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Bacillus megaterium  NCT-2 is a nitrate-uptake bacterial, which shows high bioremediation capacity in secondary salinization soil, including nitrate-reducing capacity, phosphate solubilization, and salinity adaptation. To gain insights into the bioremediation capacity at the genetic level, the complete genome sequence was obtained by using a multiplatform strategy involving HiSeq and PacBio sequencing. The NCT-2 genome consists of a circular chromosome of 5.19 Mbp and ten indigenous plasmids, totaling 5.88 Mbp with an average GC content of 37.87%. The chromosome encodes 5,606 genes, 142 tRNAs, and 53 rRNAs. Genes involved in the features of the bioremediation in secondary salinization soil and plant growth promotion were identified in the genome, such as nitrogen metabolism, phosphate uptake, the synthesis of organic acids and phosphatase for phosphate-solubilizing ability, and Trp-dependent IAA synthetic system. Furthermore, strain NCT-2 has great ability of adaption to environments due to the genes involved in cation transporters, osmotic stress, and oxidative stress. This study sheds light on understanding the molecular basis of using  B. megaterium  NCT-2 in bioremediation of the secondary salinization soils.

Genomic Analysis of Bacillus megaterium NCT-2 Reveals Its Genetic Basis for the Bioremediation of Secondary Salinization Soil