Seawater carbonate chemistry and raw data of percent cover of benthic species obtained from field surveys

Percent cover of 215 benthic species was quantified using two approaches with scuba diving: i) visual census techniques in Shallow Reef (benthic surveys were performed from 0.5 to 3 m depth) and Reef habitats (benthic surveys at ~10 m depth) dominated by algae and ii) photographic surveys in Caves (benthic surveys at ~3 m depth) and Deep Reef habitats (benthic surveys at ~ 40 m depth) dominated by sessile invertebrate animals. For visual censuses, 12 quadrats (25x25 cm) were haphazardly placed at Vent 1 and Vent 3 and the two corresponding ambient pH sites (n = 3 sites per habitat, n = 36 quadrats for Shallow Reefs and Reefs, respectively). For photographic surveys, 48–54 and 24 photoquadrats (25x25 cm) were taken at Vent 2 and Vent 4 and the two corresponding reference sites with ambient pH for each habitat (n = 3 sites per habitat, n = 144 photographic quadrats for Caves and n = 72 photographic quadrats for Deep Reefs, respectively). Both types of quadrats (visual censuses in the field and photographs in the lab) were divided into a grid of 25 squares (5 cm x 5 cm each). Percentage cover was quantified by counting the number of squares filled in the grid by the species and expressing the final values as relative percentages.