Linking microbial community assembly and function: diversity, multitrophic interactions and post-disturbance microbiome reassembly

Abstract

Microbes are the motors of terrestrial ecosystems. They mobilize nutrients, promote plant growth and suppress plant diseases. Diverse microbial communities are however under increased pressure due to intensive agricultural practices, as well as more frequent and severe climatic extremes, such as drought or flooding. In order to protect soil fertility, it is therefore important to understand how microbial diversity impacts soil functioning and how this is affected by disturbances. In this thesis, I examined how bacterial diversity, multitrophic interactions and post-disturbance community reassembly impact microbial community functioning. Bacterial diversity was shown to positively influence plant growth promotion via increased nutrient mobilization. Further, interactions of bacteria with other soil organisms, such as protists that feed on bacteria, can modulate the effect of beneficial bacteria by upregulating bacterial secondary metabolite production. It is also suggested that minor disturbance to the bacterial community or the creation of niches can further increase the establishment success of beneficial bacteria in soil and in the root zone (the rhizosphere). Strong disturbances to soil microbial communities not only decreased soil bacterial diversity, but also selected for slow-growing organisms with high efficiency. Decreases in soil diversity further constrained the bacterial communities that can colonize plant root surfaces, illustrating long-lasting effects of disturbances on ecosystems even after apparent recovery. Overall, the results of this thesis emphasize the potential of using multispecies consortia for improving the establishment and functioning of plant-beneficial bacteria in the rhizosphere and illustrate the long-term effects disturbances can have on soil and rhizosphere microbial communities.