Vertical microbial fluxes in a modern permanently redox‐stratified lake provide insights into organic carbon sequestration and benthic–pelagic coupling during the Proterozoic Eon

Microbial processes regulating carbon cycling in ancient oceans remain poorly understood, yet characterizing these processes is critical for understanding early Earth biogeochemistry. Here, we investigate microbial communities associated with sinking particles regulating carbon cycling in meromictic Fayetteville Green Lake, a mid‐Proterozoic marginal ocean analog. The lake's photic zone spans oxic through sulfidic conditions, where prokaryotic photoautotrophs contribute to sinking fluxes and organotrophs mediate remineralization across redox and irradiance gradients. To characterize microbial communities in the sinking flux over time and redox condition, we sequenced 16S rRNA amplicons recovered from sediment traps throughout the lake's water column over the course of an annual photoautotroph bloom. Purple sulfur bacteria dominated deep fluxes, while cyanobacteria and green sulfur bacteria contributed variably across depths but were more abundant in suspended communities. As the bloom waned, chemoautotrophic Epsilonbacteraeota gained dominance in deeper fluxes, possibly due to niche partitioning. The shallow flux was remineralized by microbes exposed to temporally fluctuating biogeochemical conditions. Putative temporal changes in the availability and quality of organic matter and terminal electron acceptors thus promoted a succession of low‐diversity communities with few dominant hydrolytic and acidogenic clades. Unchanging conditions at depth promoted higher diversity microbial communities with niches for specialists dominated by sulfur‐metabolizing and fermentative clades. These findings improve our understanding of carbon cycling in the ancient ocean and offer insights into future shifts under climate change and meromixis in lakes.