Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
Nat Microbiol. 2024 Feb;9(2):464-476. doi: 10.1038/s41564-023-01578-6. Epub 2024 Jan 16.
Methane-dependent nitrate and nitrite removal in anoxic environments is thought to rely on syntrophy between ANME-2d archaea and bacteria in the genus 'Candidatus Methylomirabilis'. Here we enriched and purified a single Methylomirabilis from paddy soil fed with nitrate and methane, which is capable of coupling methane oxidation to nitrate reduction via nitrite to dinitrogen independently. Isotope labelling showed that this bacterium we name 'Ca. Methylomirabilis sinica' stoichiometrically performed methane-dependent complete nitrate reduction to dinitrogen gas. Multi-omics analyses collectively demonstrated that 'M. sinica' actively expressed a well-established pathway for this process, especially including nitrate reductase Nap. Furthermore, 'M. sinica' exhibited a higher nitrate affinity than most denitrifiers, implying its competitive fitness under oligotrophic nitrogen-limited conditions. Our findings revise the paradigm of methane-dependent denitrification performed by two organisms, and the widespread presence of 'M. sinica' in public databases suggests that the coupling of methane oxidation and complete denitrification in single cells substantially contributes to global methane and nitrogen budgets.
在缺氧环境中,甲烷依赖型硝酸盐和亚硝酸盐的去除被认为依赖于 ANME-2d 古菌与“产甲烷菌属”细菌之间的共生关系。在这里,我们从以硝酸盐和甲烷为食的稻田土壤中富集和纯化了一株单一的产甲烷菌,它能够通过亚硝酸盐将甲烷氧化偶联到硝酸盐还原为氮气。同位素标记表明,我们命名为“Ca. Methylomirabilis sinica”的这种细菌能够将甲烷依赖性完全硝酸盐还原为氮气。多组学分析共同表明,“M. sinica”积极表达了这一过程的成熟途径,特别是包括硝酸盐还原酶 Nap。此外,“M. sinica”表现出比大多数反硝化菌更高的硝酸盐亲和力,这意味着它在贫营养氮限制条件下具有竞争优势。我们的发现修正了由两种生物完成的甲烷依赖型反硝化作用的范例,并且“M. sinica”在公共数据库中的广泛存在表明,单个细胞中甲烷氧化和完全反硝化的偶联对全球甲烷和氮预算有重大贡献。