In partial fulfillment of the requirements for the degree of

Master of Science in Bioinformatics

in the

School of Biological Sciences

Natalie Miller

Will defend her thesis

“Metagenome-based Quantification of the Urban Effects on the Chattahoochee River”

April 21st, 2026

2:00 PM (EST) in EBB 4029

Zoom Link: https://gatech.zoom.us/j/91878010913?pwd=Mhbbrp4zUQ0bBkjjFCMqB03afW4wYa.1

Thesis Advisor:

Dr. Kostas Konstantinidis

School of Biological Sciences, School of Civil and Environmental Engineering

Georgia Institute of Technology

Committee Members:

Dr. Joel Kostka

School of Biological Sciences

Georgia Institute of Technology

Dr. Katherine Graham

School of Civil and Environmental Engineering

Georgia Institute of Technology

Abstract:

The Chattahoochee River serves as a major freshwater resource in the southeastern United States. Atlanta is by far the largest metropolitan area on the river, with up to 1/3 of the river flow being used by its ~6 million inhabitants. The sources of fecal pollution in the river, and more importantly their relative contributions, remain essentially speculative since previous studies targeted only specific microbial indicators. We addressed this gap using short-read shotgun metagenomic sequencing of nine riverine sampling sites transecting the Atlanta metropolitan area, including three sites located downstream of the city every ~20km and three wastewater treatment plants (influent and effluent samples) within the city, across three sampling times (periods) within a year (2018), in the summertime. We recovered 190 good-to-high quality representative metagenome-assembled genomes (rMAGs) and used their relative abundance to infer the impact of the city on the indigenous freshwater microbial communities. We noted substantial fecal pollution within the Atlanta area, including elevated abundance of beta-lactamase antibiotic resistance genes (up to a 4.56-fold increase) and human-associated and wastewater-derived MAGs in the high vs. the low precipitation sampling period. Consistently, SourceApp (Lindner et al., ES&T, 2025) and further analysis revealed that untreated sewage MAGs comprised up to 2.5% of the total river metagenomes, indicating sewage escape events. However, all these taxa and genes that peaked in abundance within the city limits were largely undetectable 20 or 40 km downstream, indicating substantial resilience of the ecosystem against pollution and/or dilution of fecal pollution.