Ecological and Evolutionary Factors Shaping Animal-Bacterial Symbioses: Insights from Insects & Gut Symbionts

Animal bacterial symbioses are pervasive and underlie the success of many groups. Here, I study ecological and evolutionary factors that shape interactions between a host and gut associates. In this dissertation, I interrogate interactions between the carpenter ant (Camponotus) and its associated gut microbiota to ask the following questions: What are the resident microbiota of the Camponotine gastrointestinal tract? How does persistent gut association affect rates of molecular evolution in gut symbionts? How are gut microbiota transmitted between social hosts? How does gut community composition and structure vary across host development? What evolutionary factors facilitate adaptation to the gut? How do the genomes of gut associates respond to selective pressures associated with persistent gut habitation? I use a combination of next generation sequencing, anaerobic isolate culturing, computational modeling, and comparative genomics to illustrate evolutionary consequences of persistent host association on the genomes of gut associates. In chapter one, I characterize the gut community of C. chromaiodes and describe two novel lineages in the Acetobacteraceae (AAB). I demonstrate rapid evolutionary rates, deleterious evolution at 16S rRNA, and deep divergence of a monophyletic clade of ant associated AAB. In chapter two, I design a novel molecular tool to prevent amplification of nontarget DNA in 16S based community screens. I then use this tool to characterize the gut microbiota of C. chromaiodes across several developmental stages and incipient colonies. I argue that highly similar bacterial profiles between a colony queen and offspring are indicative of reliable vertical transmission of gut bacteria. In chapter three, I isolate and culture two strains of AAB gut associates from C. chromaiodes, as well as an associate in the Lactobacillaceae, and perform whole genome sequencing. I use comparative genomic analyses to delineate patterns of genomic erosion and rampant horizontal gene transfer on AAB gut isolates that lead to genomes with mosaic metabolic pathways.

Taken together, this dissertation establishes a new model system for assessing evolutionary consequences of symbioses with gut bacteria. These results provide novel insights into the repercussions of bacterial adaptation to a host gut tract. They establish a foundation to interrogate questions unique to persistent extracellular gut symbionts. Finally, they delineate distinct forces shaping the functional capacity of symbiont genomes: gene loss through reductive evolution and gene acquisition via horizontal transfer from diverse community members.