Five centuries of lake deoxygenation and microbial shifts revealed by sedimentary DNA

Expanding global deoxygenation is a major ecological crisis. Oxygen loss in aquatic systems is reshaping ecosystems, altering biodiversity, nutrient cycles, and ecosystem functioning. Microbial communities, as key biogeochemical mediators, are highly responsive to oxygen availability, yet their long-term trajectories under sustained oxygen loss remain poorly understood. This limits our ability to anticipate ecosystem responses to climate-driven deoxygenation. We reconstructed five centuries of microbial and oxygen dynamics in meromictic Lake Montcortès (southern Pyrenees) using sedimentary deoxyribonucleic acid (DNA) and X-ray fluorescence spectroscopy of varved sediments. Average volume of anoxic water (VAW) increased from 545,560 m³ in the preindustrial period (1500–1750 Common Era) to 558,692 m³ after 1905, with greater persistence from 1937 onward. Instrumental data (2013–2020) confirmed this trend, with VAW peaking at 1,018,400 m³ and anoxia reaching 11.5 m and anoxia occurring below 11.5 m depth. Microbial communities gradually shifted from suboxic-adapted taxa to anaerobic assemblages dominated by sulfate-reducing bacteria and methanogenic archaea, reflecting historical anthropogenic pressures and recent warming-driven anoxia. Despite compositional change, core functional traits persisted, with no evidence of abrupt regime shifts indicating microbial resilience under long-term redox stratification. The timing of stratification intensification in Lake Montcortès coincides with the mid-20th century onset of the Anthropocene, as defined by the Anthropocene Working Group. Its annually resolved varved sediments, combined with clear geochemical and microbial signals of anthropogenic impact, support its proposal as a candidate Global Boundary Stratotype Section and Point Global (GSSP or “golden spike”). • Varved sediments provide a high-resolution, continuous 500-year microbial archive • sedaDNA reveals microbial diversity under early suboxic lake conditions • Hemp retting and land-use change trigger microbial redox reorganization • Prolonged stratification fosters anaerobic functional adaptation • Climate warming intensifies microbial shifts under sustained anoxia