Methyloprofundus sedimenti gen. nov., sp nov., an obligate methanotroph from ocean sediment belonging to the 'deep sea-1' clade of marine methanotrophs

We report the isolation and growth characteristics of a gammaproteobacterial methane-oxidizing bacterium (Methylococcaceae strain WF1(T), 'whale fall 1') that shares 98% 16S rRNA gene sequence identity with uncultivated free-living methanotrophs and the methanotrophic endosymbionts of deep-sea mussels, <= 94.6% 16S rRNA gene sequence identity with species of the genus Methylobacter and <= 93.6% 16S rRNA gene sequence identity with species of the genera Methylomonas and Methylosarcina. Strain WF1(T) represents the first cultivar from the 'deep sea-1' clade of marine methanotrophs, which includes members that participate in methane oxidation in sediments and the water column in addition to mussel endosymbionts. Cells of strain WF1(T) were elongated cocci, approximately 1.5 mu m in diameter, and occurred singly, in pairs and in clumps. The cell wall was Gram-negative, and stacked intracytoplasmic membranes and storage granules were evident. The genomic DNA G+C content of WF1(T) was 40.5 mol%, significantly lower than that of currently described cultivars, and the major fatty acids were 16:0, 16:1 omega 9c, 16:1 omega 9t, 16:1 omega 8c and 16:2 omega 9,14. Growth occurred in liquid media at an optimal temperature of 23 degrees C, and was dependent on the presence of methane or methanol. Atmospheric nitrogen could serve as the sole nitrogen source for WF1(T), a capacity that had not been functionally demonstrated previously in members of Methylobacter. On the basis of its unique morphological, physiological and phylogenetic properties, this strain represents the type species within a new genus, and we propose the name Methyloprofundus sedimenti gen. nov., sp. nov. The type strain of Methyloprofundus sedimenti is WF1(T) (=LMG 28393(T)=ATCC BAA-2619(T)).