Degree Type


Date of Award


Degree Name

Doctor of Philosophy


Agricultural and Biosystems Engineering


Agricultural and Biosystems Engineering

First Advisor

Michelle L. Soupir

Second Advisor

Thomas B. Moorman


Increases in swine production, coupled with shifts towards confined animal feeding operations has led to large concentrations of manure in centralized locations. The nutrient rich material is often applied to agricultural land as organic fertilizer. While manure application is beneficial for crops, the medium also contains antibiotic resistant bacteria and pathogens of human concern. These potentially harmful microbial constituents have been identified in ground and surface waters surrounding animal confinements. However, less is known regarding the fate and transport manure associated microbial constituents in the environment post manure application. The studies described in this dissertation include monitoring the transport of antibiotic resistance genes and pathogens to surface water at the watershed scale and tracking manure associated bacteria through the soil profile into drainage waters.

Specific objectives of the first study were to determine concentrations of macrolide resistance genes (erm genes) in artificial drainage and surface water, determine ratios of erm genes to 16S rRNA gene abundance in surface and drainage waters, identify correlations between erm genes and temporal variation, and identify correlations between flow measurements and erm gene concentrations. Erm gene concentrations ranged from below limits of quantification to >107 copies 100 mL-1, with 89% of surface water samples testing positive for ermB or ermF. When normalized to 16S rRNA gene concentrations, both genes were significantly greater (p<0.0001) in artificial drainage waters when compared to surface waters. These results coupled with temporal trends indicated surface water erm gene concentrations are likely affected by typical manure application timing and periods of increased artificial drainage.

Objectives of the second study were to quantify genera harboring known species of manure-borne pathogenic bacteria and naturally occurring soil pathogens, identify pathogenic genera temporal trends and their transportation routes to surface water. Results identified significant increases in abundances of Bacteroides, Clostridium sensu stricto and Acinetobacter following typical manure application timing. Transport pathways to surface waters of pathogenic genera were also determined by assessing surface and drainage waters concentrations. Enterobacter surface water concentrations were mainly influenced by artificial drainage, while Clostridium sensu stricto primarily reached surface water through overland flow. These results will help inform mitigation strategies to reduce pathogen transport through agroecosystems.

Objectives from the third study include: identification of genera stimulated by manure application in soil and drainage, identification highly abundant genera specific to the manure microbiome and tracking manure specific genera in soil and drainage over the course of a typical drainage season. Sequences related to twelve orders of bacteria comprised the majority of OTUs stimulated by manure application. Of the twelve orders, Proteobacteria were most prevalent, followed by Bacteroidetes, Firmicutes, Actinobacteria and Spirochaetes. While the majority of these manure stimulated OTUs began to decrease prior to the end of the experiment, relative abundances of sequences matching Rhizobiales and Actinomyecetales continued to increase. The twelve orders contained variable responses in associated drainage over the course of the experiment. A “manure-specific core” of five genera were also identified, which constituted 13% of manure communities. All core manure genera returned to pre-manure relative abundances by the end of the experiment, except Clostridium sensu stricto.


Copyright Owner

Elizabeth Luby Rieke



File Format


File Size

98 pages