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

Mino, Sayaka; Shiotani, Taiki; Nakagawa, Satoshi; Takai, Ken; Sawabe, Tomoo

doi:10.1016/j.syapm.2020.126170

Cited by 12 publications

(9 citation statements)

References 36 publications

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“…Three copies of 16S rRNA gene were found in the genome, which were identical to each other. The genome size of ISO32 T is similar to that of H. urashimensis SSM-sur55 T (2 297 889 bp) [7] but smaller than that of H. thermophila EP1-55-1 % T (2 551 102 bp) [6]. The DNA G+C content of the genome of ISO32 T was 51.1 %, which is similar to that of H. urashimensis SSM-sur55 T (52.8 %) (Table 1) but higher than that of H. thermophila EP1-55-1 % T (33.6 %) [6,27].…”

Section: Genome Propertiesmentioning

confidence: 68%

“…The genome size of ISO32 T is similar to that of H. urashimensis SSM-sur55 T (2 297 889 bp) [7] but smaller than that of H. thermophila EP1-55–1 % T (2 551 102 bp) [6].…”

Section: Resultsmentioning

confidence: 99%

“…Overall genome relatedness indices between ISO32 T and related strains were calculated as described previously [27]. In silico DNA–DNA hybridization (DDH) values of ISO32 T against Hydrogenimonas urashimensis SSM-sur55 T [7], Hydrogenimonas thermophila EP1-55–1 % T [6] and Nitratiruptor tergarcus MI55-1 T [32] were calculated using the Genome-to-Genome Distance Calculator [33] with BLAST+ as a local alignment tool. Results of recommended formula 2 were considered.…”

Section: Methodsmentioning

confidence: 99%

“…A previous study revealed a close relationship of its hydrogenases with hydrogenases of pathogenic epsilonproteobacteria rather than with hydrogenases of deep-sea epsilonproteobacteria [8]. In addition, a couple of strains of members of this genus have been characterized as nitrous-oxide reducers that possibly contribute to the removal of N 2 O in deep-sea hydrothermal environments [7,9]. Although the importance of this genus in terms of taxonomy as well as applications has been recognized with respect to the described species, the available strains and metagenome-assembled genomes are still limited, both in terms of number and origin.…”

Section: Introductionmentioning

confidence: 99%

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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

Mino,

Fukazawa,

Tsuchiya

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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A novel mesophilic, hydrogen- and thiosulfate-oxidizing bacterium, strain ISO32T, was isolated from diffuse-flow hydrothermal fluids from the Crab Spa vent on the East Pacific Rise. Cells of ISO32T were rods, being motile by means of a single polar flagellum. The isolate grew at a temperature range between 30 and 55 °C (optimum, 43 °C), at a pH range between 5.3 and 7.6 (optimum, pH 5.8) and in the presence of 2.0–4.0 % NaCl (optimum, 2.5 %). The isolate was able to grow chemolithoautotrophically with molecular hydrogen, thiosulfate or elemental sulfur as the sole electron donor. Thiosulfate, elemental sulfur, nitrate and molecular oxygen were each used as a sole electron acceptor. Phylogenetic analysis of 16S rRNA gene sequences placed ISO32T in the genus Hydrogenimonas of the class Epsilonproteobacteria , with Hydrogenimonas thermophila EP1-55–1 %T as its closest relative (95.95 % similarity). On the basis of the phylogenetic, physiological and genomic characteristics, it is proposed that the organism represents a novel species within the genus Hydrogenimonas , Hydrogenimonas cancrithermarum sp. nov. The type strain is ISO32T (=JCM 39185T =KCTC 25252T). Furthermore, the genomic properties of members of the genus Hydrogenimonas are distinguished from those of members of other thermophilic genera in the orders Campylobacterales ( Nitratiruptor and Nitrosophilus ) and Nautiliales ( Caminibacter , Nautilia and Lebetimonas ), with larger genome sizes and lower 16S rRNA G+C content values. Comprehensive metabolic comparisons based on genomes revealed that genes responsible for the Pta–AckA pathway were observed exclusively in members of mesophilic genera in the order Campylobacterales and of the genus Hydrogenimonas . Our results indicate that the genus Hydrogenimonas contributes to elucidating the evolutionary history of Epsilonproteobacteria in terms of metabolism and transition from a thermophilic to a mesophilic lifestyle.

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Section: Genome Propertiesmentioning

confidence: 68%

“…The genome size of ISO32 T is similar to that of H. urashimensis SSM-sur55 T (2 297 889 bp) [7] but smaller than that of H. thermophila EP1-55–1 % T (2 551 102 bp) [6].…”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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

Mino,

Fukazawa,

Tsuchiya

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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“…The autotrophs in the enriched microecosystem were Hydrogenomonas and Desulfurobacterium , which belong to ecologically significant autotrophic groups Campylobacterota and Aquificae respectively, in hydrothermal vents (Nakagawa and Takai, 2008). Hydrogenomonas isolations were reported to be chemolithoautotrophs capable of using molecular hydrogen as the sole energy source and molecular oxygen, nitrate or sulfur species (S 2 O 3 2− , S 0 ) as electron acceptors to support growth (Mino et al ., 2021). Our enriched Hydrogenomonas shows the same capability in the genome for both carbon fixation and electron donors/acceptors.…”

Section: Resultsmentioning

confidence: 99%

Cultivation and metabolic insights of an uncultured clade, Bacteroidetes VC2.1 Bac22 (Candidatus Sulfidibacteriales ord. nov.), from deep‐sea hydrothermal vents

Leng

Zhao

Xiao

2022

Environmental Microbiology

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Bacteroidetes VC2.1 Bac22 (referred to as VC2.1) is an uncultured clade that is widely distributed in marine ecosystems, including hydrothermal vents, oxygen-minimum zones and other anoxic, sulfiderich environments. However, the lack of cultured representatives and sequenced genomes of VC2.1 limit our understanding of its physiology, metabolism and ecological functions. Here, we obtained a stable coculture of VC2.1 with autotrophic microbes by establishing an autotrophy-based enrichment from a hydrothermal vent chimney sample. We recovered a high-quality metagenome-assembled genome (MAG) that belonged to VC2.1. Phylogenetic analyses of both 16S rRNA genes and conserved protein markers suggested that VC2.1 belongs to a novel order in the Bacteroidetes phylum, which we named Candidatus Sulfidibacteriales. The metabolic reconstruction of this MAG indicated that VC2.1 could utilize polysaccharides, protein polymers and fatty acids as well as flexibly obtain energy via NO/N 2 O reduction and polysulfide reduction. Our results reveal the ecological potential of this novel Bacteroidetes for complex organic carbons mineralization and N 2 O sinks in deep-sea hydrothermal vents. Furthermore, guided by the genome information, we designed a new culture medium in which starch, ammonium and polysulfide were used as the carbon source, nitrogen source and electron acceptor respectively, to isolate VC2.1 successfully.

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Nitrosophilus kaiyonis sp. nov., a hydrogen-, sulfur- and thiosulfate-oxidizing chemolithoautotroph within “Campylobacteria” isolated from a deep-sea hydrothermal vent in the Mid-Okinawa Trough

et al. 2022

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

Cited by 12 publications

References 36 publications

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

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

Cultivation and metabolic insights of an uncultured clade, Bacteroidetes VC2.1 Bac22 (Candidatus Sulfidibacteriales ord. nov.), from deep‐sea hydrothermal vents

Nitrosophilus kaiyonis sp. nov., a hydrogen-, sulfur- and thiosulfate-oxidizing chemolithoautotroph within “Campylobacteria” isolated from a deep-sea hydrothermal vent in the Mid-Okinawa Trough

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