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

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 r...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 115; no. 28; pp. 7368 - 7373
Main Authors Walters, William A., Jin, Zhao, Youngblut, Nicholas, Wallace, Jason G., Sutter, Jessica, Zhang, Wei, González-Peña, Antonio, Peiffer, Jason, Koren, Omry, Shi, Qiaojuan, Knight, Rob, del Rio, Tijana Glavina, Tringe, Susannah G., Buckler, Edward S., Dangl, Jeffery L., Ley, Ruth E.
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 10.07.2018
National Academy of Sciences, Washington, DC (United States)
Subjects
Agronomy
BASIC BIOLOGICAL SCIENCES
Biological Sciences
Corn
field study
Flowers & plants
Genetic effects
Genotype & phenotype
Genotypes
heritability
Inbreeding
maize
Microbiomes
Microbiota
Plant growth
Plant roots
Rhizosphere
Selective breeding
soil microbiome
Soil microorganisms
Soil sciences
field study
maize
heritability
rhizosphere
soil microbiome
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Summary: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.
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USDOE
National Science Foundation (NSF)
AC02-05CH11231
USDA Agricultural Research Service
Edited by Jeffrey I. Gordon, Washington University School of Medicine in St. Louis, St. Louis, MO, and approved May 23, 2018 (received for review January 18, 2018)
Author contributions: W.A.W., Z.J., J.G.W., J.P., O.K., E.S.B., J.L.D., and R.E.L. designed research; W.A.W., Z.J., J.S., W.Z., J.P., O.K., Q.S., T.G.d.R., S.G.T., and J.L.D. performed research; W.A.W., Z.J., N.Y., J.G.W., J.S., A.G.-P., R.K., and R.E.L. analyzed data; and W.A.W., N.Y., J.G.W., J.S., and R.E.L. wrote the paper.
ISSN:0027-8424
1091-6490
1091-6490
DOI:10.1073/pnas.1800918115