Influence of sediment and stream transport on detecting a source of environmental DNA

Abstract

Environmental DNA (eDNA) can be used for early detection, population estimations, and assessment of potential spread of invasive species, but questions remain about factors that influence eDNA detection results. Efforts are being made to understand how physical, chemical, and biological factors—settling, resuspension, dispersion, eDNA stability/decay—influence eDNA estimations and potentially population abundance. In a series of field and controlled mesocosm experiments, we examined the detection and accumulation of eDNA in sediment and water and the transport of eDNA in a small stream in the Lake Michigan watershed, using the invasive round goby fish (Neogobius melanostomus) as a DNA source. Experiment 1: caged fish (average n = 44) were placed in a stream devoid of round goby; water was collected over 24 hours along 120-m of stream, including a simultaneous sampling event at 7 distances from DNA source; stream monitoring continued for 24 hours after fish were removed. Experiment 2: round goby were placed in laboratory tanks; water and sediment were collected over 14 days and for another 150 days post-fish removal to calculate eDNA shedding and decay rates for water and sediment. For samples from both experiments, DNA was extracted, and qPCR targeted a cytochrome oxidase I gene (COI) fragment specific to round goby. Results indicated that eDNA accumulated and decayed more slowly in sediment than water. In the stream, DNA shedding was markedly lower than calculated in the laboratory, but models indicate eDNA could potentially travel long distances (up to 50 km) under certain circumstances. Collectively, these findings show that the interactive effects of ambient conditions (e.g., eDNA stability and decay, hydrology, settling-resuspension) are important to consider when developing comprehensive models. Results of this study can help resource managers target representative sites downstream of potential invasion sites, thereby maximizing resource use.

Integrating physiology and environmental dynamics to operationalize environmental DNA (eDNA) as a means to monitor freshwater macro‐organism abundance

“…by increasing the value of S p ) (Curtis et al, 2020; Jane et al, 2015; Pont et al, 2018). Additionally, eDNA can accumulate in benthic sediment, particularly when decay rates in sediment are slower than in the water column (Barnes et al, 2014; Nevers et al, 2020; Turner et al, 2015). Increased turbulence could resuspend FPOM (including eDNA) during extreme discharge events, obscuring the relationship between organism abundance and eDNA (Jane et al, 2015; Shogren et al, 2017).…”

Comparison of species-specific qPCR and metabarcoding methods to detect small pelagic fish distribution from open ocean environmental DNA

“…In recent years, a new technique for investigating fish distribution in water, environmental DNA method, has been developed. Environmental DNA (eDNA) is DNA that creatures shed into their living environment, including water, sediment, soil, and even air [ 1 – 4 ]. Surveys using eDNA have been performed in rivers, lakes, and coastal areas [ 5 – 9 ].…”

Estimating number of European eel (Anguilla anguilla) individuals using environmental DNA and haplotype count in small rivers

“…Various studies have shown that eDNA can be detected in standing water days after the source of the DNA has been removed, see, for example, Barnes et al ( 2014 ), but in running water samples of several liters has often been necessary to compensate for the reduced probability of detection caused by removal of eDNA by water flow (Rees et al, 2014 ). Field experiments in rivers with low discharge (<100 liters/second) has shown that eDNA concentrations are relatively stable the first 24 h after the source of DNA has been removed, but that eDNA concentration decreases with increased discharge (Jane et al, 2015 ; Nevers et al, 2020 ). The discharge when we collected the sample was much higher, and this should have reduced the probability of detection even more.…”