Marine Protected Areas (MPAs) aim to preserve species, habitats, and the Nature Contributions to People they support. In the sub-Antarctic MPAs Namuncurá – Burdwood Bank I and II, the primary conservation features are the rich and abundant benthic assemblages across two distinct habitats: the plateau and the slope of the bank. Currently, these MPAs face significant threats from anthropogenic CO2 emissions, which drive climate change and ocean acidification processes. Here, we establish an ecological baseline by analysing the diversity and structural patterns of benthic assemblages to evaluate MPA effectiveness, monitor climate change impacts, and inform management strategies. Comparisons were performed across three areas: the MPA, the Beagle Channel, and the Atlantic shelf of Tierra del Fuego, and between zones and habitats within the MPA. Sampling was conducted at depths of 90–710 m using bottom trawls, with megafauna identified to the lowest possible taxonomic level. Uni- and multivariate analyses revealed marked differences across areas. A total of 236 taxa were distinguished, but only 16 were shared among all the three areas, while 167 were unique to the MPAs. The habitats were characterized by different biotas, with sponges (mainly Demospongiae) dominating shallower environments and calcifying taxa, such as corals and echinoderms, predominating in deeper habitats. High β-diversity turnover within the MPAs suggests that the current zonation may inadequately protect benthic habitats, which is further exacerbated by ocean acidification predictions. Our findings highlight the biodiversity and conservation value in two opensea sub-Antarctic MPAs, providing a basis for effective management and the assessment of ecological responses to environmental change.
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