The development of manure application recommendations has not taken into account the survival, movement and biotic interactions of bacteria in agricultural soils, and in fact may enhance survival of bacteria applied to soils. Implementation of biocriteria TMDL should include the fate of bacteria in the soil ecosystem, especially of tile-drained agricultural systems, as tile-drainage can impact surface-water quality. The land application of animal waste is only possible if the applied cells die off. Overall, we are finding that E coli are dying off once they are introduced into soil. Cells that find their way in to water also die off by the rate of decline in both cases is controlled by the environment. The rate of die off in soil is controlled by the key overarching environmental conditions: temperature and moisture. Warm and wet conditions tend to favor die off while dry and cold conditions tend to favor more stability in the population numbers. In stream water die off is controlled by, we suggest, active predation by protozoa. We also suggest that cold conditions tend to enhance the survivability of the cells by lessening the activity of the predator. Given the findings of these studies, it is clear that the interaction of bacteria introduced into agricultural soils by manure application needs to account for environmental factors such as soil moisture, temperature and other biotic interactions. Further investigation into the exact mechanism of predation and the interaction of fecal bacteria in the plant rhizoshpere is needed.