Montreal, Sep 5 (The Conversation) — The increasing threats of climate change and human activities on freshwater ecosystems like lakes and rivers have heightened the importance of monitoring the species within them. Traditional methods, such as capturing animals, often fall short in keeping up with rapid ecological changes. What if we could monitor these species without capturing or observing them directly? We can achieve this by analyzing the DNA and RNA they leave behind in the water.
Every organism deposits tiny traces in its environment—be it skin cells, waste products, or microscopic fragments, all carrying genetic material unique to each species. When scientists collect a water sample or a soil sample, or even filter the air, they gather something known as environmental DNA (eDNA) or RNA (eRNA). This can reveal the presence or history of certain species in that area.
Recent research has proven that eRNA, once thought to be too unstable for fieldwork, is reliably detectable in freshwater environments.
Our Research — DNA molecules take time to fully degrade in aquatic environments. Consequently, eDNA may derive from existing organisms or those that vanished weeks prior. On the contrary, RNA degrades quickly, which unexpectedly becomes advantageous. This fragility provides a real-time snapshot of currently active organisms.
At McGill University's Gault Nature Reserve, researchers utilize the Large Experimental Array of Ponds (LEAP) with 96 cattle-tank "ponds," each containing roughly 1,000 liters of water from nearby Lake Hertel. These mesocosms mimic real freshwater ecosystems, allowing scientists to examine how freshwater communities react to rapid environmental changes, such as shifts in pH and temperature.
A mesocosm is a human-constructed tank that replicates a real freshwater ecosystem, large enough to include microbes, plankton, and natural water but controlled to test specific factors and replicate experiments. You can think of them as large outdoor aquariums used for scientific study.
Within our study, we experimented with these mesocosms at LEAP by adding a solution with the DNA and RNA of water fleas (Daphnia pulex) into one of the water mesocosms. These organisms are common in freshwater but absent from Lake Hertel itself. In doing so, we tracked how eDNA and eRNA behaved over time. We then transferred 10% of the water volume to successive mesocosms, diluting the solution until it reached a 10,000-fold dilution. Water samples were collected right after introducing the solution to the initial tanks and continued for 24 days, spanning nine collections.
Using digital PCR, a highly sensitive technology also utilized during the COVID-19 pandemic to track the virus in wastewater, we measured DNA and RNA concentrations over time. This allowed us to precisely quantify the degradation rates of DNA and RNA, comparing their persistence under identical conditions.
We also investigated the differences among RNA types: messenger RNA (mRNA), which carries transient instructions on protein synthesis, and ribosomal RNA (rRNA), a more stable component of cellular protein-making machinery.
Findings — Our research found that RNA degrades faster than DNA once released into water. Notably, mRNA degraded more rapidly than rRNA. Despite RNA's quick degradation, sensitive detection methods like digital PCR still identified both DNA and RNA at a 10,000-fold dilution. This underscores digital PCR's potential for real-time monitoring of active life in freshwater systems.
The study demonstrates that environmental RNA, which dissipates soon after an organism dies, can disclose recent biological activity. mRNA, in particular, offers a better snapshot of active life in aquatic systems. This enables scientists and environmental managers to detect changes swiftly and take action to protect freshwater ecosystems.
The Future of eRNA — Environmental RNA has the potential to uncover not just species presence, but also their health status and life stages. For instance, one study indicated that changes in gene activity due to heat stress could be detected in mRNA from a water sample, offering insights into organismal health in ecosystems. Additionally, eRNA can differentiate between tadpoles and adult amphibians, facilitating the monitoring of life stages in the wild without capturing animals.
These findings point towards eRNA becoming a powerful, non-invasive tool for biodiversity monitoring. With ongoing research, environmental RNA could aid in tracking life within freshwater ecosystems and reveal how species adapt to rapid changes in the world. (The Conversation)
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