Environmental Conditions Influence eDNA Persistence in Aquatic Systems

Abstract

Environmental DNA (eDNA) surveillance holds great promise for improving species conservation and management. However, few studies have investigated eDNA dynamics under natural conditions, and interpretations of eDNA surveillance results are clouded by uncertainties about eDNA degradation. We conducted a literature review to assess current understanding of eDNA degradation in aquatic systems and an experiment exploring how environmental conditions can influence eDNA degradation. Previous studies have reported macrobial eDNA persistence ranging from less than 1 day to over 2 weeks, with no attempts to quantify factors affecting degradation. Using a SYBR Green quantitative PCR assay to observe Common Carp ( Cyprinus carpio ) eDNA degradation in laboratory mesocosms, our rate of Common Carp eDNA detection decreased over time. Common Carp eDNA concentration followed a pattern of exponential decay, and observed decay rates exceeded previously published values for aquatic macrobial eDNA. Contrary to our expectations, eDNA degradation rate declined as biochemical oxygen demand, chlorophyll, and total eDNA (i.e., from any organism) concentration increased. Our results help explain the widely divergent, previously published estimates for eDNA degradation. Measurements of local environmental conditions, consideration of environmental influence on eDNA detection, and quantification of local eDNA degradation rates will help interpret future eDNA surveillance results.

Characterization, optimization, and validation of environmental DNA (eDNA) markers to detect an endangered aquatic mammal

“…Together, these findings suggest amplicons of less than 150 bp may not be the only, or best, solution for different eDNA sampling strategies. For example, while our primers were able to detect YFP eDNA spanning from days to weeks, a time-span reflecting similar values seen in other studies of aquatic fauna such as in fish and amphibians (Dejean et al 2011), many environmental factors can potential interact with DNA to preserve or degrade it (Barnes et al 2014); factors include the abundance of focal species, total eDNA present (from all organisms), and other abiotic and biotic factors, including temperature, pH, biochemical oxygen demand, and conductivity (Thomsen et al 2012a;Barnes et al 2014). However, there is also a relationship between DNA length and the particles it binds with within an environment (e.g.…”

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

“…Methodological papers trying to make approximations between fish biomass, abundance and eDNA detection probability were also published during the same time period by Dejean et al (2011) and Takahara, Minamoto, Yamanaka, Hideyuki & Kawabata (2012). Recently, studies have been focused on modeling persistence and detection using multiple biotic and abiotic factors such as vectors, system volume, sample volume, eDNA dynamics, stream flow, discharge and particle size (Piaggio, Engeman, Hopken, Humphrey, Keacher, Bruce, & Michael, 2013;Schmidt, Kery, Ursenbasher, Hyman, & Collins, 2013;Barnes, Turner, Jerde, Renshaw, Chadderton, & Lodge, 2014;Pilliod, Goldberg, Arkle, & Waits, 2014;Turner, Barnes, Charles, Jones, Xu, Jerde, & Lodge, 2014).…”

“…In addition to density, size and life history features of the target taxa, eDNA persistence can be influenced by other biotic factors such as bacterial and fungal concentrations (Dejean et al, 2011). The role of abiotic factors on eDNA persistence has also been reported (e.g., oxygen concentration, nuclease activity, pH, conductivity, Uv radiation, pH and temperature) (Shapiro, 2008;Dejean et al 2011;Barnes et al, 2014). Nonetheless, the effect of these factors has been studied independently and only one of these studies had measured how covariation of these factors (specific environmental conditions) affects persistence .…”

“…Nonetheless, the effect of these factors has been studied independently and only one of these studies had measured how covariation of these factors (specific environmental conditions) affects persistence . Other abiotic factors related to the system that can also affect persistence include: stream flow, currents, tidal oscillations, type of sediment, and salinity (Corinaldesi, Beolchini, & Dell'Anno, 2008;Golberg et al, 2011;Barnes et al, 2014). For example, eDNA persistence in freshwater lentic systems has been shown to be as great as 30 days (Ficetola et al, 2008) while for marine systems (open and highly dynamic systems) it only averages approximately seven days (Foote et al, 2012;Thomsen et al, 2012b).…”

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

“…2012a; Barnes et al . 2014). Nevertheless, where organisms’ generation of eDNA outpaces the combined forces of degradation and transport we expect to see a significant biological signal of species living in sampled habitats.…”