Phytoplankton-induced nitrification suppression limits sediment nitrogen removal via nitrate diffusion in shallow illuminated eutrophic lake

Widespread shallow lakes/ponds receive substantial anthropogenic reactive nitrogen (N) inputs to be vulnerable components of global aquatic ecosystems. However, the mechanisms governing N retention in these systems remain inadequately explored. We combined ¹⁵N tracer-labeling techniques and molecular analysis to quantify N transformation networks, including ammonium (NH₄⁺) uptake, remineralization, nitrate (NO₃⁻) uptake and nitrification in water column versus sedimentary N removal capacity in a tropical shallow lake (<1 m depth) in southern China. High-resolution diel monitoring (every 2 h over 36 h) revealed pronounced diel fluctuations in NH₄⁺, driven by daytime phytoplankton uptake (up to 8.5 µM h⁻¹) and NH₄⁺ regeneration from particulate organic nitrogen (PN) (up to 12.3 µM h⁻¹) in diel rhythms. In contrast, NO₃⁻ remained stable, with negligible uptake by phytoplankton or production via nitrification. The reciprocal transfer between NH₄⁺ and PN formed a closed N cycle loop. Nitrification was nearly absent despite ample NH₄⁺ availability at night, as evidenced by low nitrifier gene abundances (amo A = 0 copies/mL, amo B ≤ 8 × 10³ copies/mL), suggesting competitive exclusion by phytoplankton. This suppression of nitrification restricted NO₃⁻ supply to sediments and likely limited denitrification particularly contributed from the overlying water diffusion, though measured denitrification rates indicated strong potential under elevated NO₃⁻ conditions. This study elucidated the pivotal role of diel N cycling and ecological niche competition in driving N retention and self-purification capacity in eutrophic well-lit shallow systems.