Spatial Complexity and Rare-Taxon Turnover Structures Benthic Coral Reef eDNA Communities.

Environmental DNA (eDNA) metabarcoding has transformed spatial biodiversity assessments, although its capacity to distinguish persistent from dynamic elements of ecological communities through time remains largely unknown. We asked to what degree eDNA signals on coral reefs are temporally consistent representations of community composition or are dominated by short-lived fluctuations, and how this distinction influences interpretation of biodiversity data through time. We assessed these questions in Hawaiian coral reef communities over 2 years, replicated with two universal eDNA markers (nuclear 18S and mitochondrial COI). Our analyses revealed that community composition differed strongly among sites, while within-site assemblages were relatively stable through time. Despite high per-sample richness, a smaller core of reef taxa, including sponges, annelids, and red algae, were consistently detected across sites and sampling dates, indicating that eDNA reliably captures dominant community members despite natural variability in DNA production, degradation, and transport. This core assemblage anchored site distinctiveness, while temporal variation was driven by the appearance and disappearance of a comparatively large number of rare or transient taxa. This temporal variation was detectable but smaller in magnitude and associated with environmental factors such as wind, waves, tides, and lunar cycles, highlighting their role in modulating patterns of taxon detectability. Overall, eDNA signals primarily reflect underlying spatial heterogeneity rather than transient fluctuations, demonstrating that routine eDNA surveys can robustly track community dynamics across space and time. By identifying the ecological and environmental correlates of eDNA signal variation, our study demonstrates that spatially structured community differences dominate eDNA profiles on coral reefs and allow persistent biodiversity patterns to be distinguished from short-term temporal variability. Although eDNA integrates biological and physical processes distinct from direct observation, the resulting patterns are highly similar to those generated by visual reef surveys, in which strong site-level differentiation is maintained by a small set of persistent taxa, while a large pool of rare species contributes to transient variability. The convergence between molecular and observational approaches links eDNA-derived biodiversity patterns to underlying community assembly processes and enhances ecological interpretation of molecular data in tropical reef ecosystems.