Bacterial community structure along the estuary–ocean gradient based on 16S rRNA gene profiling

Microorganisms inhabiting the estuarine and marine zones of the Patos Lagoon estuary play key ecological roles and warrant attention due to their potential implications for human health. The biochemical interactions that occur in this transitional environment contribute to the uniqueness of one of the world’s largest choked lagoons. This study determines the bacterial composition in the Patos Lagoon estuary and adjacent marine area using 16S rRNA amplicon sequencing. It represents the first application of high-throughput sequencing to comprehensively assess the estuarine–marine microbiota of this system. Variations in temperature, salinity, dissolved oxygen, and nutrient concentrations were the primary drivers of community structure. Higher temperatures combined with reduced oxygen levels were associated with increased microbial density and a predominance of Proteobacteria, particularly in areas subjected to greater anthropogenic influence. Conversely, regions under lower human impact exhibited more stable environmental conditions, lower microbial densities, and a more balanced taxonomic distribution. These findings underscore the strong influence of environmental variability on microbial communities along the estuary–ocean continuum. The seasonal shifts and site-specific differences observed highlight the dynamic nature of coastal ecosystems and reinforce the importance of continuous microbial monitoring.