Visualization of metabolic dynamics during pattern formation in bacteria

• Project/Area Number: 16K07333
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Cell biology
• Research Institution: Tohoku University
• Principal Investigator: Robert Martin 東北大学, 高度教養教育・学生支援機構, 准教授 (90365487)
• Research Collaborator: SHOJI Wataru ; SAIGUSA Daisuke ; ISOBE Hiroyuki ; MORI Hirotada
• Project Period (FY): 2016-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000); Fiscal Year 2018: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2017: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2016: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: gene expression / bacterial colony / biofilm / division of labor / time-lapse fluorescence / differentiation / pattern formation / metabolic activity / fluorescent reporter / fusion protein / cyclic di-nucleotides / bacterial macro-colonies / fluorescence / c-di-GMP / bacterial colonies / bacterial strains / 細胞間情報伝達 / メタボロミックス / 生化学 / 微生物代謝 / 複雑系

Outline of Final Research Achievements

We studied pattern formation and the dynamics of gene expression in the bacterium E. coli growing into large colony and biofilm structures on solid media. We tested various environmental conditions leading to different patterns and then investigated the spatio-temporal distribution of gene expression within those structures using fluorescent protein reporters.

Our results show that E. coli can form various types of structures depending on agar hardness and nutritional conditions. The resulting colonies develop complex wrinkle and ring structures in which the profiles of gene expression vary and can result in preferential expression in ring-like structures near the center or periphery of the colony or within wrinkles. Our work thus reveals the complexity of spatio-temporal organization in colonies and suggests that bacterial cells that are otherwise genetically identical can display division of labor leading to different physiological properties within large collectives.

Academic Significance and Societal Importance of the Research Achievements

Understanding bacterial colonies and biofilms is important as they represent communities as they occur in nature and in host organisms and are a major challenge for drug resistance some industrial processes. Our results reveal the emergent complexity of gene expression within these structures.

Research Products

• [Journal Article] Complexity and Possible Emergence of Intelligence in Bacterial Collectives (2018)
  • Author(s): Robert, Martin
  • Journal Title: Journal of Cognitive Science Volume: 19 Pages: 283-284
  • Open Access / Int'l Joint Research
• [Presentation] Structural and functional complexity within E. coli microcolonies and biofilms. (2019)
  • Author(s): Martin Robert
  • Organizer: E. coli systems biology workshop: Annual meeting in Awaji. (Awaji, Hyogo, Japan)
  • Invited
• [Presentation] Gene expression patterns in growing E. coli biofilms and macro-colonies. (2019)
  • Author(s): Xiang Zhou, Wataru Shoji and Martin Robert
  • Organizer: E. coli systems biology workshop: Annual meeting in Awaji. (Awaji, Hyogo, Japan)
• [Presentation] Patterns of metabolic gene expression within Escherichia coli biofilms and macro-colonies. (2018)
  • Author(s): Martin Robert
  • Organizer: Advances in Physics of Emergent orders in Fluctuations (APEF 2018) Tokyo, Japan
• [Presentation] Metabolic activity within Escherichia coli macrocolonies and biofilms. (2018)
  • Author(s): Xiang Zhou, Wataru Shoji and Martin Robert
  • Organizer: The 19th International Conference on Systems Biology (ICSB 2018), Lyon, France
  • Int'l Joint Research
• [Presentation] 2.Exploring spatiotemporal patterns of metabolic gene expression within E. coli biofilms and macro-colonies. (2018)
  • Author(s): Martin Robert
  • Organizer: Systems and synthetic E. coli biology: Annual meeting in Awaji.
  • Invited
• [Presentation] Connecting bacterial metabolic dynamics with biofilm structure and colony pattern formation. (2018)
  • Author(s): Martin Robert
  • Organizer: The seventh Para Limes complexity conference.
  • Int'l Joint Research
• [Presentation] Exploring metabolic function during bacterial colony pattern formation. (2017)
  • Author(s): M. Robert
  • Organizer: Systems and synthetic E. coli biology: Annual meeting in Awaji.
  • Place of Presentation: Awaji Yumebutai, Hyogo, Japan
  • Year and Date: 2017-03-15
  • Invited
• [Presentation] Metabolic activity and bacterial colony pattern formation. (2016)
  • Author(s): M. Robert
  • Organizer: Interdisciplinary application of non-linear science.
  • Place of Presentation: Kagoshima, Japan
  • Year and Date: 2016-11-03
  • Int'l Joint Research