Salinity Negatively Impacts Protistan and Fungal Community Stability and Shapes Assembly Processes in Freshwater Ecosystems

In freshwater lakes, protistan and fungal communities play crucial roles in the microbial loop as bacterivorous consumers, facilitating nutrient cycling and maintaining microbial balance by controlling bacterial populations. However, understanding of their functional roles and community assembly across varying environmental gradients in different lake ecosystems remains limited. In this study, we used 18S rRNA gene amplicon sequencing and multivariate statistical analyses to investigate the spatiotemporal and biogeographical patterns of protistan and fungal communities in the water column of two different lake systems in Croatia. Our results revealed that these complex communities were dominated by Chlorophyta, Ciliophora and Cryptophyta as well as Ascomycota, Basidiomycota and Chytridiomycota. Null model analysis showed that stochastic processes dominated most of the prokaryotic and fungal communities across sampled lakes and fractions, with seasonally salty Lake Crniševo having more prominent variable selection due to the presence of a salinity gradient. Also, it was discovered that salinity had a negative influence on the stability of both protistan and fungal communities in Lake Crniševo, acting as a major selective pressure. These results provide valuable insights into the community stability and assembly mechanisms of protistan and fungal communities in lake ecosystems and their responses to environmental changes.