Functional and genomic analyses of plant growth promoting traits in Priestia aryabhattai and Paenibacillus sp. isolates from tomato rhizosphere

Abstract

This study investigated plant growth-promoting (PGP) mechanisms in Priestia aryabhattai VMYP6 and Paenibacillus sp. VMY10, isolated from tomato roots. Their genomes were initially assessed in silico through various approaches, and these observations were then compared with results obtained in vitro and in vivo. Both possess genes associated with the production of siderophores, indole acetic acid (IAA) and cytokinins (CKs), all of which have been shown to promote plant growth. The two strains were able to produce these compounds in vitro. Although both genomes harbor genes for phosphorus solubilization, only VMY10 demonstrated this ability in vitro. Genes linked to flagellar assembly and chemotaxis were identified in the two cases. Both strains were able to colonize plant roots, even though VMYP6 lacked motility and no flagella were observed microscopically. In the greenhouse, tomato plants inoculated with the strains showed increased biomass, leaf area, and root length. These findings underscore the importance of integrating in vitro assays, genomic analyses, and plant trials to gain a comprehensive insight into the PGP mechanisms of rhizobacteria like VMYP6 and VMY10. Such insight may contribute to improving the selection of strains used as biofertilizers in tomato, a major crop worldwide.

Fig. 1

Phylogenetic trees for VMYP6 and VMY10 with their related strains. A total of 133 and 136 common ancestral genes were identified across all studied strains using BLASTN searches with an E-value of 10^–30. Genes of P. megaterium ATCC 14581 (a) and P. illinoisensis NBRC 15959 (b) were respectively used as queries. The identified genes were aligned and trimmed individually. For the Priestia genus (a), genes with at least 80% query coverage and 80% identity were selected. For the Paenibacillus genus (b), the selection criteria were set at 90% query coverage and 90% identity. The trees were built with the RAxML algorithm, and visualized and annotated using iTOL. Tree reliability was assessed through bootstrapping with 200 and 300 replicates, respectively, using the MRE-based Bootstopping criterion. Type strains are indicated with a blue star.

Fig. 2

PGP genes identified in Priestia aryabhattai VMYP6 and Paenibacillus sp. VMY10. A total of 504 and 390 annotated genes are respectively shown for VMYP6 (a) and VMY10 (b). BLASTP was implemented first, then RAST, and finally PSI-BLAST. Only non-redundant genes identified by each method are shown.

Fig. 3

Transmission electron micrographs of VMYP6 and VMY10. The arrows indicate the flagellar basal bodies (a). Swimming motility of VMYP6 and VMY10 on a soft agar plate. Bacteria were stabbed in the center of the agar plate and incubated at 28 °C for 15 h. The ‘ ↔ ’ indicates positive motility by diffuse growth around the inoculation point.

Fig. 4

Scanning electron micrographs of the root surface of 10-day-old tomato plants: uncolonized control treatment; colonization by VMYP6; colonization by VMY10.

Fig. 5

Effect of treatment with VMYP6 and VMY10 on plant growth attributes in tomato plants 75 days after sowing: (a) leaf dry weight; (b) stem dry weight; (c) leaf area; and (d) root length. Bars represent mean values ± standard deviation (SD) of three independent replicates. FW: Fresh weight. For each variable, different lowercase letters between columns indicate significant differences at P < 0.05 according to Fisher’s LSD test.