Date of Award:


Document Type:


Degree Name:

Doctor of Philosophy (PhD)



Committee Chair(s)

Michelle A. Baker


Michelle A. Baker


Zachary T. Aanderud


Bethany T. Neilson


John M. Stark


Wayne A. Wurtsbaugh


Bacteria within biofilms are an essential component of stream ecosystems, influencing the movement of carbon (C), nitrogen (N), and phosphorus (P) in watersheds. To better understand the ecological effects of human activities on stream ecosystems, my research examined how nutrients and pharmaceuticals, common pollutants in streams worldwide, influence bacterial assemblages in stream biofilms. First, I tested how nutrients (N, P, iron) and pharmaceuticals (caffeine, diphenhydramine) influenced biofilm bacterial microbiomes (taxa present in at least 75% of samples of a contaminant treatment). Nutrients allowed taxa known for their ability to thrive in nutrient-rich environments to dominate microbiomes, pharmaceuticals supported a rich microbiome that included unique taxa with contaminant-degrading abilities, and nutrients plus pharmaceuticals fostered microbiomes with unique cyanobacterial taxa. The distinctly different effects of nutrients and pharmaceuticals on bacterial microbiomes contribute to our understanding of the unique ecological ramifications of these two common pollutant classes. Next, I examined bacterial assemblages contributing to two nutrient cycling processes using DNA stable isotope probing (DNA-SIP), a technique which identifies bacteria that use an isotopically-labeled compound by tracking the movement of an isotopic label into bacterial genetic material. I performed a 13C-hemicellulose DNA-SIP experiment to identify and compare bacteria which assimilate this common organic C compound under N and/or P enriched conditions. N and P had distinctly different effects on bacterial assemblages metabolizing 13C-hemicellulose. N enabled certain abundant taxa to dominate, P enhanced assemblage richness and stability, and N plus P supported C metabolism by families which were abundant in initial assemblages. My results demonstrate the potential for changes in the absolute and relative amount of N and P to uniquely influence bacterial assemblages contributing to organic C processing. Last, I performed a DNA-SIP experiment to identify and compare bacteria which metabolized inorganic (15N-ammonium [15NH4+], 15N-nitrate [15NO3-]) and organic (15N-glycine) N forms in streams. 15NH4+ was generally metabolized by low and variably abundant families, 15NO3- was metabolized by a rich assemblage which included a family known to be able to assimilate this less preferred N form and 15N-glycine stimulated families which were rare in baseline assemblages. These results suggest distinctly different bacterial assemblages may remove different inorganic and organic N forms from stream water columns. Overall, my results provide insight into how anthropogenic pollutants influence bacterial microbiomes and identify bacteria contributing to C and N cycling in stream environments.