Nitrosophilus alvini gen. nov., sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the East Pacific Rise, inferred by a genome-based taxonomy of the phylum “Campylobacterota”

Abstract

A novel bacterium, strain EPR55-1T, was isolated from a deep-sea hydrothermal vent on the East Pacific Rise. The cells were motile rods. Growth was observed at temperatures between 50 and 60°C (optimum, 60°C), at pH values between 5.4 and 8.6 (optimum, pH 6.6) and in the presence of 2.4–3.2% (w/v) NaCl (optimum, 2.4%). The isolate used molecular hydrogen as its sole electron donor, carbon dioxide as its sole carbon source, ammonium as its sole nitrogen source, and thiosulfate, sulfite (0.01 to 0.001%, w/v) or elemental sulfur as its sole sulfur source. Nitrate, nitrous oxide (33%, v/v), thiosulfate, molecular oxygen (0.1%, v/v) or elemental sulfur could serve as the sole electron acceptor to support growth. Phylogenetic analyses based on both 16S rRNA gene sequences and whole genome sequences indicated that strain EPR55-1T belonged to the family Nitratiruptoraceae of the class “Campylobacteria”, but it had the distinct phylogenetic relationship with the genus Nitratiruptor. On the basis of the physiological and molecular characteristics of the isolate, the name Nitrosophilus alvini gen. nov. sp. nov. is proposed, with EPR55-1T as the type strain (= JCM 32893T = KCTC 15925T). In addition, it is shown that “Nitratiruptor labii” should be transferred to the genus Nitrtosophilus; the name Nitrosophilus labii comb. nov. (JCM 34002T = DSM 111345T) is proposed for this organism. Furthermore, 16S rRNA gene-based and genome-based analyses showed that Cetia pacifica is phylogenetically associated with Caminibacter species. We therefore propose the reclassification of Cetia pacifica as Caminibacter pacificus comb. nov. (DSM 27783T = JCM 19563T). Additionally, AAI thresholds for genus classification and the reclassification of subordinate taxa within “Campylobacteria” are also evaluated, based on the analyses using publicly available genomes of all the campylobacterial species.

Hydrogenimonas urashimensis sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the Southern Mariana Trough

“…The ANI and in silico DDH values between strain SSM-sur55 T and H. thermophila EP1-55-1% T were found to be 72.7% and 17.4%, respectively, well below the species threshold (95-96% and 70%, respectively) [34]. Strain SSM-sur55 T shared AAI values of 71.4% with H. thermophila EP1-55-1% T that considerably above the recently proposed AAI genus threshold among "Campylobacterota" (60-62%) (35). These results also support the proposal that the isolate is a novel species within the genus Hydrogenimonas.…”

Hydrogenimonas cancrithermarum sp. nov., a hydrogen- and thiosulfate-oxidizing mesophilic chemolithoautotroph isolated from diffuse-flow fluids on the East Pacific Rise, and an emended description of the genus Hydrogenimonas

“…tergarcus MI55-1 T were 75.4 %, 76.4 % and 57.1 %, respectively. The values against species of the genus Hydrogenimonas were above the threshold value of 60–62 % for the genus-level boundary for members of the class Epsilonproteobacteria [45]. These results indicate that ISO32 T represents a novel species within the genus Hydrogenimonas .…”

“…Comparison of physiological characteristics of ISO32 T with species of the class Epsilonproteobacteria isolated from deep-sea hydrothermal ventsStrains: 1, ISO32 T ; 2, Hydrogenimonas thermophila EP1-55-1 % T[6]; 3, Hydrogenimonas urashimensis SSM-sur55 T[7]; 4, Nitratiruptor tergarcus MI55-1 T[33];5, Nitrosophilus alvini EPR55-1 T[45]; 6, Nitrosophilus kaiyonis MOT50 T[27];7, Nitrosophilus labii HRV44 T[62]. nd, Not determined; −, negative; *, poor growth.…”

A Simple and Effective Method for Solid Medium Cultivation of Strictly Hydrogen- and Sulfur-oxidizing Chemolithoautotrophs Predominant in Deep-‍sea Hydrothermal Fields

“…3 ). These colonies showed at least 99% similarity in their 16S rRNA gene sequence to Nitrosophilus labii , a moderately thermophilic chemolithoautotroph of the phylum Campylobacterota , originally isolated from the East Pacific Rise ( Shiotani et al , 2020 ).…”