Metagenomic and metaproteomic analysis of the microbial communities of marine sponges

Marine sponges harbour complex communities of diverse microorganisms, which have been postulated to form intimate symbiotic relationship with their host. Despite the importance of this symbiosis - from both the ecological and biotechnological perspectives - little is known about the functional properties of the bacterial symbionts and their interactions with the host. This thesis presents the characterisation of the microbial communities associated with two sponges, Cymbastela concentrica and Rhopaloeides odorabile, from the eastern coast of Australia.A functional genomic analysis of an uncultured Deltaproteobacterium in the sponge C. concentrica showed that this organism represents a novel phylogenetic clade and lives in association with a cyanobacterium within the sponge tissue. The result also provide an overview of the predicted functional and ecological properties as well as the complex interactions of this bacterium with its surrounding. An integrated metaproteogenomic approach was used to characterise the microbial community associated with C. concentrica. The result unveiled the expression of specific proteins involved in the transport of typical sponge metabolites, respiration, stress protection and molecular interactions (e.g. eukaryotic-like proteins). This analysis highlighted the requirement for the microbial community to respond to variable environmental conditions.A subsequent study investigated the genomic and functional properties of an uncultured Phyllobacteriaceae phylotype. This organism was predicted to be capable of using host-derived compounds and to carry out anaerobic respiration through nitrate reduction. Functional signatures associated with survival using defence and host-symbiont interactions were also identified.The impact of elevated water temperature on the microbial communities within R. odorabile was investigated with ametaproteogenomic approach. Changes in taxonomic composition, species richness, genomic content and expressed functional profile of sponge microbial communities were observed during thermal stress. In particular, putative symbiotic functions, such as metabolite transport, metabolism of sponge-specific substrates and maintenance of cellular structure, were identified in unstressed sponge communities, but were absent in stress samples. The decline in expression of symbiont functions in stressed sponge sample demonstrated that sponge necrosis is likely to be caused by the disturbance of interactions within the sponge holobiont, rather than as a result of pathogen infection