Habitat and Hydrodynamics Influence Coral Reef and Seagrass Microbial and Exometabolite Dynamics

Coral reef and seagrass ecosystems provide critical storm protection and economic revenue to tropical coastal communities. Effective monitoring and restoration strategies are essential given increasing impacts from climate change and human development. Microorganisms, and the metabolites they produce and consume, are key drivers of coastal ecosystem function. However, microbially-mediated metabolite recycling remains poorly understood, limiting its inclusion in conservation and restoration strategies. Here we examine how seawater exometabolites and microorganisms in coastal ecosystems vary in relation to habitat (seagrass or coral reef), temporal scales and hydrodynamics. We characterized benthic seawater from two St. John, U.S. Virgin Islands coral reefs (Yawzi and Tektite) and one seagrass meadow at dawn and mid-day over four consecutive days. Using quantitative metabolomics and SSU rRNA gene amplicon sequencing, we found that habitat served as the primary driver of exometabolite and microbial community composition, while daily changes and hydrodynamics strongly influenced system variability. Hydrodynamic modeling indicated offshore water intrusion at mid-day at Yawzi reef, likely driving exometabolite and microbial shifts towards oligotrophic taxa (e.g., SAR11, SAR86). In contrast, a high percentage of coastal source water in the seagrass habitat maintained stable exometabolite pools and supported diverse microbial communities. These findings demonstrate that coastal habitat and hydrodynamics strongly influence exometabolite and microbial assemblages, with lesser contributions from temporal changes. Integrating exometabolites, microorganisms, and hydrodynamics provides new insights into coastal ecosystem functioning useful for habitat monitoring and restoration strategies.