Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer
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40168_2025_Article_2105.pdf
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Author(s)
Fan, Yupeng
Wang, Dongyu
Yang, Joy X.
Ning, Daliang
He, Zhili
Zhang, Ping
Rocha, Andrea M.
Xiao, Naijia
Michael, Jonathan P.
Walker, Katie F.
Date Issued
April 28, 2025
Journal
Microbiome
Publisher
BioMed Central
Citation
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).
Version
Final published version
Abstract
Background Microbial taxonomic diversity declines with increased environmental stress. Yet, few studies have explored whether phylogenetic and functional diversities track taxonomic diversity along the stress gradient. Here, we investigated microbial communities within an aquifer in Oak Ridge, Tennessee, USA, which is characterized by a broad spectrum of stressors, including extremely high levels of nitrate, heavy metals like cadmium and chromium, radionuclides such as uranium, and extremely low pH (< 3). Results Both taxonomic and phylogenetic α-diversities were reduced in the most impacted wells, while the decline in functional α-diversity was modest and statistically insignificant, indicating a more robust buffering capacity to environmental stress. Differences in functional gene composition (i.e., functional β-diversity) were pronounced in highly contaminated wells, while convergent functional gene composition was observed in uncontaminated wells. The relative abundances of most carbon degradation genes were decreased in contaminated wells, but genes associated with denitrification, adenylylsulfate reduction, and sulfite reduction were increased. Compared to taxonomic and phylogenetic compositions, environmental variables played a more significant role in shaping functional gene composition, suggesting that niche selection could be more closely related to microbial functionality than taxonomy. Conclusions Overall, we demonstrated that despite a reduced taxonomic α-diversity, microbial communities under stress maintained functionality underpinned by environmental selection.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics
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Creative Commons Attribution-NonCommercial-NoDerivatives
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DOI of Published Version
https://doi.org/10.1186/s40168-025-02105-x
