Study of Exogenous DNA Degradation in Ladoga Lake Water

Environmental DNA (eDNA) is genetic material obtained directly from samples of various natural substrates, rather than directly from a living organism. The use of eDNA simplifies monitoring of secretive and low-abundance species that are difficult to detect using classical environmental survey methods. Understanding the capabilities and limitations of eDNA-based methods requires information about the influence of various factors on the rate of degradation of nucleic acids in the environment. We studied the rate of DNA degradation at a temperature of 14°C in water from Svirskaya Bay of Lake Ladoga with pH 7.3 in the absence of light. For this purpose, highly specific primers and a TaqMan probe were developed and tested for the D-loop fragment of mitochondrial DNA of the domestic chicken (Gallus gallus domesticus). The choice of this particular genetic material as exogenous DNA was due to the minimal risk of contamination of natural water in the sampling area. At the start of the experiment, chicken DNA (galDNA) was added to the water samples to a concentration of 50 μg/L and detected by real-time PCR after 6 h and 1, 2, 3, 8, and 14 days. Using the developed protocol, we identified target D-loop sequences in natural water samples during the first three days of the experiment, with trace amounts of galDNA detected up to eight days.