Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley

• Published in: Cell host & microbe 2015-03, Vol.17 (3), p.392-403
• Main Authors: Bulgarelli, Davide, Garrido-Oter, Ruben, Münch, Philipp C., Weiman, Aaron, Dröge, Johannes, Pan, Yao, McHardy, Alice C., Schulze-Lefert, Paul
• Format: Article
• Language: English
• Subjects: Bacteria; Bacteria - classification; Bacteria - genetics; Cluster Analysis; Comamonadaceae; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; DNA, Ribosomal - chemistry; DNA, Ribosomal - genetics; Flavobacteriaceae; Hordeum - microbiology; Hordeum vulgare; Metagenomics; Microbiota; Molecular Sequence Data; Phylogeny; Plant Roots - microbiology; Resource; Rhizobiaceae; RNA, Ribosomal, 16S - genetics; Sequence Analysis, DNA
• ISSN: 1931-3128; 1934-6069
• DOI: 10.1016/j.chom.2015.01.011

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. [Display omitted] •A small number of bacterial families dominate the root-enriched barley microbiota•The host genotype determines the profile of a subset of community members•Functions relevant for host interactions are enriched in root-associated taxa•Genes mediating host, bacteria, and phage interactions show signs of positive selection Microbial communities inhabiting the root interior and surrounding soil contribute to plant growth. Bulgarelli et al. examine the microbiota that populates the roots of barley (Hordeum vulgare) and present evidence that integrated actions of microbe-microbe and host-microbe interactions drive root microbiota establishment through physiological processes occurring at the root-soil interface.