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

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.

Keywords: commensalism; microbiota; phylogenomics; plant immunity; rhizobiales; symbiosis.

Graphical abstract

Figure 1

Conserved Microbiota Membership of the Bacterial Order Rhizobiales Analysis of Rhizobiales community diversity using data from five previous 16S rRNA gene amplicon surveys covering root, rhizosphere, and nodule samples of a taxonomically diverse panel of plant hosts grown in a variety of natural and agricultural soils. (A) Aggregated relative abundances of Rhizobiales in each host and compartment (n = 453). Percentages show the average contribution of Rhizobiales to each subset of samples. (B) Analysis of beta-diversity of Rhizobiales between samples across hosts and compartments (indicated by different colors and shapes, respectively). Dashed lines correspond to a Gaussian distribution fitted to each cluster (95% confidence interval). See also Figures S1 and S2 and Tables S1 and S2.

Figure 2

Convergent Evolution of Nitrogen-Fixing Symbiosis in Rhizobiales Phylogenetic tree of rhizobia and maximum likelihood reconstruction of ancestral symbiotic genotypes. Phylogenetic tree of sequenced isolates (n = 1,314) inferred from aligned single-copy marker genes using a Bayesian approach. Different taxonomic groups are indicated by the various colors in the first ring. The second ring depicts newly sequenced isolates in gray (n = 944). Green branches correspond to likely gains of symbiosis genes whereas those in red correspond to probable losses. See also Figures S2 and S3 and Table S1.

Figure 3

Conserved Rhizobiales Root Growth Promotion Activity in Arabidopsis thaliana Binary interaction experiments between isolates from Rhizobiales or sister lineages and germ-free A. thaliana wild-type plants (Col-0) grown on agarose media. Macroscopic plant phenotypes after co-cultivation on agarose media containing individual isolates were recorded after 3 weeks. (A) Primary root length relative to mock control for each treatment as well as an additional heat-killed bacteria control (n = 1,487). (B) Shoot fresh weight relative to mock control for each treatment and a heat-killed bacteria control (n = 247). Different shapes depict data points from seven separate full-factorial replicates. Asterisks indicate statistical significance corresponding to a Dunnett's test with false discovery rate correction (α = 0.05). See also Figures S4 and S5 and Table S4.

Figure 4

Interference with Root Meristem Homeostasis by Rhizobium 129E (A) Confocal micrographs in the meristematic zone (MZ) (indicated by dotted lines) of the roots of transgenic A. thaliana (Wave_131Y) expressing a plasma membrane-targeted yellow fluorescent protein inoculated with 129E or with a mock control. Arrowheads indicate the place of transition from cell division to cell elongation. Bars correspond to 50 μm. (B) Number of cells within the MZ was recorded with primary root length at 5, 10, 14, 19, and 27 days post inoculation (n = 65). Shaded areas indicate means ±SD. Letters indicate statistical significance corresponding to Tukey's HSD test (α = 0.05) and asterisks highlight significant difference between mock and Rhizobium 129E-treated roots within each time point. See also Figure S6 and Table S4.

Figure 5

Transcriptional Interference with MAMP-Triggered Responses (A) Time course measurement of primary root growth under high P_i (625 μM) and low P_i (50 μM) conditions (n = 2,323). Letters indicate statistical significance corresponding to Tukey's HSD test corrected for multiple comparisons (α = 0.05). (B) Heatmaps showing expression level (log₂ counts per million; log2cpm), expression pattern (gene-wise median-centered Z scores), response to Rhizobium 129E (log₂ fold changes; logFC; green and magenta colors indicate up- and downregulation, respectively) and significance (false discovery rate-corrected p values <0.05). Co-expressed gene clusters (cluster) are defined by k-means clustering (k = 21). (C) Enrichment analysis of the clusters 1, 15, 13, and 6 identified defense-related gene ontology categories. Gene numbers used for the analysis are shown in parentheses. (D) Comparison of plant responses to Rhizobium 129E at 16 days post inoculation and to chronic 1 μM flg22 treatment for 12 days (Castrillo et al., 2017). DEG, differentially expressed genes. Asterisks indicate statistical significance corresponding to one sample t test (μ = 0) with Bonferroni's correction for multiple comparisons (α = 0.05). See also Figure S4 and Tables S4 and S5.

Figure 6

Root Commensals Interfere with MAMP-Triggered Growth Outputs (A) FLAGELLIN SENSITIVE2 (FLS2)-dependent root growth inhibition induced by chronic exposure to 1 μM flg22 for 14 days was repressed by inoculation with Rhizobium 129E (n = 302). (B) The ability to interfere with flg22-induced root growth inhibition is specific to Rhizobium 129E and Sphingomonadales 1497 (n = 1,424). Root growth promotion activity of the other Rhizobiales isolates was abolished in wild-type plants but not in the mutant lacking the flg22 receptor protein FLS2. Open (left boxplots) and closed shapes (right boxplots) within each condition indicate mock and flg22 treatment (1 μM), respectively. Letters indicate statistical significance corresponding to Tukey's HSD test corrected for multiple comparisons (α = 0.05). Different shapes depict data points from full-factorial biological replicates. See also Figure S7 and Table S4.

Figure 7

Modularity of Commensal Root Growth Promotion and Interference with MAMP Responses Primary root growth under binary and tripartite inoculations was measured in the presence and absence of 1 μM flg22 (n = 1,219). Functional profiles of tested isolates are summarized on the left. Individual isolates or combinations of isolates were mono- or co-inoculated with germ-free A. thaliana. Inoculated isolates are depicted in the bottom table with colors. Left and right boxplots within each condition with open and closed shapes indicate mock and flg22 treatments, respectively. Different shapes depict data points from full-factorial biological replicates. Letters indicate statistical significance corresponding to Tukey's HSD test corrected for multiple comparisons (α = 0.05). See also Figure S7 and Table S4.