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Degradation modeling of water environmental DNA: Experiments on multiple DNA sources in pond and seawater
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Degradation modeling of water environmental DNA: Experiments on multiple DNA sources in pond and seawater
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Journal Article
Degradation modeling of water environmental DNA: Experiments on multiple DNA sources in pond and seawater
2021
Overview
Environmental DNA (eDNA) analysis 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, for example, cells and fragmental DNA. We experimentally evaluated the degradation rates of eDNA derived from multiple sources, including fragmental DNA (internal PCR control [IPC]), free cells (from Oncorhynchus kisutch), and resident 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 resident species (Cyprinus carpio in the pond and Trachurus japonicus in the sea). We found that eDNA derived from both cells and fragmental DNA decreased exponentially in both the sea and pond samples. The degradation of eDNA from resident 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 was 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 quantify eDNA behavior in natural environments. We conducted the experiments for degradation of eDNA from cell and fragmental DNA. eDNA from inhabiting species showed similar behavior to that derived from cells. A simple exponential model was mostly useful to evaluate eDNA degradation.
