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Gene repression using the endonucleolytically deactivated dCas9 protein and sgRNAs (CRISPR interference or CRISPRi) is a useful approach to study gene functions. Here, we established CRISPRi in  Paenibacillus sonchi  genomovar Riograndensis SBR5, a plant growth promoting bacterium. CRISPRi system with sgRNAs targeting SBR5 endogenous genes  spo0A ,  yaaT  and  ydjJ  and plasmid-borne  gfpUV  was constructed and analyzed. Flow cytometry analysis revealed a significant decrease of reporter protein GFPUV signal in  P. sonchi  strains expressing  gfpUV  sgRNA in comparison with non-targeting controls. CRISPRi-based repression of chromosomal genes for regulation of sporulation  spo0A  and  yaaT  decreased sporulation and increased biofilm formation in SBR5. Repression of the sorbitol catabolic gene  ydjJ  revealed decreased specific activity of YdjJ in crude cell extracts and reduced biomass formation from sorbitol in growth experiments. Our work on CRISPRi-based gene repression serves as basis for gene function studies of the plant growth promoter  P. sonchi  SBR5. To our knowledge, the present study presents the first tool for gene repression established in  Paenibacillus  species.Key points  •  CRISPRi toward gene repression was applied for the first time in Paenibacillus.   •  CRISPRi of spo0A and yaaT depleted spores and increased biofilms in SBR5.   •  CRISPRi-based ydjJ repression decreased specific activity of sorbitol dehydrogenase.

CRISPR interference-based gene repression in the plant growth promoter Paenibacillus sonchi genomovar Riograndensis SBR5