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Metagenomic analysis of microbial community in uranium-contaminated soil

  • Genomics, transcriptomics, proteomics
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Abstract

Uranium tailing is a serious pollution challenge for the environment. Based on metagenomic sequencing analysis, we explored the functional and structural diversity of the microbial community in six soil samples taken at different soil depths from uranium-contaminated and uncontaminated areas. Kyoto Encyclopedia of Genes and Genomes Orthology (KO) groups were obtained using a Basic Local Alignment Search Tool search based on the universal protein resource database. The KO-pathway network was then constructed using the selected KOs. Finally, alpha and beta diversity analyses were performed to explore the differences in soil bacterial diversity between the radioactive soil and uncontaminated soil. In total, 30–68 million high-quality reads were obtained. Sequence assembly yielded 286,615 contigs; and these contigs mostly annotated to 1699 KOs. The KO distributions were similar among the six soil samples. Moreover, the proportion of the metabolism of other amino acids (e.g., beta-alanine, taurine, and hypotaurine) and signal transduction was significantly lower in radioactive soil than in uncontaminated soil, whereas the proportion of membrane transport and carbohydrate metabolism was higher. Additionally, KOs were mostly enriched in ATP-binding cassette transporters and two-component systems. According to diversity analyses, Actinobacteria and Proteobacteria were the dominant phyla in radioactive and uncontaminated soil, and Robiginitalea, Microlunatus, and Alicyclobacillus were the dominant genera in radioactive soil. Taken together, these results demonstrate that soil microbial community, structure, and functions show significant changes in uranium-contaminated soil. The dominant categories such as Actinobacteria and Proteobacteria may be applied in environmental governance for uranium-contaminated soil in southern China.

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Acknowledgments

This study was supported by national nuclear facilities decommissioning and radioactive waste management key scientific research projects of China (No. 14ZG6101). We wish to express our warm thanks to the Engineering Research Center of Biomass Materials, Ministry of Education, Southwest University of Science and Technology.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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The authors declare that they have no competing interests.

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Correspondence to Xuegang Luo.

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Yan, X., Luo, X. & Zhao, M. Metagenomic analysis of microbial community in uranium-contaminated soil. Appl Microbiol Biotechnol 100, 299–310 (2016). https://doi.org/10.1007/s00253-015-7003-5

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  • DOI: https://doi.org/10.1007/s00253-015-7003-5

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