Characterization of Prokaryotic Communities, Core Microbiome, and Functional Potential in the Tam Giang–Cau Hai Lagoon System

The Tam Giang–Cau Hai lagoon system comprises five interconnected lagoon units: Tam Giang, Tam Thanh–Sam, Ha Trung, Thuy Tu, and Cau Hai. To our knowledge, this is the first 16S rRNA-based characterization of prokaryotic communities encompassing all five lagoon units using high-throughput amplicon sequencing and bioinformatic analyses. Alpha-diversity indices revealed differences in microbial richness and diversity among lagoon units, while beta-diversity analyses indicated differences in community composition. The sediment microbiome was dominated by major bacterial phyla, including Proteobacteria, Chloroflexi, Acidobacteriota, Desulfobacterota, Actinobacteriota, Nitrospirota, Bacteroidota, and Myxococcota, with several genera consistently detected across multiple lagoon units. UpSet analysis identified 426 ASVs shared among all five lagoon units, representing 0.36% of total ASV richness but 20.86% of total reads, indicating substantial spatial turnover alongside an abundant shared microbial fraction. Core microbiome analysis, based on prevalence and relative-abundance criteria, identified 91 core ASVs. Predicted functional profiles differed among lagoon units, while shared predicted functions were mainly associated with energy and carbon metabolism, biosynthesis, membrane transport, and genetic information processing. These findings indicate substantial taxonomic and predicted functional heterogeneity among lagoon units while retaining a conserved fraction of microbial taxa and predicted functions. The study provides a system-wide baseline for future investigations integrating environmental measurements and temporal sampling to elucidate the factors underlying these spatial patterns.