Abstract
Community assembly processes determine patterns of species distribution and abundance which are central to the ecology of microbiomes. When studying plant root microbiome assembly, it is typical to sample at the whole plant root system scale. However, sampling at these relatively large spatial scales may hinder the observability of intermediate processes. To study the relative importance of these processes, we employed millimetre-scale sampling of the cell elongation zone of individual roots. Both the rhizosphere and rhizoplane microbiomes were examined in fibrous and taproot model systems, represented by wheat and faba bean, respectively. Like others, we found that the plant root microbiome assembly is mainly driven by plant selection. However, based on variability between replicate millimetre-scale samples and comparisons with randomized null models, we infer that either priority effects during early root colonization or variable selection among replicate plant roots also determines root microbiome assembly.
Highlights
It is broadly recognized that distinct assembly rules govern the establishment of microbiota around, on, and inside the plant root
The experiments were carried out under controlled greenhouse conditions with photoperiods of 16 h/21 °C days, 8 h/16 °C nights, and regularly irrigated with tap water. Both plant species were harvested 21 days after sowing: wheat plants were at tillering stage and faba bean plants were at growth stage
Contrariwise, Acidobacteria and Firmicutes dropped in the faba bean compartments compared to
Summary
It is broadly recognized that distinct assembly rules govern the establishment of microbiota around, on, and inside the plant root. Previous studies on plant root microbiomes have suggested a two-step selection process whereby microbiomes associated with root compartments become distinguished from the surrounding soil communities [2]. During this process, soil properties, vegetation history [3], and plant rhizodeposition have been found to be accountable for microbial enrichment in the rhizosphere soil [4, 5]. During the second step, the host plant genotype influences and hereby fine-tunes the composition of the rhizoplane and endosphere communities [6, 7] Both the immune system [8, 9] and the developmental stage of the plant [10, 11] are key factors that influence the assembly of root-associated microbiomes
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