Abstract
Elevated ammonium concentrations in deltaic groundwater pose a widespread environmental challenge, yet the microbial mechanisms linking depositional history to ammonium dynamics remain poorly understood. The Pearl River Delta, with the highest naturally occurring groundwater ammonium concentrations documented globally, provides a unique natural system to investigate these processes. Here, by integrating geochemical and metagenomic data, we show that fermentation-related genes are the most prevalent across all depositional zones, suggesting fermentation as the potential primary pathway for ammonium production, with the functional potential declining as sedimentary organic matter becomes increasingly recalcitrant with sediment age. Secondary mechanisms shift from nitrate reduction to nitrite ammonification across terrestrial-to-marine-dominated zones, reflecting salinity-driven metabolic partitioning. Notably, the marine-derived genus Brevirhabdus emerges as a key taxon linking depositional history to present-day biogeochemistry, demonstrating remarkable metabolic versatility. These findings demonstrate that paleo-depositional and hydrogeological evolution fundamentally shape microbial landscapes and dictate groundwater quality in deltaic systems worldwide.
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Acknowledgements
This research was supported by the National Natural Science Foundation of China (Grant No. 42407109, to M.Q.L.; Grant No. 42130702, to J.J.J.; Grant Nos. 32225003, 32393970, 32393971, and 92251306, to M.L.), the Guangdong Major Project of Basic and Applied Basic Research (Grant No. 2023B0303000017, to M.L.), the Shenzhen Science and Technology Program (Grant No. KCXFZ20240903092800002, to M.L.), the Shenzhen University 2035 Program for Excellent Research (Grant No. 2022B002, to M.L.), the Shenzhen University Special Funding Initiative (Grant No. 2024T001, to M.L.), the Synthetic Biology Research Center of Shenzhen University (Grant No. 868-000003010601, to M.L.), the Guangdong-Hong Kong Joint Laboratory for Soil and Groundwater Pollution Control (Grant No. 2023B1212120001, to J.J.J. and H.L.L.), the Guangdong Provincial Key Laboratory for Soil and Groundwater Pollution Control (Grant No. 2023B1212120002, to H.L.L.), and the High-level University Special Fund (Grant No. G03050K001, to H.L.L.). Computational resources were provided by the Intelligent Computing Center of Shenzhen University. We thank Shuo Shi for sharing the data, and Eddie Ho, Zijun Tan, and Yurong Song for their valuable assistance during fieldwork. The authors used AI-assisted tools (Claude, Anthropic) for language editing to improve the clarity and grammar of the manuscript. The authors take full responsibility for the integrity of the content.
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Lu, M., Jiao, J.J., Luo, X. et al. Microbial drivers of ammonium accumulation in Holocene sediments of the Pearl River Delta. Nat Commun (2026). https://doi.org/10.1038/s41467-026-72058-8
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DOI: https://doi.org/10.1038/s41467-026-72058-8
