Abstract/Summary

Interactions between plants and microbes are believed to have facilitated the conquest of land and to this day profoundly affect the success of plants. Naturally occurring soil microbes – especially the subset that live associatively with plant roots – offer the potential to contribute to the sustainable intensification of agriculture by a variety of means, including the suppression of plant diseases and provision of nutrients. However, the effects of different agricultural management practices and cropping systems on the proliferation of beneficial microbes may determine the manifestation of these functions. The design of the Broadbalk winter wheat experiment at Rothamsted has ensured that a diverse range of biotic and abiotic selective pressures associated with different combinations of such treatments have acted continuously on resident soil microbes over the last 180 years, both directly and mediated via continuously cultivated crop plants. This thesis presents an investigation into the utility of this living experiment to advance our understanding of the plant microbiome under various environmental stressors principally surrounding nutrient limitations. The central role of inorganic nitrogen amendments in structuring the rhizosphere microbiome at Broadbalk was revealed by a bacterial 16S rRNA gene amplicon sequencing survey in tandem with robust soil chemical analyses. A high-throughput, culture collection pipeline was developed to integrate functional characterisations of resultant rhizosphere microbial communities by screening isolate libraries in vitro. The role of mineral nitrogen inputs dominated outcomes, and no enrichment of putatively plant growth promoting (PGP) microbial traits relevant to nutrient limitations in the plots from which they were cultured were exhibited, potentially a result of thorough geochemical depletions through repeated cropping. This multifaceted approach towards understanding the nature of selection for PGP microbial associations holds significant promise and the data and biological resources generated can be further leveraged to develop microbial solutions to problems faced by contemporary agricultural systems.