Microbial ecology in hypersaline coastal lagoons: A model for climate-induced coastal salinisation and eutrophication

Coastal lagoons are critical ecosystems providing essential habitats and ecosystem services, including carbon sequestration, nutrient cycling, and fisheries support. Yet, many coastal lagoons face growing threats from salinisation and eutrophication driven by climate change and human activities. Climate-induced salinisation arises from multiple factors, including elevated temperatures, enhanced evaporation, reduced precipitation and freshwater inputs, and rising sea levels that trigger upwelling and direct saline intrusion to lagoons. These fragile and complex environments offer valuable models for understanding how coastal zones worldwide respond to global change. This review examines how salinity shapes microbial community composition and biogeochemical processes in hypersaline lagoons. Elevated salinity reduces microbial α-diversity, favouring salt-tolerant taxa and restructuring nitrogen and carbon cycling. Key processes, such as nitrification, denitrification, and methane production are disrupted, altering nutrient retention, organic matter decomposition, and greenhouse gas emissions. Increased salinity also intensifies eutrophication, creating positive feedback loops that weaken ecosystem health and reduce carbon sequestration. Microbial communities exhibit adaptive responses, including osmoregulatory strategies and horizontal gene transfer, which support resilience under rising salinity. By synthesising evidence on these interactions, the review illustrates the importance of understanding microbial-mediated processes to inform the conservation and management strategies for coastal lagoons under climate and anthropogenically-induced salinity change. • Climate-driven salinisation and eutrophication threaten many coastal lagoons. • Elevated salinity and nutrients reduce microbial α-diversity and health. • Salinity disrupts nitrification/denitrification, altering N retention and fluxes. • Salinity modifies C cycling, altering OM decomposition and GHG fluxes. • Understanding microbial processes under rising salinity informs lagoon management.