Fecal contamination can be controlled by environmental DNA analysis

“Who is peeing in water?” This question is not as common as it seems. However, there are a lot of scientific facts behind it. It takes years of research to determine the source of fecal contaminants, an important public health issue. Rose Ragot, a doctoral student, and Richard Villemur, a professor at the Institut national de la Recherche scientifique (INRS), are currently working on genetic primers. These primers are a short DNA sequence that can be used as a starting point to sequence. Primers are useful in identifying potential sources of fecal contamination in water, especially in urban and agricultural environments. Their work was published by the journalEnvironmental Monitoring and Assessment

Fecal contamination can be diffused, meaning that there could be multiple sources within a few kilometers of the affected area. To manage this pollution, it is important to find the right genetic indicators in the feces. For example, human contamination could be a sign of faulty wastewater treatment infrastructure and leaking septic tank. Bovine contamination is more likely from poor manure management or field runoff.

The primers were used to identify the majority mammals and birds that are responsible for fecal pollution. Professor Villemur explains that these small genetic sequences, which are based on mitochondrialDNA, are not bacterial indicators that are geographically specific.

Effective DNA sequencing

These primers act as a read button for environmental DNA analysis. Sequencing uses PCR amplification. It is the same method used in COVID testing. The primers tell the device which DNA fragments should be replicated in a large amount of identical copies to determine the species. This innovative approach does away with the need to perform a PCR analysis on every possible source.

Rose Ragot, a biology doctoral student, sampled four rivers in order to prove the effectiveness of these primers under real-life conditions. She began by analyzing the water in Rivire L’Assomption. This water flows through Joliette, before crossing an agricultural area. She also collected a sample of Rivire Bayonne, which flows through an agricultural area just upstream from Berthierville, where poultry, pigs and cattle are raised.

Ragot says that Rivire L’Assomption was contaminated by human and bovine fecal bacteria. This high level of contamination could partly be explained by a sewage system overflow from a rainstorm that occurred a few days before. Rose Ragot will continue to analyze almost 100 samples from these rivers for the remainder of her doctorate in collaboration with Fondation Rivires as well as watershed organizations in the area.

Primers are used to identify the species of mammals, birds, fish, and amphibians present in the environment. Based on the amount of DNA found, we can profile species and determine their relative abundance. Professor Villemur states that it is very helpful in wildlife management to track the presence of invasive species that are more sensitive to pollution. Villemur and Ragot will investigate this application in their future research.

Rose Ragot, Richard Villemur and Richard Villemur published the article “eDNA profiling in mammals, birds and fish of surface water by mitochondrial metagenomics – application for source tracking fecal contamination” on January 8. Environmental Monitoring and Assessment.

Provided by
Institut national de la recherche scientifique – INRS