Characterization and Whole-Genome Sequencing of Phytobacter palmae WL65, a Plant Growth-Promoting Rhizobacterium First Isolated from Rice Rhizosphere Soil in Thailand

Pisit Thamvithayakorn, Cherdchai Phosri, Vineet Vishal and Nuttika Suwannasai ()
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Pisit Thamvithayakorn: Department of Microbiology, Faculty of Science, Srinakharinwirot University, 114 Sukhumvit 23, Watthana, Bangkok 10110, Thailand
Cherdchai Phosri: Department of Biology, Faculty of Science, Nakhon Phanom University, Nakhon Phanom 48000, Thailand
Vineet Vishal: Department of Botany, Dr Shyama Prasad Mukherjee University, Ranchi 834008, Jharkhand, India
Nuttika Suwannasai: Department of Microbiology, Faculty of Science, Srinakharinwirot University, 114 Sukhumvit 23, Watthana, Bangkok 10110, Thailand

Agriculture, 2025, vol. 15, issue 7, 1-18

Abstract: Phytobacter palmae WL65, isolated from the rice rhizosphere, was confirmed as P. palmae through whole-genome analysis. WL65 exhibited key plant growth-promoting (PGP) characteristics, including nitrogen fixation ( nifA , nifB , nifD , nifE , nifF , nifH , nifJ , nifK , nifL , nifS , nifU , nifW , and nifX ), phosphate solubilization ( pstA , pstB , pstC , pstS , phnC , phnD , phnE , and phnV ), siderophore production ( fhuA , fhuB , fhuC , fhuD , fhuF , feoA , feoB , feoC , acrA , acrB , acrE , acrR , and acrZ ), and phytohormone biosynthesis ( trpA , trpB , trpC , trpE , trpGD , trpR , and trpS ). WL65 also contains an enterobactin biosynthetic gene cluster, essential for iron acquisition and enhancing both bacterial survival and plant growth. This study provides the first genomic insights into the PGP characteristics of P. palmae . The application of WL65 in rice cultivation as a biostimulant resulted in effective root colonization, supported by biofilm formation genes ( pgaA , pgaB , pgaC ), which enhance bacterial adhesion. The treatment significantly improved rice growth, increasing plant height (5.8%), panicle length (10.2%), and seed yield (34.5%). Soil analysis revealed improved nutrient availability, including increased organic matter (21%), phosphorus (38.4%), potassium (29.8%), and calcium (27%) levels. These findings suggest that WL65 is a promising biofertilizer candidate for improving soil fertility and nutrient uptake in sustainable agriculture.

Keywords: Phytobacter; nitrogen-fixing bacteria; PGP; rice (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2025
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