Transcriptome and sRNA analyses of the response of Bacillus subtilis to ammonia nitrogen

Abstract:

To explore the molecular mechanism of denitrification by Bacillus subtilis and screen out candidate genes and small RNA (sRNA) related to the response of B. subtilis to ammonia nitrogen. Transcriptome sequencing and sRNA analysis were performed on B. subtilis in both an ammonia-rich environment and a control group. The relative expression changes in differentially expressed genes were analyzed using real-time PCR. The results showed that each sequencing sample yielded approximately 1.40 × 107 reads on average. There were 3918 differentially expressed genes in the control and treatment groups as per DESeq2 analysis, which enriched 176 signaling pathways in the KEGG database, including eight signaling pathways (bacterial two-component system pathway, arginine biosynthesis, purine metabolism, and so on) adapted to the ammonia-rich environment. We found that epsA, tasA, SinR, glnR, glnA, tnrA, and ureABC genes may be involved in the response of B. subtilis to ammonia nitrogen in water. Sixty-two annotated strains of B. subtilis sRNA were obtained. The prediction and analysis results of sRNA target genes revealed that there are 3960 potential target genes involved in carbohydrate transport and metabolism, amino acid transport and metabolism, and transcription processes. Among them, the target genes corresponding to sRNA2073 and sRNA2182 were sinR and tnrA, respectively. Real-time PCR analysis showed that the relative expression changes of argH, codY, argG, glnA and glnR were consistent with transcriptome sequencing. These results provide reference data for further exploring the molecular mechanism of nitrogen removal by B. subtilis in wastewater.