Methanococcoides cohabitans sp. nov., a marine methylotrophic methanogen isolated from an anaerobic methane-oxidizing enrichment culture.

Abstract

Enrichment cultures of archaea and bacteria performing the anaerobic oxidation of methane (AOM) regularly contain persistent methanogens. Here, we isolated the marine methanogen Methanococcoides cohabitans sp. nov. strain LMO-2^T from a long-term AOM enrichment culture from the Northern Gulf of Mexico. Strain LMO-2^T is Gram-stain-negative, irregular 0.5-1 µm coccus without flagella. It utilizes a variety of methylated compounds including methanol, monomethylamine, dimethylamine and trimethylamine for growth and methanogenesis. However, it does not grow on formate, acetate, dimethyl sulphate, H₂/CO₂, betaine and choline. The optimal conditions for growth were observed within a temperature range of 30-35 °C, a pH range of 7.0-8.0 and a salinity range of 2-4% NaCl. Based on the similarity and phylogeny of the 16S rRNA gene and genomic sequence, strain LMO-2^T is classified within the genus Methanococcoides. Among the isolated type strains of the genus, strain LMO-2^T exhibited the highest 16S rRNA gene sequence identity with Methanococcoides vulcani SLH33^T (99.4%). The digital DNA-DNA hybridization and average nucleotide identity based on genome sequence showed that strain LMO-2^T shared the highest similarity with Methanococcoides orientis LMO-1^T, with values of 27.3% and 83.4%, respectively. In conclusion, we isolated a methylotrophic methanogen from an AOM culture, and the isolated strain LMO-2^T represented a novel species of the genus Methanococcoides, for which the name Methanococcoides cohabitans sp. nov. is proposed. The type strain is LMO-2^T (=CGMCC 1.18051^T=KCTC 25774^T).