Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia

Cell Host & Microbe
Ruben Garrido-OterPaul Schulze-Lefert

Abstract

Rhizobia are a paraphyletic group of soil-borne bacteria that induce nodule organogenesis in legume roots and fix atmospheric nitrogen for plant growth. In non-leguminous plants, species from the Rhizobiales order define a core lineage of the plant microbiota, suggesting additional functional interactions with plant hosts. In this work, genome analyses of 1,314 Rhizobiales isolates along with amplicon studies of the root microbiota reveal the evolutionary history of nitrogen-fixing symbiosis in this bacterial order. Key symbiosis genes were acquired multiple times, and the most recent common ancestor could colonize roots of a broad host range. In addition, root growth promotion is a characteristic trait of Rhizobiales in Arabidopsis thaliana, whereas interference with plant immunity constitutes a separate, strain-specific phenotype of root commensal Alphaproteobacteria. Additional studies with a tripartite gnotobiotic plant system reveal that these traits operate in a modular fashion and thus might be relevant to microbial homeostasis in healthy roots.

Citations

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Datasets Mentioned

BETA
GSE87336

Methods Mentioned

BETA
transgenic
PCR
RNA-seq
Illumina sequencing
Amplicon Sequencing

Software Mentioned

RNAmmer
R
Hierarchical Genome Assembly Process ( HGAP ) assembler
UCHIME
QIIME
hmmsearch
Trimmomatic
Clustal Omega
compareCluster
edgeR R package

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