Degradation factors of environmental DNA suggested by meta-analyses

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Tatsuya Saito, Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan and Hideyuki Doi, Graduate School of Information Science, University of Hyogo, Kobe, Japan

Background/Question/Methods
Environmental DNA (eDNA) methods have been developed to detect organisms' distributions and abundance/biomass in various environments. eDNA degradation is critical for eDNA evaluation, but, the dynamics and mechanisms of eDNA degradation are largely unknown, especially when considering different eDNA sources, e.g., cell-derived and fragmental DNA. In this study, we conducted the degradation experiments and a meta-analysis.
Firstly, we experimentally evaluated the degradation rates of eDNA derived from multiple sources, including fragmental DNA (the DNA of internal positive control, IPC), free cells from Oncorhynchus kisutch, and the resident species. As a meta-analysis, we complied the degradation rates of eDNA from 28 studies. We also collected the related factors, including water sources, water temperature, DNA regions, and PCR amplicon lengths of the measured DNA.
Results/Conclusions
Our results of the degradation experiments showed that eDNA derived from the both cell-derived and fragmental DNA decreased exponentially in the both sea and pond samples. The degradation of eDNA from the resident species showed similar behavior to the cell-derived eDNA. Our results of meta-analysis suggested that water temperature and PCR amplicon length were significantly related to the degradation rate of eDNA. From the simulation based on the 95% quantile model, we predicted the maximum degradation rate of eDNA in various combinations of water temperature and PCR amplicon length. The simulation would contribute to suppress false negatives when detecting trace amounts of eDNA of the species such as endangered and rare species in natural habitats.