Abstract
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 – Pcb1692) against these endophytes/plant pathogens. The results showed growth inhibition of several Proteobacteria by Pcb1692 depends either on carbapenem or pyocin production. Whereas for targeted Firmicutes, only the Pcb1692 pyocin seems to play a role in growth inhibition. Furthermore, production of carbapenem by Pcb1692 was observably dependent on the presence of environmental iron and oxygen. Additionally, upon deletion of fur, slyA and expI 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.IMPORTANCESoft 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 – Pcb1692, 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 Pcb1692 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.
Highlights
For phytopathogenic bacteria, more is known about interactions with their hosts and virulence factors recruited to enforce successful colonization while relatively less is known about microbe–microbe interactions and how such interactions impact on niche colonizations (Bhunia, 2018; Glazebrook and Roby, 2018; Rodriguez-Moreno et al, 2018; Xin et al, 2018)
The results showed that while wildtype Pcb1692 produced a clear zone of inhibition when cultured on a lawn of P. atrosepticum, the Pcb mutant strains did not produce this clear zone associated with carbapenem production (Figures 7A,C)
To evaluate the host range of killing by the Pcb1692 S-type pyocin, the overlay assay was repeated with different bacteria and the results show that bacteriocins produced by Pcb1692 can inhibit growth of P. atrosepticum, Pectobacterium carotovorum subsp. carotovorum WPP14 (Pcc), Pectobacterium carotovorum subsp. odoriferum (Pco), D. dadantii, S. typhimurium, and E. coli but not the type strains of S. marcescens and D. chrysanthemi including some environmental strains of Pcc isolated from South Africa (Supplementary Table S4)
Summary
More is known about interactions with their hosts and virulence factors recruited to enforce successful colonization while relatively less is known about microbe–microbe interactions and how such interactions impact on niche colonizations (Bhunia, 2018; Glazebrook and Roby, 2018; Rodriguez-Moreno et al, 2018; Xin et al, 2018). Bacteria exist in complex multispecies communities which are mostly characterized by competition and to a lesser extent, cooperation (Stubbendieck and Straight, 2015; Bauer et al, 2018; García-Bayona and Comstock, 2018). In these interactions, survival depends on the ability to compete for resources in a given niche. A growing number of studies have shown the role, mechanism of action and targets of T6SS, T5SS, and bacteriocins in bacterial competitions (Aoki et al, 2010; Bernal et al, 2018). There is a need to study these systems collectively and under similar experimental conditions in order to gain better insight into their relative contribution to bacterial competition
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