Metagenomic Profiling Unveils the Microbial Composition of Urban River Tributaries: Impact of Human Activities on Water Quality

Anthropogenic activities have a negative impact on aquatic environments and the organisms living in them. Aquatic ecosystems are widely used in multiple human activities. For this reason, multiple strategies have been implemented to evaluate the microbial presence, including studies related to the microbial ecology of these environments and New Generation Sequencing (NGS) analysis, which has gained popularity. In this study, we descriptively determined water quality by analyzing samples from four tributaries of the Bogotá River using physicochemical and microbiological methods, complemented by shotgun metagenomics. The results revealed the circulation of microbial communities, including bacteria associated with some genera reported to be important in bioremediation processes, as well as others with pathogenic potential. We found molecular markers of interest in health, such as those related to antimicrobial resistance (predominantly those associated with resistance to aminoglycoside, macrolide, fluoroquinolone, and tetracycline antibiotics, which are widely used in animal production systems). The panorama is worrisome in the final section of the affluents where they are more impacted by human communities, revealing the possible anthropic impact after passing through a city as populated as Bogotá D.C in Colombia. This study allowed us to obtain high-quality metagenome-assembled genomes for species such as Aliarcobacter cryaerophilus, Acinetobacter johnsonii, and Succinivibrio, which were characterized using a comparative genomic approach. We present the current state of the sampled points, obtaining basic information and providing a starting point for future research strategies and also to figure out the most proper treatment of aquatic environments in developing countries.