Draft genome sequence data of a psychrophilic tundra soil methanotroph, Methylobacter psychrophilus Z-0021 (DSM 9914)

Antti Juhani Rissanen; Rahul Mangayil; Mette Marianne Svenning; Ramita Khanongnuch

doi:10.1016/j.dib.2022.108689

Draft genome sequence data of a psychrophilic tundra soil methanotroph, Methylobacter psychrophilus Z-0021 (DSM 9914)

Data Brief. 2022 Oct 21:45:108689. doi: 10.1016/j.dib.2022.108689. eCollection 2022 Dec.

Authors

Antti Juhani Rissanen^{1

2}, Rahul Mangayil^{1

3}, Mette Marianne Svenning⁴, Ramita Khanongnuch¹

Affiliations

¹ Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, FI-33014 Tampere, Finland.
² Natural Resources Institute Finland, Latokartanonkaari 9, FI-00790 Helsinki, Finland.
³ Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland.
⁴ Department of Arctic and Marine Biology, UiT, The Arctic University of Norway, Tromsø 9037, Norway.

Abstract

Psychrophilic methanotrophic bacteria are abundant and play an important role in methane removal in cold methanogenic environments, such as boreal and arctic terrestrial and aquatic ecosystems. They could be also applied in the bioconversion of biogas and natural gas into value-added products (e.g., chemicals and single-cell protein) in cold regions. Hence, isolation and genome sequencing of psychrophilic methanotrophic bacteria are needed to provide important data on their functional capabilities. However, psychrophilic methanotroph isolates and consequently their genome sequences are rare. Fortunately, Leibniz Institute, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH was able to revive the long-extinct pure culture of a psychrophilic methanotrophic tundra soil isolate, Methylobacter psychrophilus Z-0021 (DSM 9914), from their stocks during 2022. Here, we describe the de novo assembled genome sequence of Methylobacter psychrophilus Z-0021 comprising a total of 4691082 bp in 156 contigs with a G+C content of 43.1% and 4074 coding sequences. The preliminary genome annotation analysis of Z-0021 identified genes encoding oxidation of methane, methanol and formaldehyde, assimilation of carbon and nitrate, and N₂ fixation. In pairwise genome-to-genome comparisons with closely related methanotrophic strains, the strain Z-0021 had an average nucleotide identity (ANI) of 92.9% and 78.2% and a digital DNA-DNA hybridization (dDDH) value of 50.6% and 22% with a recently described psychrophilic, lake isolate, Methylobacter sp. S3L5C and a psychrotrophic, arctic wetland soil isolate, Methylobacter tundripaludum SV96, respectively. In addition, the respective similarities between genomes of the strains S3L5C and SV96 were 78.1% ANI and 21.8% dDDH. Comparison to widely used ANI and dDDH thresholds to delineate unique species (<95% ANI and <70% dDDH) suggests that Methylobacter psychrophilus Z-0021, Methylobacter tundripaludum SV96 and Methylobacter sp. S3L5C are different species. The draft genome of Z-0021 has been deposited at GenBank under the accession JAOEGU000000000.

Keywords: Arctic; Boreal; Cold ecosystem; Methane; Methanotroph; Methylobacter; Psychrophilic; Tundra.