적 요

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).

Conflict of Interest

The authors declare no notable conflict of interest.

  1. Awala SI, Bellosillo LA, Gwak JH, Nguyen NL, Kim SJ, Lee BH, and Rhee SK. 2020. Methylococcus geothermalis sp. nov., a methanotroph isolated from a geothermal field in the Republic of Korea. Int. J. Syst. Evol. Microbiol. 70, 5520-5530.
    Pubmed CrossRef
  2. Bowman JP. 2015. Methylococcus. In Trujillo ME, Dedysh S, DeVos P, Hedlund B, Kämpfer P, Rainey FA, Whitman WB (ed.). Bergey's Manual of Systematics of Archaea and Bacteria. John Wiley & Sons, Inc, Hoboken, New Jersey, USA.
  3. Bowman JP, Sly LI, Nichols PD, and Hayward AC. 1993. Revised taxonomy of the methanotrophs: description of Methylobacter gen. nov., emendation of Methylococcus, validation of Methylosinus and Methylocystis species, and a proposal that the family Methylococcaceae includes only the group I methanotrophs. Int. J. Syst. Evol. Microbiol. 43, 735-753.
  4. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, and Eichler EEEichler EE, et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563-569.
    Pubmed CrossRef
  5. Hurt RA, Qiu X, Wu L, Roh Y, Palumbo A, Tiedje JM, and Zhou J. 2001. Simultaneous recovery of RNA and DNA from soils and sediments. Appl. Environ. Microbiol. 67, 4495-4503.
    Pubmed KoreaMed CrossRef
  6. Malashenko IP, Romanovskaia VA, Bogachenko VN, and Shved AD. 1975. Thermophilic and thermotolerant bacteria that assimilate methane. Mikrobiologiia 44, 855-862.
  7. Semrau JD. 2011. Bioremediation via methanotrophy: overview of recent findings and suggestions for future research. Front. Microbiol. 2, 209.
    Pubmed KoreaMed CrossRef
  8. Semrau JD and DiSpirito AA. 2019. Methanotrophy - environmental, industrial and medical applications. Curr. Issues Mol. Biol. 33, 1-22.
    Pubmed CrossRef
  9. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, and Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614-6624.
    Pubmed KoreaMed CrossRef
  10. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, and Young SKYoung SK, et al. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963.
    Pubmed KoreaMed CrossRef

June 2022, 58 (2)