Traditional aquatic monitoring methods are often difficult to perform, potentially inefficient or destructive, time- and cost consuming in terms of manpower, and dependent on diminishing taxonomic expertize. For aquatic disease monitoring, surveillance methods commonly involves scarifying a large amount of aquatic animals, such as fish and crayfish, for monitoring of infectious pathogens.

Environmental DNA or RNA (eDNA/eRNA) refers to genetic material from virus, whole microbial cells, or shed from multicellular organisms via metabolic waste, secretes, damaged tissue, skin cells etc that can be detected by sampling the non-living environment (e.g. water, soil) and provide information about the macro- and microorganisms and viral agents that are or were recently present. A common definition of eDNA is “genetic material obtained from environmental samples without any obvious signs of biological source material”.

eDNA monitoring is particularly useful for early detection of aquatic invasive species and diseases, allowing the detection of invasive species and pathogens at low density at any life stage or season. In sources of concern, e.g. ship ballast, aquaculture, or highrisk habitats, eDNA monitoring can alert regulatory authorities before the establishment of alien species or disease outbreaks. Early detection is crucial for preventing biological invasions in recipient ecosystems, and (if possible) eradicate earlier for lower costs and reduced hazard. Further, early warning of emerging disease outbreaks may allow early control and mitigation measures.

Targeted eDNA monitoring differ from large scale metagenomics aiming to describe all present organisms in a community, to more targeted approaches aiming to locating and quantifying species of management concern. For this purpose, quantitative PCR (qPCR) or droplet digital PCR (ddPCR) designed for detection and quantification at specific species/gene levels has proved powerful, and a rapidly growing body of studies have shown its suitability for inventory and monitoring of endangered species, invasive species, wild-life diseases and diseases of concern in aquaculture.

Unlike soil and sediment samples where eDNA traces can persist for centuries, it seems that waterborne eDNA can yield near-realtime estimates for local species frequencies, since the DNA concentration rapidly decreases to sub-detectable levels once organisms are removed from the environment.