The eDNA Toolkit enables users to detect longitudinal discontinuities in river fauna and flora caused by barriers. This is specifically useful to understand and predict the consequences of human modifications of freshwater ecosystems and get a better grasp of how human-altered environments shape species interactions across taxa.
Environmental DNA (eDNA) is considered to be more sensitive, cost effective and faster than traditional survey methods, as sample collection for eDNA does not impact directly upon species or their habitats, requires no taxonomical knowledge, and is generally less time consuming. Combined with metagenomics, eDNA is rapidly becoming the tool of choice for the early detection of multiple taxa, including aquatic invasive species, as well as for the study of current and past community dynamics. eDNA represents a mixture of genetic material of different qualities (i.e. at various decay stages), including chromosomes, plasmids contained in cells, as well as extracellular DNA fragments, free in the environment or adsorbed onto particles. Environmental DNA from fish is detectable for between 7 – 25 days in freshwater but only 7 days for marine fish.
We have optimised and validated several eDNA-based meta-barcoding protocols for freshwater fish, invertebrates and macrophytes. The eDNA assays developed in AMBER allow users to infer presence/absence data for several targeted species from small water samples. Community-wide and species-specific markers were developed for the detection of native and invasive aquatic species using Next Generation Sequencing (metabarcoding) and real time PCR (qPCR).