Short-term thermal stratification induces hypoxia-related nutrient pulses which reshapes cyanobacterial dynamics in a shallow lake.

The reduction of external nutrient loading is a common target to address lake eutrophication, however internal nutrient dynamics can significantly delay recovery. In shallow systems, the role of episodic thermal stratification in nutrient dynamics and phytoplankton bloom ecology is often overlooked. We studied 45 years of data from the polymictic Lake Müggelsee, where short-lived stratification events strongly altered oxygen conditions, triggered pulses of soluble reactive phosphorus (SRP) and dissolved inorganic nitrogen (DIN) and had consequences for cyanobacterial community dynamics. The DIN:SRP ratio in the bottom-water was typically below the Redfield ratio, indicating that internal cycles reinforce the N-limiting conditions. Nostocales, particularly Dolichospermum, were closely associated with periods of thermal stratification, likely reflecting the improved light and temperature environment favorable for N₂-fixation. Buoyancy regulation played a key role in this response, as a greater proportion of Dolichospermum and Aphanizomenon biomass was concentrated within the upper 3.5 m of the water column compared to other cyanobacteria. Phycocyanin profiles indicated that some cyanobacteria undergo vertical migrations during stratified periods and appear to cross the thermocline into more nutrient-rich hypolimnetic waters, potentially conferring an advantage to taxa with high vertical migration velocities. However, Microcystis exhibited an unexpected association with more mixed conditions, suggesting a stronger reliance on nutrient redistribution following mixing events rather than direct access to hypolimnetic nutrient pools. Together, these findings demonstrate that episodic stratification fundamentally shapes nutrient availability and cyanobacterial niche partitioning in shallow lakes, with important implications for bloom development and lake management.