Site-specific bacterial microbiome patterns across contrasting anthropogenic settings in the upper Chicamocha River, Colombia: a full-length 16S rRNA gene pilot survey

High-mountain urban rivers in tropical South America remain underrepresented in molecular monitoring studies, limiting the identification of bacterial assemblages associated with local anthropogenic pressures. This study characterized bacterial microbiome composition, diversity, and 16S rRNA gene-based predicted functional profiles at five sites in the upper Chicamocha River, Colombia, representing contrasting settings, including a wastewater treatment plant (WWTP)-influenced reach, a thermoelectric cooling pond, agrolivestock influence, and a downstream municipal-industrial reach. Full-length 16S rRNA gene amplicon sequencing using PacBio HiFi generated 737,344 high-quality reads and 4921 amplicon sequence variants. Bacterial assemblages showed site-specific patterns, with high multisite Sørensen dissimilarity mainly attributable to taxon turnover. Ammonium was the only physicochemical variable significantly associated with community ordination. The WWTP-influenced site showed high relative abundance of the phyla Bacillota and Campylobacterota, particularly of the genus Arcobacter, whereas the cooling pond showed increased representation of the genus Sphingorhabdus. Flavobacterium was most abundant at agrolivestock-influenced sites, while the genera Limnohabitans and Polynucleobacter dominated the downstream site. Functional inference suggested site-associated KEGG profiles, including predicted xenobiotic-biodegradation pathways and categories annotated to membrane transport, motility, and antimicrobial drug resistance. These findings provide a preliminary molecular monitoring baseline and identify candidate taxa and pathways for targeted validation in future watershed surveillance, supporting the development of molecular monitoring strategies for undersampled Andean high-mountain urban rivers.