Endophytic microorganisms: identification, prospection of functional genes for promoting growth and biological control of diseases in common beans

Abstract

The common bean (Phaseolus vulgaris L.) is a crop of great economic and social importance in Brazil. One of the challenges faced is the emergence of diseases caused by phytopathogenic fungi, such as Colletotrichum lindemuthianum, Sclerotinia sclerotiorum, Pseudocercospora griseola, and Rhizoctonia solani, which cause anthracnose, white mold, angular leaf spot, and damping-off, reducing grain productivity and quality. Biological control with beneficial microorganisms has effectively reduced these pathogens, decreasing the need for chemical fungicides. The study of genomes of endophytic bacteria involved in biological control promises to discover new molecules and deepen knowledge, contributing to agricultural biotechnology. This study aimed to evaluate strains of endophytic bacteria of different species for their potential in the biological control of bean fungal diseases, relating it to the genetic content in their genomes. The DNA of Pseudomonas strains UFLA 02-281, UFLA02-293, and UFLA03-18 was extracted for genome sequencing. The species-level classification was performed by calculating the ANI (Average Nucleotide Identity), considering values below 96% indicative of new species. Functional analysis of the genomes of these strains and strain UFLA03-10, previously classified as Paenibacillus peoriae, was conducted. Strains UFLA 02- 281, UFLA02-293, UFLA03-18, and UFLA03-10 were tested in vitro to observe antagonism with strains of the fungi Colletotrichum lindemuthianum, Sclerotinia sclerotiorum, Pseudocercospora griseola, and Rhizoctonia solani, and in vivo to assess the control of these strains on anthracnose, white mold, angular leaf spot, and damping-off, inoculated alone and co-inoculated with the fungus CML4019 (Induratia coffeanna). Strain UFLA 02-281 was classified as Pseudomonas xanthosomatis, UFLA 02-293 as Pseudomonas cremoris and UFLA 03-18 as Pseudomonas bananamidigenes. Genes related to plant growth promotion and biological control of diseases were detected in all four bacterial strains, as genes linked to the production of antimicrobial metabolites such as bce, hcn, toxA, kinB and induction of resistance such as butA, metN, dacA for biological control, and genes related to the production of hormones such as the genes of the trpA, trpB, ald, and ydcU and nutrient metabolism such as the genes pst, pho, fix, glnA, nit among others, which promote plant growth. In vitro and in vivo assays showed that among the bacterial strains studied, UFLA03-10 controled more efficiently the fungi and deseases. The endophytic fungus inoculated alone, CML4019, controlled the disease, especially in assays evaluating damping-off and anthracnose. Among the co- inoculations, UFLA02-281 + CML4019 showed favorable results in at least one of the cultivars evaluated in the four in vivo assays. The results of in vitro and in vivo tests showed that when inoculated or co-inoculated, these strains showed promising results in controlling diseases caused by fungi. These results show that the strains evaluated in this study have the potential to be used as biological control agents in agricultural systems.