Integrating active and passive environmental DNA sampling into coral reef monitoring: implications for...

Environmental DNA (eDNA) has transformed biodiversity monitoring, but its application for long-term ecological assessment remains limited by uncertainty in the temporal stability and consistency of eDNA signals, as well as by specialized workflows that limit accessibility for community-led programs. Expanding participation in biomonitoring requires approaches that are both logistically feasible and scientifically robust. Here, we evaluated eDNA tools for coral reef monitoring in Hawai i by comparing (1) coral-specific genetic markers for tracking benthic community dynamics through time, and (2) passive eDNA samplers (PEDS) as a low-effort alternative to active filtration. This research was conducted with local stewardship organizations on O ahu, Hawai i, positioning eDNA as a complementary tool to place-based ecological knowledge that can inform conservation strategies and enhance ecological monitoring.

Across five broad taxonomic markers, we detected diverse reef communities spanning 17 phyla, with consistent regional differences in community composition, including clear differentiation in algal assemblages. Passive samplers recovered comparable taxonomic richness to active filtration when sampling effort was standardized, but showed greater variability among replicates, whereas active methods more consistently detected rare and transient taxa. Despite this, passive samplers captured similar broad-scale community patterns with reduced logistical effort. For coral monitoring, all three markers (12S, 16S, ITS2) showed strong correlations with visual cover and detected more genera than visual surveys. Among these, 16S showed the strongest and most consistent performance across temporal replicates, while ITS2 showed greater temporal variability.

Accessible eDNA approaches can generate ecologically meaningful data for reef monitoring when matched to specific objectives. Passive samplers provide a scalable, low-barrier option for widespread community biomonitoring, while active filtration remains important for detecting rare taxa. A multimarker approach enabled detection of native, endemic, and nuisance taxa, offering an ecosystem-level perspective for management. Given the relatively slow pace of change in coral assemblages, periodic eDNA surveys may provide a useful and practical longer-term complement to rapid visual assessments of coral cover. Integrating these tools with local stewardship efforts can expand participation in eDNA biomonitoring while supporting conservation in urbanized, culturally significant reef systems.