Redefining the Expanding Diversity and Co-evolutionary Patterns in Microbial Communities within Ants

My PhD research begins to address the gaps in our knowledge of bacteria and viruses infecting ants. I have combined high throughput sequencing technologies and bioinformatic analyses with evolutionary and ecological principles to begin to understand multi-scale microbial dynamics.In Chapter 1, to begin to decipher the history of ancient viral infections in ants, I uncovered viral fragments which had endogenized (inserted themselves) into ant genomes, analyzed across all currently sequenced ant genomes. I discovered a large diversity of viruses that had infected ant genomes, many of which appear to be functional and conserved with long-term beneficial associations with certain ant species. These viral fragments often clustered by groups of related ant species implying potential for co-divergence of ants and these viruses. Genetic conservation of these viral fragments over long time spans suggest that certain viruses may be playing a role in providing some level of immune protection to the ant, as can be seen in co-opted viral functional proteins in the genomes of other species. Subsequently, for Chapter 2, I aimed to discover viruses currently infecting ants. I investigated the composition and diversity of viral communities of a phylogenetically broad group of ant species across both pristine and fragmented habitats in South America. This is the first study to explore and document the "virome" in ants, yielding results that begin to elucidate whether certain viral communities tend to associate with specific ant species depending on distinctions in their phylogenetic relationships and ecology. I found extraordinarily high levels of diversity and abundance within all ant species sampled. My findings reveal that certain viral groups are much more diverse in particular ant groups and harbor species-specific viral groups. Strikingly, the vast majority of the viruses I identified within ants represent bacteriophage (viruses which infect bacteria) and circular ssDNA viruses. These newly discovered bacteriophages tend to co-occur with bacterial groups which are known to be symbiotic with specific ant species. Finally, within Chapter 3, I tested whether bacterial communities within twelve species of the genus Cephalotes (turtle ants) varied across different sections of their gut compartments based on the digestive function of each compartment. I found that gut compartments play an important role in structuring the microbial community within Cephalotes ants. My results document that gut compartment-specific signatures of microbial diversity, composition, and abundance have been conserved over Cephalotes evolutionary history, signifying that this symbiosis has been largely stable for more than 50 million years. The foundational work of my dissertation research provides an initial characterization of ant microbiomes by uncovering bacterial and viral community diversity and structure across ant groups. My current research indicates that viruses and symbiotic bacteria both structure ant microbial communities and each may play an important role throughout ant evolution. My research confirms that ants can be established as a model ecosystem in which to study multifaceted microbial dynamics.