Abstract:Background Root-knot nematodes severely threaten tomato production, while chemical control faces multiple drawbacks. Beneficial microbial strains have become ideal agents for nematode management because of their high efficacy, safety, environmental friendliness, and low risk of resistance development. However, the genetic basis of these biocontrol strains remains largely unknown, which limits their practical application.Objective To identify the genes involved in the biosynthesis of nematicidal metabolites by Serratia ureilytica strain CD3, elucidate the nematicidal mechanisms, and investigate the evolutionary relationships and genetic specificity among Serratia species, thereby providing a theoretical foundation for the field application of strain CD3.Methods The in vitro nematicidal activity of strain CD3 against root-knot nematodes was determined via the immersion method, and the genome was revealed by PacBio sequencing and Illumina sequencing. The genomic data were annotated via multiple databases, followed by comparative genomic analysis with nine other Serratia strains: ELP1.10, Db11, T6, 8927, YD25, A1, 626, C.1, and AS9.Results The indoor toxicity test showed that the corrected mortality rates of nematodes treated with the fermentation broth and supernatant of the strain for 24 h were 100.00% and 85.41%, respectively, which were significantly higher than those of the control. The whole genome sequencing results indicated that strain CD3 had only one chromosome with a size of 5 074 029 bp and the average GC content of 59.72%. A total of 4 619 coding genes were predicted, with a total length of 4 442 538 bp, accounting for 88.75% of the total genome length. Its genome contained ten secondary metabolite gene clusters. PHI annotation identified 1 747 pathogenicity-related genes, among which 52 were directly related to nematodes. CAZy database annotation identified 114 carbohydrate-active enzymes, including GH18 and CE4 with nematicidal activity. VFDB database annotation identified 220 virulence factor-related genes. Comparative genomics analysis showed that the ten Serratia strains had differences in basic characteristics such as genome size and gene number. Strain CD3 contained 246 mobile genetic elements, including two prophages. CAZy database annotation indicated that strain CD3 had a small number of carbohydrate enzymes but a number of nematicidal enzymes comparable to that of other strains. VFDB database annotation showed that the number of pathogenicity-associated genes varied among the ten strains, being the largest in strain CD3. average nucleotide identity (ANI) analysis and collinearity analysis results indicated that S. ureilytica T6 and 8927 had the highest homology with strain CD3. The pangenome results showed that strains of Serratia had open genomes and could acquire new genetic information from the environment. The pangenome map based on COG annotation indicated that strain CD3 had 54 unique genes. We analyzed the molecular characteristics of S. ureilytica strain CD3 at the genome level, which is of great significance for the comprehensive utilization of this strain.Conclusion Strain CD3 kills nematodes by disrupting the cuticle, secreting toxins, and releasing nematicidal metabolites, while exhibiting strong environmental adaptability, demonstrating excellent potential for biocontrol.
