Environmental DNA (eDNA) methods have been developed to detect organism distribution and abundance/biomass in various environments. eDNA degradation is critical for eDNA evaluation. However, the dynamics and mechanisms of eDNA degradation are largely unknown, especially when considering different eDNA sources, e.g., cells and fragmental DNA.
We experimentally evaluated the degradation rates of eDNA derived from multiple sources, including fragmental DNA, free cells, and inhabiting species. We conducted the experiment with pond and seawater to evaluate the differences between freshwater and marine habitats. We quantified the eDNA copies of free cells, fragmental DNA, and inhabiting species (Cyprinus carpio in the pond and Trachurus japonicus in the sea). We used sea, pond, and purified water as DNA-free samples and divided each into 12 bottles. Each bottle was added a solution of isolated cells (from Oncorhynchus kisutch) and fragmental DNA (from an internal positive control, IPC). The seawater and pond water contained the eDNA of Japanese jack mackerel (Trachurus japonicus) and common carp (Cyprinus carpio), respectively. We used O. kisutch tissue for the isolated cells because the species was not distributed in the sampling region. We conducted the experiment for 7 days. A Sterivex filter was used to filter 500-mL samples of water and 1.5 mL of the filtrate from each bottle was collected. After extracting eDNA from the filtrate and the Sterivex filter, the copy number of each type of DNA contained in the Sterivex samples and filtrate were estimated by quantitative real-time PCR.
Results/Conclusions
Our results show that eDNA derived from both cells and fragmental DNA decreased exponentially in both the sea and pond samples. The degradation of eDNA from inhabiting species showed similar behavior to the cell-derived eDNA. We evaluated three degradation models with different assumptions and degradation steps and found that a simple exponential model is effective in most cases. Our findings on cell- and fragmental DNA-derived eDNA provide fundamental information about the eDNA degradation process and can be applied to elucidate eDNA behavior in natural environments.