Ecological restoration aims to reverse biodiversity loss and recover ecological function, yet success is often judged against historical reference states that may be altered, unclear, or absent—particularly in marine systems. Reliance on taxon richness alone can obscure shifts in community structure, successional dynamics, and the emergence of key or undesirable taxa, limiting effective evaluation.
We assessed biodiversity recovery on modular shellfish reefs using environmental DNA (eDNA) metabarcoding, combining taxon-specific richness models with multivariate analyses of community composition across a four-year age gradient (9, 21, and 42 months). Genus richness increased rapidly after deployment but varied among taxonomic groups. Molluscs reached comparable richness by nine months and 42 months, while crustaceans and fishes showed consistently high early richness. Five of nine groups changed significantly over time, with both increasing (flatworms, macroalgae) and decreasing (cnidarians, sponges, roundworms) trends.
Community composition showed strong age-related structuring. Younger reefs were distinct, while older reefs converged in composition, indicating successional assembly. Trait-based shifts included increases in non-benthic crustaceans, larger-bodied fishes, and free-living flatworms.
These findings show that while richness recovers quickly, community composition changes more gradually. Integrating richness and composition provides a stronger framework for evaluating restoration, with eDNA offering a scalable, non-invasive tool for monitoring biodiversity and guiding adaptive management.