The TEX86 proxy, based on the distribution of isoprenoid glycerol dialkyl glycerol tetraethers (iGDGTs) from planktonic Thaumarchaeota, is widely used to reconstruct sea surface temperature (SST). Recent observations of species‐specific and regionally dependent TEX86‐SST relationships in cultures and the modern ocean raise the question of whether nonthermal factors may have impacted TEX86 paleorecords. Here we evaluate the effects of ecological changes on TEX86 using one Pliocene and two Pleistocene sapropels from the Mediterranean Sea. We find that TEX86‐derived SSTs deviate from U37normalK’‐derived SSTs before, during, and after each sapropel event. U37normalK’‐derived SSTs vary by less than 6 °C, while TEX86‐derived SSTs vary by up to 15 °C within a single record. Compound‐specific carbon isotope compositions indicate minimal confounding influence on TEX86 from exogenous sources. Some of the variation can be accounted for by changes in nitrogen cycling intensity affecting thaumarchaeal iGDGT biosynthesis, as demonstrated by an inverse relationship between TEX86 and δ15NTN. TEX86‐derived SSTs also consistently show warm anomalies in the Pleistocene, while the Pliocene samples exhibit both warmer and cooler relative offsets. These anomalies result from systematic differences between Plio‐Pleistocene iGDGT distributions and both modern Mediterranean and modern, globally distributed core top samples. Through characteristic GDGT distributions, we suggest the existence of three distinct endemic populations of Thaumarchaeota in the Pliocene, Pleistocene, and modern Mediterranean Sea, respectively. Importantly, these communities prevailed during both sapropel and oligotrophic conditions. Our results demonstrate that ecological and community‐specific effects must be considered when applying the TEX86 proxy to paleorecords.

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compound-specific δ 13 C diatom-diazotroph symbioses N 2 -fixation Mediterranean sapropels Elevated organic matter (OM) export flux promotes marine anoxia, thus increasing carbon sequestration efficiency and decreasing atmospheric carbon dioxide levels. However, the mechanisms that trigger and sustain anoxic events-particularly those associated with nutrient-poor, oligotrophic surface watersremain poorly constrained. Mediterranean Sea sapropels are well-preserved sediments deposited during episodic anoxic events throughout the Plio-Pleistocene; as such, they may provide unique insight into the biogeochemical and ecological drivers of-and responses to-marine anoxia. Using biomarker distributions, we demonstrate that anaerobic ammonium oxidizing (anammox) bacteria and diazotrophic endosymbionts of mat-and/or raft-forming diatoms were both abundant during sapropel events, particularly in the Ionian and Libyan seas. In these sapropels, the carbon isotope compositions of anammox biomarkers directly capture progressive 13 C-depletion in deep-water dissolved inorganic carbon, indicating sustained carbon sequestration. To explain these observations, we propose a reinforcing feedback whereby initial nutrient and/or circulation perturbations promote fixed nitrogen loss via intensified anammox and heterotrophic denitrification, which in turn favors proliferation of rapidly sinking diatom-diazotroph symbiotic consortia, increases OM burial flux, and sustains anoxia. This mechanism resolves the long-standing conundrum that small and buoyant diazotrophs are apparently associated with high OM export during periods of marine anoxia and oligotrophy.