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

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Abstract

The streptomycete strain AtB-42 was previously selected from a consortium of 300 rhizospherecompetentisolates. It exerted a strong antagonism in vitro against phytopathogenic fungi and canreduce by 30% the severity of corky root of tomato (Pyrenochaeta lycopersici) in the field. Otherisolates, such as StB-8, resulted ineffective in vitro and in greenhouse assays. Multilocus sequenceanalysis using five genes (atpD, gyrB, rpoB, recA and trpB) revealed Streptomyces fulvissimus DSM40593 as the strain closest to AtB-42, and S. globisporus C-1027 the closest to StB-8. In order to unveilthe antagonism mechanism, we subjected AtB-42 and StB-8 to genome sequencing (Illumina) andmetabolomics analysis (LC-MS qTOF). The 7866 and 7086 protein-coding genes predicted in AtB-42and StB-8, respectively, formed 4838 orthologous clusters (shared between the strains), while 166clusters were unique to AtB-42 and 101 unique to StB-8. However, gene ontology enrichment analysiswas not informative in explaining the mechanism of antagonism. Furthermore, 19 secondary metabolitebiosynthetic gene clusters were found exclusively in AtB-42, other 18 solely in StB-8, while 19 wereshared between them. Hence, the 19 AtB-42-specific secondary metabolites could be putativelyinvolved in its antifungal activity, and include antibiotics such as oxazolomycin, macrotetrolide,sporolide, meridamycin, desotamide, platencin, fredericamycin, albachelin, kirromycin, the NRPSbleomycin and pactamycin, alkylresorcinol (type III PKS), nanchangmycin (saccharide), auricin (type IIPKS), roseoflavin, the biofilm inhibitor cahuitamycins and the siderophore griseobactin. Surprisingly,these substances were not detected by LC-MS qTOF, but deoxyvalidamine, which is the componentpseudo-amino-sugar of validamycin, was found uniquely in AtB-42.

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  • Bubici G.; Vinale F.; Staropoli A.; Prigigallo M. I.; Monfreda R.

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2018

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