The ability of a sponge to filter large volumes of water and retain microbial communities makes them candidates for use as bio-indicators. Amphimedon compressa is a marine sponge (phylum Porifera, class Demospongiae) abundant in the Caribbean and the southern Gulf of Mexico known to produce useful natural products, such as cytotoxins, antifouling agents, antibiotics, anti-inflammatory and antiviral compounds. Forty to sixty percent of sponge biomass can consist of microbes. However, sponges and their seasonal fluctuations in microbial communities as endosymbionts have not been widely studied. Seasonal fluctuations of specifically targeted Amphimedon microbial symbionts, such as Halovibrio, Vibrio sp., Myxobacteria uncultured cyanobacteria, and Enterococci will be measured with real-time quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). This will yield a dynamic profile of microbes within their host. This research will also determine the potential effects of natural and anthropogenic events on the interactions between sponges and their microbes, as well as provide scientific insight into which microbes are truly symbiotic. Environmental factors that may affect microbial counts, such as temperature and salinity, will be examined and correlated with targeted microbial abundances. Data on how these events may influence the population structure of microbes within sponges will provide an understanding of microbial dynamics and fluxes within the ocean's ecosystem. This research is collaborative among different scientific facilities, and develops a broader knowledgebase of sponge physiology and microbial ecology. Lastly, as residents of endangered coral reefs, sponge responses to environmental changes may enhance critical habitat management programs.