Cascade reservoir development alters the hydrological regimes of the river continuum, inducing thermal and oxygen stratification, and creating sediment gradients that affect downstream nitrogen (N) speciation. Traditional models rely on physical interception estimates while overlooking the metabolic feedback of in-reservoir bacterial communities. This study investigated water column and sediment N-cycling dynamics across the Lancang-Mekong River cascade (exemplified by the stratified Xiaowan Reservoir) and the undammed Nu River, combining vertical profiling, in situ flux measurements, and metagenomic sequencing.

Our results show that cascade damming does not disrupt river-scale bacterial continuity; however, flow deceleration and sediment sorting create strong spatial compartmentalization within reservoirs. Conditionally rare and abundant taxa (CRAT) exhibit distinct free-living (FL) and particle-associated (PA) lifestyle differentiation, linking hydrodynamic gradients to localized functional zones and molecular regulation.

Specifically, at the reservoir tail under oxic conditions, FL-CRAT dominate active nitrification under ArcAB regulation, maintaining high nitrification potential and suppressing anaerobic pathways. In the transition region, flow deceleration enriches PA-CRAT in deeper layers, where ArcAB/ANR oxygen-sensing systems drive dynamic nitrification-denitrification coupling, cAMP regulators facilitate organic carbon utilization, and DNR/NNR systems control nitrous oxide release, forming a carbon-nitrogen coupling hot zone. Near the dam front, prolonged water residence limits denitrification substrates. Consequently, both FL and PA CRAT establish a sophisticated nitrogen-sensing network centered on PII-GlnK and GlnL/GlnG systems. This network precisely senses intracellular carbon-to-nitrogen ratios and energy levels to coordinately regulate dissimilatory nitrate reduction to ammonium (DNRA) via complementary nirBD and nrfAH pathways, promoting sediment ammonium release.

Overall, this study provides a novel hydrodynamics-lifestyle-multilevel regulation perspective on how microbial communities adapt to reservoir heterogeneity, yielding critical insights into how cascade damming alters the bioavailability of exported nitrogen along the river-estuary-bay continuum.