Integrating active and passive environmental DNA sampling into coral reef assessments: implications for community-based biomonitoring in Hawaiʻi

Background 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 workflows that require specialized equipment and analytical support. Broader use of eDNA in community-based monitoring will depend on approaches that are both logistically practical and scientifically reliable. Here, we conducted two complementary studies of eDNA methods for coral reef monitoring in Hawaiʻi. First, we compared coral-specific genetic markers for tracking benthic community dynamics through time. Second, we compared passive eDNA samplers (PEDS) as a low-effort alternative to active filtration. This research was conducted in collaboration with local stewardship organizations on Oʻahu, Hawaiʻi, to assess how eDNA sampling could complement existing reef-monitoring activities and provide additional information relevant to conservation planning. Results Across five broad taxonomic markers (16S, 18S, 23S, COI, MFU), we detected diverse reef assemblages spanning 17 phyla, with consistent differences in community composition between the two O‘ahu study regions, Ke‘ehi and Maunalua Bay (~ 12 km apart), 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 ecological 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 (23 vs. 17 site-genera detections, a 35% increase). Among these, 16S showed the strongest and most consistent performance across temporal replicates, while ITS2 showed greater temporal variability. Conclusions eDNA approaches can generate ecologically meaningful data for reef monitoring when matched to specific objectives. Passive samplers offer a relatively simple option for expanding spatial and temporal biomonitoring, while active filtration remains important for detecting rare taxa. A multi-marker 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 may increase monitoring capacity, provided that requirements for laboratory processing, bioinformatic analysis, taxonomic validation, and interpretation are adequately supported.