Functional consequences of Caribbean coral reef habitat degradation

Coral reefs are declining worldwide. The abundance of corals has decreased alongside the 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 biological functions. An urgent challenge is to understand the 15 functional consequences of these shifts in order 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 custom made tent was placed over communities dominated by either one of five 20 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. Measured fluxes were then translated into responsible biogeochemical processes by solving a system of differential equations describing the contribution of each process to the measured chemical fluxes. Estimated processes are low compared to those known for reef flats worldwide. No real gain in primary habitat is recorded, with negative or very modest net community calcification rates by all communities. Similarly, 25 net production of biomass through photosynthesis is relatively low during the day and remineralisation of organic matter at night is relatively high in comparison, resulting in net heterotrophy over the survey period by most communities. Estimated recycling through nitrification and denitrification are high but denitrification does not fully counterbalance nutrient release from aerobic mineralisation, rendering all substrates sources of nitrogen. A multivariate pairwise analysis revealed that there is no significant difference between processes occurring on any of the assemblages, suggesting functional homogenisation 30 between distinct substrate types. We infer that the amount and type of organic matter released by abundant algal turfs and cyanobacterial mats on this reef, likely enhances heterotroph activity, and stimulates the proliferation of less diverse copiotrophic microbial populations, rendering the studied reef net heterotrophic and the overall biogeochemical ‘behaviour’ similar regardless of substrate type.