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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. Sphingomonas sp. Z392 can significantly reduce the ammonia level in broiler coops. However, the mechanisms of ammonia nitrogen reduction by Sphingomonas sp. Z392 remain unclear. To explore the mechanisms of ammonia reduction by Sphingomonas sp. Z392, the transcriptome and metabolome analysis of Sphingomonas sp. Z392 under high ammonium sulfate level were conducted. It was found that the transcription levels of genes related to purine metabolism (RS01720, RS07605, purM, purC, purO) and arginine metabolism (glsA, argB, argD, aguA, aguB) 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 ncd2 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 Sphingomonas 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 ncd2 gene on ammonia removal, ncd2 was successfully overexpressed and knocked out in Sphingomonas sp. Z392. ncd2 Overexpression exhibited the most ammonia reduction capability, the ammonia concentration of ncd2 overexpression group decreased by 43.33% than that of without Sphingomonas sp. group, and decreased by 14.17% than that of Sphingomonas sp. Z392 group. In conclusion, Sphingomonas 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, ncd2 might be one of the key genes to reduce ammonia.
Pubmed ID: 40376685
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NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP.
View all literature mentionsSoftware package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
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