Poor Water Quality and Microbial Contamination in the main Santa Marta's Rivers: A Combined Approach Using Conventional Methods and Next-Generation Sequencing
Water quality assessment is crucial for evaluating the suitability of water resources for human consumption worldwide. In Santa Marta city, the water supply and sewage systems have limited coverage and inadequate treatment in both urban and rural areas. In some regions, water is sourced directly from the river or cisterns without treatment. This study aimed to evaluate the physicochemical and microbiological parameters, along with the diversity of prokaryotic and eukaryotic communities, using next-generation sequencing (NGS). The study also included PCR detection of public health pathogens, such as Giardia intestinalis and Cryptosporidium spp., which are of concern in Santa Marta's primary drinking water sources. Samples were collected from eight sites between May 2023 and February 2024, with four sites along the Manzanares River and four on the Gaira River. PCR was used to detect the genetic material of Giardia intestinalis and Cryptosporidium spp. in water samples. Microbial communities were characterized through ribosomal marker amplification using Oxford Nanopore high-throughput sequencing. The 16S-rRNA gene was targeted for prokaryotic communities using primers 27F/1492R, while the 18S-rRNA gene was targeted for eukaryotic communities with primers 566F/1289R. Physicochemical parameters, such as pH and temperature, remained stable across sampling sites, while conductivity and oxygen levels showed significant variations. Traditional microbiological analysis revealed elevated coliform levels, and PCR detected Cryptosporidium spp., but not Giardia intestinalis. Amplicon-based sequencing identified 872 prokaryotic taxonomic units, corresponding to     Moraxellaceae, Rhizobiaceae, Comamonadaceae, Xanthobacteraceae, and Rhodobacteraceae, and 349 eukaryotic taxonomic units, predominantly fungi, including Lomentospora, Phytophthora, Fonseca, Fusarium, and Coccidioides, alongside two protozoan genera, Trichomonas and Sarcocystis. Alpha and beta diversity analyses revealed no significant differences between the rivers. High-throughput sequencing results complement traditional physicochemical and microbiological analyses, highlighting microbial diversity and contamination risks in the rivers, emphasizing the need for improved water quality management to mitigate public health risks.