AUTHOR=Chen Yanyan , Lin Yijing , Zhu Jingyi , Zhou Jiayin , Lin Haoyi , Fu Yiting , Zhou Yan 

TITLE=Transcriptomic analysis of nitrogen metabolism pathways in Klebsiella aerogenes under nitrogen-rich conditions

JOURNAL=Frontiers in Microbiology

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1323160

DOI=10.3389/fmicb.2024.1323160

ISSN=1664-302X

ABSTRACT=<p>The acceleration of the nitrogen cycle and the nitrogen excess observed in some coastal waters has increased interest into understanding the biochemical and molecular basis of nitrogen metabolism in various microorganisms. To investigate nitrogen metabolism of a novel heterotrophic nitrification and aerobic denitrification bacterium <italic>Klebsiella aerogenes</italic> strain (B23) under nitrogen-rich conditions, we conducted physiological and transcriptomic high-throughput sequencing analyses on strain B23 cultured on potassium nitrate–free or potassium nitrate–rich media. Overall, <italic>K. aerogenes</italic> B23 assimilated 82.47% of the nitrate present into cellular nitrogen. Further, 1,195 differentially expressed genes were observed between <italic>K. aerogenes</italic> B23 cultured on potassium nitrate–free media and those cultured on potassium nitrate-rich media. Gene annotation and metabolic pathway analysis of the transcriptome were performed using a series of bioinformatics tools, including Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Non-Redundant Protein Database annotation. Accordingly, the nitrogen metabolism pathway of <italic>K. aerogenes</italic> B23 was analyzed; overall, 39 genes were determined to be involved in this pathway. Differential expression analysis of the genes involved in the nitrogen metabolism pathway demonstrated that, compared to the control, <italic>FNR</italic>, <italic>NarK</italic>/<italic>14945</italic>, <italic>fdx</italic>, <italic>gshA</italic>, <italic>proB</italic>, <italic>proA</italic>, <italic>gapA</italic>, <italic>argH</italic>, <italic>artQ</italic>, <italic>artJ</italic>, <italic>artM</italic>, <italic>ArgR</italic>, <italic>GAT1</italic>, <italic>prmB</italic>, <italic>pyrG</italic>, <italic>glnS</italic>, and <italic>Ca1</italic> were significantly upregulated in the nitrogen-treated <italic>K. aerogenes</italic> B23; these genes have been established to be involved in the regulation of nitrate, arginine, glutamate, and ammonia assimilation. Further, <italic>norV</italic>, <italic>norR</italic>, and <italic>narI</italic> were also upregulated in nitrogen-treated <italic>K. aerogenes</italic> B23; these genes are involved in the regulation of NO metabolism. These differential expression results are important for understanding the regulation process of key nitrogen metabolism enzyme genes in <italic>K. aerogenes</italic> B23. Therefore, this study establishes a solid foundation for further research into the expression regulation patterns of nitrogen metabolism–associated genes in <italic>K. aerogenes</italic> B23 under nitrogen-rich conditions; moreover, this research provides essential insight into how <italic>K. aerogenes</italic> B23 utilizes nutritional elements.</p>