Bottom-trawling affects the viability of climate refugia for vulnerable marine ecosystem indicator taxa

Bottom trawling significantly impacts benthic ecosystems, including deep-sea habitats. International guidelines recognize Vulnerable Marine Ecosystems (VMEs) as ecologically critical ecosystems at risk from fishing. In New Zealand, spatial protection measures aim to mitigate some effects of bottom trawling but remain insufficient to preserve essential habitats of VME indicator taxa under current and future climatic conditions. Using the dynamic Relative Benthic Status (dRBS) approach and density predictions for 10 VME indicator taxa, we evaluated the historical impacts of bottom trawling across New Zealand's seas, focusing on primary habitats and climate refugia predicted under future scenarios (SSP2-4.5, SSP3-7.0). Our results show that bottom trawling is expected to have impacted all assessed taxa across the study region, albeit with different intensities. Areas identified as climate refugia were particularly affected, showing the greatest reductions in both taxon density and habitat extent. Overall density losses were similar among taxa within internal climate refugia (i.e., current high-density areas predicted to maintain high densities in the future) at approximately 7–8 % and external refugia (i.e., new areas where certain taxa were predicted to expand into in the future) at approximately 9–10 % under both climate scenarios. Nevertheless, the predicted reduction in current-day density was higher in internal refugia (on average 4000 individuals per km 2 ) compared to external refugia (on average 500 individuals per km 2 ). Habitat extent reductions were also greater in internal refugia (∼10 %) than in external refugia (∼4 %). Identifying and protecting climate refugia must be a conservation priority, as they represent areas where taxa may persist or expand under future climates. Careful consideration of these areas is required to reduce extinction risk and ensure the long-term conservation of ecosystem services. • The dRBS model assessed how historical bottom trawling affected the distribution of 10 VME indicator taxa. • Scleractinian corals show the greatest density and extent loss, with an approximate 10 % decline across regions. • Bottom trawling impacted all taxa; climate refugia showed the highest density losses (7–10 %). • Climate refugia aid resilience to change, but bottom trawling threatens their viability and raises extinction risk. • Conservation planning should address both global and local threats to current and future climate refugia.