Even when species count decreases under stress, groups of microbes compensate to sustain essential functions.

The Science

Water underground contains small life forms called microbes, which include bacteria, viruses, and fungi. These microbes act to break down harmful chemicals, but little is known about how this critical function is affected by stress. In this study, ENIGMA scientists compared microbes in wells with clean water to wells with water contaminated by metals and other waste. The team found that even when many types of microbes disappeared, the jobs those microbes did still occurred. This suggests microbes can switch roles, or that different types of microbes can fill the same role, a concept known as functional redundancy.

Image showing the location of different wells on a topographical map. — Geographical location of the study site, which consisted of several wells across a watershed in Oak Ridge, Tennessee, USA. Samples include water from a range of wells, uncontaminated to high-contaminated wells.

The Impact

This study shows that microbes do useful work, like breaking down contaminants, even when their numbers drop or the kinds of microbes change. The results could also help scientists build better models to predict how contamination affects life underground.

The Summary

Scientists studied microbes living in groundwater at a site contaminated with metal, acid, and other waste. They compared wells with high, medium, low, and no levels of contamination. At high levels, the variety of microbes dropped. But the key functions they performed—like breaking down nitrogen and sulfur compounds—remained. In other words, while microbial variety can fall, critical processes or functions may remain stable.

Contact

Yupeng Fan
University of Oklahoma
Yupeng.Fan-1@ou.edu

zhou-jizhong-joe — Jizhong Zhou, University of Oklahoma

Jizhong Zhou
George Lynn Cross Research Professor; Director, Institute for Environmental Genomics (IEG)
Department of Microbiology & Plant Biology, University of Oklahoma
jzhou@ou.edu

Funding

This study by ENIGMA – Ecosystems and Networks Integrated with Genes and Molecular Assemblies (http://enigma.lbl.gov), a Science Focus Area Program at Lawrence Berkeley National Laboratory, is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Biological & Environmental Research, under contract number DE-AC02-05CH11231

Publication

Fan, Y., Wang, D., Yang, J.X. et al. Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer. Microbiome 13, 106 (2025). OSTI:2563555 https://doi.org/10.1186/s40168-025-02105-x