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

Abstract

We report the isolation and growth characteristics of a gammaproteobacterial methane-oxidizing bacterium (Methylococcaceae strain WF1, "whale fall 1" that shares 98% 16S rRNA identity with uncultivated free-living methanotrophs and the methanotrophic endosymbionts of deep sea mussels, 94.6% 16S rRNA identity with Methylobacter species, and 93.6% 16S rRNA identity with Methylomonas and Methylosarcina species. Strain WF1 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. WF1 cells were elongated cocci approximately 1.5 µm in diameter, and occurred singly, in pairs and clumps. The cell wall was Gram negative, and stacked intracytoplasmic membranes and storage granules were evident. The genomic GC content of WF1 was 40.5%, significantly lower than currently described cultivars, and the major fatty acids were 16:0, 16:1 ω9c, 16:1 ω9t, 16:1 ω8c and 16:2 ω9, 14. Growth occurred in liquid media at an optimal temperature of 23oC, and was dependent on the presence of methane or methanol. Atmospheric nitrogen could serve as the sole nitrogen source for WF1, a capacity that had not been functionally demonstrated in members of Methylobacter. On the basis of unique morphological, physiological, and phylogenetic properties this strain represents the type species within a new genus, and we propose the name Methyloprofundus sedimenti (type strain WF1 = BCCM LMG 28393 = ATCC BAA-2619).

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