Young Scholar Presentation: Characterization and Implications of Novel Rumen Viral and Methanogen Diversity Discovered through Targeted Genomic Approaches

Rumen microbes play a critical role in energy acquisition for the ruminant host. Consequently, an improved understanding of the composition, function, and interactions of rumen microbial populations would provide novel opportunities to enhance rumen fermentation, host efficiency, and health. However, our knowledge of the diversity and function of the complex rumen ecosystem has been stifled by the inability to culture the vast majority of microbial life. Using targeted culture-independent techniques, we explored rumen viral and methanogen diversity, as well as interactions between these populations to better understand the rumen ecosystem. Viruses have been shown to influence ecosystem function through top-down and bottom-up effects resulting from cell lysis, horizontal gene transfer, active lysogeny, and metabolic reprogramming. For the first time, we investigated the response of rumen viruses to dietary modulation and demonstrated dietary total digestible nutrient content best explains the variation in viral populations. While rumen viruses were dynamic, core viral groups, mainly characterized by unknown viruses, suggest a potential role for viruses in structuring the rumen microbiome. Additionally, we identified glycosidic hydrolases among the virally encoded auxiliary metabolic genes, signifying viruses augment the breakdown of carbohydrates to boost host microbe energy production and in turn, viral replication. In addition to metagenomic approaches, in a separate study we utilized microfluidic enabled single cell genomics to describe novel methanogens not previously found in the rumen. These single cell genomics studies are ongoing and have implications for methane mitigation strategies, as well as answering fundamental questions regarding the evolution of methanogenesis. Metabolic predictions indicate the discovered methanogens use different substrates to produce methane and this is reflected in their differential abundance on contrasting diets. Lastly, from these methanogen genomes we were able to identify temperate viral signatures suggestive of a viral influence on methanogenesis. In summary, through targeted approaches we were able to document novel features and dynamics of rumen viruses and methanogens in ways that would have not been possible through traditional approaches. This work builds foundational knowledge regarding the diversity and roles of viruses and methanogens in rumen ecosystem function necessary for future hypotheses. Further, the methods employed here can be adapted to study other populations and will help push us toward our goal of manipulating the rumen microbiome to favor certain phenotypes.