Chalcone analogues on the control of Meloidogyne incognita and genomic studies of the biocontrol agent Bacillus velezensis

Abstract

Root-knot nematodes, Meloidogyne spp., are economically important plant pathogens and distributed worldwide. Among the strategies used to control these pathogens are chemical nematicides. However, the overuse of these toxic molecules in agriculture causes serious environmental problems. Hence the need for sustainable strategies, such as the use of natural compounds and biological agents. Chalcones are intermediate and final products in the flavonoid biosynthesis route. They have a wide spectrum of important biological activities. In this work, the activity of 12 chalcone analogues against the root-knot nematode Meloidogyne incognita was studied. Three of them showed strong nematicidal and nematostatic action against second stage juveniles of M. incognita. Chalcone (1E,4E)-1,5-di(4-nitrophenyl)-2-butylpenta-1,4-dien-3-one (compound 6) showed higher nematicidal activity than the commercial nematicide Carbofuran, and when applied in infested tomato plants, it reduced the number of nematode galls and eggs by 51% and 68%, respectively. In in silico study, this chalcone presumably acts by inhibiting the cytochrome P450 enzyme, which is important in the oxidation of various substances in nematode physiology. Also in this work, we studied the complete genomic sequence of the strain Bacillus velezensis UFLA258, which is a biological control agent of plant pathogens, since its obtaining, followed by assembly and annotation. In addition, using a comparative genomic approach, in silico evaluations were performed with all complete B. velezensis genomes available in the database, plus genomes of nearby species Bacillus amyloliquefaciens and Bacillus siamensis. Thus, the B. velezensis UFLA258 genome consists of a single chromosome of 3.95 Mbp in length, with an average GC content of 46.69%. It contains 3,949 protein coding genes and 27 RNA genes. Analysis based on mean nucleotide identity (ANI), DNA-DNA hybridization (dDDH), and complete sequence phylogeny of the rpoB gene confirmed that 19 strains deposited in the database as B. amyloliquefaciens were indeed B. velezensis. Although these species are phylogenetically close, combined analyzes of various genomic traits, such as the presence of biosynthetic genes encoding secondary metabolites, CRISPr/Cas arrays, ANI, dDDH, and other strain information, including source isolation, have allowed their unambiguous classification like these three species. This genomic analysis extends knowledge about related species, B. velezensis, B. amyloliquefaciens and B. siamensis, with an emphasis on taxonomic status.