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Article

Effects of Environmental Chemical Pollutants on Microbiome Diversity: Insights from Shotgun Metagenomics

1
Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
2
The Geneva Foundation, Silver Spring, MD 20910, USA
3
U.S. Army Engineer Research and Development Center Environmental Laboratory, Vicksburg, MS 39180, USA
4
Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, MS 39759, USA
*
Authors to whom correspondence should be addressed.
Toxics 2025, 13(2), 142; https://doi.org/10.3390/toxics13020142
Submission received: 20 January 2025 / Revised: 8 February 2025 / Accepted: 10 February 2025 / Published: 19 February 2025
(This article belongs to the Special Issue Feature Papers in the Novel Methods in Toxicology Research)

Abstract

Chemical exposure in the environment can adversely affect the biodiversity of living organisms, particularly when persistent chemicals accumulate over time and disrupt the balance of microbial populations. In this study, we examined how chemical contaminants influence microorganisms in sediment and overlaying water samples collected from the Kinnickinnic, Milwaukee, and Menomonee Rivers near Milwaukee, Wisconsin, USA. We characterized these samples using shotgun metagenomic sequencing to assess microbiome diversity and employed chemical analyses to quantify more than 200 compounds spanning 16 broad classes, including pesticides, industrial products, personal care products, and pharmaceuticals. Integrative and differential comparative analyses of the combined datasets revealed that microbial density, approximated by adjusted total sequence reads, declined with increasing total chemical concentrations. Protozoan, metazoan, and fungal populations were negatively correlated with higher chemical concentrations, whereas certain bacterial (particularly Proteobacteria) and archaeal populations showed positive correlations. As expected, sediment samples exhibited higher concentrations and a wider dynamic range of chemicals compared to water samples. Varying levels of chemical contamination appeared to shape the distribution of microbial taxa, with some bacterial, metazoan, and protozoan populations present only at certain sites or in specific sample types (sediment versus water). These findings suggest that microbial diversity may be linked to both the type and concentration of chemicals present. Additionally, this study demonstrates the potential roles of multiple microbial kingdoms in degrading environmental pollutants, emphasizing the metabolic versatility of bacteria and archaea in processing complex contaminants such as polyaromatic hydrocarbons and bisphenols. Through functional and resistance gene profiling, we observed that multi-kingdom microbial consortia—including bacteria, fungi, and protozoa—can contribute to bioremediation strategies and help restore ecological balance in contaminated ecosystems. This approach may also serve as a valuable proxy for assessing the types and levels of chemical pollutants, as well as their effects on biodiversity.
Keywords: microbiome; metagenomic; chemical pollutants; toxicity; biodiversity microbiome; metagenomic; chemical pollutants; toxicity; biodiversity

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MDPI and ACS Style

Muhie, S.; Gautam, A.; Mylroie, J.; Sowe, B.; Campbell, R.; Perkins, E.J.; Hammamieh, R.; Garcia-Reyero, N. Effects of Environmental Chemical Pollutants on Microbiome Diversity: Insights from Shotgun Metagenomics. Toxics 2025, 13, 142. https://doi.org/10.3390/toxics13020142

AMA Style

Muhie S, Gautam A, Mylroie J, Sowe B, Campbell R, Perkins EJ, Hammamieh R, Garcia-Reyero N. Effects of Environmental Chemical Pollutants on Microbiome Diversity: Insights from Shotgun Metagenomics. Toxics. 2025; 13(2):142. https://doi.org/10.3390/toxics13020142

Chicago/Turabian Style

Muhie, Seid, Aarti Gautam, John Mylroie, Bintu Sowe, Ross Campbell, Edward J. Perkins, Rasha Hammamieh, and Natàlia Garcia-Reyero. 2025. "Effects of Environmental Chemical Pollutants on Microbiome Diversity: Insights from Shotgun Metagenomics" Toxics 13, no. 2: 142. https://doi.org/10.3390/toxics13020142

APA Style

Muhie, S., Gautam, A., Mylroie, J., Sowe, B., Campbell, R., Perkins, E. J., Hammamieh, R., & Garcia-Reyero, N. (2025). Effects of Environmental Chemical Pollutants on Microbiome Diversity: Insights from Shotgun Metagenomics. Toxics, 13(2), 142. https://doi.org/10.3390/toxics13020142

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