Mitochondrial DNA in the environment: towards the development of better animal-specific markers for fecal source tracking

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Numerous sources can contribute to fecal contamination of water and soil. As many waterborne pathogenic microorganisms are associated with fecal pollution, monitoring such contamination in water quality assessments is of great importance for public health. Indeed, fecal pollution of surface water and groundwater can have a great impact on public health (drinking water) and local economy (agriculture and recreational activities). The microbiological quality of water is primarily monitored using fecal indicator organisms, such as coliforms. However, these indicators do not identify the source of the fecal matter. Several fecal source tracking (FST) methods have been developed to address the issue of host-specific contributions to fecal contamination. Host-specific genetic markers detected by PCR methods indicate the presence of fecal contamination from specific animal species. Most of these genetic markers rely on the presence of microorganisms in the intestinal (fecal) matter that are associated with specific animal host. Despite their number, none of these markers are completely and sufficiently specific and sensitive. Therefore, it is essential to develop novel genetic markers and innovative methods for FST.*** Recently developed FST genetic markers rely on the important release of colonic epithelium cells in the intestinal lumen. These cells contain numerous copies of mitochondria with their genome (mtDNA). In the early 2000s, my team has been the first group to develop mtDNA-based FST markers; such markers are now used by other groups. mtDNA sequences are highly species-specific; substantial differences in mtDNA can be found between closely related species. Building on these sequence variations, we designed species-specific primers that can be used for PCR. We and others have demonstrated that mtDNA from human, bovine and porcine are present and detectable in untreated domestic sewage, agricultural soil runoff, swine farm effluents and water from rivers with known pollution sources. Despite the successful detection of mtDNA in environmental samples, the detection of such markers can be challenging in environmental water and soil. This problem stems from our lack of knowledge on the dynamics of mtDNAs in the environment.*** The overall aim of this research program is to characterize the fate of mtDNAs in various water and soil environments with the ultimate goal of developing improved mtDNA detection as a robust FST method. The aims of the research program will address the fate and transport of animal-specific mtDNA markers in various environmental situations well controlled in laboratory settings as well as in experimental field plots. The development of improved animal-specific markers identifying the exact sources of fecal matter is essential for implementing effective preventive or remedial strategies.**