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Methane-dependent complete denitrification by a single Methylomirabilis bacterium.

Xiangwu Yao1,2, Jiaqi Wang2, Mingyue He2

  • 1Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.

Nature Microbiology
|January 16, 2024
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A novel bacterium, Candidatus Methylomirabilis sinica, independently removes methane and nitrate. This finding revises the understanding of methane-dependent denitrification and its role in global nutrient cycling.

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Area of Science:

  • Environmental microbiology
  • Biogeochemical cycles
  • Anaerobic respiration

Background:

  • Methane-dependent nitrate and nitrite removal in anoxic environments is typically attributed to syntrophy between ANME-2d archaea and 'Candidatus Methylomirabilis' bacteria.
  • This process is crucial for regulating methane and nitrogen budgets in various ecosystems.

Purpose of the Study:

  • To isolate and characterize a single microorganism capable of independent methane oxidation coupled to complete nitrate reduction.
  • To elucidate the metabolic pathways and competitive advantages of this organism under nutrient-limited conditions.

Main Methods:

  • Enrichment and purification of a novel bacterium from paddy soil.
  • Isotope labeling experiments to trace metabolic pathways.
  • Multi-omics analyses (genomics, transcriptomics, proteomics) to identify expressed genes and proteins.
  • Determination of nitrate affinity.

Main Results:

  • Isolation of 'Candidatus Methylomirabilis sinica' (M. sinica), a bacterium performing methane-dependent complete nitrate reduction to dinitrogen gas independently.
  • 'M. sinica' utilizes a well-established denitrification pathway, including nitrate reductase Nap.
  • The bacterium exhibits high nitrate affinity, suggesting competitive fitness in oligotrophic, nitrogen-limited environments.
  • Widespread presence of 'M. sinica' indicated in public databases.

Conclusions:

  • The study revises the paradigm of methane-dependent denitrification, demonstrating its occurrence within a single bacterial species.
  • 'M. sinica' plays a significant role in global methane and nitrogen cycling.
  • The findings highlight the importance of single-organism processes in biogeochemical transformations.