M ethanocaldococcus bathoardescens sp. nov., a hyperthermophilic methanogen isolated from a volcanically active deep-sea hydrothermal vent

Abstract

A hyperthermophilic methanogen, strain JH146T , was isolated from 26 6C hydrothermal vent fluid emanating from a crack in basaltic rock at Marker 113 vent, Axial Seamount in the northeastern Pacific Ocean. It was identified as an obligate anaerobe that uses only H 2 and CO 2 for growth. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain is more than 97 % similar to other species of the genus Methanocaldococcus. Therefore, overall genome relatedness index analyses were performed to establish that strain JH146 T represents a novel species. For each analysis, strain JH146 T was most similar to Methanocaldococcus sp. FS406-22, which can fix N 2 and also comes from Marker 113 vent. However, strain JH146 T differs from strain FS406-22 in that it cannot fix N 2 . The average nucleotide identity score for strain JH146 T was 87 %, the genome-to-genome direct comparison score was 33-55 % and the species identification score was 93 %. For each analysis, strain JH146 T was below the species delineation cut-off. Full-genome gene synteny analysis showed that strain JH146 T and strain FS406-22 have 97 % genome synteny, but strain JH146 T was missing the operons necessary for N 2 fixation and assimilatory nitrate reduction that are present in strain FS406-22. Based on its whole genome sequence, strain JH146 T is suggested to represent a novel species of the genus Methanocaldococcus for which the name Methanocaldococcus bathoardescens is proposed. The type strain is JH146 T (5DSM 27223 T 5KACC 18232 T ).The genus Methanocaldococcus was proposed when the order Methanococcales was reclassified to reduce the diversity of each genus within the order (Boone et al., 1993). It consists of strictly hyperthermophilic, hydrogenotrophic methanogens that are obligately anaerobic and coccoidal (Boone et al., 1993;Whitman & Jeanthon, 2006). In this study, the complete genome sequence of a strain of the genus Methanocaldococcus, strain JH146 T , was used to establish the novelty of the strain. The strain was isolated from 26 u C hydrothermal fluid that was flowing from a crack in basaltic rock at Marker 113 vent at Axial Seamount on the Juan de Fuca Ridge in the northeastern Pacific Ocean (Ver Eecke et al., 2012, 2013). The strain used only H 2 as its electron donor and CO 2 as its sole electron acceptor and carbon source (Ver Eecke et al., 2013). Strain JH146 T grew within the temperature range of 48-90 u C with an optimum temperature of 82 u C, within the pH range of 4.5-9.0 with an optimum pH of 7.0 and within the chlorinity range of 127-974 mM chloride with an optimum chlorinity of 358 mM (Ver Eecke et al., 2013). Its phenotypic characteristics were very similar to all other species of the genus Methanocaldococcus (Table 1).The phylogenetic relatedness of strain JH146T to other species of the genus Methanocaldococcus was determined using 16S rRNA gene sequences obtained from the Ribosomal Database Project (Cole et al., 2007) and comparing them via MEGABLAST (McGinnis & Madden, 2004). Strain JH146T showed 99.7 % s...

Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent fluids

“…S8). On the tree, the two Methanocaldococcus MAGs clustered with the sequenced Methanocaldococcus bathoardescens JH146 isolated from Marker 113 vent (Ver Eecke et al, 2013;Stewart et al, 2015).…”

Hydrogen Limitation and Syntrophic Growth among Natural Assemblages of Thermophilic Methanogens at Deep-sea Hydrothermal Vents

“…Methanocaldococcus bathoardescens JH146 (DSM 27223; Ver Eecke et al, 2013 ; Stewart et al, 2015 ), Methanothermococcus sp. strain BW11 (DSM 100453; Stewart et al, 2016 ), and Thermo-coccus paralvinellae ES1 (DSM 27261; Pledger and Baross, 1989 ; Hensley et al, 2014 , 2016 ) were used for pure and co-culture experiments from our hyperthermophile culture collection.…”

Diversity of methanogenic archaea from the 2012 terrestrial hot spring (Valley of Geysers, Kamchatka)

“…Members of two orders of hydrogenotrophic methanogens, Methanococcales and Methanopyrales, are usually detected in and isolated from the samples from such ecotopes (Jones et al, 1983;Kurr et al, 1991;Takai et al, 2004;Flores et al, 2012;Stewart et al, 2015). These deep-sea thermophilic methanogens are lithoautotrophs that utilize hydrogen as the sole energy source and thus act as producers of organic matter in deep-sea hydrothermal ecosystems.…”