Currently, livestock manure, biosolids, and non-agricultural source materials are applied to farmland in Ontario for nutrient management purposes. While composting reduces the concentration of nutrients and pathogens in these materials, it does not eliminate them. Data on potential microbial contamination of soil and surface water after compost application onto agricultural lands exists, but few studies have focused on the fate of emerging bacterial and viral pathogens and environmentally-hardy protozoans in composted deadstock, biosolids, and cracked bedrock aquifers. As such, the objective of this study is to compare the effects of different compost types on the fate of pathogenic microbial contaminants (bacterial, parasitic, and viral) and nutrients (nitrates, orthophosphates, and ammonia) in surface and groundwater resources in agricultural watersheds in Ontario, with a particular focus on the use of composted deadstock and biosolids. Our study thus has clear implications for the health, safety, and sustainability of rural communities and agricultural ecosystems.

Significant numbers of human microbial pathogens are present in urban and rural sewage. Although most pathogens can be removed from sewage by various treatment processes, many survive treatment only to be discharged into the effluent and enter receiving waters. There are two types of pollution that need to be mitigated in order to protect public health: a) point-source pollution, which enters the environment at distinct locations through a direct route of discharge of treated or untreated sewage; and b) non-point pollution, which are generally diffuse and intermittent and may be attributable to the run-off from urban and agricultural areas, leakage from sewers and septic systems, and sewer overflows. This problem is exacerbated in agricultural and in remote northern communities; in the former due to excessive applications of animal manure and agricultural chemicals onto cropland and in the latter due to challenges in the management and operations of sewage treatment plants. In 2009, Aboriginal Affairs and Northern Development Canada (AANDC, formerly INAC) assessed the efficacy of 740 wastewater treatment facilities in First Nations communities and found that 60 were high risk and failed to meet the standards outlines in the Canadian Guidelines for Effluent Quality and Wastewater Treatment and Federal Establishments.

Pathogens pose a significant threat to human, animal and agricultural health therefore there is a need for rapid, reliable and sensitive detection tools that can be used for a broad spectrum of targeted microorganisms from mostly complex environmental matrices. Treatment of source water contaminated by Cryptosporidium and Giardia presents a particular challenge to water-quality managers due to: the ubiquity of protozoa in wastewater effluents, the widespread infection of domestic animals and wildlife, the resistance of protozoans (especially Cryptosporidium) to traditional disinfection methods, and the uncertain relationship between the presence of protozoans and faecal indicator bacteria typically used in water quality monitoring. Also, treatment efficiency for bacterial, viral and protozoan pathogens is compromised in circumstances where treatment plant capacity is challenged by growths in population size, or where treatment conditions are not optimal (e.g. temperatures and residence times are too low to completely remove pathogens). The objective of this work is to develop a new research team with a focus on waterborne microbial pathogens in the environment to improve our understanding of the short- and long-term impacts of current practices on ecosystems, and consequently on the health and wellbeing of Canadians.