Geomicrobiology Research Group
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Institute for Geo-Resources and Environment
National Institute of Advanced Industrial Science and Technology
Central 7, 1-1-1 Higashi, Tsukuba, 305-8567, JAPAN.
Tel.: +81-298-61-2000

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Geomicrobiology Research Group.
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Member



Name Position Email(*)
Dr. Hideyoshi Yoshioka Group Leader hi-yoshioka
Dr. Susumu Sakata Chief Senior Researcher su-sakata
Dr. Mio Takeuchi Senior Researcher takeuchi-mio
Dr. Hanako Mochimaru Senior Researcher h-mochimaru
Dr. Taiki Katayama Senior Researcher katayama.t
Dr. Daisuke Mayumi Senior Researcher mayumi-daisuke
Dr. Masanori Kaneko Senior Researcher m-kaneko
Dr. Konomi Suda Researcher suda-konomi
Dr. Makoto Matsushita Researcher m-matsushita
Dr. Satoshi Furota Researcher sato.furota
Ms. Tomomi Ujiie Technical Staff
Ms. Yumi Shinotsuka Technical Staff
Ms. Kuniko Syuin Technical Staff
Ms. Fumie Nozawa Technical Staff
Ms. Chiwaka Miyako Technical Staff
Ms. Keiko Shintate Technical Staff
Ms. Chihiro Amano Technical Staff
Ms. Misa Takenouchi Technical Staff
Ms. Miyuki Kobayashi Technical Staff
Ms. Yuu Hashimoto Technical Staff
Ms. Ayami Ishikawa Technical Staff

(*)@aist.go.jp


Dr. Susumu Sakata
Research Fields Organic Geochemistry, Biogeochemistry
Research Topics
  • Distribution of geomicrobes assessed by lipid biomarkers
  • Isotopic fractionation associated with microbial processes
  • Origin of natural gas
Comment My Motto:Constant dropping wears away a stone.

Publication
  • Mayumi D., Mochimaru H., Tamaki H., Yamamoto K., Yoshjoka H., Suzuki Y., Kamagata Y., Sakata S.(2016) Methane production from coal by a single methanogen. Science354 (6309), 222-225.
  • Mochimaru H., Tamaki H., Katayama T., Imachi H., Sakata S., Kamagata Y. (2016) Methanomicrobium antiquum sp. nov., a hydrogenotrophic methanogen isolated from deep sedimentary aquifers in a natural gas field. in press.
  • Katayama T., Yoshioka H., Takahashi H.A., Amo M., Fujii T., Sakata S.(2016) Changes in microbial communities associated with gas hydrates in subseafloor sediments from the Nankai Trough.FEMS Microbiology Ecology, in press
  • Yoshioka H, Mochimaru H, Sakata S. Takeda H, Yoshida S.(2015) Methane production potential of subsurface microbes in Pleistocene sediments from a natural gas field of the dissolved-in-water type, central Japan. Chemical Geology 419, 92-101.
  • Katayama T., Yoshioka H., Muramoto Y., Usami J., Fujiwara K., Yoshida S., Kamagata Y., Sakata S. (2015) Physicochemical impacts associated with natural gas development on methanogenesis in deep sand aquifers. The ISME Journal 9, 436-446.
  • Takeuchi M., Yamagishi T., Kamagata Y., Oshima K., Hattori M., Katayama T., Hanada S., Tamaki H., Marumo K., Maeda H., Nedachi M., Iwasaki W., Suwa Y., Sakata S. (2015) Tepidicaulis marinus gen. nov., sp. nov., a novel marine bacterium reducing nitrate to nitrous oxide strictly under microaerobic conditions. International Journal of Systematic and Evolutionary Microbiology, in press (doi: 10.1099/ijs.0.000167).
  • Oba M., Sakata S., Fujii T. (2015) Archaeal polar lipids in deep marine sediments from the Nankai Trough. Archaeal polar lipids in subseafloor sediments from the Nankai Trough: Implications for the distribution of methanogens in the deep marine subsurface. Organic Geochemistry 78, 153-160.
  • Takeuchi M., Kamagata Y., Oshima K., Hanada S., Tamaki H., Marumo K., Maeda H., Nedachi M., Hattori M., Iwasaki W., Sakata S. (2014) Methylocaldum marinum sp. nov., a thermotolerant, methane oxidizing bacterium isolated from marine sediments, and emended description of the genus Methylocaldum. International Journal of Systematic and Evolutionary Microbiology 64, 3240-3246. 
  • Komatsu T., Kato S., Hirata K., Takashima R., Ogata Y., Oba M., Naruse H., Ta P.H., Nguyen P.D., Dang H.T., Doan T.N., Nguyen H.H., Sakata S., Kaiho K., Konigshof P. (2014) Devonian - Carboniferous transition containing a Hangenberg Black Shale equivalent in the Pho Han Formation on Cat Ba Island, northeastern Vietnam. Palaeogeography, Palaeoclimatology, Palaeoecology 404, 30-43.
  • Katayama T., Yoshioka H., Mochimaru H., Meng X.Y., Muramoto Y., Usami J., Ikeda, H., Kamagata Y., Sakata S. (2014) Methanohalophilus levihalodurans sp. nov., a slightly halophilic, methylotrophic methanogen isolated from natural gas-bearing deep aquifers, and emended description of the genus Methanohalophilus. International Journal of Systematic and Evolutionary Microbiology 64, 2089-2093.
  • Takeuchi M., Oshima K., Yamagishi T., Katayama T., Hanada S., Tamaki H., Kamagata Y., Marumo K., Nedachi M., Maeda H., Sakata S. (2014) Methyloceanibacter cenitepidus gen. nov., sp. nov., a facultatively methylotrophic bacterium isolated from marine sediments near a hydrothermal vent. International Journal of Systematic and Evolutionary Microbiology 64, 462-468.
  • Mayumi D., Dolfing J., Sakata S., Maeda H., Miyagawa Y., Ikarashi M., Tamaki H., Takeuchi M., Nakatsu C. H., and Kamagata Y. (2013) Carbon dioxide concentration dictates alternative methanogenic pathways in oil reservoirs. Nature Communications, DOI: 10.1038/ncomms2998.
  • Sakata S., Maekawa T., Igari S., and Sano Y. (2012) Geochemistry and origin of natural gases dissolved in brines from gas fields in southwest Japan. Geofluids, 12, 327-335.
  • Kobayashi H., Endo K., Sakata S., Mayumi D., Kawaguchi H., Ikarashi M., Miyagawa Y., Maeda H., Sato K. (2012) Phylogenetic diversity of microbial communities associated with the crude-oil, large-insoluble-particle, and formation-water components of the reservoir fluid from a non-flooded high-temperature biodegraded petroleum reservoir. Journal of Bioscience and Bioengineering 113, 204-210.
  • Kobayashi H., Kawaguchi H., Endo K., Mayumi D., Sakata S., Ikarashi M., Miyagawa Y., Maeda H., Sato K. (2012) Analysis of methane production by microorganisms indigenous to a depleted oil reservoir for application in Micobial Enchance Oil Recovery. Journal of Bioscience and Bioengineering 113, 84-87.
  • Takeuchi M., Yoshioka H., Seo Y., Tanabe S., Tamaki H., Kamagata Y., Takahashi H. A., Igari S., Mayumi D., Sakata S. (2011) A distinct freshwater-adapted subgroup of ANME-1 dominates active archaeal communities in terrestrial subsurfaces in Japan. Environmental Microbiology 13, 3206-3218.
  • Mayumi D., Mochimaru H., Yoshioka H., Sakata S., Maeda H., Miyagawa Y., Ikarashi M., Takeuchi M., Kamagata Y. (2011) Evidence for syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis in the high-temperature petroleum reservoir of Yabase oil field (Japan). Environmental Microbiology 13, 1995-2006.
  • Yoshioka H., Maruyama A., Nakamura T., Higashi Y., Fuse H., Sakata S., Bartlett D. H. (2010) Activities and distribution of methanogenic and methane-oxidizing microbes in marine sediments from the Cascadia Margin. Geobiology 8, 223-233.
  • Maeda H., Miyagawa Y., Ikarashi M., Mayumi D., Mochimaru H., Yoshioka H., Sakata S., Kobayashi H., Sato K. (2010) Research for Microbial Conversion of Residual Oil into Methane in Depleted Oil Fields to Develop New EOR Process. Proceedings of Abudabi Oil and Gas Conference and Exhibition 2010, Abudabi. OnePetro, No. 138135-MS.
  • Yoshioka H., Sakata S., Cragg B., Parkes J., Fujii T. (2009) Microbial methane production rates in gas hydrate-bearing sediments from the eastern Nankai Trough, off central Japan. Geochemical Journal 43, 315-321.
  • Takahashi S., Oba M., Kaiho K., Yamakita S., Sakata S. (2009) Panthalassic oceanic anoxia at the end of the Early Triassic: a cause of delay in the recovery of life after the end-Permian mass extinction. Palaeogeography, Palaeoclimatology, Palaeoecology 274, 185-195.
  • Mochimaru H., Tamaki H., Hanada S., Imachi H., Nakamura K., Sakata S., Kamagata Y. (2009) Methanolobus profundi sp. nov., a new methylotrophic methanogen isolated from deep subsurface sediments in a natural gas field. International Journal of Systematic and Evolutionary Microbiology 59, 714-718.
  • Maeda H., Miyagawa Y., Ikarashi M., Kobayashi H., Sato K., Sakata S., Mochimaru H. (2009) Development of microbial conversion process of residual oil to methane in depleted oil fields. SPE 122573 Proceedings of Asia Pacific Oil and Gas Conference and Exhibition 2009, Jakarta. OnePetro, No. 122573-MS.
  • Sakata S., Hayes J. M., Rohmer M., Hooper A., Seeman M. (2008) Stable carbon isotopic compositions of lipids isolated from an ammonia-oxidizing chemoautotroph. Organic Geochemistry 39, 1725-1734.
  • Yoshioka H., Sakata S., Kamagata Y. (2008) Hydrogen isotope fractionation by Methanothermobacter thermoautotrophicus in coculture and pure culture conditions. Geochimica et Cosmochimica Acta 72, 2687-2694.
  • Mochimaru H., Yoshioka H., Tamaki H., Nakamura K., Kaneko N., Sakata S., Imachi H., Sekiguchi Y., Uchiyama H., Kamagata Y. (2007) Microbial diversity and methanogenic potential in high temperature natural gas associated water in Japan. Extremophiles 11, 453-461.
  • Oba M., Sakata, S., Tsunogai U. (2006) Polar and neutral isopranylglycerol ether lipids as biomarkers of archaea in near-surface sediments from the Nankai Trough. Organic Geochemistry 37, 1643-1654.
  • Yamanaka T., Sakata S. (2004) Abundance and distribution of fatty acids in hydrothermal vent sediments of the western Pacific Ocean. Organic Geochemistry 35, 573-582.
  • Sakata S., Sano Y., Maekawa T., Igari S. (1997) Hydrogen and carbon isotopic composition of methane as evidence for biogenic origin of natural gases from the Green Tuff Basin, Japan.  Organic Geochemistry 26, 399-407.
  • Sakata S., Hayes J.M., McTaggart A.R., Evans R.A., Leckrone K.J., Togasaki R. K. (1997) Carbon isotopic fractionation associated with lipid biosynthesis by a cyanobacterium: Relevance for interpretation of biomarker records. Geochimica et Cosmochimica Acta 61, 5379-5389.
  • Maekawa, T., Sakata, S., Igari, S., Imai, N. (1997) Organic geochemistry of the sources and generation environment for gas hydrate methane. Proceedings of the International Workshops on Gas Hydrate Studies. 328-339.
  • Higashihara M., Igari S., Maekawa T., Noda T., Sakata S., Asada N., Miyatake, A. (1996)  C5+ hydrocarbons in fumarolic gases from the Kakkonda (Takinoue) geothermal area, Japan. Geochemical Journal 31, 63-73.
  • Maekawa, T., Ito, S., Sakata S., Igari S., Imai N. (1995) Pressure and temperature conditions for methane hydrate dissociation in sodium chloride solutions. Geochemical Journal 29, 325-329.
  • Sakata, S., Matsuhisa, Y., Igari, S. (1994) Organic geochemistry of petroleum from the Green Tuff basin, Japan. Organic Geochemistry 21, 27-34.
  • Igari, S., Sakata, S. (1992) Fractionation of light hydrocarbons through GC columns packed with rocks and minerals - Implications for natural gas migration. Geochemical Journal 26, 37-43.
  • Fukushima K., Kondo H., Sakata S. (1992) Geochemistry of hydroxy acids in sediments-I. Some freshwater and brackish water lakes in Japan. Organic Geochemistry 18, 913-922.
  • Fukushima K., Uzaki M., Sakata, S. (1992) Geochemistry of hydroxy acids in sediments-II. Estuarine and coastal marine environments. Organic Geochemistry 18, 923-932.
  • Sakata S. (1991) Carbon isotope geochemistry of natural gases from the Green Tuff Basin, Japan. Geochimica et Cosmochimica Acta 55, 1395-1405.
  • Sakata,S., Takahashi, M., Igari, S., Suzuki, N. (1989) Origin of light hydrocarbons from volcanic rocks in the Green Tuff region of Northeast Japan. Chemical Geology 74, 241-248.
  • Igari, S., Sakata, S. (1989) Origin of natural gas of dissolved-in water type in Japan inferred from chemical and isotopic compositions: Occurrence of dissolved gas of thermogenic origin.  Geochemical Journal 23, 139-142.
  • Sakata, S., Akiyama, M. (1989) Steroid and hopanoid hydrocarbons in the Miocene formations from the MITI-Hamayuchi borehole in northern Hokkaido, Japan. Geochemical Journal 23, 237-244.
  • Sakata S., Suzuki N., Kaneko N. (1988) A biomarker study of petroleum from the Neogene Tertiary sedimentary basins in Northeast Japan. Geochemical Journal 22, 89-105.
  • Igari, S., Sakata, S. (1988) Chemical and isotopic compositions of natural gases from the Japanese major oil and gas fields: Origin and compositional change due to migration. Geochemical Journal 22, 257-263.

Dr. Hideyoshi Yoshioka
Research Fields Geomicrobiology, Organic Geochemistry
Research Topics
  • Microbial activity of subsurface biosphere in methane hydrate-bearing regions and water-soluble gas deposits
  • Methane production and oxidation in subsurface environments
Comment I am looking for research topics that surprise everyone, excite me, and finally contribute to our society.

Publication
  • Mayumi D., Mochimaru H., Tamaki H., Yamamoto K., Yoshjoka H., Suzuki Y., Kamagata Y., Sakata S.(2016) Methane production from coal by a single methanogen. Science354 (6309), 222-225.
  • Katayama T., Yoshioka H., Takahashi H.A., Amo M., Fujii T., Sakata S.(2016) Changes in microbial communities associated with gas hydrates in subseafloor sediments from the Nankai Trough.FEMS Microbiology Ecology, in press
  • Jiang N, Yoshioka H, Yamamoto K, Soga K (2016) Ureolytic activities of a urease-producing bacterium and purified urease enzyme in the anoxic condition:Implication for subseafloor sand production control by microbially induced carbonate precipitation (MICP), Ecological Engineering 90, 96-104.        
  • Yoshioka H, Mochimaru H, Sakata S. Takeda H, Yoshida S.(2015) Methane production potential of subsurface microbes in Pleistocene sediments from a natural gas field of the dissolved-in-water type, central Japan. Chemical Geology 419, 92-101.
  • Katayama T., Yoshioka H., Muramoto Y., Usami Y., Fujiwara K., Yoshida S., Kamagata Y. and Sakata S.(2015) Physicochemical impacts associated with natural gas development on methanogenesis in deep sand aquifers. ISME Journal 9, 436−446.
  • Aoki M, Ehara M, Saito Y, Yoshioka H, Miyazaki M, Saito Y, Miyashita A,Kawakami S, Yamaguchi T, Ohashi A, Nunoura T, Takai K, Imachi H.(2014) A Long-term cultivation of an anaerobic methane-oxidizing microbial community from deep-sea methane-seep sediment using a continuous-flow bioreactor. PLoS One 9:e105356.
  • Katayama T., Yoshioka H., Mochimaru H., Muramoto Y., Usami J., Ikeda H., Kamagata Y., Sakata S. (2014) Methanohalophilus levihalophilus gen. nov., sp. nov., a methylotrophic methanogen isolated from deep aquifers in a natural gas field, and an emended description of the genus Methanohalophilus. International Journal of Systematic and Evolutionary Microbiology, doi:10.1099/ijs.0.063677-0.
  • Hosam E. Maruyama A., Stokes H., Yoshioka H., Mitani Y. (2014) Novel integrons and gene cassettes from a Cascadian submarine gas hydrate-bearing core. FEMS Microbiology Ecology 87, 343-356.
  • Takeuchi M., Yoshioka H., Seo Y., Tanabe S., Tamaki H., Kamagata Y., Takahashi H.,, Igari S., Mayumi D., Sakata S. (2011) A distinct freshwater-adapted subgroup of ANME-1 dominates active archaeal communities in terrestrial subsurfaces in Japan. Environmental Microbiology, 13(12), 3206-3218.
  • Yoshioka H., Maruyama A., Nakamura T., Higashi Y., Fuse H., Sakata S., and Bartlett D.H. (2010) Activities and distribution of methanogenic and methane-oxidizing microbes in marine sediments from the Cascadia Margin. Geobiology, 8, 223-233.
  • Yoshioka H., Sakata S., Cragg B.A., Parkes R.J., and Fuji T. (2009) Methane production rates in sediments from the eastern Nankai Trough, off central Japan. Geochemical Journal, 43, 315-321.
  • Suzuki Y., Takahashi M., Yoshioka H., Takeno N., and Ito K. (2009) Biogeochemical profiles in deep sedimentary rocks in an inland fore-arc basin, Central Japan. Chemical Geology, 259, 107-119.
  • Yoshioka H., Sakata S., and Kamagata Y. (2008) Hydrogen isotope fractionation by Methanothermobacter thermoautotrophicus in coculture and pure culture conditions. Geochimica et Cosmochimica Acta, 72, 2687-2694.
  • Mochimaru H., Yoshioka H., Tamaki H., Nakamura K., Kaneko N., Sakata S., Imachi H., Sekiguchi Y. (2007) Microbial diversity and methanogenic potential in a high temperature natural gas field in Japan. Extremophiles, 11, 453–461.
  • Mochimaru H., Uchiyama H., Yoshioka H., Imachi H., Hoaki T., Tamaki H., Nakamura K., Sekiguchi Y., Kamagata Y. (2007) Methanogen diversity in deep subsurface gas-associated water at the Minami-kanto gas field in Japan. Geomicrobiology Journal, 24, 93-100.
  • Yoshioka, H. and Ishiwatari, R. (2005) An improved ruthenium tetroxide oxidation of marine and lacustrine kerogens: Possible origin of low-molecular-weight acids and benzenecaroboxylic acids. Organic Geochemistry, 36, 83-94.
  • Yoshioka H. Takeda, N. (2003) Analysis of organic compounds in coal macerals by infrared laser micropyrolysis. Journal of Analytical and Applied Pyrolysis 71, 137-149.
  • Ueno, Y., Yoshioka, H., Maruyama, S., and Isozaki, Y. (2003) Carbon and nitrogen isotope geochemistry of kerogen in ca. 3.5 Ga hydrothermal silica dikes in the North Pole area, Western Australia. Geochim Cosmochim Acta, 68, 573-589.
  • Yoshioka H., Asahara Y., Tojo B., Kawakami S.-i. (2003) Systematic variations, in C, O, and Sr isotopes and elemental concentrations in Neoproterozoic carbonates in Namibia: implications for a glacial to interglacial transition. Precambrian Research. 124, 69-85.
  • Yoshioka, H. and Ishiwatari, R. (2003) Low molecular weight compounds and biological markers generated by ruthenium tetroxide oxidation of a type II kerogen: Implications for molecular structure and diagenetic reaction. Research in Organic Geochemistry, 18, 11-21.
  • Sarkar, A., Yoshioka, H., Ebihara, M., and Naraoka, H. (2003) Geochemical and organic carbon isotope studies across the continental Permo-Triassic boundary of Raniganj basin, Eastern India. Palaeogeo Palaeoclim Palaeoecol. 191, 1-14.
  • Yoshioka, H. and Ishiwatari, R. (2002) Characterization of organic matter generated by Green River shale by infrared laser pyrolysis. Geochemical Journal, 36, 73-82.
  • Ueno, Y., Yurimoto, H., Yoshioka, H., Komiya, T., and Maruyama, S. (2002) Ion microprobe analysis of graphite from ca. 3.8 Ga metasediments, Isusa supracrustal belt, Western Greenland: Relationship between metamorphism and carbon isotopic composition. Geochim Cosmochim Acta, 66, 1257-1268.

Dr. Mio Takeuchi
Research Fields Geomicrobiology
Research Topics
  • Anaeroic oxidation of methane in the terrestrial subsurface environments
  • Bioremediation of subsurface contamination with chlorinated ethenes
  • Aerobic methane-oxidizing microbial community in marine sediments
Personal URL http://staff.aist.go.jp/takeuchi-mio/
Comment I want to introduce you exciting activities of unseen microbes living in subsurface environments! My present research mainly focuses on microbial activity related to methane, which is an important energy source and also a greenhouse gas.

Publication
  • Takeuchi M., Yamagishi T., Kamagata Y., Oshima K., Hattori M., Katayama T., Hanada S., Tamaki H., Marumo K., Maeda H., Nedachi M., Iwasaki W., Suwa Y., Sakata S. (2015) Tepidicaulis marinus gen. nov., sp. nov., a novel marine bacterium reducing nitrate to nitrous oxide strictly under microaerobic conditions. International Journal of Systematic and Evolutionary Microbiology, in press (doi: 10.1099/ijs.0.000167).
  • Takeuchi M., Kamagata Y., Oshima K., Hanada S., Tamaki H., Marumo K., Maeda H., Nedachi M., Hattori M., Iwasaki W., Sakata S. (2014) Methylocaldum marinum sp. nov., a thermotolerant, methane-oxidizing bacterium isolated from marine sediments, and emended description of the genus Methylocaldum. Int J Syst Evol Microbiol 64: 3240-3246
  • Takeuchi M., Katayama T., Yamagishi T., Hanada S., Tamaki H., Kamagata Y., Oshima K., Hattori M., Marumo K., Nedachi M., Maeda H., Suwa Y., Sakata S. (2014) Methyloceanibacter caenitepidi gen. nov., sp. nov., a novel facultatively methylotrophic bacterium isolated from marine sediments near the hydrothermal vent area. Int J Syst Evol Microbiol 64: 462-468.
  • Machida, I., Suzuki, Y., Takeuchi, M. (2013) Carbon-14 age and chemical evolution of Ca (HCO3) 2-type groundwater of age less than 8,000 years in a confined sandy and muddy Pleistocene aquifer, Japan. Hydrogeol J 21: 1289-1305.
  • Mayumi, D., Dolfing, J., Sakata, S., Maeda, H., Miyagawa, Y., Ikarashi, M., Tamaki, H., Takeuchi, M., Nakatsu, C. H., Kamagata, Y. (2013) Carbon dioxide concentration dictates alternative methanogenic pathways in oil reservoirs. Nature Communications DOI: 10.1038/ncomms2998.
  • Yamagishi T., Takeuchi M., Wakiya Y., Waki Y. (2013) Distribution and characterization of anammox in a swine wastewater activated sludge facility. Wat Sci Technol 67: 2330-2336.
  • Imase M., Ohko Y., Takeuchi M., Hanada S. (2013) Estimating the viability of Chlorella exposed to oxidative stresses based around photocatalysis. Int. Biodeterior. Biodegrad. 78: 1-6.
  • Takeuchi M., Yoshioka H., Seo Y., Tanabe S., Tamaki H., Kamagata Y., Takahashi H. A., Igari S., Mayumi D., Sakara S. (2011) A distinct freshwater-adapted subgroup of ANME-1 dominates active archaeal communities in terrestrial subsurfaces in Japan. Environ. Microbiol. 13, 3206-3218.
  • Takeuchi M., Kawabe Y., Watanabe E., Oiwa T., Takahashi M., Nanba K., Kamagata Y., Hanada S., Ohko Y., Komai T. (2011) Comparative study of microbial dechlorination of chlorinated ethenes in an aquifer and a clayey aquitard, J. Contam. Hydrol. 124, 14-24.
  • Fukushima M., Furubayashi, K., Fujisawa, N., Takeuchi, M., Komai, T., Ootsuka, K., Yamamoto, M., Kawabe, Y., and Horiya, S. (2011) Characterization of humic acids in sediments from dam reservoirs by pyrolysis-gas chromatography/mass spectrometry using tetramethylammonium hydroxide: Influence of the structural features of humic acids on iron(II) binding capacity. J. Anal. Appl. Pyrol. 91, 323-331.
  • Uchiyama M., Hara M., Takeuchi M., Kimura K. (2011) Electric conductivity and pH profiles of pore water extracted from the latest Pleistocene to Holocene sediments in the Tokyo and the Nakagawa Lowlands, central Japan. Bull. Geol. Surv. Japan 62, 85-104. (Japanese)
  • Waki M., Yasuda T., Suzuki K., Sakai T., Suzuki N., Suzuki R., Matsuba K., Yokoyama H., Ogino A., Tanaka Y., Ueda S., Takeuchi M., Yamagishi T., Suwa Y. (2010) Rate determination and distribution of anammox activity in activated sludge treating swine wastewater. Biores. Technol. 101, 2685-2690.
  • Mayumi D., Mochimaru H., Yoshioka H., Sakata S., Maeda H., Miyagawa Y., Ikarashi M., Takeuchi M., and Kamagata Y. (2010) Evidence for syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis in the high-temperature petroleum reservoir of Yabase oil field (Japan). Environ. Microbiol. 13, 1995-2006.
  • Machida I., Suzuki Y., and Takeuchi M. (2010) The 14C age of confined groundwater in as sandy-muddy Pleistocene, Chapter 6 in International Association of Hydrologists Selected papers, 16, CRC Press, (Edited by Taniguchi, M. and Holman, I.P.), 67-78.
  • Takeuchi M., Kawahata H., Gupta L.P., Itouga M., Sakakibara H., Ohta H., Komai T., Ono Y. (2009) Chemistry of fly ash and cyclone ash leachate from waste materials and effects of ash leachates on bacterial growth, nitrogen transformation activity and metal accumulation. J. Hazard. Mater. 165,967-973.
  • Ohko Y., Nagao Y., Okano K., Sugiura N., Fukuda A., Yang Y., Negishi N., Takeuchi M., Hanada S. (2009) Prevention of Phormidium tenue Biofilm Formation by TiO2 Photocatalysis. Microb. Environ. 24, 241-245.
  • Takeuchi M., Hanada S., Tanabe S., Tamaki H., Miyachi Y., Nakazawa T., Komai T., Uchiyama M., Kimura K., Kamagata,Y. (2009) Bacterial and archaeal 16S rRNA genes in late Pleistocene to Holocene muddy sediments from the Kanto Plain of Japan. Geomicrobiol. J. 26, 104-118.
  • Takeuchi M., Kawahata H., Gupta L.P., Kita N., Morishita Y., Ono Y., Komai T. (2007) Arsenic resistance and removal by marine and non-marine bacteria. J. Biotechnol. 127, 434-442.
  • Takeuchi M., Nanba N., Furuya K., Komai T. (2006) Bioremediation of subsurface contamination with volatile chloro-organic compounds (VCOCs) using methane-oxidizing bacteria- Bioremediation trend-, Geo-pollution Science, Medical Geology and Urban Geology 2: 98-109. (Japanese)
  • Lallan Prasad G., Kawahata H, Takeuchi M, Ohta H, Ono Y. (2006) Impact of Changes in Redox Conditions on Leaching of Some Elements from MSW Fly Ash. Resour. Geol. 56, 191-196.
  • Lallan Prasad G., Kawahata H., Takeuchi M., Ohta H., Ono Y. (2005) Temperature and pH dependence of some metals leaching from fly ash of municipal solid waste. Resour. Geol. 55, 357-372.
  • Takeuchi M., Nanba N., Iwamoto H., Nirei H., Kusuda T., Kazaoka O., Owaki M., Furuya K. (2005) In situ bioremediation of cis-dichloroethylene-contaminated aquifer utilizing methane-rich groundwater from uncontaminated aquifer. Wat. Res. 39, 2438-2444.
  • Takeuchi M., Terada A., Nanba K., Kanai Y., Owaki M., Yoshida T., Kuroiwa T., Nirei H., Komai T. (2005) Distribution and Fate of Biologically Formed Organoarsenicals in Coastal Marine Sediment. Appl. Organometal. Chem. 19, 945-951.
  • Takeuchi M., Nanba K., Nirei H., Yoshida M., Furuya K. (2004) Natural groundwater of a gas field utilizable for a bioremediation of trichloroethylene-contamination. Environmen. Geol. 45, 891-898.
  • Takeuchi M., Nanba K., Tanaka T., Takahashi A., Nirei, H. (2004) Effects of a high pressure water jet on trichloroethylene-degrading, methane-oxidizing bacteria. Journal of Jet Flow Engineering, 21, 4-12.
  • Takeuchi M., Nanba K., Iwamoto H., Nirei H., Kusuda T., Kazaoka O. and Furuya K. (2001) Distribution of methanotrophs in trichloroethylene-contaminated aquifers in a natural gas field. Geomicrobiol. J.18, 387-399.
  • Takeuchi M., Nanba K., Iwamoto H., Nirei H., Kazaoka O., Furuya, K. (2000) Distribution and Seasonal Variation of Methanotrophs in Trichloroethylene Contaminated Groundwater. Wat. Res. 34, 3717-3724.

Dr. Hanako Mochimaru
Research Fields Geomicrobiology, Anaerobic microbiology
Research Topics
  • Microbial diversity and methanogenic potential in deep subsurface gas fields.
  • Isolation of novel microorganisms from deep subsurface environments.
  • Crude oil biodegradation coupled to methane production in high-temperature oil reservoirs.
Comment Between you and me, my special interest is to find new methanogens.

Publication
  • Mayumi D., Mochimaru H., Tamaki H., Yamamoto K., Yoshjoka H., Suzuki Y., Kamagata Y., Sakata S.(2016) Methane production from coal by a single methanogen. Science354 (6309), 222-225.
  • Mochimaru H., Tamaki H., Katayama T., Imachi H., Sakata S., Kamagata Y. (2016) Methanomicrobium antiquum sp. nov., a hydrogenotrophic methanogen isolated from deep sedimentary aquifers in a natural gas field. in press.
  • Yoshioka H, Mochimaru H, Sakata S. Takeda H, Yoshida S.(2015) Methane production potential of subsurface microbes in Pleistocene sediments from a natural gas field of the dissolved-in-water type, central Japan. Chemical Geology 419, 92-101.
  • Katayama T., Yoshioka H., Mochimaru H., Muramoto Y., Usami J., Ikeda H., Kamagata Y., Sakata S. (2014) Methanohalophilus levihalophilus gen. nov., sp. nov., a methylotrophic methanogen isolated from deep aquifers in a natural gas field, and an emended description of the genus Methanohalophilus. International Journal of Systematic and Evolutionary Microbiology, 64, 2089-2093.
  • Nakamura K., Takahashi A., Mori C., Tamaki H., Mochimaru H., Nakamura K., Takamizawa K., Kamagata Y. (2013) Methanothermobacter tenebrarum sp. nov., a hydrogenotrophic thermophilic methanogen isolated from gas-associated formation water of a natural gas field in Japan. International Journal of Systematic and Evolutionary Microbiology 63, 715-722.
  • Nakamura K., Tamaki H., Kang M. S., Mochimaru H., Lee S. T., Nakamura K., Kamagata Y. (2011) A Six-well Plate Method: Less Laborious and Effective Method for Cultivation of Obligate Anaerobic Microorganisms. Microbes & Environments 26, 301-306.
  • Nakamura H., Narihiro T., Tsuruoka N., Mochimaru H., Matsumoto R., Tanabe Y., Hagiya K., Ikeba K., Maruyama A., Hanada S. (2011) Evaluation of the aflatoxin biosynthetic genes for identification of the Aspergillus section Flavi. Microbes & Environments 26, 367-369.
  • Mayumi D., Mochimaru H., Yoshioka H., Sakata S., Maeda H., Miyagawa Y., Ikarashi M., Takeuchi M., Kamagata Y. (2011) Evidence for syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis in the high-temperature petroleum reservoir of Yabase oil field (Japan). Environmental Microbiology 13, 1995-2006.
  • Mochimaru H., Tamaki H., Hanada S., Imachi H., Nakamura K., Sakata S., Kamagata Y. (2009) Methanolobus profundi sp. nov., a methylotrophic methanogen isolated from deep subsurface sediments in a natural gas field. International Journal of Systematic and Evolutionary Microbiology 59, 714-718.
  • Miyashita A, Mochimaru H, Kazama H, Ohashi A, Yamaguchi T, Nunoura T, Horikoshi K, Takai K, Imachi H. (2009) Development of 16S rRNA gene-targeted primers for detection of archaeal anaerobic methanotrophs (ANMEs). FEMS Microbiol Lett.297, 31-37.
  • Mochimaru H., Uchiyama H., Yoshioka H., Imachi H., Hoaki T., Tamaki H., Nakamura K., Sekiguchi Y., Kamagata Y. (2007) Methanogen diversity in deep subsurface gas-associated water at the Minami-kanto gas field in Japan. Geomicrobiology Journal 24. 93-100.
  • Mochimaru H., Yoshioka H., Tamaki H., Nakamura K., Kaneko N., Sakata S., Imachi H., Sekiguchi Y., Uchiyama H., Kamagata Y. (2007) Microbial diversity and methanogenic potential in a high temperature natural gas field in Japan. Extremophiles 11, 453-461.

Dr. Taiki Katayama
Research Fields Geomicrobiology, Microbial Physiology
Research Topics
  • Biogenic methane production in gas hydrate-bearing subseafloor sediments, natural gas field of dissolved-in-water type and sedimentary coastal sediments: studies on microbial community structure and distribution, methanogenic activity and pathway and environmental factors that may influence methanogenesis.
  • Cultivation of as-yet-unknown bacteria and archaea in deep subsurface environments.
  • Development of enhanced microbial recovery in natural gas field, Japan.
Comment Art is I; Science is we. (Claude Bernard)

Publication
  • Mochimaru H., Tamaki H., Katayama T., Imachi H., Sakata S., Kamagata Y. (2016) Methanomicrobium antiquum sp. nov., a hydrogenotrophic methanogen isolated from deep sedimentary aquifers in a natural gas field. in press.
  • Katayama T., Yoshioka H., Takahashi H.A., Amo M., Fujii T., Sakata S.(2016) Changes in microbial communities associated with gas hydrates in subseafloor sediments from the Nankai Trough.FEMS Microbiology Ecology, in press
  • Takeuchi M., Yamagishi T., Kamagata Y., Oshima K., Hattori M., Katayama T., Hanada S., Tamaki H., Marumo K., Maeda H., Nedachi M., Iwasaki W., Suwa Y., Sakata S. (2015) Tepidicaulis marinus gen. nov., sp. nov., a novel marine bacterium reducing nitrate to nitrous oxide strictly under microaerobic conditions. International Journal of Systematic and Evolutionary Microbiology, in press (doi: 10.1099/ijs.0.000167).
  • Kanno M., Katayama T. (equal contribution), Morita N., Tamaki H., Hanada S., Kamagata Y. (2015) Catenisphaera adipataccumulans gen. nov., sp. nov., a member of the family Erisipelotrichaceae isolated from an anaerobic digester. International Journal of Systematic and Evolutionary Microbiology 65, 805-810.
  • Katayama T., Yoshioka H., Muramoto Y., Usami J., Fujiwara K., Yoshida S., Kamagata Y., Sakata S. (2015) Physicochemical impacts associated with natural gas development on methanogenesis in deep sand aquifers. The ISME Journal 9, 436-446.
  • Katayama T., Yoshioka H., Mochimaru H., Muramoto Y., Usami J., Ikeda H., Kamagata Y., Sakata S. (2014) Methanohalophilus levihalophilus gen. nov., sp. nov., a methylotrophic methanogen isolated from deep aquifers in a natural gas field, and an emended description of the genus Methanohalophilus. International Journal of Systematic and Evolutionary Microbiology, 64, 2089-2093.
  • Takeuchi M., Katayama T., Yamagishi T., Hanada S., Tamaki H., Kamagata Y., Oshima K., Hattori M., Marumo K., Nedachi M., Maeda H., Suwa Y., Sakata S. (2014)Methyloceanibacter caenitepidi gen. nov., sp. nov., a novel facultatively methylotrophic bacterium isolated from marine sediments near a hydrothermal vent. International Journal of Systematic and Evolutionary Microbiology 64, 462-468.
  • Katayama T., Kanno M., Morita N., Hori T., Narihiro T., Mitani Y., Kamagata Y. (2014) An oleaginous bacterium that accumulates long-chain free fatty acids in its cytoplasm. Applied and Environmental Microbiology 80, 1126-1131.
  • Kanno M., KatayamaT. (equal contribution), Tamaki H., Mitani Y., Mou K., Hori T., Narihiro T., Morita N., Yumoto I., Kimura N., Hanada S., Kamagata Y. (2013) Isolation of butanol- and isobutanol-tolerant bacteria and physiological characterization of their butanol tolerance. Applied and Environmental Microbiology 79, 6998-7005.
  • Puspita I.D., Uehara M., Katayama T., Kikuchi Y., Kitagawa W., Kamagata Y., Asano K., Nakatsu C.H., Tanaka, M. (2013) Resuscitation promoting factor (Rpf) from Tomitella biformata AHU1821T promotes growth and resuscitates non-dividing cells. Microbes and Environments 28, 58-64.
  • Katayama T., Tanaka M. (2012) Microorganisms in a permafrost ice wedge and their resuscitation promoting factors. Chapter 10, pp.177-188 in Cold-Adapted Microorganisms (Edited by Yumoto I.) Caister Academic Press.
  • Pudjiraharti S., Takesue N., Katayama T., Lisdiyanti P., Hanafi M., Tanaka M., Sone T., Asano K. (2011) Actinomycete Nonomuraea sp. isolated from Indonesian soil is a new producer of inulin fructotransferase. Journal of Bioscience and Bioengineering 111, 671-674.
  • Katayama T., Kato T., Tanaka M., Douglas T. A.. Brouchkov A., Abe A., Sone T., Fukuda M. Asano K. (2010) Tomitella biformata gen. nov., sp. nov., a novel member of the suborder Corynebacterineae isolated from a permafrost ice wedge. International Journal of Systematic and Evolutionary Microbiology 60, 2803-2807.
  • Katayama T., Kato T., Tanaka M., Douglas T. A.. Brouchkov A., Fukuda M. Tomita F., Asano K. (2009) Glaciibacter superstes gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from a permafrost ice wedge. International Journal of Systematic and Evolutionary Microbiology 59, 482-486.
  • Katayama T., Tanaka M., Moriizumi J., Nakamura T., Brouchkov A., Douglas T.A., Fukuda M., Tomita F., Asano K. (2007) Phylogenetic analysis of bacteria preserved in a permafrost ice wedge for 25,000 years. Applied and Environmental Microbiology 73, 2360-2363.

Dr. Daisuke Mayumi
Research Fields Geomicrobiology
Research Topics
  • Elucidation of methanogenic crude oil biodegradation in oil reservoirs.
  • Evaluation of effects of geological CO2 storage on the microbial ecosystem in oil reservoirs.
  • Identification of novel anaerobic microbes in oil reservoirs.
  • Stable isotope analyses addressing the process of the methane hydrate production.
Comment I seek the possibility of microbes in deep subsurface for industry.

Publication
  • Mayumi D., Mochimaru H., Tamaki H., Yamamoto K., Yoshjoka H., Suzuki Y., Kamagata Y., Sakata S.(2016) Methane production from coal by a single methanogen. Science354 (6309), 222-225.
  • Mayumi D., Dolfing, J., Sakata, S., Maeda, H., Miyagawa, Y., Ikarashi, M., Tamaki, H., Takeuchi, M., Nakatsu, CH., Kamagata, Y. (2013) Carbon dioxide concentration dictates alternative methanogenic pathways in oil reservoirs. Nature Communications 4:1998 doi: 10.1038/ncomms2998.
  • Mayumi D., Mochimaru, H., Yoshioka, H., Sakata, S., Maeda, H., Miyagawa, Y., Ikarashi, M., Takeuchi, M., Kamagata, Y. (2010) Evidence for syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis in the high-temperature petroleum reservoir of Yabase oil field (Japan). Environmental Microbiology 13(8), 1995-2006.
  • Mayumi D., Yoshimoto, T., Uchiyama, H., Nomura N., Nakajima-Kambe T. (2010) Seasonal change in methanotrophic diversity and populations in a rice field soil assessed by DNA-stable isotope probing and quantitative real-time PCR. Microbes and Environments 25, 156-163.
  • Mayumi D., Akutsu-Shigeno Y., Uchiyama H., Nomura N., Nakajima-Kambe T. (2008) Identification and characterization of novel poly(DL-lactic acid) depolymerases from metagenome. Applied Microbiology and Biotechnology 79, 743-750.

Dr. Masanori Kaneko
Research Fields Organic Geochemistry, Biogeochemistry
Research Topics
  • Development of application of the Function-Specific-compound-analysis.
  • Studies on biogeochemical processes based on biomarker and isotope analyses.
Comment I'm trying to find something new in the biogeochemical cycle by the analytical developments and its applications.

Publication
  • Kaneko, M., Takano, Y., Ogawa, N.O., Sato, Y., Yoshida, N., Ohkouchi, N. (2016) Estimation of methanogenesis by quantification of coenzyme F430 in marine sediments. Geochemical Journal, 50(6), 453-460.
  • Inagaki, F., Hinrichs, U., K., Kubo, Y., Bowles, W., M., Heuer, B., V., Hong, L., W., Hoshino, T., Ijiri, A., Imachi, H., Ito, M., Kaneko, M., Lever, A., M., Lin, S., Y., Methe, A., B., Morita, S., Morono, Y., Tanikawa, W., Bihan, M., Bowden, A., S., Elvert, M., Glombitza, C., Gross, D., Harrington, J., G., Hori, T., Li, K., Limmer, D., Liu, H., C., Murayama, M., Ohkouchi, N., Ono, S., Park, S., Y., Phillips, C., S., Prieto-Mollar, X., Purkey, M., Riedinger, N., Sanada, Y., Sauvage, J., Snyder, G., Susilawati, R., Takano, Y., Tasumi, E., Terada, T., Tomaru, H., Trembath-Reichert, E., Wang, T., D., Yamada, Y.(2015) Exploring deep microbial life in coal-bearing sediment down to similar to 2.5 km below the ocean floor. Science 349, 420-424.
  • Kaneko, M., Takano, Y., Chikaraishi, Y., Ogawa, N.O., Asakawa, S., Watanabe, K., Shima, S., Krueger, M., Matsushita, M., Kimura, H., and Ohkouchi, N. (2014) Quantitative analysis of coenzyme F430 in environmental samples: a new diagnostic tool for methanogenesis and anaerobic methane oxidation. Analytical Chemistry, 86(7), 3633-3638.         
  • Kaneko, M. and Poulson, S.R. (2013) The rate of oxygen isotope exchange between nitrate and water. Geochimica et Cosmochimica Acta, 118, 148-156.
  • Kaneko, M., Naraoka, H., Takano, Y., and Ohkouchi, N. (2013) Distribution and isotopic signatures of archaeal lipid biomarkers associated with gas hydrate occurrences on the northern Cascadia Margin. Chemical Geology, 343, 76-84.
  • Takano, Y., Kaneko, M., Kahnt, J., Imachi, H., Shima, S., and Ohkouchi, N. (2013) Detection of coenzyme F430 in deep sea sediments: A key molecule for biological methanogenesis. Organic Geochemistry, 58, 137-140.
  • Nishizawa, M., Koba, K., Makabe, A., Yoshida, N., Kaneko, M., Hirao, S., Ishibashi, J., Yamanaka, T., Shibuya, T., Kikuchi, T., Hirai, M., Miyazaki, J., Nunoura, T., Takai, K. (2013) Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream. Geochimica et Cosmochimica Acta, 113, 152-173.
  • Chikaraishi Y., Kaneko, M., and Ohkouchi N. (2012) Stable hydrogen and carbon isotopic compositions of long-chain (C21-C33) n-alkanes and n-alkenes in insects. Geochimica et Cosmochimica Acta, 95(15), 53-62.
  • Igisu, M., Takai, K., Ueno, Y., Nishizawa, M., Nunoura, T., Hirai, M., Kaneko, M., Naraoka, H., Shimojima, M., Hori, K., Nakashima, S., Ohta, H., Maruyama, S., and Isozaki, Y. (2012) Domain-level identification and quantification of relative prokaryotic cell abundance in microbial communities by Micro-FTIR spectroscopy. Environmental Microbiology Reports, 4, 42-49.
  • Kaneko, M. and Poulson, S. (2012) Rate of oxygen isotope exchange between selenate and water. Environmental Science and Technology, 46, 4539-4545.
  • Kaneko, M., Kitajima, F., and Naraoka, H. (2011) Stable hydrogen isotope measurement of archaeal ether-bound hydrocarbons. Organic Geochemistry, 42, 166-172.
  • Kaneko, M., Oba, Y., and Naraoka, H. (2010) Vertical carbon isotope change in acetate in a surface sediment from the northwestern Pacific Ocean. Research in Organic Geochemistry, 26, 73-79.
  • Kaneko, M., Shingai, H., Pohlman, J.W., and Naraoka, H. (2010) Chemical and isotopic signature of bulk organic matter and hydrocarbon biomarkers within mid-slope accretionary sediments of the northern Cascadia margin gas hydrate system. Marine Geology, 275, 166-177.
  • Pohlman, J.W., Kaneko, M., Heuer, V.B., Coffin, R.B., and Whiticar, M. (2009) Methane sources and production in the northern Cascadia margin gas hydrate system. Earth and Planetary Science Letters, 287, 504-512.

Dr. Konomi Suda
Research Fields Geochemistry, History of the Earth
Research Topics
  • Methanogenic crude oil biodegradation in oil reservoirs.
  • Origin of low-molecular-weight organic compounds in serpentinite-hosted hydrothermal systems.
Comment I am studying to make clear the relationships between rock, water and life.

Publication
  • Suda, K., Gilbert, A., Yamada, K., Yoshida, Y., Ueno, Y. (2017) Compound- and position-specific carbon isotopic signatures of abiogenic hydrocarbons from on-land serpentinite-hosted Hakuba Happo hot spring in Japan. Geochimica et Cosmochimica Acta, 206, 201-215.
  • Gilbert, A., Yamada, K., Suda, K., Ueno, Y., Yoshida, Y. (2016) Measurement of position−specific 13C isotopic composition of propane at the nanomole level. Geochimica et Cosmochimica Acta, 177, 205-216.
  • Suda, K., Ueno, Y., Yoshizaki, M., Nakamura, H., Kurokawa, K., Nishiyama, E., Yoshino, K., Hongoh, Y, Kawachi, K, Omori, S., Yamada, K., Yoshida, N., Maruyama, S. (2014) Reply to comment on "Origin of methane in serpentinite−hosted hydrothermal systems: The CH4−H2−H2O hydrogen isotope systematics of the Hakuba Happo hot spring” by Suda et al. [Earth Planet. Sci. Lett. 386(2014) 112−125]. Earth and Planetary Science Letters 401, 376-377.
  • Suda, K., Ueno, Y., Yoshizaki, M., Nakamura, H., Kurokawa, K., Nishiyama, E., Yoshino, K., Hongoh, Y, Kawachi, K, Omori, S., Yamada, K., Yoshida, N., Maruyama, S. (2014) Origin of methane in serpentinite−hosted hydrothermal systems: The CH4−H2−H2O hydrogen isotope systematics of the Hakuba Happo hot spring. Earth and Planetary Science Letters 386, 112−125.           



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