Rumen protozoa shape microbiome composition and metabolic output of fermentation

Background: Eukaryotic ciliate protozoa are an integral part of the rumen microbiome where they account for up to half of the microbial biomass. Protozoa are known to reside in tight association with their surrounding prokaryotic community - either as predators or involved in mutualistic interactions. Nonetheless, the extent of the ecological effect of protozoa on the microbial community as well as their effect on the rumen metabolic output remains largely understudied. Results: Our study shows that ciliate protozoa determine the metabolic output of the rumen microbiome as well as impose ecological effects on the prokaryotic community. By conducting microcosms experiments over time we find that volatile fatty acids and methane production are highly increased in the presence of protozoa. Analyzing the structure of the prokaryotic community in the presence of protozoa shows that predation enables several species to colonize previously occupied ecological niches. Furthermore, we observe specificity in predation-resistant species across all treatments, while predation susceptible species depends mainly on the source environment. Our results suggest that ecological models describing predation dynamics are applicable when studying host-associated communities. Conclusions: We conclude that protozoa have a large impact on the rumen ecosystem structure that may determine the overall rumen productivity. Our study further provides insights into natural dynamics as well as the multifaceted role of microbial eukaryotes in host-associated habitats. Thus, when studying the rumen microbial ecosystem, cross-domain interactions between protozoa and prokarya need to be taken into consideration.