Defense Date


Document Type


Degree Name

Master of Science



First Advisor

Rima Franklin


Antibiotic resistance spread within aquatic bacterial communities, particularly ones in urban areas, is in part driven by wastewater inflows that may contain both elevated concentrations of antibiotics and increased abundance of antibiotic resistant bacteria. These can be transmitted into the environment via release of treated wastewater, since removal of these compounds by most wastewater treatment facilities is inadequate, or by release of untreated waste from leaking wastewater treatment networks and overflow of combined sewer systems. This study used the James River and the City of Richmond wastewater network as a model urban waterway to study both types of impacts. Shotgun metagenomic sequencing was used to compare water column, biofilm, and sediment microbial communities from five sites along the James River flow path. Data were analyzed to assess how microbial community diversity, the distribution of wastewater indictor organisms, and the abundance of antibiotic resistance genes changed with varied wastewater exposure.

Alpha diversity was mainly driven by habitat rather than site along the flow path. Beta diversity was primarily a product of ecosystem type and whether the samples were collected from a river or stream site. While taxonomic differences existed between the three habitats, biofilm and sediments communities were much more closely related than suspended bacteria. Additionally, while the taxonomic makeup of river and stream water communities differed, differences between the functional gene presence were not statistically significant. Multidrug resistance, total ARG abundance, and metal resistances was highest within sediment samples and lowest in water samples, although for individual ARG there was not a pattern that resistance followed within the habitats. However, sewer overflows and wastewater influent change the bacterial community composition of in all habitats and increase the presence of potentially pathogenic bacteria within the urban waterway. Without alteration to our wastewater treatment protocols and infrastructure, freshwater ecosystems will continue to be a reservoir of antibiotic resistance.


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