Assessment of water quality and microbial contamination in Santa Marta’s major rivers using conventional methods and next-generation sequencing

Water quality assessment is critical for determining the suitability of water resources for human consumption. In Santa Marta, northern Colombia, limited access to potable water and sewage systems, along with poor treatment infrastructure, poses a significant risk to both urban and rural communities. In some areas, untreated water is sourced directly from rivers or cisterns. Despite being a public health concern, molecular surveillance of waterborne pathogens remains limited. In this study, we integrated next-generation sequencing (NGS) with conventional physicochemical and microbiological analyses to assess water quality in the Gaira and Manzanares rivers. A total of 24 water samples were collected from eight sites along these rivers between August 2023 and February 2024. Microbial communities were characterized using Oxford Nanopore sequencing targeting the 16S-rRNA and 18S-rRNA genes. Physicochemical variables evidenced high levels of contamination, as elevated concentrations of nitrates, phosphates, ammonium, BOD, and COD were detected across the sampling sites. Other parameters, such as pH and temperature, remained stable, while conductivity and dissolved oxygen varied across sites. Microbiological analyses indicated elevated coliform levels, and Cryptosporidium spp. DNA, but not Giardia intestinalis DNA, was detected by PCR. Sequencing analysis revealed 1080 prokaryotic and 149 eukaryotic taxa, including environmental bacteria, Escherichia-Shigella group, and important taxa like Enterocytozoon. Diversity analyses showed that prokaryotic community structure was significantly influenced by basin location (upstream vs. downstream), whereas eukaryotic communities were primarily structured by river identity. Overall, integrating NGS with conventional methods provided a comprehensive characterization of microbial diversity and contamination risks in these tropical river systems, highlighting the urgent need to strengthen water management and public health strategies in Santa Marta and similar regions.