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  • Perspective
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Core microbiomes for sustainable agroecosystems

Nature Plants volume 4, pages 247–257 (2018)Cite this article

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A Publisher Correction to this article was published on 14 August 2018

This article has been updated

Abstract

In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary research strategies to optimize microbiome functions in agroecosystems. Informatics now allows us to identify members and characteristics of ‘core microbiomes’, which may be deployed to organize otherwise uncontrollable dynamics of resident microbiomes. Integration of microfluidics, robotics and machine learning provides novel ways to capitalize on core microbiomes for increasing resource-efficiency and stress-resistance of agroecosystems.

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Fig. 1: Entangled webs of below-ground interactions.
Fig. 2: Managing native biomes using core microorganisms.
Fig. 3: Microbial network information for controlling microbiomes in agroecosystems.
Fig. 4: Preparing and deploying core microbiomes.
Fig. 5: Agroecosystem management.

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Change history

  • 14 August 2018

    Owing to a technical error, this Perspective was originally published without its received and accepted dates; the dates “Received: 31 December 2017; Accepted: 23 March 2018” have now been included in all versions.

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Acknowledgements

We thank Takashi Akagi and three anonymous reviewers for their insightful comments on the manuscript. This work was financially supported by JSPS KAKENHI Grant (26711026), JST PRESTO (JPMJPR16Q6), and the Funding Program for Next Generation World-Leading Researchers of Cabinet Office, the Government of Japan (GS014) to H.T, DOE Award DE-SC0016097 to KGP, and by a European Research Council Grant (335542) to E.T.K.

Author information

Author notes

  1. Yasunori Ichihashi

    Present address: RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan

Authors and Affiliations

  1. Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan

    Hirokazu Toju & Masayuki Ushio

  2. PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan

    Hirokazu Toju, Kei Hiruma, Shinji Fukuda, Masayuki Ushio, Shinji Nakaoka, Kentaro Yoshida, Ryo Sugiura & Yasunori Ichihashi

  3. Department of Biology, Stanford University, Stanford, CA, USA

    Kabir G. Peay

  4. Department of General Systems Studies, University of Tokyo, Meguro, Tokyo, Japan

    Masato Yamamichi

  5. Department of Bioresource Science, College of Agriculture, Ibaraki University, Ami, Ibaraki, Japan

    Kazuhiko Narisawa

  6. Department of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan

    Kei Hiruma

  7. Genetic Resource Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan

    Ken Naito

  8. Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan

    Shinji Fukuda

  9. Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan

    Shinji Fukuda

  10. Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan

    Shinji Fukuda

  11. Institute of Industrial Sciences, The University of Tokyo, Tokyo, Japan

    Shinji Nakaoka

  12. Graduate School of Agriculture, Kyoto University, Kyoto, Japan

    Yusuke Onoda

  13. Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, Japan

    Kentaro Yoshida

  14. Institute of Plant Sciences, University of Bern, Bern, Switzerland

    Klaus Schlaeppi

  15. Department of Agroecology and Environment, Agroscope, Zurich, Switzerland

    Klaus Schlaeppi

  16. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing, China

    Yang Bai

  17. Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Science & John Innes Centre, Beijing, China

    Yang Bai

  18. Hokkaido Agricultural Research Center, NARO (National Agriculture and Food Research Organization), Memuro, Hokkaido, Japan

    Ryo Sugiura

  19. RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan

    Yasunori Ichihashi

  20. Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan

    Kiwamu Minamisawa

  21. Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands

    E. Toby Kiers

Authors
  1. Hirokazu Toju
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  2. Kabir G. Peay
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  3. Masato Yamamichi
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  4. Kazuhiko Narisawa
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  5. Kei Hiruma
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  6. Ken Naito
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  7. Shinji Fukuda
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  8. Masayuki Ushio
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  9. Shinji Nakaoka
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  10. Yusuke Onoda
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  11. Kentaro Yoshida
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  12. Klaus Schlaeppi
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  13. Yang Bai
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  14. Ryo Sugiura
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  15. Yasunori Ichihashi
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  16. Kiwamu Minamisawa
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  17. E. Toby Kiers
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Contributions

H.T. designed the study and wrote the first draft. H.T. and E.T.K. edited the final version of the manuscript based on discussion with all the authors.

Corresponding author

Correspondence to Hirokazu Toju.

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The authors declare no competing interests.

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Toju, H., Peay, K.G., Yamamichi, M. et al. Core microbiomes for sustainable agroecosystems. Nature Plants 4, 247–257 (2018). https://doi.org/10.1038/s41477-018-0139-4

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  • DOI: https://doi.org/10.1038/s41477-018-0139-4

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