Dual Assembly Pathways of Bacterial–Fungal Communities in Water and Sediments of a Seasonally Ice-Covered Shallow Lakes

Seasonal freeze–thaw transitions reorganize lake microbiomes, yet the coupling of environmental filters, biotic interactions, and assembly mechanisms across habitats remains unclear. We profiled bacteria and fungi in the water and sediment of Lianhuan Lake during winter (frozen) and spring (thawed) using amplicon sequencing, co-occurrence networks, and assembly models. Despite sharp physicochemical differences, α-diversity remained stable, while β-diversity was mainly driven by habitat (water vs. sediment), with seasonal turnover detectable, particularly for bacteria. Network analysis revealed a clear winter-to-spring shift: the frozen-water (FW) network was complex with high connectivity and 15% cross-domain edges, while frozen sediment (FS) was less connected but more modular. After thaw, both habitats showed reduced connectivity, with thawed sediment (TS) displaying the strongest modularity and an increase in cross-domain links (~16%). Keystone taxa shifted seasonally and by habitat: FW was dominated by peripheral taxa like Polaromonas , Pseudomonas , and Candidatus Limnoluna ; FS had connectors such as the families Comamonadaceae and Ilumatobacteraceae. In spring, Luteolibacter and Rhodoferax dominated water, while Flavobacterium and Sutcliffiella took over sediment. Environmental drivers varied by season and habitat: in winter water, pH was the dominant organising factor, with permanganate index (COD Mn ) and ammonia nitrogen (NH 3 -N) as secondary hubs, while NH 3 -N became central after thaw. In sediments, sediment total nitrogen (STN) and sediment organic matter (SOM) promoted bacterial links in winter, but SOM had a negative effect after thaw. Assembly analyses suggested selection-driven processes, with dispersal-assisted selection for water bacteria (neutral community model (NCM) R 2 ≈ 0.76), stronger determinism for sediment bacteria (R 2 ≈ 0.30), and for fungi, assembly governed jointly by heterogeneous selection and dispersal limitation rather than by a single dominant process. These results highlight how freeze–thaw cycles reshape cross-kingdom networks and microbial assembly, providing insights for monitoring seasonally frozen lakes.