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Comparative analysis of DNA-SIP and magnetic-nanoparticle mediated isolation (MMI) on unraveling dimethoate degraders

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Abstract

Microorganisms are crucial in the bioremediation of organophosphorus pesticides. However, most functional microorganisms (> 99%) are yet to be cultivated. This study applied two cultivation-independent approaches, DNA-SIP and magnetic-nanoparticle mediated isolation (MMI), to identify the functional microorganisms in degrading dimethoate in agricultural soils. MMI identified five dimethoate degraders: Pseudomonas, Bacillus, Ramlibacter, Arthrobacter, and Rhodococcus, whereas DNA-SIP identified three dimethoate degraders: Ramlibacter, Arthrobacter, and Rhodococcus. Also, MMI showed higher resolution than DNA-SIP in identifying functional microorganisms. Two organic phosphohydrolase (OPH) genes: ophC2 and ophB, were involved in dimethoate metabolism, as revealed by DNA-SIP and MMI. The degradation products of dimethoate include omethoate, O,O,S-trimethyl thiophosphorothioate, N-methyl-2-sulfanylacetamide, O,O-diethyl S-hydrogen phosphorodithioate, O,O,O-trimethyl thiophosphate, O,O,S-trimethyl thiophosphorodithioate, and O,O,O-trimethyl phosphoric. This study emphasizes the feasibility of using SIP and MMI to explore the functional dimethoate degraders, expanding our knowledge of microbial resources with cultivation-independent approaches.

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Acknowledgements

The authors would like to thank the National Natural Science Foundation of China (Nos. 42177359 and 41807119), the Natural Science Foundation of Beijing (No. 8212030), the Fundamental Research Funds for the Central Universities (Nos. FRF-TP-20-010A3 and FRF-IDRY-22-001), and the Open Fund of National Engineering Laboratory for Site Remediation Technologies (No. NEL-SRT201907).

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Authors and Affiliations

  1. School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, China

    Luning Lian, Yi Xing & Bo Jiang

  2. Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, China

    Luning Lian, Yi Xing & Bo Jiang

  3. National Environmental and Energy Science and Technology International Cooperation Base, University of Science & Technology Beijing, Beijing, 100083, China

    Luning Lian, Yi Xing & Bo Jiang

  4. College of New Energy and Environment, Jilin University, Changchun, 130021, China

    Dayi Zhang

  5. Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China

    Longfei Jiang

  6. College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China

    Mengke Song

  7. National Engineering Laboratory for Site Remediation Technologies, Beijing, 100015, China

    Bo Jiang

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  1. Luning Lian
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  2. Yi Xing
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  3. Dayi Zhang
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Correspondence to Yi Xing or Bo Jiang.

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Conflict of Interest The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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Highlights

• Dimethoate degraders were identified via MMI and DNA-SIP.

• MMI identified Pseudomonas, Bacillus, Ramlibacter, Arthrobacter, and Rhodococcus.

• DNA-SIP identified Ramlibacter, Rhodococcus and Arthrobacter.

• Both ophB and ophC2 were involved in dimethoate metabolism.

• MMI shows higher resolution than DNA-SIP in identifying functional microbes.

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Lian, L., Xing, Y., Zhang, D. et al. Comparative analysis of DNA-SIP and magnetic-nanoparticle mediated isolation (MMI) on unraveling dimethoate degraders. Front. Environ. Sci. Eng. 18, 5 (2024). https://doi.org/10.1007/s11783-024-1765-x

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  • DOI: https://doi.org/10.1007/s11783-024-1765-x

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