- Thermococcus indicus sp. nov., a Fe(III)-reducing hyperthermophilic archaeon isolated from the Onnuri Vent Field of the Central Indian Ocean ridge
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Jae Kyu Lim , Yun Jae Kim , Jhung-Ahn Yang , Teddy Namirimu , Sung-Hyun Yang , Mi-Jeong Park , Yong Min Kwon , Hyun Sook Lee , Sung Gyun Kang , Jung-Hyun Lee , Kae Kyoung Kwon
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J. Microbiol. 2020;58(4):260-267. Published online April 1, 2020
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DOI: https://doi.org/10.1007/s12275-020-9424-9
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A strictly anaerobic, dissimilatory Fe(III)-reducing hyperthermophilic
archaeon, designated as strain IOH1T, was isolated
from a new deep-sea hydrothermal vent (Onnuri Vent Field)
area in the Central Indian Ocean ridge. Strain IOH1T showed
> 99% 16S rRNA gene sequence similarity with Thermococcus
celericrescens TS2T (99.4%) and T. siculi DSM 12349T (99.2%).
Additional three species T. barossii SHCK-94T (99.0%), T. celer
Vu13T (98.8%), and T. piezophilus (98.6%) showed > 98.6%
of 16S rRNA gene sequence similarity, however, the maximum
OrthoANI value is 89.8% for the genome of T. celericrescens
TS2T. Strain IOH1T cells are coccoid, 1.2–1.8 μm
in diameter, and motile by flagella. Growth was at 70–82°C
(optimum 80°C), pH 5.4–8.0 (optimum pH 6.0) with 2–4%
(optimum 3%) NaCl. Growth of strain IOH1T was enhanced
by starch, pyruvate, D(+)-maltose and maltodextrin as a carbon
sources, and elemental sulfur as an electron acceptor;
clearly different from those of related species T. celecrescens
DSM 17994T and T. siculi DSM 12349T. Strain IOH1T, T. celercrescence
DSM 17994T, and T. siculi DSM 12349T reduced
soluble Fe(III)-citrate present in the medium, whereas the
amount of total cellular proteins increased with the concomitant
accumulation of Fe(II). We determined a circular chromosome
of 2,234 kb with an extra-chromosomal archaeal
plasmid, pTI1, of 7.7 kb and predicted 2,425 genes. The DNA
G + C content was 54.9 mol%. Based on physiological properties,
phylogenetic, and genome analysis, we proposed that
strain IOH1T (= KCTC 15844T = JCM 39077T) is assigned to
a new species in the genus Thermococcus and named Thermococcus
indicus sp. nov.
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Citations
Citations to this article as recorded by  - Fluid chemistry evolution in deep-sea hydrothermal environments: Unraveling mineral-fluid-microorganism interactions through continuous culture experiment
Lise Artigue, Valérie Chavagnac, Christine Destrigneville, David François, Françoise Lesongeur, Anne Godfroy
Deep Sea Research Part I: Oceanographic Research Papers.2025; 218: 104456. CrossRef - Iron’s irony: speciation, complexation & microbial processing of Fe in hydrothermal plumes
Solveig I. Bühring, Stefanie Böhnke-Brandt, Alexander Diehl, Martha Gledhill, Laura Haffert, Charlotte Kleint, Andrea Koschinsky, Sinikka Lennartz, Mirjam Perner, Sylvia G. Sander, Christoph Völker, Ying Ye
Communications Earth & Environment.2025;[Epub] CrossRef - 湖泊铁硫循环微生物研究进展
Yuan Yuan, Yongqin Liu
Earth Science-Journal of China University of Geosciences.2025; 50(3): 887. CrossRef -
Caloranaerobacter longqiensis sp. nov., a novel thermophilic member of the family Thermohalobacteraceae with the ability of ferric iron reduction from deep-sea hydrothermal sulphide
Guangyu Li, Jingwen Cheng, Xiupian Liu, Xiaoteng Fu, Yingbao Gai, Zhisheng Zhu, Jianning Wang, Xiaobo Zhang, Xiang Zeng, Zongze Shao
International Journal of Systematic and Evolutionary Microbiology
.2025;[Epub] CrossRef - Macrobenthic communities in the polymetallic nodule field, Indian Ocean, based on multicore and box core analysis
Santosh Gaikwad, Sabyasachi Sautya, Samir Damare, Maria Brenda Luzia Mascarenhas-Pereira, Vijayshree Gawas, Jayesh Patil, Mandar Nanajkar, Sadiq Bukhari
Frontiers in Marine Science.2024;[Epub] CrossRef -
Thermococcus argininiproducens sp. nov., an arginine biosynthesis archaeal species isolated from the Central Indian Ocean ridge
Yeong-Jun Park, Jae Kyu Lim, Yun Jae Kim, Sung-Hyun Yang, Hyun Sook Lee, Sung Gyun Kang, Jung-Hyun Lee, Youngik Yang, Kae Kyoung Kwon
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef - Spatial comparison and temporal evolution of two marine iron-rich microbial mats from the Lucky Strike Hydrothermal Field, related to environmental variations
Aina Astorch-Cardona, Mathilde Guerre, Alain Dolla, Valérie Chavagnac, Céline Rommevaux
Frontiers in Marine Science.2023;[Epub] CrossRef - Formate and hydrogen in hydrothermal vents and their use by extremely thermophilic methanogens and heterotrophs
James F. Holden, Harita Sistu
Frontiers in Microbiology.2023;[Epub] CrossRef - Microbiome and environmental adaption mechanisms in deep-sea hydrothermal vents
WeiShu ZHAO, Xiang XIAO
SCIENTIA SINICA Vitae.2022;[Epub] CrossRef - Limitations of microbial iron reduction under extreme conditions
Sophie L Nixon, Emily Bonsall, Charles S Cockell
FEMS Microbiology Reviews.2022;[Epub] CrossRef - Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology
.2021;[Epub] CrossRef - Thermococcus aciditolerans sp. nov., a piezotolerant, hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent chimney in the Southwest Indian Ridge
Xue-Gong Li, Hong-Zhi Tang, Wei-Jia Zhang, Xiao-Qing Qi, Zhi-Guo Qu, Jun Xu, Long-Fei Wu
International Journal of Systematic and Evolutionary Microbiology.2021;[Epub] CrossRef - Microorganisms from deep-sea hydrothermal vents
Xiang Zeng, Karine Alain, Zongze Shao
Marine Life Science & Technology.2021; 3(2): 204. CrossRef
- Paradesulfovibrio onnuriensis gen. nov., sp. nov., a chemolithoautotrophic sulfate-reducing bacterium isolated from the Onnuri vent field of the Indian Ocean and reclassification of Desulfovibrio senegalensis as Paradesulfovibrio senegalensis comb. nov.
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Yun Jae Kim , Jhung-Ahn Yang , Jae Kyu Lim , Mi-Jeong Park , Sung-Hyun Yang , Hyun Sook Lee , Sung Gyun Kang , Jung-Hyun Lee , Kae Kyoung Kwon
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J. Microbiol. 2020;58(4):252-259. Published online February 27, 2020
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DOI: https://doi.org/10.1007/s12275-020-9376-0
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956
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An anaerobic, rod-shaped, mesophilic, chemolithoautotrophic,
sulfate-reducing bacterial strain IOR2T was isolated from
a newly found deep-sea hydrothermal vent (OVF, Onnuri
Vent Field) area in the central Indian Ocean ridge (11°2488
S 66°2542E, 2021 m water depth). The 16S rRNA gene sequence
analysis revealed that the strain IOR2T was most closely
related to Desulfovibrio senegalensis BLaC1T (96.7%).
However, it showed low similarity with the members of the
family Desulfovibrionaceae, such as Desulfovibrio tunisiensis
RB22T (94.0%), D. brasiliensis LVform1T (93.9%), D. halophilus
DSM 5663T (93.7%), and Pseudodesulfovibrio aespoeensis
Aspo-2T (93.2%). The strain IOR2T could grow at 23–
42°C (optimum 37°C), pH 5.0–8.0 (optimum pH 7.0) and
with 0.5–6.5% (optimum 3.0%) NaCl. The strain could use
lactate, pyruvate, H2, and glycerol as electron donors and sulfate,
thiosulfate, and sulfite as electron acceptors. The major
fatty acids of the strain IOR2T were iso-C15:0, iso-C17:0, anteiso-
C15:0, and summed feature 9 (C16:0 methyl/iso-C17:1ω9c).
Both the strains IOR2T and BLaC1T could grow with CO2 and
H2 as the sole sources of carbon and energy, respectively. Genomic
evidence for the Wood-Ljungdahl pathway in both
the strains reflects chemolithoautotrophic growth. The DNA
G + C content of the strain IOR2T and BLaC1T was 58.1–60.5
mol%. Based on the results of the phylogenetic and physiologic
studies, Paradesulfovibrio onnuriensis gen. nov., sp.
nov. with the type strain IOR2T (= KCTC 15845T = MCCC
1K04559T) was proposed to be a member of the family Desulfovibrionaceae.
We have also proposed the reclassification
of D. senegalensis as Paradesulfovibrio senegalensis comb. nov.
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Citations
Citations to this article as recorded by - Sulfate-Reducing Bacteria Isolated from an Oil Field in Kazakhstan and a Description of Pseudodesulfovibrio karagichevae sp. nov.
Salimat K. Bidzhieva, Tatyana P. Tourova, Denis S. Grouzdev, Salima R. Samigullina, Diyana S. Sokolova, Andrey B. Poltaraus, Alexander N. Avtukh, Vera M. Tereshina, Andrey V. Mardanov, Nurlan S. Zhaparov, Tamara N. Nazina
Microorganisms.2024; 12(12): 2552. CrossRef - Sulfur fertilization integrated with soil redox conditions reduces Cd accumulation in rice through microbial induced Cd immobilization
Quan Zhang, Hai-Fei Chen, Dao-You Huang, Xiao-Bin Guo, Chao Xu, Han-Hua Zhu, Bo Li, Tong-Tong Liu, Ren-Wei Feng, Qi-Hong Zhu
Science of The Total Environment.2022; 824: 153868. CrossRef - Pseudodesulfovibrio sediminis sp. nov., a mesophilic and neutrophilic sulfate-reducing bacterium isolated from sediment of a brackish lake
Ayaka Takahashi, Hisaya Kojima, Miho Watanabe, Manabu Fukui
Archives of Microbiology.2022;[Epub] CrossRef - Diversity and biogenesis contribution of sulfate-reducing bacteria in arsenic-contaminated soils from realgar deposits
Xianbin Zhu, Liyuan Chen, Hongzhong Pan, Lei Wang, Xun Zhang, Dan Wang
Environmental Science and Pollution Research.2022; 29(21): 31110. CrossRef - A sulfate-reducing bacterial genus, Desulfosediminicola gen. nov., comprising two novel species cultivated from tidal-flat sediments
Jaeho Song, Juchan Hwang, Ilnam Kang, Jang-Cheon Cho
Scientific Reports.2021;[Epub] CrossRef - Desulfomarina profundi gen. nov., sp. nov., a novel mesophilic, hydrogen-oxidizing, sulphate-reducing chemolithoautotroph isolated from a deep-sea hydrothermal vent chimney
Yurina Hashimoto, Akihiro Tame, Shigeki Sawayama, Junichi Miyazaki, Ken Takai, Satoshi Nakagawa
International Journal of Systematic and Evolutionary Microbiology.2021;[Epub] CrossRef -
Pseudodesulfovibrio mercurii sp. nov., a mercury-methylating bacterium isolated from sediment
Cynthia C. Gilmour, Ally Bullock Soren, Caitlin M. Gionfriddo, Mircea Podar, Judy D. Wall, Steven D. Brown, Joshua K. Michener, Maria Soledad Goñi Urriza, Dwayne A. Elias
International Journal of Systematic and Evolutionary Microbiology
.2019;[Epub] CrossRef
- Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus
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Jhung-Ahn Yang , Sung-Hyun Yang , Junghee Kim , Kae Kyoung Kwon , Hyun-Myung Oh
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J. Microbiol. 2017;55(7):583-591. Published online June 30, 2017
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DOI: https://doi.org/10.1007/s12275-017-7172-2
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955
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2
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7
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Abstract
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Here we report the comparative genomic analysis of strain
UJ101 with 15 strains from the family Flavobacteriaceae,
using the CGExplorer program. Flavobacteriales bacterium
strain UJ101 was isolated from a xanthid crab, Atergatis reticulatus,
from the East Sea near Korea. The complete genome
of strain UJ101 is a 3,074,209 bp, single, circular chromosome
with 30.74% GC content. While the UJ101 genome
contains a number of annotated genes for many metabolic
pathways, such as the Embden–Meyerhof pathway, the pentose
phosphate pathway, the tricarboxylic acid (TCA) cycle,
and the glyoxylate cycle, genes for the Entner-Douddoroff
pathway are not found in the UJ101 genome. Overall, carbon
fixation processes were absent but nitrate reduction and
denitrification pathways were conserved. The UJ101 genome
was compared to genomes from other marine animals (three
invertebrate strains and 5 fish strains) and other marine animal-
derived genera. Notable results by genome comparisons
showed that UJ101 is capable of denitrification and nitrate
reduction, and that biotin-thiamine pathway participation
varies among marine bacteria; fish-dwelling bacteria, freeliving
bacteria, invertebrate-dwelling bacteria, and strain
UJ101. Pan-genome analysis of the 16 strains in this study
included 7,220 non-redundant genes that covered 62% of
the pan-genome. A core-genome of 994 genes was present
and consisted of 8% of the genes from the pan-genome. Strain
UJ101 is a symbiotic hetero-organotroph isolated from xanthid
crab, and is a metabolic generalist with nitrate-reducing
abilities but without the ability to synthesize biotin. There
is a general tendency of UJ101 and some fish pathogens to
prefer thiamine-dependent glycolysis to gluconeogenesis. Biotin
and thiamine auxotrophy or prototrophy may be used
as important markers in microbial community studies.
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Citations
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Frontiers in Nutrition.2025;[Epub] CrossRef - The hepatopancreas microbiome of velvet crab, Necora puber
Signe Martin, Cindy Smith, Kelly Stewart, William Barr, Deborah Cheslett, Ian O'Connor, Fiona Swords, Umer Zeeshan Ijaz, Katie O'Dwyer
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Science of The Total Environment.2022; 823: 153710. CrossRef - Climate Warming Enhances Wetland Soil Hono and Nox Emissions, Induces Shifts in Soil Fungal Community, and Decreases Soil Abundance of Nitrogen Cycling Genes
Dianming Wu, Lingling Deng, Yihua Sun, Ruhai Wang, Li Zhang, Rui Wang, Yaqi Song, Zhiwei Gao, Haroon Haider, Yue Wang, Lijun Hou, Min Liu
SSRN Electronic Journal .2021;[Epub] CrossRef -
Changes of the intestinal microbiota along the gut of Japanese Eel (
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P. Zhu, M.K.‐S. Wong, X. Lin, T.F. Chan, C.K.C. Wong, K.P. Lai, W.K.F. Tse
Letters in Applied Microbiology.2021; 73(4): 529. CrossRef - Out From the Shadows – Resolution of the Taxonomy of the Family Cryomorphaceae
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Frontiers in Microbiology.2020;[Epub] CrossRef
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