Effects of Microbial Activity and Environmental Parameters on the Degradation of Extracellular Environmental DNA from a Eutrophic Lake

Abstract

Extracellular DNA (exDNA) pool in aquatic environments is a valuable source for biomonitoring and bioassessment. However, degradation under particular environmental conditions can hamper exDNA detectability over time. In this study, we analyzed how different biotic and abiotic factors affect the degradation rate of extracellular environmental DNA using 16S rDNA sequences extracted from the sediment of a eutrophic lake and Anabaena variabilis cultured in the laboratory. We exposed the extracted exDNA to different levels of temperature, light, pH, and bacterial activity, and quantitatively analyzed the concentration of exDNA during 4 days. The solution containing bacteria for microbial activity treatment was obtained from the lake sediment using four consecutive steps of filtration; two mesh filters (100 μm and 60 μm mesh) and two glass fiber filters (2.7 μm and 1.2 μm pore-sized). We found that temperature individually and in combination with bacterial abundance had significant positive effects on the degradation of exDNA. The highest degradation rate was observed in samples exposed to high microbial activity, where exDNA was completely degraded within 1 day at a rate of 3.27 day^-1. Light intensity and pH had no significant effects on degradation rate of exDNA. Our results indicate that degradation of exDNA in freshwater ecosystems is driven by the combination of both biotic and abiotic factors and it may occur very fast under particular conditions.

Keywords: biomonitoring; degradation; extracellular DNA; freshwater environment; light; microbial activity; pH; temperature.

Figure 1

ExDNA concentration in samples exposed to different temperatures. (A) Changes in exDNA concentration detected under different temperature treatments (5 °C, 15 °C, 25 °C, and 35 °C). (B) Total exDNA degradation (%) at the end of the experiment (4 days). Different letters indicate statistically significant differences defined by p < 0.05 between treatments. Error bars represent the standard deviations among replicates within the treatments.

Figure 2

ExDNA concentration in samples exposed to different bacterial abundance and temperatures. (A–C) Changes in exDNA concentration detected under different bacterial treatments (no bacteria added and diluted bacterial solutions by 10⁰, 10⁻², and 10⁻⁵-fold) at different temperatures (5 °C, 25 °C, and 35 °C). Average bacterial abundance before dilutions was 1.6 ± 0.12 × 10⁷ cells/mL. (D–F) Total exDNA degradation (%) at the end of the experiments (4 days). NO BAC: no bacteria added. Different letters indicate statistically significant differences defined by p < 0.05 between treatments. Error bars represent the standard deviations among replicates within treatments.

Figure 3

ExDNA concentration in samples exposed to different light intensity levels and temperatures. (A,B) Changes in exDNA concentration detected under different light treatments at different temperatures (5 °C and 35 °C). (C,D) Total exDNA degradation (%) at the end of the experiments (4 days). Different letters indicate statistically significant differences defined by p < 0.05 treatments between treatments. Error bars represent the standard deviations among replicates within treatments.

Figure 4

ExDNA concentration in samples exposed to different pH levels combined and temperatures. (A,B) Changes in exDNA concentration detected under different pH levels at different temperatures (5 °C and 35 °C). (C,D) Total exDNA degradation (%) at the end of the experiments (4 days). Different letters indicate statistically significant differences defined by p < 0.05 between treatments. Error bars represent the standard deviations among replicates within treatments.