Higher variability of bacterial communities across space than over time in Antarctic lakes, and contrasting assembly processes

As sentinels of environmental changes, Antarctic lakes are ideal systems for studying the temporal and spatial dynamics of microbial communities. However, the relative magnitude and underlying mechanisms driving these variations remain poorly understood. Studying the spatiotemporal variation of microbial communities is crucial to provide a robust baseline for predicting ecosystem responses to global changes. Here, we investigated the spatial and inter-annual variation of bacterial community structure and their underlying assembly processes across sediment and water habitats in 11 lakes on the Fildes Peninsula, Maritime Antarctica, sampled during austral summers from 2017 to 2023, using 16S rRNA gene sequencing. The communities primarily clustered by habitat, with higher diversity in sediment (characterized by Rhodoferax, Intraporangiaceae, and Vicinamibacterales) compared to water (characterized by Polaromonas, Flavovacterium, and Sporichthyaceae). Spatial turnover of communities dominated over inter-annual variation in both habitats. Accordingly, the temporal core microbiome showed greater stability than the spatial core. The conserved bacterial communities (core communities) over time and across space exhibited a strikingly similar taxonomic composition. Community assembly processes differed between habitats, with a stronger contribution of dispersal limitation in sediment, versus ecological drift in water, as expected from the differences in connectivity within each habitat. Spatial and temporal variations in sediment were driven by globally similar assembly processes. In contrast, in water communities, different assembly processes explained the spatial and temporal variation. These insights emphasize the need to consider both spatial and temporal scales and various habitat types when predicting future bacterial dynamics in Antarctic lakes in a changing environment.