A systematic approach to evaluate the influence of environmental conditions on eDNA detection success in aquatic ecosystems

Abstract

The use of environmental DNA (eDNA) to determine the presence and distribution of aquatic organisms has become an important tool to monitor and investigate freshwater communities. The successful application of this method in the field, however, is dependent on the effectiveness of positive DNA verification, which is influenced by site-specific environmental parameters. Factors affecting eDNA concentrations in aquatic ecosystems include flow conditions, and the presence of substances that possess DNA-binding properties or inhibitory effects. In this study we investigated the influence of different environmental parameters on the detection success of eDNA using the invasive goby Neogobius melanostomus. In a standardized laboratory setup, different conditions of flow, sediment-properties, and fish density were compared, as well as different potential natural inhibitors such as algae, humic substances, and suspended sediment particles. The presence of sediment was mainly responsible for lower eDNA detection in the water samples, regardless of flow-through or standing water conditions and a delayed release of eDNA was detected in the presence of sediment. Humic substances had the highest inhibitory effect on eDNA detection followed by algae and siliceous sediment particles. The results of our study highlight that a successful application of eDNA methods in field surveys strongly depends on site-specific conditions, such as water flow conditions, sediment composition, and suspended particles. All these factors should be carefully considered when sampling, analyzing, and interpreting eDNA detection results.

Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement

“…However, we discovered that several aspects of eDNA metabarcoding require further optimization prior to implementation in established monitoring programs. The impact of vertical zonation on eDNA patterns (Minamoto et al, ), temporal stability (Bista et al, ), abiotic influences on eDNA persistence (Stoeckle et al, ), and the correlation between eDNA signal strength and true abundance (Jo et al, ), have received little attention to date and require more investigation. In agreement with the growing body of eDNA studies in the literature, the data from the Aramoana site indicate that eDNA metabarcoding surveys, when appropriately executed, will be a powerful tool in the management and conservation of marine environments.…”

Development and application of environmental DNA surveillance for the threatened crucian carp (Carassius carassius)

“…We found that crucian carp density (CPUE) positively influenced eDNA detection probability and DNA copy number. Density is frequently reported to improve detection probability of aquatic species due to more eDNA deposition in the environment (Buxton, Groombridge, Zakaria, & Griffiths, ; Schmelzle & Kinziger, ; Stoeckle et al., ), but this relationship is highly variable across study systems and species due to influence of external factors (Buxton, Groombridge, & Griffiths, ; Goldberg et al., ; Strickler et al., ). For example, increase in water temperature coincided with breeding activity and heightened DNA release in other fish and amphibian species (Buxton, Groombridge, Zakaria, & Griffiths, ; Bylemans et al., ).…”

“…Links established between eDNA and pH support greater detectability, concentration, and persistence of eDNA in more alkaline waters (Barnes et al., ; Goldberg et al., ; Strickler et al., ). Conductivity relates to total dissolved solids (TDS) and sediment type, which can impair eDNA detection due to release of inhibitory substances and their capacity to bind DNA (Buxton, Groombridge, & Griffiths, ; Stoeckle et al., ). Vegetated ponds reduce UV exposure thereby preserving eDNA (Barnes et al., ), and are susceptible to terrestrialisation which can create anoxic conditions that may slow eDNA degradation (Barnes et al., ; Pilliod et al., ; Weltz et al., ).…”

“…Environmental variables play a substantial role in abundance/biomass estimation by influencing the ecology of eDNA (Barnes et al., ). Variables examined have included temperature, pH, salinity, conductivity, anoxia, sediment type, and UV light (Barnes et al., ; Buxton, Groombridge, & Griffiths, ; Buxton, Groombridge, Zakaria, & Griffiths, ; Goldberg, Strickler, & Fremier, ; Keskin, ; Pilliod, Goldberg, Arkle, & Waits, ; Robson et al., ; Stoeckle et al., ; Strickler, Fremier, & Goldberg, ; Takahara et al., ; Weltz et al., ). However, these variables are not always measured and only a handful of studies have assessed their effects in ponds (Buxton, Groombridge, & Griffiths, ; Buxton, Groombridge, Zakaria, & Griffiths, ; Goldberg et al., ; Takahara et al., ).…”

Environmental DNA improves Eastern Hellbender (Cryptobranchus alleganiensis alleganiensis) detection over conventional sampling methods

“…For example, the various physiochemical factors of lotic freshwater environments such as turbidity and conductivity are suggested to influence eDNA detection (Buxton, Groombridge, & Griffiths, 2017). However, studies rarely consider the importance of these factors in their sampling and analysis of eDNA data (Stoeckle et al, 2017). Comparative modelling approaches that also account for eDNA detection rates allow decision-makers to weigh the costs and benefits of sampling methods to better understand population declines, fill data gaps, and improve monitoring programs (Jackson et al, 2016;Nichols et al, 2008).…”