Detection,  Projects

Early Detection at the Molecular Level!

By convention, early detection of invasive species including aquatic invasive species typically relies on visual observation of the species causing harm or the symptoms thereof. In many cases we visually observe swallowwort (Cynanchum spp.) growing on the land or perhaps we catch a northern snakehead (Channa argus) while fishing for pike. From an ecological function perspective we see for example, canopy dieback indicating a possible forest pest or we may observe changes in aquatic food web abundance indicating the presence an aquatic invasive species. Unfortunately and according to the invasives curve[1], by the time a species is detected and the public takes notice, the invasive is already populated and the management thereof becomes difficult at best. Genuine early detection means detecting the presence of a species before it has the opportunity to populate and cause irreplaceable harm to the ecosystem of concern.

Aquatic invasive species often pose a unique level of difficulty when it comes to early detection. Simply put, many aquatic animals are hidden beneath the water’s surface and the invasion curve becomes skewed. The use of environmental DNA may offer a unique solution to the early detection of aquatic organisms.

As aquatic animals such as fish swim through the water, they constantly release biological material into the water. Materials such as scales, mucus and waste contain genetic material specific to that species. It is this genetic material that can be detected within water samples and amplified to allow for the unmistakable identification of a species and alluding to its presence within the area where the water sample was taken.

Genetics is one discipline that has an abundance of terminology barely understandable by those non-geneticists; however some basics may pertinent here. Once detected the amplification of DNA is done with a polymerase chain reaction (PCR). PCR is a method where an enzyme (polymerase), amplifies a short specific part of the DNA (amplicon) in cycles. In every cycle the number of short specific sections of DNA is doubled, leading to an exponential amplification of targets. In qPCR, exactly the same procedure happens but with two major differences: first the amplified DNA is fluorescently labelled (usually with cyanine based fluorescent dyes) and second, the amount of the fluorescence released during amplification is directly proportional to the amount of amplified DNA. The higher the initial number of DNA molecules in the sample, the faster the fluorescence will increase during the PCR cycles. The result looks similar to a barcode found on almost all goods purchased at your local grocery store. This barcode holds an enormous amount of information specific to that product (species).1a

Over the next two summers the partners of the SLELO PRISM in cooperation with The Nature Conservancy and The Department of Microbiology and Immunology at Cornell University, will undertake a project to assess the feasibility of using eDNA as an early detection tool for aquatic invasive species. Over 400 water samples will be collected from four strategic locations along Eastern Lake Ontario and assessed using qPCR for the presence of certain AIS. Underwater video technology (UVT) combined with eDNA will also be used as a citizen science component to assess the validity of UVT as an early detection tool as well.

[1] The invasion curve. Adapted from Invasive Plants and Animals Policy Framework, State of Victoria, Department of Primary Industries, 2010.

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