Nuanced effects of wastewater disinfection upgrades on the microbial community dynamics of an urban river system

Microorganisms such as coliform-forming bacteria are commonly used indicators in assessing freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; rather, they exist within the context of expansive and interactive microbial communities which vary through space and time. As such, the elucidation of spatio-temporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, as well as for improving our overall understanding of the relationship between the microbial community and ecosystem health. In this study, we conducted a seven-year (2013-2019) time-series investigation of the microbial community in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades in its wastewater disinfection processes and sewage overflow management system in an effort to improve river water quality. Using both culture-independent and culture-dependent approaches, we compared the microbial ecology of the CAWS between pre-intervention and post-intervention time points. Fecal coliform assays and differential abundance analyses of the community demonstrate the impactful contribution of the intervention in removing key microbial taxa from the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations of such community dynamics can be consistent even when perturbed.