Ecophysiology of yet-to-be cultured subsurface archaea using environmental omics and cultivation based approach

• Project/Area Number: 18H02426
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Review Section: Basic Section 43050:Genome biology-related
• Research Institution: National Institute of Advanced Industrial Science and Technology
• Principal Investigator: Tamaki Hideyuki 国立研究開発法人産業技術総合研究所, 生命工学領域, 研究グループ長 (00421842)
• Project Period (FY): 2018-04-01 – 2021-03-31
• Project Status: Completed (Fiscal Year 2020)
• Budget Amount: ¥17,290,000 (Direct Cost: ¥13,300,000、Indirect Cost: ¥3,990,000); Fiscal Year 2020: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000); Fiscal Year 2019: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000); Fiscal Year 2018: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
• Keywords: 未知微生物 / 未知アーキア / 陸域地下圏 / メタゲノム / 培養 / 物質循環 / 新生物機能 / 生理生態 / アーキア / 環境ゲノム情報解析 / メタン / 炭素循環 / 地下圏環境 / 環境ゲノム / 分離・培養 / 難培養 / 生物機能 / 培養技術

Outline of Final Research Achievements

Archaea, the third group of the whole creature, is the most unknown organism on the Earth due to the quite small number of the axenic cultures. In the present study, we conducted polyphasic approaches including cultivation, isolation, environmental omics, and geochemical analyses and revealed diversity and ecophysiology of archaea and the associated bacteria thriving in the terrestrial deep subsurface (oil and gas fields, coal seams, hot springs, subsurface aquifer, etc).

Academic Significance and Societal Importance of the Research Achievements

陸域地下圏環境は、エネルギー資源や水資源を涵養する場であり、地球規模の物質循環にも多大な影響を及ぼす環境である。本研究では、陸域地下圏の未知アーキア・未知バクテリアの実態を解き明かし、地下圏環境に特有の根源有機物がどのように分解されメタンや二酸化炭素に至るのかを明らかにするものであり、天然ガス資源であるメタンの成因や地球規模での炭素循環に解明に資する研究である。また陸域地下圏から培養に成功した門や科レベルで新規な地下微生物とその新生物機能の発見の成果は、物質循環に果たす役割の解明だけでなく生物の細胞構造や系統進化に新たな洞察をもたらす学術的価値と波及効果の高い成果である。

Research Products

• [Int'l Joint Research] イリノイ大学/イリノイ州立地質研究所/イリノイ州立水質研究所(米国)
• [Int'l Joint Research] イリノイ大学/イリノイ州立地質研究所/イリノイ州立水質研究所(米国)
• [Journal Article] Methanogenic crude oil degradation induced by an exogenous microbial community and nutrient injections (2021)
  • Author(s): Suda Konomi、Ikarashi Masayuki、Tamaki Hideyuki、Tamazawa Satoshi、Sakata Susumu、Haruo Maeda、Kamagata Yoichi、Kaneko Masanori、Ujiie Tomomi、Shinotsuka Yumi、Wakayama Tatsuki、Iwama Hiroki、Osaka Noriko、Mayumi Daisuke、Yonebayashi Hideharu
  • Journal Title: Journal of Petroleum Science and Engineering Volume: 201 Pages: 108458-108458
  • DOI: 10.1016/j.petrol.2021.108458
  • Peer Reviewed / Open Access
• [Journal Article] Desulfovibrio subterraneus sp. nov., a mesophilic sulfate-reducing deltaproteobacterium isolated from a deep siliceous mudstone formation (2021)
  • Author(s): Ueno Akio、Tamazawa Satoshi、Tamamura Shuji、Murakami Takuma、Kiyama Tamotsu、Inomata Hidenori、Amano Yuki、Miyakawa Kazuya、Tamaki Hideyuki、Naganuma Takeshi、Kaneko Katsuhiko
  • Journal Title: International Journal of Systematic and Evolutionary Microbiology Volume: 71 Issue: 2 Pages: 004683-004683
  • DOI: 10.1099/ijsem.0.004683
  • Peer Reviewed / Open Access
• [Journal Article] Unique metabolic strategies in Hadean analogues reveal hints for primordial physiology (2021)
  • Author(s): Nobu Masaru Konishi、Nakai Ryosuke、Tamazawa Satoshi、Mori Hiroshi、Toyoda Atsushi、Ijiri Akira、Suzuki Shino、Kurokawa Ken、Kamagata Yoichi、Tamaki Hideyuki
  • Journal Title: bioRxiv Volume: 1 Pages: 1-1
  • DOI: 10.1101/2021.04.20.440570
  • Open Access
• [Journal Article] Sakamoto S, Nobu MK, Mayumi D, Tamazawa S, Kusada H, Yonebayashi H, Iwama H, Ikarashi M, Wakayama T, Maeda H, Sakata S, Tamura T, Nomura N, (2021)
  • Author(s): Sakamoto S, Nobu MK, Mayumi D, Tamazawa S, Kusada H, Yonebayashi H, Iwama H, Ikarashi M, Wakayama T, Maeda H, Sakata S, Tamura T, Nomura N,
  • Journal Title: Syst. Appl. Microbiol. Volume: 44 Issue: 1 Pages: 126154-126154
  • DOI: 10.1016/j.syapm.2020.126154
  • Peer Reviewed / Open Access
• [Journal Article] Isolation of a member of the candidate phylum ‘Atribacteria’ reveals a unique cell membrane structure (2020)
  • Author(s): Katayama Taiki、Nobu Masaru K.、Kusada Hiroyuki、Meng Xian-Ying、Hosogi Naoki、Uematsu Katsuyuki、Yoshioka Hideyoshi、Kamagata Yoichi、Tamaki Hideyuki
  • Journal Title: Nature Communications Volume: 11 Issue: 1 Pages: 6381-6381
  • DOI: 10.1038/s41467-020-20149-5
  • Peer Reviewed / Open Access
• [Journal Article] An iron corrosion-assisted H2-supplying system: a culture method for methanogens and acetogens under low H2 pressures (2020)
  • Author(s): Souichiro Kato, Motoko Takashino, Kensuke Igarashi, Hanako Mochimaru, Daisuke Mayumi, Hideyuki Tamaki
  • Journal Title: Scientific Reports Volume: 10 Issue: 1 Pages: 1-9
  • DOI: 10.1038/s41598-020-76267-z
  • Peer Reviewed / Open Access
• [Journal Article] 未知の微生物を"培養"して新たな生物機能を探る (2020)
  • Author(s): 玉木秀幸
  • Journal Title: バイオサイエンスとインダストリー Volume: 78 Pages: 458-459
• [Journal Article] Isolation of an archaeon at the prokaryote-eukaryote interface (2020)
  • Author(s): Imachi Hiroyuki、Nobu Masaru K.、Nakahara Nozomi、Morono Yuki、Ogawara Miyuki、Takaki Yoshihiro、Takano Yoshinori、Uematsu Katsuyuki、Ikuta Tetsuro、Ito Motoo、Matsui Yohei、Miyazaki Masayuki、Murata Kazuyoshi、Saito Yumi、Sakai Sanae、Song Chihong、Tasumi Eiji、Yamanaka Yuko、Yamaguchi Takashi、Kamagata Yoich
  • Journal Title: Nature Volume: 577 Issue: 7791 Pages: 519-525
  • DOI: 10.1038/s41586-019-1916-6
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Cultivation Renaissance in the Post-Metagenomics Era: Combining the New and Old (2019)
  • Author(s): Tamaki Hideyuki
  • Journal Title: Microbes and Environments Volume: 34 Issue: 2 Pages: 117-120
  • DOI: 10.1264/jsme2.ME3402rh
  • NAID: 130007668647
  • ISSN: 1342-6311, 1347-4405
  • Peer Reviewed / Open Access
• [Journal Article] Improvement of terrestrial groundwater sampling method affects microbial community analysis (2019)
  • Author(s): Ueno A, Tamazawa S, Tamamura S, Aramaki N, Badrul AKMA, Murakami T, Yamaguchi S, Yamagishi J, Tamaki H, Mayumi D, Naganuma T, Kaneko K
  • Journal Title: Geomicrobiol. J. Volume: 36 Pages: 303-316
  • Peer Reviewed
• [Journal Article] Diversity and geochemical community assembly processes of the living rare biosphere in a sand-and-gravel aquifer ecosystem in the Midwestern United States (2019)
  • Author(s): Yamamoto K, Hackley CK, Kelly RW, Panno VS, Sekiguchi Y, Sanford RA, Liu WT, Kamagata Y, Tamaki H
  • Journal Title: Sci. Rep. Volume: 9 Issue: 1 Pages: 1-11
  • DOI: 10.1038/s41598-019-49996-z
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Improvement of terrestrial groundwater sampling method affects microbial community analysis (2019)
  • Author(s): Akio Ueno, Satoshi Tamazawa, Shuji Tamamura, Noritaka Aramaki, A. K. M. Alam Badrul, Takuma Murakami, Shinji Yamaguchi, Junya Yamagishi, Hideyuki Tamaki, Daisuke Mayumi, Takeshi Naganuma & Katsuhiko Kaneko
  • Journal Title: Geomicrobiology Journal Volume: 36 Issue: 4 Pages: 303-316
  • DOI: 10.1080/01490451.2018.1534900
  • Peer Reviewed
• [Journal Article] Aggregatilinea lenta gen. nov., sp. nov., a slow-growing, facultatively anaerobic bacterium isolated from subseafloor sediment, and proposal of the new order Aggregatilineales ord. nov. within the class Anaerolineae of the phylum Chloroflexi (2019)
  • Author(s): Nakahara Nozomi、Nobu Masaru K.、Takaki Yoshihiro、Miyazaki Masayuki、Tasumi Eiji、Sakai Sanae、Ogawara Miyuki、Yoshida Naoko、Tamaki Hideyuki、Yamanaka Yuko、Katayama Arata、Yamaguchi Takashi、Takai Ken、Imachi Hiroyuki
  • Journal Title: International Journal of Systematic and Evolutionary Microbiology Volume: 69 Issue: 4 Pages: 1185-1194
  • DOI: 10.1099/ijsem.0.003291
  • Peer Reviewed / Open Access
• [Journal Article] Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism (2018)
  • Author(s): Hidalgo‐Ahumada Catalina A. P.、Nobu Masaru K.、Narihiro Takashi、Tamaki Hideyuki、Liu Wen‐Tso、Kamagata Yoichi、Stams Alfons J M、Imachi Hiroyuki、Sousa Diana Z
  • Journal Title: Environmental Microbiology Volume: 20 Issue: 12 Pages: 4503-4511
  • DOI: 10.1111/1462-2920.14388
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Isolation of previously uncultured slow-growing bacteria by using a simple modification in the preparation of agar media (2018)
  • Author(s): Souichiro Kato, Ayasa Yamagishi, Serina Daimon, Kosei Kawasaki, Hideyuki Tamaki, Wataru Kitagawa, Ayumi Abe, Michiko Tanaka, Teruo Sone, Kozo Asano, Yoichi Kamagata
  • Journal Title: Appl. Environ. Microbiol. Volume: 84 Issue: 19
  • DOI: 10.1128/aem.00807-18
  • Peer Reviewed
• [Presentation] 深部地下圏でメトキシ芳香族化合物分解を担う新規共生細菌の生存戦略 (2021)
  • Author(s): 坂本 幸子、NOBU MASARU KONISHI、眞弓 大介、玉澤 聡、米林英治、岩間弘樹、五十嵐雅之、若山樹、前田 治男、坂田 将、田村 具博、野村暢彦、鎌形 洋一、玉木 秀幸
  • Organizer: 日本農芸化学会2021年度仙台大会
• [Presentation] 深部地下圏でメトキシ芳香族化合物分解を担う新規共生細菌の発見及び生存戦略 (2021)
  • Author(s): 坂本 幸子、NOBU MASARU KONISHI、眞弓 大介、玉澤 聡、米林英治、岩間弘樹、五十嵐雅之、若山樹、前田 治男、坂田 将、田村 具博、野村暢彦、鎌形 洋一、玉木 秀幸
  • Organizer: 第15回日本ゲノム微生物学会年会
• [Presentation] 14Cおよび希ガス同位体を用いた白馬八方蛇紋岩温泉メタンの起源研究 (2020)
  • Author(s): 須田好、阿瀬貴博、宮入陽介、横山祐典、松井洋平、上田修裕、齋藤拓也、佐藤友彦、澤木佑介、中井 亮佑、玉木 秀幸、高橋 浩、森川 徳敏
  • Organizer: 2020年度 日本地球化学会第67回年会
• [Presentation] Radiocarbon and noble gas isotope study to constrain origin of methane in Hakuba Happo serpentinite-hosted hot spring (2020)
  • Author(s): 須田好、阿瀬貴博、宮入陽介、横山祐典、松井洋平、上田修裕、齋藤拓也、佐藤友彦、澤木佑介、中井 亮佑、玉木 秀幸、高橋 浩、森川 徳敏
  • Organizer: JpGU-AGU Joint Meeting
  • Int'l Joint Research
• [Presentation] 単離培養から紐解く稀少微生物たちの実態と多様性 (2020)
  • Author(s): 中井 亮佑、玉木 秀幸
  • Organizer: 日本農芸化学会2020年度大会
  • Invited
• [Presentation] 深部地下圏環境におけるメトキシ芳香族化合物（MACs）分解メタン生成共生系の発見 (2020)
  • Author(s): 坂本 幸子、延 優、眞弓 大介、玉澤 聡、五十嵐 雅之、若山 樹、前田 治男、坂田 将、鎌形 洋一、玉木 秀幸
  • Organizer: 日本農芸化学会2020年度大会優秀発表賞講演
  • Invited
• [Presentation] Cultivation Renaissance for discovery of novel functions of uncultured fastidious microorganisms (2019)
  • Author(s): 玉木秀幸
  • Organizer: BioJapan2019
  • Int'l Joint Research / Invited
• [Presentation] Discovery of a novel subsurface syntrophic niche: methoxylated aromatic compound degradation (2019)
  • Author(s): S Sakamoto, MK Nobu, D Mayumi, S Tamazawa, M Ikarashi, T Wakayama, H Maeda, S Sakata, Y Kamagata, H Tamaki
  • Organizer: 8th IWA Microbial Ecology and Water Engineering Specialist Conference (MEWE2019)
  • Int'l Joint Research
• [Presentation] 深部地下圏環境におけるメトキシ芳香族化合物分解メタン生成共生系の発見 (2019)
  • Author(s): 坂本 幸子、延 優、眞弓 大介、玉澤 聡、五十嵐 雅之、若山 樹、前田 治男、坂田 将、鎌形 洋一、玉木 秀幸
  • Organizer: 日本微生物生態学会第33回大会
• [Presentation] 未知の微生物を”培養”して深淵な生命機能を探る (2018)
  • Author(s): 玉木秀幸
  • Organizer: 第32回日本微生物生態学会
  • Invited
• [Presentation] 冥王代類似環境微生物：環境ゲノム情報と培養技術で紐解くその存在と未知機能 (2018)
  • Author(s): 玉木秀幸
  • Organizer: 日本進化学会第20回大会シンポジウム
  • Invited
• [Presentation] New candidates for acetogenesis in early Earth (2018)
  • Author(s): Nobu Masaru Konishi, Ryosuke Nakai, Satoshi Tamazawa, Hiroshi Mori, Atsushi Toyoda, Itsuki Ijiri, Shino Suzuki, Ken Kurokawa, Yoichi Kamagata, Hideyuki Tamaki
  • Organizer: Hadean Bioscience International Symposium 2018
  • Int'l Joint Research / Invited
• [Presentation] Unique acetogenic microorganisms inhabiting the serpentinite-hosted Hakuba Happo hot spring (2018)
  • Author(s): Ryosuke Nakai, Nobu Masaru Konishi, Satoshi Tamazawa, Hiroshi Mori, Atsushi Toyoda, Itsuki Ijiri, Shino Suzuki, Ken Kurokawa, Yoichi Kamagata, Hideyuki Tamaki
  • Organizer: Hadean Bioscience International Symposium 2018
• [Presentation] 鉄腐食反応を利用した低水素濃度環境を好むメタン生成菌・酢酸生成菌の新規培養法 (2018)
  • Author(s): 加藤 創一郎、高篠 素子、五十嵐 健輔、持丸 華子、眞弓 大介、玉木 秀幸
  • Organizer: 日本微生物生態学会第32回大会
• [Remarks] 地下で発見！ゲノムが膜で包まれたバクテリア
  • URL: https://www.aist.go.jp/aist_j/press_release/pr2020/pr20201214/pr20201214.html
• [Remarks] 真核生物誕生の鍵を握る微生物「アーキア」の培養に成功
  • URL: https://www.aist.go.jp/aist_j/press_release/pr2020/pr20200116/pr20200116.html