Source: Journal of Geophysical Research: Biogeosciences
Underground environments like soil and aquifers teem with microbial life. These tiny microbes play a big role in cycling nutrients and breaking down or transforming pollutants. However, scientists still struggle to reliably model how microbes grow and decay.
Most studies of groundwater microbe communities focus on free-floating planktonic microbes, which make up less than 10% of an aquifer’s microbial population. The majority of microbes in groundwater are attached to sediment, making examination more difficult. Many studies are also done in labs, rather than on site.
Strobel et al. set out to study whether tracking biomarkers, such as specific genes produced by microbes during their life cycles, can improve models aimed at predicting how well microbes degrade pollutants in aquifers. They conducted research in southwestern Germany’s Ammer River floodplain, where groundwater sources with low oxygen levels and sediment with a high organic carbon content were ideal for microbial denitrification (the reduction of nitrate to nitrogen gas) to occur. The team constructed two 8.4-meter-deep wells surrounded by PVC casings and inserted seven microbial trapping devices (MTDs)—containers of sterilized sediment packed into a filter that served as a proxy for the microbial community in the aquifer matrix—into one of the wells. The MTDs remained submerged for 4.5 months prior to any experiments to allow the microbial community time to adapt to the environment and proliferate.
During a roughly 10-day period, while the MTDs were in the outflow well, the researchers injected nitrate-rich groundwater at the inflow well and extracted groundwater from the outflow well. The presence of nitrate, a pollutant that comes from sources such as fertilizer and sewage waste, spurred the microbial community into the process of denitrification. The team monitored the concentration of nitrate at the outflow and periodically withdrew an MTD to be transported to a lab for DNA analysis.
The growing abundance of key denitrification genes (napA and narG) in the earlier samples, followed by a decline in the later samples, indicated a dynamic microbial response to the added nitrate. The researchers’ efforts to use mathematical models to match their observations showed the importance of microbial growth during denitrification to control the extent of nitrate removal. The researchers note that though MTDs do not act as a perfect proxy for studying real aquifers, overall, the findings provide insight into the use of biomarkers to track biogeochemical processes, such as denitrification, in nature. (Journal of Geophysical Research: Biogeosciences, https://doi.org/10.1029/2025JG009181, 2025)
—Rebecca Owen (@beccapox.bsky.social), Science Writer
Citation: Owen R. (2026), Microbial genes could improve our understanding of water pollution, Eos, 107, https://doi.org/10.1029/2026EO260015. Published on 13 January 2026.
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