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

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.

Pattern and causes of the establishment of the invasive bacterial potato pathogen Dickeya solani and of the maintenance of the resident pathogen D. dianthicola

“…The capacity of D. solani to cause rotting at a lower bacterial load than D. dianthicola is likely at least partly due to a higher expression of the pel genes coding for Pel enzymes, especially PelE that acts as an initiator of the plant cell wall degradation (Duprey et al, 2016). (Charkowsky, 2018;Shyntum et al, 2019;Toth et al, 2011).…”

“…By modulating the synthesis of virulence factors, the quorum-sensing signals participate in the transition from an oligotroph lifestyle in soils and surface waters, where Dickeya and Pectobacterium bacteria are rare, to a copiotroph lifestyle on a plant host, where they increase in number by several orders of magnitude (Laurila et al, 2008;Potrykus et al, 2016). Functional differences such as metabolic capacities have been identified between D. solani and D. dianthicola by comparative genomics, transcriptomics and biochemical approaches (Bellieny-Rabelo et al, 2019;Raoul des Essarts et al, 2019), but fitness differences within host plants remain only partially investigated (Czajkowski et al, 2010(Czajkowski et al, , 2013Raoul des Essarts et al, 2019;Shyntum et al, 2019). Whether the potato host could be differentially exploited by D. dianthicola and D. solani and whether the two pathogens stably coexist by using different ecological niches or compete directly when exploiting this host remain unsolved questions, despite their importance for understanding the D. solani invasion.…”

Pectobacterium brasiliense: Genomics, Host Range and Disease Management

“…In addition, Pbr 1692 is known to be more aggressive and typically outcompetes other members of SRP [ 60 ]. The production of several antimicrobial compounds by Pbr 1692 could contribute to its capacity to effectively colonize different types of ecological niches [ 61 ].…”

Pattern and causes of the establishment of the invasive bacterial potato pathogen Dickeya solani and of the maintenance of the resident pathogen D. dianthicola

“…Beside the tripartite interaction between potato plant host, D. solani and D. dianthicola , additional environmental (soil and climate) and biological factors (microbiota includingPectobacterium species) may facilitate or limit D. solani establishment (Charkowsky 2018;Shyntum et al, 2019;Toth et al, 2011). Competition and facilitation processes have been well studied in pathogenic fungi (Al-Naimi, Garrett, & Bockus, 2005;Abdullah et al, 2017;Gladieux et al, 2015;Zhan & McDonald, 2013).…”

“…By modulating the synthesis of virulence factors, the quorum-sensing signals participate in the transition from an oligotroph lifestyle in soils and surface waters, where Dickeya and Pectobacterium bacteria are rare, to a copiotroph lifestyle on a plant host, where they increase in number by several orders of magnitude (Laurila et al, 2008;Potrykus et al, 2016). Functional differences such as metabolic capacities have been identified between D. solani and D. dianthicola by comparative genomics, transcriptomics and biochemical approaches (Bellieny-Rabelo et al, 2019;Raoul des Essarts et al, 2019), but fitness differences within host plants remain only partially investigated (Czajkowski et al, 2013;Czajkowski, de Boer, Velvis, & van der Wolf, 2010;Raoul des Essarts et al, 2019;Shyntum et al, 2019). Whether the potato host could be differentially exploited byD.…”