Geogenic Ammonium Enrichment in Alluvial-Lacustrine Aquifer Systems: Coupled Controls of Microbial Pathways and Organic Matter Composition

Elevated geogenic ammonium (NH₄⁺) reported globally in alluvial-lacustrine aquifer systems is generally attributed to the mineralization of natural organic matter (OM). However, the contribution of microbial nitrogen (N) metabolism remains unclear. This study integrated hydrogeochemical profiling, metagenomic sequencing, and molecular-level OM characterization to elucidate how microbial nitrogen transformation and organic N mineralization could drive geogenic NH₄⁺ accumulation in groundwater. A distinct shift in microbial N metabolism pathways was identified along the NH₄⁺ enrichment gradient. Under N-limited and strongly reducing conditions, N fixation and dissimilatory reduction of nitrate to ammonium provided additional NH₄⁺ sources, whereas nitrification served as the primary sink by oxidizing NH₄⁺ to nitrate. At low NH₄⁺ levels, NH₄⁺ was mainly produced via deamination of simple mono-N compounds (CHO+1N) found in highly unsaturated low-oxygen (O) compounds and low-O polyphenols. In contrast, at high NH₄⁺ levels, urease-mediated hydrolysis of multi-N compounds (CHO+nN) in highly unsaturated high-O compounds became dominant. Co-occurrence network analysis revealed tight, pathway-specific linkages between functional genes and NH₄⁺-associated OM compounds, highlighting the substrate-dependent nature of geogenic NH₄⁺ production. These findings could advance our understanding of microbially mediated NH₄⁺ enrichment mechanisms and offer implications for the management of NH₄⁺ and other geogenic contaminants in organic-rich aquifers.