Assessing Bacterial Community Assembly and Function for Improved Biological Removal of Pathogens and Contaminants in Stormwater Filtration Systems

ASSESSING BACTERIAL COMMUNITY ASSEMBLY AND FUNCTION FOR IMPROVED BIOLOGICAL REMOVAL OF PATHOGENS AND CONTAMINANTS IN STORMWATER FILTRATION SYSTEMS

by Andrea Naimah Fraser

A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy

Baltimore, Maryland August 2020

Abstract

Pathogens and nutrients are consistently top pollutants of waterbodies around the world. Stormwater runoff is a major source of these pollutants, though with proper treatment, such as engineered filtration, water quality can potentially be improved for safe infiltration, discharge or reuse of runoff. Microorganisms are ubiquitous in stormwater, thus microbial community development on filtration based remediation systems requires consistent maintenance, which is far from optimized in practice. Previous work has demonstrated that biofilm microorganisms that colonize stormwater filters can lead to biofouling, as well as differ substantially in their remediation potential. However, few studies have investigated either the variation of the community in stormwater, or tested remediation ability with natural communities that are representative of variation from different potential treatment locations. Here we assessed the natural bacterial community structure variability of urban stormwater with 16S rRNA gene sequencing at a variety of runoff locations. We inferred the presence of potential pathogens and organisms associated with remediation functions (e.g. denitrification) from their sequence classification. Overall, we found high variability in stormwater bacterial community structure across rooftop, roadway, and Municipal Separate Storm Sewer outfall samples, but substantially less variability in potential for contaminant remediation. We also tested whether microbial community functional potential (e.g. pathogen presence and nitrate removal) in experimental filtration systems was sensitive to inoculum community composition, deposition and drift during biofilm assembly in experimental filtration

ii columns. Potentially pathogenic and denitrifying organisms increased in total abundance in experimental filtration columns over a one month growth period.

Additionally, inoculation of filters with stormwater microbial communities provided significantly better pathogen removal than single isolate, sand, and control columns. Filters inoculated with stormwater communities performed similarly despite substantial taxonomic differences in inoculum communities taken from different runoff locations. Model pathogen initial removal performance had significant correlation with inoculum community diversity while biofilm presence was anti-correlated with the amount of E. coli remobilized in a subsequent simulated storm event. A similar approach could be used to investigate other pathogens of concern, varied chemistry and environmental conditions associated with stormwater or drinking, waste and other water treatment systems.

Committee: Sarah Preheim, Harihar Rajaram, Grace Brush, Jocelyne DiRuggiero, Genee Smith, and Edward Bouwer, may he rest in peace.

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iv Preface

Let us be reminded…

“Nature does not strive to classify things; humans do.

Despite many gray areas where classification of organisms is not easy (and sometimes does not seem to make much sense), classification is essential for our organization of knowledge and for communication among scientists, practitioners, and others...

The principles of engineering lead to quantitative tools while the principles of microbiology often are more observational. Quantification is essential if processes are to be reliable and cost-effective. However, the complexity of the microbial communities involved in environmental biotechnology often is beyond quantitative description; unquantifiable observations are of the utmost value.”

Rittmann, Bruce E., and Perry L. McCarty. Envi