Quantifying functional consequences of habitat degradation on a Caribbean coral reef

Coral reefs are declining worldwide. The abundance of corals has decreased alongside a rise of filter feeders, turf, and algae in response to intensifying human pressures. This shift in prevalence of functional groups alters the biogeochemical processes in tropical water ecosystems, thereby influencing reef functioning. An urgent challenge is to understand the functional consequences of these shifts to develop suitable management strategies that aim at preserving the biological functions of reefs.Here, we quantify biogeochemical processes supporting key reef functions (i.e. net community calcification (NCC) and production (NCP) and nutrient recycling) in situ for five different benthic assemblages currently dominating shallow degraded Caribbean reef habitats. To this end, a transparent custom-made enclosure was placed over communities dominated by either one of five functional groups – coral, turf and macroalgae, bioeroding sponges, cyanobacterial mats, or sand – to determine chemical fluxes between these communities and the overlying water, during both day and night. To account for the simultaneous influence that distinct biogeochemical processes have on measured variables, the rates were then derived by solving a model consisting of differential equations describing the contribution of each process to the measured chemical fluxes.Inferred rates were low compared to those known for reef flats worldwide. Reduced accretion potential was recorded, with negative or very modest net community calcification rates for all communities. Net production during the day was also low, suggesting limited accumulation of biomass through photosynthesis and remineralisation of organic matter at night was relatively high in comparison, resulting in net heterotrophy over the survey period for most communities. Estimated recycling processes (i.e. nitrification and denitrification) were high but did not fully counterbalance nutrient release from aerobic mineralisation, rendering all subs