Stenotrophomonas sp. C3, a Potential Drought Alleviator in Capsicum annuum L.: Metabolomic and Genomic Characterization

Morphological, metabolomic, and genomic aspects of an endophytic bacterial strain Stenotrophomonas sp. C3 isolated from the xerophytic plant Cereus hexagonous L. were characterized. This strain was previously reported to enhance drought tolerance in Capsicum annuum L. seedlings. To understand the effects of drought stress on Stenotrophomonas sp. C3, a detailed analysis on its morphological changes, biofilm production, and metabolite synthesis was conducted. In response to its drought conditions, the organism displayed adaptive features such as aggregation, clumping, robust biofilm production, and the generation of the osmolyte glucosylglycerol. The genomic characteristics of the organism were analyzed by whole genome sequencing (WGS) analysis. This has demonstrated Stenotrophomonas sp. C3 to have a genome size of 3 701 554 bp, an N50 value of 3 684 702 and a mean G+C content of 66.68%. The sequencing analysis identified stress-responsive genes, exopolysaccharide production genes, chemotaxis-related genes, flagella formation genes, and the genes coding for the enzymes involved in antioxidant defense and osmolyte production as well. Furthermore, genes associated with the plant growth promotion, specifically those linked to phosphate and nitrogen metabolism could be predicted. The pan-genome analysis of plant-derived Stenotrophomonas maltophilia strains sourced from public databases disclosed a total of 8619 gene clusters which included 2031 core genes and 6588 shell genes depicting an absence of softcore genes and cloud genes. This observation highlighted the considerable gene content variation among different strains of Stenotrophomonas maltophilia.