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

有许多来源可导致粪便污染水和土壤。由于许多水生病原微生物与粪便污染有关，因此在水质评估中监测粪便污染对公众健康具有重要意义。的确，地表水和地下水的粪便污染会对公众健康（饮用水）和当地经济（农业和娱乐活动）产生重大影响。水的微生物质量主要是用粪便指示生物，如大肠菌群来监测的。然而，这些指标并不能确定粪便的来源。几种粪便源追踪（FST）方法已经开发出来，以解决宿主对粪便污染的特异性贡献问题。通过PCR方法检测到的宿主特异性遗传标记表明存在来自特定动物物种的粪便污染。大多数这些遗传标记依赖于肠道（粪便）物质中与特定动物宿主相关的微生物的存在。尽管它们数量众多，但没有一种是完全和足够的特异性和敏感性。因此，开发新的遗传标记和创新的FST方法是必要的。

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.