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Biodegradation analysis of pendimethalin by Planococcus citreus strain PD6 using FTIR and further in silico characterization for dehydrogenase as potential regulatory enzyme of degradation pathway

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Abstract

Degradation of pendimethalin by microorganisms is an approach seeking more attention nowadays. This study aims to isolate a new strain of Planococcus, which is capable of degrading pendimethalin from the soil in rice field. Identification of this coccus bacterium was done by phylogenetic analysis of 16S rRNA gene sequence. Strain PD6 was found to grow potentially on pendimethalin supplemented minimal salt medium and degraded 50 mg L−1 pendimethalin in monosubstrate system. Fourier transform infrared (FTIR) spectroscopy was performed to check degradation of pendimethalin by Planococcus, which was demonstrated by changing chemical bonding and stretching patterns. This study was further extended to predict possible first enzyme of pendimethalin-degradation pathway. Molecular docking was performed to check efficient binding of dehydrogenase with pendimethalin. This strain of Planococcus degraded pendimethalin with relatively high efficiency in minimal salt media and is presented as another possible bacterium other than species of Bacillus and Pseudomonas which are already demonstrated as potential in vitro pendimethalin-degrading bacteria. Moreover, docking reveals that dehydrogenases having more chance to prove as first regulatory enzyme of pendimethalin-degradation pathway.

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Acknowledgements

The scientific discussion with Dr. A.K. Verma (Department of Biochemistry CBSH, GBPUAT, India) and Dr. Anita Sharma (Department of Microbiology CBSH, GBPUAT, India) are gratefully acknowledged.

Funding

The work was partially supported by DST (Department of Science and Technology)—FIST (Fund for Improvement of S&T) India.

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  1. Department of Biochemistry, College of Basic Science and Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India

    Neha Trivedi & Ashutosh Dubey

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  1. Neha Trivedi
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  2. Ashutosh Dubey
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Research problem design, experiment design and objectives were decided by Dr. Ashutosh Dubey. Experimentation and data analysis was done by Dr. Neha Trivedi. Both the authors have equal contribution in manuscript writing and further editing.

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Correspondence to Neha Trivedi.

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Trivedi, N., Dubey, A. Biodegradation analysis of pendimethalin by Planococcus citreus strain PD6 using FTIR and further in silico characterization for dehydrogenase as potential regulatory enzyme of degradation pathway. Syst Microbiol and Biomanuf 3, 719–729 (2023). https://doi.org/10.1007/s43393-022-00142-3

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