AIST 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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Publication

2024

Katayama T., Nobu M.K., Imachi H., Hosogi N., Meng X.-Y., Morinaga K., Yoshioka H., Takahashi H. A., Kamagata Y., Tamaki H. (2024) A Marine Group A isolate relies on other growing bacteria for cell wall formation. Nature Microbiology, https://doi.org/10.1038/s41564-024-01717-7.
Kawamoto H., Watanabe M., Mochimaru H., Nakahara N., Meng X.-Y., Sakamoto S., Morinaga K., Katayama T., Yoshioka H., Nomura N., Tamaki H. (2024) Atrimonas thermophila gen. nov., sp. nov., a novel anaerobic thermophilic bacterium of the phylum Atribacterota isolated from deep subsurface gas field and proposal of Atrimonadaceae fam. nov. within the class Atribacteria in the phylum Atribacterota. Systematic and Applied Microbiology 47, https://doi.org/10.1016/j.syapm.2024.126515.
Gotore O., Watanabe M., Okano K., Miyata N., Katayama T., Yasutaka T., Semoto Y., Hamai T. (2024) Effects of batch and continuous-flow operation on biotreatment of Mn(II)-containing mine drainage. Journal of Environmental Sciences 152, 401-415, https://doi.org/10.1016/j.jes.2024.05.038.

2023

Katayama T., Ikawa R., Koshigai M., Sakata S. (2023) Microbial methane formation in deep aquifers associated with the sediment burial history at a coastal site. Biogeosciences 20, 5199–5210, https://doi.org/10.5194/bg-20-5199-2023.
Hirakata Y., Mei R., Morinaga K., Katayama T., Tamaki H., Meng X.-Y, Watari T., Yamaguchi T., Hatamoto M., Nobu K. M. (2023) Identification and cultivation of anaerobic bacterial scavengers of dead cells. The ISME Journal 17, 2279–2289, https://doi.org/10.1038/s41396-023-01538-2.

2022
Katayama T., Yoshioka H., Kaneko M., Amo M., Fujii T., Takahashi H. A., Yoshida S., Sakata S. (2022) Cultivation and biogeochemical analyses reveal insights into methanogenesis in deep subseafloor sediment at a biogenic gas hydrate site. The ISME Journal, https://doi.org/10.1038/s41396-021-01175-7.

2021

Urai A., Matsushita M., Park H.-D, Imachi H., Ogawara M., Iwata H., Kaneko M., Ogawa, N. O., Ohkouchi N. and Takano Y. (2021) Detection of planktonic coenzyme factor 430 in a freshwater lake: small‑scale analysis for probing archaeal methanogenesis. Progress in Earth and Planetary Science 8:62, https://doi.org/10.1186/s40645-021-00450-7.
Kaneko M., Takano Y., Kamo M., Morimoto K., Nunoura T., Ohkouchi N. (2021) Insights into the Methanogenic Population and Potential in Subsurface Marine Sediments Based on Coenzyme F430 as a Function-Specific Biomarker. JACS Au 2021, 1(10), 1743–1751, https://doi.org/10.1021/jacsau.1c00307.
Takeuchi M., Yoshioka H. (2021) Acetate excretion by a methanotroph, Methylocaldum marinum S8, under aerobic conditions. Bioscience, Biotechnology, and Biochemistry 85, Issue 11, 2326–2333.
Kurth J.M., Nobu M.K., Tamaki H., de Jonge N., Berger S., Jetten S.M., Yamamoto K., Mayumi D., Sakata S., Bai L., Cheng L., Nielsen J.L., Kamagata Y., Wagner T., Welte C.U. (2021) Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds.The ISME Journal, 15, 3549–3565. https://doi.org/10.1038/s41396-021-01025-6.
Suda K., Ikarashi M., Tamaki H., Tamazawa S., Sakata S., Maeda H., Kamagata Y., Kaneko M., Ujiie T., Shinotsuka Y., Wakayama T., Iwama H., Mayumi D., Yonebayashi H. (2021) Methanogenic crude oil degradation induced by an exogenous microbial community and nutrient injections. Journal of Petroleum Science and Engineering, https://doi.org/10.1016/j.petrol.2021.108458.
Yoshikawa M., Zhang M., Kawabe Y., Katayama T.(2021) Effects of ferrous iron supplementation on reductive dechlorination of tetrachloroethene and on methanogenic microbial community. FEMS Microbiology Ecology, Volume 97, Issue 5, https://doi.org/10.1093/femsec/fiab069.
Takeuchi M., Fujiwara-Nagata E., Katayama T. et al. (2021) Skin bacteria of rainbow trout antagonistic to the fish pathogen Flavobacterium psychrophilum. Scientific Reports 11, 7518. https://doi.org/10.1038/s41598-021-87167-1.
Sakamoto S., Nobu M.K., Mayumi D., Tamazawa S., Kusada H., Ikarashi M., Wakayama T., Iwama H., Yonebayashi H., Maeda H., Sakata S., Tamura T., Nomura N., Kamagata Y., Tamaki H. (2021) Koleobacter methoxysyntrophicus gen. nov., sp. nov., a novel anaerobic bacterium isolated from deep subsurface oil field and proposal of Koleobacteraceae fam. nov. and Koleobacterales ord. nov. within the class Clostridia of the phylum Firmicutes. Systematic and Applied Microbiology, https://doi.org/10.1016/j.syapm.2020.126154.

2020

Katayama T., Nobu M., Kusada H., Meng X., Hosogi N., Uematsu K., Yoshioka H., Kamagata Y., and Tamaki H. (2020) Isolation of a member of the candidate phylum ‘Atribacteria’ reveals a unique cell membrane structure. Nature Communications, DOI: 10.1038/s41467-020-20149-5.
Heuer V. B., Inagaki F., Morono Y., Kubo Y., Spivack A. J., Viehweger B., Treude T., Beulig F., Schubotz F., Tonai S., Bowden S. A., Cramm M., Henkel S., Hirose T., Homola K., Hoshino T., Ijiri A., Imachi H., Kamiya N., Kaneko M., Lagostina L., Manners H., McClelland H. -L., Metcalfe K., Okutsu N., Pan D., Raudsepp M. J., Sauvage J., Tsang M. -Y., Wang D. T., Whitaker E., Yamamoto Y., Yang K., Maeda L., Adhikari R. R., Glombitza C., Hamada Y., Kallmeyer J., Wendt J., Wörmer L., Yamada Y., Kinoshita M., Hinrichs K. -U. (2020) Temperature limits to deep subseafloor life in the Nankai Trough subduction zone. Science, Vol. 370, pp. 1230-1234.
Yoshioka H., Takeuchi M., Sakata S., Takahashi M., Tanabe S., Inamura A., Yasuhara M. (2020) Microbial methane production and oxidation in the Holocene mud beneath the Kanto Plain of central Japan. Geochemical Journal, Vol. 54 (No. 4), pp. 243-254.
Aoyagi T., Inaba T., Aizawa H., Mayumi D., Sakata S., Charfi A., Suh C., Lee J., Sato Y., Ogata A., Habe H., Hori T. (2020) Unexpected diversity of acetate degraders in anaerobic membrane bioreactor treating organic solid waste revealed by high-sensitivity stable isotope probing. Water Research 176, 115750.
Yusuke Miyajima, Ayaka Saito, Hiroyuki Kagi, Tatsunori Yokoyama, Yoshio Takahashi, Takafumi Hirata (2020) Incorporation of U, Pb, and rare earth elements in calcite through crystallization from amorphous calcium carbonate: simple preparation of reference materials for microanalysis. Geostandards and Geoanalytical Research, 45, 189-205.
Krzysztof Hryniewicz, Yusuke Miyajima, Kazutaka Amano, Magdalena N. Georgieva, Michal Jakubowicz, Robert G. Jenkins, Andrzej Kaim (2020) Formation, diagenesis and fauna of cold seep carbonates from the Miocene Taishu Group of Tsushima (Japan). Geological Magazine, DOI: 10.1017/s001675682000103x.

2019

Takeuchi Mio, Haruka Ozaki, Satoshi Hiraoka, Kamagata Yoichi, Sakata Susumu, Hideyoshi Yoshioka, Iwasaki Wataru (2019) Possible cross-feeding pathway between a methanotroph and a facultative methylotroph. PlosONE 14, e0213535.
Katayama T., Yoshioka H., Yamanaka T., Mio Takeuchi, Muramoto Y., Usami J., Ikeda H. and Sakata S. (2019) Microbial community structure in deep natural gas-bearing aquifers subjected to sulfate-containing fluid injection. Journal of Bioscience and Bioengineering 127, 45-51.
Xiyang Dong, Chris Greening, Jayne E. Rattray, Anirban Chakraborty, Maria Chuvochina, Daisuke Mayumi, Jan Dolfing, Carmen Li, James M. Brooks, Bernie B. Bernard, Ryan A. Groves, Ian A.Lewis & Casey R. J. Hubert (2019). Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments. Nature Communications 10, 1816, DOI: 10.1038/s41467-019-09747-0.

2018
Yoshinori Takano, Yoshito Chikaraishi, Hiroyuki Imachi, Yosuke Miyairi, Nanako O. Ogawa, Masanori Kaneko, Yusuke Yokoyama, Martin Krüger, Naohiko Ohkouchi(2018) Insight into anaerobic methanotrophy from 13C/12C-amino acids and 14C/12C-ANME cells in seafloor microbial ecology. Scientific reports 8:14070, DOI:10.1038/s41598-018-31004-5.

　　　

2017

Yuji Sano, Naoya Kinoshita, Takanori Kagoshima, Naoto Takahata, Susumu Sakata, Tomohiro Toki, Shinsuke Kawagucci, Amane Waseda, Tefang Lan, Hsinyi Wen, Ai-Ti Chen, Tsanyao F. Yang, Zheng Guodong, Yama Tomonaga, Emilie Roulleau and Daniele L. Pinti (2017) Origin of methane-rich natural gas at the West Pacific convergent plate boundary. Scientific Reports 67, Article number 15646.
Tamazawa S., Mayumi D., Mochimaru H., Sakata S., Maeda H., Wakayama T., Ikarashi M., Kamagata Y., Tamaki H. (2017) Petrothermobacter organivorans gen. nov., sp. nov., a novel thermophilic, strictly anaerobic bacterium of the phylum Deferribacteres isolated from a deep subsurface oil reservoir. International Journal of Systematic and Evolutionary Microbiology 67, 3982-3986.
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.

2016

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. 66, 4873-4877.
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, 92, fiw093.
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.

2015

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.
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, 65, 1749-1754..
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.
Kaneko, M., Takano, Y., Ogawa, N.O., Sato, Y., Yoshida, N., Ohkouchi, N. (2015) Estimation of methanogenesis by quantification of coenzyme F430 in marine sediments. Geochemical Journal, in press
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.
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.

2014

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.
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.
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.
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.

2013

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.
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.

2012

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.

2011

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.
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.
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.
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.
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.

2010

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.
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.
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.

2009

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., 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.
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.
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.
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.

2008

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.

2007

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.
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.