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Strand-specific RNA-seq analysis of the Acidithiobacillus ferrooxidans transcriptome in response to magnesium stress

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Abstract

Bioleaching is a promising process for 350 million tons Jinchuan low-grade pentlandite. But, Jinchuan pentlandite has lots of magnesium and high concentration of Mg2+ is harmful to bioleaching microorganisms. Thus, finding a way to improve the adaption of microorganisms to Mg2+ is a key for bioleaching. In the study, we found that oxidizing activity, bioleaching ability and biofilm formation of A.f were inhibited by Mg2+ stress. In addition, we analyzed mRNA and small RNA (sRNA) of Acidithiobacillus ferrooxidans (A.f) under Mg2+ stress by strand-specific RNA-sequencing (ssRNA-seq). After the bioinformatics process, 2475 coding genes were obtained, and there were 33 differential expression genes (DEGs) in 0.1 M-VS-Con, including 28 down-regulated and 5 up-regulated, whereas 52 DEGs were obtained in 0.5 M-VS-Con, including 28 down-regulated and 24 up-regulated. Gene ontology analysis showed most of DEGs were involved in catalytic activity, metabolic process and single-organism process. Furthermore, we identified 636 sRNA and some differential expression sRNA that may respond to Mg2+ stress. Further analysis of DEGs suggested that Mg2+ stress reduced biofilm formation perhaps through inhibiting Type IV Pili-related gene expression and inhibited bacterial activity perhaps through affecting carbon fixation. The study provided the foundation to understand the mechanisms of Mg2+ resistance in A.f and may be helpful to improve bioleaching ability for pentlandit.

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Acknowledgements

This work was supported by National Natural Science Foundation of China (31660026), the Fundamental Research Funds for the Central Universities of China (lzujbky-2016-152) and the Gansu Province Science Foundation for Distinguished Young Scholars (Grant no. 1308RJDA014).

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Authors and Affiliations

  1. Institute of Microbiology, School of Life Sciences, Lanzhou University, Tianshui Road No. 222, Lanzhou, 730000, People’s Republic of China

    Deping Tang, Jiangong Duan, Qiyu Gao, Yang Zhao & Hongyu Li

  2. The School of Chemical and Biological Engineering, Lanzhou Jiaotong University, West Anning Road No. 88, Lanzhou, 730070, People’s Republic of China

    Deping Tang

  3. Institute for Microbial and Biochemical Pharmacy, School of Pharmacy, Lanzhou University, Donggang Road No. 199, Lanzhou, 730020, People’s Republic of China

    Yang Li, Peng Chen, Zhengrong Wu, Ruixiang Xu & Hongyu Li

  4. Institute of Biology, Gansu Academy of Sciences, South Dingxi Road No. 229, Lanzhou, 730000, People’s Republic of China

    Jianping Zhou

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  1. Deping Tang
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  2. Jiangong Duan
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  3. Qiyu Gao
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  5. Yang Li
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  6. Peng Chen
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  7. Jianping Zhou
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  8. Zhengrong Wu
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  9. Ruixiang Xu
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  10. Hongyu Li
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Correspondence to Hongyu Li.

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Communicated by Erko Stackebrandt.

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Tang, D., Duan, J., Gao, Q. et al. Strand-specific RNA-seq analysis of the Acidithiobacillus ferrooxidans transcriptome in response to magnesium stress. Arch Microbiol 200, 1025–1035 (2018). https://doi.org/10.1007/s00203-018-1503-5

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  • DOI: https://doi.org/10.1007/s00203-018-1503-5

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