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Pseudomonas stutzeri  A1501 is a model strain used to study associative nitrogen fixation, and it possesses the nitrogen regulatory NtrC protein in the core genome. Nitrogen sources represent one of the important factors affecting the efficiency of biological nitrogen fixation in the natural environment. However, the regulation of NtrC during nitrogen metabolism in  P. stutzeri  A1501 has not been clarified. In this work, a phenotypic analysis of the  ntrC  mutant characterized the roles of NtrC in nitrogen metabolism and the oxidative stress response of  P. stutzeri  A1501. To systematically identify NtrC-controlled gene expression, RNA-seq was performed to further analyse the gene expression differences between the wild-type strain and the ∆ ntrC  mutant under nitrogen fixation conditions. A total of 1431 genes were found to be significantly altered by  ntrC  deletion, among which 147 associative genes had NtrC-binding sites, and the pathways for nitrogen fixation regulation, nitrogenous compound acquisition and catabolism and nitrate assimilation were discussed. Furthermore, the oxidative stress-related gene ( katB ), which was upregulated by  ntrC  deletion, was suggested to be a potential target gene of NtrC, thus highlighting the importance of NtrC in nitrogenase protection against oxygen damage. Based on these findings, we propose that NtrC is a high-ranking element in the regulatory network of  P. stutzeri  A1501 that controls a variety of nitrogen metabolic and oxidative stress responsive traits required for adaptation to complex rhizosphere environments.   Supplementary Information  The online version contains supplementary material available at 10.1007/s11274-021-03144-w.

world journal of microbiology and biotechnology incorporating the mircen journal of applied microbiology and biotechnology/world journal of microbiology and biotechnology

Master regulator NtrC controls the utilization of alternative nitrogen sources in Pseudomonas stutzeri A1501