Comparative Analysis of Microbial Community Composition in Tropical Aquatic Ecosystems

Aquatic ecosystems provide vital ecological services to global health through facilitating biogeochemical cycles, providing water for drinking & industrial usage, supporting fisheries, and preserving biodiversity. Critical elements such as climate change and growing anthropogenic pressures are causing changes in microbial communities, leading to far-reaching consequences for human health. Systematic analysis of microbial communities based on overall genomic diversity reveals the interplay between microorganisms and environmental factors, responsible for indicative features of aquatic ecosystems. In this study, we conducted a 16S and 18S rRNA gene amplicon-based metagenomic analysis across four types of tropical aquatic habitats. 16S data showed the bacterial phylum Pseudomonadota dominated 38% to 83% of the total prokaryotic communities with Limnohabitans and Marinobacterium being the most abundant genera across all the aquatic habitats except for the pond, which was dominated by the phylum Bacteroidota around 42% with the genera Macellibacteroides. For eukaryotic communities, 18S data showed that a phylum of single-celled fungi Cryptomycota was the most dominant in the pond, brown algae Ochrophyta was dominant in around half of the canal and lake ecosystems. Conversely, the green algae Chlorophyta was the predominant eukaryotic phylum in marine ecosystems. Poteriospumella, Spumella and Chrysamoeba were the most abundant eukaryotic genera across all habitats, while more than 60% of eukaryotic genera remained unclassified, particularly in marine samples. Our findings provide a comprehensive picture of the diverse freshwater and marine microbiomes, highlighting the differential abundance, taxonomic distribution, community structure, and potential functional roles of microbial assemblages across diverse tropical aquatic habitats. These patterns are influenced by environmental factors and geographic location, laying the foundation for future ecological and conservation studies. Moreover, understanding these microbial communities can offer valuable insights into ecosystem health and potential pathogen reservoirs, contributing to improved strategies for environmental monitoring and public health protection.