Multiomics-based analysis of the mechanism of ammonia reduction in Sphingomonas

Ammonia is the primary component of malodorous substances in chicken farms. Currently, the microbial ammonia reduction is considered a potential method due to its low cost, high safety, and environmental friendliness. <i>Sphingomonas</i> sp. Z392 can significantly reduce the ammonia level in broiler coops. However, the mechanisms of ammonia nitrogen reduction by <i>Sphingomonas</i> sp. Z392 remain unclear. To explore the mechanisms of ammonia reduction by <i>Sphingomonas</i> sp. Z392, the transcriptome and metabolome analysis of <i>Sphingomonas</i> sp. Z392 under high ammonium sulfate level were conducted. It was found that the transcription levels of genes related to purine metabolism (<i>RS01720</i>, <i>RS07605</i>, <i>purM</i>, <i>purC</i>, <i>purO</i>) and arginine metabolism (<i>glsA</i>, <i>argB</i>, <i>argD</i>, <i>aguA</i>, <i>aguB</i>) were decreased under high ammonium sulfate environment, and the levels of intermediate products such as ornithine, arginine, IMP, and GMP also were also decreased. In addition, the <i>ncd2</i> gene in nitrogen metabolism was upregulated, and intracellular nitrite content increased by 2.27 times than that without ammonium sulfate. These results suggested that under high ammonium sulfate level, the flux of purine and arginine metabolism pathways in <i>Sphingomonas</i> sp. Z392 might decrease, while the flux of nitrogen metabolism pathway might increase, resulting in increased nitrite content and NH₃ release. To further verify the effect of the <i>ncd2</i> gene on ammonia removal, <i>ncd2</i> was successfully overexpressed and knocked out in <i>Sphingomonas</i> sp. Z392. <i>ncd2</i> Overexpression exhibited the most ammonia reduction capability, the ammonia concentration of <i>ncd2</i> overexpression group decreased by 43.33% than that of without <i>Sphingomonas</i> sp. group, and decreased by 14.17% than that of <i>Sphingomonas</i> sp. Z392 group. In conclusion, <i>Sphingomonas</i> sp. Z392 might reduce the release of NH₃ by reducing the flux of purine and arginine metabolisms, while enhancing ammonia assimilation to form nitrite. In this context, <i>ncd2</i> might be one of the key genes to reduce ammonia.