Large-scale replicated field study of maize rhizosphere identifies heritable microbes

William A. Walters, Zhao Jin, Nicholas Youngblut, Jason G. Wallace, Jessica Sutter, Wei Zhang, Antonio González-Peña, Jason Peiffer, Omry Koren, Qiaojuan Shi, Rob Knight, Tijana Glavina Del Rio, Susannah G. Tringe, Edward S. Buckler, Jeffery L. Dangl, Ruth E. Ley

Research output: Contribution to journalArticlepeer-review

398 Scopus citations

Abstract

Soil microbes that colonize plant roots and are responsive to differences in plant genotype remain to be ascertained for agronomically important crops. From a very large-scale longitudinal field study of 27 maize inbred lines planted in three fields, with partial replication 5 y later, we identify root-associated microbiota exhibiting reproducible associations with plant genotype. Analysis of 4,866 samples identified 143 operational taxonomic units (OTUs) whose variation in relative abundances across the samples was significantly regulated by plant genotype, and included five of seven core OTUs present in all samples. Plant genetic effects were significant amid the large effects of plant age on the rhizosphere microbiome, regardless of the specific community of each field, and despite microbiome responses to climate events. Seasonal patterns showed that the plant root microbiome is locally seeded, changes with plant growth, and responds to weather events. However, against this background of variation, specific taxa responded to differences in host genotype. If shown to have beneficial functions, microbes may be considered candidate traits for selective breeding.

Original languageEnglish
Pages (from-to)7368-7373
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume115
Issue number28
DOIs
StatePublished - 10 Jul 2018

Bibliographical note

Publisher Copyright:
© 2018 National Academy of Sciences. All rights reserved.

Funding

We thank Sherry Flint-Garcia, Stephen Moose, Ayme Spor, and Lynn Marie Johnson for assistance. This work was supported by NSF Inspire Track II Grants IOS-1343020 (to R.E.L. and J.L.D.), IOS-0958184 (to R.E.L.), and IOS-0958245 (to J.L.D.). Support was provided by the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation (J.L.D.), NSF Grants IOS-0820619 and IOS-1238014 (to J.P., J.G.W., and E.S.B.), the United States Department of Agriculture Agricultural Research Service (E.S.B.), the University of Georgia (J.G.W.), the David and Lucile Packard Foundation, and the Max Planck Society (R.E.L. and W.A.W.). This work was funded by the Joint Genome Institute (JGI) Director’s Discretionary Grand Challenge Program. Work conducted by the US Department of Energy (DOE) JGI, a DOE Office of Science User Facility, is supported by the Office of Science of the US DOE under Contract DE-AC02-05CH11231. ACKNOWLEDGMENTS. We thank Sherry Flint-Garcia, Stephen Moose, Ayme Spor, and Lynn Marie Johnson for assistance. This work was supported by NSF Inspire Track II Grants IOS-1343020 (to R.E.L. and J.L.D.), IOS-0958184 (to R.E.L.), and IOS-0958245 (to J.L.D.). Support was provided by the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation (J.L.D.), NSF Grants IOS-0820619 and IOS-1238014 (to J.P., J.G.W., and E.S.B.), the United States Department of Agriculture Agricultural Research Service (E.S.B.), the University of Georgia (J.G.W.), the David and Lucile Packard Foundation, and the Max Planck Society (R.E.L. and W.A.W.). This work was funded by the Joint Genome Institute (JGI) Director’s Discretionary Grand Challenge Program. Work conducted by the US Department of Energy (DOE) JGI, a DOE Office of Science User Facility, is supported by the Office of Science of the US DOE under Contract DE-AC02-05CH11231.

FundersFunder number
DOE Office of Science
Joint Genome Institute
Office of Science of the US DOE
US Department of Energy
United States Department of Agriculture Agricultural Research Service
National Science FoundationIOS-0958184, IOS-0958245, IOS-1343020
David and Lucile Packard Foundation
Howard Hughes Medical Institute
U.S. Department of Energy
Directorate for Biological Sciences1343020, 1238014, 0958245, 0958184, 0820619
U.S. Department of Agriculture
Gordon and Betty Moore FoundationIOS-0820619, IOS-1238014
National Sleep Foundation
Office of ScienceDE-AC02-05CH11231
University of Georgia
Max-Planck-Gesellschaft

    Keywords

    • Field study
    • Heritabilit
    • Maize
    • Rhizosphere
    • Soil microbiome

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