Environmental DNA analysis to manage faecal contamination

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“Who pees in the water? As unlikely as it may seem, there is a lot of science behind this question. Determining the source of faecal contamination, an important public health problem, requires years of research. Doctoral student Rose Ragot and Professor Richard Villemur of the National Institute for Scientific Research (INRS) are working on genetic primers, a short DNA sequence that serves as a starting point for sequencing. The primers make it possible to identify potential sources of faecal contamination, particularly in water flowing in urban and agricultural areas. Their work has been published in the journal Environmental monitoring and assessment.

Faecal contamination being diffuse, there may be several sources, several kilometers from the affected area. It is therefore necessary to find the right genetic indicators in the faeces to manage this pollution. For example, human contamination may indicate faulty wastewater treatment infrastructure or leaking septic tanks. A source of bovine contamination is more likely to be runoff from fields or poor manure management.

The research group found primers to identify the majority of mammals and birds, the main contributors to fecal contamination. “Unlike bacterial indicators which vary geographically according to diet, these small genetic sequences are species-specific because they are based on mitochondrial DNA,” explains Professor Villemur.

Efficient DNA sequencing

These primers serve as a sort of play button for environmental DNA analysis. Sequencing is done by PCR amplification, the same technique used in COVID testing. Primers tell the device which DNA fragments need to be replicated in a large number of identical copies to determine which species are present. By considering all species at once, this innovative approach eliminates the need to perform PCR analysis for every possible source.

Biology doctoral student Rose Ragot sampled four rivers to demonstrate the effectiveness of these baits in real conditions. She first analyzed the water from the L’Assomption River, which crosses the city of Joliette before crossing an agricultural area. She also took a sample of the Bayonne River, which crosses an agricultural area upstream of the municipality of Berthierville where cattle, pigs and poultry are raised.

“Human and bovine faecal contamination has been observed at the L’Assomption River,” says Ragot. An overflow of the sewer network during a storm a few days earlier would partly explain this high level of contamination. For the rest of her doctorate, Rose Ragot is continuing to analyze nearly 100 samples from these rivers, in collaboration with the Fondation Rivières and the region’s watershed organizations.

In addition to tracking sources of fecal contamination, baits are used to determine which species of mammals and birds, as well as fish and amphibians, are present in the environment. “We can profile species and even know their relative abundance based on the percentage of DNA found. Monitoring the presence of species that are more invasive and more tolerant to pollution, for example, is very useful in wildlife management,” explains Professor Villemur. Ragot and Villemur will explore this application in their future work.

The article “eDNA profiling of mammals, birds, and fish of surface waters by mitochondrial metagenomics: application for source tracking of fecal contamination in surface waters”, by Rose Ragot and Richard Villemur, was published on January 8 in the journal Environmental monitoring and assessment.


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More information:
Rose Ragot et al, eDNA profiling of surface water mammals, birds and fish by mitochondrial metagenomics: application for source monitoring of faecal contamination in surface waters, Environmental monitoring and assessment (2022). DOI: 10.1007/s10661-021-09668-w

Provided by the National Institute for Scientific Research – INRS

Quote: Environmental DNA analysis to manage fecal contamination (2022, February 24) retrieved February 24, 2022 from https://phys.org/news/2022-02-environmental-dna-analysis-fecal-contamination.html

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