Complete genome sequence of a Methylomonas sp. nov. 2F7 isolated from rice paddy soil in South Korea

Abstract

Objective

This Data Note reports the complete genome sequence and associated functional-genomic data of Methylomonas sp. strain 2F7, a methane-oxidizing bacterium isolated from rice paddy soil in South Korea. These data were generated to support comparative genomic analyses of methanotrophic bacteria and to document the genome-based taxonomic position and C1 metabolism gene repertoire of strain 2F7.

Data description

The dataset includes Oxford Nanopore Technologies MinION raw reads, a two-replicon genome assembly, annotation summaries, functional classifications, a phylogenetic analysis, average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) comparisons, and a curated C1 metabolism gene table. The genome consists of a 4,979,984-bp chromosome and a 23,603-bp plasmid, with an overall G+C content of 51.4%. Annotation identified 4,520 genes, including 4,429 coding sequences (CDSs), nine rRNA genes, 46 tRNA genes, and four ncRNAs. The 16S rRNA gene sequence showed the highest similarity to Methylomonas fluvii EbBᵀ, whereas ANI/dDDH analysis identified Methylomonas rosea WSC-7ᵀ as the closest related type strain by genome-distance criteria, with ANI/dDDH values of 89.6% and 38.0%, respectively. Additional ANI/dDDH comparisons with M. fluvii EbBᵀ and M. defluvii OY6ᵀ yielded values of 89.3%/37.4% and 89.4%/36.9%, respectively. These genome-based values fall below accepted species-boundary thresholds and support placement of strain 2F7 as a putative novel species within the genus Methylomonas. The curated gene table documents pMMO-like and sMMO gene clusters and genes involved in methanol oxidation, formaldehyde oxidation, and ribulose monophosphate (RuMP)–linked C1 assimilation.

Objective

Methane-oxidizing bacteria are major biological sinks for methane in wetland and rice paddy ecosystems. Strain 2F7 was recovered during a project aimed at enriching, isolating, and characterizing methanotrophs and methylotrophs from Korean rice paddy and wetland soils. Surface soil samples were enriched in mineral medium under a methane-containing headspace [1], and candidate methanotrophs were screened by amplification of the pmoA marker gene [2] and 16 S rRNA gene sequencing. Strain 2F7 was assigned to the genus Methylomonas and selected for whole-genome sequencing because it maintained stable growth during purification and carried methanotroph-associated molecular markers.

The objective of this Data Note is to make publicly available the raw sequencing data, genome assembly, genome annotation, and comparative-genomic files generated for strain 2F7. This genomic resource provides a foundation for future studies investigating methane biogeochemistry in wetland ecosystems and the evolutionary biology of type I methanotrophs. The dataset also includes ANI and dDDH comparisons with closely related type strains [3, 4], whose values fall below widely used species-boundary thresholds and support the treatment of strain 2F7 as a putative novel species within the genus Methylomonas. No formal species name is proposed here; a formal taxonomic description will require additional polyphasic evidence and culture collection deposition.

Data description

Data files 1–9 and Data sets 1–3 are summarized in Table 1. Data file 1 provides a circular genome map of strain 2F7 [5]. Data file 2 summarizes genome features, including genome size, G + C content, replicon composition and predicted gene categories. Data files 3 and 4 provide COG and GO functional classifications of predicted proteins, and Data file 5 presents KEGG pathway enrichment and pathway mapping results. Data file 6 contains the 16 S rRNA gene-based phylogenetic tree. Data file 7 provides ANI and dDDH heatmap data for closely related type strains [3, 4], and Data file 8 contains a core-genome phylogenomic tree for 2F7 and related Methylomonas strains. Data file 9 is an Excel workbook providing a curated C1 metabolism gene table.

Table 1.

Overview of data files/datasets

Label	Name of data file/data set	File types (file extension)	DOI or accession number & reference
Data file 1	Circular genome map of Methylomonas sp. strain 2F7	PDF (.pdf)	Figshare (https://doi.org/10.6084/m9.figshare.32134384) [13]
Data file 2	Genome features	PDF (.pdf)	Figshare (https://doi.org/10.6084/m9.figshare.32134501) [14]
Data file 3	COG functional categorization of predicted proteins	PDF (.pdf)	Figshare (https://doi.org/10.6084/m9.figshare.32134528) [15]
Data file 4	GO classification of annotated genes	PDF (.pdf)	Figshare (https://doi.org/10.6084/m9.figshare.32134531) [16]
Data file 5	KEGG pathway enrichment analysis	PDF (.pdf)	Figshare (https://doi.org/10.6084/m9.figshare.32134537) [17]
Data file 6	Phylogenetic tree based on 16 S rRNA sequence	PDF (.pdf)	Figshare (https://doi.org/10.6084/m9.figshare.32134540) [18]
Data file 7	ANI and dDDH heatmap of closely related type strain genomes	PDF (.pdf)	Figshare (https://doi.org/10.6084/m9.figshare.32134552) [19]
Data file 8	Phylogenomic tree based on core genome sequences of Methylomonas sp. 2F7 and closely related type strains	PDF (.pdf)	Figshare (https://doi.org/10.6084/m9.figshare.32134555) [20]
Data file 9	Curated gene table for C1 metabolism	Excel (.xlsx)	Figshare (https://doi.org/10.6084/m9.figshare.32134561) [21]
Data set 1	Raw sequencing data	FASTQ (.fastq)	NCBI Sequence Read Archive. https://identifiers.org/ncbi/insdc.sra:SRR38272862 [22]
Data set 2	Chromosome assembly sequence	FASTA (.fna)	NCBI GenBank/INSDC. Chromosome CP195203 https://identifiers.org/ncbi/insdc:CP195203 [23]
Data set 3	Plasmid assembly sequence	FASTA (.fna)	NCBI GenBank/INSDC. Plasmid CP195204. https://identifiers.org/ncbi/insdc: CP195204 [24]

For whole-genome sequencing, genomic DNA was extracted from a seven-day culture using the Wizard Genomic DNA Purification Kit (Promega, Madison, WI, USA) after centrifugation of cells at 14,000 rpm for 10 min. The genomic DNA was sequenced using an Oxford Nanopore MinION platform. Raw reads are available as Data set 1 under SRA accession SRR38272862, comprising one MinION WGS run with 31,067 spots and 170.6 Mb of sequence data. Reads were assembled de novo using Flye [6], and genome completeness was assessed with CheckM [7]. Annotation was performed using Prokka [8] and the NCBI Prokaryotic Genome Annotation Pipeline [9, 10], and KEGG Orthology mapping was performed with BlastKOALA [11] and iPath3 [12].

The deposited genome assembly contains two replicons: chromosome CP195203 and plasmid CP195204. The chromosome is 4,979,984 bp and the plasmid is 23,603 bp, for a total assembly size of 5,003,587 bp. PGAP annotation identified 4,520 total genes, 4,461 CDSs (4,429 coding sequences, 32 pseudogenes), nine rRNA genes, 46 tRNA genes and four ncRNAs. Data file 9 lists methane monooxygenase, methanol oxidation, PQQ biosynthesis, formaldehyde oxidation, formate oxidation, RuMP-pathway and serine-cycle-associated genes identified in the 2F7 genome.

Limitations

The dataset is based on a single isolate, and phenotypic measurements such as methane oxidation rate, copper-switch behavior and enzyme activity assays are not included. C1 metabolism functions were inferred computationally via genome annotation and pathway mapping; therefore, they require experimental validation. The pMMO-associated genes are described conservatively as pmoA/amoA-like where the automated annotation uses amoA-like terminology; final functional assignment will require curated phylogenetic or biochemical evidence. The taxonomic statement is genome-based and does not constitute valid publication of a new species name. Although genome-based comparisons support strain 2F7 as a putative novel species within the genus Methylomonas, formal taxonomic description will require culture collection deposition and additional polyphasic characterization, including physiological, biochemical, phenotypic, chemotaxonomic and ecological analyses. Because strain 2F7 has been successfully isolated and maintained in culture, it represents a valuable resource for future studies on polyphasic taxonomy, methane oxidation and methane mitigation in rice paddy soil environments.

Abbreviations

ANI

Average nucleotide identity

CDS

Coding sequence

dDDH

digital DNA-DNA hybridization

MMO

Methane monooxygenase

ONT

Oxford nanopore Technologies

pMMO

particulate methane monooxygenase

PQQ

Pyrroloquinoline quinone

RuMP

Ribulose monophosphate

sMMO

soluble methane monooxygenase

Author contributions

YJG performed genome analysis. SEJ wrote the manuscript. SCK performed microbial culture and DNA extraction. KBK contributed to comparative genomic analysis, taxonomic interpretation, and manuscript revision. HJL conceived the overall study design and wrote the manuscript. All authors read and approved the final manuscript.

Funding

Not applicable.

Data availability

The genome assembly is available in GenBank under accession numbers CP195203 and CP195204, associated with BioProject PRJNA1279808 and BioSample SAMN49505834. Raw Oxford Nanopore reads are available under SRA accession SRR38272862.

Declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.