Bacterial partitioning across water and sediment geochemical gradients in the Knysna estuary, South Africa

Introduction Estuaries support diverse biological communities and are essential for various socioeconomic activities, being characterised by the mixing of oceanic and riverine waters. However, increasing anthropogenic pressures have led to widespread habitat degradation and nutrient pollution, with nearly half of South Africa’s estuaries currently affected. Bacterial communities play important roles in the functioning of ecological and geochemical processes in estuaries. This study assessed the bacterial community structure and its relationship to environmental drivers in the water and sediments of the Knysna Estuary. Methods The incorporation of 16S rRNA gene metabarcoding analyses with elemental profiling, conducted through inductively coupled plasma mass spectrometry, provided a comprehensive understanding of how bacterial assemblages are associated with different biogeochemical conditions within this dynamic estuarine system. The study identified 18 phyla, with Proteobacteria predominating across both water (52.33%) and sediment (40.67%) samples. At the family and genus taxonomic levels, clear segregation was observed, as bacterial taxa unique to each sampling type were identified. Significant differences were observed between habitats in terms of Shannon and Simpson alpha diversity and beta diversity, with the results indicating a partitioning of bacterial communities between water and sediment, with sediments acting as a richer and more compositionally heterogeneous microbial reservoir. Results Multivariate analysis, using redundancy analysis (RDA) and species response curves revealed that the salinity and pH gradients, as well as the distribution of nutrients and trace metals, were primarily associated with variation in bacterial communities in both habitats, with the genus Synechococcus displaying strong sensitivity. The bacterial communities exhibited wider ecological tolerances, reflecting the fluctuating conditions in the estuary. In contrast, sediment communities were more specialised and more strongly associated with local geochemistry, particularly the concentrations of metals (Co, Pb, Ni), nutrients (P, Ca), and ions. Discussion This study enhances our understanding of the relationships between geochemical gradients and bacterial diversity in the water and sediments of the Knysna Estuary, thereby establishing a baseline for future research and informing targeted monitoring and intervention practices.