Most marine sponges establish a persistent association with a wide array of phylogenetically and physiologically diverse microbes. To date, the role of these symbiotic microbial communities in the metabolism and nutrient cycles of the sponge-microbe consortium remains largely unknown. We identified and quantified the microbial communities associated with three common Mediterranean sponge species, Dysidea avara, Agelas oroides and Chondrosia reniformis (Demospongiae) that cohabitate coralligenous community. For each sponge we quantified the uptake and release of dissolved organic carbon (DOC) and nitrogen (DON), inorganic nitrogen and phosphate. Low microbial abundance and no evidence for DOC uptake or nitrification were found for D. avara. In contrast A. oroides and C. reniformis showed high microbial abundance (30% and 70% of their tissue occupied by microbes respectively) and both species exhibited high nitrification and high DOC and NH4+ uptake. Surprisingly, these unique metabolic pathways were mediated in each sponge species by a different, and host specific, microbial community. The functional convergence of microbial consortia found in these two sympatric sponge species, suggest that these metabolic processes may be of special relevance to the success of the holobiont.