Elevated level of arsenic negatively influences nifH gene expression of isolated soil bacteria in culture condition as well as soil system

Abstract

Comprehensive studies on the effect of arsenic (As) on free-living diazotrophs that play a crucial role in soil fertility by nitrogen fixation are still scanty. Here, we isolated three free-living bacteria from rice field with potential nitrogen-fixing ability and investigated the impact of As on their nifH gene expression and extracellular polysaccharide (EPS) production in culture condition and soil system. 16S rRNA sequence analysis showed that the isolated bacteria were affiliated to β-Proteobacteria, γ-Proteobacteria and Firmicutes. As(III) exposure to bacterial isolates followed by RT-qPCR analysis revealed that elevated levels of As reduced the expression of nifH gene in selective bacteria, both in culture medium and soil condition. We also noticed reduced production of EPS under higher concentration of As. All the three bacteria showed high tolerance to As(III), able to oxidize As and exhibited significant plant growth-promoting traits. This investigation indicated that an environment exposed with higher concentration of As might perturbed the activity of free-living diazotrophs in agricultural soil system.

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Acknowledgements

This work was supported by Extra Mural Research grant (No. EMR/2016/003761) from DST-SERB, Government of India. Sincere acknowledgement is also due to Miss. Priyanka Chowdhury, Department of Biochemistry and Biophysics, University of Kalyani and Miss Sarmistha Majumdar, Bioinformatics centre, Bose Institute, Kolkata, for their kind assistance during qPCR and homology modelling, respectively.

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Supplementary figure S1

Photograph of a set of biomixture prepared for assessment of the impact of Arsenic on diazotrophic bacterial activity. In each biomixture, three different isolates were being exposed in the presence or absence of variable concentration of arsenic with sterile agricultural soil and incubated for three months. Please see Table 1 for detail description of the biomixtures (DOC 309 kb)

Supplementary figure S2

Slandered curve plotting log starting quantity of the 16S rRNA (a) and nifH (b) gene in terms of copy number vs. threshold cycle. PCR efficiency was 95% and 95.6% for 16S rRNA and nifH gene, respectively (DOC 130 kb)

Supplementary figure S3

Restriction digestion pattern of amplified 16S rRNA genes of isolates collected from rice field (DOCX 390 kb)

Supplementary figure S4

Structural alignment of the modelled structure shows that they can achieve highly similar scaffold of secondary structural elements of the experimentally reported structure. (a) A cartoon in green colour representing the model Burkholderia sp. EIKU9 and red cartoon represents Burkholderia vietnamiensis (AQM36706.1) (b) Yellow and red cartoon represent the model Bacillus sp. EIKU10 and Azotobacter chroococcum (ACF22078.1), respectively (c) model (Klebsiella sp. EIKU11 is shown in blue cartoon and cartoon in red for Klebsiella pneumoniae (AAO85881.1) (DOC 4726 kb)

Supplementary material 5 (DOC 34 kb)

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Chakraborty, A., Aziz Chowdhury, A., Bhakat, K. et al. Elevated level of arsenic negatively influences nifH gene expression of isolated soil bacteria in culture condition as well as soil system. Environ Geochem Health 41, 1953–1966 (2019). https://doi.org/10.1007/s10653-019-00261-2

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Keywords

  • Free-living N2-fixing bacteria
  • Arsenic contamination
  • nifH gene expression
  • Extracellular polysaccharide
  • Plant growth-promoting trait