Ocean acidification is widely expected to suppress marine ecosystem functioning, yet how it reshapes biodiversity-ecosystem functioning (BEF) relationships is poorly understood. Using in situ benthic chambers along a natural CO₂ gradient at Vulcano Island (Mediterranean Sea), we measured community metabolism (community respiration (CR), net (NCP) and gross (GCP) community production) and macrophyte community structure in 19 chambers across ambient (~8.1) and low pH (~7.5) conditions.

NCP was significantly higher at the acidified site while CR remained unchanged, revealing a shift of the community trophic balance toward autotrophy consistent with CO₂ fertilisation. Critically, taxonomic diversity (species richness, Shannon, Pielou) did not predict NCP. Functioning was instead predicted by the community-weighted mean (CWM) of species pH tolerance, a trait-based descriptor of functional structure, which was strongly and positively correlated with NCP. Variance partitioning attributed ~23% of the variation in NCP to functional identity and essentially none to species richness, while the acidification-tolerant green alga Caulerpa prolifera emerged as the single strongest predictor.

These results indicate that ocean acidification does not simply suppress benthic functioning but reorganises it, shifting the predictor of functioning from taxonomic diversity to the functional identity of tolerant species through a selection effect. We argue that trait-based frameworks, rather than taxonomic metrics, are essential to anticipate the functional trajectories of marine ecosystems - including the maintenance or enhancement of ecosystem functioning despite deep compositional turnover - under low pH scenarios.