Bottom-trawling fisheries are a common threat to the health of continental margins worldwide. Together with numerous environmental and biological processes, physical disturbance induced by trawlers can largely shape the benthic habitats and their associated assemblages. At the SW Portuguese Margin, crustacean bottom trawlers have exploited deep-sea habitats for a few decades, but its effects on the benthic biodiversity are practically unknown. During the spring-summer of 2013 and 2014, several Remotely Operated Vehicle (ROV) video transects were used to investigate mega-epibenthic abundance, composition, and diversity in soft-sediment areas subjected to varying trawling pressures off Sines and Setúbal (200–800 m). Differences in mega-epibenthic assemblages were linked with environmental changes (depth, grain size, primary productivity) and trawling disturbance. The effect of trawling was assessed between segments with similar habitat characteristics, i.e., muddy-sand bottoms between 300 and 500 m. Areas subjected to intensive trawling pressure showed a generally flattened seabed, with abundant recent trawl marks (up to 3 scars.100 m−1), indicating that the seabed physical integrity was compromised. Significant negative correlations were detected between various mega-epibenthic diversity indices [S, H′, and ET(20)] and trawling pressure (h.cell−1.y−1). Furthermore, the distinct mega-epibenthic assemblages and absence of several sessile erect morphospecies at both low and highly disturbed locations by trawling off Sines, namely all seapen morphospecies found in non-trawled areas, demonstrates the negative influence of trawling fisheries on the benthic component of the study area. Also, low dissimilarity between assemblages from the main fishing grounds and the adjacent low-disturbance locations, suggests that the potentially negative influence of trawling can extend beyond the targeted areas (e.g., by the plumes of re-suspended sediments). The observed deleterious effects of trawling on mega-epibenthic fauna together with the intensification of trawling pressure in the study area, stress the need for adequate monitoring programs and regulatory measures to halt the long-term loss of biodiversity and allow the sustainability of fisheries at the SW Portuguese Margin.
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