Genomic and transcriptomic analyses of Bacillus methylotrophicus NJ13 reveal a molecular response strategy combating Ilyonectria robusta causing ginseng rusty root rot

To explain the molecular mechanism of the biocontrol exerted by Bacillus methylotrophicus NJ13 against Ilyo-nectria robusta, this study mainly focused on the following aspects. (i) Background: I. robusta is a dominant species of soil-borne pathogen causing ginseng rusty root rot. The ginseng endophytic bacteria B. methylotrophicus NJ13 can effectively inhibit the growth of I. robusta DQX01 and control the disease. (ii) Methods: Through in vitro antagonism experiments and microscopic observation, the inhibitory effect of the strain NJ13 against strain DQX01 was determined. The whole genome of NJ13 was sequenced by using the Illumina NovaSeq PE150 platform, and the gene expression pattern of NJ13 against DQX01 was revealed by using RNA-seq. (iii) Results: NJ13 could significantly inhibit the growth of DQX01, leading to the mycelial and conidia of DQX01 appearing abnormal and swollen. The genome of NJ13 consists of a circular chromosome of 3,929,584 bp, with 4024 coding DNA sequences (CDSs). The number of NJ13 differentially expressed genes (DEGs) (| log2 (fold change) | > 1, q < 0.005) was 691, of which 233 were upregulated and 458 downregulated. (iv) Conclusions: According to both in vivo and in vitro experiments, NJ13 shows good antagonistic activity against DQX01. Secondary metabolite gene clusters probably regulate the good antagonistic effect, as demon-strated through the analysis of strain NJ13's genome. When the strain NJ13 interacted with DQX01, a defensive response within B. methylotrophicus NJ13 was triggered. The transcriptomic profiling of NJ13 could provide an explanation for this phenomenon.