Differential decay of multiple environmental nucleic acid components.

Area of Science:

• Environmental DNA (eDNA) and RNA analysis
• Biodiversity monitoring
• Molecular ecology

Background:

• Environmental nucleic acids (eNA), including DNA and RNA, are vital for biodiversity assessment.
• Accurate interpretation of eNA detections hinges on understanding their environmental persistence and degradation rates.
• Variability in eNA stability complicates precise spatiotemporal monitoring efforts.

Purpose of the Study:

• To quantify the degradation rates of different environmental nucleic acid (eNA) components from bottlenose dolphins (Tursiops truncatus).
• To assess the influence of eNA type (mitochondrial eDNA, ribosomal eRNA, messenger eRNA) and eDNA fragment length on decay rates.
• To evaluate the potential of combining multiple eNA types as a molecular clock for inferring eNA age.

Main Methods:

• A controlled decay experiment was conducted over seven days at 15°C.
• Six eNA components from Tursiops truncatus were analyzed: mitochondrial eDNA of varying lengths, ribosomal eRNA, and messenger eRNA.
• Quantification of target eNAs was performed using digital droplet PCR (ddPCR).

Main Results:

• eNA degradation followed a biphasic exponential model with an initial rapid loss phase (approx. 24 hours) followed by slower degradation.
• Mitochondrial messenger eRNA exhibited the shortest persistence, degrading within four hours.
• Ribosomal eRNA degraded faster than its eDNA counterpart, and longer eDNA fragments degraded more rapidly than shorter fragments.

Conclusions:

• eDNA fragment length can serve as a proxy for degradation, aiding in age estimation.
• Integrating multiple eNA components with distinct stabilities offers a molecular clock approach to enhance spatiotemporal resolution in eNA monitoring.
• Distinguishing between RNA types (ribosomal vs. messenger) is critical due to their divergent stability and interpretability in environmental studies.