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Cell Host Microbe. 2015 Mar 11;17(3):392-403. doi: 10.1016/j.chom.2015.01.011. Epub 2015 Feb 26.

Structure and function of the bacterial root microbiota in wild and domesticated barley.

Author information

  • 1Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK.
  • 2Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Department of Algorithmic Bioinformatics, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
  • 3Department of Algorithmic Bioinformatics, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany.
  • 4Department of Algorithmic Bioinformatics, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
  • 5Department of Algorithmic Bioinformatics, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany. Electronic address: alice.mchardy@helmholtz-hzi.de.
  • 6Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany. Electronic address: schlef@mpipz.mpg.de.

Abstract

The microbial communities inhabiting the root interior of healthy plants, as well as the rhizosphere, which consists of soil particles firmly attached to roots, engage in symbiotic associations with their host. To investigate the structural and functional diversification among these communities, we employed a combination of 16S rRNA gene profiling and shotgun metagenome analysis of the microbiota associated with wild and domesticated accessions of barley (Hordeum vulgare). Bacterial families Comamonadaceae, Flavobacteriaceae, and Rhizobiaceae dominate the barley root-enriched microbiota. Host genotype has a small, but significant, effect on the diversity of root-associated bacterial communities, possibly representing a footprint of barley domestication. Traits related to pathogenesis, secretion, phage interactions, and nutrient mobilization are enriched in the barley root-associated microbiota. Strikingly, protein families assigned to these same traits showed evidence of positive selection. Our results indicate that the combined action of microbe-microbe and host-microbe interactions drives microbiota differentiation at the root-soil interface.

PMID:
25732064
PMCID:
PMC4362959
DOI:
10.1016/j.chom.2015.01.011
[PubMed - indexed for MEDLINE]
Free PMC Article
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