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

Jun YANG; Rikuan ZHENG; Jie ZHU; Shimei WU; Chaomin SUN

doi:10.1007/s00343-026-5326-y

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

Updated：2026-05-07

- Metagenomic, cultural, and transcriptomic insights into deep-sea Pseudomonadota bacteria with denitrification capability
- Metagenomic, cultural, and transcriptomic insights into deep-sea Pseudomonadota bacteria with denitrification capability
- 海洋湖沼学报(英文) 2026年页码：1-13
- Affiliations：
  
  1.College of Life Sciences, Qingdao University, Qingdao 266071, China
  2.Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266000, China
  3.Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266003, China
  4.College of Earth Science, University of Chinese Academy of Sciences, Beijing 101408, China
- Author bio：
  
  shimeiwu2016@126.com
  sunchaomin2020@126.com
- Funds：
  
  the NSFC Innovative Group Grant(42221005);the Science and Technology Innovation Project of Laoshan Laboratory(LSKJ202203103;2022QNLM030004-3);the Shandong Provincial Natural Science Foundation(ZR2024ZD49;ZR2021ZD28);the Taishan Scholars Program(tstp20230637;tsqn202312264)
- DOI：10.1007/s00343-026-5326-y
  中图分类号：
- 收稿：2025-09-03，
  
  修回：2025-10-27，
  
  网络首发：2026-05-07，
- Accepted：
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Jun YANG, Rikuan ZHENG, Jie ZHU, 等. Metagenomic, cultural, and transcriptomic insights into deep-sea Pseudomonadota bacteria with denitrification capability[J/OL]. 海洋湖沼学报(英文), 2026,1-13.

YANG Jun,ZHENG Rikuan,ZHU Jie,et al.Metagenomic, cultural, and transcriptomic insights into deep-sea Pseudomonadota bacteria with denitrification capability[J].Journal of Oceanology and Limnology,
Jun YANG, Rikuan ZHENG, Jie ZHU, 等. Metagenomic, cultural, and transcriptomic insights into deep-sea Pseudomonadota bacteria with denitrification capability[J/OL]. 海洋湖沼学报(英文), 2026,1-13. DOI： 10.1007/s00343-026-5326-y.

YANG Jun,ZHENG Rikuan,ZHU Jie,et al.Metagenomic, cultural, and transcriptomic insights into deep-sea Pseudomonadota bacteria with denitrification capability[J].Journal of Oceanology and Limnology, DOI：.

摘要

Abstract

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 upregu

lated under anoxic conditions

suggesting adaptive responses to energy stress and environmental sensing. These findings enhance our understanding of

stutzeri

273’s potential role in nitrogen cycling within fluctuating oxygen environments and offer new insights into microbial nitrogen loss in deep-sea habitats.

关键词

Keywords

references

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