Novel isolation technology illuminates ecophysiology and diversity of nitrifiers

• Project/Area Number: 16K18609
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Biodiversity/Systematics
• Research Institution: Waseda University
• Principal Investigator: Fujitani Hirotsugu 早稲田大学, ナノ・ライフ創新研究機構, 次席研究員(研究院講師) (50708617)
• Project Period (FY): 2016-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2018: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2017: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2016: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
• Keywords: アンモニア酸化 / 亜硝酸酸化 / 分離培養 / ゲノム / 代謝物 / セルソーター / バイオリアクター / 亜硝酸酸化細菌 / 硝化 / Nitrotoga / Nitrospira / Nitrobacter / 土壌 / 有機物 / 海水 / 微生物生態 / 系統 / 多様性 / 窒素循環

Outline of Final Research Achievements

Nitrification is a key reaction of biogeochemical nitrogen cycle and catalyzed by ammonia oxidizers and nitrite oxidizers. Generally, nitrifiers are difficult to cultivate and isolate under laboratory conditions resulting that their eco-physiological characteristics are still unknown. In this study, we aimed to develop novel cultivation and isolation methods for uncultured nitrifiers and obtain novel nitrifiers. Isolates were characterized physiologically and genomically.

Academic Significance and Societal Importance of the Research Achievements

本研究で開発された分離培養技術は，工学的な培養技術と分光技術をベースとした独創的な手法である。本手法は，硝化細菌をはじめとする環境微生物全般に広く一般化できるポテンシャルを持っている。また，本研究によって，系統学的に新規な硝化細菌を特徴付けることができた。硝化細菌の生理生態を明らかにすることで，過剰な窒素化合物の流出や温室効果ガスの抑制など環境問題の解決に向け，微生物学的知見を拡充することができた。

Research Products

• [Int'l Joint Research] デンマーク工科大学(デンマーク)
• [Int'l Joint Research] デンマーク工科大学(デンマーク)
• [Journal Article] Genomic analysis of two phylogenetically distinct Nitrospira species reveals their genomic plasticity and functional diversity (2018)
  • Author(s): Norisuke Ushiki, Hirotsugu Fujitani, Yu Shimada, Tomohiro Morohoshi, Yuji Sekiguchi, Satoshi Tsuneda
  • Journal Title: Frontiers in Microbiology Volume: 8
  • DOI: 10.3389/fmicb.2017.02637
  • Peer Reviewed / Open Access
• [Journal Article] Enrichment and physiological characterization of a cold-adapted nitrite oxidizer Nitrotoga sp. from an eelgrass sediment (2017)
  • Author(s): Kento Ishii, Hirotsugu Fujitani, Tatsunori Nakagawa, Reiji Takahashi, Satoshi Tsuneda
  • Journal Title: Applied and Environmental Microbiology Volume: 83 Issue: 14
  • DOI: 10.1128/aem.00549-17
  • Peer Reviewed
• [Journal Article] Nitrite oxidation kinetics of two Nitrospira strains: the quest for competition and ecological niche differentiation (2017)
  • Author(s): Norisuke Ushiki, Masaru Jinno, Hirotsugu Fujitani, Toshikazu Suenaga, Akihiko Terada, Satoshi Tsuneda
  • Journal Title: Journal of Bioscience and Bioengineering Volume: 123 Issue: 5 Pages: 581-589
  • DOI: 10.1016/j.jbiosc.2016.12.016
  • NAID: 40021205367
  • Peer Reviewed / Acknowledgement Compliant
• [Presentation] 見過ごされたアンモニア酸化細菌：Nitrosomonas属の新規な生理学，ゲノミクス，環境分布 (2019)
  • Author(s): 藤谷拓嗣，菊池脩太，石井拳人，関口勇地，常田聡
  • Organizer: 第13回日本ゲノム微生物学会年会
• [Presentation] 網羅的遺伝子発現解析による硝化菌の形態変化がもたらす生存戦略の解明 (2019)
  • Author(s): 一色理乃，藤谷拓嗣，田中大器，関口哲志，常田 聡
  • Organizer: 第13回日本ゲノム微生物学会年会
• [Presentation] ピルビン酸存在下での亜硝酸酸化細菌Nitrotogaの混合栄養的な増殖様式 (2019)
  • Author(s): 石井拳人，藤谷拓嗣，関口勇地，常田 聡
  • Organizer: 第13回日本ゲノム微生物学会年会
• [Presentation] Genomic and physiological characteristics of novel nitrite-oxidizing Nitrospira isolated from a drinking water treatment plant (2018)
  • Author(s): Hirotsugu Fujitani, Kengo Momiuchi, Kento Ishii, Masaru Jinno, Norisuke Ushiki, Yuji Sekiguchi, Satoshi Tsuneda
  • Organizer: 17th International society for microbial ecology
  • Int'l Joint Research
• [Presentation] Growth variability at the single-cell level affects culturability of environmental microorganisms (2018)
  • Author(s): Rino Isshiki, Hirotsugu Fujitani, Daiki Tanaka, Tetsushi Sekiguchi, Satoshi Tsuneda
  • Organizer: 17th International society for microbial ecology
  • Int'l Joint Research
• [Presentation] Isolation process and genomic analysis of nitrite oxidizer Nitrotoga sp. provide insights on physiological characteristics and clues to promote the growth (2018)
  • Author(s): Kento Ishii, Hirotsugu Fujitani, Yuji Sekiguchi, Satoshi Tsuneda
  • Organizer: 32th Japanese Society Microbial Ecology Annual Meeting and 10th Asian Symposium on Microbial Ecology,
  • Int'l Joint Research
• [Presentation] Growth heterogeneity in pure cultures affects the culturability (2018)
  • Author(s): Rino Isshiki, Hirotsugu Fujitani, Daiki Tanaka, Tetsushi Sekiguchi, Satoshi Tsuneda
  • Organizer: 32th Japanese Society Microbial Ecology Annual Meeting and 10th Asian Symposium on Microbial Ecology
  • Int'l Joint Research
• [Presentation] Cultivation of novel nitrite oxidizer Nitrospira from acidic soil (2018)
  • Author(s): Yu Takahashi, Hirotsugu Fujitani, Yuhei Hirono, Masahito Hayatsu, Satoshi Tsuneda
  • Organizer: 32th Japanese Society Microbial Ecology Annual Meeting and 10th Asian Symposium on Microbial Ecology
  • Int'l Joint Research
• [Presentation] 革新的分離培養技術による新規なcomammox細菌の獲得と生存戦略の解明 (2017)
  • Author(s): 野町真名実，藤谷拓嗣，長谷部吉昭，江口正浩，常田 聡
  • Organizer: 第19回化学工学会学生発表会
  • Place of Presentation: 東京
  • Year and Date: 2017-03-04
• [Presentation] Nitrospiraの亜硝酸酸化活性を制御するQuorum-sensing機構の発見 (2017)
  • Author(s): 牛木章友，藤谷拓嗣，諸星知広，常田 聡
  • Organizer: 第11回日本ゲノム微生物学会年会
  • Place of Presentation: 藤沢
  • Year and Date: 2017-03-02
• [Presentation] セルソーターによって分取された凝集体内の微生物間相互作用の解明 (2017)
  • Author(s): 石井拳人，藤谷拓嗣，常田 聡
  • Organizer: 第11回日本ゲノム微生物学会年会
  • Place of Presentation: 藤沢
  • Year and Date: 2017-03-02
• [Presentation] Comparative genomics of phylogenetically distinct two Nitrospira strains isolated from activated sludge (2017)
  • Author(s): Norisuke Ushiki, Hirotsugu Fujitani, Yu Shimada, Tomohiro Morohoshi, Yuji Sekiguchi, Satoshi Tsuneda
  • Organizer: 5th International Conference on Nitrification
  • Int'l Joint Research
• [Presentation] Growth heterogeneity in pure cultures of nitrifiers (2017)
  • Author(s): Rino Isshiki, Hirotsugu Fujitani, Daiki Tanaka, Tetsushi Sekiguchi, Satoshi Tsuneda
  • Organizer: 5th International Conference on Nitrification
  • Int'l Joint Research
• [Presentation] Genome-informed isolation of nitrite oxidizer Nitrotoga sp. (2017)
  • Author(s): Kento Ishii, Hirotsugu Fujitani, Tatsunori Nakagawa, Reiji Takahashi, Satoshi Tsuneda
  • Organizer: 5th International Conference on Nitrification
  • Int'l Joint Research
• [Presentation] 硝化菌単一菌株集団でみられる形態と増殖能の不均一性 (2017)
  • Author(s): 一色 理乃, 藤谷 拓嗣, 田中 大器, 関口 哲志, 常田 聡
  • Organizer: 環境微生物系学会合同大会2017
• [Presentation] ゲノムから推定する遅増殖性Nitrotogaの活性促進因子 (2017)
  • Author(s): 石井 拳人, 藤谷 拓嗣, 常田 聡
  • Organizer: 環境微生物系学会合同大会2017
• [Presentation] 完全アンモニア酸化能を保持するComammox細菌の分離培養と生理生態 (2017)
  • Author(s): 野町 真名実, 藤谷 拓嗣, 長谷部 吉昭, 江口 正浩, 常田 聡
  • Organizer: 環境微生物系学会合同大会2017
• [Presentation] 微生物凝集体ソーティングによる未培養な亜硝酸酸化細菌Nitrotogaの獲得と生存戦略 (2016)
  • Author(s): 石井拳人，藤谷拓嗣，中川達功，高橋令二，常田 聡
  • Organizer: 第31回日本微生物生態学会
  • Place of Presentation: 横須賀
  • Year and Date: 2016-10-22
• [Presentation] Ammonia concentration determines ecological niche differentiation of Nitrospira as nitrite-oxidizers in activated sludge (2016)
  • Author(s): Hirotsugu Fujitani, Masaru Jinno, Norisuke Ushiki, Toshikazu Suenaga, Akihiko Terada, Satoshi Tsuneda
  • Organizer: 6th International Conference Microbial Ecology and Water Engineering
  • Place of Presentation: Copenhagen
  • Year and Date: 2016-09-04
  • Int'l Joint Research
• [Presentation] Direct isolation of microcolonies from activated sludge opens the window of unrecognized genus Nitrosomonas as ammonia oxidizers (2016)
  • Author(s): Hirotsugu Fujitani, Takuma Abe, Norisuke Ushiki, Satoshi Tsuneda
  • Organizer: 16th International Society for Microbial Ecology
  • Place of Presentation: Montreal
  • Year and Date: 2016-08-21
  • Int'l Joint Research
• [Presentation] Comparative genomic analysis of phylogenetically distinct two Nitrospira strains isolated from a wastewater treatment plant (2016)
  • Author(s): Norisuke Ushiki, Hirotsugu Fujitani, Yuji Sekiguchi, Satoshi Tsuneda
  • Organizer: 16th International Society for Microbial Ecology
  • Place of Presentation: Montreal
  • Year and Date: 2016-08-21
  • Int'l Joint Research
• [Presentation] Physiological characterization of Nitrotoga-like bacteria enriched from coastal sand (2016)
  • Author(s): Kento Ishii, Hirotsugu Fujitani, Tatsunori Takahashi, Reiji Takahashi, Satoshi Tsuneda
  • Organizer: 16th International Society for Microbial Ecology
  • Place of Presentation: Montreal
  • Year and Date: 2016-08-21
  • Int'l Joint Research
• [Presentation] 新規な分離培養技術によって獲得された硝化細菌の生理・ゲノム特性 (2016)
  • Author(s): 藤谷拓嗣，牛木章友，神野 大，安部拓磨，常田 聡
  • Organizer: 環境バイオテクノロジー学会
  • Place of Presentation: 広島
  • Year and Date: 2016-06-13