What in the world is eDNA and why should we care?

 

What is eDNA?

1. Short for environmental DNA. (Deoxyribonucleic acid)

2. eDNA is the genetic material that is shed by an organism into the environment. – skin, eggs, waste, gametes, mucous, scales, you name it – anything a species can shed, drop, or left behind. 

3. Similar to a perpetrator leaving DNA at a crime scene (through saliva, or sweat), it is the specific signature that is left behind in the environment. 

4. What we can do, is collect samples of the environment itself (instead of the species), extract the DNA and compare it to known sequences unique to that target species, thereby determining its presence or absence from that sample location.

 

How do we do this? 

1. We can accomplish this is by filter the sampling;

2. Then extracting & releasing the DNA from the filter through a chemical and physical treatment, putting it into solution;

3. We then put the DNA solution through a series of washes;

4. And what we are left with is the eluted & Preserved DNA. 

There are few different approaches that can be used in eDNA. Most common are what’s called qPCR, short for quantitative Polymerase Chain Reaction; and, Metabarcoding:

1. qPCR is where one or a few species are targeted for detection;

2. Species specific assays are designed using specific primers and probes.

3. qPCR rapidly multiply copies of the target DNA, and these copies are measured for amplification; 

4. If the samples amplify the target DNA, the target species is noted at present, and vice versa;

Then there is Metabarcoding: 

1. this is essentially where all species can potentially be detected within each sample. 

2. All DNA sequences captured are identified in the sample by comparing them to known DNA sequences. 

3. These sequences are catalogued in various databases, and universal primers are used to amplify these species.

4. Multiple spatial samples can be taken and entire species distributions could then be catalogued. 

 

Analysis of indicator species and invasive species (as health markers).

For instance we are using (currently analyzing) the contrasting native and invasive species as indicators of the current health of lake ontario. 

In the last decade there has been a big movement to repopulate the native Atlantic Salmon to the waters of Lake ontario. Salmons are an amazing marker for water health because they are part of a very intricately connected web of biodiversity. They feed humans, bears and other larger marine species - salmon come into contact with around 137 different species in their journey to sea and back. They are such an important food source that without them our lakes would change dramatically. They also bring nutrients from the sea back to freshwater lakes where they spawn and later die, feeding forests with valuable nutrients. 

The opposite can almost be said for the zebra mussel or quagga mussel populations which are our invasive species marker. They can harm native ecosystems when found in large densities: they out-compete other filter feeders causing a decline in plankton and other marine microorganisms which are the base of the marine food chain, starving out competitors. And they adhere to all hard surfaces which include other native mussels, turtles or crustaceans.

Analysing both of these species through the barcoding methods previously described, can give us a glimpse into our efforts for rewilding species, and the health of the marine food chain. We can then use this data to create collective bioregional action to sustain a healthy ecosystem.

 

Analysis of E-DNA as a future safeguard of evolutionary data

Speculatively to be kept as a record of the current species living in this great freshwater body (since we can expect most certainly that by 2050 the population numbers, or biodiversity will have changed) We can use this information in the future as a “library” or “archive” to determine what, why and how environments have changed and perhaps even preserve DNA from species that may no longer (sadly) exist in 2050.

 

Everyone can be a scientist. The world needs place based people to be observing, analysing and recording data to monitor the health of our environments! And most importantly to communicate and make accessible this biological data through media, community efforts, storytelling and art!