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RIKEN BioResource Research Center (BRC®) Plant-Microbe Symbiosis Research and Development Team

Team Leader: Yasunori Ichihashi (Ph.D.)

Research Summary

Yasunori  Ichihashi(Ph.D.)

Since most agricultural crops grow in soil, where is one of the richest microbial ecosystems on Earth, plants and microbes are strongly associated with each other. Elucidation of the plant-microbe symbiosis should contribute to building a sustainable solution for world food and environmental problems. Our team will develop the "Agricultural Digital Twin", which is a system that simulates agroecosystems in cyberspace, and the "Symbiotic Microorganism Resource", which is a solution for engineering agriculture. Through collaborative researches with domestic and international communities, we aim to fully understand regulatory mechanism behind the plant-microbe symbiosis and provide a research platform leading to industrial applications.

Main Research Fields

  • Biology

Related Research Fields

  • Agricultural Sciences
  • Complex Systems

Keywords

  • Plant-Microbe Symbiosis
  • Multi-omics
  • Agricultural Digital Twin
  • Symbiotic Microorganism Resource
  • Green Digital Transformation

Selected Publications

  • 1. Miyamoto H, Shigeta K, Suda W, Ichihashi Y, Nihei N, Matsuura M, Tsuboi A, Tominaga N, Aono M, Sato M, Taguchi S, Nakaguma T, Tsuji N, Ishii C, Matsushita T, Shindo C, Ito T, Kato T, Kurotani A, Shima H, Moriya S, Wada S, Horiuchi S, Satoh T, Mori K, Nishiuchi T, Miyamoto H, Kodama H, Hattori M, Ohno H, Kikuchi J, Yokota Hirai M.:
    "An agroecological structure model of compost – soil - plant interactions for sustainable organic farming"
    ISME COMMUN. 3, 28 (2023)
  • 2. Fujiwara F, Miyazawa K, Nihei N, Ichihashi Y.:
    "Agroecosystem Engineering Extended from Plant-Microbe Interactions Revealed by Multi-Omics Data"
    Bioscience, Biotechnology, and Biochemistry 87(1), 21-27 (2023)
  • 3. Dang T, Kumaishi K, Usui E, Kobori S, Sato T, Toda Y, Yamasaki Y, Tsujimoto H, Ichihashi Y, Iwata H.:
    "Stochastic variational variable selection for high-dimensional microbiome data"
    Microbiome 10(1), 236 (2022)
  • 4. Kumaishi K, Usui E, Suzuki K, Kobori S, Sato T, Toda Y, Takanashi H, Shinozaki S, Noda M, Takakura A, Matsumoto K, Yamasaki Y, Tsujimoto H, Iwata H, Ichihashi Y.:
    "High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profiling"
    Sci. Rep. 12, 19289 (2022)
  • 5. Choi SW, Kumaishi K, Motohashi R, Enoki H, Chacuttayapong W, Takamizo T, Saika H, Endo E, Yamada T, Hirose A, Koizuka N, Kimura S, Kawakatsu Y, Koga H, Ito E, Shirasu K, Ichihashi Y.:
    "Oxicam-type nonsteroidal anti-inflammatory drugs enhance Agrobacterium-mediated transient transformation in plants"
    Plant Biotechnology 39(3), 323-327 (2022)
  • 6. Fujii T, Minami M, Watanabe T, Sato Takumi Kumaishi K, Ichihashi Y.:
    "Characterization of inter-annual changes in soil microbial lora of Panax ginseng cultivation fields in Shimane Prefecture of Western Japan by DNA metabarcoding using next-generation sequencing"
    J. Nat. Med. 75, 1067–1079 (2021)
  • 7. 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 F-S, 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(25), 14552-14560 (2020)
  • 8. Notaguchi M, Kurotani K, Sato Y, Tabata R, Kawakatsu Y, Okayasu K, Sawai Y, Okada R, Asahina M, Ichihashi Y, Shirasu K, Suzuki T, Niwa M, Higashiyama T.:
    "Cell–cell adhesion in plant grafting is facilitated by β-1,4-glucanases"
    Science 369(6504), 698-702 (2020)
  • 9. Toju H, Peay KG, Yamamichi M, Narisawa K, Hiruma K, Naito K, Fukuda S, Ushio M, Nakaoka S, Onoda Y, Yoshida K, Schlaeppi K, Bai Y, Sugiura R, Ichihashi Y, Minamisawa K, Kiers ET.:
    "Core microbiomes for sustainable agroecosystems"
    Nat. Plants 4, 247-257 (2018)
  • 10. Ichihashi Y, Fukushima A, Shibata A, Shirasu K.:
    "High Impact Gene Discovery: Simple Strand-Specific mRNA Library Construction and Differential Regulatory Analysis Based on Gene Co-Expression Network"
    Methods Mol. Biol. 1830, 163-189 (2018)

Recent Research Results

Related Links

Lab Members

Principal investigator

Yasunori Ichihashi
Team Leader

Core members

Megumi Narukawa
Research & Development Scientist
Shuhei Yabe
Research & Development Scientist
Shinichi Yamazaki
Postdoctoral Researcher
Nao Okuma
Special Postdoctoral Researcher
Kie Kumaishi
Technical Staff II
Yui Nose
Technical Staff II
Fuki Fujiwara
Junior Research Associate

Contact Information

BioResource Center Main Building
3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
Email: yasunori.ichihashi [at] riken.jp

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