HKU scientists identify fermentation as key ammonium source beneath Pearl River Delta

A hidden microbial engine beneath China’s Pearl River Delta may be responsible for producing and preserving some of the highest natural groundwater ammonium concentrations ever recorded. A new study led by researchers at The University of Hong Kong and Shenzhen University identifies microbial fermentation as the likely dominant pathway generating ammonium in the delta’s deep sediments, offering a biological explanation for a groundwater problem previously attributed mainly to buried organic matter and poor circulation. The findings reveal how microorganisms living in sediments deposited thousands of years ago continue to influence groundwater chemistry today, potentially affecting water supplies across one of the world’s most densely populated regions.

Groundwater beneath the Pearl River Delta can contain exceptionally high levels of ammonium, a reduced form of nitrogen that is chemically distinct from ammonia but often discussed alongside it in environmental monitoring. At these concentrations, the water may be unsuitable for drinking unless it undergoes treatment. The delta’s unusual chemistry has long been linked to nitrogen-rich organic material buried in fine-grained sediments, where slow groundwater movement allows dissolved compounds to accumulate. Yet the precise microbial processes converting buried organic nitrogen into ammonium, and the organisms carrying out those reactions, have remained difficult to identify. The new research connects those missing biological details with the delta’s geological history and present-day hydrogeology.

The team examined 36 sediment samples collected from three boreholes drilled across different parts of the delta. The cores represented terrestrial-dominated, transitional and marine-dominated depositional environments and extended through sediments recording roughly 13,000 years of geological change. As the Pearl River shifted and sea levels changed, different sections of the delta were periodically influenced by riverine, coastal or marine conditions. Those environments left behind sediments with contrasting grain sizes, salinities, mineral compositions and quantities of organic matter. By studying these layers together, the researchers were able to compare microbial communities not only across space, from land toward the sea, but also through time, from relatively young shallow deposits to older and deeper sediments.

Geochemical measurements were combined with metagenomic sequencing, a technique that analyzes genetic material recovered directly from environmental samples. Rather than trying to grow individual microorganisms in the laboratory, the researchers reconstructed fragments of their genomes from the sediment DNA. This approach produced 770 representative metagenome-assembled genomes, or MAGs, providing a detailed catalogue of the microorganisms and metabolic capabilities preserved beneath the delta. The genetic data showed that microbial communities changed substantially along the land–sea gradient. Bacteria generally displayed broader metabolic flexibility, allowing them to respond to variations in organic substrates, salinity and electron acceptors. Archaea, by contrast, tended to retain more conserved functional traits across the different sedimentary settings.

Among the genes detected, those associated with fermentation were the most abundant in all three depositional zones. Fermentation is an anaerobic metabolic process in which microorganisms break down organic compounds without using oxygen as the final electron acceptor. In oxygen-poor sediments, this process can transform complex organic matter into smaller molecules such as organic acids, alcohols, carbon dioxide and hydrogen. Nitrogen-containing compounds released during the degradation of proteins and other biomolecules can ultimately contribute to ammonium formation. The researchers’ results suggest that fermentation is the central microbial route supporting ammonium production across the delta, although the genetic evidence indicates a pathway’s potential rather than a direct measurement of every reaction occurring in the sediment.

Fermentation-related genes became less abundant with increasing depth and sediment age. This pattern is consistent with the progressive depletion of easily degradable organic matter as sediments mature. Freshly buried material provides relatively accessible substrates for microbial metabolism, but over thousands of years the most reactive compounds are consumed, leaving behind more resistant organic matter that is harder to break down. The decline in fermentation potential with depth therefore suggests that ammonium production may be strongest in zones where suitable organic substrates remain available. In the marine-dominated part of the delta, however, the consequences may be particularly pronounced because fine, organic-rich deposits can simultaneously support microbial activity and restrict groundwater movement. Ammonium generated in these sediments may consequently remain trapped for millennia.

The researchers also identified important differences in other nitrogen-processing reactions. In the terrestrial-dominated sediments, genes involved in nitrate reduction were the second most abundant nitrogen-cycling genes. Nitrate reduction converts nitrate into nitrite, an intermediate compound that can then enter several microbial pathways. In the more saline transitional and marine-dominated sediments, genes associated with the direct reduction of nitrite to ammonium became more prominent. This shift suggests that salinity, as well as the availability of nitrate and nitrite, helps determine which biochemical routes dominate in different parts of the delta. The result is a layered microbial nitrogen cycle in which the same broad environmental system can host different ammonium-producing reactions depending on its depositional history and chemical conditions.

One organism stood out in the genetic analysis: the marine-associated bacterial genus Brevirhabdus. The researchers suggest that this group may be an important contributor to ammonium cycling in the sediments. Its presence may represent a biological legacy of earlier marine conditions, even where the modern environment has changed. The organism carries genes linked to fermentation and to the conversion of nitrite into ammonium, giving it the potential to connect carbon degradation with nitrogen transformation. Its discovery also illustrates why geological history matters in groundwater science. Microbes introduced or enriched during an ancient depositional phase can remain embedded in buried sediments and continue influencing chemical reactions long after the surrounding landscape has changed.

“Our findings move beyond the general understanding that buried organic matter is the source of ammonium,” said Professor Jimmy Jiujiu Jiao of HKU, who co-led the study. “We have identified the microbial pathways and organisms that are likely responsible for producing it and shown how these processes vary across sediments formed under different environmental conditions.” The study’s first author, Meiqing Lu, conducted her doctoral training under Jiao at HKU before joining Meng Li’s research group at Shenzhen University as a postdoctoral researcher. The work also involved scientists from the Southern University of Science and Technology, The Hong Kong University of Science and Technology and East China Normal University.

The findings could help reshape how groundwater ammonium is assessed in deltas around the world. Conventional surveys often focus on measuring ammonium concentrations and identifying the organic-rich layers that may supply nitrogen. Incorporating microbial genes, sediment age, salinity and depositional history could make it possible to predict where ammonium is most likely to accumulate before contamination becomes a major water-management challenge. Such information may guide the placement of monitoring wells, improve estimates of natural treatment requirements and help distinguish zones where ammonium production is still active from those where the available organic substrates have largely been exhausted. Because many major cities depend on deltaic groundwater, understanding this hidden microbial chemistry could become increasingly important as water demand, land use and climate-driven changes place additional pressure on freshwater resources.

News Publication Date: 6 May 2026

Web References: https://doi.org/10.1038/s41467-026-72058-8

References: “Microbial drivers of ammonium accumulation in Holocene sediments of the Pearl River Delta,” Nature Communications