Draft genome sequence data of methanotrophic Methylovulum psychrotolerans strain S1L and Methylomonas paludis strain S2AM isolated from hypoxic water column layers of boreal lakes

Abstract

Methanotrophic bacteria inhabit a wide range of natural (e.g. wetlands, lakes and soils) and anthropogenic (e.g. wastewater treatment plants and landfills) environments. They play a crucial role in mitigating atmospheric emissions of the greenhouse gas methane. There is also a growing interest in applying methanotrophs in the bioconversion of biogas - and natural gas - methane into value-added products (e.g. chemicals and single-cell protein). Hence, isolation and genome sequencing of methanotrophic bacteria is needed to provide important data on their functional capabilities. Here, we describe the de novo assembled draft genome sequences of Methylovulum psychrotolerans strain S1L isolated from hypoxic water column layer of boreal Lake Lovojärvi (Southern Finland), comprising total of 5090628 bp in 11 contigs with G+C – content of 50.9% and containing 4554 coding sequences. The draft genome of strain S1L represents the first published genome of M. psychrotolerans strain isolated from lake ecosystems. In addition, we present the genome sequence of Methylomonas paludis strain S2AM, isolated from water column of boreal Lake Alinen Mustajärvi (Southern Finland), comprising 3673651 bp in 1 contig with G+C – content of 48.2% and 3294 coding sequences. The draft genome of strain S2AM represents the first published genome of M. paludis . The preliminary genome annotation analysis of both S1L and S2AM identified genes encoding oxidation of methane, methanol, formaldehyde and formate, assimilation of carbon, ammonium and nitrate, N 2 fixation, as well as various enzymes enabling the survival in hypoxic conditions, i.e. high-affinity oxidase, hemerythrins, fermentation enzymes (for production of acetate, succinate and H 2 ) and respiratory nitrite reductases. The draft genomes have been deposited at GenBank under the accession JAGVVN000000000 for S1L and CP073754 for S2AM.

Characterization and genome analysis of a psychrophilic methanotroph representing a ubiquitous Methylobacter spp. cluster in boreal lake ecosystems

“…Lake water samples from a small humic and O 2 -stratified lake, Lake Lovojärvi in southern Finland (61° 04’N, 25° 02’E), were used as the isolation source [ 22 ]. The sampling was conducted at the hypoxic layer (5.75 m depth, temperature 5.2 °C, pH 6.5, and dissolved O 2 concentration (DO) < 0.3 mg l −1 ) (Supplementary Fig.…”

“…Library preparation and sequencing for long reads (PacBio Sequel SMRT Cell 1M v2) and short reads (Illumina NovaSeq 6000 platform) were done by Novogene Co. Ltd. (Beijing, China) as previously described by Rissanen et al [ 22 ]. The genomes were de novo assembled using a hybrid assembly strategy in Unicycler (version 0.4.8) with default parameters and “–mode normal” [ 27 ].…”

Characterization and genome analysis of a psychrophilic methanotroph representing a ubiquitousMethylobacterspp. cluster in boreal lake ecosystems

“…Lake water sample from small humic and O 2 -stratified lake, Lake Lovojärvi in southern Finland (61° 04’N, 25° 02’E), was used as the isolation source (Rissanen et al, 2021a). The sampling was conducted at the hypoxic layer (5.75 m depth, temperature 5.2 °C, pH 6.5 and dissolved O 2 concentration < 0.3 mg l -1 ) (Fig.…”

“…Library preparation and sequencing for long reads (PacBio Sequel SMRT Cell 1M v2) and short reads (Illumina NovaSeq 6000 platform) were done by Novogene Co. Ltd. (Beijing, China) as previously described by (Rissanen et al, 2021a). The genomes were de novo assembled using hybrid assembly strategy in Unicycler (version 0.4.8) with default parameters and "-mode normal" (Wick et al, 2017).…”

Enigmatic persistence of aerobic methanotrophs in oxygen-limiting freshwater habitats

“…Future research could focus on isolating and characterizing lake-associated methanotrophic strains that are capable of thriving under microoxic and anoxic conditions (e.g. [ 94 ]). This would enable, for instance, investigation of the role of bacteriohemerythrin (Bhr), gas vesicles, high-affinity oxidases, and extracellular electron transfer in the microbial oxidation of CH 4 under varying O 2 conditions.…”