Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades

Sho M Kodera; Anukriti Sharma; Cameron Martino; Melissa Dsouza; Mark Grippo; Holly L Lutz; Rob Knight; Jack A Gilbert; Cristina Negri; Sarah M Allard

doi:10.1186/s40793-023-00470-4

Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades

Environ Microbiome. 2023 Feb 19;18(1):10. doi: 10.1186/s40793-023-00470-4.

Authors

Sho M Kodera¹, Anukriti Sharma², Cameron Martino^{3

4}, Melissa Dsouza⁵, Mark Grippo⁶, Holly L Lutz^{1

3

7}, Rob Knight^{3

8

9

10}, Jack A Gilbert^{11

12

13}, Cristina Negri¹⁴, Sarah M Allard^{15

16}

Affiliations

¹ Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
² Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
³ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
⁴ Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
⁵ Merck Inc., Cambridge, MA, USA.
⁶ Environmental Science Division, Argonne National Laboratory, University of Chicago, Lemont, IL, USA.
⁷ Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
⁸ Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
⁹ Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
¹⁰ Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
¹¹ Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA. [email protected].
¹² Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. [email protected].
¹³ Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA. [email protected].
¹⁴ Environmental Science Division, Argonne National Laboratory, University of Chicago, Lemont, IL, USA. [email protected].
¹⁵ Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA. [email protected].
¹⁶ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. [email protected].

Abstract

Background: Microorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013-2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention.

Results: Examinations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in 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.

Conclusions: This study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed.

Keywords: 16S rRNA gene sequencing; Dynamics; Fecal coliform; Microbiome; Wastewater.