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Yao X, Wang J, He M, Liu Z, Zhao Y, Li Y, Chi T, Zhu L, Zheng P, Jetten MSM, Hu B. Methane-dependent complete denitrification by a single Methylomirabilis bacterium. Nat Microbiol 2024; 9:464-476. [PMID: 38228857 DOI: 10.1038/s41564-023-01578-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 12/08/2023] [Indexed: 01/18/2024]
Abstract
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.
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Affiliation(s)
- Xiangwu Yao
- 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
| | - Jiaqi Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Mingyue He
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Zishu Liu
- 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
| | - Yuxiang Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yufen Li
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Taolve Chi
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Lin Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- 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
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Baolan Hu
- 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.
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
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Quitón-Tapia S, Trueba-Santiso A, Garrido JM, Suárez S, Omil F. Metalloenzymes play major roles to achieve high-rate nitrogen removal in N-damo communities: Lessons from metaproteomics. BIORESOURCE TECHNOLOGY 2023:129476. [PMID: 37429551 DOI: 10.1016/j.biortech.2023.129476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/12/2023]
Abstract
Nitrite-driven anaerobic methane oxidation (N-damo) is a promising biological process to achieve carbon-neutral wastewater treatment solutions, aligned with the sustainable development goals. Here, the enzymatic activities in a membrane bioreactor highly enriched in N-damo bacteria operated at high nitrogen removal rates were investigated. Metaproteomic analyses, with a special focus on metalloenzymes, revealed the complete enzymatic route of N-damo including their unique nitric oxide dismutases. The relative protein abundance evidenced that "Ca. Methylomirabilis lanthanidiphila" was the predominant N-damo species, attributed to the induction of its lanthanide-binding methanol dehydrogenase in the presence of cerium. Metaproteomics also disclosed the activity of the accompanying taxa in denitrification, methylotrophy and methanotrophy. The most abundant functional metalloenzymes from this community require copper, iron, and cerium as cofactors which was correlated with the metal consumptions in the bioreactor. This study highlights the usefulness of metaproteomics for evaluating the enzymatic activities in engineering systems to optimize microbial management.
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Affiliation(s)
- Silvana Quitón-Tapia
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Alba Trueba-Santiso
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain.
| | - Juan M Garrido
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Sonia Suárez
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Francisco Omil
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
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