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Nitrogen is important for crop productivity and usually added in form of urea into the soil which negatively affects the environment. It is important to utilize nitrogen fixing bacteria for improving the nitrogen content of soil in India. Here, we have isolated nitrogen fixing-bacteria Pseudomonas mendocina S10 from rhizospheric soil and studied its nitrogenase activity along with its survival under sterile soil conditions. Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR and Real-time quantitative PCR were employed to investigate the population and nifH transcripts level respectively in presence of ammonium and moisture additives. Strain S10 was capable of growth and expressing nifH transcripts in the presence of 2.5 mM ammonium and 20 percent water availability. Population of isolated strain and it’s nifH mRNA was found at low levels when exposed to 5 mM ammonium for 60 days of incubation period. However, viable bacterial count and nifH transcript levels remained low in the presence of 1.25 mM ammonium and zero percent water content. These findings indicate that isolated strain could tolerate ammonium up to 5 mM for 60 days and can maintained their cell viability in low moisture conditions. Results revealed the advantage of using gene expression to evaluate the physiological state of microorganism’s population in soil.