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RIKEN Center for Sustainable Resource Science Plant Symbiosis Research Team

Team Leader: Makoto Hayashi (Ph.D.)

Research Summary

Makoto  Hayashi(Ph.D.)

Nitrogen is the most heavily used fertilizer in the present agriculture. Its production and use however damage the ecosystem due to the emission of greenhouse gases. Soil bacteria called rhizobia infect legume roots, and fix atmospheric nitrogen in root nodules. Consequently, if cereals such as rice, corn and wheat establish symbiosis with rhizobia, we can dramatically reduce the use of nitrogen fertilizer, resulted in ecosystem-friendly, sustainable agriculture. In order to achieve our goal, we aim to confer the ability to fix nitrogen on cereals, by elucidating molecular-genetic and biochemical functions of nodulation and symbiotic nitrogen fixation, as well as by investigating evolutionary aspects of legume-rhizobia symbiosis.

Main Research Fields

  • Biology

Related Research Fields

  • Agricultural Sciences


  • Plant-microbe interaction/Symbiosis
  • Biological interaction

Selected Publications

  • 1. Ichihashi Y, Hakoyama T, Iwase A, Shirasu K, Sugimoto K, Hayashi M.:
    "Common Mechanisms of Developmental Reprogramming in Plants—Lessons from Regeneration, Symbiosis, and Parasitism"
    Front. Plant Sci. 11: 1084 (2020).
  • 2. Ichihashi Y, Date Y, Shino A, Shimizu T, Shibata A, Kumaishi K, Funahashi F, Wakayama K, Yamazaki K, Umezawa A, Sato T, Kobayashi M, Kamimura M, Kusano M, Che FS, O Brien M, Tanoi K, Hayashi M, Nakamura R, Shirasu K, Kikuchi J, Nihei N.:
    "Multi-omics analysis on an agroecosystem reveals the significant role of organic nitrogen to increase agricultural crop yield"
    Proc. Natl. Acad. Sci. USA 117: 14552-14560 (2020).
  • 3. Shimoda Y, Nishigaya Y, Yamaya-Ito H, Inagaki N, Umehara Y, Hirakawa H, Sato S, Yamazaki T, Hayashi M.:
    "The rhizobial autotransporter determines the symbiotic nitrogen fixation activity of Lotus japonicus in a host-specific manner"
    Proc. Natl. Acad. Sci. USA 117: 1806-1815 (2020).
  • 4. Soyano T, Shimoda Y, Kawaguchi M, Hayashi M.:
    "A shared gene drives lateral root development and root nodule symbiosis pathways in Lotus"
    Science 366: 1021-1023 (2019).
  • 5. Shimoda Y, Imaizumi-Anraku H, Hayashi M.:
    "Kinase activity-dependent stability of calcium/calmodulin-dependent protein kinase of Lotus japonicus"
    Planta 250: 1773-1779 (2019).
  • 6. Liu M, Soyano T, Yano K, Hayashi M, Kawaguchi M.:
    "ERN1 and CYCLOPS coordinately activate NIN signaling to promote infection thread formation in Lotus japonicus"
    J. Plant Res. 132: 641-653 (2019).
  • 7. Sogawa A, Yamazaki A, Yamasaki H, Komi M, Manabe T, Tajima S, Hayashi M, Nomura M.:
    "SNARE Proteins LjVAMP72a and LjVAMP72b Are Required for Root Symbiosis and Root Hair Formation in Lotus japonicus"
    Front. Plant Sci. 9: 1992 (2019).
  • 8. Sugimoto K, Xu L, Paszkowski U, Hayashi M.:
    "Multifaceted Cellular Reprogramming at the Crossroads Between Plant Development and Biotic Interactions"
    Plant Cell Physiol. 59: 651-655 (2018).
  • 9. Yamaya-Ito H, Shimoda Y, Hakoyama T, Sato S, Kaneko T, Hossain MS, Shibata S, Kawaguchi M, Hayashi M, Kouchi H, Umehara Y.:
    "Loss-of-function of ASPARTIC PEPTIDASE NODULE- INDUCED 1 (APN1) in Lotus japonicus restricts efficient nitrogen-fixing symbiosis with specific Mesorhizobium loti strains"
    Plant J. 93: 5-16 (2018).
  • 10. Shimomura A, Arima S, Hayashi M, Maymon M, Hirsh AM, Suzuki A.:
    "Blue light does not inhibit nodulation in Sesbania rostrata"
    Plant Signal. Behav. 12: e1268313 (2017).

Recent Research Results

Related Links

Lab Members

Principal investigator

Makoto Hayashi
Team Leader

Core members

Tsuneo Hakoyama
Research Scientist
Akihiro Yamazaki
Research Scientist
Kai Battenberg / Kai Tsujii
Postdoctoral Researcher
Teruki Sugiyama
Postdoctoral Researcher
Atsuko Hirota
Technical Staff I
Shouko Yamazaki
Technical Staff II

Contact Information

1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama City, Kanagawa,
230-0045, Japan
Tel: +81-(0)45-503-9493
Fax: +81-(0)45-503-9492

Email: makoto.hayashi [at] riken.jp