The evolutionary ecology of root-associated bacteria

Abstract

Complex communities are formed by association of plant roots with microbes in soil, and significantly determine plant nutrition, stress tolerance, and pathogen resistance. These communities are potentially shaped by differential microbial colonisation of roots, competition between colonizing strains, and selective recruitment of microbes by plants - all these processes are poorly understood. To better understand community assembly in the root and how it can affect plant growth and health, this thesis explored experimentally the ecological factors shaping microbial communities. I found that plant host species rather than soils defined microbial communities, although community assembly appears to differ between plant species, as both relatively invariant and dynamic assembly patterns are observed. Phenotypic characterization of rhizobacteria isolates indicated that bacterial functions define root-associated bacteria beyond phylogenetic identities, so that differential colonization and selection are plausible mechanisms for assembly. Nevertheless, isolate host origin was not an important predictor of colonization ability in a gnotobiotic in planta experimental system, although competitive or mutualistic interactions could be very important for colonization and plant growth outcomes. An additional chapter exploring the microbial ecology of a ‘replant’ disease in a commercial orchard confirmed that disease risk associated with soil legacy was associated with changes in diversity and abundance of unculturable phyla. This project highlights the potential of culture-independent approaches, but also their limitations. Microbial function and microbe-microbe interactions are clearly important for rhizobacterial community assembly, but their elucidation may require more data-intensive approaches. In terms of predicting which microbes might colonize particular plants and whether colonization is likely to be beneficial, this thesis only scratched the surface of the problem. Perhaps not surprisingly, environmental context is very important for understanding when rhizobacteria are likely to be beneficial, while the complexities of bacterial competition and mutualism suggest that stochasticity is important in determining which microbes are successful on which plant.