Comparative Analysis of Microbial Community Structure and Composition across Tropical Freshwater Ecosystems Using 16S rRNA Metagenomics

Understanding the microbial diversity of freshwater bodies provides insight into their trophic status, habitat type, and degree of contamination. This study represents the first attempt to evaluate the taxonomic composition and microbial diversity of three freshwater bodies (Iyiube Lake, Abala Lake, and Iyioku River) located in Enugu East, Nigeria. Genomic DNA was isolated from the collected water samples, and the compositions of the microbial communities were characterized using the 16S rRNA sequencing method. The results of metagenomics analysis identified a total of 31 phyla, 81 classes, 139 orders, 177 families, and 209 genera. The two dominant bacterial phyla identified in the present study are Proteobacteria and Acidobacteria. Additionally, other prevalent phyla identified are Chloroflexi, Bacteroidota, Verrucomicrobiota, Myxococcota, and Nitrospirota. Among the bacterial phyla present in the freshwater ecosystems studied, Fusobacteria was the least prevalent phylum, only detected in Abala Lake. Additional phyla unique to single freshwater bodies are Sumerlaeota, DTB120, Deferrisomatota, Hydrogenedentes, Elusimicrobiota, and NB1-j, suggesting niche differentiation. Thus, when compared to other freshwater bodies, Iyiube Lake exhibits the largest abundance of Acidobacteria, which may indicate anthropogenic influence because of high sewage deposit. This study provides the first baseline inventory of bacterial assemblages in these tropical freshwater systems, underscoring their ecological uniqueness and the potential of specific taxa as bioindicators for environmental monitoring and freshwater ecosystem restoration in the tropical regions.