Frontiers in Microbiology (Apr 2025)

Transcriptome analysis of nitrogen assimilation preferences in Burkholderia sp. M6-3 and Arthrobacter sp. M7-15

  • Ran Liu,
  • Ran Liu,
  • Hongyi Qin,
  • Qian Wang,
  • Cheng Chu,
  • Yunbin Jiang,
  • Huan Deng,
  • Cheng Han,
  • Cheng Han,
  • Wenhui Zhong,
  • Wenhui Zhong,
  • Wenhui Zhong

DOI
https://doi.org/10.3389/fmicb.2025.1559884
Journal volume & issue
Vol. 16

Abstract

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IntroductionAmmonium (NH4+) and nitrate (NO3−) are the two main forms of inorganic nitrogen (N) that exist in soil and both can be absorbed and utilized by plants. As a vast and crucial biome, soil microorganisms are responsible for mediating the inorganic N assimilation process and enhancing nitrogen use efficiency. Understanding how these microorganisms assimilate different forms of inorganic nitrogen is crucial. There are a handful of microorganisms that play a dominant role in the process of soil inorganic nitrogen assimilation and have a significant advantage in abundance. However, microbial preferences for ammonium or nitrate, as well as differences in their metabolic pathways under co-existing ammonium and nitrate conditions, remain unclear.MethodsIn this study, two microbial strains with nitrogen assimilation advantages, Burkholderia sp. M6-3 and Arthrobacter sp. M7-15 were isolated from an acidic Chinese soil and then incubated by different sources of inorganic N to investigate their N preferences. Furthermore, RNA sequencing-based transcriptome analysis was used to map the metabolic pathways of the two strains and explore their explanatory potential for N preferences.ResultsThe results showed that strain M6-3 preferred to utilize NH4+ while strain M7-15 preferred to utilize NO3−. Although both strains shared similar nitrogen metabolic pathways, the differential expression of the glutamine synthetase-coding gene glnA played a crucial role in regulating their inorganic N preferences. This inconsistency in glnA expression may be attributed to GlnR, a global regulator of nitrogen utilization.DiscussionThis research strengthens the theoretical basis for exploring the underlying causes of differential preferences for inorganic N forms and provided key clues for screening functional microorganisms to ultimately enhance inorganic nitrogen use efficiency.

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