Potential drivers of fungal diversity in the sediment and water of the Knysna Estuary, South Africa

Estuaries serve as dynamic biodiversity networks, where microbial communities respond to environmental changes. However, the ecological functions and environmental factors shaping fungal assemblages in temperate South African estuaries remain largely unexplored. By integrating molecular data from ITS metabarcoding with physicochemical and elemental profiling, this study assessed the relationships between environmental variables and fungal communities in the sediment and water of the Knysna Estuary. Ascomycota was the most dominant phylum observed in the sediments, accounting for a mean relative abundance of 32.58%. Water communities largely belonged to unassigned phyla (57.68%). Similar genera were observed across habitats, where sediments illustrated an overall higher relative abundance between identified genera. Diversity indices in both sample types were mainly not statistically significant ( p ≥ 0.05), and the fungal community composition was similar across habitats. Fungal community response was assessed using Redundancy Analysis (RDA) and species response curves. Herein, phosphorus availability and ionic composition were associated with fungal taxa composition in water samples, where sediment communities differed in relation to the presence of specific elements, such as Pb and Zn. Additionally, the genera Aspergillus and Fusarium showed response patterns consistent with metal tolerance, whereas Rhizopus showed a pattern consistent with metal sensitivity. To the best of our knowledge, this study is the first to investigate the fungal communities in the Knysna Estuary. These findings advance our understanding of the fungal ecology in this estuary and emphasize the value of integrating molecular fungal data with elemental and physicochemical characterisation for estuarine health assessment and management.