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We assembled communities of bacteria and exposed them to different nutrient concentrations with or without predation by protists. Taxa that were rare in the field were less abundant at low nutrient concentrations than common taxa, independent of predation. However, some taxa that were rare in the field became highly abundant in the assembled communities, especially under ample nutrient availability. This high abundance points at a possible competitive advantage of some rare bacterial taxa under nutrient-rich conditions. In contrast, the abundance of most rare bacterial taxa decreased at low resource availability. Since low resource availability will be the prevailing situation in most soils, our data suggests that under those conditions poor competitiveness for limiting resources may contribute to bacterial rarity. Interestingly, taxa that were rare in the field and most successful under predator-free conditions in the lab also tended to be more reduced by predation than common taxa. This suggests that predation contributes to rarity of bacterial taxa in the field. We further discuss whether there may be a trade-off between competitiveness and predation resistance. The substantial variability among taxa in their responses to competition and predation suggests that other factors, for example abiotic conditions and dispersal ability, also influence the local abundance of soil bacteria. This article is protected by copyright. All rights reserved.

Root-colonizing bacteria can support plant growth and help fend off pathogens. It is clear that such bacteria benefit from plant-derived carbon, but it remains ambiguous why they invest in plant-beneficial traits. We suggest that selection via protist predation contributes to recruitment of plant-beneficial traits in rhizosphere bacteria. To this end, we examined the extent to which bacterial traits associated with pathogen inhibition coincide with resistance to protist predation. We investigated the resistance to predation of a collection of Pseudomonas spp. against a range of representative soil protists covering three eukaryotic supergroups. We then examined whether patterns of resistance to predation could be explained by functional traits related to plant growth promotion, disease suppression and root colonization success. We observed a strong correlation between resistance to predation and phytopathogen inhibition. In addition, our analysis highlighted an important contribution of lytic enzymes and motility traits to resist predation by protists. We conclude that the widespread occurrence of plant-protective traits in the rhizosphere microbiome may be driven by the evolutionary pressure for resistance against predation by protists. Protists may therefore act as microbiome regulators promoting native bacteria involved in plant protection against diseases.

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.