Downloaded from www.microbiologyresearch.org by IP: 54.70.40.11 On: Fri, 07 Dec 2018 05:31:33 Geofilum rubicundum gen. nov., sp. nov., isolated from deep subseafloor sediment Masayuki Miyazaki, 1 Osamu Koide, 2 Tohru Kobayashi, 2 Kozue Mori, 3 Shigeru Shimamura, 1 Takuro Nunoura, 1 Hiroyuki Imachi, 1 Fumio Inagaki, 4 Takahiko Nagahama, 2 Yuichi Nogi, 2 Shigeru Deguchi 2 and Ken Takai 1 Correspondence Masayuki Miyazaki miyazakim@jamstec.go.jp 1 Subsurface Geobiology Advanced Research (SUGAR) project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan 2 Soft Matter and Extremophiles Research Team, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan 3 Marine Bioresource Exploration Research Team and Institute of Biogeosciences (BioGeos), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan 4 Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine- Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan A novel, facultatively anaerobic bacterium (strain JAM-BA0501 T ) was isolated from a deep subseafloor sediment sample at a depth of 247 m below seafloor off the Shimokita Peninsula of Japan in the north-western Pacific Ocean (Site C9001, 1180 m water depth). Cells of strain JAM- BA0501 T were Gram-negative, filamentous, non-spore-forming and motile on solid medium by gliding. Phylogenetic analysis based on the 16S rRNA gene sequence of strain JAM-BA0501 T indicated a distant relationship to strains representing genera within the order Bacteroidales, such as Alkaliflexus imshenetskii Z-7010 T (91.1 % similarity), Marinilabilia salmonicolor ATCC 19041 T (86.2 %) and Anaerophaga thermohalophila Fru22 T (89.3 %). The new isolate produced isoprenoid quinones with menaquinone MK-7 as the major component, and the predominant fatty acids were iso-C 15 : 0 and anteiso-C 15 : 0 . The DNA G+C content of the isolate was 42.9 mol%. Based on its taxonomic distinctiveness, strain JAM-BA0501 T is considered to represent a novel species of a new genus within the family Marinilabiliaceae, for which the name Geofilum rubicundum gen. nov., sp. nov. is proposed. The type strain of Geofilum rubicundum is JAM- BA0501 T (5JCM 15548 T 5NCIMB 14482 T ). The family Marinilabiliaceae within the order Bacteroi- dales was proposed by Ludwig et al. (2008). At the time of writing, this family includes three genera, namely Marinilabilia, Alkaliflexus and Anaerophaga. Marinilabilia salmonicolor was originally described as a species of the genus Cytophaga by Veldkamp (1961) to accommodate a novel, facultatively anaerobic, agar-degrading bacterium isolated from marine sediment. Based on phylogenetic affiliation as well as physiological and chemotaxonomic characteristics, this bacterium was transferred to a novel genus, Marinilabilia, by Nakagawa & Yamasato (1996). The genus Alkaliflexus was described and proposed by Zhilina et al. (2004) for a novel, anaerobic, low-O 2 -tolerant, alkaliphilic bacterium isolated from soda lake sediments. The genus Anaerophaga was erected to accommodate a novel, strictly anaerobic, thermophilic bacterium isolated from an oilfield (Denger et al., 2002). All recognized members of the family are facultatively or strictly anaerobic heterotrophs. A diversity of aerobic heterotrophic bacteria were isolated from subseafloor sediment samples cored from offshore of the Shimokita Peninsula, Japan, by the deep-earth research drilling vessel Chikyu in 2006 from multiple sample depths down to 365 m below the seafloor (drilling site C9001C, 41 u 10.63809 N 142 u 12.0819 E: see Kobayashi et al., 2008). The depth of overlying seawater at Site C9001C is 1180 m. Preliminary phylogenetic analysis based on 16S rRNA gene sequences showed that several isolates might represent Abbreviations: ML, maximum-likelihood; NJ, neighbour-joining. The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain JAM-BA0501 T is AB362265. One supplementary table and three supplementary figures are available with the online version of this paper. International Journal of Systematic and Evolutionary Microbiology (2012), 62, 1075–1080 DOI 10.1099/ijs.0.032326-0 032326 G 2012 IUMS Printed in Great Britain 1075