Unveiling chlorpyrifos mineralizing and tomato plant-growth activities of Enterobacter sp. strain HSTU-ASh6 using biochemical tests, field experiments, genomics, and in silico analyses

Abstract

The chlorpyrifos-mineralizing rice root endophyte Enterobacter sp. HSTU-ASh6 strain was identified, which enormously enhanced the growth of tomato plant under epiphytic conditions. The strain solubilizes phosphate and grew in nitrogen-free Jensen’s medium. It secreted indole acetic acid (IAA; 4.8 mg/mL) and ACC deaminase (0.0076 μg/mL/h) and hydrolyzed chlorpyrifos phosphodiester bonds into 3,5,6-trichloro-2-pyridinol and diethyl methyl-monophosphate, which was confirmed by Gas Chromatography – Tandem Mass Spectrometry (GC–MS/MS) analysis. In vitro and in silico (ANI, DDH, housekeeping genes and whole genome phylogenetic tree, and genome comparison) analyses confirmed that the strain belonged to a new species of Enterobacter. The annotated genome of strain HSTU-ASh6 revealed a sets of nitrogen-fixing, siderophore, acdS, and IAA producing, stress tolerance, phosphate metabolizing, and pesticide-degrading genes. The 3D structure of 28 potential model proteins that can degrade pesticides was validated, and virtual screening using 105 different pesticides revealed that the proteins exhibit strong catalytic interaction with organophosphorus pesticides. Selected docked complexes such as α/β hydrolase–crotoxyphos, carboxylesterase–coumaphos, α/β hydrolase–cypermethrin, α/β hydrolase–diazinon, and amidohydrolase–chlorpyrifos meet their catalytic triads in visualization, which showed stability in molecular dynamics simulation up to 100 ns. The foliar application of Enterobacter sp. strain HSTU-ASh6 on tomato plants significantly improved their growth and development at vegetative and reproductive stages in fields, resulting in fresh weight and dry weight was 1.8–2.0-fold and 1.3–1.6-fold higher in where urea application was cut by 70%, respectively. Therefore, the newly discovered chlorpyrifos-degrading species Enterobacter sp. HSTU-ASh6 could be used as a smart biofertilizer component for sustainable tomato cultivation.

GC/MS Profiling, Antibacterial, Anti-Quorum Sensing, and Antibiofilm Properties of Anethum graveolens L. Essential Oil: Molecular Docking Study and In-Silico ADME Profiling

“…The OPLS3e force field was applied for ligand preparation. Tautomer creation, ionization state at pH 7.0 ± 1.0 utilizing Epik, charged group neutralization, and optimization of the hydrogen bond and ligand 3D geometry are all included in the ligand preparation process [ 74 , 75 , 76 ]. Protein PDB IDs 1HD2, 1JIJ, 2XCT, 2UV0, and 3IX3 are downloaded by the protein data bank and processed for the modeling study.…”

Characterization of Growth-Promoting Activities of Consortia of Chlorpyrifos Mineralizing Endophytic Bacteria Naturally Harboring in Rice Plants—A Potential Bio-Stimulant to Develop a Safe and Sustainable Agriculture

“…Endophytes exhibit cell wall hydrolytic and lignin-related dye-degrading enzyme activities, facilitating their penetration into host plants as symbionts. Additionally, their anti-microbial activities enable them to protect themselves and resist pathogenic strains during symbiosis, thus promoting healthier plants [ 20 , 21 , 37 , 38 ]. Furthermore, pesticide-degrading endophytes can contribute to the remediation of soil and plants by alleviating pesticide contamination [ 7 , 37 , 39 ].…”

Design, synthesis, biological evaluation, and in silico studies of quinoxaline derivatives as potent p38α MAPK inhibitors

“…The RMSF analysis focuses on residue fluctuations, revealing the impact of such fluctuations on the flexibility of functionally significant residues that affect the protein. [54,55] indicating that throughout the 100-ns simulation period, the 4a-4F9W complex remained stable.…”