Metatranscriptomic analysis reveals active microbes and genes responded to short-term Cr(VI) stress
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Metatranscriptomic analysis reveals active microbes and genes responded to short-term Cr(VI) stress Zhengsheng Yu1,2 Yaxin Pei1,2 Shuai Zhao2 Apurva Kakade2 Aman Khan1 Monika Sharma2 Hajira Zain2 Pengya Feng2 Jing Ji1,2 Tuoyu Zhou1 Haoyang Wang3 Jingyuan Wu4 Xiangkai Li 1,2 ●
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Accepted: 10 October 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract 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. Keywords Short-term Cr(VI) stress Active microbes Dormant microbes Function-unknown genes Rare genera ●
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Introduction
These authors contributed equally: Zhengsheng Yu, Yaxin Pei Supplementary information The online version of this article (https:// doi.org/10.1007/s10646-020-02290-5) contains supplementary material, which is available to authorized users. * Xiangkai Li [email protected] 1
Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000 Gansu, PR China
2
Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000 Gansu, PR China
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McMaster University, 1280 Main Street West, Hamilton, ON, Canada
4
The First Clinical Medical College, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000 Gansu, PR China
Microorganisms play an important role in global biogeochemical cycles, such as carbon, nitrogen, sulfur, and metal cycling (Anantharaman et al. 2018; Francis et al. 2007; Klaus-Joerger et al. 2001; Worden et al. 2015). The relationship between microbial com
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