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Sally Attia:
Patterns and Processes of the Microbiome Assembly at a Small-Scale of the Plant Root Microenvironments

Date: 31-08-2020    Supervisor: Søren J. Sørensen & Jonas S. Madsen

Understanding the fundamental ecological processes that drive the local community assembly is a significant challenge, especially, in the microbial community ecology. When it comes to the plant roots-housed microbiomes, ecological processes, both deterministic (e.g., the host plant filtering and microbial interactions) and stochastic (e.g., ecological drift and colonization history) display essential roles in the assembly of root-associated microbiomes. Though, their relative influence on the root microbiome assembly remains inadequately unexplored. When studying plant root microbiome assembly, it is typical to sample at the scale of the whole plant root system. However, sampling at these relatively large spatial scales may hinder the observability of the relative influence of these processes. Therefore, we employed small-scale sampling of the cell elongation zone of individual roots, where both the rhizosphere and rhizoplane microbiomes were examined in fibrous and taproot model systems, represented by wheat and faba bean, respectively.

Through three studies, this thesis aimed to: 1) explore the relative influence of the microbial interactions and stochastic processes on the local composition of the rhizosphere- and rhizoplane-associated microbiomes, 2) investigate the effects of biotic soil-borne legacies on the assembly of the contemporary root-associated microbiomes, and 3) test intra- and inter-species antagonism among bacterial strains of Bacillus spp. and Pseudomonas spp. that were co-isolated from small subsections of individual plant root rhizosphere samples of wheat and faba bean.

In Manuscript I we revealed that it is not only the selective effects of the host plant that drives the root microbiome assembly, but local interactions among co-existing species also largely influence the assembly of the individual root-associated communities. Moreover, stochastic factors also had a crucial minor role in the microbiome assembly that only observed between different rhizocompartments from the same plant. Nevertheless, these results only realized through a small-scale sampling of defined plant rhizocompartments.

In Manuscript II Intriguingly, we found that the assembly of the root microbiomes is a combined action between stochastic and deterministic processes; however, biotic soil-borne legacy impacts the balance between those two processes, which may affect the strength of the relationship between environmental factors and ecosystem processes.

In Manuscript III we found that the occurrence of antagonism was much higher among species belonging to the same genus rather than between species of different genera. However, the antagonistic propensity was species-dependent as the antagonism among Bacillus species was more severe (4.4% interactions) than that of Pseudomonas species (1.2% interactions). Antagonism was also more prevalent between strains originated from the same plant species than those originated from different plant species, inferring competition between conspecifics