Protozoa populations are ecosystem engineers that shape prokaryotic community structure and function of the rumen microbial ecosystem

Unicellular eukaryotes are an integral part of many microbial ecosystems communities where they are known to interact with their surrounding prokaryotic community, either as predators or as a mutualistic habitat. Within the rumen, one of the most complex host associated microbial habitats, ciliate protozoa represent the main microeukaryotes, accounting for up to 50% of the microbial biomass. Nonetheless, the extent of the ecological effect of protozoa on the microbial community and on the rumen metabolic output remains largely understudied. To assess the role of protozoa on the rumen ecosystem, we established an ex-vivo system in which distinct protozoa subcommunities were introduced to native rumen prokaryotic community. We show that the different protozoa communities exert a strong and differential impact on the composition of the prokaryotic community, as well as its function including methane production. Furthermore, the presence of protozoa increases prokaryotic diversity with a differential effect on specific bacterial populations such as Gammaproteobacteria, Prevotella and Spirochetes. Our results suggest that protozoa mitigate the effect of competitive exclusion between bacterial species, thereby contributing to the maintenance of prokaryotic diversity in the rumen. Our findings put forward the rumen protozoa populations as potentially important ecosystem engineers for future microbiome modulation strategies.