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Meloidogyne incognita is one of the most destructive plant-parasitic nematodes worldwide, causing severe economic losses in agricultural production. Biocontrol bacteria can effectively control M. incognita, with significant differences in control efficacy among different strains. However, the mechanisms underlying differences in control efficacy remain unclear. Objective To explore the mechanisms responsible for the different efficacy of various biocontrol bacteria against nematodes. Methods The differences in nematicidal activity between two biocontrol bacterial strains, B133 and B104, were analyzed. Comparative genomics and metabolomics techniques were employed to investigate the genetic composition and metabolic mechanisms influencing the nematicidal activity of the two strains. Result From 24 h to 120 h of fermentation, the nematicidal activity of strain B133 was significantly higher than that of strain B104, reaching peaks of 77% and 54%, respectively, at the time point of 60 h. Whole-genome comparative analysis revealed that strain B133 possessed a larger genome size and a greater number of coding genes than strain B104. The phylogenetic trees conducted based on 16S rRNA gene or the housekeeping gene gyrB indicated that strains B133 and B104 were two different subspecies of Priestia megaterium. Predictions based on the virulence factors database (VFDB) and Kyoto encyclopedia of genes and genomes (KEGG) database showed that strain B133 harbored 22 unique virulence genes and 75 unique metabolism genes compared with strain B104. Meanwhile, the metabolites in the fermentation filtrate (60 h) were determined. Principal component analysis demonstrated significant differences in metabolite profiles between the two strains. Compared with that of strain B104, the fermentation filtrate of strain B133 had 40 increased metabolites (P<0.05), such as galactinol, 4-aminobenzoic acid, lumichrome, anthranilic acid, trehalose, and 3-methylthiopropionic acid. Moreover, through integrated genomics-metabolomics analyses, cysteine and methionine metabolism was identified as a key pathway influencing nematicidal activity. This pathway involves an L-lactic dehydrogenase (LDH) gene unique to strain B133 and 3-methylthiopropanoic acid with an elevated level and a positive correlation with the nematicidal effect of the strain. Conclusion By coupling genomics and metabolomics, this study reveals the different functional gene clusters and potential related metabolites of different subspecies of P. megaterium, laying a theoretical foundation and a practical basis for the targeted screening, modification, and industrial development of efficient biocontrol agents for nematodes.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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