Host genotype and age shape the leaf and root microbiomes of a wild perennial plant

Maggie R. Wagner (), Derek S Lundberg, Tijana G. del Rio, Susannah G. Tringe, Jeffery L. Dangl and Thomas Mitchell-Olds
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Maggie R. Wagner: Program in Genetics and Genomics, Duke University
Derek S Lundberg: Curriculum in Genetics and Molecular Biology, Carolina Center for Genome Sciences, University of North Carolina
Tijana G. del Rio: Department of Energy Joint Genome Institute
Susannah G. Tringe: Department of Energy Joint Genome Institute
Jeffery L. Dangl: Curriculum in Genetics and Molecular Biology, Carolina Center for Genome Sciences, University of North Carolina
Thomas Mitchell-Olds: Program in Genetics and Genomics, Duke University

Nature Communications, 2016, vol. 7, issue 1, 1-15

Abstract: Abstract Bacteria living on and in leaves and roots influence many aspects of plant health, so the extent of a plant’s genetic control over its microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies, because they poorly simulate true environmental heterogeneity, may misestimate or totally miss the influence of certain host genes on the microbiome. Here we report a large-scale field experiment to disentangle the effects of genotype, environment, age and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta (Brassicaceae), a perennial wild mustard. Host genetic control of the microbiome is evident in leaves but not roots, and varies substantially among sites. Microbiome composition also shifts as plants age. Furthermore, a large proportion of leaf bacterial groups are shared with roots, suggesting inoculation from soil. Our results demonstrate how genotype-by-environment interactions contribute to the complexity of microbiome assembly in natural environments.

Date: 2016
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DOI: 10.1038/ncomms12151

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