Community-level eDNA decay patterns in marine zooplankton: Implications for optimizing eDNA-based marine environmental monitoring

Environmental DNA (eDNA) has the potential to greatly transform marine ecological monitoring, yet its capacity for accurate biodiversity estimates is constrained by its decay process. Previous research has largely focused on laboratory-cultured single species, and thus the dynamics of mixed-species eDNA from natural communities remain poorly understood. Here, we conducted a 10-day time-series experiment to track the community-level eDNA decay process following the complete removal of zooplankton, employing an integrated approach of morphological analysis, quantitative PCR (qPCR), metabarcoding, and metagenomics. Our results reveal that the decay of marine zooplankton eDNA is a complex, heterogeneous process. Total community eDNA declined rapidly during the first two days (0-2 d), followed by a slower decline (4-10 d), as quantified by qPCR. Crucially, the taxonomic composition of the detectable eDNA pool changed substantially over time: the relative read abundance of copepods declined sharply after only two days, whereas that of medusae persisted high throughout the experiment. Furthermore, methodological comparison revealed significant discrepancies in temporal trajectories between metabarcoding and metagenomics regarding the detected community composition. To optimize eDNA-based marine environmental monitoring, we propose matching target taxa and molecular methods to the temporal scale of interest. Short-lived signals of copepods might support timely, near-snapshot assessments of recent environmental change by eDNA metabarcoding, whereas long-lived medusa eDNA appears to integrate occurrence over time. Taxon-specific signal persistence and method-dependent detectability should therefore be considered when interpreting eDNA monitoring data. This framework can strengthen the reliability of eDNA-based biodiversity assessments and support more effective marine ecosystem monitoring.