Technical Abstract: Outbreaks of foodborne illnesses caused by pathogenic bacteria are increasingly being linked to fresh produce. Animal manure is a potential pathogen reservoir, and the close proximity of dairy operations and croplands in California cannot be ignored. We have worked on developing improved detection methods for pathogens, and on understanding how manure management systems affect the chemical environment on dairies. Our long-term goals are to develop integrated manure management systems that reduce pathogen numbers on dairies, thereby reducing chances for food contamination in the field. Data on molecular detection techniques for Mycobacterium avium ssp. paratuberculosis, manure separation equipment, aerosol microbial transmission, and abiotic environmental analysis are presented.