Fusarium antagonism potential and metabolomics analysis of endophytic bacteria isolated from Crotalaria retusa L., a traditional medicinal plant in Côte d’Ivoire

Sixty-four endophytic bacteria were isolated from roots, stems, and leaves of Crotalaria retusa L., a medicinal plant well-known for its antimicrobial properties in Côte d'Ivoire. Taxonomic characterization revealed that these bacteria were mainly dominated by the genera Pseudomonas, Rhizobium, Bacillus, and Inquilinus. The antagonistic activities of the endophytic bacteria against two phytopathogenic fungi affiliated with the genus Fusarium were tested using in vitro coculture. Isolates belonging to the genus Inquilinus showed the highest inhibitory activities against Fusarium oxysporum f. sp. cubense, ranging from 40% to 57%, while the highest inhibitory activities against Fusarium graminearum were obtained with Bacillus isolates (∼66%). Finally, a metabolomic study of the leaves, stems, and seeds of the plant and of the endophytes presenting antifungal activity was carried out using LC-MS/MS analysis of the methanolic extracts of all active endophytic isolates. The identified metabolites of interest from the endophytes were mainly peptides, lipids, and steroids. Two pyrrolizidine alkaloids, monocrotaline and senecionine, were detected in the plant organs but not in the endophytic bacterial extracts. These results highlighted the potential of C. retusa L. plant and its endophytic microbiome as a source of bioactive molecules of interest and biocontrol agents against phytopathogenic Fusarium spp.