Comparative genomics reveals expanded cell-surface signaling and siderophore scavenging repertoires in Pectobacterium

Iron acquisition in gram-negative bacteria relies on TonB-dependent receptors (TBDRs), some of which initiate cell-surface signaling (CSS) by activating extracytoplasmic function (ECF) sigma factors that induce cognate transport pathways. Although well characterized in Pseudomonas , CSS systems remain poorly explored in plant-associated bacteria. Surveying 6,847 plant-associated bacterial genomes revealed near-ubiquitous CSS systems in Pseudomonas and Pectobacterium , with markedly lower strain-to-strain variation in the latter. In 902 high-contiguity Pectobacteriaceae genomes, Pectobacterium averaged 5.03 CSS modules per genome, compared with 0.67 in Dickeya , despite their shared soft-rot lifestyle. De novo clustering identified 14 distinct CSS systems across the family, with nine found in Pectobacterium . The ferredoxin receptor gene fusA was conserved in 572 of 586 Pectobacterium genomes; however, only 126 carried fusA under CSS regulation. These strains were phylogenetically dispersed but formed a single fusA clade, a pattern consistent with co-acquisition of the receptor and regulator as a transferable module. Pectobacterium also encoded a more diverse repertoire of siderophore receptors than related taxa, suggesting broader potential for siderophore utilization across bacterial lineages. Notably, the predicted amonabactin-like biosynthetic gene cluster and its putative cognate TBDR were highly conserved within Pectobacterium but rare elsewhere in the family, supporting its potential role in the endogenous siderophore system in the genus. These findings reveal an expanded genomic repertoire of CSS systems and siderophore receptors in Pectobacterium , providing a framework for investigating their roles in environmental sensing and iron acquisition.