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The complexity of plant microbial communities provides a rich model for investigating biochemical and regulatory strategies involved in interbacterial competition. Within these niches, the soft rot  Enterobacteriaceae  (SRE) represents an emerging group of plant–pathogens causing soft rot/blackleg diseases resulting in economic losses worldwide in a variety of crops. A preliminary screening using next-generation sequencing of 16S rRNA comparatively analyzing healthy and diseased potato tubers, identified several taxa from  Proteobacteria  to  Firmicutes  as potential potato endophytes/plant pathogens. Subsequent to this, a range of molecular and computational techniques were used to determine the contribution of antimicrobial factors such as bacteriocins, carbapenem and type VI secretion system (T6SS), found in an aggressive SRE ( Pectobacterium carotovorum  subsp.  brasiliense  strain PBR1692 –  Pcb 1692) against these endophytes/plant pathogens. The results showed growth inhibition of several  Proteobacteria  by  Pcb 1692 depends either on carbapenem or pyocin production. Whereas for targeted  Firmicutes , only the  Pcb 1692 pyocin seems to play a role in growth inhibition. Furthermore, production of carbapenem by  Pcb 1692 was observably dependent on the presence of environmental iron and oxygen. Additionally, upon deletion of  fur ,  sly A and  exp I regulators, carbapenem production ceased, implying a complex regulatory mechanism involving these three genes. Finally, the results demonstrated that although T6SS confers no relevant advantage during  in vitro  competition, a significant attenuation in competition by the mutant strain lacking a functional T6SS was observed  in planta .   IMPORTANCE  Soft rot  Enterobacteriaceae  (SRE) represents important phytopathogens causing soft rot/blackleg diseases in a variety of crops leading to huge economic losses worldwide. These pathogens have been isolated alongside other bacteria from different environments such as potato tubers, stems, roots and from the soil. In these environments, SREs coexist with other bacteria where they have to compete for scarce nutrients and other resources. In this report, we show that  Pectobacterium carotovorum  subsp.  brasiliense  strain PBR1692 –  Pcb 1692, which represents one of the SREs, inhibits growth of several different bacteria by producing different antimicrobial compounds. These antimicrobial compounds can be secreted inside or outside the plant host, allowing  Pcb 1692 to effectively colonize different types of ecological niches. By analyzing the genome sequences of several SREs, we show that other SREs likely deploy similar antimicrobials to target other bacteria.

frontiers in microbiology

The Impact of Type VI Secretion System, Bacteriocins and Antibiotics on Bacterial Competition of Pectobacterium carotovorum subsp. brasiliense and the Regulation of Carbapenem Biosynthesis by Iron and the Ferric-Uptake Regulator