Date of Award

December 2018

Degree Type


Degree Name

Master of Science


Freshwater Sciences

First Advisor

Ryan J Newton

Committee Members

Timothy Grundl, Matthew Smith


16S rRNA gene sequencing, Microbial Community Compostion, Microbial Ecology, Nitrate Phosphate Experiments, Riverbank Inducement, Shallow Groundwater


Placing groundwater wells next to riverbanks to draw in surface water, known as riverbank inducement (RBI), is common and proposed as a promising and sustainable practice for municipal and public water production across the globe. However, these systems require further investigation to determine risks associated with river infiltration especially with rivers containing wastewater treatment plant (WWTP) effluent. Since microbes drive biogeochemical transformations in groundwater and largely affect water quality, it is important to understand how the microbial communities in drinking water wells are affected by river infiltration. This study investigated if, and to what extent, the microbial community in a shallow groundwater aquifer in southeastern Wisconsin is affected by river infiltration. The study area includes an active RBI well, a previously active RBI well, a pristine background well, and the Fox River in Waukesha, WI. After targeting both DNA and RNA for V4 16S rRNA gene sequencing, the results show the microbial community compositions of the groundwater sites significantly differ from each other and from the Fox River. Microbial community compositions correlated with Total Dissolved Phosphorus (TDP) and Total Nitrogen (TN). Amplicon sequence variants (ASVs) associated with river bacteria were found in all groundwater wells, however, these taxa were always more abundant in the active RBI well with similar distribution patterns to the river. The aquifer microbial community composition was over 50% Unclassified organisms. Some ASVs showed evidence of intron splicing in the 16S rRNA gene, a rarely recorded feature in bacteria. The aquifer microbial communities also contained common subsurface organisms and recently discovered CPR and DPANN superphyla organisms. The taxa affiliations suggest heterotrophic, fermentative, and symbiotic lifestyles, and suggest anaerobic metabolisms related to nitrate and sulfate reduction. Microbial affiliation results are consistent with free energy flux predictions for the groundwater wells. Lab experiments indicated the water itself may be C limited and that additional nitrate from river infiltration may initially accumulate in the system, which could impact required water treatment processes.