Natural Resources, School of


First Advisor

Daniel Snow

Date of this Version



A thesis presented to the faculty of the Graduate College at the University of Nebraska in partial fulfillment of requirements for the degree of Master of Science

Major: Natural Resource Sciences

Under the supervision of Professor Daniel Snow

Lincoln, Nebraska, November 2023


Copyright 2023, Paula R. Guastello


The Nebraska Water Quality Index, under development by the Nebraska Department of Environment and Energy, summarizes in a single value eight environmental parameters that have been monitored in Nebraska for nearly 20 years. Water quality parameters including those used in the Nebraska Water Quality Index have been shown in previous studies to impact bacterial growth. As such, this index has the potential to correlate with the freshwater microbial community. Here, I relate the Nebraska Water Quality Index to microbial community composition and structure using 16S rRNA gene amplicon sequence data collected from the North Platte River Basin, Nebraska. This index was chosen because data were readily available as the Nebraska Department of Environment and Energy collected the water samples, the parameter criteria are tailored to Nebraska’s water quality standards, and the index is flexible to account for missing values. From among the samples sequenced, 376 ASVs were identified and classified into 45 bacterial orders and the order “Chloroplast,” representing algae. Nebraska Water Quality Index ratings were related to the microbial community in terms of structure and composition: Gini-Simpson alpha diversity was significantly negatively related to index ratings, as were the relative abundances of several bacterial orders: Absconditabacteriales, Burkholderiales, Campylobacterales, Oscillospirales, Rhizobiales, and Vicinamibacteria Subgroup 17. Index ratings were positively related to Flavobacteriales and Saccharimonadales. Nitrogen played a substantial role in water quality and was related to microbial community structure and composition. Total nitrogen concentration exceeding water quality standards was found in 26 of the 28 samples. Total nitrogen concentration was significantly correlated with total coliform/E. coli cell count, Gini-Simpson alpha diversity, and the relative abundances of Campylobacterales, Oscillospirales, and Vicinamibacteria Subgroup 17. Together these data indicate that the application of the Nebraska Water Quality Index may help identify sites warranting further examination of the aquatic microbial community. Additionally, microbial community data may further help determine sources of contamination, such as whether fecal bacteria originate from current or previous livestock presence.

Advisor: Daniel Snow