Study on novel functions of nitrogen fixation and hydrogen utilization in bacteria of the order Bacteroidales

• Project/Area Number: 26292047
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Applied microbiology
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: OHKUMA Moriya 国立研究開発法人理化学研究所, バイオリソースセンター, 室長 (10270597)
• Co-Investigator(Kenkyū-buntansha): 野田 悟子 山梨大学, 総合研究部, 准教授 (80342830)
• Co-Investigator(Renkei-kenkyūsha): HONGOH Yuichi 東京工業大学, 生命理工学研究科, 教授 (90392117)
• Research Collaborator: YUKI Masahiro ; INOUE Jun-ichi
• Project Period (FY): 2014-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥16,640,000 (Direct Cost: ¥12,800,000、Indirect Cost: ¥3,840,000); Fiscal Year 2016: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2015: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2014: ¥7,020,000 (Direct Cost: ¥5,400,000、Indirect Cost: ¥1,620,000)
• Keywords: 微生物機能 / 窒素固定 / 水素代謝 / 共生 / シングルセルゲノム / 還元的酢酸生成 / Bacteroidales目細菌 / スピロヘータ / ゲノム / 生態 / 進化 / 微生物 / 生態学 / 分類学 / 微生物ゲノム / 微生物進化 / 生物多様性 / 難培養微生物

Outline of Final Research Achievements

We found bacterial species in the order Bacteroidales that harbor genes for nitrogen fixation or genes homologous to archaea for hydrogen utilization in the genomes, and we detected the respective activities in their representative cultured strains. We identified an endosymbiotic spirochete species of a termite-gut cellulolytic protist species that contributes to the activities for both nitrogen fixation and hydrogen-utilizing reductive acetogenesis in the gut. Through single-cell genome sequencing, we investigated functions and symbiotic mechanisms of this endosymbiont and two ectosymbiotic Bacteroidales species attached onto cell surface of termite-gut protists.

Research Products

• [Int'l Joint Research] University of Sydney(Australia)
• [Int'l Joint Research] リバプール大(英国)
• [Journal Article] Desulfovibrio trichonymphae’, an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut. (2017)
  • Author(s): Kuwahara, H., Yuki, M., Izawa, K., Ohkuma, M., Hongoh, Y
  • Journal Title: ISME J. Volume: 11(3) Pages: 766-776
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Comparison of intracellular “Ca. Endomicrobium trichonymphae” genomovars illuminates the requirement and decay of defense systems against foreign DNA (2016)
  • Author(s): Izawa, K., H. Kuwahara, K. Kihara, M. Yuki, N. Lo, T. Ito, M. Ohkuma, Y. Hongoh
  • Journal Title: Genome Biol. Evol. Volume: 8(10) Issue: 10 Pages: 3099-3107
  • DOI: 10.1093/gbe/evw227
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Nitrogen fixation and nifH diversity in human gut microbiota (2016)
  • Author(s): Igai, K., M. Itakura, S. Nishijima, H. Tsurumaru, W. Suda, T. Tsutaya, E. Tomitsuka, K. Tadokoro, J. Baba, S. Odani, K. Natsuhara, A. Morita, M. Yoneda, A. R. Greenhill, P. F. Horwood, J. Inoue, M. Ohkuma, Y. Hongoh, T. Yamamoto, P. M. Siba, M. Hattori, K. Minamisawa, M. Umezaki
  • Journal Title: Sci. Rep. Volume: 6 Issue: 1 Pages: 31942-31942
  • DOI: 10.1038/srep31942
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Bacteroides caecicola sp. nov. and Bacteroides gallinaceum sp. nov., isolated from the caecum of an Indonesian chicken (2016)
  • Author(s): Irisawa, T., S. Saputra, M. Kitahara, M. Sakamoto, S. Tiani, T. Yulineri, A. Dinoto, M. Ohkuma
  • Journal Title: Int. J. Syst. Evol. Microbiol. Volume: 66 Issue: 3 Pages: 1431-1437
  • DOI: 10.1099/ijsem.0.000899
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] 難培養微生物のシングルセルゲノム解析 (2016)
  • Author(s): 雪 真弘、大熊 盛也
  • Journal Title: バイオサイエンスとインダストリー Volume: 74(6) Pages: 488-491
  • NAID: 40021006286
• [Journal Article] The outset of another nitrogenase (2016)
  • Author(s): Ohkuma, M.
  • Journal Title: Environ Microbiol Volume: 18 Issue: 1 Pages: 4-4
  • DOI: 10.1111/1462-2920.13001
• [Journal Article] Dominant ectosymbiotic bacteria of cellulolytic protists in the termite gut also have the potential to digest lignocellulose (2015)
  • Author(s): Yuki M., Kuwahara H., Shintani M., Izawa K., Sato T., Starns D., Hongoh Y., Ohkuma M.
  • Journal Title: Environmental Microbiology Volume: 17 Issue: 12 Pages: 4942-4953
  • DOI: 10.1111/1462-2920.12945
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Acetogenesis from H2 plus CO2 and nitrogen fixation by an endosymbiotic spirochete of a termite-gut cellulolytic protist (2015)
  • Author(s): Ohkuma, M., S. Noda, S. Hattori, T. Iida, M. Yuki, D. Starns, J. Inoue, A.C. Darby, and Y. Hongoh
  • Journal Title: Proc Natl Acad Sci USA Volume: 112 Issue: 33 Pages: 10224-10230
  • DOI: 10.1073/pnas.1423979112
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] High quality draft genome sequence of Bacteroides barnesiae type strain BL2T (DSM 18169T) from chicken caecum (2015)
  • Author(s): Sakamoto, M., A. L. Lapidus, J. Han, S. Trong, M. Haynes, T. B. K. Reddy, N. Mikhailova, M. Huntemann, A. Pati, N. N. Ivanova, R. Pukall, V. M. Markowitz, T. Woyke, H.-P. Klenk, N. C. Kyrpides, and M. Ohkuma
  • Journal Title: Stand Genomic Sci Volume: 10 Issue: 1 Pages: 48-48
  • DOI: 10.1186/s40793-015-0045-6
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Distribution and Evolution of Nitrogen Fixation Genes in the Phylum <i>Bacteroidetes</i> (2015)
  • Author(s): Inoue, J., Oshima K., Suda, W., Sakamoto, M., Iino, T., Noda, S., Hongoh, Y., Hattori, M. and Ohkuma, M.
  • Journal Title: Microbes and Environments Volume: 30 Issue: 1 Pages: 44-50
  • DOI: 10.1264/jsme2.ME14142
  • NAID: 130005061711
  • ISSN: 1342-6311, 1347-4405
  • Peer Reviewed / Open Access
• [Presentation] シロアリ腸内原生生物細胞表面共生細菌のmicrodiversity解析にもとづく伝播様式についての考察 (2016)
  • Author(s): 猪飼 桂、望月 悠司、雪 真弘、大熊 盛也、本郷 裕一
  • Organizer: 日本微生物生態学会第31回大会
  • Place of Presentation: 横須賀文化会館（神奈川県・横須賀市）
  • Year and Date: 2016-10-23
• [Presentation] 長期に隔離された共生微生物群集では群集レベルの競争が生じるか？ (2016)
  • Author(s): 北出 理、佐藤 渚、野田 悟子、飯田 敏也、大熊 盛也
  • Organizer: 日本微生物生態学会第31回大会
  • Place of Presentation: 横須賀文化会館（神奈川県・横須賀市）
  • Year and Date: 2016-10-23
• [Presentation] シロアリ腸内の難培養性細菌のシングルセルゲノム解析 (2016)
  • Author(s): 大熊盛也、雪 真弘、David Starns、桑原宏和、本郷裕一
  • Organizer: 日本微生物資源学会第23回大会
  • Place of Presentation: 千葉大学（千葉県・千葉市）
• [Presentation] バイオマスの循環を支えるシロアリの多重共生系 (2016)
  • Author(s): 野田悟子、雪真弘、大熊盛也
  • Organizer: 日本水環境学会シンポジウム
  • Place of Presentation: 秋田県立大学（秋田県・秋田市）
• [Presentation] シロアリ腸内の原生生物の細胞内で効率的に働く共生細菌 (2015)
  • Author(s): 大熊盛也
  • Organizer: 第38回日本分子生物学会年会 第88回日本生化学会大会 合同大会
  • Place of Presentation: 神戸国際会議場（兵庫県・神戸）
  • Year and Date: 2015-12-04
  • Invited
• [Presentation] Single-cell genomics of Bacteroidales ectosymbionts of termite-gut protists (2015)
  • Author(s): Masahiro Yuki, Hirokazu Kuwahara, David Starns, Kazuki Izawa, Yuichi Hongoh, Moriya Ohkuma
  • Organizer: 2nd International Symposium, Matryoshka-type Evolution of Eukaryotic Cells
  • Place of Presentation: 筑波大学大学会館（茨城県・つくば市）
  • Year and Date: 2015-10-01
  • Int'l Joint Research
• [Presentation] Comparative genomics of the nitrogen-fixing endosymbionts of the cellulolytic protists Pseudotrichonympha spp. in the gut of termites (2015)
  • Author(s): Agent Pramono, Akinori Yamada,Hirokazu Kuwahara,Takako Mabuchi,Osamu Kitade, Nathan Lo, Atsushi Toyoda, Takehiko Ito, Moriya Ohkuma, Yuichi Hongoh
  • Organizer: 2nd International Symposium, Matryoshka-type Evolution of Eukaryotic Cells
  • Place of Presentation: 筑波大学大学会館（茨城県・つくば市）
  • Year and Date: 2015-10-01
  • Int'l Joint Research
• [Presentation] CO2 and N2-fixing endosymbionts of termite-gut cellulolytic pritists (2015)
  • Author(s): Ohkuma, M.
  • Organizer: 2nd International Symposium, Matryoshka-type Evolution of Eukaryotic Cells
  • Place of Presentation: 筑波大学大学会館（茨城県・つくば市）
  • Year and Date: 2015-09-30
  • Int'l Joint Research / Invited
• [Presentation] シロアリ腸内の原生生物細胞内の細菌の共生と進化 (2015)
  • Author(s): 大熊盛也
  • Organizer: 日本進化学会第17回大会
  • Place of Presentation: 中央大学後楽園キャンパス（東京都・東京）
  • Year and Date: 2015-08-21
  • Invited
• [Presentation] シロアリ腸内原生生物に細胞表面共生するSymbiothrix dinenymphaeの１細胞ゲノム解析 (2015)
  • Author(s): 雪真弘、桑原宏和、新谷政己、伊澤和輝、本郷裕一、大熊盛也
  • Organizer: 日本農芸化学会2015年度大会
  • Place of Presentation: 岡山 岡山大学津島キャンパス
  • Year and Date: 2015-03-28
• [Presentation] Bacteroidetes門細菌の窒素固定に関する諸解析 (2015)
  • Author(s): 井上潤一、本郷裕一、坂本光央、大島健志朗、服部正平、大熊盛也
  • Organizer: 日本農芸化学会2015年度大会
  • Place of Presentation: 岡山 岡山大学津島キャンパス
  • Year and Date: 2015-03-27
• [Presentation] 高等シロアリ腸内に共生する優占種細菌3種のシングル・セルゲノム解析 (2014)
  • Author(s): 雪 真弘、桑原 宏和, ,新谷 政己, 本郷 裕一, 大熊 盛也
  • Organizer: 環境微生物系学会合同大会2014
  • Place of Presentation: 浜松 アクトシテｨ浜松
  • Year and Date: 2014-10-22
• [Presentation] Single cell genomic insights into Treponema diversity in the gut of the higher termite Nasutitermes takasagoensis. (2014)
  • Author(s): David Starns、雪 真弘, 桑原 宏和, 本郷 裕一, Darby Alistair, 大熊 盛也
  • Organizer: 環境微生物系学会合同大会2014
  • Place of Presentation: 浜松 アクトシテｨ浜松
  • Year and Date: 2014-10-22
• [Presentation] Metabolic integration across endosymbiotic communities (2014)
  • Author(s): Moriya Ohkuma
  • Organizer: Arthur M. Sackler Coloquium "Symbioses becoming permanent: The origins and evolutionary trajectories of organelles"
  • Place of Presentation: Irvine CA, USA
  • Year and Date: 2014-10-17
  • Invited
• [Presentation] Nitrogen fixation and evolution of nif genes in the phylum Bacteroidetes (2014)
  • Author(s): Jun-ichi Inoue, Mitsuo Sakamoto, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma
  • Organizer: 15th International Symposium on Microbial Ecology (ISME15)
  • Place of Presentation: Seoul, South Korea
  • Year and Date: 2014-08-26
• [Presentation] Molecular studies of termite-gut protists on cellulose utilization (2014)
  • Author(s): Moriya Ohkuma
  • Organizer: 17th Congress of International Union for the Study of Social Insects
  • Place of Presentation: Cairns, Australia
  • Year and Date: 2014-07-16
  • Invited
• [Book] 第７章シロアリ共生微生物 共生微生物―生物と密接に関わるミクロな生命体― 大野博司（編） (2016)
  • Author(s): 大熊盛也
  • Publisher: 化学同人
• [Remarks] シロアリ腸内の原生生物の表面共生細菌がリグノセルロース分解に寄与
  • URL: http://www.riken.jp/pr/press/2015/20150706_1/
• [Remarks] シロアリは腸内微生物によって高効率にエネルギーと栄養を獲得
  • URL: http://www.riken.jp/pr/press/2015/20150512_2/