Resilience and reassembly of redox-structured microbial functional networks after rare holomixis in a meromictic lake

Abstract-short Land-locked meromictic lakes are characterized by long-term stratification and steep redox gradients that sustain vertically structured microbial communities and tightly coupled biogeochemical processes. Because complete overturns of the lake are rare, the dynamics of microbial reassembly after redox gradients collapse and subsequently recover remain poorly resolved. We investigated a mixing–restratification transition in Lake Shira (Siberia) with depth-stratified sampling of oxic, chemocline, anoxic, and water–sediment interface layers across four stages: intermittent holomictic (IH), complete holomictic (CH), developing meromictic (DM), and stable meromictic (M). 16S rRNA gene amplicons showed that CH homogenized the water column, dominated by Gamma - and Alphaproteobacteria , Campylobacteria , and Cyanobacteriia . As stratification re-formed (DM–M), communities became strongly depth-partitioned, with Desulfobacterota and other anaerobes re-established in sulfidic deep waters and assemblages concentrating near the redox transition. Nanopore metagenomics reconstructed 401 MAGs, revealing stage- and depth-specific functional repertoires consistent with redox zonation. Core MAGs, including Yoonia spp., persisted across phases, suggesting functional continuity underpinning rapid ecosystem recovery. These data provide a system-wide view of biogeochemical reassembly during collapse and restoration of stratification meromictic lake.