Soil Protists: From Traits To Ecological Functions

Abstract

The best-known function of soil protists is as bacteria feeders, protists consume bacteria prey and further release the nutrients which were locked in bacteria biomass, those nutrients benefit the remaining bacteria and plant root. Moreover, protists do not feed on all prey bacteria equally, this selective feeding by protists can lead to shifting prey bacterial community structure, which may be linked with changes in soil community functioning. Given the lack of a generalized pattern of protists predation, the central question of this thesis is whether the effects of protist predation can be predicted. I proposed to use protist traits as a means to address this question. Due to the focus of previous work on only one model protists and some closely related protists, I then collected and isolated 20 protists species with diverse morphotypes to investigate the central question. I started by clarifying the taxonomic affiliations of the protists isolates used in this thesis, with a special focus on Heterolobosea amoeba, which are widespread and diverse in soil. Given the lack of morphologically useful characteristics in Heterolobosea amoeba, I further combined morphological characterization and molecular tools to identify these species and proposed a new species Vahlkampfia soli. This first soil Vahlkampfia species highlights the need for additional efforts in the future to cultivate previously unknown soil protists. I continued to investigate the relationship between protist traits and their effects on prey bacterial community structure. I measured a range of protists traits across my target 20 protist species covering the main phylogenetic lineages found in soil. I further used microcosm experiments to assess the effect of each species on the structure of a semi-natural soil bacterial community. This work revealed that protists traits, especially cell volume, could be linked to their predation effect on the bacterial community. It was critical that cell volume calculations were not only based upon cell size but also considered geometric morphotype. To understand the functionality of protists, I then examined how protist predation and competition with other soil bacteria communities affect the stability of bacterial cooperative interactions. I utilized two types of bacterial strains, one is a cooperator bacterial strain that produces the public goods, the other one is defector bacterial strain that takes advantage of public goods without contributing to their production. I combined these two types of bacteria in the presence of competing soil bacterial communities and protists. This work revealed that multitrophic interactions strongly impacted microbial cooperation, in particular, competition increased the net benefit of cooperation at low and intermediate resource availabilities, however, predation followed the opposite pattern. Moreover, multitrophic interactions constrained the defector invasion and promote cooperation, but this effect strongly depended on resource availability. Finally, I synthesized existing knowledge on soil protists and demonstrate their importance as regulators of the rhizosphere microbiome. I then addressed the known and hypothesized consequences of protists on microbiome functionality and plant performance. I also presented a framework to guide efforts to harness protists as a microbiome enhancer in sustainable agriculture.