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PLoS Biol. 2017 Mar 28;15(3):e2001793. doi: 10.1371/journal.pbio.2001793. eCollection 2017 Mar.

Research priorities for harnessing plant microbiomes in sustainable agriculture.

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Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.
Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America.
Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America.
Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America.
Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, United States of America.
MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America.
The James Hutton Institute, Invergowrie, Dundee, Scotland.
College of Natural Sciences and Mathematics, University of West Alabama, Livingston, Alabama, United States of America.
Genome Center, University of California, Davis, California, United States of America.
Bioagricultural Sciences and Pest Management, Colorado State University, Ft Collins, Colorado, United States of America.
Howard Hughes Medical Institute, Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.


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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