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

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.