Fine-scale fish associations across mesophotic and deep coral fore-reef habitats

Abstract Coral reefs are threatened by climate change and overfishing, putting pressure on these sensitive ecosystems. Mesophotic habitats (> 30 m) contain diverse marine assemblages in depths where coral cover declines, yet they remain poorly studied compared to shallow coral habitats. We surveyed fish assemblages using stereo-video transects recorded with a Remotely Operated Vehicle (ROV) across six benthic mesophotic habitats in a multiple use marine park across the northern Ningaloo Reef, Western Australia. We analysed 11.9 km of stereo-video transects identifying, measuring, and counting 19,211 fish (263 species). There were significant differences in fish assemblage composition among habitats for both count and biomass data. Coral habitats supported the highest average number of species, individuals, and biomass. Notably, fish lengths were equally higher in rhodolith and coral habitats, while mesophotic habitats supported distinct assemblages including recreationally targeted and endemic species. We recorded environmental data (longitude, latitude, depth, temperature, light, and salinity) with each deployment, and all variables contributed significantly to variation in fish assemblages (biomass and count). Multivariate analyses revealed that habitat type, depth, light, and salinity influenced fish community composition, with habitat and light intensity being the strongest predictors. Stereo-ROV transects proved effective for quantifying fine-scale fish habitat associations in mesophotic zones. These habitats are underrepresented in no-take sanctuary zones of Ningaloo Marine Park, despite their unique biota. We emphasise the ecological importance of deeper reef and mesophotic habitats and the need for spatially explicit management that incorporates fish–habitat relationships across depth gradients to safeguard biodiversity and sustain fisheries.