Methanoculleus horonobensis sp. nov., a methanogenic archaeon isolated from a deep diatomaceous shale formation

Abstract

A methanogenic organism from the domain Archaea , designated strain T10T, was isolated from groundwater sampled from a deep diatomaceous shale formation located in Horonobe, Hokkaido, Japan. The strain utilized H2/CO2 and formate as substrates for methanogenesis. Cells were strictly anaerobic, Gram-negative-staining, flagellated, irregular coccoids, 0.7–1.6 µm in diameter, and occurred singly. The strain grew at 25–45 °C (optimum 37–42 °C), at pH 5.8–8.2 (optimum pH 6.7–6.8) and in the presence of 0–1.3 M NaCl (optimum 0.1–0.2 M NaCl). The G+C content of the genomic DNA was 62.9 mol%. 16S rRNA gene sequencing revealed that, although the strain is a member of the genus Methanoculleus , it clearly differed from all described species of this genus (95.5–98.3 % sequence similarity). Values for DNA–DNA hybridization with type strains of closely related Methanoculleus species were less than 50 %. Phenotypic and phylogenetic features of strain T10T clearly indicate that it represents a novel species of the genus Methanoculleus , for which the name Methanoculleus horonobensis sp. nov. is proposed. The type strain is T10T ( = DSM 21626T = JCM 15517T).

Methanogenic archaea database containing physiological and biochemical characteristics

“…In this respect, methanogens are extremely variable (). The DNA G+C content ranged from 23 mol% for Methanosphaera cuniculi (Biavati et al , 1988) to 62 mol% for Methanoculleus horonobensis (Shimizu et al , 2013), Methanothermobacter defluvii (Kotelnikova et al , 1993) and Methanoculleus chikugoensis (Dianou et al , 2001). It has been suggested that the DNA G+C content is correlated with factors such as genome size, whether or not the bacterium is free-living, aerobiosis, nitrogen utilization or temperature (Hildebrand et al , 2010).…”

Methanosarcina subterranea sp. nov., a methanogenic archaeon isolated from a deep subsurface diatomaceous shale formation

“…In this study, we characterized strain HC-2 T , a methylotrophic methanogen belonging to the genus Methanosarcina isolated from groundwater in a terrestrial deep diatomaceous shale formation. The methanogenic substrates for this strain differed from those of other isolates from the same site (Shimizu et al, 2011(Shimizu et al, , 2013. Our results suggest a variety of terminal processes for carbon cycling in the stratum.…”

“…Since the late twentieth century, several methanogens have been isolated from the deep subsurface environment (Kotelnikova et al, 1998;Mikucki et al, 2003;Kendall et al, 2006;Doerfert et al, 2009;Mochimaru et al, 2009;Shimizu et al, 2011Shimizu et al, , 2013Katayama et al, 2014). It is now clear that methanogens are associated with carbon cycling in the earth's crust.…”

Methanoculleus sediminis sp. nov., a methanogen from sediments near a submarine mud volcano

“…Table 1. Comparison of physiological characteristics of strain S3Fa T and type strains of related species of the genus Methanoculleus Strains: 1, S3Fa T (data from this study); 2, M. marisnigri JR1 T (Romesser et al, 1979); 3, M. submarinus Nankai-1 T (Mikucki et al, 2003); 4, M. chikugoensis MG62 T (Dianou et al, 2001); 5, M. thermophilus CR-1 T (Rivard & Smith, 1982); 6, M. palmolei INSLUZ T (Zellner et al, 1998); 7, M. bourgensis MS2 T (Ollivier et al, 1986); 8, M. receptaculi ZC-2 T (Cheng et al, 2008); 9, M. hydrogenitrophicus HC T (Tian et al, 2010); 10, M. horonobensis T10 T (Shimizu et al, 2013); 11, M. taiwanensis CYW4 T (Weng et al, 2015). All strains have irregular coccus-shaped cells.…”

“…The genus Methanoculleus comprises hydrogenotrophic methanogens that have been isolated from diverse habitats, including marine and river sediments, wetland, paddy field soil, anaerobic digesters, oilfields and a deep diatomaceous shale formation (Blotevogel et al, 1991;Cheng et al, 2008;Corder et al, 1983;Dianou et al, 2001;Mikucki et al, 2003;Ollivier et al, 1986;Rivard & Smith, 1982;Romesser et al, 1979;Shimizu et al, 2013;Tian et al, 2010;Weng et al, 2015;Zellner et al, 1998). Methanoculleus submarinus Nankai-1 T (Mikucki et al, 2003) and Methanoculleus taiwanensis CYW4 T (Weng et al, 2015) were isolated from marine sediments associated with gas (methane) hydrates.…”