Environmental and Genetic Factors Affecting Pathogen Persistence in Animal Waste and Transfer to Crops

<ol> <li> The identification of factors contributing to the persistence and horizontal
transfer of MAP and other pathogens on dairy farms. We will examine the role
alternate protozoan hosts play in MAP persistence and horizontal transfer. We will
also perform functional genomic analysis of MAP in the environment to elucidate clues
about the strategies employed by this organism for environmental survival.

<li> The development of methodologies for the reduction of pathogens in waste. Two of
the most common waste treatment methodologies are aerobic and anaerobic digestion,
but little is known about the effect these processes have on the microbial population
structure, pathogen levels, and volatile compound missions. The bacterial community
structure, chemical composition and volatile compounds emitted from animal waste,
aerobic and anaerobic digesters, and holding tanks receiving effluent will be
characterized. We will also analyze the effect of diet and dietary supplements on the
microbial population structure, pathogen levels, and volatile compound emissions from
animal waste and animal waste treatment systems.
<li> Pathogen transfer from manure and CAFOs (confined animal feeding operations) to
crops. We will use high volume aerosol collection and agar impaction devices to
collect bacteria from aerosols near CAFOs. Aerosol samples will be evaluated for
pathogens using culture and non-culture based methods. We will examine the bacterial
community structure and pathogen levels on crops fertilized with waste using culture
and non-culture based methods and compare them to those of plants fertilized with
only chemical fertilizers. We will study the colonization of crop plants by
Salmonella enterica grown in soil amended with manure spiked with pathogens using
standard culture and quantitative PCR methods.</ol>