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Core microbiomes for sustainable agroecosystems

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

This article has been updated


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.

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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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.

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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.

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Correspondence to Hirokazu Toju.

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Toju, H., Peay, K.G., Yamamichi, M. et al. Core microbiomes for sustainable agroecosystems. Nature Plants 4, 247–257 (2018).

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