Open AccessNitrosophilus 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”
Author(s) -
Taiki Shiotani,
Sayaka Mino,
Wakana Sato,
Sayo Nishikawa,
Masanori Yonezawa,
Stefan M. Sievert,
Tomoo Sawabe
Publication year - 2020
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0241366
Subject(s) - thiosulfate , sulfur , hydrothermal vent , biology , 16s ribosomal rna , phylogenetic tree , botany , hydrothermal circulation , bacteria , gene , chemistry , genetics , organic chemistry , paleontology
A novel bacterium, strain EPR55-1 T , 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 EPR55-1 T 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 EPR55-1 T as the type strain (= JCM 32893 T = KCTC 15925 T ). In addition, it is shown that “ Nitratiruptor labii ” should be transferred to the genus Nitrtosophilus ; the name Nitrosophilus labii comb. nov. (JCM 34002 T = DSM 111345 T ) 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 27783 T = JCM 19563 T ). 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.