Assessing Microbial Diversity at Watering Points Along the Isiukhu River, Kenya Using 16S rRNA Sequencing

Abstract

Aims: 1) assess microbial diversity in water and sediment samples from watering points and springs along the upper reaches of river isiukhu, kakamega county, kenya, 2) utilize advanced molecular techniques, specifically 16s rRNA sequencing, to understand microbial communities, including both cultivable and non-cultivable microbes and 3) evaluate the influence of anthropogenic and environmental factors on microbial assemblages in freshwater ecosystems. Study Design:  The research employs a cross-sectional study design with random sampling of microbial communities from multiple locations along the river. Place and Duration of Study: the study was conducted in kakamega county, kenya, along the upper reaches of river isiukhu, between GPS coordinates 34.8372 and 0.2970 in the forest, and 34.7448 and 0.2557 downstream. Methodology: Nine sampling points were established for collecting water and sediment samples, resulting in 54 water samples and 18 sediment samples. Genomic DNA was extracted directly from 1 liter of water and sediment samples. 16s rRNA sequencing was performed on the extracted DNA, with sequence reads generated from an illumina miseq run. Taxonomy assignment was conducted using qiime pipeline scripts, matching against the ribosomal database project (RDP) and green genes. Data visualization was performed using the emperor online tool. Results: The analysis identified 1,549 operational taxonomic units (OTUS), comprised of 99% bacteria and 1% archaea. Forty phyla were detected, with predominant groups being proteobacteria (34%), bacteroidetes (17%), firmicutes (6%), and verrucomicrobia (5%). Sites ranked by faith’s phylogenetic diversity index included spring 1 at lianila (243) as the highest and the confluence site (43) as the lowest. Conclusion: The study reveals significant microbial diversity along river isiukhu, highlighting the impact of anthropogenic and environmental factors on microbial assemblages, and contributing to water conservation and management efforts. Anthropogenic factors could help explain the spatial variability in the composition of microbes seen here. This study begins to shed more light into the richness in freshwater microbiomes thus availing important data for monitoring and conservation of environment.