From deployment to functioning ecosystems: assessing taxonomic richness and community composition on modular shellfish reefs using environmental DNA metabarcoding

Abstract

Ecological restoration success is commonly assessed against historical reference states that are often altered, poorly defined, or absent, particularly in marine systems. Reliance on taxon richness alone can further obscure changes in community structure, successional trajectories, and the emergence of functionally important taxa at restoration sites. We assessed biodiversity recovery on modular shellfish reef structures using environmental DNA (eDNA) metabarcoding, combining taxon-specific richness models with multivariate community composition analyses across a four-year age gradient (9, 21, and 42 months). Genus richness increased rapidly following reef deployment but differed strongly among taxon groups. Dominant groups, particularly Mollusca, showed similar richness in nine-month-old and 42-month-old reefs; crustaceans and fishes also showed high, consistent richness early in development. Five of nine taxon groups displayed significant richness changes through time, with increasing (flatworms and macroalgae) and decreasing (cnidarians, sponges, and roundworms) trajectories. Community composition showed pronounced age-related structuring: younger reefs were compositionally distinct from older reefs, and within-age variability declined markedly with age, consistent with convergent successional assembly. Trait-based patterns indicated shifts towards non-benthic crustaceans, larger-bodied fish, and free-living flatworms in older reefs. These results show that modular shellfish structures are rapidly colonised by a wide taxonomic range within 9 months, producing early richness gains. However, the identity and relative representation of those taxa continue to change, generating structured compositional shifts undetectable from richness alone. Integrated richness-composition frameworks focused on ecological trajectories provide a more robust basis for evaluating restoration success than strict reference states. Environmental DNA metabarcoding offers a scalable, non-invasive monitoring approach capable of capturing both early richness gains and longer-term community assembly dynamics in data-limited marine systems.