Differential Decay of Multiple eNA Components from a Cetacean

Abstract

Environmental nucleic acids (eNA), such as DNA and RNA, are powerful tools for monitoring biodiversity. Yet, interpreting eNA detections requires understanding of their environmental persistence. We conducted a decay experiment using seawater from an open enclosure to track degradation of six eNA components derived from Tursiops truncatus: mitochondrial eDNA of varying lengths, ribosomal eRNA, and messenger eRNA. Targets were quantified over seven days via digital droplet PCR (ddPCR). Decay followed a biphasic exponential model with rapid initial loss ([~]24 hours at 15 {degrees}C), followed by slower degradation. Cytb messenger eRNA was least stable, disappearing within four hours. Ribosomal eRNA persisted longer but degraded slightly faster than its eDNA counterpart ({lambda} = 0.236 vs. 0.165 hr-{superscript 1}). Longest eDNA fragments decayed more rapidly ({lambda} = 0.190 hr-1) than shorter ones ({lambda} = 0.114 hr-1). These findings support the use of eDNA fragment length as a proxy for degradation state and reinforce that combining multiple eNA components with distinct stabilities can potentially provide a molecular clock for inferring eNA age. This approach improves the spatiotemporal resolution of eNA-based monitoring, particularly for rare marine-mammal that act as point sources. We also emphasize the importance of explicitly distinguishing between RNA types (ribosomal vs. messenger) in environmental studies, given their divergent stability and interpretability.