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

Abstract

Up until now, 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.

Authors:
 [1];  [2];  [1];  [3];  [1];  [2];  [4];  [2]; ORCiD logo [5];  [2];  [6];  [7]; ORCiD logo [7]; ORCiD logo [8];  [9];  [10]
  1. Max Planck Institute for Developmental Biology, Tubingen (Germany)
  2. Cornell Univ., Ithaca, NY (United States)
  3. Univ. of Georgia, Athens, GA (United States)
  4. Univ. of California, San Diego, La Jolla, CA (United States)
  5. Cornell Univ., Ithaca, NY (United States); Bar Ilan Univ., Safed (Israel)
  6. Univ. of Georgia, Athens, GA (United States); Univ. of California, San Diego, La Jolla, CA (United States)
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  8. United States Dept. of Agriculture - Agricultural Research Service, Ithaca, NY (United States); Cornell Univ., Ithaca, NY (United States)
  9. Univ. of North Carolina, Chapel Hill, NC (United States)
  10. Max Planck Institute for Developmental Biology, Tubingen (Germany); Cornell Univ., Ithaca, NY (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE; National Science Foundation (NSF); USDA Agricultural Research Service
OSTI Identifier:
1482534
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 115; Journal Issue: 28; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; maize; rhizosphere; soil microbiome; heritability; field study

Citation Formats

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, Glavina del Rio, Tijana, Tringe, Susannah G., Buckler, Edward S., Dangl, Jeffery L., and Ley, Ruth E. Large-scale replicated field study of maize rhizosphere identifies heritable microbes. United States: N. p., 2018. Web. doi:10.1073/pnas.1800918115.
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, Glavina del Rio, Tijana, Tringe, Susannah G., Buckler, Edward S., Dangl, Jeffery L., & Ley, Ruth E. Large-scale replicated field study of maize rhizosphere identifies heritable microbes. United States. doi:10.1073/pnas.1800918115.
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, Glavina del Rio, Tijana, Tringe, Susannah G., Buckler, Edward S., Dangl, Jeffery L., and Ley, Ruth E. Mon . "Large-scale replicated field study of maize rhizosphere identifies heritable microbes". United States. doi:10.1073/pnas.1800918115. https://www.osti.gov/servlets/purl/1482534.
@article{osti_1482534,
title = {Large-scale replicated field study of maize rhizosphere identifies heritable microbes},
author = {Walters, William A. and Jin, Zhao and Youngblut, Nicholas and Wallace, Jason G. and Sutter, Jessica and Zhang, Wei and González-Peña, Antonio and Peiffer, Jason and Koren, Omry and Shi, Qiaojuan and Knight, Rob and Glavina del Rio, Tijana and Tringe, Susannah G. and Buckler, Edward S. and Dangl, Jeffery L. and Ley, Ruth E.},
abstractNote = {Up until now, 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.},
doi = {10.1073/pnas.1800918115},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
issn = {0027-8424},
number = 28,
volume = 115,
place = {United States},
year = {2018},
month = {6}
}

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Works referenced in this record:

Maize association population: a high-resolution platform for quantitative trait locus dissection
journal, November 2005