- 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
- Oxygen-mediated growth enhancement of an obligate anaerobic archaeon Thermococcus onnurineus NA1
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Seong Hyuk Lee , Hwan Youn , Sung Gyun Kang , Hyun Sook Lee
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J. Microbiol. 2019;57(2):138-142. Published online January 31, 2019
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DOI: https://doi.org/10.1007/s12275-019-8592-y
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1,016
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4
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Abstract
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Thermococcus onnurineus NA1, an obligate anaerobic hyperthermophilic
archaeon, showed variable oxygen (O2) sensitivity
depending on the types of substrate employed as an
energy source. Unexpectedly, the culture with yeast extract
as a sole energy source showed enhanced growth by 2-fold
in the presence of O2. Genome-wide transcriptome analysis
revealed the upregulation of several antioxidant-related genes
encoding thioredoxin peroxidase (TON_0862), rubrerythrin
(TON_0864), rubrerythrin-related protein (TON_0873),
NAD(P)H rubredoxin oxidoreductase (TON_0865), or thioredoxin
reductase (TON_1603), which can couple the detoxification
of reactive oxygen species with the regeneration
of NAD(P)+ from NAD(P)H. We present a plausible mechanism
by which O2 serves to maintain the intracellular redox
balance. This study demonstrates an unusual strategy of an
obligate anaerobe underlying O2-mediated growth enhancement
despite not having heme-based or cytochrome-type
proteins.
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Citations
Citations to this article as recorded by - Exploration of formate as a liquid organic hydrogen carrier in biohydrogen production through evolutionary and process engineering of hyperthermophilic archaeon
Hae-Chang Jung, Sung-Mok Lee, Ji-in Yang, Seong Hyuk Lee, Hyun Sook Lee, Sung Gyun Kang
Bioresource Technology.2025; 425: 132318. CrossRef - The aerobic biosphere as an O2 sink before the Great Oxygenation Event: geobiological feedback to solid Earth and surface oxidation
Eric Runge, Sara Vulpius, Daniel Herwartz, Andreas Pack, Caroline Brachmann, Lena Noack
Geo-Bio Interfaces.2025;[Epub] CrossRef - How low can they go? Aerobic respiration by microorganisms under apparent anoxia
Jasmine S Berg, Soeren Ahmerkamp, Petra Pjevac, Bela Hausmann, Jana Milucka, Marcel M M Kuypers
FEMS Microbiology Reviews.2022;[Epub] CrossRef - Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii
David Moreira, Yvan Zivanovic, Ana I. López-Archilla, Miguel Iniesto, Purificación López-García
Nature Communications.2021;[Epub] CrossRef
- Metagenomic analysis reveals the contribution of anaerobic methanotroph-1b in the oxidation of methane at the Ulleung Basin, East Sea of Korea
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Jin-Woo Lee , Kae Kyoung Kwon , Jang-Jun Bahk , Dong-Hun Lee , Hyun Sook Lee , Sung Gyun Kang , Jung-Hyun Lee
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J. Microbiol. 2016;54(12):814-822. Published online November 26, 2016
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DOI: https://doi.org/10.1007/s12275-016-6379-y
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931
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Abstract
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We have previously identified a sulfate methane transition
zone (SMTZ) within the methane hydrate-bearing sediment
in the Ulleung Basin, East Sea of Korea, and the presence of
ANME-1b group in the sediment has been shown by phylogenetic
analysis of a 16S rRNA gene. Herein, we describe
taxonomic and functional profiling in the SMTZ sample by
metagenomic analysis, comparing with that of surface sediment.
Metagenomic sequences of 115 Mbp and 252 Mbp
were obtained from SMTZ and surface sediments, respectively.
The taxonomic profiling using BLASTX against the
SEED within MG-RAST showed the prevalence of methanogens
(19.1%), such as Methanosarcinales (12.0%) and
Methanomicrobiales (4.1%) predominated within the SMTZ
metagenome. A number of 185,200 SMTZ reads (38.9%) and
438,484 surface reads (62.5%) were assigned to functional
categories, and methanogenesis-related reads were statistically
significantly overrepresented in the SMTZ metagenome.
However, the mapping analysis of metagenome reads to the
reference genomes, most of the sequences of the SMTZ metagenome
were mapped to ANME-1 draft genomes, rather
than those of methanogens. Furthermore, the two copies of
the methyl-coenzyme M reductase gene (mcrA) segments
of the SMTZ metagenome were clustered with ANME-1b in
the phylogenetic cluster. These results indicate that ANME-
1b reads were miss-annotated to methanogens due to limitation
of database. Many of key genes necessary for reverse
methanogenesis were present in the SMTZ metagenome,
except for N5,N10-methenyl-H4MPT reductase (mer) and CoBCoM
heterodisulfide reductase subunits D and E (hdrDE). These data suggest that the ANME-1b represents the primary
player the anaerobic methane oxidation in the SMTZ,
of the methane hydrate-bearing sediment at the Ulleung
Basin, East Sea of Korea.
-
Citations
Citations to this article as recorded by - Methane seepage intensity distinguish microbial communities in sediments at the Mid-Okinawa Trough
Youzhi Xin, Nengyou Wu, Zhilei Sun, Hongmei Wang, Ye Chen, Cuiling Xu, Wei Geng, Hong Cao, Xilin Zhang, Bin Zhai, Dawei Yan
Science of The Total Environment.2022; 851: 158213. CrossRef - Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments
Anna J. Wallenius, Paula Dalcin Martins, Caroline P. Slomp, Mike S. M. Jetten
Frontiers in Microbiology.2021;[Epub] CrossRef -
Roles of Organohalide-Respiring
Dehalococcoidia
in Carbon Cycling
Yi Yang, Robert Sanford, Jun Yan, Gao Chen, Natalie L. Cápiro, Xiuying Li, Frank E. Löffler, Nick Bouskill
mSystems.2020;[Epub] CrossRef - Community structure and distribution of benthic Bacteria and Archaea in a stratified coastal lagoon in the Southern Gulf of Mexico
Santiago Cadena, M. Leopoldina Aguirre-Macedo, Daniel Cerqueda-García, Francisco J. Cervantes, Jorge A. Herrera-Silveira, José Q. García-Maldonado
Estuarine, Coastal and Shelf Science.2019; 230: 106433. CrossRef
- Dimethyl sulfoxide reduction by a hyperhermophilic archaeon Thermococcus onnurineus NA1 via a cysteine-cystine redox shuttle
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Ae Ran Choi , Min-Sik Kim , Sung Gyun Kang , Hyun Sook Lee
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J. Microbiol. 2016;54(1):31-38. Published online January 5, 2016
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DOI: https://doi.org/10.1007/s12275-016-5574-1
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922
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0
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9
Crossref
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Abstract
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A variety of microbes grow by respiration with dimethyl sulfoxide
(DMSO) as an electron acceptor, and several distinct
DMSO respiratory systems, consisting of electron carriers
and a terminal DMSO reductase, have been characterized.
The heterotrophic growth of a hyperthermophilic archaeon
Thermococcus onnurineus NA1 was enhanced by the addition
of DMSO, but the archaeon was not capable of reducing
DMSO to DMS directly using a DMSO reductase. Instead, the
archaeon reduced DMSO via a cysteine-cystine redox shuttle
through a mechanism whereby cystine is microbially reduced
to cysteine, which is then reoxidized by DMSO reduction.
A thioredoxin reductase-protein disulfide oxidoreductase
redox couple was identified to have intracellular cystine-reducing
activity, permitting recycle of cysteine. This study presents
the first example of DMSO reduction via an electron
shuttle. Several Thermococcales species also exhibited enhanced
growth coupled with DMSO reduction, probably by
disposing of excess reducing power rather than conserving
energy.
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Citations
Citations to this article as recorded by - H2-dependent reduction of rubredoxin by FrhAGB hydrogenase in Thermococcus onnurineus NA1
Ji-in Yang, Hye-Jin Park, Young Jun An, Bo Gyoung Choi, Myeong-Eun Jegal, Hyun-Myung Oh, Sung Gyun Kang, Hyun Sook Lee
Applied Microbiology and Biotechnology.2026;[Epub] CrossRef - Outstanding lithium storage performance of a copper coordination complex [Cu(DMSO)2]Cl2 as anode material for lithium-ion batteries
Youkui Wang, Ruili Zhao, Jiamiao Ma, Jiamin Zhao, Yanmeng Cai, Qing Yuan, Jinsheng Zhao
Journal of Energy Storage.2025; 116: 116045. CrossRef - Heavy Metal-Resistant Biohybrid System Boosts Dissimilatory Nitrate Reduction to Ammonium for Agronomic Sustainability
Jialin Chi, Shiyin Wu, Liping Fang, Kai Liu, Shaochen Huang, Wenjun Zhang, Fangbai Li
ACS Sustainable Chemistry & Engineering.2024; 12(44): 16444. CrossRef - Phenotypic and genomic characterization of Bathyarchaeum tardum gen. nov., sp. nov., a cultivated representative of the archaeal class Bathyarchaeia
Maria A. Khomyakova, Alexander Y. Merkel, Dana D. Mamiy, Alexandra A. Klyukina, Alexander I. Slobodkin
Frontiers in Microbiology.2023;[Epub] CrossRef -
Direct Electron Transfer between the
frhAGB
-Encoded Hydrogenase and Thioredoxin Reductase in the Nonmethanogenic Archaeon
Thermococcus onnurineus
NA1
Hae-Chang Jung, Jae Kyu Lim, Tae-Jun Yang, Sung Gyun Kang, Hyun Sook Lee, Haruyuki Atomi
Applied and Environmental Microbiology.2020;[Epub] CrossRef - A peroxiredoxin of Thermus thermophilus HB27: Biochemical characterization of a new player in the antioxidant defence
Gabriella Fiorentino, Patrizia Contursi, Giovanni Gallo, Simonetta Bartolucci, Danila Limauro
International Journal of Biological Macromolecules.2020; 153: 608. CrossRef - A Reexamination of Thioredoxin Reductase from Thermoplasma acidophilum, a Thermoacidophilic Euryarchaeon, Identifies It as an NADH-Dependent
Enzyme
Dwi Susanti, Usha Loganathan, Austin Compton, Biswarup Mukhopadhyay
ACS Omega.2017; 2(8): 4180. CrossRef - Redox regulation of SurR by protein disulfide oxidoreductase in Thermococcus onnurineus NA1
Jae Kyu Lim, Hae-Chang Jung, Sung Gyun Kang, Hyun Sook Lee
Extremophiles.2017; 21(3): 491. CrossRef - Exploring membrane respiratory chains
Bruno C. Marreiros, Filipa Calisto, Paulo J. Castro, Afonso M. Duarte, Filipa V. Sena, Andreia F. Silva, Filipe M. Sousa, Miguel Teixeira, Patrícia N. Refojo, Manuela M. Pereira
Biochimica et Biophysica Acta (BBA) - Bioenergetics.2016; 1857(8): 1039. CrossRef
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