Natural bacterial assemblages in Arabidopsis thaliana tissues become more distinguishable and diverse during host development

To study the spatial and temporal dynamics of bacterial colonization under field conditions, we planted and sampled Arabidopsis thaliana during two years at two Michigan sites and surveyed colonists with 16S rRNA gene amplicon sequence variants (ASVs). Mosaic and dynamic bacterial assemblages revealed the plant as a patchwork of tissue habitats that differentiated with age. ASV prevalence patterns varied not only between roots and the phyllosphere but among phyllosphere tissues. Increasing assemblage diversity indicated that variants dispersed more widely over time, decreasing the importance of stochastic variation in early colonization relative to tissue differences. As tissues underwent developmental transitions, the root and phyllosphere assemblages became more distinct. This pattern was driven by common variants rather than those restricted to a particular tissue or transiently present at one developmental stage. Patterns also depended critically on fine phylogenetic resolution: when ASVs were grouped at coarse taxonomic levels, their associations with host tissue and age disappeared. Thus, the observed spatial and temporal variation in colonization depended upon bacterial traits that were less conserved than the family-level metabolic functions recently reported to govern ex situ plant microbiome assembly. Some colonists were consistently more successful at entering specific tissues, as evidenced by their repeatable spatial prevalence distributions across sites and years. However, these variants did not overtake plant assemblages, which instead became more even over time. Together, these results suggested that the increasing effect of tissue type was related to colonization bottlenecks for specific ASVs rather than to their ability to dominate other colonists once established.