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The plant microbiome represents an enormous untapped resource for discovering novel genes and bioactive compounds. Previously, we isolated  Pseudomonas  sp. SH-C52 from the rhizosphere of sugar beet plants grown in a soil suppressive to the fungal pathogen  Rhizoctonia solani  and showed that its antifungal activity is, in part, attributed to the production of the chlorinated 9-amino-acid lipopeptide thanamycin (Mendes et al.,  2011 ). To get more insight into its biosynthetic repertoire, the genome of  Pseudomonas  sp. SH-C52 was sequenced and subjected to  in silico , mutational and functional analyses. The sequencing revealed a genome size of 6.3 Mb and 5579 predicted ORFs. Phylogenetic analysis placed strain SH-C52 within the  Pseudomonas corrugata  clade.  In silico  analysis for secondary metabolites revealed a total of six non-ribosomal peptide synthetase (NRPS) gene clusters, including the two previously described NRPS clusters for thanamycin and the 2-amino acid antibacterial lipopeptide brabantamide. Here we show that thanamycin also has activity against an array of other fungi and that brabantamide A exhibits anti-oomycete activity and affects phospholipases of the late blight pathogen  Phytophthora infestans . Most notably, mass spectrometry led to the discovery of a third lipopeptide, designated thanapeptin, with a 22-amino-acid peptide moiety. Seven structural variants of thanapeptin were found with varying degrees of activity against  P. infestans . Of the remaining four NRPS clusters, one was predicted to encode for yet another and unknown lipopeptide with a predicted peptide moiety of 8-amino acids. Collectively, these results show an enormous metabolic potential for  Pseudomonas  sp. SH-C52, with at least three structurally diverse lipopeptides, each with a different antimicrobial activity spectrum.

Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds