Skip to main content
ARS Home » Southeast Area » Oxford, Mississippi » National Sedimentation Laboratory » Water Quality and Ecology Research » Research » Publications at this Location » Publication #298252

Title: Age-related shifts in the density and distribution of genetic marker water quality indicators in cow and calf feces

item SHANKS, ORIN - Us Environmental Protection Agency (EPA)
item KELTY, CATHERINE - Us Environmental Protection Agency (EPA)
item PEED, LINDSAY - Us Environmental Protection Agency (EPA)
item SIVAGANESAN, MANO - Us Environmental Protection Agency (EPA)
item MOONEY, THOMAS - University Of Cincinnati
item Jenkins, Michael

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/17/2013
Publication Date: 3/1/2014
Publication URL:
Citation: Shanks, O.C., Kelty, C.A., Peed, L., Sivaganesan, M., Mooney, T., Jenkins, M. 2014. Age-related shifts in the density and distribution of genetic marker water quality indicators in cow and calf feces. Applied and Environmental Microbiology. 80:1588-1594.

Interpretive Summary: To keep dairy operations producing milk cows must also produce calves. Both cows and calves produce large quantities of manure that can contaminate recreational surface waters. Because calves are prone to infections from pathogenic microorganisms that also can infect humans, it is important to be able to determine if surface water pollution is from calves on dairies in agricultural watersheds. Scientists at USEPA, the University of Cincinnati, and USDA-ARS collected manure from cow-calf pairs from the time of the calf’s birth to the time of its weaning. The researchers analyzed manure of both cow and calf for particular genetic markers. Results of their research showed that the microbial composition of calf manure was distinct from its mother until it was weaned and no common genetic markers were observed. This difference between calf and cow indicated a need for developing genetic markers for identifying calves as sources of surface water pollution that can put public health at risk. This is important information for state and federal environmental protection agencies and managers of watersheds impacted by dairies and cow-calf operations.

Technical Abstract: Calves (= 226 kg body mass) make up about 16% of the current bovine population in the United States and can excrete high levels of human pathogens. We describe the density and distribution of genetic markers from 11 PCR- and real-time quantitative PCR-based assays including CF128, CF193, Bac2, Bac3, CowM2, CowM3, GenBac3, Entero1, EC23S857, CampF2, and ttr-6 commonly used to help assess ambient surface water quality. Each assay was tested against a collection of 381 individual bovine fecal samples representing 31 mother and calf pairings collected over a 10 month time period from time of birth through weaning. Genetic markers reported to be associated with ruminant and/or bovine fecal pollution were completely absent in calves for up to approximately 115 days from birth suggesting that physiological changes in calf ruminant function impact host-associated genetic marker shedding. In addition, general fecal indicator markers for Bacteroidales, E. coli, and Enterococcus spp. exhibited three separate trends across time indicating that these bacteria respond differently to age-related physiological and dietary changes during calf development. Results of this study suggest that currently available PCR-based water quality indicator technologies can under- or overestimate fecal pollution originating from calves and identify a need for novel calf-associated source identification methods.