# Changes in Microbial Community Assemblages Due To Urban Pollution, Detected via rRNA Gene Amplicon Sequencing in the Magdalena River, Mexico City

## TL;DR

This study shows how urban pollution in Mexico City's Magdalena River changes microbial communities, with different bacteria and microeukaryotes dominating based on pollution levels.

## Contribution

The study identifies new microbial taxa in tropical urban rivers, expanding knowledge beyond temperate systems.

## Key findings

- Bacterial genera like Rhizobacter and Flavobacterium were common in less polluted areas, while Arcobacter and Acinetobacter dominated in heavily polluted sites.
- Peri-urban sites showed higher bacterial diversity, and Ciliophora and Chlorophyta made up over 75% of microeukaryotic abundance.
- Urban influence altered microbial composition, with some taxa previously unrecorded in tropical urban rivers.

## Abstract

As freshwater sources become increasingly polluted and depleted, the delicate balance of aquatic environments is disrupted, leading to cascading effects throughout entire ecosystems. This disruption manifests in various ways, including changes in water chemistry, temperature fluctuations, and the introduction of contaminants, all of which contribute to alterations in microbial communities. We applied eDNA metabarcoding to characterize microbial communities along an anthropogenic pollution gradient in the Magdalena River, a tropical river in Mexico City. Sampling was conducted at four sites representing different levels of human influence. Results revealed differences in both bacterial and microeukaryotic community compositions between sites. In areas with low to moderate disturbance, bacterial genera associated with nitrogen cycling and plant–microbe interactions (e.g., Rhizobacter, Rhodoferax, and Flavobacterium) were predominant, whereas in more heavily impacted sites, genera linked to enteric, nosocomial, or fecal sources (e.g., Arcobacter, Acinetobacter, and Aeromonas) dominated. Peri-urban sites exhibited higher alpha diversity at the phylum level for bacteria, and microeukaryotic communities; two phyla account for over 75% of the relative abundance throughout the year (Ciliophora & Chlorophyta). Statistical analysis showed that water quality influences microbial composition in the sites. These findings demonstrate that urban influence alter microbial community composition, showing similar patterns to other studies. Our study, however, also discovered certain taxa that had not been previously recorded in tropical urban rivers, thereby broadening the existing knowledge, which has primarily been based on temperate systems. This research offers one of the initial thorough evaluations of microbial communities in urban rivers in Mexico and highlights the potential of eDNA metabarcoding as a valuable tool for environmental monitoring.

Changing microbial communities (eukaryotic and prokaryotic) and physicochemical variables along a human influence gradient. Left circles in any of the sites show the characteristic and most abundant prokaryotic groups; right circles show the characteristic and most abundant microeukaryotic groups. The figure also shows the most common groups of bacteria and eukarya over all sites (lower left corner)

The online version contains supplementary material available at 10.1007/s00248-025-02580-7.