Isolation and whole genome analysis of bacterial strains assimilating inorganic nitrogen in acidic dryland red soils

Abstract:

Inorganic nitrogen assimilation performed by microorganisms can immobilize chemical fertilizer nitrogen that is not directly absorbed by crops after application to the soil, which can reduce the losses of chemical nitrogen fertilizer and the risk of environmental nitrogen pollution. Soil inorganic nitrogen assimilation is performed by functional microbial populations rather than a large number of redundant microorganisms. [Objective] The enrichment, isolation, identification, and whole genome sequencing of dominant inorganic nitrogen-assimilating bacteria in acidic dryland red soil and clarification of the nitrogen assimilation capacity of the strains in soil can provide strain resources and a theoretical basis for the application of chemical nitrogen fertilizer in acidic soil and the research on the nitrogen transformation process. [Methods] We added KNO₃ or (NH₄)₂SO₄ as the inorganic nitrogen source and glucose as the carbon source into the acidic dryland red soil. Then, we performed strain enrichment under aerobic conditions and screened the dominant bacterial strains assimilating inorganic nitrogen by the gradient dilution isolation method. We verified the inorganic nitrogen assimilation ability of the strains by soil recolonization experiments, and employed whole genome sequencing to analyze the nitrogen metabolic pathways of different strains. [Results] The relative abundance of 16S rRNA genes of dominant inorganic nitrogen-assimilating microorganisms in acidic dryland red soils increased from 0.20%-0.94% to 20.2%-30.2% after one week of enrichment. We isolated three dominant inorganic nitrogen-assimilating strains, which were identified as Burkholderia sp. M6-3, Bacillus funiculus M2-4, and Arthrobacter sp. M7-15. The inorganic nitrogen assimilation rates of strains M6-3, M2-4, and M7-15 in sterilized soil were (1.28±0.61), (0.17±0.07), and (0.16±0.02) mg/(kg·d), respectively. M6-3 possessed a more complete metabolic pathway and more functional genes related to nitrogen assimilation than the other two strains. In terms of nitrogen metabolic pathways and functional activity, Burkholderia sp. M6-3 was dominant in the assimilation of inorganic nitrogen in acidic dryland red soils. [Conclusion] This study confirmed that low-abundance microbial taxa play a dominant role in the inorganic nitrogen assimilation of acidic dryland red soil, and revealed the metabolic process of inorganic nitrogen assimilation at the genomic level of the strains. The above results provide strain resources and a theoretical basis for the study of chemical nitrogen fertilizer application and transformation process in the acidic dryland red soil.