Resilience and re-establishment of sulfide- and redox-structured microbial networks after holomixis in a meromictic lake

Abstract

Land-locked meromictic lakes sustain persistent redox stratification that structures microbial niches and sulfur–nitrogen–carbon cycling. Whole-lake overturns are unusual in such systems, and the temporal dynamics of microbial community re-establishment and functional recovery during holomictic restratification remain poorly understood. We tracked a mixing–re-stratification sequence in meromictic Lake Shira (Siberia) using depth-resolved sampling across oxic, chemocline, anoxic, and water–sediment interface layers in four hydrodynamic regimes: transitional holomixis, complete holomixis (CH), developing meromixis (DM), and stable meromixis (M). 16S rRNA amplicons showed that CH homogenized the water column and reduced depth structure, whereas DM–M rapidly re-established strong vertical partitioning, including recovery of Desulfobacterota and other anaerobic lineages in sulfidic deep waters and enrichment at the redox transition. Nanopore metagenomics reconstructed 401 metagenome-assembled genomes (MAGs) and revealed stage- and layer-specific functional repertoires consistent with redox zonation, oxic regimes enriched in sulfur oxidation, phototrophy-related traits and anoxic regimes enriched in sulfate reduction, and anaerobic nitrogen transformation. A conserved set of core MAGs, including Yoonia spp., persisted among regimes, suggesting a functional backbone that may promote rapid ecosystem recovery after overturn. These findings provide time-and depth-resolved, and genome-resolved evidence that microbial reassembly after holomixis is not simply a return of the former community composition, but that microbial succession is a process of functional reorganization. Persistence of core MAGs, re-establishment of redox-specific assemblages, and redistribution of shared metabolic modules contribute to the recovery of stratified ecosystem functions as meromictic stratification collapses and re-establishes. Video Abstract