Multiomics profiling of transcriptional and metabolic responses of Bacillus siamensis LSZ23 to corn straw

Abstract

Agricultural straw is an abundant yet underutilised lignocellulosic resource whose microbial valorisation requires cellulolytic strains that sustain enzyme production under substrate-imposed stress. Although Bacillus siamensis is valued for plant growth promotion and biocontrol, its lignocellulose-degrading capacity and regulation remain largely unexplored. B. siamensis LSZ23, isolated from humic soil in Inner Mongolia, China, produced a balanced cellulolytic system (CMCase 0.321, β-glucosidase 0.275, avicelase 0.240 and FPase 0.209 U/mL in 24 h LB culture) and reduced sterilised corn straw dry mass by 19.5% within 20 d in solid-state culture (109 CFU/g), with scanning electron microscopy revealing extensive fibre-bundle disruption. Its 4.12 Mb genome (46% GC, 4,120 protein-coding genes) encodes 570 predicted carbohydrate-active enzyme (CAZyme) genes, with marked expansion of glycoside hydrolase family GH1, and harbours 31 orthogroups absent from four reference genomes, notably oligosaccharide ATP-binding cassette transporters and starch-processing enzymes. Upon straw exposure, transcriptomics (173 differentially expressed genes) and metabolomics (1,094 differentially abundant metabolites) indicated coordinated reprogramming rather than simple enzyme amplification: motility and chemotaxis genes were repressed, the biofilm-matrix gene tapA was induced, carbon uptake shifted transcriptionally towards a phosphotransferase system-mediated cellobiose route, and the glutamine synthetase-glutamate synthase pathway and de novo purine biosynthesis were downregulated, consistent with reduced high-cost anabolism. Purine metabolism was jointly significant across both omics. Lignin-derived phenolics accumulated alongside five upregulated MarR-family transcriptional regulators, although their ligand-regulon relationships remain undetermined. These findings provide a multiomics framework for LSZ23-mediated lignocellulose bioconversion and identify it as a candidate hydrolytic partner for straw degrading consortia.