Genomic Features of Stenotrophomonas rhizophila IS26 Suggest Potential for Aflatoxin B1 Reduction in Aspergillus flavus-Contaminated Maize

Aspergillus flavus produces aflatoxin B1 (AFB1), a carcinogenic mycotoxin affecting food and feed safety. This study investigated the biocontrol potential of the endophytic Stenotrophomonas rhizophila strain IS26 against toxigenic Aspergillus flavus NRRL 3251 in maize grain assay and through genome mining. Live IS26 cells achieved 86.30 ± 0.67% AFB1 inhibition on maize grains (vs. 22.82 ± 1.91% heat-killed, 13.77 ± 5.72% cell-free supernatant), distinguishing contact-dependent from diffusible mechanisms. In addition, phenotypic and biochemical characteristics, as well as protease, amylase and esterase enzymatic activities of S. rhizophila strain IS26 were tested. Whole-genome sequencing of S. rhizophila strain IS26 was performed, and assembly of 5,189,077 paired-end Illumina reads yielded 42 contigs, resulting in a total genome assembly size of 4.09 Mb with a GC content of 66.4%. The NCBI Prokaryotic Genome Automatic Annotation Pipeline (NCBI-PGAAP) was used to forecast 3,624 genes. Using RAST annotation, the genome of S. rhizophila strain IS26 was estimated to have 304 subsystems, with 27% subsystem coverage. Genome mining revealed genes potentially contributing to AFB1 down-regulation, including polyamine biosynthesis pathways, oxidative stress response factors (alkyl hydroperoxide reductase), and zinc-chelating peptide production (cysteine- and histidine-rich). Additionally, carbohydrate-active enzymes (CAZymes), including Glycoside Hydrolases (GHs) and Carbohydrate Esterases (CEs), were identified, which may have a role in facilitating AFB1 degradation. These findings suggest S. rhizophila strain IS26 reduces AFB1 accumulation on A. flavus-contaminated maize grains, potentially through biosynthetic gene down-regulation and/or enzymatic degradation. These findings establish IS26 as a maize grain biocontrol candidate requiring functional validation of proposed mechanisms through gene expression and food matrix studies for sustainable aflatoxin management.