Molecular mechanisms of host-symbiont recognition in a highly specific sponge-archaeal symbiosis

Evolution of multicellular eukaryotes is intimately associated with microbial interactions resulting in diversification and niche expansion. This long history of co-evolution is evident in metabolic interdependence, and reliance of animal (i.e. metazoan) ecosystems on their microbiota for healthy development and function. Specific recognition between interacting partners is essential for establishing and successfully maintaining interspecies associations, and involves host immunity and symbiont-encoded factors. Sponges represent the most deeply branching animal phylum with the potential to shed new light on the evolution of innate immunity and host-microbe interactions within the metazoa. Marine sponges harbour diverse microbial communities that contribute to higher order ecosystem functions including primary production and nutrient cycling. However, molecular mechanisms mediating symbiont recognition and host immune signalling in sponge symbioses are unknown. This knowledge gap stems from the fact that most sponge-associated microbes remain uncultivated and no sponge host/symbiont culture systems exist. In this thesis, I used cultivation-independent approaches including environmental genomics, transcriptomics, and proteomics in combination with homology modeling and community composition profiling to identify molecular determinants of sponge symbiosis in the sponge Dragmacidon mexicanum. Community composition profiling indicated that D. mexicanum is a high microbial abundance sponge harbouring a specific microbial community dominated by the Thaumarchaeaote Cenarchaeum symbiosum. Comparative genomics and gene expression profiling identified potential symbiont-encoded proteins including serine protease inhibitors (serpins) with the potential to mediate host-microbe interactions that were not found in closely related free-living Thaumarchaeaota, consistent with C. symbiosum’s adaptation to a symbiotic lifestyle. Biochemical assays were subsequently used to characterize serpin activity and infer function. Immunity determinants previously unreported in sponges were identified, enabling near-complete reconstruction of innate immune signalling pathways and partial adaptive immunity pathways. Thus, this work expanded the known complexity of sponge immune signalling and suggests a more ancient origin of certain pathways than previously recognized. The composition of sponge innate immunity may reflect the complex nature of sponge-associated microbiota, which likely acquired adaptive features to thrive in the host milieu. Taken together, this thesis provides novel insights into the evolution of host-microbial recognition, archaeal adaptations to a symbiotic lifestyle, and molecular interactions between archaea and eukaryotic cells.Science, Faculty ofMicrobiology and Immunology, Department ofGraduat