How environmental RNA can give us real-time picture of freshwater biodiversity

As climate change and human activity threaten freshwater ecosystems like lakes and rivers, it's more important than ever to know how the species that inhabit them are being impacted. But traditional methods of monitoring species, such as catching animals, are challenging to implement and can miss rapid changes. What if we could track life without capturing or directly observing individual animals? It turns out we can, by reading the DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid) they leave behind in the water.

Every living thing leaves tiny traces in its environment — skin cells, waste or microscopic fragments we cannot see. These fragments carry genetic material unique to each species on Earth. So, when scientists sample one bottle of water, a few grams of soil, or even filter the air, they are actually collecting what's called environmental DNA (eDNA) or RNA (eRNA), which can tell us which species are (or have been) present in an area.

Recent studies have demonstrated that eRNA, previously considered too unstable for field use, can be reliably detected in freshwater ecosystems. Our research DNA molecules take time to completely disappear in the aquatic environment. That means eDNA might come from organisms living there now — or from ones that disappeared weeks ago.

However, RNA breaks down quickly. That fragility turns out to be an advantage: it gives us a snapshot of what's alive and active in the moment, offering a powerful new way of tracking living organisms in real time. At McGill University's Gault Nature Reserve, researchers use the Large Experimental Array of Ponds (LEAP): 96 cattle-tank “ponds,” each holding about 1,000 litres of water drawn from nearby Lake Hertel. Known as mesocosms, they allow the researchers to test how freshwater communities respond to rapid changes in their environment, such as pH and temperature.

A mesocosm is a human-made outdoor tank that mimics a real freshwater ecosystem — big enough to include microbes, plankton and natural water, yet controlled so scientists can test isolated factors and repeat experiments. You can think of them as giant outdoor aquariums for science.