A guest blog by Dr Chloe Robinson.
Freshwater systems, including rivers, lakes and wetlands, are complex and dynamic habitats, home to a wide variety of species. This complexity coupled with the often large surface area covered by freshwater, makes aquatic species difficult to both detect and monitor over time. Traditional monitoring methods, including trapping, electrofishing and seine netting, often miss species which are rare (naturally exist in low abundance) and can be bias towards size of the species targeted, meaning some aquatic species remain undetected despite their presence in the system. The problems with not detecting species which are actually there include 1) misrepresentation of the existing community of species and 2) the lack of detection of aquatic invasive species in their early stages of invasion. Similar to rare species, invasive species are normally in low numbers at the start of their invasion of a new river or lake, meaning they are often missed with traditional monitoring methods.
Luckily, as technology advances, so do our methods of monitoring freshwater ecosystems. Through developments in DNA extraction techniques and sequencing, it is now possible to detect and monitor aquatic species using the DNA they leave behind in the water. Environmental DNA (eDNA) is defined as DNA found in an environmental sample (water, soil, permafrost, sediment), which has been shed from an animal in the form of urine, faeces, dead skin cells or through death and decomposition. We are able to collect these environmental samples and accurately identify all of the species which have been present in a freshwater ecosystem and/or we can target one particular species and look for presence and distribution across a variety of sample types. This methodology is particularly useful for detecting aquatic invasive species; if we can use eDNA techniques to find evidence of a new invasive species invasion, we can target areas for intensive investigation and removal of the invasive species before they become established, spread and potentially start impacting negatively on the local environment.
eDNA methods have been previously used to detect and monitor some aquatic invasive species individually including topmouth gudgeon (Pseudorasbora parva) and Chinese mitten crab (Eriocheir sinensis), and for detecting a combination of native, invasive and invasive pathogen species such as native white-clawed crayfish (Austropotamobius pallipes), invasive American signal crayfish (Pacifastacus leniusculus) and fungal-like pathogen Aphanomyces astaci. To detect these species, 15 mL water samples are collected from a combination of rivers and lakes, which are then processed in the laboratory to separate the DNA from the water. DNA is then multiplied in a PCR machine, using a technique which is designed to produce a ‘flag’ on the screen when DNA from a target species is present in a sample. This enables us to essentially map out where the target species is across samples and sites.
Our previous research has used eDNA to investigate evidence of coexistence of native and invasive crayfish in absence of crayfish plague pathogen A. astaci and compare eDNA with standard trapping protocols for crayfish species. We determined that eDNA was far more sensitive than trapping for determining presence of both crayfish species and successfully detected the A. astaci pathogen in infected rivers (Robinson et al., 2018). Secondly, we applied eDNA as a method to assess the success of previous attempts to eradicate topmouth gudgeon, where we found that DNA from this fish species was present in ponds where trapping failed to successfully detect any fish (Robinson et al., 2019a). Additionally, we have applied eDNA to look at the effects of river barriers on 1) upstream migration of Chinese mitten crabs and 2) the downstream transport of eDNA from American signal crayfish. In this study, we concluded that barriers had limited the upstream migration of mitten crabs and the presence of barriers could potentially be slowing the downstream movement of eDNA from signal crayfish upstream (Robinson et al., 2019b).
The above applications of eDNA show the fine-scale accuracy that can be achieved when using eDNA to detect and monitor aquatic species. The future of eDNA involves further technological and experimental development to allow for quantification of species abundance and use of eDNA to study the variability of genetic material in target species populations (population genetics). These advancements will enable management strategies to be put in place for conserving native species, controlling aquatic invasive species, and for overall preservation of freshwater ecosystems.
-Dr Chloe V Robinson (Centre for Biodiversity Genomics, University of Guelph. Canada)
- Robinson, C. V., Uren Webster, T. M., Cable, J., James, J. & Consuegra, S. (2018). Simultaneous detection of invasive signal crayfish, endangered white-clawed crayfish and the crayfish plague pathogen using environmental DNA. Biological Conservation, 222, 241-252. https://doi.org/10.1016/j.biocon.2018.04.009.
- Robinson, C. V., Garcia de Leaniz, C., Rolla, M., & Consuegra, S. (2019a). Monitoring the eradication of the highly invasive topmouth gudgeon (Pseudorasbora parva) using a novel eDNA assay. Environmental DNA, early view. https://doi.org/10.1002/edn3.12.
- Robinson, C. V., Garcia de Leaniz, C., & Consuegra, S. (2019b). Effect of artificial barriers on the distribution of the invasive signal crayfish and Chinese mitten crab. Scientific Reports, 9, 7230. | https://doi.org/10.1038/s41598-019-43570-3.