Using bacterial and mitochondrial DNA markers to assess fecal pollution sources in stream water and sediments of a mixed land-use watershed.

This article focuses on identifying sources of fecal contamination in water and sediment within the Middle Tallapoosa watershed in Alabama, USA, and assessing the impact of rainfall on microbial water quality. Using quantitative polymerase chain reaction (qPCR) assays targeting human-, cattle-, and chicken-associated genetic markers (HF183, CowM3, LA35, and Chicken-ND5), the study found that human and cattle markers were consistently present in water regardless of precipitation, while chicken markers appeared mainly after significant rainfall events. Escherichia coli concentrations were significantly higher in sediments than in water and correlated positively with antecedent rainfall and streamflow, indicating sediment resuspension as a key factor in contamination. The findings highlight the importance of including sediment analysis in microbial water quality assessments and suggest that humans and cattle are primary contamination sources in this mixed land-use watershed, with episodic poultry contamination linked to storm runoff.