Genome comparison identifies different bacillus species in a bast fibre-retting bacterial consortium and provides insights into pectin degrading genes

Abstract

Retting of bast fbres requires removal of pectin, hemicellulose and other non-cellulosic materials from plant stem tissues by a complex microbial community. A microbial retting consortium with high-efciency pectinolytic bacterial strains is efective in reducing retting-time and enhancing fbre quality. We report comprehensive genomic analyses of three bacterial strains (PJRB 1, 2 and 3) of the consortium and resolve their taxonomic status, genomic features, variations, and pan-genome dynamics. The genome sizes of the strains are ~3.8Mb with 3729 to 4002 protein-coding genes. Detailed annotations of the protein-coding genes revealed diferent carbohydrate-degrading CAZy classes viz. PL1, PL9, GH28, CE8, and CE12. Phylogeny and structural features of pectate lyase proteins of PJRB strains divulge their functional uniqueness and evolutionary convergence with closely related Bacillus strains. Genome-wide prediction of genomic variations revealed 12461 to 67381 SNPs, and notably many unique SNPs were localized within the important pectin metabolism genes. The variations in the pectate lyase genes possibly contribute to their specialized pectinolytic function during the retting process. These fndings encompass a strong foundation for fundamental and evolutionary studies on this unique microbial degradation of decaying plant material with immense industrial signifcance. These have preponderant implications in plant biomass research and food industry, and also posit application in the reclamation of water pollution from plant materials