Environmental DNA (eDNA) detection has emerged as a powerful tool for monitoring aquatic organisms, but much remains unknown about the dynamics of aquatic eDNA over a range of environmental conditions. DNA concentrations in streams and rivers will depend not only on the equilibrium between DNA entering the water and DNA leaving the system through degradation, but also on downstream transport. To improve understanding of the dynamics of eDNA concentration in lotic systems, we introduced caged trout into two fishless headwater streams and took eDNA samples at evenly spaced downstream intervals. This was repeated 18 times from mid-summer through autumn, over flows ranging from approximately 1-96 L/s. We used quantitative PCR to relate DNA copy number to distance from source. We found that regardless of flow, there were detectable levels of DNA at 239.5 m. The main effect of flow on eDNA counts was in opposite directions in the two streams. At the lowest flows, eDNA counts were highest close to the source and quickly trailed off over distance. At the highest flows, DNA counts were relatively low both near and far from the source. Biomass was positively related to eDNA copy number in both streams. A combination of cell settling, turbulence and dilution effects is probably responsible for our observations. Additionally, during high leaf deposition periods, the presence of inhibitors resulted in no amplification for high copy number samples in the absence of an inhibition-releasing strategy, demonstrating the necessity to carefully consider inhibition in eDNA analysis.

No abstract

Environmental DNA (eDNA) is being rapidly adopted as a tool to detect rare animals. Quantitative PCR (qPCR) using probe-based chemistries may represent a particularly powerful tool because of the method’s sensitivity, specificity, and potential to quantify target DNA. However, there has been little work understanding the performance of these assays in the presence of closely related, sympatric taxa. If related species cause any cross-amplification or interference, false positives and negatives may be generated. These errors can be disastrous if false positives lead to overestimate the abundance of an endangered species or if false negatives prevent detection of an invasive species. In this study we test factors that influence the specificity and sensitivity of TaqMan MGB assays using co-occurring, closely related brook trout (Salvelinus fontinalis) and bull trout (S. confluentus) as a case study. We found qPCR to be substantially more sensitive than traditional PCR, with a high probability of detection at concentrations as low as 0.5 target copies/µl. We also found that number and placement of base pair mismatches between the Taqman MGB assay and non-target templates was important to target specificity, and that specificity was most influenced by base pair mismatches in the primers, rather than in the probe. We found that insufficient specificity can result in both false positive and false negative results, particularly in the presence of abundant related species. Our results highlight the utility of qPCR as a highly sensitive eDNA tool, and underscore the importance of careful assay design.

The concentration of dissolved oxygen in aquatic systems helps regulate biodiveristy 1, 2 , nutrient biogeochemistry 3 , greenhouse gas emissions 4 , and drinking water quality 5 . The long-term declines in dissolved oxygen concentrations in coastal and ocean waters have been linked to climate warming and human activity 6, 7 , but little is known about changes in dissolved oxygen concentrations in lakes. While dissolved oxygen solubility decreases with increasing water temperatures, long-term lake trajectories are not necessarily predictable. Oxygen losses in warming lakes may be amplified by enhanced decomposition and stronger thermal stratification 8, 9 or they may increase as a result of enhanced primary production 10 . Here we analyse 45,148 dissolved oxygen and temperature profiles from 393 temperate lakes spanning 1941-2017. We find that a decline in dissolved oxygen is widespread in surface and deep-water habitats. The decline in surface waters is primarily associated with reduced solubility under warmer water temperatures, although surface dissolved oxygen increased in a subset of highly-productive warming lakes, likely due to increasing phytoplankton production. In contrast, the decline in deep waters is associated with stronger thermal stratification and water clarity losses, but not with changes in gas solubility. Our results suggest that climate change and declining water clarity have altered the physical and chemical environment of lakes. Freshwater dissolved oxygen losses are 2.5-10 times greater than observed in the world's oceans 6, 7 and could threaten essential lake ecosystem services 2,3,5,11 .