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A poultry litter marker gene correlates with pathogen and indicator bacteria deposition on, growth in and transport from poultry bedding. Kameswari Sirisha Mantha Poultry is one of the major contributors of inputs to U.S. environmental waters due to the large number of poultry grown per year in the U.S. and litter disposal practices. Two studies were conducted during this research: (1) to determine the temporal rate of deposition and growth or decay of microorganisms in poultry litter originating from poultry feces and (2) the release and transport of poultry litter associated microorganisms from soiled poultry litter applied as fertilizer through soil columns under simulated rainfall. First, deposition studies were conducted to evaluate the deposition rate of microorganisms on poultry bedding during the growth of poultry. The studies were designed to simultaneously evaluate the growth or decay of microorganisms after deposition on the poultry bedding (i.e., wood shavings). A secondary objective of this study was to determine if there is a correlation between the poultry litter marker gene and indicator bacteria (FIB) and pathogens during deposition. Culture and qPCR analysis revealed growth of Enterococcus, Staphylococcus and Bacteroidales in the litter for up to four weeks after deposition in feces. In contrast after deposition of E. coli on the litter, the concentrations of E. coli declined after the soiled litter was separated from the poultry. The poultry litter marker Brevibacterium sp. LA35 was found to increase in the litter over time as the birds aged, but was not observed to grow in the soiled litter after deposition with feces. The deposition study aids in our understanding of the deposition, survival and growth of microorganisms from poultry feces in and on poultry litter. The next study conducted evaluated the release and transport of pathogens (Salmonella sp.), FIB (Enterococcus, and E. coli) and MST markers (LA35 and Bacteroidales) from poultry litter under simulated rainfall events through soil columns. The transport and attenuation of microorganisms was observed through an acid washed sand column and loamy sand soil columns over 10 to 30 pore volumes of deionized water. The qPCR analysis revealed that the breakthrough of pathogens and MST markers were correlated. These soil column studies aid in our understanding of the release, transport and attenuation of pathogens from poultry litter applied as an agricultural fertilizer.