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Transformation of TNT, 2,4-DNT, and PETN by Raoultella planticola M30b and Rhizobium radiobacter M109 and exploration of the associated enzymes

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Abstract

The nitrated compounds 2,4-dinitrotoluene (2,4-DNT), 2,4,6-trinitrotoluene (TNT), and pentaerythritol tetranitrate (PETN) are toxic xenobiotics widely used in various industries. They often coexist as environmental contaminants. The aims of this study were to evaluate the transformation of 100 mg L−1 of TNT, 2,4-DNT, and PETN by Raoultella planticola M30b and Rhizobium radiobacter M109c and identify enzymes that may participate in the transformation. These strains were selected from 34 TNT transforming bacteria. Cupriavidus metallidurans DNT was used as a reference strain for comparison purposes. Strains DNT, M30b and M109c transformed 2,4-DNT (100%), TNT (100, 94.7 and 63.6%, respectively), and PETN (72.7, 69.3 and 90.7%, respectively). However, the presence of TNT negatively affects 2,4-DNT and PETN transformation (inhibition > 40%) in strains DNT and M109c and fully inhibited (100% inhibition) 2,4-DNT transformation in R. planticola M30b.

Genomes of R. planticola M30b and R. radiobacter M109c were sequenced to identify genes related with 2,4-DNT, TNT or PETN transformation. None of the tested strains presented DNT oxygenase, which has been previously reported in the transformation of 2,4-DNT. Thus, unidentified novel enzymes in these strains are involved in 2,4-DNT transformation. Genes encoding enzymes homologous to the previously reported TNT and PETN-transforming enzymes were identified in both genomes. R. planticola M30b have homologous genes of PETN reductase and xenobiotic reductase B, while R. radiobacter M109c have homologous genes to GTN reductase and PnrA nitroreductase. The ability of these strains to transform explosive mixtures has a potentially biotechnological application in the bioremediation of contaminated environments.

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Data availability

All relevant data appear in the article and its Supporting Information files. The raw data of the transformation experiments appear in the Online Resource file “Raw data.xlsx”. Strains R. planticola M30b and R. radiobacter M109c are available in the bacteria collection of the Microbiology Department of the School of Science at Pontificia Universidad Javeriana (CMPUJ, Bogota, Colombia) under codes CMPUJ470 and CMPUJ471, respectively. CMPUJ collection are register in World Federation for Culture Collections. The genome sequences of strains R. planticola M30b and R. radiobacter M109c are deposited in the GeneBank database under accession Nos. GCA_006757685.1 and GCA_006757705.1, respectively. Sequences of the fosmids M30b_B4 and M109c_G12 are deposited in the GeneBank database under accession Nos. MT009031 and MT009032, respectively.

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Acknowledgments

The authors thank Dr. Jim Spain for providing the reference strain and Drs. Johanna Husserl and Howard Junca for contributing their knowledge and advice towards the development of this study.

Funding

This work was funded by INDUMIL (Colombian Military Industry—https://www.indumil.gov.co/). Colciencias (Colombian Innovation Agency—https://minciencias.gov.co/) awarded Hernan Avellaneda "Convocatoria 727 de 2015". The funders had no role in study design, data collection and analysis, decision to publish, or manuscript preparation. Soil sampling was approved by the Colombian National Authority of Environmental Licenses (Autoridad Nacional de Licencias Ambientales—ANLA) under Scientific Research Permit on Biodiversity No. 545 dated September 18, 2009 and amended by Resolution No. 450 dated May 15, 2013.

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  1. Facultad de Ciencias, Departamento de Biología, Unidad de Saneamiento y Biotecnología Ambiental (USBA), Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá, DC, Colombia

    Hernán Avellaneda, Ziv Arbeli & Fabio Roldan

  2. Facultad de Ciencias, Departamento de Biología, Biología de Plantas y Sistemas Productivos, Pontificia Universidad Javeriana, Bogotá, Colombia

    Wilson Teran

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  1. Hernán Avellaneda
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All authors contributed to the study conception and design. Material preparation, data collection, and analysis were performed by Hernán Avellaneda. The first draft of the manuscript was written by Hernán Avellaneda and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Fabio Roldan.

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Pontificia Universidad Javeriana ethics committee approved the present study in session held on April 11th.

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Avellaneda, H., Arbeli, Z., Teran, W. et al. Transformation of TNT, 2,4-DNT, and PETN by Raoultella planticola M30b and Rhizobium radiobacter M109 and exploration of the associated enzymes. World J Microbiol Biotechnol 36, 190 (2020). https://doi.org/10.1007/s11274-020-02962-8

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