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Metatranscriptomic analysis reveals active microbes and genes responded to short-term Cr(VI) stress


Heavy metals have been severely polluting the environment. However, the response mechanism of microbial communities to short-term heavy metals stress remains unclear. In this study, metagenomics (MG) and metatranscriptomics (MT) was performed to observe the microbial response to short-term Cr(VI) stress. MG data showed that 99.1% of species were similar in the control and Cr(VI) treated groups. However, MT data demonstrated that 83% of the microbes were active in which 58.7% increased, while the relative abundance of 41.3% decreased after short-term Cr(VI) incubation. The MT results also revealed 9% of microbes were dormant in samples. Genes associated with oxidative stress, Cr(VI) transport, resistance, and reduction, as well as genes with unknown functions were 2–10 times upregulated after Cr(VI) treatment. To further confirm the function of unknown genes, two genes (314 and 494) were selected to detect the Cr(VI) resistance and reduction ability. The results showed that these genes significantly increased the Cr(VI) remediation ability of Escherichia coli. MT results also revealed an increase in the expression of some rare genera (at least two times) after Cr(VI) treatment, indicating these rare species played a crucial role in microbial response to short-term Cr(VI) stress. In summary, MT is an efficient way to understand the role of active and dormant microbes in specific environmental conditions.

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All the raw datasets have been deposited into NCBI’s Sequence Read Achieve under accession number SRP154829.


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This study was funded by the National Natural Science Foundation grant (Grant no. 31870082), the Gansu Province Major Science and Technology Projects (Grant no. 17ZD2WA017), and the Fundamental Research Funds for the Central Universities (Grant no. lzujbky-2018-it47, lzujbky-2018-103).

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Correspondence to Xiangkai Li.

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Yu, Z., Pei, Y., Zhao, S. et al. Metatranscriptomic analysis reveals active microbes and genes responded to short-term Cr(VI) stress. Ecotoxicology 30, 1527–1537 (2021).

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  • Short-term Cr(VI) stress
  • Active microbes
  • Dormant microbes
  • Function-unknown genes
  • Rare genera