Environmental DNA: contactless tool for detecting shy organisms

Imagine this scenario. You are playing a game of hide and seek in water with someone and that someone is so good at hiding, that you are really not able to find him using your eyes. Luckily enough you have a small trick in your pocket. And that trick is just a syringe with water filter. By using that syringe, you are able to find him. Sounds good to you? That’s exactly what you can do using environmental DNA. And of course, some other equipment.

As environmental DNA is considered every DNA residual that you can find in the environment without the need of finding the targeted organisms. And it doesn’t matter if they are great mammals or microscopic pathogens. Everything that leave behind DNA can be detected. Obviously it´s not always easy, there are many things that can go wrong during the process. And what even is the process? Firstly you have to sample the water (or any other environment, but the water is the most convenient one) using the filter that has small enough pores to catch the DNA particles. After that you have to extract the DNA from the filter and using PCR find out what DNA you manage to capture.

Sometimes you find nothing, but that’s also the part of the process, especially when you are looking for pathogens, when finding nothings is actually good news. And what can go wrong? You may even filter the DNA you are looking for but it will be in so low amount that it would seem as falsely negative. Sometimes the filters gets too dirty before you can find the high enough amount of DNA. Or you can filter also some small crustaceans, that can eat out your DNA. Or you can make a storage mistake. Many things can occur.

But what for is this all good, that you would go through such trouble? It can be useful tool for nature protection. If you are searching for same rare shy species, you only need to find the water, not them. And suddenly seemingly empty waters could be full of life so they are worth protecting. Using techniques such as metabarcoding, you are able to target a lot of species, which can make this tool also really fast.

All of this, detecting the pathogens and organism, such as amphibians and their pathogenous fungi of genus Batrachochytrium are main goals of my dissertation. Of course, there is more to it, but I don´t want to take the pleasure of reading the thesis afterwards with any secrets to it. So stay tuned for the finished thing.