Complete genome sequence and mass spectrometry assist mining siderophore turnerbactin analogs in a non-model Pseudoduganella strain with biocontrol potential

Abstract

Plant-associated biocontrol bacteria play a pivotal role in advancing sustainable agriculture by minimizing the reliance on toxic chemical pesticides. The order Burkholderiales is an underexplored yet highly promising group of microorganisms, characterized by a broad ecological distribution and considerable potential for application in sustainable agricultural systems. In this study, we aimed to isolate and characterize a potential biocontrol strain belonging to Burkholderiales, with the goal of contributing to eco-friendly agricultural practices and mining previously unexploited secondary metabolites. A novel bacterial strain, Pseudoduganella sp. D-3-1, was isolated from Cangma Mountain and characterized to possess potent antifungal activity and a high iron-chelating capacity. Whole-genome sequencing revealed that its complete genome spans 6,875,892 bp and encodes 6035 predicted coding sequences (CDSs), including a complete violacein biosynthesis pathway. Genome mining uncovered a diverse array of secondary metabolite biosynthetic gene clusters (BGCs), notably a non-ribosomal peptide synthetase (NRPS) gene cluster, designated the pseudodubactin cluster, which encodes a catecholate-type siderophore structurally related to turnerbactin. Through high-resolution electrospray ionization mass spectrometry (HR-ESI-MS), gene knockout, heterologous expression, and bioinformatics analysis, four turnerbactin analogs (1-4) were identified for the first time from Pseudoduganella sp., including two novel compounds: pseudodubactin A (2), and pseudodubactin B (4). Additionally, HR-ESI-MS analysis detected two uncharacterized siderophores, designated as compound 5 and compound 6, that are structurally distinct from the turnerbactin analogs. These findings indicate that Pseudoduganella sp. D-3-1 is a promising source of bioactive natural products, particularly violacein and diverse siderophores, highlighting its potential as a biological control agent for sustainable and eco-friendly agriculture.