Methylocystis borbori sp.nov., a novel methanotrophic bacterium from the sludge of a freshwater lake and its metabolic properties

Abstract

A novel methanotrophic strain 9N^T was isolated from the sludge of a freshwater lake. Cells were aerobic, Gram-stain-negative, non-motile pleomorphic rods with intracytoplasmic membrane systems that appropriate type-II methanotrophs and hemispherical and spherical exocellular formations on the perimeter of the cell wall surface. The novel isolate grows only on methane or methanol as the sole carbon and energy source, at 10–37 °C (optimum 28–30 °C), pH 4.5–9.0 (optimum 7.0–7.5), up to 1% NaCl (optimum 0.3–0.5%). Methanol supported the growth of the strain 9N^T in a wide range of concentrations from 0.05 to 5.0% (v/v) with an optimum of 0.5% (v/v). The major fatty acids were C_18:1ω8c and C_18:1ω7c. Based on 16S rRNA gene sequence phylogenetic analysis, strain 9N^T was closely related to representatives of the genus Methylocystis (96.5–98.3%). The genome of strain 9N^T was 3.34 Mbp in size with 63.5% of G + C content. The average nucleotide identity and digital DNA–DNA hybridization values between strain 9N^T and closely related type strains of genus Methylocystis were 78.0–82.4% and 20.9–24.3%, respectively. The careful genome annotation of the novel strain shows it possessed genes for the detoxification of arsenate and cyanides as well as genes potentially involved in plant growth promotion (such as biosynthesis of indoles, cytokinins, polyhydroxybutyrate, siderophore production, and nitrogen fixation). Based on the phylogenetic, phenotypic, chemotaxonomic and genomic data, we propose Methylocystis borbori sp. nov. as novel species of the genus Methylocystis. The type strain is 9N^T (= VKM B-3616^T = KCTC 92566^T).