Physiological survival mechanism of bacterial community inhabiting in oligotrophic environments

• Project/Area Number: 25870295
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Environmental dynamic analysis; Ecology/Environment
• Research Institution: Shizuoka University
• Principal Investigator: KIMURA Hiroyuki 静岡大学, 理学(系)研究科(研究院), 准教授 (30377717)
• Project Period (FY): 2013-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2014: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2013: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
• Keywords: バクテリア / 海洋細菌 / 極限環境 / 貧栄養環境 / トランスクリプトーム / RNA / 生存戦略 / RNA発現 / small RNA / 定量RT-PCR

Outline of Final Research Achievements

Transfer-messenger RNA is small RNA that employs both tRNA and mRNA-like properties as it rescues stalled ribosomes during nutrient shortage. Here, we surveyed transcriptional responses of transfer-messenger RNA-containing bacterial strains in the medium of various nutrient conditions. Consequently, transfer-messenger RNA showed significant up-regulation in the nutrient-limiting growth conditions.
We collected seawater samples from open ocean (oligotrophic environment) and coastal area (eutrophic environment). We then performed transcriptomic analyses targeting total RNA extracted from the bacterial communities in the seawater samples. Transfer-messenger RNA was expressed at significantly higher levels in the seawater sample derived from the open ocean. In total, our results suggest the importance of transfer-messenger RNA as essential components for nutrient-limiting growth conditions in these bacteria.

Research Products

• [Journal Article] Biogas production using anaerobic groundwater containing a subterranean microbial community associated with the accretionary prism (2015)
  • Author(s): Baito K., Imai S., Matsushita M., Otani M., Sato Y., Kimura H.
  • Journal Title: Microbial Biotechnology Volume: ー Issue: 5 Pages: 837-845
  • DOI: 10.1111/1751-7915.12179
  • Peer Reviewed / Open Access
• [Journal Article] Quantitative analysis of coenzyme F430 in environmental samples: a new diagnostic tool for methanogenesis and anaerobic methane oxidation (2014)
  • Author(s): Kaneko, M., Takano, Y., Chikaraishi, Y., Ogawa, N.O., Asakawa, S., Watanabe, K., Shima, S., Krueger, M., Matsushita, M., Kimura, H., Ohkouchi, N.
  • Journal Title: Analytical Chemistry Volume: 86 Issue: 7 Pages: 3633-3638
  • DOI: 10.1021/ac500305j
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Thermotoga profunda sp. nov., and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs (2014)
  • Author(s): Mori K., Yamazoe A.,Hosoyama A, Ohji S., Fujita N., Ishibashi J., Kimura H., Suzuki K.
  • Journal Title: International Journal of Systematic and Evolutionary Microbiology Volume: 64 Issue: Pt_6 Pages: 2128-2136
  • DOI: 10.1099/ijs.0.060137-0
  • Peer Reviewed
• [Journal Article] Growth temperatures of archaeal communities can be estimated from the guanine-plus-cytosine contents of 16S rRNA gene fragments (2013)
  • Author(s): Hiroyuki Kimura, Kousuke Mori, Toshiro Yamanaka, Jun-Ichiro Ishibashi
  • Journal Title: Environmental Microbiology Reports Volume: Vol.5 Issue: 3 Pages: 468-474
  • DOI: 10.1111/1758-2229.12035
  • Peer Reviewed
• [Journal Article] First occurrence of Alviniconcha from Japanese waters (Gastropoda: Provannidae) (2013)
  • Author(s): Yoshihiro Fujiwara, Takashi Okutani, Hiroyuki Kimura
  • Journal Title: Venus Volume: 71 Pages: 217-219
  • NAID: 130005155524
  • Peer Reviewed
• [Presentation] ゲノム上にG+C含量の異なる2 種類の16S rRNA 遺伝子を有する好塩性古細菌の生理生態 (2015)
  • Author(s): 佐藤 悠、藤原健智、木村浩之
  • Organizer: 第16回静岡ライフサイエンスシンポジウム
  • Place of Presentation: 静岡大学 (静岡県静岡市)
  • Year and Date: 2015-03-07 – 2015-03-08
• [Presentation] G+C含量の異なる2種類の16S rRNA遺伝子を使い分ける好塩性古細菌Haloarculaの生態 (2014)
  • Author(s): 佐藤 悠、木村浩之
  • Organizer: 環境微生物系学会合同大会2014
  • Place of Presentation: アクトシティー浜松 (静岡県浜松市)
  • Year and Date: 2014-10-21 – 2014-10-24
• [Presentation] Microbial methane production and carbon-nitrogen cycles in subterranean environments associated with the accretionary prism in Southwest Japan (2014)
  • Author(s): Kimura H.
  • Organizer: 13th Japan-Taiwan International Workshop on Hydrological and Geochemical Research for Earthquake Prediction
  • Place of Presentation: 独立行政法人産業技術総合研究所 (茨城県つくば市)
  • Year and Date: 2014-09-02 – 2014-09-03
  • Invited
• [Presentation] Haloarcula strains regulate transcription of multiple 16S rRNA genes in response to environmental temperatures (2014)
  • Author(s): Sato Y., Kimura H.
  • Organizer: 15th International Symposium on Microbial Ecology (ISME-15)
  • Place of Presentation: Coex Convention Center (Seoul, Korea)
  • Year and Date: 2014-08-24 – 2014-08-29
• [Presentation] 好塩性古細菌は環境温度によりG+C含量の異なる16S rRNA遺伝子を選択的に転写する
  • Author(s): 佐藤 悠、木村浩之
  • Organizer: 第29回日本微生物生態学会大会
  • Place of Presentation: 鹿児島大学（鹿児島県鹿児島市）
• [Presentation] 全ゲノム解析を用いた新種提案 －温泉環境から分離した新規Thermotoga－
  • Author(s): 森浩二、細山 啓、山副敦司、黄地祥子、木村浩之、石橋純一郎、鈴木健一朗
  • Organizer: 第29回日本微生物生態学会大会
  • Place of Presentation: 鹿児島大学（鹿児島県鹿児島市）
• [Book] 環境と微生物の事典 (2014)
  • Author(s): 日本微生物生態学会
  • Total Pages: 432
  • Publisher: 朝倉出版
• [Remarks] 静岡大学理学部地球科学科 木村研究室ホームページ
  • URL: http://www.ipc.shizuoka.ac.jp/~shkimur/top.html
• [Remarks] 静岡大学大学院理学研究科地球科学専攻木村研究室ホームページ
  • URL: http://www.ipc.shizuoka.ac.jp/~shkimur/top.html