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Emerging strategies for precision microbiome management in diverse agroecosystems

Abstract

Substantial efforts to characterize the structural and functional diversity of soil, plant and insect-associated microbial communities have illuminated the complex interacting domains of crop-associated microbiomes that contribute to agroecosystem health. As a result, plant-associated microorganisms have emerged as an untapped resource for combating challenges to agricultural sustainability. However, despite growing interest in maximizing microbial functions for crop production, resource efficiency and stress resistance, research has struggled to harness the beneficial properties of agricultural microbiomes to improve crop performance. Here, we introduce the historical arc of agricultural microbiome research, highlighting current progress and emerging strategies for intentional microbiome manipulation to enhance crop performance and sustainability. We synthesize current practices and limitations to managing agricultural microbiomes and identify key knowledge gaps in our understanding of microbe-assisted crop production. Finally, we propose research priorities that embrace a holistic view of crop microbiomes for achieving precision microbiome management that is tailored, predictive and integrative in diverse agricultural systems.

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Fig. 1: The major sectors of crop-associated microbial communities (soil, plant and insect) are shaped by key agricultural practices.
Fig. 2: The future of microbiome-informed management requires integration of management practices, host-specific factors and customized microbial biotechnology.
Fig. 3: Third-generation microbiome management will be tailored across different farming systems, use predictive analytics to optimize management, and integrate across management, microbial biotechnology and host genetics.

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Acknowledgements

We thank L. Hoagland for her comments and guidance during the preparation of the manuscript, Purdue Entomology Women’s Writing Group for continued support, motivation and accountability, and funding provided by Purdue University through the 2019 Elevating the Visibility of Agricultural Research: 150th Anniversary Review program.

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E.F. and L.E. conceived and wrote the manuscript. A.I.-P., I.K. and C.H.N. provided conceptual guidance, contributed the body of literature reviewed and edited the manuscript.

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French, E., Kaplan, I., Iyer-Pascuzzi, A. et al. Emerging strategies for precision microbiome management in diverse agroecosystems. Nat. Plants 7, 256–267 (2021). https://doi.org/10.1038/s41477-020-00830-9

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