Objective:
To develop or refine methodology and conduct analysis of bacterial, viral, and protozoan pathogens in manure, agricultural runoff, and forage materials. To collaborate with other scientists in the interpretation of data and writing of manuscripts for journal publcation.

Approach:
Improved management of dairy farms requires successfully managing its nutrient flows, both to maximize nutrient use by animals and crops in order to optimize profit, and to minimize nutrient loss to the environment in order to optimize sustainability. While much of our research project focuses on improving nutrient management, another critical area of concern is the transport of manure-derived pathogens from agricultural fields and their potential to contaminate surface waters. This SCA adds the pathogen component to experiments designed to evaluate crop, soil, and manure management effects on transport of contaminants in surface runoff from manured fields. This includes an ongoing experiment that employs a paired-watershed design to compare packages of practices, both conventional and improved nutrient/crop/soil systems at a landscape scale. Other planned replicated plot studies will examine the effect of manure application methods on nutrient and pathogen transport from alfalfa-grass mixtures, and assess the effects of timing of dairy slurry application on the forage quality, silage fermentation characteristics, and pathogen survival in alfalfa forages. Water samples will be collected by one or both of the following methods, depending on the study design and availability of runoff: 1) Unconcentrated ambient samples taken by an automated ISCO sampler (paired watershed) or other sampling techniques (plot studies); 2) Novel glass wool filtration technology for simultaneously concentrating protozoa, bacteria, and virus pathogens, as well as indicators like E. coli. Forage samples will be analyzed directly without concentration. E. coli will be quantified by the chromogenic substrate method in a most-probable-number format. Cryptosporidium species will be quantified by immunofluorescent microscopy, and Salmonella and Campylobacter species will be enumerated by standard culture techniques. One or more viruses (types to be determined from manure analyses) will be detected by quantitative real-time RT-PCR. We will also explore quantifying Cryptosporidium, Salmonella, and Campylobacter in runoff and forage samples by qPCR.