Global environmental change drives diversity loss and shifts in community structure. A key challenge is to better understand the impacts on ecosystem function and to connect species and trait diversity of assemblages with the possible consequences for ecosystem function. Here we quantify shifts in species composition and trait diversity associated with ocean acidification (OA) by using field measurements at marine CO₂ vent systems spanning four reef habitats across different depths in a temperate coastal ecosystem. We find that both species and trait diversity decreased and that ecosystem properties (understood as the interplay between species, traits, and ecosystem function) shifted with acidification. Furthermore, shifts in trait categories such as autotrophs, filter feeders, herbivores, and habitat-forming species were habitat-specific, indicating that OA may produce divergent responses across habitats and depths. Combined, these findings reveal the importance of connecting species and trait diversity of marine benthic habitats with key ecosystem properties to anticipate the impacts of global environmental change. Our results also generate new insights into the predicted general and habitat-specific ecological consequences of OA.

Sampling design of benthic 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.

Trait characterization of benthic species. The trait diversity of benthic assemblages was assessed using seven traits, which were chosen to provide an overview of each species’ ecological strategy. The traits were: 1) morphological form, 4 categories: a) encrusting, b) filaments, c) massive, and d) tree-like; 2) feeding, 6 categories: a) autotroph, b) filter feeders, c) herbivores/grazers, d) carnivores, e) detritivores, and f) parasites; 3) growth rates, 3 categories: 1) extreme low (<1 cm/year), 2) moderate (1–5 cm/year), 3) high (>5–10 cm/year; 4) calcification, 2 categories: a) without and b) with calcareous structures; 5) mobility, 2 categories: a) sessile and b) vagile; 6) age at reproductive maturity, 2 categories: 1) < than 1 year, 2) > than 1 year; and 7) chemical defenses, 2 categories: 1) no and 2) yes (see Table S5 for a detailed description of the seven traits and categories). 

Bayesian Dirichlet-Multinomial Model. We used Bayesian models to predict the probability of a species’ cover belonging to a specific trait category across habitats and between pH conditions. We applied a Bayesian Dirichlet-Multinomial model (DMM) to analyze benthic cover for the four functional traits (morphological form, feeding activity, growth rate, and calcification).