Microbial Nitrogen Transformation in Hyporheic–riparian Zones: Integrating Molecular Ecology and Biogeochemical Perspectives

Abstract

Hyporheic–riparian zones (HRZs) function as critical biogeochemical hotspots, where dynamic exchanges between surface water and groundwater establish steep physicochemical gradients that regulate nitrogen (N) cycling at the terrestrial–aquatic interface. Here, we synthesises advances in the understanding of microbial N transformation pathways within HRZs from integrated biogeochemical, hydrological, and molecular ecological perspectives. We critically evaluated major microbially mediated processes, including nitrification, comammox, denitrification, dissimilatory nitrate reduction to ammonium (DNRA), anaerobic ammonium oxidation (anammox), and iron-coupled ammonium oxidation (feammox), in relation to redox stratification, hydrological residence time, organic carbon availability, and sediment heterogeneity. Emphasis is placed on emerging evidence for coupled anaerobic N-loss pathways and their sensitivity to transient hydrological exchange. Recent applications of metagenomics, stable isotope probing, and microbial network analysis have substantially advanced the mechanistic understanding of functional diversity and pathway interactions governing ecosystem N fate. We further assessed how anthropogenic pressures eutrophication, flow regulation, and climate-driven hydrological variability alter microbial community structure and N-cycling efficiency. Despite considerable progress, critical knowledge gaps persist in linking ecohydrological dynamics with microbial functional ecology at spatiotemporal scales. Future research integrating multi-omics, high-resolution isotope tracing, and predictive modelling frameworks is essential for advancing mechanistic understanding and informing the sustainable management of N cycling in HRZ ecosystems.