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<p>In marine ecosystems, nitrogen cycling is vital for ecological balance, especially in anoxic and micro-aerobic environments like deep-sea sediments. Facultative anaerobes, such as <i>Pseudomonas</i> species, are key players due to their ability to adapt to varying oxygen levels and perform denitrification. Metagenomic analysis showed that <i>Pseudomonas</i> species possess the genomic potential for the most complete denitrification pathways among the taxa studied, emphasizing their ecological importance in deep-sea nitrogen cycling. We isolated denitrifying strains from deep-sea cold seep environments and confirmed their activity using chromogenic assays. Among them, <i>Pseudomonas stutzeri</i> 273, a facultative anaerobic denitrifier, was chosen for further study. Growth experiments showed that while biomass accumulation was delayed in anoxic sealed environments, nitrate reduction occurred actively, indicating energy metabolism is driven by denitrification. Genomic analysis revealed a complete denitrification pathway, and transcriptomic profiling highlighted significant upregulation of denitrification genes under oxygen-limited conditions, particularly during early growth phases. Additionally, genes related to peptidoglycan biosynthesis, flagellar assembly, motility, and flavin adenine dinucleotide (FAD)-dependent redox reactions were upregulated under anoxic conditions, suggesting adaptive responses to energy stress and environmental sensing. These findings enhance our understanding of <i>P. stutzeri</i> 273’ s potential role in nitrogen cycling within fluctuating oxygen environments and offer new insights into microbial nitrogen loss in deep-sea habitats.</p>

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Metagenomic, cultural, and transcriptomic insights into deep-sea Pseudomonadota bacteria with denitrification capability

  • 期刊论文

  • 发表日期：

    2026年5月12日

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  • Jun Yang,
  • Rikuan Zheng,
  • Jie Zhu,
  • Shimei Wu,
  • Chaomin Sun

摘要

In marine ecosystems, nitrogen cycling is vital for ecological balance, especially in anoxic and micro-aerobic environments like deep-sea sediments. Facultative anaerobes, such as Pseudomonas species, are key players due to their ability to adapt to varying oxygen levels and perform denitrification. Metagenomic analysis showed that Pseudomonas species possess the genomic potential for the most complete denitrification pathways among the taxa studied, emphasizing their ecological importance in deep-sea nitrogen cycling. We isolated denitrifying strains from deep-sea cold seep environments and confirmed their activity using chromogenic assays. Among them, Pseudomonas stutzeri 273, a facultative anaerobic denitrifier, was chosen for further study. Growth experiments showed that while biomass accumulation was delayed in anoxic sealed environments, nitrate reduction occurred actively, indicating energy metabolism is driven by denitrification. Genomic analysis revealed a complete denitrification pathway, and transcriptomic profiling highlighted significant upregulation of denitrification genes under oxygen-limited conditions, particularly during early growth phases. Additionally, genes related to peptidoglycan biosynthesis, flagellar assembly, motility, and flavin adenine dinucleotide (FAD)-dependent redox reactions were upregulated under anoxic conditions, suggesting adaptive responses to energy stress and environmental sensing. These findings enhance our understanding of P. stutzeri 273’ s potential role in nitrogen cycling within fluctuating oxygen environments and offer new insights into microbial nitrogen loss in deep-sea habitats.