Research priorities for harnessing plant microbiomes in sustainable agriculture

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Busby, Posy E.
- ORCID: 0000-0002-2837-9820
- Other Affiliation: Department of Botany and Plant Pathology; Oregon State University
Soman, Chinmay
- Other Affiliation: Department of Natural Resources and Environmental Sciences; University of Illinois at Urbana Champaign
Wagner, Maggie R.
- Other Affiliation: Department of Plant Pathology; North Carolina State University
Friesen, Maren L.
- Other Affiliation: Department of Plant Biology; Michigan State University
Kremer, James
- Other Affiliation: MSU-DOE Plant Research Laboratory; Michigan State University
Bennett, Alison
- Other Affiliation: The James Hutton Institute
Morsy, Mustafa
- Other Affiliation: College of Natural Sciences and Mathematics; University of West Alabama
Eisen, Jonathan A.
- Other Affiliation: Genome Center; University of California
Leach, Jan E.
- Other Affiliation: Bioagricultural Sciences and Pest Management; Colorado State University
Dangl, Jeffery L.
- Affiliation: College of Arts and Sciences, Department of Biology

Abstract

Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is to integrate beneficial plant microbiomes—i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance—into agricultural production. This integration will require a large-scale effort among academic researchers, industry researchers, and farmers to understand and manage plant-microbiome interactions in the context of modern agricultural systems. Here, we identify priorities for research in this area: (1) develop model host–microbiome systems for crop plants and non-crop plants with associated microbial culture collections and reference genomes, (2) define core microbiomes and metagenomes in these model systems, (3) elucidate the rules of synthetic, functionally programmable microbiome assembly, (4) determine functional mechanisms of plant-microbiome interactions, and (5) characterize and refine plant genotype-by-environment-by-microbiome-by-management interactions. Meeting these goals should accelerate our ability to design and implement effective agricultural microbiome manipulations and management strategies, which, in turn, will pay dividends for both the consumers and producers of the world food supply.

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