Article 1 Microbial Community Composition and Antibiotic 2 Resistance Genes Within a North Carolina Urban 3 Water System 4 Kevin Lambirth 1,2 , Matthew Tsilimigras 1 , Anju Lulla 1 , James Johnson 2 , Abrar Al-Shaer 3 , Orion 5 Wynblatt 2 , Shannon Sypolt, Cory Brouwer 1,2 , Sandra Clinton 1 , Olya Keen 1 , Molly Redmond 1 , 6 Anthony Fodor 1 , and Cynthia Gibas 2, * 7 1 The University of North Carolina at Charlotte; 9201 University City Blvd, Charlotte NC, 28223 8 2 The University of North Carolina at Charlotte, Bioinformatics Services Division; 150 N Research Campus 9 Dr, Kannapolis NC, 28081 10 3 The University of North Carolina at Chapel Hill; 135 Dauer Drive, Chapel Hill NC, 27599 11 * Correspondence: cgibas@uncc.edu; Tel.: 704-687-8378 12 13 Abstract: Wastewater treatment plants (WWTPs) are thought to be potential incubators of 14 antibiotic resistance. Persistence of commonly used antibiotics in wastewater may increase the 15 potential for selection of resistance genes transferred between bacterial populations, some of which 16 may pose a threat to human health. In this study, we measured the concentrations of ten antibiotics 17 in wastewater plant influents and effluents, and in surface waters up- and downstream from two 18 Charlotte area treatment facilities. We performed Illumina shotgun sequencing to assay the 19 microbial community and resistome compositions at each site across four time points from late 20 winter to mid-summer of 2016. Antibiotics are present throughout wastewater treatment, and 21 elevated concentrations of multiple antibiotics are maintained in moving stream water downstream 22 of effluent release. While some human gut and activated sludge associated taxa are detectable 23 downstream, these seem to attenuate with distance while the core microbial community of the 24 stream remains fairly consistent. We observe slight suppression of functional pathways in the 25 downstream microbial communities, including amino acid, carbohydrate and nucleic acid 26 metabolism as well as nucleotide and amino acid scavenging. Nearly all antibiotic resistance genes 27 (ARGs) and potentially pathogenic taxa are removed in the treatment process, though a few ARG 28 markers are elevated downstream of effluent release. Taken together, these results represent 29 baseline measurements which future studies can utilize to help to determine which factors control 30 the movement of antibiotics and resistance genes through aquatic urban ecosystems before, during 31 and after wastewater treatment. 32 Keywords: metagenomics; antibiotic resistance; wastewater; environmental ecology 33 34 1. Introduction 35 Urbanization has the potential to affect surface water quality and alter microbial community 36 composition [1-4]. One mechanism by which human activity directly affects surface waters is 37 through the wastewater treatment process, in which human waste is collected, treated, and the 38 residual water eventually released back into surface waterways [3,5,6]. Pharmaceuticals and 39 antimicrobial compounds that are not fully metabolized or that are disposed of improperly make 40 treated wastewater a significant source of pharmaceuticals in surface waters [7]. Significant effects 41 of pharmaceuticals, including metformin, estrogens, and illegal drugs on native flora and fauna have 42 recently been reported as well [8-11]. 43 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 14 September 2018 doi:10.20944/preprints201809.0255.v1 © 2018 by the author(s). Distributed under a Creative Commons CC BY license. Peer-reviewed version available at Water 2018, 10, 1539; doi:10.3390/w10111539