Urbanized bays are vulnerable to fecal bacterial pollution and the extent of this pollution, in marine recreational waters, is commonly assessed by quantifying enterococci concentrations. Recent reports have questioned the utility of enterococci as an indicator of fecal bacterial pollution in subtropical bays impaired by non-point source pollution, and enterococci data alone cannot identify fecal bacterial sources (i.e., hosts). The purpose of this study was to assess relationships between rainfall, fecal bacterial pollution, antimicrobial resistance, and microbial diversity in an urbanized subtropical bay. Thus, a comprehensive bacterial source tracking (BST) study was conducted using a combination of traditional and modern BST methodologies. Findings show that rainfall was directly correlated with elevated enterococci concentrations, including the increased prevalence of Enterococcus faecium, although it was not correlated with an increase in the prevalence of antimicrobial-resistant strains. Rainfall was also correlated with decreased microbial diversity. By contrast, neither rainfall nor enterococci concentrations were directly correlated with the concentrations of three omnipresent host-associated fecal markers (i.e., human, canine, and gull). Notably, the human fecal marker (HF183) was inversely correlated with enterococci concentrations, signifying that traditional enterococci data alone is not an accurate proxy for human fecal waste in urbanized subtropical bays. IMPORTANCE The presence of human enteric pathogens, stemming from fecal pollution, is a serious environmental and public health concern in recreational waters. Accurate assessments of fecal pollution are therefore needed to properly assess exposure risks and guide water quality policies and practices. In this study, the absence of a direct correlation between enterococci and source-specific human and animal markers disputes the utility of enterococci as an indicator of fecal pollution. Moreover, the inverse correlation between enterococci and the human-specific HF183 marker indicates that recreational beach advisories, triggered by elevated enterococci concentrations, are a misleading and ineffective practice. This study clearly demonstrates that a multiparameter approach that includes the quantitation of host-specific markers, as well as analyses of microbial diversity, is a more effective means of assessing water quality in urbanized subtropical bays.

Stormwater runoff is an important nonpoint source of fecal pollution in coastal environments. In anticipation of future coastal urbanization and altered weather patterns, it is increasingly important to understand the impact of rainfall; therefore, the purpose of this study was to determine how rainfall impacts water quality along an estuarine ecocline in the northwestern Gulf of Mexico (GOM). Decreasing levels of enterococci were detected along the ecocline from land to sea, with the highest concentrations measured immediately downstream of a wastewater treatment plant (WWTP). Human-, canine-, and gull-associated markers were detected consistently throughout the study, but they were not correlated with enterococci and they did not experience a significant trend along the ecocline. Antecedent rainfall was associated with significant changes in bacterial community structure and increased human marker concentrations. These results question the utility of enterococci as a fecal pollution indicator in the northwestern GOM and suggest that increased rainfall frequency or intensity could negatively impact water quality in this region. Taken together, these results clearly demonstrate the need for a data-based approach to water quality management that incorporates modern water quality indicators such as host-associated markers and microbial community composition.