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

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.

Authors:
ORCiD logo [1];  [2];  [3]; ORCiD logo [3];  [4];  [1]
  1. Duke Univ., Durham, NC (United States). Dept. of Biology
  2. Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Biology
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Biology, Dept. of Microbiology and Immunology
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1379512
Grant/Contract Number:  
AC02-05CH11231; SC0010423
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; microbiome; plant ecology; plant genetics

Citation Formats

Wagner, Maggie R., Lundberg, Derek S., del Rio, Tijana G., Tringe, Susannah G., Dangl, Jeffery L., and Mitchell-Olds, Thomas. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. United States: N. p., 2016. Web. doi:10.1038/ncomms12151.
Wagner, Maggie R., Lundberg, Derek S., del Rio, Tijana G., Tringe, Susannah G., Dangl, Jeffery L., & Mitchell-Olds, Thomas. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. United States. doi:10.1038/ncomms12151.
Wagner, Maggie R., Lundberg, Derek S., del Rio, Tijana G., Tringe, Susannah G., Dangl, Jeffery L., and Mitchell-Olds, Thomas. Tue . "Host genotype and age shape the leaf and root microbiomes of a wild perennial plant". United States. doi:10.1038/ncomms12151. https://www.osti.gov/servlets/purl/1379512.
@article{osti_1379512,
title = {Host genotype and age shape the leaf and root microbiomes of a wild perennial plant},
author = {Wagner, Maggie R. and Lundberg, Derek S. and del Rio, Tijana G. and Tringe, Susannah G. and Dangl, Jeffery L. and Mitchell-Olds, Thomas},
abstractNote = {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.},
doi = {10.1038/ncomms12151},
journal = {Nature Communications},
issn = {2041-1723},
number = ,
volume = 7,
place = {United States},
year = {2016},
month = {7}
}

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Cited by: 80 works
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Works referenced in this record:

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006

  • DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
  • Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
  • DOI: 10.1128/AEM.03006-05