Core microbiomes for sustainable agroecosystems

Hirokazu Toju^{1

2}, Kabir G Peay³, Masato Yamamichi⁴, Kazuhiko Narisawa⁵, Kei Hiruma^{6

7}, Ken Naito⁸, Shinji Fukuda^{6

9

10

11}, Masayuki Ushio^{12

6}, Shinji Nakaoka^{6

13}, Yusuke Onoda¹⁴, Kentaro Yoshida^{6

15}, Klaus Schlaeppi^{16

17}, Yang Bai^{18

19}, Ryo Sugiura^{6

20}, Yasunori Ichihashi^{6

21

22}, Kiwamu Minamisawa²³, E Toby Kiers²⁴

Affiliations

¹ Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan. toju.hirokazu.4c@kyoto-u.ac.jp.
² PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan. toju.hirokazu.4c@kyoto-u.ac.jp.
³ Department of Biology, Stanford University, Stanford, CA, USA.
⁴ Department of General Systems Studies, University of Tokyo, Meguro, Tokyo, Japan.
⁵ Department of Bioresource Science, College of Agriculture, Ibaraki University, Ami, Ibaraki, Japan.
⁶ PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
⁷ Department of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan.
⁸ Genetic Resource Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan.
⁹ Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.
¹⁰ Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan.
¹¹ Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan.
¹² Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan.
¹³ Institute of Industrial Sciences, The University of Tokyo, Tokyo, Japan.
¹⁴ Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
¹⁵ Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, Japan.
¹⁶ Institute of Plant Sciences, University of Bern, Bern, Switzerland.
¹⁷ Department of Agroecology and Environment, Agroscope, Zurich, Switzerland.
¹⁸ State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing, China.
¹⁹ Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Science & John Innes Centre, Beijing, China.
²⁰ Hokkaido Agricultural Research Center, NARO (National Agriculture and Food Research Organization), Memuro, Hokkaido, Japan.
²¹ RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.
²² RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan.
²³ Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan.
²⁴ Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.

PMID: 29725101
DOI: 10.1038/s41477-018-0139-4

Review

Core microbiomes for sustainable agroecosystems

Hirokazu Toju et al. Nat Plants. 2018 May.

. 2018 May;4(5):247-257.

doi: 10.1038/s41477-018-0139-4.

Authors

Affiliations

¹ Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan. toju.hirokazu.4c@kyoto-u.ac.jp.
² PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan. toju.hirokazu.4c@kyoto-u.ac.jp.
³ Department of Biology, Stanford University, Stanford, CA, USA.
⁴ Department of General Systems Studies, University of Tokyo, Meguro, Tokyo, Japan.
⁵ Department of Bioresource Science, College of Agriculture, Ibaraki University, Ami, Ibaraki, Japan.
⁶ PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
⁷ Department of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan.
⁸ Genetic Resource Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan.
⁹ Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.
¹⁰ Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan.
¹¹ Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan.
¹² Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan.
¹³ Institute of Industrial Sciences, The University of Tokyo, Tokyo, Japan.
¹⁴ Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
¹⁵ Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, Japan.
¹⁶ Institute of Plant Sciences, University of Bern, Bern, Switzerland.
¹⁷ Department of Agroecology and Environment, Agroscope, Zurich, Switzerland.
¹⁸ State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing, China.
¹⁹ Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Science & John Innes Centre, Beijing, China.
²⁰ Hokkaido Agricultural Research Center, NARO (National Agriculture and Food Research Organization), Memuro, Hokkaido, Japan.
²¹ RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.
²² RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan.
²³ Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan.
²⁴ Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.

PMID: 29725101
DOI: 10.1038/s41477-018-0139-4

Erratum in

Publisher Correction: Core microbiomes for sustainable agroecosystems.
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. Toju H, et al. Nat Plants. 2018 Sep;4(9):733. doi: 10.1038/s41477-018-0245-3. Nat Plants. 2018. PMID: 30108297

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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Core microbiomes for sustainable agroecosystems

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Core microbiomes for sustainable agroecosystems

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