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

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.


a b s t r a c t
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 prelimi-nary genome annotation analysis of Z-0021 identified genes encoding oxidation of methane, methanol and formaldehyde, assimilation of carbon and nitrate, and N 2 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.  Repository: The assembled whole-genome shotgun data (.fasta) has been deposited at GenBank under the accession number JAOEGU0 0 0 0 0 0 0 0 0 ( https://www.ncbi.nlm.nih.gov/nuccore/JAOEGU0 0 0 0 0 0 0 0 0 ). The raw sequence data (.fastq) have been deposited in the SRA database under the Bioproject PRJNA883059 ( https://www.ncbi.nlm.nih.gov/sra/PRJNA883059 ) and Biosample SAMN30959511.

Value of the Data
• Draft genome sequence data of Methylobacter psychrophilus Z-0021 provide fundamental knowledge on the functional potential of psychrophilic methanotrophs mitigating methane emissions from cold, boreal and arctic terrestrial and aquatic ecosystems, and give insights into their biotechnical applicability. • This data can be utilized by researchers in biogeochemistry, (environmental) microbiology, biotechnology and circular economy. • This data can be used in predicting the function of methanotrophs in natural, cold ecosystems under variating physicochemical conditions as well as in developing methane-based bioproduct platforms to be utilized in cold regions.

Objective
Psychrophilic (i.e., cold-loving) methanotrophic bacteria are widely distributed and play an important role in methane removal in cold, boreal and arctic soil and aquatic ecosystems [1][2][3] . They could also be applied in the bioconversion of biogas-and natural gas methane into valueadded products in cold environments [4] . Therefore, genomic data of psychrophilic methanotrophs is needed to provide important insights into their functional capabilities. However, psychrophilic methanotroph isolates and consequently their genomes are currently rare [3] . A psychrophilic methanotroph, Methylobacter psychrophilus Z-0021, was isolated from tundra soil during the 1990s [5] . Despite being deposited into All-Russian Collection of Microorganisms -VKM (VKM), the isolate was not available as a pure culture at early-mid 20 0 0s when a psychrotrophic, methanotrophic arctic wetland soil isolate, Methylobacter tundripaludum SV96 was characterized, thus, restricting a DNA-DNA hybridization comparison between SV96 and Z-0021 isolates [6] . Leibniz Institute, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH (DSMZ) had also received a culture of the strain, but it had been contaminated (personal communication with DSMZ staff). Fortunately, DSMZ could re-purify the strain from their stocks and make it publicly available during 2022 ( https://www.dsmz.de/collection/catalogue/details/ culture/DSM-9914 ). We hereby provide the first draft genome of Methylobacter psychrophilus Z-0021 (DSM 9914).

Experimental Design, Materials and Methods
DSMZ repurified Methylobacter psychrophilus Z-0021 (DSM 9914) from their stocks and made it publicly available during 2022 (see details of the strain Z-0021 and its cultivation conditions: https://www.dsmz.de/collection/catalogue/details/culture/DSM-9914 ).
For this work, the DNA extraction, as well as the genome sequencing and genome assembly of Z-0021 was ordered as a commercial service from DSMZ. Genomic DNA extraction was carried out using MasterPure TM Gram Positive DNA Purification Kit from Epicentre®Biotechnologies Germany according to the manufacturer ś instructions. Sequencing library was prepared using Nextera XT DNA Library Preparation Kit (Illumina®, USA). Library was sequenced on NextSeq 550 Sequencing System using NextSeq 500/550 High Output Kit v2.5 (Illumina®, USA).

Ethics Statement
This work meets the ethical requirements for publication. Furthermore, this work did not involve human subjects, animal experiments and data collected from social media platforms.

Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.