The impact of type VI secretion system, bacteriocins and antibiotics on competition amongst Soft-RotEnterobacteriaceae: Regulation of carbapenem biosynthesis by iron and the transcriptional regulator Fur
Authors: Shyntum Divine Yutefar , Nkomo Ntombikayise , Gricia Alessandro Rino , Shigange Ntwanano Luann , Bellieny-Rabelo Daniel , Moleleki Lucy Novungayo 
Published: December 2018

Plant microbial communities’ complexity provide a rich model for investigation on biochemical and regulatory strategies involved in interbacterial competition. Within these niches, the soft rotEnterobacteriaceae(SRE) comprise an emerging group of plant-pathogens inflicting soft rot/black-leg diseases and causing economic losses worldwide in a variety of crops. In this report, a range of molecular and computational techniques are utilized to survey the contribution of antimicrobial factors such as bacteriocins, carbapenem antibiotic and type VI secretion system (T6SS) in interbacterial competition among plant-pathogens/endophytes using an aggressive SRE as a case study (Pectobacterium carotovorumsubsp.brasiliensestrain PBR1692 –Pcb1692). A preliminary screening using next-generation sequencing of 16S rRNA comparatively analysing healthy and diseased potato tubers, followed byin vitrocompetition assays, corroborated the aggressiveness ofPcb1692 against several relevant taxa sharing this niche ranging from Proteobacteria toFirmicutes. The results showed growth inhibition of several Proteobacteria by Pcb1692 depends either on carbapenem or pyocin production. Whereas for targetedFirmicutes, only pyocin seems to play a role in growth inhibition byPcb1692. Further analyses elucidated that although T6SS confers no relevant advantage duringin vitrocompetition, a significant attenuation in competition by the mutant strain lacking a functional T6SS was observedin planta. Furthermore, production of carbapenem byPcb1692 was observably dependent on the presence of environmental iron and oxygen. Additionally, upon deletion offur, slyA andexpI regulators, carbapenem production ceased, implying a complex regulatory mechanism involving these three genes. Potential Fur binding sites found upstream ofslyA,carR andexpR inPectobacteriumgenomes harboring carbapenem-associated genes further suggests a conserved regulatory pattern in the genus, in which carbapenem might be modulated in response to iron through the control exerted by Fur over secondary regulators. Furthermore, we unveiled the striking role played by S-pyocin in growth inhibition within the SRE group.

Authors Summary

For many phytopathogenic bacteria, more is known about interactions within the host and virulence factors used for host colonisation while relatively less is known about microbe-microbe interactions and factors that shape niche colonisation. The soft rotEnterobacteriaceae(SRE) comprise an emerging group of phytopathogens causing soft rot/black-leg diseases in a variety of crops leading to huge economic losses worldwide. In this report, a range of molecular and computational techniques are utilized to survey the contribution of antimicrobial factors such as bacteriocins, carbapenem antibiotic and type VI secretion system (T6SS) in interbacterial competition among plant-pathogens/endophytes using an aggressive SRE as a case study (Pcb1692). Our results show thatPcb1692 inhibits growth of other SRE and several potato endophytes using either the type VI secretion, carbapenem or bacteriocins. Carbapenem plays a role in both inter and intrabacterial competitionin vitro, while thePcb1692T6SS plays a role in interbacterial competitionin planta(in potato tubers). We also demonstrate that carbapenem regulation requires the presence of environmental iron and oxygen in a complex network consisting ofPcb1692 Fur, SlyA, and ExpI. The presence of these gene homologs in several SREs suggests that they too can deploy similar antimicrobials to target other bacteria.