Dr. Zilles' research interests lie at the intersection of environmental engineering and microbiology. In systems such as biological wastewater treatment, a more complete understanding of the microbial ecology and physiology may be applied to the development of process improvements. Current research areas include the microbial physiology of enhanced biological phosphorus removal, the effects of agricultural antibiotic use on antibiotic resistance levels in swine waste treatment systems and manure-amended soils, the microbial ecology of denitrification in tile drainage bioreactors, and gene expression and genetic adaptation for herbicide degradation in a model dynamic soil system.