Archaeal hunting: cultivation of uncultured fastidious Archaea

• Project/Area Number: 24687011
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Partial Multi-year Fund
• Research Field: Biodiversity/Systematics
• Research Institution: Japan Agency for Marine-Earth Science and Technology
• Principal Investigator: IMACHI Hiroyuki 独立行政法人海洋研究開発機構, 深海・地殻内生物圏研究分野, 主任研究員 (20361933)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥27,430,000 (Direct Cost: ¥21,100,000、Indirect Cost: ¥6,330,000); Fiscal Year 2014: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000); Fiscal Year 2013: ¥10,400,000 (Direct Cost: ¥8,000,000、Indirect Cost: ¥2,400,000); Fiscal Year 2012: ¥9,880,000 (Direct Cost: ¥7,600,000、Indirect Cost: ¥2,280,000)
• Keywords: アーキア / 分離培養 / 16S rRNA遺伝子 / メタン / 古細菌 / 生態学 / 微生物 / バイオリアクター / メタン生成菌

Outline of Final Research Achievements

Cultured enrichments and isolates are important in developing our understanding of microbial physiology, genetics, and ecology. However, many microorganisms, particularly members of the domain Archaea, remain uncultured under laboratory conditions. In this study, I attempted to cultivate and isolate uncultured Archaea using a new cultivation technique I developed and molecular techniques. As a result, I successfully obtained three anaerobic methane-oxidizing microbial communities that contain phylogenetically diverse of uncultured archaeal groups. The single cell genome analysis for one of the enriched microbial communities revealed that an uncultured archaeal group might have a unique sulfur metabolism gene. Unfortunately, isolates of the uncultured archaeal group was not obtained during the period of this study, but the enrichments and single cell genome analysis provide new information about the uncultured archaea.

Research Products

• [Journal Article] Presence of a novel methanogenic archaeal lineage in anaerobic digesters inferred from mcrA and 16S rRNA gene phylogenetic analyses (2015)
  • Author(s): Saito Y, Aoki M, Hatamoto M, Yamaguchi T, Takai K and Imachi H
  • Journal Title: Journal of Water and Environmental Technology Volume: 13 Pages: 279-289
  • NAID: 130005076093
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Spirochaeta psychrophila sp. nov., a psychrophilic spirochaete isolated from subseafloor sediment, and emended description of the genus Spirochaeta (2014)
  • Author(s): Miyazaki, M., S. Sakai, Y. Yamanaka, Y. Saito, K. Takai and H. Imachi
  • Journal Title: International Journal of Systematic and Evolutionary Microbiology Volume: 64 Issue: Pt_8 Pages: 2798-2804
  • DOI: 10.1099/ijs.0.062463-0
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] A long-term cultivation of an anaerobic methane-oxidizing microbial community from deep-sea methane-seep sediment using a continuous-flow bioreactor (2014)
  • Author(s): Aoki M, Ehara M, Saito Y, Yoshioka H, Miyazaki M, Saito Y, Miyashita A, Kawakami S, Yamaguchi T, Ohashi A, Nunoura T, Takai K, and Imachi H
  • Journal Title: PLOS ONE Volume: 9 Issue: 8 Pages: 1-14
  • DOI: 10.1371/journal.pone.0105356
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Complete genome sequence of Methanoregula formicica SMSPT, a mesophilic hydrogenotrophic methanogen isolated from a methanogenic upflow anaerobic sludge blanket reactor (2014)
  • Author(s): Yamamoto, K., H. Tamaki, H. Cadillo-Quiroz, H. Imachi, N. Kyrpides, T. Woyke, L. Goodwin, S. H. Zinder, Y. Kamagata and W-T. Liu
  • Journal Title: Genome Annoucement Volume: 2 Issue: 5
  • DOI: 10.1128/genomea.00870-14
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Complete genome sequence of Methanolinea tarda NOBI-1T, a hydrogenotrophic methanogen isolated from methanogenic digester sludge (2014)
  • Author(s): Yamamoto, K., H. Tamaki, H. Cadillo-Quiroz, H. Imachi, N. Kyrpides, T. Woyke, L. Goodwin, S. H. Zinder, Y. Kamagata and W-T. Liu
  • Journal Title: Genome Annoucement Volume: 2 Issue: 5
  • DOI: 10.1128/genomea.00876-14
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Sphaerochaeta multiformis sp. nov., an anaerobic, psychrophlic bacterium isolated from subseafloor sediment, and emended description of the genus Sphaerochaeta (2014)
  • Author(s): Miyazaki, M., S. Sakai, K. M. Ritalahti, Yayoi Saito, Y. Yamanaka, Yumi Saito, A. Tame, K. Uematsu, F. E. Loeffler, K. Takai and H. Imachi
  • Journal Title: International Journal of Systematic and Evolutionary Microbiology Volume: 64 Issue: Pt_12 Pages: 4147-4154
  • DOI: 10.1099/ijs.0.068148-0
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] 海底堆積物中のメタン生成および酸化反応を担う微生物 (特集 地球温暖化と海洋微生物) (2014)
  • Author(s): 青木仁孝、井町寛之
  • Journal Title: 生物の科学 遺伝 Volume: 687 Pages: 486-491
• [Journal Article] Pelolinea submarina gen. nov., sp. nov., an anaerobic, filamentous bacterium of the phylum Chloroflexi isolated from subseafloor sediment (2014)
  • Author(s): Imachi, H., S. Sakai, J. S. Lipp, M. Miyazaki, Y. Saito, Y. Yamanaka, K.-U. Hinrichs, F. Inagaki and Ken Takai
  • Journal Title: International Journal of Systematic and Evolutionary Microbiology Volume: 64 Issue: Pt_3 Pages: 812-818
  • DOI: 10.1099/ijs.0.057547-0
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Biological CO_2 conversion to acetate in subsurface coal-sand formation using a high-pressure reactor system (2013)
  • Author(s): Ohtomo, Y., Ijiri, A., Ikegawa, Y., Tsutsumi, M., Imachi, H., Uramoto, G., Hoshino, T., Morono, Y., Sakai, S., Saito, Y., Tanikawa, W., Hirose, T., and Inagaki, F
  • Journal Title: Frontiers in Microbiology Volume: Article no. 361 Pages: 4-4
  • DOI: 10.3389/fmicb.2013.00361
  • Peer Reviewed / Open Access
• [Journal Article] Detection of coenzyme F430 in deep sea sediments : A key molecule for biological methanogenesis (2013)
  • Author(s): Takano, Y.
  • Journal Title: Organic Geochemistry Volume: 58 Pages: 137-140
  • Peer Reviewed
• [Presentation] 持続的CO2還元を可能にするバイオリアクターについて (2015)
  • Author(s): 井町寛之
  • Organizer: 平成26年度水溶性天然ガス田の生産に係る技術検討会 第4回水溶性天然ガス（ガス田）を対象とした炭素循環の可能性検討会
  • Place of Presentation: 独立行政法人石油天然ガス・金属鉱物資源機構東京本部、東京都港区
  • Year and Date: 2015-01-23
  • Invited
• [Presentation] Cultivation of methanogenic microbial community from the deeply buried coalbeds in the ocean (2014)
  • Author(s): Imachi H, Tasumi E, Ijiri A, Konno U, Morono Y, Ito M, Takai K, Inagaki F and IODP Expedition 337 Scientists
  • Organizer: 9th International Symposium on Subsurface Microbiology (ISSM)
  • Place of Presentation: Pacific Grove, CA, USA
  • Year and Date: 2014-10-06
• [Presentation] Cultivation of methanogenic community from 2-km deep subseafloor coalbeds using a down-flow hanging sponge bioreactor (2014)
  • Author(s): Imachi, H., Tasumi, E., Ijiri, A., Konno, U., Morono, Y., Ito, M., Takai, K., Inagaki, F. and IODP Expedition 337 Scientists
  • Organizer: 15th International Symposium on Microbial Ecology (ISME15)
  • Place of Presentation: Seoul, South Korea
  • Year and Date: 2014-08-25
• [Presentation] 海底下メタン菌の連続リアクター培養とCO2資源化への応用 (2014)
  • Author(s): 井町寛之
  • Organizer: シンポジウム「海底下の炭化水素資源・炭素循環と地球生命工学」
  • Place of Presentation: 東京大学理学部小柴ホール、東京都文京区
  • Year and Date: 2014-01-24
  • Invited
• [Presentation] Cultivation of methanogenic community from 2-km deep subseafloor coalbeds using a continuous-flow bioreactor (2013)
  • Author(s): Imachi, H.
  • Organizer: AGU2013 Fall Meeting
  • Place of Presentation: San Francisco, CA, USA
  • Year and Date: 2013-12-10
• [Presentation] 深海堆積物からの嫌気共生細菌の培養とその分離の試み (2013)
  • Author(s): 斎藤弥生
  • Organizer: 第29回日本微生物生態学会大会
  • Place of Presentation: 鹿児島大学郡元キャンパス、鹿児島県鹿児島市
  • Year and Date: 2013-11-23
• [Presentation] Cultivation of methanogenic microbial community from 2-km deep subseafloor coalbeds using a continuous-flow bioreactor (2013)
  • Author(s): 井町寛之
  • Organizer: 第29回日本微生物生態学会大会
  • Place of Presentation: 鹿児島大学郡元キャンパス、鹿児島県鹿児島市
  • Year and Date: 2013-11-23
• [Presentation] A long-term cultivation of an anaerobic methane-oxidizing sulfate-reducing community by a down-flow hanging sponge bioreactor (2013)
  • Author(s): Aoki, M.
  • Organizer: The 5th Taiwan-Japan-Korea International Symposium on Microbial Ecology
  • Place of Presentation: National Central University, Jhongli, Taiwan
  • Year and Date: 2013-11-01
• [Presentation] 嫌気的メタン酸化反応に関与する海底下未知アーキアの培養 (2013)
  • Author(s): 青木仁孝
  • Organizer: 第47回日本水環境学会年会
  • Place of Presentation: 大阪工業大学大宮キャンパス
  • Year and Date: 2013-03-10
• [Presentation] 廃水処理リアクターを用いた嫌気的メタン酸化反応を担う未知アーキアの培養 (2012)
  • Author(s): 青木仁孝
  • Organizer: 第67回土木学会年次講演会
  • Place of Presentation: 名古屋大学東山キャンパス
  • Year and Date: 2012-09-05
• [Presentation] Sponges as microbial habitats : cultivation of fastidious subseafloor sedimentary microbes using continuous-flow bioreactor. (2012)
  • Author(s): Imachi, H.
  • Organizer: International Society for Microbial Ecology 14 (ISME14)
  • Place of Presentation: Copenhagen, Denmark
  • Year and Date: 2012-08-22
• [Book] Family Methanocellaceae. In The Prokaryotes 4th Edition. Other Major Lineages of Bacteria and The Archaea (2014)
  • Author(s): Sakai, S., R. Conrad and H. Imachi
  • Total Pages: 1028
  • Publisher: Springer
• [Book] Chapter 2.6 Cultivation of Subseafloor Prokaryotic Life, In Earth and Life Processes Discovered from Subseafloor Environment - A Decade of Science Achieved by the Integrated Ocean Drilling Program (IODP) (2014)
  • Author(s): Engelen, B. and Imachi, H
  • Total Pages: 789
  • Publisher: Elsevier