Comparative genomics and metabolomics of Streptomyces fulvissimus AtB-42, a biological control agent against soil-borne phytopathogenic fungi

"The streptomycete strain AtB-42 was previously selected from a consortium of 300 rhizospherecompetent isolates. It exerted a strong antagonism in vitro against phytopathogenic fungi and can reduce by 30% the severity of corky root of tomato (Pyrenochaeta lycopersici) in the field. Other isolates, such as StB-8, resulted ineffective in vitro and in greenhouse assays. Multilocus sequence analysis using five genes (atpD, gyrB, rpoB, recA and trpB) revealed Streptomyces fulvissimus DSM 40593 as the strain closest to AtB-42, and S. globisporus C-1027 the closest to StB-8. In order to unveil the antagonism mechanism, we subjected AtB-42 and StB-8 to genome sequencing (Illumina) and metabolomics analysis (LC-MS qTOF). The 7866 and 7086 protein-coding genes predicted in AtB-42 and StB-8, respectively, formed 4838 orthologous clusters (shared between the strains), while 166 clusters were unique to AtB-42 and 101 unique to StB-8. However, gene ontology enrichment analysis was not informative in explaining the mechanism of antagonism. Furthermore, 19 secondary metabolite biosynthetic gene clusters were found exclusively in AtB-42, other 18 solely in StB-8, while 19 were shared between them. Hence, the 19 AtB-42-specific secondary metabolites could be putatively involved in its antifungal activity, and include antibiotics such as oxazolomycin, macrotetrolide, sporolide, meridamycin, desotamide, platencin, fredericamycin, albachelin, kirromycin, the NRPS bleomycin and pactamycin, alkylresorcinol (type III PKS), nanchangmycin (saccharide), auricin (type II PKS), roseoflavin, the biofilm inhibitor cahuitamycins and the siderophore griseobactin. Surprisingly, these substances were not detected by LC-MS qTOF, but deoxyvalidamine, which is the component pseudo-amino-sugar of validamycin, was found uniquely in AtB-42."