Temporal variability in temperate mesophotic ecosystems revealed with over a decade of monitoring with an autonomous underwater vehicle.

Rocky reef temperate mesophotic ecosystems (TMEs) are increasingly recognised for their spatial extent and high biodiversity. Platforms such as autonomous underwater vehicles (AUVs) allow large-scale collection of benthic imagery, facilitating descriptions of TMEs, but these efforts currently remain geographically restricted. Furthermore, descriptions of temporal changes in TMEs are extremely rare and typically limited to a single site with few repeated surveys, leaving critical gaps in our understanding of ecosystem variability. Here, we report on temporal changes in abundance and size structure of sessile biota across TMEs in three Australian Marine Parks (AMPs) across decadal time scales, using AUV-collected benthic imagery, enhanced with AI tools for estimating biota size. Our results challenge the common assumption of TME stability, revealing significant fluctuations in key biota over 2-13-year periods. At the phyla-level, cnidaria exhibited threefold changes and bryozoa fivefold changes at individual sites over ∼5 years. Some individual morphospecies also showed more than twofold change over ∼5 years. We found that higher-level taxonomic/morphological groupings could track changes in dominant taxa, but often masked significant trends at the morphospecies level. Size structure data offer important insights into the population dynamics that abundance or cover data alone could not capture, particularly in terms of recruitment events and size shifts. Our findings highlight that mesophotic ecosystems are dynamic and underscore the need for ongoing monitoring to better understand the temporal changes within TMEs and to inform the development of effective indicators. Coupling image-based surveys with physical data collection such as temperature data should be a priority in future monitoring to better link biotic changes to environmental drivers.