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.