Methylocaldum marinum sp. nov., a thermotolerant, methane-oxidizing bacterium isolated from marine sediments, and emended description of the genus Methylocaldum

Abstract

Methylocaldum marinum sp. nov., a thermotolerant, methane-oxidizing bacterium isolated from marine sediments, and emended description of the genus Methylocaldum Genetic Research Section, Atmosphere and Ocean Research Institute, the University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8564, JapanAn aerobic, methane-oxidizing bacterium (strain S8 T ) was isolated from marine sediments in Kagoshima Bay, Japan. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain is closely related to members of the genus Methylocaldum (97.6-97.9 % similarity) within the class Gammaproteobacteria. Strain S8 T was a Gram-staining-negative, non-motile, coccoid or short rod-shaped organism. The temperature range for growth of strain S8 T was 20-47 6C (optimum growth at 36 6C). It required NaCl (.0.5 %), tolerated up to 5 % NaCl and utilized methane and methanol. The major cellular fatty acid and major respiratory quinone were C 16 : 0 and 18-methylene ubiquinone 8, respectively. The DNA G+C content was 59.7 mol%. Strain S8 T possessed mmoX, which encodes soluble methane monooxygenase, as well as pmoA, which encodes the particulate methane monooxygenase. On the basis of this morphological, physiological, biochemical and genetic information, the first marine species in the genus Methylocaldum is proposed, with the name Methylocaldum marinum sp. nov. The type strain is S8 T (5NBRC 109686 T 5DSM 27392 T ). An emended description of the genus Methylocaldum is also provided.The methane cycle in the ocean has been the subject of increased attention in recent years. It has been reported that methane is produced not only in anaerobic environments but also in aerobic environments such as the water at the surface of the ocean, possibly through the decomposition of methylphosphonate (Karl et al. 2008) or via methanogenesis (Grossart et al., 2011). On the seafloor, destabilization of methane hydrate due to changes in ocean temperature has been found to occur in the North American margin (Phrampus & Hornbach, 2012), possibly 3Present address: Faculty of Science, Toyama University, 3190 Gofuku, Toyama-shi, Toyama 930-8555, Japan.4Present address: Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan.Abbreviations: RuMP, ribulose monophosphate; sMMO, soluble methane monooxygenase.The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA, mmoX, pmoA and cbbL gene sequences of strain S8 T are AB894129, AB900160, AB900159 and AB922600, respectively.

Large‐scale biogeography and environmental regulation of methanotrophic bacteria across boreal inland waters

“…We found this genus throughout the boreal landscape and in different types of ecosystems, supporting that this group may be composed of generalists (Knief, ). This contrasts with the reports of Methylocaldum strains that appear to occupy very specific habitats, such as hydrothermal vents or landfill soils (Takeuchi et al, ; Zhang, Kong, Xia, Su, & He, ), implying thermotolerant and thermophilic properties (Bodrossy, Holmes, Holmes, Kovacs, & Murrell, ). We identified OTUs belonging to the genus Methylomonas , which has been described as an acid‐tolerant genus inhabiting acidic peatlands (Knief, ).…”

New Methyloceanibacter diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase

“…Despite their crucial role in marine carbon cycling, only a handful of marine methanol oxidizers and even fewer methane oxidizers, the latter all belonging to the Gammaproteobacteria , have been isolated and physiologically characterized (Sieburth et al , ; Lidstrom, ; Fuse et al , ; Giovannoni et al , ; Boden et al , ; Huggett et al , ; Hirayama et al , ; Hirayama et al , ; Takeuchi et al , ; Tavormina et al , ; Jimenez‐Infante et al , ). Most methanotrophic surveys focused on high methane‐loaded systems like mud vulcanoes (Niemann et al , ), vent fields (Nercessian et al , ) and methane gas seeps (Inagaki et al , ; Yan et al , ; Håvelsrud et al , ).…”

A new cell morphotype among methane oxidizers: a spiral-shaped obligately microaerophilic methanotroph from northern low-oxygen environments

“…One additional type of gammaproteobacterial methanotrophs, type X, was originally proposed for Methylococcus capsulatus, which, in addition to ribulose monophosphate pathway, possesses ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), a key enzyme in the Calvin-Benson cycle (Whittenbury and Dalton, 1981;Whittenbury, 1981). Several Methylococcus-related methanotrophs have been described including the genera Methylocaldum (Bodrossy et al, 1997;Takeuchi et al, 2014), Methyloparacoccus (Hoefman et al, 2014) and Methylogaea (Geymonat et al, 2010). Members of these genera form a monophyletic cluster in pmoA gene-based trees and are lately addressed as type Ib methanotrophs.…”