Recently, the research teams of Prof. Meng Li from Shenzhen University and Prof. Jiu Jimmy Jiao from The University of Hong Kong collaborated to publish a research paper in the high-impact journal Nature Communications. The study, entitled "Microbial Drivers of Ammonium Accumulation in Holocene Sediments of the Pearl River Delta," investigates the microbial mechanisms underlying high ammonium concentrations in groundwater within the Pearl River Delta. Dr. Meiqing Lu is the first author of the paper, while Prof. Jiu Jimmy Jiao and Prof. Meng Li serve as co-corresponding authors. Shenzhen University is the lead institution, with collaborative contributions from The University of Hong Kong, Southern University of Science and Technology, The Hong Kong University of Science and Technology, and East China Normal University.
The Pearl River Delta hosts the highest naturally occurring groundwater ammonium concentrations reported globally, making it an ideal natural laboratory for investigating ammonium enrichment mechanisms in delta environments. This study combines geochemical and metagenomic analyses from 36 sediment samples collected from three boreholes spanning approximately 13,000 years, covering terrestrial-dominated, transitional, and marine-dominated depositional environments.
Metagenomic analysis recovered 770 representative metagenome-assembled genomes (MAGs), revealing significant spatial variation in microbial communities and ammonium-related metabolic potentials along the land-sea gradient. The researchers found that Archaea and bacteria adopt fundamentally different adaptive strategies: Archaea exhibited evolutionary conservatism, while bacteria demonstrated greater biochemical plasticity. Fermentation-related genes were the most abundant across all depositional zones, indicating that fermentation is likely the primary microbial pathway for ammonium production. This potential for fermentation decreased with increasing sediment depth and age, reflecting the progressive aging of organic matter, which limits the availability of substrates for microbial ammonium production.
Among secondary ammonium-producing pathways, distinct patterns of gene abundance emerged along the land-sea gradient. In the terrestrial-dominated zone, nitrate reduction genes ranked second after fermentation genes, whereas in the transitional and marine-dominated zones, nitrite ammonification genes surpassed nitrate reduction genes to become the second most abundant. This suggests that salinity gradients may influence the metabolic partitioning between different ammonium-producing pathways. Furthermore, the marine-derived genus Brevirhabdus was identified as a key taxon linking depositional history to contemporary ammonium cycling, demonstrating notable metabolic versatility. Evolutionary analysis indicated widespread purifying selection on critical functional genes, with differentiated adaptive responses to both depth and salinity gradients.
This study establishes a mechanistic framework that integrates depositional history, hydrogeochemistry, and microbial function, providing new scientific insights for understanding and managing groundwater in delta regions worldwide.
Fig. 1 Conceptual model of historical depositional processes, biogeochemical zonation and microbial ammonium metabolism.
This research was supported by the National Natural Science Foundation of China, the Guangdong Major Project of Basic and Applied Basic Research, the Shenzhen Science and Technology Program, the Shenzhen University 2035 Program for Excellent Research, the Shenzhen University Special Funding Initiative, the Synthetic Biology Research Center of Shenzhen University, the Guangdong-Hong Kong Joint Laboratory for Soil and Groundwater Pollution Control, the Guangdong Provincial Key Laboratory for Soil and Groundwater Pollution Control, and the High-level University Special Fund.
Paper link: https://www.nature.com/articles/s41467-026-72058-8
