Biocontrol activity and whole genome sequence analysis of Pseudomonas piscis Liu et al. R19 against Pectobacterium brasiliense Portier et al. isolated from soft rot-infected bok choy (Brassica rapa L.) in Davao City, Philippines

Soft rot disease caused by Pectobacterium spp. is one of the most destructive plant diseases causing significant production losses in a wide range of host crops worldwide. Current management strategies in controlling soft rot disease including cultural and chemical practices are effective to a limited extent only: hence, the need for a sustainable alternative which is biological control. Biological control is the suppression of plant pathogens using living organisms and is recognized as a tool for disease control in sustainable agriculture. In this study, bacteria were initially isolated from four soft rot-infected bok choy in a farm in Davao City [Philippines]. Of the 17 isolates, 15 were found to be pathogenic in bok choy, and four of these isolates (SRBs 4, 10, 16 and 26) were identified as Pectobacterium brasiliense based on 16S rRNA gene sequence analysis. Results of host range assessment showed that P. brasiliense SRB26 was pathogenic to tomato, bell pepper, potato, kimchi cabbage, and radish indicative of its broad host range. The bok choy rhizosphere was then explored to isolate bacteria with antagonistic activity against P. brasiliense SRB26. Two isolates, R17 and R19, were found to exhibit antagonism against P. brasiliense SRB26 in vitro and in vivo. Moreover, application of both antagonists via the preventive approach resulted in the greatest reduction of tissue maceration by P. brasiliense SRB26. Isolate R19 was also found to exhibit better suppression than isolate R17. Analysis of the 16S rRNA gene sequences showed that isolates R17 and R19 belonged to the genus Pseudomonas. Draft genome analysis established the taxonomic assignment of R19 as Pseudomonas piscis and confirmed the presence of genes involved in biocontrol mechanisms such as production of antimicrobial compounds and siderophores, Type VI secretion system, quorum quenching and induction of systemic resistance in Pseudomonas piscis R19. Further experiments, however, are needed to be performed to determine which among the identified mechanisms are directly associated with the antibacterial activity of P. piscis R19.