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

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.