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Screening of <i>Bacillus</i> with antagonistic effects on paddy mold pathogens to provide strain resources for biological control of mold in <i>Oryza sativa</i> L. screening of <i>Bacillus</i> isolates antagonistic towards <i>Aspergillus tubingensis</i> from rhizosphere soil of healthy paddy; classification and identification of antagonistic strains by biological characteristics and 16S rDNA sequence analysis; transcriptome sequencing after RNA extraction from Bacillus-treated <i>Aspergillus tubingensis</i>; and extraction of inhibitory crude proteins of <i>Bacillus</i> by ammonium sulfate precipitation; inhibitory crude protein and <i>Bacillus</i> spp. were treated separately for <i>A. tubingensis</i> and observed by scanning electron microscopy (SEM). An antagonistic strain of <i>Bacillus</i>, named B7, was identified as <i>Paenibacillus polymyxa</i> by 16S rDNA identification and phylogenetic evolutionary tree comparison analysis. Analysis of the transcriptome results showed that genes related to secondary metabolite biosynthesis such as antifungal protein were significantly downregulated. SEM results showed that the mycelium of <i>A. tubingensis</i> underwent severe rupture after treatment with <i>P. polymyxa</i> and antifungal proteins, respectively. In addition, the sporocarp changed less after treatment with <i>P. polymyxa</i>, and the sporangium stalks had obvious folds. <i>P. polymyxa</i> B7 has a good antagonistic effect against <i>A. tubingensis</i> and has potential for biocontrol applications of paddy mold pathogens.