Ken Takai

Summary

Affiliation: Japan Agency for Marine-Earth Science and Technology
Country: Japan

Publications

  1. ncbi Hydrogenivirga caldilitoris gen. nov., sp. nov., a novel extremely thermophilic, hydrogen- and sulfur-oxidizing bacterium from a coastal hydrothermal field
    Satoshi Nakagawa
    Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606 8502, Japan
    Int J Syst Evol Microbiol 54:2079-84. 2004
  2. ncbi Deep-sea vent epsilon-proteobacterial genomes provide insights into emergence of pathogens
    Satoshi Nakagawa
    Subground Animalcule Retrieval Program and Extremophiles Research Program, Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Proc Natl Acad Sci U S A 104:12146-50. 2007
  3. ncbi Acquired thermotolerance and temperature-induced protein accumulation in the extremely thermophilic bacterium Rhodothermus obamensis
    K Takai
    Laboratory of Marine Microbiology, Division of Applied Bioscience, Graduate School of Agriculture, Kyoto University, Kyoto 606 01, Japan
    J Bacteriol 180:2770-4. 1998
  4. ncbi Deferribacter desulfuricans sp. nov., a novel sulfur-, nitrate- and arsenate-reducing thermophile isolated from a deep-sea hydrothermal vent
    Ken Takai
    Subground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Japan Marine Science and Technology Center, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 53:839-46. 2003
  5. ncbi Sulfurimonas paralvinellae sp. nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of Thiomicrospira denitrificans as Su
    Ken Takai
    Subground Animalcule Retrieval SUGAR Program, Japan Agency for Marine Earth Science and Technology, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 56:1725-33. 2006
  6. ncbi Marinobacter alkaliphilus sp. nov., a novel alkaliphilic bacterium isolated from subseafloor alkaline serpentine mud from Ocean Drilling Program Site 1200 at South Chamorro Seamount, Mariana Forearc
    Ken Takai
    Subground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Extremophiles 9:17-27. 2005
  7. ncbi Hydrogenimonas thermophila gen. nov., sp. nov., a novel thermophilic, hydrogen-oxidizing chemolithoautotroph within the epsilon-Proteobacteria, isolated from a black smoker in a Central Indian Ridge hydrothermal field
    Ken Takai
    Subground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Japan Marine Science and Technology Centre, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 54:25-32. 2004
  8. ncbi Cell proliferation at 122 degrees C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation
    Ken Takai
    Subground Animalcule Retrieval Program, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Proc Natl Acad Sci U S A 105:10949-54. 2008
  9. ncbi Isolation and physiological characterization of two novel, piezophilic, thermophilic chemolithoautotrophs from a deep-sea hydrothermal vent chimney
    Ken Takai
    Sunground Animalcule Retrieval SUGAR Program, Japan Agency for Marine Earth Science and Technology, Yokosuka 237 0061, Japan
    Environ Microbiol 11:1983-97. 2009
  10. ncbi Spatial distribution of marine crenarchaeota group I in the vicinity of deep-sea hydrothermal systems
    Ken Takai
    Subground Animalcule Retrieval Project, Frontier Research System for Extremophiles, Japan Marine Science and Technology Center, Yokosuka 237 0061, Japan
    Appl Environ Microbiol 70:2404-13. 2004

Detail Information

Publications79

  1. ncbi Hydrogenivirga caldilitoris gen. nov., sp. nov., a novel extremely thermophilic, hydrogen- and sulfur-oxidizing bacterium from a coastal hydrothermal field
    Satoshi Nakagawa
    Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606 8502, Japan
    Int J Syst Evol Microbiol 54:2079-84. 2004
    ..nov., sp. nov. is IBSK3(T) (=JCM 12173(T)=ATCC BAA-821(T))...
  2. ncbi Deep-sea vent epsilon-proteobacterial genomes provide insights into emergence of pathogens
    Satoshi Nakagawa
    Subground Animalcule Retrieval Program and Extremophiles Research Program, Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Proc Natl Acad Sci U S A 104:12146-50. 2007
    ..Our comparative genomic analysis suggests that there are previously unrecognized evolutionary links between important human/animal pathogens and their nonpathogenic, symbiotic, chemolithoautotrophic deep-sea relatives...
  3. ncbi Acquired thermotolerance and temperature-induced protein accumulation in the extremely thermophilic bacterium Rhodothermus obamensis
    K Takai
    Laboratory of Marine Microbiology, Division of Applied Bioscience, Graduate School of Agriculture, Kyoto University, Kyoto 606 01, Japan
    J Bacteriol 180:2770-4. 1998
    ..These results suggested that this extreme thermophile has developed temperature-induced responses that include increased survival under hyperthermal conditions, changes in protein composition, and also the production of novel HSPs...
  4. ncbi Deferribacter desulfuricans sp. nov., a novel sulfur-, nitrate- and arsenate-reducing thermophile isolated from a deep-sea hydrothermal vent
    Ken Takai
    Subground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Japan Marine Science and Technology Center, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 53:839-46. 2003
    ..thermophilus BMA(T) on the basis of its physiological and genetic properties. The name Deferribacter desulfuricans sp. nov. (type strain SSM1(T) = JCM 11476(T) = DSM 14783(T)) is proposed...
  5. ncbi Sulfurimonas paralvinellae sp. nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of Thiomicrospira denitrificans as Su
    Ken Takai
    Subground Animalcule Retrieval SUGAR Program, Japan Agency for Marine Earth Science and Technology, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 56:1725-33. 2006
    ..nov. (type strain DSM 1251(T)=ATCC 33889(T)). In addition, an emended description of the genus Sulfurimonas is proposed...
  6. ncbi Marinobacter alkaliphilus sp. nov., a novel alkaliphilic bacterium isolated from subseafloor alkaline serpentine mud from Ocean Drilling Program Site 1200 at South Chamorro Seamount, Mariana Forearc
    Ken Takai
    Subground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Extremophiles 9:17-27. 2005
    ..Based on the physiological and molecular properties of the new isolate, we propose the name Marinobacter alkaliphilus sp. nov., type strain: ODP1200D-1.5T (JCM12291T and ATCC BAA-889T)...
  7. ncbi Hydrogenimonas thermophila gen. nov., sp. nov., a novel thermophilic, hydrogen-oxidizing chemolithoautotroph within the epsilon-Proteobacteria, isolated from a black smoker in a Central Indian Ridge hydrothermal field
    Ken Takai
    Subground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Japan Marine Science and Technology Centre, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 54:25-32. 2004
    ..nov., sp. nov. is proposed, with strain EP1-55-1%T (=JCM 11971T=ATCC BAA-737T) as the type strain...
  8. ncbi Cell proliferation at 122 degrees C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation
    Ken Takai
    Subground Animalcule Retrieval Program, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Proc Natl Acad Sci U S A 105:10949-54. 2008
    ..4 per thousand, which is one of the smallest effects ever reported. This observation will shed light on the sources and production mechanisms of deep-sea methane...
  9. ncbi Isolation and physiological characterization of two novel, piezophilic, thermophilic chemolithoautotrophs from a deep-sea hydrothermal vent chimney
    Ken Takai
    Sunground Animalcule Retrieval SUGAR Program, Japan Agency for Marine Earth Science and Technology, Yokosuka 237 0061, Japan
    Environ Microbiol 11:1983-97. 2009
    ..nov., sp. nov. is proposed. The piezophilic cultivation technique can be a powerful tool to isolate and characterize the previously uncultivated phylotypes in the deep-sea hydrothermal vent environments...
  10. ncbi Spatial distribution of marine crenarchaeota group I in the vicinity of deep-sea hydrothermal systems
    Ken Takai
    Subground Animalcule Retrieval Project, Frontier Research System for Extremophiles, Japan Marine Science and Technology Center, Yokosuka 237 0061, Japan
    Appl Environ Microbiol 70:2404-13. 2004
    ..These profiles were markedly different from the profiles of epsilon-Proteobacteria, which are abundant in the low temperatures of deep-sea hydrothermal environments...
  11. ncbi Methanotorris formicicus sp. nov., a novel extremely thermophilic, methane-producing archaeon isolated from a black smoker chimney in the Central Indian Ridge
    Ken Takai
    Subground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Japan Marine Science and Technology Center, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 54:1095-100. 2004
    ..The name Methanotorris formicicus sp. nov. is proposed for this isolate; the type strain is Mc-S-70T (=JCM 11930T=ATCC BAA-687T)...
  12. ncbi Geochemical and microbiological evidence for a hydrogen-based, hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) beneath an active deep-sea hydrothermal field
    Ken Takai
    Subground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Japan Marine Science and Technology Center JAMSTEC, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Extremophiles 8:269-82. 2004
    ..These results imply that a HyperSLiME, consisting of methanogens and fermenters, occurs in this tectonically active subsurface zone, strongly supporting the existence of hydrogen-driven subsurface microbial communities...
  13. ncbi [Microorganisms in deep biosphere and hydrothermal system: potential roles in the co-evolution of earth and life]
    Ken Takai
    Tanpakushitsu Kakusan Koso 50:1649-59. 2005
  14. ncbi Thiomicrospira thermophila sp. nov., a novel microaerobic, thermotolerant, sulfur-oxidizing chemolithomixotroph isolated from a deep-sea hydrothermal fumarole in the TOTO caldera, Mariana Arc, Western Pacific
    Ken Takai
    Subground Animalcule Retrieval SUGAR Project, Japan Agency for Marine Earth Science and Technology JAMSTEC, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 54:2325-33. 2004
    ..nov. is proposed (type strain, I78(T)=JCM 12397(T)=DSM 16397(T))...
  15. ncbi Enzymatic and genetic characterization of carbon and energy metabolisms by deep-sea hydrothermal chemolithoautotrophic isolates of Epsilonproteobacteria
    Ken Takai
    Subground Animalcule Retrieval Program, Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Appl Environ Microbiol 71:7310-20. 2005
    ....
  16. ncbi Lebetimonas acidiphila gen. nov., sp. nov., a novel thermophilic, acidophilic, hydrogen-oxidizing chemolithoautotroph within the 'Epsilonproteobacteria', isolated from a deep-sea hydrothermal fumarole in the Mariana Arc
    Ken Takai
    Subground Animalcule Retrieval SUGAR Project, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 55:183-9. 2005
    ..It is, therefore, proposed that strain Pd55T (=JCM 12420T=DSM 16356T) represents the type strain of a novel species in a new genus, Lebetimonas acidiphila gen. nov., sp. nov...
  17. ncbi Sulfurihydrogenibium subterraneum gen. nov., sp. nov., from a subsurface hot aquifer
    Ken Takai
    Subground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Japan Marine Science and Technology Center, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 53:823-7. 2003
    ..The name Sulfurihydrogenibium subterraneum gen. nov., sp. nov. is proposed for this novel species; the type strain is HGMK1(T) (= JCM 11477(T) = ATCC BAA-562(T) = DSM 15120(T))...
  18. ncbi Hydrogenobacter subterraneus sp. nov., an extremely thermophilic, heterotrophic bacterium unable to grow on hydrogen gas, from deep subsurface geothermal water
    K Takai
    Subground Animalcules Retrieval SUGAR Project, Frontier Research for Deep sea Environments, Japan Marine Science and Technology Center, Yokosuka
    Int J Syst Evol Microbiol 51:1425-35. 2001
    ..The name Hydrogenobacter subterraneus sp. nov. is proposed; the type strain is HGP1T (= JCM 10560T = IFO 16485T)...
  19. ncbi Distribution of archaea in a black smoker chimney structure
    K Takai
    Subground Animalcule Retrieval SUGAR Project, Frontier Research Program for Deep sea Extremophiles, Japan Marine Science and Technology Center, Yokosuka 237 0061, Japan
    Appl Environ Microbiol 67:3618-29. 2001
    ..The results of the culture-dependent analysis supported in part the view that changes in archaeal community structures in these microhabitats are associated with the geochemical and physical dynamics in the black smoker chimney...
  20. ncbi Thermosipho japonicus sp. nov., an extremely thermophilic bacterium isolated from a deep-sea hydrothermal vent in Japan
    K Takai
    Deep sea Microorganisms Research Group DEEP STAR, Japan Marine Science and Technology Center JAMSTEC, Yokosuka
    Extremophiles 4:9-17. 2000
    ..On the basis of the physiological and molecular properties, we propose that the new isolate represents a new species, which we name Thermosipho japonicus sp. nov. (type strain: IHB1; JCM10495)...
  21. ncbi Archaeal diversity and community development in deep-sea hydrothermal vents
    Ken Takai
    Subsurface Geobiology Advanced Research SUGAR Project, Japan Agency for Marine Earth Science and Technology JAMSTEC, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Curr Opin Microbiol 14:282-91. 2011
    ....
  22. ncbi Isolation and metabolic characteristics of previously uncultured members of the order aquificales in a subsurface gold mine
    Ken Takai
    Sunground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Japan Marine Science and Technology Center, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Appl Environ Microbiol 68:3046-54. 2002
    ..Their versatile energy-generating systems may reflect the geochemical conditions of their habitat in the geothermally active subsurface gold mine...
  23. ncbi Methanothermococcus okinawensis sp. nov., a thermophilic, methane-producing archaeon isolated from a Western Pacific deep-sea hydrothermal vent system
    Ken Takai
    Subground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Japan Marine Science and Technology Center, Yokosuka
    Int J Syst Evol Microbiol 52:1089-95. 2002
    ..The name Methanothermococcus okinawensis sp. nov is proposed, with the type strain IH1T (=JCM 11175T=DSM 14208T)...
  24. ncbi Isolation and phylogenetic diversity of members of previously uncultivated epsilon-Proteobacteria in deep-sea hydrothermal fields
    Ken Takai
    Japan Marine Science and Technology Center, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    FEMS Microbiol Lett 218:167-74. 2003
    ..The successful cultivation will enable the subsequent characterization of physiological properties and ecological impacts of a diversity of epsilon-Proteobacteria in the deep-sea hydrothermal environments...
  25. ncbi Genetic diversity of archaea in deep-sea hydrothermal vent environments
    K Takai
    Deep Sea Microorganisms Research Group, Japan Marine Science and Technology Center, Yokosuka 237 0061, Japan
    Genetics 152:1285-97. 1999
    ..These findings expand our view of the genetic diversity of archaea in deep-sea hydrothermal vent environments and of the phylogenetic organization of archaea...
  26. ncbi Thermaerobacter marianensis gen. nov., sp. nov., an aerobic extremely thermophilic marine bacterium from the 11,000 m deep Mariana Trench
    K Takai
    Deep sea Micro organisms Research Group DEEPSTAR, Japan Marine Science and Technology Center JAMSTEC, Yokosuka, Japan
    Int J Syst Bacteriol 49:619-28. 1999
    ..On the basis of the physiological and molecular properties of the new isolate, the name Thermaerobacter marianensis gen. nov., sp. nov. (type strain 7p75aT = JCM 10246T) is proposed...
  27. ncbi ppc, the gene for phosphoenolpyruvate carboxylase from an extremely thermophilic bacterium, Rhodothermus obamensis: cloning, sequencing and overexpression in Escherichia coli
    K Takai
    Division of Applied Bioscience, Graduate School of Agriculture, Kyoto University, Japan
    Microbiology 144:1423-34. 1998
    ..Comparison of the deduced amino acid sequences of the thermophilic and mesophilic PEPCs revealed distinct or common preferences for specific amino acid composition and substitutions in the two thermophilic enzymes...
  28. ncbi Sulfurivirga caldicuralii gen. nov., sp. nov., a novel microaerobic, thermophilic, thiosulfate-oxidizing chemolithoautotroph, isolated from a shallow marine hydrothermal system occurring in a coral reef, Japan
    Ken Takai
    Subground Animalcule Retrieval SUGAR Program, Japan Agency for Marine Earth Science and Technology, JAMSTEC, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 56:1921-9. 2006
    ..It is suggested that the novel isolates represent the type species of a new genus, for which the name Sulfurivirga caldicuralii gen. nov., sp. nov. (type strain MM1(T)=JCM 13439(T)=DSM 17737(T)) is proposed...
  29. ncbi Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes
    K Takai
    Deep Sea Microorganisms Research Group, Japan Marine Science and Technology Center, Yokosuka 237 0061, Japan
    Appl Environ Microbiol 66:5066-72. 2000
    ..Our findings indicate that this method is applicable to culture-independent molecular analysis of microbial communities in various environments...
  30. ncbi Culture-dependent and -independent characterization of microbial communities associated with a shallow submarine hydrothermal system occurring within a coral reef off Taketomi Island, Japan
    Hisako Hirayama
    Subground Animalcule Retrieval SUGAR Program, Extremobiosphere Research Center, JAMSTEC, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Appl Environ Microbiol 73:7642-56. 2007
    ..Our results indicate that there are unique microbial communities that are sustained by active chemosynthetic primary production rather than by photosynthetic production in a shallow hydrothermal system where sunlight is abundant...
  31. ncbi Bacterial community shift along a subsurface geothermal water stream in a Japanese gold mine
    Hisako Hirayama
    Subground Animalcule Retrieval SUGAR Project, Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology JAMSTEC, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Extremophiles 9:169-84. 2005
    ....
  32. ncbi Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the epsilon-Proteobacteria isolated from Okinawa Trough hydrothermal sediments
    Fumio Inagaki
    Subground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Japan Marine Science and Technology Center JAMSTEC, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 54:1477-82. 2004
    ..On the basis of the physiological and molecular characteristics of this isolate, the type species of a novel genus, Sulfurovum lithotrophicum gen. nov., sp. nov., is proposed. The type strain is 42BKTT (= ATCC BAA-797T = JCM 12117T)...
  33. ncbi Desulfothermus okinawensis sp. nov., a thermophilic and heterotrophic sulfate-reducing bacterium isolated from a deep-sea hydrothermal field
    Takuro Nunoura
    Subground Animalcule Retrieval SUGAR Program, Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology JAMSTEC, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 57:2360-4. 2007
    ..Based on physiological and phylogenetic characteristics, strain TFISO9(T) represents a novel species for which the name Desulfothermus okinawensis sp. nov. is proposed. The type strain is TFISO9(T) (=JCM 13304(T)=DSM 17375(T))...
  34. ncbi Distribution and phylogenetic diversity of the subsurface microbial community in a Japanese epithermal gold mine
    Fumio Inagaki
    Subground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Japan Marine Science and Technology Center, Yokosuka 237 0061, Japan
    Extremophiles 7:307-17. 2003
    ..The cultivable microbial community detected by enrichment cultivation analysis largely matched that detected by the culture-independent molecular analysis...
  35. ncbi Hydrogenivirga okinawensis sp. nov., a thermophilic sulfur-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal field, Southern Okinawa Trough
    Takuro Nunoura
    Subground Animalcule Retrieval SUGAR Program, Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 58:676-81. 2008
    ..nov. The type strain of Hydrogenivirga okinawensis is LS12-2(T) (=JCM 13302(T)=DSM 17378(T))...
  36. ncbi Kosmotoga arenicorallina sp. nov. a thermophilic and obligately anaerobic heterotroph isolated from a shallow hydrothermal system occurring within a coral reef, southern part of the Yaeyama Archipelago, Japan, reclassification of Thermococcoides shenglien
    Takuro Nunoura
    Institute of Biogeosciences, Japan Agency for Marine Earth Science and Technology, Yokosuka, Japan
    Arch Microbiol 192:811-9. 2010
    ..5.1(T), we propose the reclassification of Thermococcoides shengliensis as Kosmotoga shengliensis comb. nov. (type strain 2SM-2(T)). In addition, an emended description of the genus Kosmotoga is proposed...
  37. ncbi Geofilum rubicundum gen. nov., sp. nov., isolated from deep subseafloor sediment
    Masayuki Miyazaki
    Subsurface Geobiology Advanced Research SUGAR Project, Japan Agency for Marine Earth Science and Technology JAMSTEC, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 62:1075-80. 2012
    ..nov., sp. nov. is proposed. The type strain of Geofilum rubicundum is JAM-BA0501(T) ( = JCM 15548(T)  = NCIMB 14482(T))...
  38. ncbi Molecular characterization of potential nitrogen fixation by anaerobic methane-oxidizing archaea in the methane seep sediments at the number 8 Kumano Knoll in the Kumano Basin, offshore of Japan
    Junichi Miyazaki
    Subground Geobiology and Advanced Research Project, Institute of Biogeosciences, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Appl Environ Microbiol 75:7153-62. 2009
    ....
  39. ncbi Thioreductor micantisoli gen. nov., sp. nov., a novel mesophilic, sulfur-reducing chemolithoautotroph within the epsilon-Proteobacteria isolated from hydrothermal sediments in the Mid-Okinawa Trough
    Satoshi Nakagawa
    Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606 8502, Japan
    Int J Syst Evol Microbiol 55:599-605. 2005
    ..nov. is proposed, with Thioreductor micantisoli sp. nov. as the type species. The type strain is BKB25Ts-Y(T) (=JCM 12457(T)=DSM 16661(T))...
  40. ncbi Thiobacter subterraneus gen. nov., sp. nov., an obligately chemolithoautotrophic, thermophilic, sulfur-oxidizing bacterium from a subsurface hot aquifer
    Hisako Hirayama
    Subground Animalcule Retrieval SUGAR Project, Japan Agency for Marine Earth Science and Technology JAMSTEC, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 55:467-72. 2005
    ..On the basis of its physiological and molecular properties, strain C55T (=JCM12421T=DSM 16629T=ATCC BAA-941T) is proposed as the type strain of Thiobacter subterraneus gen. nov., sp. nov...
  41. ncbi Archaeal diversity and distribution along thermal and geochemical gradients in hydrothermal sediments at the Yonaguni Knoll IV hydrothermal field in the Southern Okinawa trough
    Takuro Nunoura
    Subsurface Geobiology and Advanced Research Project, Extremobiosphere Research Program, Institute of Biogeosciences, JAMSTEC, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Appl Environ Microbiol 76:1198-211. 2010
    ....
  42. ncbi Characterization of C1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, southern Ryukyu Arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes
    Fumio Inagaki
    Subground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Yokosuka, Japan
    Appl Environ Microbiol 70:7445-55. 2004
    ....
  43. ncbi Molecular characterization of inorganic sulfur-compound metabolism in the deep-sea epsilonproteobacterium Sulfurovum sp. NBC37-1
    Masahiro Yamamoto
    Institute of Biogeosciences, Japan Agency for Marine Earth Science and Technology JAMSTEC, Yokosuka, Japan
    Environ Microbiol 12:1144-53. 2010
    ....
  44. ncbi Exilispira thermophila gen. nov., sp. nov., an anaerobic, thermophilic spirochaete isolated from a deep-sea hydrothermal vent chimney
    Hiroyuki Imachi
    Subground Animalcule Retrieval SUGAR Program, Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology JAMSTEC, Yokosuka, Kanagawa 237 0061, Japan
    Int J Syst Evol Microbiol 58:2258-65. 2008
    ..1-80.6 %). Hence, we propose the name Exilispira thermophila gen. nov., sp. nov. The type strain of Exilispira thermophila is strain RASEN(T) (=JCM 14728(T) =NBRC 103205(T) =KCTC 5595(T))...
  45. ncbi Microbial communities associated with geological horizons in coastal subseafloor sediments from the sea of okhotsk
    Fumio Inagaki
    Subground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Japan
    Appl Environ Microbiol 69:7224-35. 2003
    ....
  46. ncbi Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field
    Satoshi Nakagawa
    Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake cho, Kitashirakawa, Kyoto 606 8502, Japan
    Environ Microbiol 7:1619-32. 2005
    ..These results provide new insight into the ecophysiological characteristics of the deep-sea hydrothermal vent epsilon-Proteobacteria, which has never been assessed by comparative analysis of the 16S rRNA genes...
  47. ncbi Nitratiruptor tergarcus gen. nov., sp. nov. and Nitratifractor salsuginis gen. nov., sp. nov., nitrate-reducing chemolithoautotrophs of the epsilon-Proteobacteria isolated from a deep-sea hydrothermal system in the Mid-Okinawa Trough
    Satoshi Nakagawa
    Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606 8502, Japan
    Int J Syst Evol Microbiol 55:925-33. 2005
    ..nov., sp. nov., with MI55-1(T) (=JCM 12459(T)=DSM 16512(T)) as the type strain, and Nitratifractor salsuginis gen. nov., sp. nov., with E9I37-1(T) (=JCM 12458(T)=DSM 16511(T)) as the type strain...
  48. ncbi Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments
    Takuro Nunoura
    Subground Animalcule Retrieval SUGAR Program, Extremebiosphere Research Center, Japan Agency for Marine Earth Science and Technology JAMSTEC, 2 15 Natsushima cho, Jokosuka, Japan
    Environ Microbiol 7:1967-84. 2005
    ..The reconstructed phylogenetic tree based on the 23S rRNA gene sequence reinforced the intermediate phylogenetic affiliation of HWCG III bridging the hyperthermophilic and non-thermophilic uncultivated Crenarchaeota...
  49. ncbi Development of 16S rRNA gene-targeted primers for detection of archaeal anaerobic methanotrophs (ANMEs)
    Ai Miyashita
    Subsurface Geobiology Advanced Research Team, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine Earth Science and Technology, Kanagawa, Japan
    FEMS Microbiol Lett 297:31-7. 2009
    ..02% of the total prokaryotic 16S rRNA gene community. The newly designed ANME group-specific primers in this study may be useful to survey the distribution and quantitative determination of ANMEs...
  50. ncbi Persephonella hydrogeniphila sp. nov., a novel thermophilic, hydrogen-oxidizing bacterium from a deep-sea hydrothermal vent chimney
    Satoshi Nakagawa
    Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606 8502, Japan
    Int J Syst Evol Microbiol 53:863-9. 2003
    ..On the basis of the physiological and molecular properties of the new isolate, the name Persephonella hydrogeniphila sp. nov. is proposed. The type strain is strain 29W(T) (= JCM 11663(T) = DSM 15103(T))...
  51. ncbi Marinithermus hydrothermalis gen. nov., sp. nov., a strictly aerobic, thermophilic bacterium from a deep-sea hydrothermal vent chimney
    Yoshihiko Sako
    Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606 8502, Japan
    Int J Syst Evol Microbiol 53:59-65. 2003
    ..The name Marinithermus gen. nov. is proposed, with Marinithermus hydrothermalis gen. nov., sp. nov. as the type species. The type strain of M. hydrothermalis gen. nov., sp. nov. is strain T1T (=JCM 11576T =DSM 14884T)...
  52. ncbi Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing epsilon-proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough
    Fumio Inagaki
    Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Marine Science and Technology Center (JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
    Int J Syst Evol Microbiol 53:1801-5. 2003
    ..On the basis of its physiological and molecular characteristics, strain OK10(T) (=ATCC BAA-671(T)=JCM 11897(T)) represents the sole species of a new genus, Sulfurimonas, for which the name Sulfurimonas autotrophica is proposed...
  53. ncbi Geomicrobiological exploration and characterization of a novel deep-sea hydrothermal system at the TOTO caldera in the Mariana Volcanic Arc
    Tatsunori Nakagawa
    Subground Animalcule Retrieval SUGAR Project, Japan Agency for Marine-Earth Science and Technology, JAMSTEC, Yokosuka 237-0061, Japan
    Environ Microbiol 8:37-49. 2006
    ..Cultivation analysis suggested that the chemolithoautotrophs might play a significant ecological role as primary producers utilizing gas and sulfur compounds provided from hydrothermal fluids...
  54. ncbi Methanofollis ethanolicus sp. nov., an ethanol-utilizing methanogen isolated from a lotus field
    Hiroyuki Imachi
    Subground Animalcule Retrieval SUGAR Program, Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology JAMSTEC, Yokosuka, Kanagawa 237 0061, Japan
    Int J Syst Evol Microbiol 59:800-5. 2009
    ..nov. is proposed. The type strain is HASU(T) (=NBRC 104120(T)=JCM 15103(T)=DSM 21041(T))...
  55. ncbi Quantification of mcrA by quantitative fluorescent PCR in sediments from methane seep of the Nankai Trough
    Takuro Nunoura
    Subground Animalcule Retrieval Program, Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology, Yokosuka, Japan
    FEMS Microbiol Ecol 57:149-57. 2006
    ..This quantification method will contribute to future investigations of methanotrophic microbial ecosystems in anoxic marine sediments...
  56. ncbi Microbial community in a sediment-hosted CO2 lake of the southern Okinawa Trough hydrothermal system
    Fumio Inagaki
    Subground Animalcule Retrieval SUGAR Program, Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology JAMSTEC, Yokosuka 237 0061, Japan
    Proc Natl Acad Sci U S A 103:14164-9. 2006
    ..Clearly, the Yonaguni Knoll is an exceptional natural laboratory for the study of consequences of CO2 disposal as well as of natural CO2 reservoirs as potential microbial habitats on early Earth and other celestial bodies...
  57. ncbi Marinitoga okinawensis sp. nov., a novel thermophilic and anaerobic heterotroph isolated from a deep-sea hydrothermal field, Southern Okinawa Trough
    Takuro Nunoura
    Subground Animalcule Retrieval SUGAR Program, Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology JAMSTEC, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Int J Syst Evol Microbiol 57:467-71. 2007
    ..nov. is proposed. The type strain is TFS10-5(T) (=JCM 13303(T)=DSM 17373(T))...
  58. ncbi Novel chemoautotrophic endosymbiosis between a member of the Epsilonproteobacteria and the hydrothermal-vent gastropod Alviniconcha aff. hessleri (Gastropoda: Provannidae) from the Indian Ocean
    Yohey Suzuki
    Frontier Research System for Extremophiles, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Appl Environ Microbiol 71:5440-50. 2005
    ....
  59. ncbi Variability in microbial community and venting chemistry in a sediment-hosted backarc hydrothermal system: Impacts of subseafloor phase-separation
    Satoshi Nakagawa
    Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake cho, Kitashirakawa, Sakyo ku, Japan
    FEMS Microbiol Ecol 54:141-55. 2005
    ..Subseafloor phase-separation and -segregation may play a key role in supplying energy and carbon sources to vent-associated chemolithoautotrophs and subvent microbial communities...
  60. ncbi Host-symbiont relationships in hydrothermal vent gastropods of the genus Alviniconcha from the Southwest Pacific
    Yohey Suzuki
    Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology, Yokosuka, Kanagawa 237 0061, Japan
    Appl Environ Microbiol 72:1388-93. 2006
    ..The results from the present study also suggest the possibility that Alviniconcha sp. types 1 and 2 separately inhabit hydrothermal vent sites approximately 120 m apart in the North Fiji Basin and 500 m apart in the Manus Basin...
  61. ncbi Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin
    Fumio Inagaki
    Subground Animalcule Retrieval Project, Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology, Yokosuka 237 0061, Japan
    Proc Natl Acad Sci U S A 103:2815-20. 2006
    ..The recognition of which microbial groups prevail under distinctive subseafloor environments is a significant step toward determining the role these communities play in Earth's essential biogeochemical processes...
  62. ncbi Microbial community in black rust exposed to hot ridge flank crustal fluids
    Satoshi Nakagawa
    Subground Animalcule Retrieval SUGAR Project, Extremobiosphere Research Center XBR, Japan Agency for Marine Earth Science and Technology JAMSTEC, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Appl Environ Microbiol 72:6789-99. 2006
    ..This report provides important insights into the phylogenetic, physiological, and trophic characteristics of subseafloor microbial ecosystems in warm ridge flank crusts...
  63. ncbi Phylogenetic and enzymatic diversity of deep subseafloor aerobic microorganisms in organics- and methane-rich sediments off Shimokita Peninsula
    Tohru Kobayashi
    Extremobiosphere Research Center of Japan Agency for Marine Earth Science and Technology JAMSTEC, 2 15 Natsushima, Yokosuka, 237 0061, Japan
    Extremophiles 12:519-27. 2008
    ..Our results indicate that microbes in the deep subseafloor environment off Shimokita are metabolically active and that the cultivable populations may have a great potential in biotechnology...
  64. ncbi Comparison of microbial communities associated with phase-separation-induced hydrothermal fluids at the Yonaguni Knoll IV hydrothermal field, the Southern Okinawa Trough
    Takuro Nunoura
    Subground Animalcule Retrieval SUGAR Program, Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology JAMSTEC, Yokosuka, Japan
    FEMS Microbiol Ecol 67:351-70. 2009
    ..The relatively consistent microbial communities found in this study could have been because of the sufficient input of hydrogen from the hydrothermal fluids rather than other chemical properties...
  65. ncbi Aeropyrum camini sp. nov., a strictly aerobic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney
    Satoshi Nakagawa
    Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606 8502, Japan
    Int J Syst Evol Microbiol 54:329-35. 2004
    ..On the basis of the molecular and physiological traits of the new isolate, the name Aeropyrum camini sp. nov. is proposed, with the type strain SY1(T) (=JCM 12091(T)=ATCC BAA-758(T))...
  66. ncbi Thermaerobacter nagasakiensis sp. nov., a novel aerobic and extremely thermophilic marine bacterium
    Takuro Nunoura
    Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606 8502, Japan
    Arch Microbiol 177:339-44. 2002
    ..The differences in physiology and DNA-DNA similarity between strain Ts1a and T. marianensis showed that strain Ts1a represents a new species of Thermaerobacter. The type strain of T. nagasakiensis is strain Ts1a (=JCM11223, DSM 14512)...
  67. ncbi Balnearium lithotrophicum gen. nov., sp. nov., a novel thermophilic, strictly anaerobic, hydrogen-oxidizing chemolithoautotroph isolated from a black smoker chimney in the Suiyo Seamount hydrothermal system
    Ken Takai
    Subground Animalcule Retrieval (SUGAR) Project, Japan Marine Science and Technology Center, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
    Int J Syst Evol Microbiol 53:1947-54. 2003
    ..ruber ED11/3LLK(T) and D. thermolithotrophum BSA(T) on the basis of physiological properties. The name Balnearium lithotrophicum gen. nov., sp. nov. is proposed for this isolate (type strain, 17S(T)=JCM 11970(T)=ATCC BAA-736(T))...
  68. ncbi Bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium Deferribacter desulfuricans SSM1
    Yoshihiro Takaki
    Microbial Genome Research Group, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine Earth Science and Technology JAMSTEC, Yokosuka, Kanagawa 237 0061, Japan
    DNA Res 17:123-37. 2010
    ..desulfuricans SSM1 thriving in the physically and chemically fluctuating environments near hydrothermal vents. This is the first genome sequence from the phylum Deferribacteres...
  69. ncbi Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group
    Takuro Nunoura
    Subsurface Geobiology and Advanced Research Project, Institute of Biogeosciences, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Nucleic Acids Res 39:3204-23. 2011
    ..The presence of such a eukaryote-type system is unprecedented in prokaryotes, and indicates that a prototype of the eukaryotic protein modifier system is present in the Archaea...
  70. ncbi Phylogenetic diversity of sulfate-reducing prokaryotes in active deep-sea hydrothermal vent chimney structures
    Tatsunori Nakagawa
    Subground Animalcule Retrieval SUGAR Project, Japan Marine Science and Technology Center, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    FEMS Microbiol Lett 232:145-52. 2004
    ..Sequence analysis of DSR clones demonstrated a diverse sulfate-reducing prokaryotic community in the active deep-sea hydrothermal chimney structures...
  71. ncbi Subseafloor microbial communities associated with rapid turbidite deposition in the Gulf of Mexico continental slope (IODP Expedition 308)
    Takuro Nunoura
    Subsurface Geobiology and Advanced Research SUGAR Project, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine Earth Science and Technology JAMSTEC, Yokosuka 237 0061, Japan
    FEMS Microbiol Ecol 69:410-24. 2009
    ..This may also explain the distributions of relatively similar archaeal communities in the Ursa Basin sediments and basement sediments in the BT Basin...
  72. ncbi Extremely high alkaline protease from a deep-subsurface bacterium, Alkaliphilus transvaalensis
    Tohru Kobayashi
    Extremobiosphere Research Center of Japan Agency for Marine Earth Science and Technology JAMSTEC, 2 15, Natsushima, Yokosuka, Japan
    Appl Microbiol Biotechnol 75:71-80. 2007
    ..ALTP is the first high-alkaline protease reported from a strict anaerobe in this family...
  73. ncbi Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance
    Satoshi Nakagawa
    Subground Animalcule Retrieval Program, Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology, Yokosuka, Japan
    FEMS Microbiol Ecol 65:1-14. 2008
    ..This review summarizes chemoautotrophy in deep-sea vents, highlighting recent biochemical and genomic discoveries...
  74. ncbi Quantification of mcrA by fluorescent PCR in methanogenic and methanotrophic microbial communities
    Takuro Nunoura
    Subground Animalcule Retrieval SUGAR Program, Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology JAMSTEC, Yokosuka, Japan
    FEMS Microbiol Ecol 64:240-7. 2008
    ..The assay can be applied to detecting and assessing the abundance of methanogens and/or ANMEs in anoxic environments that could not be detected by 16S rRNA gene sequence analyses...
  75. ncbi Hydrogen-driven subsurface lithoautotrophic microbial ecosystems (SLiMEs): do they exist and why should we care?
    Kenneth H Nealson
    Department of Earth Sciences, University of Southern California, 3651 Trousdale Parkway, Los Angeles, CA 90089 0740, USA
    Trends Microbiol 13:405-10. 2005
    ....
  76. ncbi Shifts in archaeal communities associated with lithological and geochemical variations in subsurface Cretaceous rock
    Ken Takai
    Deep-sea Microorganisms Research Group, Japan Marine Science and Technology Center, Yokosuka 237-0061 Japan
    Environ Microbiol 5:309-20. 2003
    ....
  77. ncbi Molecular analysis of deep subsurface Cretaceous rock indicates abundant Fe(III)- and S(zero)-reducing bacteria in a sulfate-rich environment
    William P Kovacik
    Microbial Ecology Program, Division of Biological Sciences, The University of Montana, Missoula, 59812, USA
    Environ Microbiol 8:141-55. 2006
    ..The presence of a phylogenetically and functionally diverse microbial community in this deep subsurface environment likely reflects the complex nature of the primary energy and carbon sources, kerogen associated with the shale...
  78. ncbi Related assemblages of sulphate-reducing bacteria associated with ultradeep gold mines of South Africa and deep basalt aquifers of Washington State
    Brett J Baker
    Dept. of Biological Sciences, University of Wisconsin-Milwaukee, 3209 N. Maryland Ave. Milwaukee, WI 53211, USA
    Environ Microbiol 5:267-77. 2003
    ..The dsr sequences recovered from the Washington State deep aquifer systems affiliated closely with the South African sequences, suggesting that Gram-positive sulphate-reducing bacteria are widely distributed in the deep subsurface...
  79. ncbi The versatile epsilon-proteobacteria: key players in sulphidic habitats
    Barbara J Campbell
    College of Marine Studies, University of Delaware, Lewes, Delaware 19958, USA
    Nat Rev Microbiol 4:458-68. 2006
    ..These integrated perspectives provide a framework for future culture- and genomic-based studies...