Beta Diversity and Rarity Assessment of Sessile Cryptobenthic Communities Across Depth and Islands Can Inform Coral Reef Conservation

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Aim This study investigates a poorly known component of coral reefs, the cryptobiome, species that live hidden within the reef matrix, essential for reef functioning and productivity. It focuses on patterns of diversity and rarity of sessile cryptobenthic communities across Mascarene islands, and across shallow and mesophotic habitats (in deep low‐light conditions). It aims to: (i) assess community uniqueness and local extinction risks for conservation, (ii) evaluate taxonomic overlap between mesophotic and shallow communities to explore mesophotic habitats as refugia for degrading shallow reefs. Location Reunion and Rodrigues islands, Mascarene Archipelago, south‐west Indian Ocean. Method Forty‐four Autonomous Reef Monitoring Structures (ARMS) were deployed on outer reef slopes at Reunion (~11 m and ~51 m depths) and at Rodrigues (~11 m depth). Seven hundred four ARMS plate photographs were analysed using a point counting method, and 138 morphospecies (MSP) were distinguished. Analyses included alpha, beta and gamma diversity, rarity and taxonomic overlap. Results Sessile cryptobenthic communities from Rodrigues and mesophotic habitats were characterized by unique MSP compositions, higher spatial heterogeneity and elevated rarity indices. A strong species turnover was observed between shallow and mesophotic habitats and taxonomic overlap assessment revealed that two‐thirds of the MSP were habitat‐exclusive, while only one‐quarter were common and shared across habitats. Main Conclusions We highlight the uniqueness and rarity of sessile cryptobenthic communities in mesophotic habitats and in shallow habitats on the southwest coast of Reunion and in Rodrigues, and the need to consider broad geographical coverage in conservation strategies to account for their spatial heterogeneity and uniqueness. The low proportion of shallow‐water MSP found in deeper habitats argues against the deep reef refugia hypothesis for sessile cryptobenthic communities in Reunion. Each habitat holds a distinct conservation value that should be recognized independently.