Genomic Insights into Pseudomonas protegens E1BL2 from Giant Jala Maize: A Novel Bioresource for Sustainable Agriculture and Efficient Management of Fungal Phytopathogens

Abstract

The relationships between plants and bacteria are essential in agroecosystems and bioinoculant development. The leaf endophytic Pseudomonas protegens E1BL2 was previously isolated from giant Jala maize, which is a native Zea mays landrace of Nayarit, Mexico. Using different Mexican maize landraces, this work evaluated the strain's plant growth promotion and biocontrol against eight phytopathogenic fungi in vitro and greenhouse conditions. Also, a plant field trial was conducted on irrigated fields using the hybrid maize Supremo. The grain productivity in this assay increased compared with the control treatment. The genome analysis of P. protegens E1BL2 showed putative genes involved in metabolite synthesis that facilitated its beneficial roles in plant health and environmental adaptation (bdhA, acoR, trpE, speE, potA); siderophores (ptaA, pchC); and extracellular enzymes relevant for PGPB mechanisms (cel3, chi14), protection against oxidative stress (hscA, htpG), nitrogen metabolism (nirD, nit1, hmpA), inductors of plant-induced systemic resistance (ISR) (flaA, flaG, rffA, rfaP), fungal biocontrol (phlD, prtD, prnD, hcnA-1), pest control (vgrG-1, higB-2, aprE, pslA, ppkA), and the establishment of plant-bacteria symbiosis (pgaA, pgaB, pgaC, exbD). Our findings suggest that P. protegens E1BL2 significantly promotes maize growth and offers biocontrol benefits, which highlights its potential as a bioinoculant.

Keywords: Pseudomonas protegens; antifungals; bacterial genome; biocontrol; maize endophyte; phytopathogen; promotion growth plant.

Figure 1

Representation of the circular genome of Pseudomonas protegens E1BL2. Using the Proksee server, the genome of Pseudomonas protegens E1BL2 was analyzed. The outermost circle represents the coding sequences of its genome assembly, which was deposited under GenBank BioProject PRJNA1078837, with BioSample ID SAMN40020743. The next circle contains the coding sequences of the Pseudomonas protegens SN15-2 * reference genome, which was phylogenetically the closest.

Figure 2

Phylogenomic tree and relevant plant-symbiosis genomic traits of Pseudomonas protegens strains and closely related species. The tree was built using the maximum likelihood method, which compared a core of 937 orthologous genes by employing 1000 bootstraps. Seven main clades were recognized. The color scale represents the percentage of genes found for each genomic trait for the 39 species analyzed; the red color represents a low percentage, while the green color represents a high percentage.

Figure 3

Growth percentage heatmap of various maize landraces inoculated with either Burkholderia metallica R3J3HD10 (Burk) or Pseudomonas protegens E1BL2 (Pseu). The growth parameters measured included the (A) stem length, (B) root length, (C) stem dry weight, and (D) root dry weight, with an uninoculated control as a negative control, Burkholderia-inoculated (Burk) as a positive control, and Pseudomonas-inoculated (Pseu) conditions. The color scale indicates the growth percentage, with green representing higher growth percentages and yellow representing lower growth percentages. The clustering dendrogram illustrates the similarity in growth responses between the different maize landraces. (E) Representative examples of treatments in Gordo maize landrace: uninoculated control, treatment with Burkholderia, and treatment with Pseudomonas.

Figure 4

Protection of the germination of Tuxpeño maize seeds by Pseudomonas protegens E1BL2 against phytopathogenic fungi. Fusarium oxysporum, Colletotrichum falcatum, Helminthosporium maydis, Curvularia sp., Pestalotia sp., Rhizoctonia sp., and Pythium sp. were assayed. The 18-point inhibition scale of the infection test was used to evaluate the fungus damage to the seeds and protection assay by endophytic bacteria. A, uninoculated control; B, safety control of P. protegens E1BL2; C, fungal infection control; D, P. protegens E1BL2 + phytopathogenic fungi. Error bars represent standard deviations (SDs). Only statistically significant differences between infection control and P. protegens E1BL2 + phytopathogen fungi were determined using one-way ANOVA (* p < 0.05).

Figure 5

Mexican maize landrace biocontrol assays of Pseudomonas protegens E1BL2 against phytopathogenic fungi at the greenhouse level. The heat map shows the percentage of the infection severity of the seedlings during the different treatments. The red bars represent the most severe plant damage, while the blue bars represent the absence of or less damage.

Figure 6

Plant field trial of P. protegens E1BL2 application in corn crop using the commercial maize hybrid Supremo. Panels (A,B) display violin plots illustrating the distribution of plant lengths (m) and yields (tons/ha), respectively, for treatments including uninoculated control, growth media, conventional fertilization, and P. protegens E1BL2 treatment, with statistically significant differences indicated by asterisks (* p < 0.05) and non-significant differences labeled as “ns”. Tukey’s test was used to compare the yields of inoculated and uninoculated plants (* p ≤ 0.05). (C) Uninoculated control, (D) conventional fertilization, and (E) P. protegens E1BL2 treatment.

Figure 7

Graphical abstract of the Pseudomonas protegens E1BL2 functions in the PGPB–plant–phytopathogen compound interactions through phenotypic information and genomic traits. The image was made with BioRender.