Rhizosphere microbiome assemblage is affected by plant development

Abstract

There is a concerted understanding of the ability of root exudates to influence the structure of rhizosphere microbial communities. However, our knowledge of the connection between plant development, root exudation and microbiome assemblage is limited. Here, we analyzed the structure of the rhizospheric bacterial community associated with Arabidopsis at four time points corresponding to distinct stages of plant development: seedling, vegetative, bolting and flowering. Overall, there were no significant differences in bacterial community structure, but we observed that the microbial community at the seedling stage was distinct from the other developmental time points. At a closer level, phylum such as Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and specific genera within those phyla followed distinct patterns associated with plant development and root exudation. These results suggested that the plant can select a subset of microbes at different stages of development, presumably for specific functions. Accordingly, metatranscriptomics analysis of the rhizosphere microbiome revealed that 81 unique transcripts were significantly (P<0.05) expressed at different stages of plant development. For instance, genes involved in streptomycin synthesis were significantly induced at bolting and flowering stages, presumably for disease suppression. We surmise that plants secrete blends of compounds and specific phytochemicals in the root exudates that are differentially produced at distinct stages of development to help orchestrate rhizosphere microbiome assemblage.

Figure 1

Multivariate analyses of the rhizosphere microbial community through plant development analyzed by 454 pyrosequencing. (a) Principal Coordinate Analysis (PCoA) for the visualization of pairwise community dissimilarity (Bray–Curtis index) of the rhizosphere microbial community at each plant developmental stage (seedling, vegetative, bolting and flowering). 95% confidence ellipses are shown around each developmental stage. (b) Principal Component Analysis (PCA) of the rhizosphere microbial community at each plant developmental stage. 95% confidence ellipses are shown around each developmental stage.

Figure 2

Relative abundance (%) of the major bacterial phyla present in the rhizosphere microbial community at each plant developmental stage.

Figure 3

Bacterial phyla that significantly (P<0.05) change with plant development. (a) Acidobacteria, (b) Actinobacteria, (c) Bacteroidetes and (d) Cyanobacteria. The bars with different letters are significantly different (ANOVA Tukey post-hoc P<0.05) from one another. Each point represents one repetition and graphs show mean±SE.