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Bicaldo IEC, Padilla KSAR, Tu TH, Chen WT, Mendoza-Pascual MU, Vicera CVB, de Leon JR, Poblete KN, Austria ES, Lopez MLD, Kobayashi Y, Shiah FK, Papa RDS, Okuda N, Wang PL, Lin LH. The methane-oxidizing microbial communities of three maar lakes in tropical monsoon Asia. Front Microbiol 2024; 15:1410666. [PMID: 39044952 PMCID: PMC11263035 DOI: 10.3389/fmicb.2024.1410666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/21/2024] [Indexed: 07/25/2024] Open
Abstract
Methane-oxidizing bacteria (MOB) is a group of planktonic microorganisms that use methane as their primary source of cellular energy. For tropical lakes in monsoon Asia, there is currently a knowledge gap on MOB community diversity and the factors influencing their abundance. Herewith, we present a preliminary assessment of the MOB communities in three maar lakes in tropical monsoon Asia using Catalyzed Reporter Deposition, Fluorescence In-Situ Hybridization (CARD-FISH), 16S rRNA amplicon sequencing, and pmoA gene sequencing. Correlation analysis between MOB abundances and lakes' physicochemical parameters following seasonal monsoon events were performed to explain observed spatial and temporal patterns in MOB diversity. The CARD-FISH analyses detected the three MOB types (I, II, and NC10) which aligned with the results from 16S rRNA amplicons and pmoA gene sequencing. Among community members based on 16S rRNA genes, Proteobacterial Type I MOB (e.g., Methylococcaceae and Methylomonadaceae), Proteobacterial Type II (Methylocystaceae), Verrucomicrobial (Methylacidiphilaceae), Methylomirabilota/NC10 (Methylomirabilaceae), and archaeal ANME-1a were found to be the dominant methane-oxidizers in three maar lakes. Analysis of microbial diversity and distribution revealed that the community compositions in Lake Yambo vary with the seasons and are more distinct during the stratified period. Temperature, DO, and pH were significantly and inversely linked with type I MOB and Methylomirabilota during stratification. Only MOB type I was influenced by monsoon changes. This research sought to establish a baseline for the diversity and ecology of planktonic MOB in tropical monsoon Asia to better comprehend their contribution to the CH4 cycle in tropical freshwater ecosystems.
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Affiliation(s)
- Iona Eunice C. Bicaldo
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Karol Sophia Agape R. Padilla
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Philippine Genome Center, University of the Philippines, Quezon City, Philippines
- Department of Science and Technology, Science Education Institute, Taguig, Philippines
| | - Tzu-Hsuan Tu
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wan Ting Chen
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
| | - Milette U. Mendoza-Pascual
- Department of Environmental Science, School of Science and Engineering, Ateneo Research Institute for Science and Engineering, Ateneo de Manila University, Quezon City, Philippines
| | | | - Justine R. de Leon
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Department of Biological Sciences, University of Santo Tomas, Manila, Philippines
| | | | | | - Mark Louie D. Lopez
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Yuki Kobayashi
- Center for Ecological Research, Kyoto University, Shiga, Japan
| | - Fuh-Kwo Shiah
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan
| | - Rey Donne S. Papa
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Department of Biological Sciences, University of Santo Tomas, Manila, Philippines
| | - Noboru Okuda
- Center for Ecological Research, Kyoto University, Shiga, Japan
- Research Center for Inland Seas, Kobe University, Kobe, Japan
- Research Institute for Humanity and Nature, Kamigamo Motoyama, Kita Ward, Kyoto, Japan
| | - Pei-Ling Wang
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
- Research Center for Future Earth, National Taiwan University, Taipei, Taiwan
| | - Li-Hung Lin
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
- Research Center for Future Earth, National Taiwan University, Taipei, Taiwan
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2
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Bai Y, Yang W, Li H, Hu Q, Wen S, Shen L, Song Y. Simultaneous methane mitigation and nitrogen removal by denitrifying anaerobic methane oxidation in lake sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:173134. [PMID: 38734096 DOI: 10.1016/j.scitotenv.2024.173134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
Methane (CH4) is a potent greenhouse gas, with lake ecosystems significantly contributing to its global emissions. Denitrifying anaerobic methane oxidation (DAMO) process, mediated by NC10 bacteria and ANME-2d archaea, links global carbon and nitrogen cycles. However, their potential roles in mitigating methane emissions and removing nitrogen from lake ecosystems remain unclear. This study explored the spatial variations in activities of nitrite- and nitrate-DAMO and their functional microbes in Changdanghu Lake sediments (Jiangsu Province, China). The results showed that although the average abundance of ANME-2d archaea (5.0 × 106 copies g-1) was significantly higher than that of NC10 bacteria (2.1 × 106 copies g-1), the average potential rates of nitrite-DAMO (4.59 nmol 13CO2 g-1 d-1) and nitrate-DAMO (5.01 nmol 13CO2 g-1 d-1) showed no significant difference across all sampling sites. It is estimated that nitrite- and nitrate-DAMO consumed approximately 6.46 and 7.05 mg CH4 m-2 d-1, respectively, which accordingly achieved 15.07-24.95 mg m-2 d-1 nitrogen removal from the studied lake sediments. Statistical analyses found that nitrite- and nitrate-DAMO activities were both significantly related to sediment nitrate contents and ANME-2d archaeal abundance. In addition, NC10 bacterial and ANME-2d archaeal community compositions showed significant correlations with sediment organic carbon content and water depth. Overall, this study underscores the dual roles of nitrite- and nitrate-DAMO processes in CH4 mitigation and nitrogen elimination and their key environmental impact factors (sediment organic carbon and inorganic nitrogen contents, and water depth) in shallow lake, enhancing the understanding of carbon and nitrogen cycles in freshwater aquatic ecosystems.
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Affiliation(s)
- Yanan Bai
- School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China; Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Wangting Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Hanyu Li
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Qinan Hu
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Sile Wen
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Lidong Shen
- School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China; Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Yuzhi Song
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China.
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3
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Schorn S, Graf JS, Littmann S, Hach PF, Lavik G, Speth DR, Schubert CJ, Kuypers MMM, Milucka J. Persistent activity of aerobic methane-oxidizing bacteria in anoxic lake waters due to metabolic versatility. Nat Commun 2024; 15:5293. [PMID: 38906896 PMCID: PMC11192741 DOI: 10.1038/s41467-024-49602-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 06/07/2024] [Indexed: 06/23/2024] Open
Abstract
Lacustrine methane emissions are strongly mitigated by aerobic methane-oxidizing bacteria (MOB) that are typically most active at the oxic-anoxic interface. Although oxygen is required by the MOB for the first step of methane oxidation, their occurrence in anoxic lake waters has raised the possibility that they are capable of oxidizing methane further anaerobically. Here, we investigate the activity and growth of MOB in Lake Zug, a permanently stratified freshwater lake. The rates of anaerobic methane oxidation in the anoxic hypolimnion reached up to 0.2 µM d-1. Single-cell nanoSIMS measurements, together with metagenomic and metatranscriptomic analyses, linked the measured rates to MOB of the order Methylococcales. Interestingly, their methane assimilation activity was similar under hypoxic and anoxic conditions. Our data suggest that these MOB use fermentation-based methanotrophy as well as denitrification under anoxic conditions, thus offering an explanation for their widespread presence in anoxic habitats such as stratified water columns. Thus, the methane sink capacity of anoxic basins may have been underestimated by not accounting for the anaerobic MOB activity.
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Affiliation(s)
- Sina Schorn
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Jon S Graf
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Philipp F Hach
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Daan R Speth
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Carsten J Schubert
- Department of Surface Waters, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Kastanienbaum, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zurich, Switzerland
| | | | - Jana Milucka
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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Li Y, Wang T, Jing H, Xiao Y. Evolutionary ecology of denitrifying methanotrophic NC10 bacteria in the deep-sea biosphere. Mol Ecol 2024; 33:e17372. [PMID: 38709214 DOI: 10.1111/mec.17372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/02/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
The NC10 phylum links anaerobic methane oxidation to nitrite denitrification through a unique O2-producing intra-aerobic methanotrophic pathway. Although numerous amplicon-based studies revealed the distribution of this phylum, comprehensive genomic insights and niche characterization in deep-sea environments were still largely unknown. In this study, we extensively surveyed the NC10 bacteria across diverse deep-sea environments, including waters, sediments, cold seeps, biofilms, rocky substrates, and subseafloor aquifers. We then reconstructed and analysed 38 metagenome-assembled genomes (MAGs), and revealed the extensive distribution of NC10 bacteria and their intense selective pressure in these harsh environments. Isotopic analyses combined with gene expression profiling confirmed that active nitrite-dependent anaerobic methane oxidation (n-DAMO) occurs within deep-sea sediments. In addition, the identification of the Wood-Ljungdahl (WL) and 3-hydroxypropionate/4-hydroxybutyrat (3HB/4HP) pathways in these MAGs suggests their capability for carbon fixation as chemoautotrophs in these deep-sea environments. Indeed, we found that for their survival in the oligotrophic deep-sea biosphere, NC10 bacteria encode two branches of the WL pathway, utilizing acetyl-CoA from the carbonyl branch for citric acid cycle-based energy production and methane from the methyl branch for n-DAMO. The observed low ratios of non-synonymous substitutions to synonymous substitutions (pN/pS) in n-DAMO-related genes across these habitats suggest a pronounced purifying selection that is critical for the survival of NC10 bacteria in oligotrophic deep-sea environments. These findings not only advance our understanding of the evolutionary adaptations of NC10 bacteria but also underscore the intricate coupling between the carbon and nitrogen cycles within deep-sea ecosystems, driven by this bacterial phylum.
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Affiliation(s)
- Yingdong Li
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
| | - Ting Wang
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
| | - Yao Xiao
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
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5
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Li R, Xi B, Wang X, Li Y, Yuan Y, Tan W. Anaerobic oxidation of methane in landfill and adjacent groundwater environments: Occurrence, mechanisms, and potential applications. WATER RESEARCH 2024; 255:121498. [PMID: 38522398 DOI: 10.1016/j.watres.2024.121498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/08/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024]
Abstract
Landfills remain the predominant means of solid waste management worldwide. Widespread distribution and significant stockpiles of waste in landfills make them a significant source of methane emissions, exacerbating climate change. Anaerobic oxidation of methane (AOM) has been shown to play a critical role in mitigating methane emissions on a global scale. The rich methane and electron acceptor environment in landfills provide the necessary reaction conditions for AOM, making it a potentially low-cost and effective strategy for reducing methane emissions in landfills. However, compared to other anaerobic habitats, research on AOM in landfill environments is scarce, and there is a lack of analysis on the potential application of AOM in different zones of landfills. Therefore, this review summarizes the existing knowledge on AOM and its occurrence in landfills, analyzes the possibility of AOM occurrence in different zones of landfills, discusses its potential applications, and explores the challenges and future research directions for AOM in landfill management. The identification of research gaps and future directions outlined in this review encourages further investigation and advancement in the field of AOM, paving the way for more effective waste stabilization, greenhouse gas reduction, and pollutant mitigation strategies in landfills.
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Affiliation(s)
- Renfei Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; School of Environment, Tsinghua University, Beijing 100084, PR China.
| | - Xiaowei Wang
- Department of Environmental Science and Engineering, Beijing Technology and Business University, Beijing 100048, PR China
| | - Yanjiao Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Ying Yuan
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
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Zhang M, Huang W, Zhang L, Feng Z, Zuo Y, Xie Z, Xing W. Nitrite-dependent anaerobic methane oxidation (N-DAMO) in global aquatic environments: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:171081. [PMID: 38387583 DOI: 10.1016/j.scitotenv.2024.171081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024]
Abstract
The vast majority of processes in the carbon and nitrogen cycles are driven by microorganisms. The nitrite-dependent anaerobic oxidation of methane (N-DAMO) process links carbon and nitrogen cycles, offering a novel approach for the simultaneous reduction of methane emissions and nitrite pollution. However, there is currently no comprehensive summary of the current status of the N-DAMO process in natural aquatic environments. Therefore, our study aims to fill this knowledge gap by conducting a comprehensive review of the global research trends in N-DAMO processes in various aquatic environments (excluding artificial bioreactors). Our review mainly focused on molecular identification, global study sites, and their interactions with other elemental cycling processes. Furthermore, we performed a data integration analysis to unveil the effects of key environmental factors on the abundance of N-DAMO bacteria and the rate of N-DAMO process. By combining the findings from the literature review and data integration analysis, we proposed future research perspectives on N-DAMO processes in global aquatic environments. Our overarching goal is to advance the understanding of the N-DAMO process and its role in synergistically reducing carbon emissions and removing nitrogen. By doing so, we aim to make a significant contribution to the timely achievement of China's carbon peak and carbon neutrality targets.
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Affiliation(s)
- Miao Zhang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China; CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garde, Chinese Academy of Sciences, Wuhan 430074, China
| | - Wenmin Huang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garde, Chinese Academy of Sciences, Wuhan 430074, China; Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan 430074, China
| | - Lei Zhang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China; CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garde, Chinese Academy of Sciences, Wuhan 430074, China
| | - Zixuan Feng
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garde, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yanxia Zuo
- Analysis and Testing Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zuoming Xie
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China.
| | - Wei Xing
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garde, Chinese Academy of Sciences, Wuhan 430074, China; Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan 430074, China.
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7
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Wang W, Zhang Y, Yin TM, Zhao L, Xu XJ, Xing DF, Zhang RC, Lee DJ, Ren NQ, Chen C. Prospect of denitrifying anaerobic methane oxidation (DAMO) application on wastewater treatment and biogas recycling utilization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167142. [PMID: 37722432 DOI: 10.1016/j.scitotenv.2023.167142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
Old-fashioned wastewater treatments for nitrogen depend on heterotrophic denitrification process. It would utilize extra organic carbon source as electron donors when the C/N of domestic wastewater was too low to ensure heterotrophic denitrification process. It would lead to non-compliance with carbon reduction targets and impose an economic burden on wastewater treatment. Denitrifying anaerobic methane oxidation (DAMO), which could utilize methane serving as electron donors to replace traditional organic carbon (methanol or sodium acetate), supplies a novel approach for wastewater treatment. As the primary component of biogas, methane is an inexpensive carbon source. With anaerobic digestion becoming increasingly popular for sludge reduction in wastewater treatment plants (WWTPs), efficient biogas utilization through DAMO can offer an environmentally friendly option for in-situ biogas recycling. Here, we reviewed the metabolic principle and relevant research for DAMO and biogas recycling utilization, outlining the prospect of employing DAMO for wastewater treatment and biogas recycling utilization in WWTPs. The application of DAMO provides a new focal point for enhancing efficiency and sustainability in WWTPs.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Yu Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Tian-Ming Yin
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Xi-Jun Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Ruo-Chen Zhang
- School of Civil and Transportation Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China; Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen 518055, China
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China.
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Jiang Q, Jing H, Li X, Wan Y, Chou IM, Hou L, Dong H, Niu Y, Gao D. Active pathways of anaerobic methane oxidization in deep-sea cold seeps of the South China Sea. Microbiol Spectr 2023; 11:e0250523. [PMID: 37916811 PMCID: PMC10715046 DOI: 10.1128/spectrum.02505-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/08/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Cold seeps occur in continental margins worldwide and are deep-sea oases. Anaerobic oxidation of methane is an important microbial process in the cold seeps and plays an important role in regulating methane content. This study elucidates the diversity and potential activities of major microbial groups in dependent anaerobic methane oxidation and sulfate-dependent anaerobic methane oxidation processes and provides direct evidence for the occurrence of nitrate-/nitrite-dependent anaerobic methane oxidation (Nr-/N-DAMO) as a previously overlooked microbial methane sink in the hydrate-bearing sediments of the South China Sea. This study provides direct evidence for occurrence of Nr-/N-DAMO as an important methane sink in the deep-sea cold seeps.
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Affiliation(s)
- Qiuyun Jiang
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, Guangdong, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
| | - Xuegong Li
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Ye Wan
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - I-Ming Chou
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Costal Research, East China Normal University, Shanghai, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Costal Research, East China Normal University, Shanghai, China
| | - Yuhui Niu
- State Key Laboratory of Estuarine and Costal Research, East China Normal University, Shanghai, China
| | - Dengzhou Gao
- State Key Laboratory of Estuarine and Costal Research, East China Normal University, Shanghai, China
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9
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Zhao Q, Lu Y. Anaerobic oxidation of methane in terrestrial wetlands: The rate, identity and metabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166049. [PMID: 37543312 DOI: 10.1016/j.scitotenv.2023.166049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/19/2023] [Accepted: 08/02/2023] [Indexed: 08/07/2023]
Abstract
The recent discovery of anaerobic oxidation of methane (AOM) in freshwater ecosystems has caused a great interest in "cryptic methane cycle" in terrestrial ecosystems. Anaerobic methanotrophs appears widespread in wetland ecosystems, yet, the scope and mechanism of AOM in natural wetlands remain poorly understood. In this paper, we review the recent progress regarding the potential of AOM, the diversity and distribution, and the metabolism of anaerobic methanotrophs in wetland ecosystems. The potential of AOM determined through laboratory incubation or in situ isotopic labeling ranges from 1.4 to 704.0 nmol CH4·g-1 dry soil·d-1. It appears that the availability of electron acceptors is critical in driving different AOM in wetland soils. The environmental temperature and salinity exert a significant influence on AOM activity. Reversal methanogenesis and extracellular electron transfer are likely involved in the AOM process. In addition to anaerobic methanotrophic archaea, the direct involvement of methanogens in AOM is also probable. This review presented an overview of the rate, identity, and metabolisms to unravel the biogeochemical puzzle of AOM in wetland soils.
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Affiliation(s)
- Qingzhou Zhao
- College of Urban and Environmental Science, Peking University, Beijing 100871, PR China
| | - Yahai Lu
- College of Urban and Environmental Science, Peking University, Beijing 100871, PR China.
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10
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Gibert-Brunet E, Tudryn A, Kong T, Tucholka P, Motavalli-Anbaran SH, Marlin C, Noret A, Lankarani M, Ahmady-Birgani H, Karimi G. Salt wedges and trapped brines of low-latitude endoreic saline lakes as potential modulators of GHG emission. Sci Rep 2023; 13:21118. [PMID: 38036673 PMCID: PMC10689730 DOI: 10.1038/s41598-023-48148-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023] Open
Abstract
Large salt lakes are long-term witnesses to climatic conditions and land use in their basins. The majority are experiencing a drastic drop in water levels due to climate change and human impact. Endoreic Lake Urmia (NW Iran), the sixth largest salt lake worldwide, is a striking example of this decline. Quantification of the relative contributions of natural variability and human impact on the lake's water supply is therefore essential. Here we present isotopic and radiocarbon analyses of surface and groundwater from the Shahr Chay River catchment, entering Lake Urmia on its western shore, and radiocarbon dating of a sedimentary core. Lake Urmia behaves like a large saltwater wedge almost entirely fed by the river and shallow groundwater. This leads to trapping of residual brines and formation of CH4 and secondary CO2 greenhouse gases, impacting sediment geochemical records and corresponding time scales for paleoenvironmental reconstructions. We conclude that (1) salt lakes functioning like a saline wedge, allowing organic matter oxidation, could contribute to increasing methane sources or reducing carbon sinks globally, and (2) endoreic basins worldwide need to be monitored before aridification-related salinization leads to the establishment of a saline wedge precluding any possibility of return to an equilibrium state.
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Affiliation(s)
| | - Alina Tudryn
- CNRS, UMR 8148-GEOPS, University of Paris-Saclay, 91405, Orsay, France
| | - Ting Kong
- CNRS, UMR 8148-GEOPS, University of Paris-Saclay, 91405, Orsay, France.
| | - Piotr Tucholka
- Faculty of Geology, Warsaw University, 02-089, Warsaw, Poland
| | | | - Christelle Marlin
- CNRS, UMR 8148-GEOPS, University of Paris-Saclay, 91405, Orsay, France
| | - Aurélie Noret
- CNRS, UMR 8148-GEOPS, University of Paris-Saclay, 91405, Orsay, France
| | - Mohammad Lankarani
- School of Geology, University-College of Science, University of Tehran, Tehran, Iran
| | | | - Gilda Karimi
- Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
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11
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Gou Y, Qin Y, Ouyang C, Zheng W, Jiang C. Research on aerobic oxidation of methane bacteria and its influencing factors in Chongqing central city section of the Yangtze River, China. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023; 45:6435-6453. [PMID: 37322172 DOI: 10.1007/s10653-023-01631-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 05/23/2023] [Indexed: 06/17/2023]
Abstract
Bacterial communities play an important role in the carbon cycle of freshwater ecosystems. In order to understand the influencing factors of bacterial community in the process of carbon cycle and search for measures to reduce carbon emissions, Chongqing central city section of the Yangtze River and its tributaries were selected to be the study area in this research. High-throughput sequencing was applied to study aerobic oxidation of methane bacteria (MOB) in sampling area. The results showed that there were spatial differences in the community diversity of aerobic MOB in the Yangtze River in central Chongqing. The Shannon index in the sediment (2.389-2.728) was higher than that in the water (1.820-2.458), and the community diversity in the middle reaches of the main river was higher than that in the upstream and the downstream. The aerobic MOB community was mainly dominated by Type II (Methylocystis). Most of operational taxonomic units (OTUs) in the top ten had high homology with MOB from river and lake sediments, and a few OTUs had high homology with MOB from paddy fields, forests and wetland soils. The main environmental factors affecting the community structure of aerobic MOB were NH4+-N, dissolved oxygen (DO), temperature (T, p ≤ 0.001), pH (p ≤ 0.05), methane (CH4) and carbon dioxide (CO2).
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Affiliation(s)
- Yujia Gou
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing, 400074, China
- Chongqing Metropolitan College of Science and Technology, Chongqing, 402160, China
| | - Yu Qin
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing, 400074, China.
| | - Changyue Ouyang
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing, 400074, China
| | - Wang Zheng
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing, 400074, China
| | - Chengyong Jiang
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing, 400074, China
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12
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Ouyang C, Qin Y, Liang Y, Gou Y. Community structure and network interaction of aerobic methane-oxidizing bacteria in Chongqing's central urban area in the Three Gorges Reservoir, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:56368-56381. [PMID: 36914933 DOI: 10.1007/s11356-023-26310-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
A reservoir is an important source of methane (CH4), which is consumed by aerobic methane-oxidizing bacteria (MOB), representing the main CH4 sink in water. The central urban area of Chongqing in the Three Gorges Reservoir (TGR) area was selected as the study area in 2021. High-throughput sequencing was used to analyze the community structure and abundance of MOBs. The results showed that Methylocystis (Type II) was the dominant MOB in water, whereas Methylococcus (Type I) and Methylocystis co-dominated the sediments. High water temperature in the study area largely accounted for the predominance of Type II MOBs in the two habitats. Moreover, the influence of environmental factors on MOB community and its interspecific relationship were significantly regulated by the operation of the TGR. In the low-water-level period, NO2--N and CO2 concentration significantly correlated with Methylocystis, whereas in the high-water-level period, the higher discharge and velocity weakened the influence of all environmental factors on Methylocystis. In addition, the scouring of sediments by increasing discharge in the high-water-level period caused a significant decrease in dissolved CH4 concentration. The decrease in substrate increased interspecific competition within the MOB community, especially between different types of MOBs, in the high-water-level period.
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Affiliation(s)
- Changyue Ouyang
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing, 400074, China
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing, 400074, China
| | - Yu Qin
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing, 400074, China.
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing, 400074, China.
| | - Yue Liang
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing, 400074, China
| | - Yujia Gou
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing, 400074, China
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing, 400074, China
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13
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Su G, Lehmann MF, Tischer J, Weber Y, Lepori F, Walser JC, Niemann H, Zopfi J. Water column dynamics control nitrite-dependent anaerobic methane oxidation by Candidatus "Methylomirabilis" in stratified lake basins. THE ISME JOURNAL 2023; 17:693-702. [PMID: 36806832 PMCID: PMC10119105 DOI: 10.1038/s41396-023-01382-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023]
Abstract
We investigated microbial methane oxidation in the water column of two connected but hydrodynamically contrasting basins of Lake Lugano, Switzerland. Both basins accumulate large amounts of methane in the water column below their chemoclines, but methane oxidation efficiently prevents methane from reaching surface waters. Here we show that in the meromictic North Basin water column, a substantial fraction of methane was eliminated through anaerobic methane oxidation (AOM) coupled to nitrite reduction by Candidatus Methylomirabilis. Incubations with 14CH4 and concentrated biomass from this basin showed enhanced AOM rates with nitrate (+62%) and nitrite (+43%). In the more dynamic South Basin, however, aerobic methanotrophs prevailed, Ca. Methylomirabilis was absent in the anoxic water column, and no evidence was found for nitrite-dependent AOM. Here, the duration of seasonal stratification and anoxia seems to be too short, relative to the slow growth rate of Ca. Methylomirabilis, to allow for the establishment of anaerobic methanotrophs, in spite of favorable hydrochemical conditions. Using 16 S rRNA gene sequence data covering nearly ten years of community dynamics, we show that Ca. Methylomirabilis was a permanent element of the pelagic methane filter in the North Basin, which proliferated during periods of stable water column conditions and became the dominant methanotroph in the system. Conversely, more dynamic water column conditions led to a decline of Ca. Methylomirabilis and induced blooms of the faster-growing aerobic methanotrophs Methylobacter and Crenothrix. Our data highlight that physical (mixing) processes and ecosystem stability are key drivers controlling the community composition of aerobic and anaerobic methanotrophs.
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Affiliation(s)
- Guangyi Su
- Department of Environmental Sciences, University of Basel, Basel, Switzerland. .,State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
| | - Moritz F Lehmann
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Jana Tischer
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Yuki Weber
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Fabio Lepori
- Department for Environment, Constructions and Design, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Mendrisio, Switzerland
| | | | - Helge Niemann
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.,Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research and Utrecht University, Texel, The Netherlands
| | - Jakob Zopfi
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.
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14
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Yang WT, Shen LD, Bai YN. Role and regulation of anaerobic methane oxidation catalyzed by NC10 bacteria and ANME-2d archaea in various ecosystems. ENVIRONMENTAL RESEARCH 2023; 219:115174. [PMID: 36584837 DOI: 10.1016/j.envres.2022.115174] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/07/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands are recognized as important sources of atmospheric methane (CH4). Currently, increasing evidence shows the potential importance of the anaerobic oxidation of methane (AOM) mediated by NC10 bacteria and a novel cluster of anaerobic methanotrophic archaea (ANME)-ANME-2d in mitigating CH4 emissions from different ecosystems. To better understand the role of NC10 bacteria and ANME-2d archaea in CH4 emission reduction, the current review systematically summarizes different AOM processes and the functional microorganisms involved in freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands. NC10 bacteria are widely present in these ecosystems, and the nitrite-dependent AOM is identified as an important CH4 sink and induces nitrogen loss. Nitrite- and nitrate-dependent AOM co-occur in the environment, and they are mainly affected by soil/sediment inorganic nitrogen and organic carbon contents. Furthermore, salinity is another key factor regulating the two AOM processes in coastal wetlands. In addition, ANME-2d archaea have the great potential to couple AOM to the reduction of iron (III), manganese (IV), sulfate, and even humics in different ecosystems. However, the study on the environmental distribution of ANME-2d archaea and their role in CH4 mitigation in environments is insufficient. In this study, we propose several directions for future research on the different AOM processes and respective functional microorganisms.
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Affiliation(s)
- Wang-Ting Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Li-Dong Shen
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Ya-Nan Bai
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
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15
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Cheng H, Yang Y, Shen L, Liu Y, Zhan X, Hu Z, Huang H, Jin J, Ren B, He Y, Jin Y, Su Z. Spatial variations of activity and community structure of nitrite-dependent anaerobic methanotrophs in river sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158288. [PMID: 36030855 DOI: 10.1016/j.scitotenv.2022.158288] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Rivers are an important site for methane emissions and reactive nitrogen removal. The process of nitrite-dependent anaerobic methane oxidation (n-damo) links the global carbon cycle and the nitrogen cycle, but its role in methane mitigation and nitrogen removal in rivers is poorly known. In the present study, we investigated the activity, abundance, and community composition of n-damo bacteria in sediment of the upper, middle, and lower reaches of Wuxijiang River (Zhejiang Province, China). The 13CH4 stable isotope experiments showed that the methane oxidation activity of n-damo was 0.11-1.88 nmol CO2 g-1 (dry sediment) d-1, and the activity measured from the middle reaches was significantly higher than that from the remaining regions. It was estimated that 3.27 g CH4 m-2 year-1 and 8.72 g N m-2 year-1 could be consumed via n-damo. Quantitative PCR confirmed the presence of n-damo bacteria, and their 16S rRNA gene abundance varied between 5.45 × 105 and 5.86 × 106 copies g-1 dry sediment. Similarly, the abundance of n-damo bacteria was significantly higher in the middle reaches. High-throughput sequencing showed a high n-damo bacterial diversity, with totally 152 operational taxonomic units being detected at 97 % sequence similarity cut-off. In addition, the n-damo bacterial community composition also varied spatially. The inorganic nitrogen (NH4+, NO2-, NO3-) level was found to be the key environmental factor controlling the n-damo activity and bacterial community composition. Overall, our results showed the spatial variations and environmental regulation of the activity and community structure of n-damo bacteria in river sediment, which expanded our understanding of the quantitative importance of n-damo in both methane oxidation and reactive nitrogen removal in riverine systems.
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Affiliation(s)
- Haixiang Cheng
- College of Chemistry and Materials Engineering, Quzhou University, Quzhou 324000, China
| | - Yuling Yang
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Lidong Shen
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Yan Liu
- Wuxi River Drinking Water Source Protection and Management Center, Quzhou 324000, China
| | - Xugang Zhan
- Quzhou Bureau of Ecology and Environment, Quzhou 324000, China
| | - Zhengfeng Hu
- Eco-environmental Science Research & Design Institute of Zhejiang Province, Hangzhou 310007, China
| | - Hechen Huang
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Jinghao Jin
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Bingjie Ren
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yefan He
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yuhan Jin
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Zhenfa Su
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
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16
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Chen J, Zhou Z, Gu JD. Distribution pattern of N-damo bacteria along an anthropogenic nitrogen input gradient from the coastal mangrove wetland to the South China sea sediments. MARINE ENVIRONMENTAL RESEARCH 2022; 181:105739. [PMID: 36084374 DOI: 10.1016/j.marenvres.2022.105739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Microbial nitrite-dependent anaerobic methane oxidation (n-damo) process is important for mitigating methane emission and anthropogenic nitrogen inputs in the marine environment. However, the distribution pattern of n-damo bacteria along an anthropogenic N-input gradient from the coastal wetland to the pristine South China Sea is poorly understood. This study investigated the diversity and abundance of n-damo bacteria in samples collected along a N-input gradient from Mai Po (MP) mangrove wetland sediments of the Pearl River Estuary (PRE) to the deep ocean sediments of the South China Sea (SCS). Retrieved 16S rDNA sequences showed a shift of n-damo community composition of complex structures with both freshwater and marine n-damo lineages in MP intertidal sediments to marine dominated characteristic in SCS sediments. The observed variation of Shannon and Chao1 indexes of n-damo bacteria shared a similar trend of a decrease at first followed by an increase along the targeting gradient with previously investigated methanogens, anaerobic methanotrophic archaea, ammonia-oxidizing archaea and ammonia-oxidizing bacteria, but had a reverse pattern with anammox bacteria. The community structure of pmoA gene sequences contained freshwater lineages only in SCS continental shelf sediments closer to the PRE, and turned to group with other marine samples in deeper and pristine sediments. Results suggested that n-damo bacteria might be a major contributor to anaerobic denitrification in the SCS sediments because their abundances were much higher than previously studied anammox bacteria in the same sample set. The distribution pattern of n-damo bacterial diversity, richness and abundance along the anthropogenic N-input gradient implies that they could be used as a bio-indicator for monitoring the anthropogenic/terrestrial inputs in marine environments.
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Affiliation(s)
- Jing Chen
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, PR China; Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region of China
| | - Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region of China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, Shantou, Guangdong, 515063, China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China.
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17
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Wang W, Zhao L, Ni BJ, Yin TM, Zhang RC, Yu M, Shao B, Xu XJ, Xing DF, Lee DJ, Ren NQ, Chen C. A novel sulfide-driven denitrification methane oxidation (SDMO) system: Operational performance and metabolic mechanisms. WATER RESEARCH 2022; 222:118909. [PMID: 35917671 DOI: 10.1016/j.watres.2022.118909] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Microbial denitrification is a crucial biological process for the treatment of nitrogen-polluted water. Traditional denitrification process consumes external organic carbon leading to an increase in treatment costs. We developed a novel sulfide-driven denitrification methane oxidation (SDMO) system that integrates autotrophic denitrification (AD) and denitrification anaerobic methane oxidation (DAMO) for cost-effective denitrification and biogas utilization in situ. Two SDMO systems were operated for 735 days, with nitrate and nitrite serving as electron acceptors, to explore the performance of sewage denitrification and characterize metabolic mechanisms. Results showed SDMO system could reach as high as 100% efficiency of nitrogen removal and biogas desulfurization without an external carbon source when HRT was 10 days and inflow nitrogen concentrations were 50-100 mgN·L-1. Besides, nitrate was a preferable electron acceptor for SDMO system. Biogas not only enhanced nitrogen removal but also intensified the DAMO, nitrogen removed through DAMO contribution doubled as original period from 2.9 mgN·(L·d)-1 to 6.2 mgN·(L·d)-1, and the ratio of nitrate removal through AD to DAMO was 1.2:1 with nitrate as electron acceptor. While nitrogen removed almost all through AD contribution and DAMO was weaken as before, the ratio of nitrate removal through AD to DAMO was 21.2:1 with nitrite as electron acceptor. Biogas introduced into SDMO system with nitrate inspired the growth of DAMO bacteria Candidatus Methylomirabilis from 0.3% to 19.6% and motivated its potentiality to remove nitrate without ANME archaea participation accompanying with gene mfnE upregulating ∼100 times. According to the reconstructed genome from binning analysis, the dramatically upregulated gene mfnE was derived from Candidatus Methylomirabilis, which may represent a novel metabolism pathway for DAMO bacteria to replace the role of archaea for nitrate reduction.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China.
| | - Bing-Jie Ni
- Center for Technology in Water and Wastewater (CTWW), School of Civil and Environmental Engineering, University of Technology Sydney (UTS), Sydney, NSW 2007, Australia
| | - Tian-Ming Yin
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Ruo-Chen Zhang
- School of Civil and Transportation Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Miao Yu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Bo Shao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Xi-Jun Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China; Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen 518055, China
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China.
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18
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Zhao Y, Jiang H, Wang X, Liu C, Yang Y. Quinolone antibiotics enhance denitrifying anaerobic methane oxidation in Wetland sediments: Counterintuitive results. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 305:119300. [PMID: 35427678 DOI: 10.1016/j.envpol.2022.119300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 03/25/2022] [Accepted: 04/10/2022] [Indexed: 06/14/2023]
Abstract
Denitrifying anaerobic methane oxidation (DAMO) plays an important role in the element cycle of wetlands. In recent years, the content of antibiotics in wetlands has gradually increased due to human activities. However, the impact of antibiotics on the ecological function of DAMO remains unclear. Here we studied the influence of three high-content quinolone antibiotics (QNs) on DAMO in the sediments of the Baiyangdian Wetland. The results show that QNs can significantly promote the potential DAMO rates. Moreover, the enhancement of potential DAMO rates is positively correlated with the dosage of QNs. This promotion effect of QNs on nitrate-DAMO can be attributed to the hormesis phenomenon or their inhibition of substrate competitors. As antibacterial agents, QNs inhibit nitrite-DAMO conducted by bacteria, but greatly promote nitrate-DAMO conducted by archaea. These results suggest that the short-term effect of QNs on DAMO in wetlands is promotion rather than inhibition.
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Affiliation(s)
- Yuewen Zhao
- Fujian Provincial Key Laboratory of Water Cycling and Eco-Geological Processes, Xiamen, 361021, China; Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, 050061, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China; Key Laboratory of Groundwater Sciences and Engineering, Ministry of Natural Resources, Shijiazhuang, 050800, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China.
| | - Xiuyan Wang
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, 050061, China; Key Laboratory of Groundwater Sciences and Engineering, Ministry of Natural Resources, Shijiazhuang, 050800, China
| | - Changli Liu
- Fujian Provincial Key Laboratory of Water Cycling and Eco-Geological Processes, Xiamen, 361021, China; Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, 050061, China
| | - Yuqi Yang
- School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
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19
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Wang Z, Li J, Xu X, Li K, Chen Q. Denitrifying anaerobic methane oxidation and mechanisms influencing it in Yellow River Delta coastal wetland soil, China. CHEMOSPHERE 2022; 298:134345. [PMID: 35307384 DOI: 10.1016/j.chemosphere.2022.134345] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 05/16/2023]
Abstract
Methane oxidation coupled to denitrification is mediated by Candidatus "Methylomirabilis oxyfera" (M. oxyfera), which belongs to the candidate phylum NC10, and plays a crucial role in the global carbon and nitrogen cycle. Using the Yellow River Delta coastal wetland as the study area, molecular biology technology and laboratory incubation were used to determine the abundance of NC10 bacteria and the denitrifying anaerobic methane oxidation (DAMO) rate in soils from different vegetation areas. The results of the electrophoresis detection show that M. oxyfera-like bacteria can be found in the four types of soils, according to the growth analysis by the system, OTU1 (SA) has been found the highest similarity to first-discovered Candidatus Methylomir-abilis oxyfera (FP565575) (over 98%); Vegetation cover significantly increased the abundance of M. oxyfera-like bacteria compared to beach areas, which abundance was significantly higher in deeper layers than in surface ones. Nitrate, nitrite, total nitrogen, and conductivity were identified as the main environmental factors affecting the DAMO rate. This study showed that both groups A and B of Candidatus M. oxyfera-like bacteria exist in the coastal wetland of the Yellow River Delta, which provides molecular biological evidence for the existence of the DAMO process therein. Moreover, it was revealed the influence mechanism of physical and chemical characteristics of each region on the DAMO rate. This is of significance for furthering our understanding of the coupled effect of the global carbon and nitrogen cycle.
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Affiliation(s)
- Zihao Wang
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Jinye Li
- College of Resource & Environment, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Xiaoya Xu
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Kun Li
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Qingfeng Chen
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China.
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20
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Ren L, Wu X, Ma D, Liu L, Li X, Song D. Nitrite-dependent anaerobic methane oxidation bacteria and potential in permafrost region of Daxing'an Mountains. Appl Microbiol Biotechnol 2022; 106:743-754. [PMID: 34982194 DOI: 10.1007/s00253-021-11739-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/07/2021] [Accepted: 12/11/2021] [Indexed: 11/02/2022]
Abstract
Nitrite-dependent anaerobic methane oxidation (n-damo) acts as a crucial link between biogeochemical carbon and nitrogen cycles. Nevertheless, very few studies have characterized n-damo microorganisms in high-latitude permafrost regions. Therefore, this study investigated the vertical distribution and diversity of n-damo bacterial communities in soil from three forest types in the permafrost regions of the Daxing'an Mountains. A total of 11 and 8 operational taxonomic units (OTUs) of n-damo 16S rRNA and pmoA genes were observed, respectively. Remarkable spatial variations in n-damo bacteria community richness, diversity, and structure were observed at different soil depths. Moreover, the abundances of n-damo bacteria (16S rRNA and pmoA genes) varied between 1.55 × 104 to 1.47 × 105 and 1.31 × 103 to 3.11 × 104 copies g-1 dry soil (ds), as demonstrated by quantitative PCR analyses. 13CH4 stable isotope tracer assays indicated that the potential n-damo rates varied from 0 to 1.26 nmol g-1 day-1, with the middle layers (20-40 cm and 40-60 cm) exhibiting significantly higher values than the upper (0-20 cm) and deeper layers (80-100 cm) in all three forest types. Redundancy analyses (RDA) indicated that total organic carbon (TOC), nitrate (NO3--N), and nitrite (NO2--N) were key modulators of the distribution of n-damo bacterial communities. This study thus demonstrated the widespread occurrence of n-damo bacteria in cold and high-latitude regions of forest ecosystems and provided important insights into the global distribution of these bacteria. KEY POINTS: • This study detected n-damo bacteria in soil samples obtained from the permafrost region of three forest types in the Daxing'an Mountains. • The community composition of n-damo bacteria was mainly affected by soil depth and not forest type. • The abundances of n-damo bacteria first increased and then decreased at higher soil depths.
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Affiliation(s)
- Lu Ren
- College of Geographical Sciences, Harbin Normal University, Harbin, 150025, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China
| | - Xiangwen Wu
- College of Geographical Sciences, Harbin Normal University, Harbin, 150025, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China
| | - Dalong Ma
- College of Geographical Sciences, Harbin Normal University, Harbin, 150025, China. .,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China.
| | - Lin Liu
- College of Geographical Sciences, Harbin Normal University, Harbin, 150025, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China
| | - Xin Li
- College of Geographical Sciences, Harbin Normal University, Harbin, 150025, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China
| | - Dandan Song
- College of Geographical Sciences, Harbin Normal University, Harbin, 150025, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China
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21
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Gambelli L, Mesman R, Versantvoort W, Diebolder CA, Engel A, Evers W, Jetten MSM, Pabst M, Daum B, van Niftrik L. The Polygonal Cell Shape and Surface Protein Layer of Anaerobic Methane-Oxidizing Methylomirabilis lanthanidiphila Bacteria. Front Microbiol 2021; 12:766527. [PMID: 34925275 PMCID: PMC8671808 DOI: 10.3389/fmicb.2021.766527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/08/2021] [Indexed: 11/25/2022] Open
Abstract
Methylomirabilis bacteria perform anaerobic methane oxidation coupled to nitrite reduction via an intra-aerobic pathway, producing carbon dioxide and dinitrogen gas. These diderm bacteria possess an unusual polygonal cell shape with sharp ridges that run along the cell body. Previously, a putative surface protein layer (S-layer) was observed as the outermost cell layer of these bacteria. We hypothesized that this S-layer is the determining factor for their polygonal cell shape. Therefore, we enriched the S-layer from M. lanthanidiphila cells and through LC-MS/MS identified a 31 kDa candidate S-layer protein, mela_00855, which had no homology to any other known protein. Antibodies were generated against a synthesized peptide derived from the mela_00855 protein sequence and used in immunogold localization to verify its identity and location. Both on thin sections of M. lanthanidiphila cells and in negative-stained enriched S-layer patches, the immunogold localization identified mela_00855 as the S-layer protein. Using electron cryo-tomography and sub-tomogram averaging of S-layer patches, we observed that the S-layer has a hexagonal symmetry. Cryo-tomography of whole cells showed that the S-layer and the outer membrane, but not the peptidoglycan layer and the cytoplasmic membrane, exhibited the polygonal shape. Moreover, the S-layer consisted of multiple rigid sheets that partially overlapped, most likely giving rise to the unique polygonal cell shape. These characteristics make the S-layer of M. lanthanidiphila a distinctive and intriguing case to study.
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Affiliation(s)
- Lavinia Gambelli
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands.,Living Systems Institute, University of Exeter, Exeter, United Kingdom.,College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, United Kingdom
| | - Rob Mesman
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Christoph A Diebolder
- Netherlands Centre for Electron Nanoscopy (NeCEN), Leiden University, Leiden, Netherlands
| | - Andreas Engel
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands
| | - Wiel Evers
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Department of Chemical Engineering, Delft University of Technology, Delft, Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Laura van Niftrik
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
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22
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Harb R, Laçin D, Subaşı I, Erguder TH. Denitrifying anaerobic methane oxidation (DAMO) cultures: Factors affecting their enrichment, performance and integration with anammox bacteria. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 295:113070. [PMID: 34153588 DOI: 10.1016/j.jenvman.2021.113070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/16/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
The recently discovered process, denitrifying anaerobic methane oxidation (DAMO), links the carbon and nitrogen biogeochemical cycles via coupling the anaerobic oxidation of methane to denitrification. The DAMO process, in this respect, has the potential to mitigate the greenhouse effect through the assimilation of dissolved methane. Denitrification via methane oxidation rather than organic matter, provides a new perspective to performing this once thought to be well established process. The two main species responsible for this process are "Candidatus Methylomirabilis oxyfera (M. oxyfera), and "Candidatus Methanoperedens nitroreducens" (M. nitroreducens). M. oxyfera is responsible of reducing nitrite while M. nitroreducens reduces nitrate to nitrite. These two microorganisms, despite their different pathways, were found to exist together in nature through a syntrophic relationship. Their co-existence with anaerobic ammonium oxidation (Anammox) bacteria was also revealed in the last decade. Anammox bacteria are chemolithoautotrophs, converting ammonium and nitrite to N2 and nitrate. They are responsible for the release of more than 50% of oceanic N2, hence play an important role in the global nitrogen cycle. Factors leading to the enrichment of DAMO cultures and their cultivation with Anammox cultures are of significance for improved nitrogen removal systems with decreased greenhouse effect, and even for further full-scale applications. This study, therefore, aims to present an updated review of the DAMO process, by focusing on the factors that might have a significant role in enrichment of DAMO microorganisms and their co-existence with Anammox bacteria. Factors such as temperature, pH, inoculum and feed type, trace metals and reactor configuration are among the ones discussed in detail. Factors, which have not been investigated, are also elucidated to provide a better understanding of the process and set research goals that will aid in the development of DAMO-centered wastewater treatment alternatives.
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Affiliation(s)
- Rayaan Harb
- Department of Environmental Engineering, Middle East Technical University, Ankara, Turkey
| | - Dilan Laçin
- Department of Environmental Engineering, Middle East Technical University, Ankara, Turkey
| | - Irmak Subaşı
- Department of Environmental Engineering, Middle East Technical University, Ankara, Turkey
| | - Tuba H Erguder
- Department of Environmental Engineering, Middle East Technical University, Ankara, Turkey.
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23
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Roland FAE, Borges AV, Bouillon S, Morana C. Nitrate-dependent anaerobic methane oxidation and chemolithotrophic denitrification in a temperate eutrophic lake. FEMS Microbiol Ecol 2021; 97:6360975. [PMID: 34468740 DOI: 10.1093/femsec/fiab124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 08/30/2021] [Indexed: 11/12/2022] Open
Abstract
While the emissions of methane (CH4) by natural systems have been widely investigated, CH4 aquatic sinks are still poorly constrained. Here, we investigated the CH4 cycle and its interactions with nitrogen (N), iron (Fe) and manganese (Mn) cycles in the oxic-anoxic interface and deep anoxic waters of a small, meromictic and eutrophic lake, during two summertime sampling campaigns. Anaerobic CH4 oxidation (AOM) was measured from the temporal decrease of CH4 concentrations, with the addition of three potential electron acceptors (NO3-, iron oxides (Fe(OH)3) and manganese oxides (MnO2)). Experiments with the addition of either 15N-labeled nitrate (15N-NO3-) or 15N-NO3- combined with sulfide (H2S), to measure denitrification, chemolithotrophic denitrification and anaerobic ammonium oxidation (anammox) rates, were also performed. Measurements showed AOM rates up to 3.8 µmol CH4 L-1 d-1 that strongly increased with the addition of NO3- and moderately increased with the addition of Fe(OH)3. No stimulation was observed with MnO2 added. Potential denitrification and anammox rates up to 63 and 0.27 µmol N2 L-1 d-1, respectively, were measured when only 15N-NO3- was added. When H2S was added, both denitrification and anammox rates increased. Altogether, these results suggest that prokaryote communities in the redoxcline are able to efficiently use the most available substrates.
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Affiliation(s)
- Fleur A E Roland
- Chemical Oceanography Unit, Université de Liège, 4000 Liège, Belgium
| | - Alberto V Borges
- Chemical Oceanography Unit, Université de Liège, 4000 Liège, Belgium
| | - Steven Bouillon
- Department of Earth and Environmental Sciences, Katholieke Universiteit Leuven (KU Leuven), 3001 Leuven, Belgium
| | - Cédric Morana
- Chemical Oceanography Unit, Université de Liège, 4000 Liège, Belgium
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24
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Benassi RF, de Jesus TA, Coelho LHG, Hanisch WS, Domingues MR, Taniwaki RH, Peduto TAG, da Costa DO, Pompêo MLM, Mitsch WJ. Eutrophication effects on CH 4 and CO 2 fluxes in a highly urbanized tropical reservoir (Southeast, Brazil). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:42261-42274. [PMID: 33797721 DOI: 10.1007/s11356-021-13573-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Shallow urban polluted reservoirs at tropical regions can be hotspots for CO2 and CH4 emissions. In this study, we investigated the relationships between eutrophication and GHG emissions in a highly urbanized tropical reservoir in São Paulo Metropolitan Area (Brazil). CO2 and CH4 fluxes and limnological variables (water and sediment) were collected at three sampling stations classified as hypereutrophic and eutrophic. Analysis of variance (ANOVA) and the principal component analysis (PCA) determined the most significant parameters to CO2 and CH4 fluxes. ANOVA showed significant differences of CO2 and CH4 fluxes between sampling stations with different trophic state. The hypereutrophic station showed higher mean fluxes for both CO2 and CH4 (5.43 ± 1.04 and 0.325 ± 0.167 g m-2 d-1, respectively) than the eutrophic stations (3.36 ± 0.54 and 0.060 ± 0.005 g m-2 d-1). The PCA showed a strong relationship between nutrients in the water column (surface and bottom) and GHG fluxes. We concluded that GHG fluxes were higher whenever the trophic state increases as observed previously in temperate and tropical reservoirs. High concentrations of nutrients in the water column in the studied area support the high production of autotrophic biomass that, when sedimented, ends up serving as organic matter for CH4 producers. These outcomes reinforce the necessity of water quality improvement and eutrophication mitigation in highly urbanized reservoirs in tropical regions.
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Affiliation(s)
- Roseli Frederigi Benassi
- Center for Engineering, Modeling and Applied Social Sciences, Federal University of ABC, Av. dos Estados, 5001 - Bangú, SP, 09210-580, Santo André, Brazil.
| | - Tatiane Araujo de Jesus
- Center for Engineering, Modeling and Applied Social Sciences, Federal University of ABC, Av. dos Estados, 5001 - Bangú, SP, 09210-580, Santo André, Brazil
| | - Lúcia Helena Gomes Coelho
- Center for Engineering, Modeling and Applied Social Sciences, Federal University of ABC, Av. dos Estados, 5001 - Bangú, SP, 09210-580, Santo André, Brazil
| | | | - Mercia Regina Domingues
- Center for Engineering, Modeling and Applied Social Sciences, Federal University of ABC, Av. dos Estados, 5001 - Bangú, SP, 09210-580, Santo André, Brazil
| | - Ricardo Hideo Taniwaki
- Center for Engineering, Modeling and Applied Social Sciences, Federal University of ABC, Av. dos Estados, 5001 - Bangú, SP, 09210-580, Santo André, Brazil
| | - Thais Araujo Goya Peduto
- Post-graduation Program in Environmental Science and Technology, Federal University of ABC, CTA/UFABC, Av. dos Estados, 5001 - Bangú, Santo André, SP, 09210-580, Brazil
| | - Danilo Oliveira da Costa
- Post-graduation Program in Environmental Science and Technology, Federal University of ABC, CTA/UFABC, Av. dos Estados, 5001 - Bangú, Santo André, SP, 09210-580, Brazil
| | - Marcelo Luiz Martins Pompêo
- Department of Ecology, Institute of Biosciences, University of Sao Paulo Rua do Matão, Trav. 14, n° 321, PO Box 05508-900, São Paulo, SP, Brazil
- Post-graduation Program in Environmental Sciences, UNESP, Campus de Sorocaba, Sorocaba, Brazil
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25
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Nie WB, Ding J, Xie GJ, Tan X, Lu Y, Peng L, Liu BF, Xing DF, Yuan Z, Ren N. Simultaneous nitrate and sulfate dependent anaerobic oxidation of methane linking carbon, nitrogen and sulfur cycles. WATER RESEARCH 2021; 194:116928. [PMID: 33618110 DOI: 10.1016/j.watres.2021.116928] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/02/2021] [Accepted: 02/11/2021] [Indexed: 06/12/2023]
Abstract
ANaerobic MEthanotrophic (ANME) archaea are critical microorganisms mitigating methane emission from anoxic zones. In previous studies, sulfate-dependent anaerobic oxidation of methane (AOM) and nitrate-dependent AOM, performed by different clades of ANME archaea, were detected in marine sediments and freshwater environments, respectively. This study shows that simultaneous sulfate- and nitrate-dependent AOM can be mediated by a clade of ANME archaea, which may occur in estuaries and coastal zones, at the interface of marine and freshwater environments enriched with sulfate and nitrate. Long-term (~1,200 days) performance data of a bioreactor, metagenomic analysis and batch experiments demonstrated that ANME-2d not only conducted AOM coupled to reduction of nitrate to nitrite, but also coupled to the conversion of sulfate to sulfide, in collaboration with sulfate-reducing bacteria (SRB). Sulfide was oxidized back to sulfate by sulfide-oxidizing autotrophic denitrifiers with nitrate or nitrite as electron acceptors, in turn alleviating sulfide accumulation. In addition, dissimilatory nitrate reduction to ammonium performed by ANME-2d was detected, providing substrates to Anammox. Metatranscriptomic analysis revealed significant upregulation of flaB in ANME-2d and pilA in Desulfococcus, which likely resulted in the formation of unique nanonets connecting cells and expanding within the biofilm, and putatively providing structural links between ANME-2d and SRB for electron transfer. Simultaneous nitrate- and sulfate-dependent AOM as observed in this study could be an important link between the carbon, nitrogen and sulfur cycles in natural environments, such as nearshore environments.
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Affiliation(s)
- Wen-Bo Nie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No.73, Huanghe Road, Nangang District, Harbin, Heilongjiang, 150090, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No.73, Huanghe Road, Nangang District, Harbin, Heilongjiang, 150090, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No.73, Huanghe Road, Nangang District, Harbin, Heilongjiang, 150090, China.
| | - Xin Tan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No.73, Huanghe Road, Nangang District, Harbin, Heilongjiang, 150090, China
| | - Yang Lu
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore
| | - Lai Peng
- School of Resources and Environmental Engineering, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No.73, Huanghe Road, Nangang District, Harbin, Heilongjiang, 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No.73, Huanghe Road, Nangang District, Harbin, Heilongjiang, 150090, China
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane QLD, 4072, Australia
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No.73, Huanghe Road, Nangang District, Harbin, Heilongjiang, 150090, China
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26
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Friese A, Bauer K, Glombitza C, Ordoñez L, Ariztegui D, Heuer VB, Vuillemin A, Henny C, Nomosatryo S, Simister R, Wagner D, Bijaksana S, Vogel H, Melles M, Russell JM, Crowe SA, Kallmeyer J. Organic matter mineralization in modern and ancient ferruginous sediments. Nat Commun 2021; 12:2216. [PMID: 33850127 PMCID: PMC8044167 DOI: 10.1038/s41467-021-22453-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 03/15/2021] [Indexed: 02/02/2023] Open
Abstract
Deposition of ferruginous sediment was widespread during the Archaean and Proterozoic Eons, playing an important role in global biogeochemical cycling. Knowledge of organic matter mineralization in such sediment, however, remains mostly conceptual, as modern ferruginous analogs are largely unstudied. Here we show that in sediment of ferruginous Lake Towuti, Indonesia, methanogenesis dominates organic matter mineralization despite highly abundant reactive ferric iron phases like goethite that persist throughout the sediment. Ferric iron can thus be buried over geologic timescales even in the presence of labile organic carbon. Coexistence of ferric iron with millimolar concentrations of methane further demonstrates lack of iron-dependent methane oxidation. With negligible methane oxidation, methane diffuses from the sediment into overlying waters where it can be oxidized with oxygen or escape to the atmosphere. In low-oxygen ferruginous Archaean and Proterozoic oceans, therefore, sedimentary methane production was likely favored with strong potential to influence Earth's early climate.
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Affiliation(s)
- André Friese
- GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - Kohen Bauer
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Clemens Glombitza
- ETH Zürich, Institute of Biogeochemistry and Pollutant Dynamics, Zürich, Switzerland
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Luis Ordoñez
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
| | - Daniel Ariztegui
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
| | - Verena B Heuer
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Aurèle Vuillemin
- GFZ German Research Centre for Geosciences, Potsdam, Germany
- Department of Earth & Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Cynthia Henny
- Research Center for Limnology, Indonesian Institute of Sciences (LIPI), Cibinong, Bogor, West Java, Indonesia
| | - Sulung Nomosatryo
- GFZ German Research Centre for Geosciences, Potsdam, Germany
- Research Center for Limnology, Indonesian Institute of Sciences (LIPI), Cibinong, Bogor, West Java, Indonesia
| | - Rachel Simister
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Potsdam, Germany
| | - Satria Bijaksana
- Faculty of Mining and Petroleum Engineering, Institut Teknologi Bandung, Bandung, Jawa Barat, Indonesia
| | - Hendrik Vogel
- Institute of Geological Sciences & Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Martin Melles
- Institute of Geology and Mineralogy, University of Cologne, Cologne, Germany
| | - James M Russell
- Department of Earth, Environmental, and Planetary Sciences, Brown University, Providence, RI, USA
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada.
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Potsdam, Germany.
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27
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Fan SQ, Xie GJ, Lu Y, Liu BF, Xing DF, Ding J, Han HJ, Ren NQ. Nitrate/nitrite dependent anaerobic methane oxidation coupling with anammox in membrane biotrickling filter for nitrogen removal. ENVIRONMENTAL RESEARCH 2021; 193:110533. [PMID: 33285154 DOI: 10.1016/j.envres.2020.110533] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/10/2020] [Accepted: 11/22/2020] [Indexed: 06/12/2023]
Abstract
Combining nitrate/nitrite dependent anaerobic methane oxidation (n-DAMO) and anaerobic ammonium oxidation (Anammox) is a promising sustainable wastewater treatment technology, which simultaneously achieve nitrogen removal and methane emission mitigation. However, the practical application of n-DAMO has been greatly limited by its extremely slow growth-rate and low reaction rate. This work proposes an innovative Membrane BioTrickling Filter (MBTF), which consist of hollow fiber membrane for effective methane supplementation and polyurethane sponge as support media for the attachment and growth of biofilm coupling n-DAMO with Anammox. When steady state with a hydraulic retention time (HRT) of 6.00 h was reached, above 99.9% of nitrogen was removed from synthetic sidestream wastewater at a rate of 3.99 g N L-1 d-1. This system presented robust capacity to withstand unstable partial nitritation effluent, achieving complete nitrogen removal at a varied nitrite to ammonium ratio in the range of 1.10-1.40. It is confirmed that n-DAMO and Anammox microorganisms jointly dominated the microbial community by pyrosequencing technology. The complete nitrogen removal potential at high-rate and efficient biomass retention (12.4 g VSS L-1) of MBTF offers promising alternative for sustainable wastewater treatment by the combination of n-DAMO and Anammox.
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Affiliation(s)
- Sheng-Qiang Fan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Yang Lu
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, 637551, Singapore
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Hong-Jun Han
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
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28
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Zhong Q, Xue D, Chen H, Liu L, He Y, Zhu D, He Z. Structure and distribution of nitrite-dependent anaerobic methane oxidation bacteria vary with water tables in Zoige peatlands. FEMS Microbiol Ecol 2020; 96:5800981. [PMID: 32149349 DOI: 10.1093/femsec/fiaa039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/06/2020] [Indexed: 11/12/2022] Open
Abstract
The recently discovered nitrite-dependent anaerobic methane oxidation (n-damo) is an important methane sink in natural ecosystems performed by NC10 phylum bacteria. However, the effect of water table (WT) gradient due to global change on n-damo bacterial communities is not well studied in peatlands. Here, we analysed the vertical distribution (0-100 cm) of n-damo bacterial communities at three sites with different WTs of the Zoige peatlands in the Qinghai-Tibetan Plateau. Using an n-damo bacterial specific 16S rRNA gene clone library, we obtained 25 operational taxonomic units (OTUs) that could be divided into Groups A, B, C, D and E (dominated by A and B). The dominant group was Group B at the high (OTU14 and OTU20) and intermediate (OTU7 and OTU8) WT sites and Group A was dominant at the low WT site (OTU6 and OTU5). Using high-throughput sequencing, we observed that n-damo bacteria mainly distributed in subsurface soils (50-60 and 20-30 cm), and their relative abundances were higher at the low WT site than at the other two sites. In addition, we found that pH and nitrate were positively correlated with Group A, while total organic carbon, total nitrogen and ammonia were positively associated with Group B. Our study provides new insights into our understanding of the response of n-damo bacteria to WT gradient in peatlands, with important implications for global change.
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Affiliation(s)
- Qiuping Zhong
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.,Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
| | - Dan Xue
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China.,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100101, China
| | - Liangfeng Liu
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
| | - Yixin He
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
| | - Dan Zhu
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
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Li X, Lai DYF, Gao D. Anaerobic oxidation of methane with denitrification in sediments of a subtropical estuary: Rates, controlling factors and environmental implications. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 273:111151. [PMID: 32758912 DOI: 10.1016/j.jenvman.2020.111151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/11/2020] [Accepted: 07/28/2020] [Indexed: 06/11/2023]
Abstract
Anaerobic oxidation of methane with denitrification (DAMO), as an important microbial process regulating methane emission, has been widely reported in freshwater ecosystems. However, the DAMO process and associated biogeochemical controls in estuaries remain poorly understood. Here, we used 13C- and 15N-labelling experiments to quantify the potential rates of DAMO and determined the crucial factors controlling the DAMO rates in the sediment of Yangtze Estuary. Potential rates of DAMO varied greatly across the estuary, ranging from 0.07 to 0.28 nmol CO2 g-1 d-1. Salinity negatively affected the DAMO and also showed an indirectly negative influence on DAMO process by high salinity inhibition on NO3- availability and denitrification. Nitrate concentrations were significantly correlated with the DAMO rates. Denitrification rates showed positive correlation with DAMO rates, implying that nitrate reduction drives the DAMO process. Sediment total organic carbon and NH4+ had important effects on DAMO rates. These results together indicate that DAMO process can occur and the DAMO rates were mainly controlled by sediment NO3- and denitrification in estuary. We further conclude that increasing NO3- load can drive the DAMO process with more important implications on methane sink in estuarine ecosystems.
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Affiliation(s)
- Xiaofei Li
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China; School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China.
| | - Derrick Y F Lai
- Department of Geography and Resource Management, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Dengzhou Gao
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai, 200241, China
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30
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Shen LD, Tian MH, Cheng HX, Liu X, Yang YL, Liu JQ, Xu JB, Kong Y, Li JH, Liu Y. Different responses of nitrite- and nitrate-dependent anaerobic methanotrophs to increasing nitrogen loading in a freshwater reservoir. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114623. [PMID: 33618455 DOI: 10.1016/j.envpol.2020.114623] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 06/12/2023]
Abstract
Nitrite (NO2-)- and nitrate (NO3-)-dependent anaerobic oxidation of methane (AOM) are two new additions in microbial methane cycle, which potentially act as important methane sinks in freshwater aquatic systems. Here, we investigated spatial variations of community composition, abundance and potential activity of NO2-- and NO3--dependent anaerobic methanotrophs in the sediment of Jiulonghu Reservoir (Zhejiang Province, China), a freshwater reservoir having a gradient of increasing nitrogen loading from upstream to downstream regions. High-throughput sequencing of total bacterial and archaeal 16S rRNA genes showed the cooccurrence of Candidatus Methylomirabilis oxyfera (M. oxyfera)-like and Candidatus Methanoperedens nitroreducens (M. nitroreducens)-like anaerobic methanotrophs in the examined reservoir sediments. The community structures of these methanotrophs differed substantially between the sediments of upstream and downstream regions. Quantitative PCR suggested higher M. oxyfera-like bacterial abundance in the downstream (8.6 × 107 to 2.8 × 108 copies g-1 dry sediment) than upstream sediments (2.4 × 107 to 3.5 × 107 copies g-1 dry sediment), but there was no obvious difference in M. nitroreducens-like archaeal abundance between these sediments (3.7 × 105 to 4.8 × 105 copies g-1 dry sediment). The 13CH4 tracer experiments suggested the occurrence of NO2-- and NO3--dependent AOM activities, and their rates were 4.7-14.1 and 0.8-2.6 nmol CO2 g-1 (dry sediment) d-1, respectively. Further, the rates of NO2--dependent AOM in downstream sediment were significantly higher than those in upstream sediment. The NO3- concentration was the key factor affecting the spatial variations of abundance and activity of NO2--dependent anaerobic methanotrophs. Overall, our results showed different responses of NO2-- and NO3--dependent anaerobic methanotrophs to increasing nitrogen loading in a freshwater reservoir.
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Affiliation(s)
- Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Mao-Hui Tian
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Hai-Xiang Cheng
- College of Chemistry and Materials Engineering, Quzhou University, Quzhou, 324000, China
| | - Xin Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yu-Ling Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jia-Qi Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jiang-Bing Xu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yun Kong
- College of Resources and Environment, Yangtze University, Hubei, Wuhan, 430100, China
| | - Jian-Hui Li
- College of Chemistry and Materials Engineering, Quzhou University, Quzhou, 324000, China
| | - Yan Liu
- Wuxijiang National Wetland Park Service, Quzhou, 324000, China
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31
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Pan H, Qin Y, Wang Y, Liu S, Yu B, Song Y, Wang X, Zhu G. Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) pathway dominates nitrate reduction processes in rhizosphere and non-rhizosphere of four fertilized farmland soil. ENVIRONMENTAL RESEARCH 2020; 186:109612. [PMID: 32668552 DOI: 10.1016/j.envres.2020.109612] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/26/2020] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
Nitrate (NO3-) reduction partitioning between denitrification, anaerobic ammonium oxidation (anammox), denitrifying anaerobic methane oxidation (DAMO), and dissimilatory nitrate reduction to ammonium (DNRA), can influence the nitrogen (N) use efficiency and crop production in arid farmland. The microbial structure, function and potential rates of denitrification, anammox, DAMO and DNRA, and their respective contributions to total NO3- reduction were investigated in rhizosphere and non-rhizosphere soil of four typical crops in north China by functional gene amplification, high-throughput sequencing, network analysis and isotopic tracing technique. The measured denitrification and DNRA rate varied from 0.0294 to 20.769 nmol N g-1 h-1and 2.4125-58.682 nmol N g-1 h-1, respectively, based on which DNRA pathway contributed to 84.44 ± 14.40% of dissimilatory NO3- reduction, hence dominated NO3- reduction processes compared to denitrification. Anammox and DAMO were not detected. High-throughput sequencing analysis on DNRA nrfA gene, and denitrification nirS and nirK genes demonstrated that these two processes did not correlate to corresponding gene abundance or dominant genus. RDA and Pearson's correlation analysis illustrated that DNRA rate was significantly correlated with the abundance of Chthiniobacter, as well as total organic matter (TOM); denitrification rate was significantly correlated with the abundance of Lautropia, so did TOM. Network analysis showed that the genus performed DNRA was the key connector in the microbial community of dissimilatory nitrate reducers. This study simultaneously investigated the dissimilatory nitrate reduction processes in rhizosphere and non-rhizosphere soils in arid farmland, highlighting that DNRA dominated NO3- reduction processes against denitrification. As denitrification results in N loss, whereas DNRA contributes to N retention, the relative contributions of DNRA versus denitrification activities should be considered appropriately when assessing N transformation processes and N fertilizer management in arid farmland fields.
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Affiliation(s)
- Huawei Pan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yu Qin
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuantao Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shiguang Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Bin Yu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiping Song
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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32
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Liu Y, Wang X, Chen Y, Zhang L, Xu K, Du Y. Anaerobic methane-oxidizing bacterial communities in sediments of a drinking reservoir, Beijing, China. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01578-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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33
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Abstract
The anaerobic oxidation of methane (AOM) is an important sink of methane that plays a significant role in global warming. However, evidence for the AOM in freshwater habitats is rare, especially in dam and weir (small-scale dam) reservoirs. Here, the AOM process was examined in freshwater sediments of a small-scale dam reservoir located in Rzeszów, SE Poland. The AOM rate was determined in the main experiment with the addition of the 13CH4 isotope marker (He+13CH4). Sediments were collected three times: in spring (in May, 15 °C), in summer (in July, 20 °C) and in autumn (in September, 10 °C). Further analysis considers the impact on AOM rate of potential electron acceptors present in pore-water (NO2−, NO3−, SO42−, and Fe3+ ions). The work suggests that an AOM process does take place in the studied reservoir sediments, with this evidenced by the presence in the headspace of an increased 13CO2 concentration deemed to derive from 13CH4 oxidation. Rates of AOM noted were of 0.36–1.42 nmol·g−1·h−1, with the most intensive oxidation in each sediment layer occurring at 20 °C. While none of the potential electron acceptors considered individually were found to have had a statistically significant influence on the AOM rate, their significance to the dynamics of the AOM process was not precluded.
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34
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van Grinsven S, Sinninghe Damsté JS, Abdala Asbun A, Engelmann JC, Harrison J, Villanueva L. Methane oxidation in anoxic lake water stimulated by nitrate and sulfate addition. Environ Microbiol 2020; 22:766-782. [PMID: 31814267 PMCID: PMC7027835 DOI: 10.1111/1462-2920.14886] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 11/21/2019] [Accepted: 12/04/2019] [Indexed: 11/30/2022]
Abstract
Methanotrophic bacteria play a key role in limiting methane emissions from lakes. It is generally assumed that methanotrophic bacteria are mostly active at the oxic-anoxic transition zone in stratified lakes, where they use oxygen to oxidize methane. Here, we describe a methanotroph of the genera Methylobacter that is performing high-rate (up to 72 μM day-1 ) methane oxidation in the anoxic hypolimnion of the temperate Lacamas Lake (Washington, USA), stimulated by both nitrate and sulfate addition. Oxic and anoxic incubations both showed active methane oxidation by a Methylobacter species, with anoxic rates being threefold higher. In anoxic incubations, Methylobacter cell numbers increased almost two orders of magnitude within 3 days, suggesting that this specific Methylobacter species is a facultative anaerobe with a rapid response capability. Genomic analysis revealed adaptations to oxygen-limitation as well as pathways for mixed-acid fermentation and H2 production. The denitrification pathway was incomplete, lacking the genes narG/napA and nosZ, allowing only for methane oxidation coupled to nitrite-reduction. Our data suggest that Methylobacter can be an important driver of the conversion of methane in oxygen-limited lake systems and potentially use alternative electron acceptors or fermentation to remain active under oxygen-depleted conditions.
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Affiliation(s)
- Sigrid van Grinsven
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
- Department of Earth Sciences, Faculty of GeosciencesUtrecht UniversityUtrechtThe Netherlands
| | - Alejandro Abdala Asbun
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
| | - Julia C. Engelmann
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
| | - John Harrison
- Washington State University Vancouver, School of the EnvironmentVancouverWA98686USA
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
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Wang S, Pi Y, Jiang Y, Pan H, Wang X, Wang X, Zhou J, Zhu G. Nitrate reduction in the reed rhizosphere of a riparian zone: From functional genes to activity and contribution. ENVIRONMENTAL RESEARCH 2020; 180:108867. [PMID: 31708170 DOI: 10.1016/j.envres.2019.108867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/27/2019] [Accepted: 10/27/2019] [Indexed: 06/10/2023]
Abstract
The increased nitrogen (N) fertilizer usage caused substantial nitrate (NO3-) leaching into groundwater and eutrophication in downstream aquatic systems. Riparian zones positioned as the link interfaces of terrestrial and aquatic environments are effective in NO3- removal. However, the microbial mechanisms regulating NO3- reduction in riparian zones are still unclear. In this study, four microbial NO3- reduction processes were explored in fine-scale riparian soil horizons by isotopic tracing technique, qPCR of functional gene, high-throughput amplicon sequencing, and phylogenetic molecular ecological network analysis. Interestingly, anaerobic ammonium oxidation (anammox) contributed to NO3- removal of up to 48.2% only in waterward sediments but not in landward soil. Denitrification was still the most significant contributor to NO3- reduction (32.0-91.8%) and N-losses (51.7-100%). Additionally, dissimilatory nitrate reduction to ammonium (DNRA) played a key role in NO3- reduction (4.4-67.5%) and was even comparable to denitrification. Community structure analysis of denitrifying, anammox, and DNRA bacterial communities targeting the related functional gene showed that spatial heterogeneity played a greater role than both temporal and soil type (rhizosphere and non-rhizosphere soil) variability in microbial community structuring. Denitrification and DNRA communities were diverse, and their activities did not depend on gene abundance but were significantly related to organic matter, suggesting that gene abundance alone was insufficient in assessing their activity in riparian zones. Based on networks, DNRA plays a keystone role among the microbial NO3- reducers. As the last line of defense in the interception of terrestrial NO3-, these findings contribute to our understanding of NO3- removal mechanisms in riparian zones, and could potentially be exploited to reduce the diffusion of NO3- pollution.
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Affiliation(s)
- Shanyun Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yanxia Pi
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yingying Jiang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Huawei Pan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xiaoxia Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xiaomin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jiemin Zhou
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Guibing Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
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Chen F, Zheng Y, Hou L, Zhou J, Yin G, Liu M. Denitrifying anaerobic methane oxidation in marsh sediments of Chongming eastern intertidal flat. MARINE POLLUTION BULLETIN 2020; 150:110681. [PMID: 31699499 DOI: 10.1016/j.marpolbul.2019.110681] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
Denitrifying anaerobic methane oxidation (DAMO) and associated microbial diversity and abundance in the marsh sediments of Chongming eastern intertidal flat, the Yangtze Estuary, were investigated using carbon-isotope tracing and molecular techniques. Co-existence of nitrate-DAMO archaea and nitrite-DAMO bacteria was evidenced, with higher biodiversity of DAMO archaea than DAMO bacteria. Abundance of DAMO archaeal mcrA gene and DAMO bacterial pmoA gene ranged from 4.2 × 103 to 3.9 × 1010 copies g-1 and from 4.5 × 105 to 6.4 × 106 copies g-1, respectively. High DAMO potential was detected, ranging from 0.6 to 46.7 nmol 13CO2 g-1 day-1 for nitrate-DAMO and from 1.3 to 39.9 nmol 13CO2 g-1 day-1 for nitrite-DAMO. In addition to playing an important role as a CH4 sink, DAMO bacteria also removed a substantial amount of reactive nitrogen (29.4 nmol N g-1 day-1) from the intertidal sediments. Overall, these results indicate the importance of DAMO bioprocess as methane and nitrate sinks in intertidal marshes.
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Affiliation(s)
- Feiyang Chen
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai, 200241, China
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai, 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai, 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai, 200241, China.
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai, 200241, China.
| | - Jie Zhou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai, 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai, 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai, 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai, 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai, 200241, China
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37
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Wang S, Liu W, Zhao S, Wang C, Zhuang L, Liu L, Wang W, Lu Y, Li F, Zhu G. Denitrification is the main microbial N loss pathway on the Qinghai-Tibet Plateau above an elevation of 5000 m. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 696:133852. [PMID: 31442722 DOI: 10.1016/j.scitotenv.2019.133852] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
Soil nitrogen (N) deficiency is the major factor contributing to low primary productivity on the Qinghai-Tibet Plateau. However, most of our understanding of N cycling is still based on human disturbed environments, and the microbial mechanisms governing N loss in low primary productivity environment remain unclear. This study explores three microbial N loss pathways in eight wetland and dryland soil profiles from the Qinghai-Tibet Plateau, at an elevation of above 5000 m with little human activity, using 15N isotopic tracing slurry technology, quantitative PCR, and high-throughput sequencing. No denitrifying anaerobic methane oxidation was detected. Anammox occurred in two of the wetland (n = 4) and dryland (n = 4) soil profiles, while denitrification widely occurred and was the dominant N loss pathway in all samples. Where denitrification and anammox co-occurred, both abundance and activity were higher in wetland than in dryland soils and higher in surface than in subsurface soils. In comparison with non-anammox sites, nitrate levels initiate anammox-related N cycling. High-throughput sequencing and network analysis of nirK, nirS, nosZ, and hzsB gene communities showed that Bradyrhizobiaceae (a family of rhizobia) may play a dominant role in N loss pathways in this region. Given the geological evolution and relatively undisturbed habitat, these findings strongly suggest that denitrification is the dominant N loss pathway in terrestrial habitats of the Qing-Tibet Plateau with minimal anthropogenic activity.
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Affiliation(s)
- Shanyun Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weiyue Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Siyan Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Cheng Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Linjie Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lu Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weidong Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yonglong Lu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Sciences and Technology, Guangzhou 510650, China
| | - Guibing Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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38
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Wang S, Wang W, Zhao S, Wang X, Hefting MM, Schwark L, Zhu G. Anammox and denitrification separately dominate microbial N-loss in water saturated and unsaturated soils horizons of riparian zones. WATER RESEARCH 2019; 162:139-150. [PMID: 31260829 DOI: 10.1016/j.watres.2019.06.052] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 06/09/2019] [Accepted: 06/19/2019] [Indexed: 06/09/2023]
Abstract
Fertilized agroecosystems may show considerable leaching of the mobile nitrogen (N) compound NO3-, which pollutes groundwater and causes eutrophication of downstream waterbodies. Riparian buffer zones, positioned between terrestrial and aquatic environments, effectively remove NO3- and serve as a hotspot for N2O emissions. However, microbial processes governing NO3- reduction in riparian zones still remain largely unclear. This study explored the underlying mechanisms of various N-loss processes in riparian soil horizons using isotopic tracing techniques, molecular assays, and high-throughput sequencing. Both anaerobic ammonium oxidation (anammox) and denitrification activity were maximized in the riparian fringe rather than in the central zones. Denitrifying anaerobic methane oxidation (damo) process was not detected. Interestingly, both contrasting microbial habitats were separated by a groundwater table, which forms an important biogeochemical interface. Denitrification dominated cumulative N-losses in the upper unsaturated soil, while anammox dominated the lower oxic saturated soil horizons. Archaeal and bacterial ammonium oxidation that couple dissimilatory nitrate reduction to ammonium (DNRA) with a high cell-specific rate promoted anammox even further in oxic subsurface horizons. High-throughput sequencing and network analysis showed that the anammox rate positively correlated with Candidatus 'Kuenenia' (4%), rather than with the dominant Candidatus 'Brocadia'. The contribution to N-loss via anammox increased significantly with the water level, which was accompanied by a significant reduction of N2O emission (∼39.3 ± 10.6%) since N-loss by anammox does not cause N2O emissions. Hence, water table management in riparian ecotones can be optimized to reduce NO3- pollution by shifting from denitrification to the environmentally friendly anammox pathway to mitigate greenhouse gas emissions.
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Affiliation(s)
- Shanyun Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Weidong Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Siyan Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xiaomin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Mariet M Hefting
- Ecology and Biodiversity Group, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Lorenz Schwark
- Institute for Geosciences, University of Kiel, Kiel, Germany
| | - Guibing Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
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Zhu B, Wang J, Bradford LM, Ettwig K, Hu B, Lueders T. Nitric Oxide Dismutase ( nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers. Front Microbiol 2019; 10:1577. [PMID: 31354671 PMCID: PMC6636425 DOI: 10.3389/fmicb.2019.01577] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/25/2019] [Indexed: 11/13/2022] Open
Abstract
Oxygenic denitrification represents a new route in reductive nitrogen turnover which differs from canonical denitrification in how nitric oxide (NO) is transformed into dinitrogen gas. Instead of NO reduction via N2O to N2, NO is proposed to be directly disproportionated into N2 and O2 in oxygenic denitrification, catalyzed by the putative NO dismutase (Nod). Although a high diversity of nod genes has been recovered from various environments, still little is known about the niche partitioning and ecophysiology of oxygenic denitrifiers. One constraint is that nod as a functional marker for oxygenic denitrifiers is not well established. To address this issue, we compared the diversity and phylogeny of nod, 16S rRNA and pmoA gene sequences of four NC10 enrichments that are capable of methane-driven oxygenic denitrification and one environmental sample. The phylogenies of nod, 16S rRNA and pmoA genes of these cultures were generally congruent. The diversity of NC10 bacteria inferred from different genes was also similar in each sample. A new set of NC10-specific nod primers was developed and used in qPCR. The abundance of NC10 bacteria inferred from nod genes was constantly lower than via 16S rRNA genes, but the difference was within one order of magnitude. These results suggest that nod is a suitable molecular marker for studying the diversity and phylogeny of methane-driven oxygenic denitrifiers, the further investigation of which may be of value to develop enhanced strategies for sustainable nitrogen or methane removal.
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Affiliation(s)
- Baoli Zhu
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Munich, Germany.,Department of Microbiology, Radboud University Nijmegen, Nijmegen, Netherlands.,Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Lauren M Bradford
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Munich, Germany
| | - Katharina Ettwig
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Munich, Germany.,Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
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40
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Guerrero-Cruz S, Stultiens K, van Kessel MAHJ, Versantvoort W, Jetten MSM, Op den Camp HJM, Kartal B. Key Physiology of a Nitrite-Dependent Methane-Oxidizing Enrichment Culture. Appl Environ Microbiol 2019; 85:e00124-19. [PMID: 30770408 PMCID: PMC6450021 DOI: 10.1128/aem.00124-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/11/2019] [Indexed: 11/20/2022] Open
Abstract
Nitrite-dependent methane-oxidizing bacteria couple the reduction of nitrite to the oxidation of methane via a unique oxygen-producing pathway. This process is carried out by members of the genus Methylomirabilis that belong to the NC10 phylum. Contrary to other known anaerobic methane oxidizers, they do not employ the reverse methanogenesis pathway for methane activation but instead a canonical particulate methane monooxygenase similar to those used by aerobic methanotrophs. Methylomirabilis-like bacteria are detected in many natural and manmade ecosystems, but their physiology is not well understood. Here, using continuous cultivation techniques, batch activity assays, and state-of-the-art membrane-inlet mass spectrometry, we determined growth rate, doubling time, and methane and nitrite affinities of the nitrite-dependent methane-oxidizing bacterium "Candidatus Methylomirabilis lanthanidiphila." Our results provide insight into understanding the interactions of these microorganisms with methanotrophs and other nitrite-reducing microorganisms, such as anaerobic ammonium-oxidizing bacteria. Furthermore, our data can be used in modeling studies as well as wastewater treatment plant design.IMPORTANCE Methane is an important greenhouse gas with a radiative forcing 28 times that of carbon dioxide over a 100-year time scale. The emission of methane to the atmosphere is controlled by aerobic and anaerobic methanotrophs, which are microorganisms that are able to oxidize methane to conserve energy. While aerobic methanotrophs have been studied for over a century, knowledge on the physiological characteristics of anaerobic methanotrophs is scarce. Here, we describe kinetic properties of "Candidatus Methylomirabilis lanthanidiphila," a nitrite-dependent methane-oxidizing microorganism, which is ecologically important and can be applied in wastewater treatment.
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Affiliation(s)
- Simon Guerrero-Cruz
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Karin Stultiens
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | | | - Wouter Versantvoort
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | | | - Boran Kartal
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
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41
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Shen L, Ouyang L, Zhu Y, Trimmer M. Spatial separation of anaerobic ammonium oxidation and nitrite‐dependent anaerobic methane oxidation in permeable riverbeds. Environ Microbiol 2019; 21:1185-1195. [DOI: 10.1111/1462-2920.14554] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/21/2019] [Accepted: 02/01/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Lidong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural MeteorologyDepartment of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology Nanjing 210044 China
- School of Biological & Chemical Sciences, Queen Mary University of London E1 4NS, London UK
| | - Liao Ouyang
- School of Biological & Chemical Sciences, Queen Mary University of London E1 4NS, London UK
| | - Yizhu Zhu
- School of Biological & Chemical Sciences, Queen Mary University of London E1 4NS, London UK
| | - Mark Trimmer
- School of Biological & Chemical Sciences, Queen Mary University of London E1 4NS, London UK
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42
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Wang J, Cai C, Li Y, Hua M, Wang J, Yang H, Zheng P, Hu B. Denitrifying Anaerobic Methane Oxidation: A Previously Overlooked Methane Sink in Intertidal Zone. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:203-212. [PMID: 30457852 DOI: 10.1021/acs.est.8b05742] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The intertidal zone is an open ecosystem rich in organic matter and plays an important role in global biogeochemical cycles. It was previously considered that methane was mainly removed by sulfate-dependent anaerobic methane oxidation (sulfate-AOM) process in marine ecosystems while other anaerobic methane oxidation processes were ignored. Recent researches have demonstrated that denitrifying anaerobic methane oxidation (DAMO), consisting of nitrite-dependent anaerobic methane oxidation (nitrite-AOM) and nitrate-dependent anaerobic methane oxidation (nitrate-AOM), can also oxidize methane. In this work, the community structure, quantity and potential methane oxidizing rate of DAMO archaea and bacteria in the intertidal zone were studied by high-throughput sequencing, qPCR and stable isotope tracing method. The results showed that nitrate-AOM and nitrite-AOM were both active in the intertidal zone and showed approximate methane oxidation rates. The copy number of 16S rRNA gene of DAMO archaea and DAMO bacteria were 104 ∼ 105 copies g-1 (dry sediment), whereas NC10 bacteria were slightly higher. The contribution rate of DAMO process to total anaerobic methane removal in the intertidal zone reached 65.6% ∼ 100%, which indicates that DAMO process is an important methane sink in intertidal ecosystem. Laboratory incubations also indicated that DAMO archaea were more sensitive to oxygen and preferred a more anoxic environment. These results help us draw a more complete picture of methane and nitrogen cycles in natural habitats.
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Affiliation(s)
- Jiaqi Wang
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Chaoyang Cai
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Yufen Li
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Miaolian Hua
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Junren Wang
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Hongrui Yang
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Ping Zheng
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Baolan Hu
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety , Hangzhou , China
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43
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Guerrero-Cruz S, Cremers G, van Alen TA, Op den Camp HJM, Jetten MSM, Rasigraf O, Vaksmaa A. Response of the Anaerobic Methanotroph " Candidatus Methanoperedens nitroreducens" to Oxygen Stress. Appl Environ Microbiol 2018; 84:e01832-18. [PMID: 30291120 PMCID: PMC6275348 DOI: 10.1128/aem.01832-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/01/2018] [Indexed: 11/20/2022] Open
Abstract
"Candidatus Methanoperedens nitroreducens" is an archaeon that couples the anaerobic oxidation of methane to nitrate reduction. In natural and man-made ecosystems, this archaeon is often found at oxic-anoxic interfaces where nitrate, the product of aerobic nitrification, cooccurs with methane produced by methanogens. As such, populations of "Ca Methanoperedens nitroreducens" could be prone to regular oxygen exposure. Here, we investigated the effect of 5% (vol/vol) oxygen exposure in batch activity assays on a "Ca Methanoperedens nitroreducens" culture, enriched from an Italian paddy field. Metagenome sequencing of the DNA extracted from the enrichment culture revealed that 83% of 16S rRNA gene reads were assigned to a novel strain, "Candidatus Methanoperedens nitroreducens Verserenetto." RNA was extracted, and metatranscriptome sequencing upon oxygen exposure revealed that the active community changed, most notably in the appearance of aerobic methanotrophs. The gene expression of "Ca Methanoperedens nitroreducens" revealed that the key genes encoding enzymes of the methane oxidation and nitrate reduction pathways were downregulated. In contrast to this, we identified upregulation of glutaredoxin, thioredoxin family/like proteins, rubrerythrins, peroxiredoxins, peroxidase, alkyl hydroperoxidase, type A flavoproteins, FeS cluster assembly protein, and cysteine desulfurases, indicating the genomic potential of "Ca Methanoperedens nitroreducens Verserenetto" to counteract the oxidative damage and adapt in environments where they might be exposed to regular oxygen intrusion.IMPORTANCE "Candidatus Methanoperedens nitroreducens" is an anaerobic archaeon which couples the reduction of nitrate to the oxidation of methane. This microorganism is present in a wide range of aquatic environments and man-made ecosystems, such as paddy fields and wastewater treatment systems. In such environments, these archaea may experience regular oxygen exposure. However, "Ca Methanoperedens nitroreducens" is able to thrive under such conditions and could be applied for the simultaneous removal of dissolved methane and nitrogenous pollutants in oxygen-limited systems. To understand what machinery "Ca Methanoperedens nitroreducens" possesses to counteract the oxidative stress and survive, we characterized the response to oxygen exposure using a multi-omics approach.
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Affiliation(s)
- Simon Guerrero-Cruz
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Geert Cremers
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Theo A van Alen
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
- Royal Netherlands Institute for Sea Research, Texel, the Netherlands
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44
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Wang B, Huang S, Zhang L, Zhao J, Liu G, Hua Y, Zhou W, Zhu D. Diversity of NC10 bacteria associated with sediments of submerged Potamogeton crispus (Alismatales: Potmogetonaceae). PeerJ 2018; 6:e6041. [PMID: 30533317 PMCID: PMC6284450 DOI: 10.7717/peerj.6041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/30/2018] [Indexed: 12/15/2022] Open
Abstract
Background The nitrite-dependent anaerobic methane oxidation (N-DAMO) pathway, which plays an important role in carbon and nitrogen cycling in aquatic ecosystems, is mediated by “Candidatus Methylomirabilis oxyfera” (M. oxyfera) of the NC10 phylum. M. oxyfera-like bacteria are widespread in nature, however, the presence, spatial heterogeneity and genetic diversity of M. oxyfera in the rhizosphere of aquatic plants has not been widely reported. Method In order to simulate the rhizosphere microenvironment of submerged plants, Potamogeton crispus was cultivated using the rhizobox approach. Sediments from three compartments of the rhizobox: root (R), near-rhizosphere (including five sub-compartments of one mm width, N1–N5) and non-rhizosphere (>5 mm, Non), were sampled. The 16S rRNA gene library was used to investigate the diversity of M. oxyfera-like bacteria in these sediments. Results Methylomirabilis oxyfera-like bacteria were found in all three sections, with all 16S rRNA gene sequences belonging to 16 operational taxonomic units (OTUs). A maximum of six OTUs was found in the N1 sub-compartment of the near-rhizosphere compartment and a minimum of four in the root compartment (R) and N5 near-rhizosphere sub-compartment. Indices of bacterial community diversity (Shannon) and richness (Chao1) were 0.73–1.16 and 4–9, respectively. Phylogenetic analysis showed that OTU1-11 were classified into group b, while OTU12 was in a new cluster of NC10. Discussion Our results confirmed the existence of M. oxyfera-like bacteria in the rhizosphere microenvironment of the submerged plant P. crispus. Group b of M. oxyfera-like bacteria was the dominant group in this study as opposed to previous findings that both group a and b coexist in most other environments. Our results indicate that understanding the ecophysiology of M. oxyfera-like bacteria group b may help to explain their existence in the rhizosphere sediment of aquatic plant.
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Affiliation(s)
- Binghan Wang
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Shanshan Huang
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Liangmao Zhang
- Laboratory of Environmental Planning and Management, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Jianwei Zhao
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Guanglong Liu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Yumei Hua
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Wenbing Zhou
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Duanwei Zhu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
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45
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Yang Y, Chen J, Li B, Liu Y, Xie S. Anaerobic methane oxidation potential and bacteria in freshwater lakes: Seasonal changes and the influence of trophic status. Syst Appl Microbiol 2018; 41:650-657. [DOI: 10.1016/j.syapm.2018.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 07/15/2018] [Accepted: 08/02/2018] [Indexed: 11/30/2022]
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46
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Martinez-Cruz K, Sepulveda-Jauregui A, Casper P, Anthony KW, Smemo KA, Thalasso F. Ubiquitous and significant anaerobic oxidation of methane in freshwater lake sediments. WATER RESEARCH 2018; 144:332-340. [PMID: 30053624 DOI: 10.1016/j.watres.2018.07.053] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 06/08/2023]
Abstract
Anaerobic oxidation of methane (AOM) is a microbial process that consumes dissolved methane (CH4) in anoxic sediments and soils and mitigates CH4 release to the atmosphere. The degree to which AOM limits global biospheric CH4 emissions is not fully understood. In marine sediments, where the process was first described, AOM is responsible for oxidizing >90% of the CH4 produced. More recently, AOM has been observed in soils, peatlands, and freshwater ecosystems. In lakes, where sediment anoxia, organic carbon turnover, and CH4 production are common, AOM is not well studied but could represent a significant CH4 sink and constraint on emissions. Here, we present evidence for the occurrence of AOM in the sediment of thirteen lakes that span a global climatic and trophic gradient. We further quantified and modeled AOM patterns and studied potential microbial controls of AOM using laboratory incubations of sediment and stable isotope measurements in three of the thirteen lakes. We demonstrate that AOM is widespread in freshwater lake sediments and accounts for 29%-34% (95% confidence interval) of the mean total CH4 produced in surface and near-surface lake sediments.
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Affiliation(s)
- Karla Martinez-Cruz
- Cinvestav, Department of Biotechnology and Bioengineering, 2508 IPN Ave., San Pedro Zacatenco, 07360, Mexico City, Mexico; Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775, Stechlin, Germany; University of Magallanes, Department of Science and Natural Resources, 01890, Manuel Bulnes Ave., Punta Arenas, Chile
| | - Armando Sepulveda-Jauregui
- Cinvestav, Department of Biotechnology and Bioengineering, 2508 IPN Ave., San Pedro Zacatenco, 07360, Mexico City, Mexico; University of Alaska Fairbanks, Water and Environmental Research Center, 1760 Tanana Loop, Fairbanks, 99775, Alaska, USA
| | - Peter Casper
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775, Stechlin, Germany
| | - Katey Walter Anthony
- University of Alaska Fairbanks, Water and Environmental Research Center, 1760 Tanana Loop, Fairbanks, 99775, Alaska, USA
| | - Kurt A Smemo
- Skidmore College, Environmental Studies and Sciences Program, 815 N. Broadway, Saratoga Springs, 12866, New York, USA
| | - Frederic Thalasso
- Cinvestav, Department of Biotechnology and Bioengineering, 2508 IPN Ave., San Pedro Zacatenco, 07360, Mexico City, Mexico; University of Alaska Fairbanks, Water and Environmental Research Center, 1760 Tanana Loop, Fairbanks, 99775, Alaska, USA.
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47
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Jiang L, Hu Z, Wang Y, Ru D, Li J, Fan J. Effect of trace elements on the development of co-cultured nitrite-dependent anaerobic methane oxidation and methanogenic bacteria consortium. BIORESOURCE TECHNOLOGY 2018; 268:190-196. [PMID: 30077879 DOI: 10.1016/j.biortech.2018.07.139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 06/08/2023]
Abstract
The aim of this work was to study the effects of key trace elements (i.e., iron, copper and molybdenum) on the development of co-cultured n-damo and methanogenic bacteria consortium, which could realize in situ CH4 production and utilization. The results showed that rational dosage, which was 50 mg/L of Fe, 1 mg/L of Cu and 5 mg/L of Mo, significantly stimulated the removal of NO2-. However, the activity of microbes was noticeably inhibited at 5 mg/L of Cu and 1 mg/L of Mo. Microbial community analysis indicated that the abundances of n-damo bacteria and methanogens showed a positive response to the rational dosage. Furthermore, the expression of key functional genes was enhanced under the rational dosage condition.
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Affiliation(s)
- Liping Jiang
- School of Environmental Science and Engineering, Shandong University, Jinan, Shandong, China
| | - Zhen Hu
- School of Environmental Science and Engineering, Shandong University, Jinan, Shandong, China.
| | - Yinan Wang
- School of Environmental Science and Engineering, Shandong University, Jinan, Shandong, China
| | - Dongyun Ru
- School of Environmental Science and Engineering, Shandong University, Jinan, Shandong, China
| | - Jianwei Li
- School of Environmental Science and Engineering, Shandong University, Jinan, Shandong, China
| | - Jinlin Fan
- National Engineering Laboratory of Coal-Fired Pollutants Emission Reduction, Shandong University, Jinan, Shandong, China
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48
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Shen LD, Ouyang L, Zhu Y, Trimmer M. Active pathways of anaerobic methane oxidation across contrasting riverbeds. ISME JOURNAL 2018; 13:752-766. [PMID: 30375505 PMCID: PMC6461903 DOI: 10.1038/s41396-018-0302-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/19/2018] [Accepted: 09/30/2018] [Indexed: 12/26/2022]
Abstract
Anaerobic oxidation of methane (AOM) reduces methane emissions from marine ecosystems but we know little about AOM in rivers, whose role in the global carbon cycle is increasingly recognized. We measured AOM potentials driven by different electron acceptors, including nitrite, nitrate, sulfate, and ferric iron, and identified microorganisms involved across contrasting riverbeds. AOM activity was confined to the more reduced, sandy riverbeds, whereas no activity was measured in the less reduced, gravel riverbeds where there were few anaerobic methanotrophs. Nitrite-dependent and nitrate-dependent AOM occurred in all sandy riverbeds, with the maximum rates of 61.0 and 20.0 nmol CO2 g−1 (dry sediment) d−1, respectively, while sulfate-dependent and ferric iron-dependent AOM occurred only where methane concentration was highest and the diversity of AOM pathways greatest. Diverse Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria and Candidatus Methanoperedens nitroreducens (M. nitroreducens)-like archaea were detected in the sandy riverbeds (16S rRNA gene abundance of 9.3 × 105 to 1.5 × 107 and 2.1 × 104 to 2.5 × 105 copies g−1 dry sediment, respectively) but no other known anaerobic methanotrophs. Further, we found M. oxyfera-like bacteria and M. nitroreducens-like archaea to be actively involved in nitrite- and nitrate/ferric iron-dependent AOM, respectively. Hence, we demonstrate multiple pathways of AOM in relation to methane, though the activities of M. oxyfera-like bacteria and M. nitroreducens-like archaea are dominant.
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Affiliation(s)
- Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.,School of Biological & Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Liao Ouyang
- School of Biological & Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Yizhu Zhu
- School of Biological & Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Mark Trimmer
- School of Biological & Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
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49
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Montag D, Schink B. Formate and Hydrogen as Electron Shuttles in Terminal Fermentations in an Oligotrophic Freshwater Lake Sediment. Appl Environ Microbiol 2018; 84:e01572-18. [PMID: 30097443 PMCID: PMC6182907 DOI: 10.1128/aem.01572-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/03/2018] [Indexed: 11/20/2022] Open
Abstract
The energetic situation of terminal fermentations in methanogenesis was analyzed by pool size determinations in sediment cores taken in the oligotrophic Lake Constance, Germany. Distribution profiles of fermentation intermediates and products were measured at three different water depths (2, 10, and 80 m). Methane concentrations were constant below 10 cm of sediment depth. Within the methanogenic zone, concentrations of formate, acetate, propionate, and butyrate varied between 1 and 40 μM, and hydrogen was between 0.5 and 5 Pa. From the distribution profiles of the fermentation intermediates, Gibbs free energy changes for their interconversion were calculated. Pool sizes of formate and hydrogen were energetically nearly equivalent, with -5 ± 5 kJ per mol difference of free energy change (ΔG) for a hypothetical conversion of formate to hydrogen plus CO2 The ΔG values for conversion of fatty acids to methanogenic substrates and their further conversion to methane and CO2 were calculated with hydrogen and with formate as intermediates. Syntrophic propionate oxidation reached energetic equilibrium with formate as the sole electron carrier but was sufficiently exergonic if at least some of the electrons were transferred via hydrogen. The energetic consequences of formate versus hydrogen transfer in secondary and methanogenic fermentations indicate that both carrier systems are probably used simultaneously to optimize the energy yields for the partners involved.IMPORTANCE In the terminal steps of methane formation in freshwater lake sediments, fermenting bacteria cooperate syntrophically with methanogens and homoacetogens at minimum energy increments via interspecies electron transfer. The energy yields of the partner organisms in these cooperations have so far been calculated based mainly on in situ hydrogen partial pressures. In the present study, we also analyzed pools of formate as an alternative electron carrier in sediment cores of an oligotrophic lake. The formate and hydrogen pools appeared to be energetically nearly equivalent and are likely to be used simultaneously for interspecies electron transfer. Calculations of reaction energies of the partners involved suggest that propionate degradation may also proceed through the Smithella pathway, which converts propionate via butyrate and acetate to three acetate residues, thus circumventing one energetically difficult fatty acid oxidation step.
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Affiliation(s)
- Dominik Montag
- Department of Biology, University of Konstanz, Constance, Germany
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Constance, Germany
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Graf JS, Mayr MJ, Marchant HK, Tienken D, Hach PF, Brand A, Schubert CJ, Kuypers MMM, Milucka J. Bloom of a denitrifying methanotroph, 'Candidatus Methylomirabilis limnetica', in a deep stratified lake. Environ Microbiol 2018; 20:2598-2614. [PMID: 29806730 DOI: 10.1111/1462-2920.14285] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 12/17/2022]
Abstract
Methanotrophic bacteria represent an important biological filter regulating methane emissions into the atmosphere. Planktonic methanotrophic communities in freshwater lakes are typically dominated by aerobic gamma-proteobacteria, with a contribution from alpha-proteobacterial methanotrophs and the NC10 bacteria. The NC10 clade encompasses methanotrophs related to 'Candidatus Methylomirabilis oxyfera', which oxidize methane using a unique pathway of denitrification that tentatively produces N2 and O2 from nitric oxide (NO). Here, we describe a new species of the NC10 clade, 'Ca. Methylomirabilis limnetica', which dominated the planktonic microbial community in the anoxic depths of the deep stratified Lake Zug in two consecutive years, comprising up to 27% of the total bacterial population. Gene transcripts assigned to 'Ca. M. limnetica' constituted up to one third of all metatranscriptomic sequences in situ. The reconstructed genome encoded a complete pathway for methane oxidation, and an incomplete denitrification pathway, including two putative nitric oxide dismutase genes. The genome of 'Ca. M. limnetica' exhibited features possibly related to genome streamlining (i.e. less redundancy of key metabolic genes) and adaptation to its planktonic habitat (i.e. gas vesicle genes). We speculate that 'Ca. M. limnetica' temporarily bloomed in the lake during non-steady-state conditions suggesting a niche for NC10 bacteria in the lacustrine methane and nitrogen cycle.
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Affiliation(s)
- Jon S Graf
- Max-Planck-Institute for Marine Microbiology, Department of Biogeochemistry, Bremen, Germany
| | - Magdalena J Mayr
- Eawag, Surface Waters-Research and Management, Kastanienbaum, Switzerland.,ETH Zurich, Institute of Biogeochemistry and Pollutant Dynamics, Zürich, Switzerland
| | - Hannah K Marchant
- Max-Planck-Institute for Marine Microbiology, Department of Biogeochemistry, Bremen, Germany
| | - Daniela Tienken
- Max-Planck-Institute for Marine Microbiology, Department of Biogeochemistry, Bremen, Germany
| | - Philipp F Hach
- Max-Planck-Institute for Marine Microbiology, Department of Biogeochemistry, Bremen, Germany
| | - Andreas Brand
- Eawag, Surface Waters-Research and Management, Kastanienbaum, Switzerland.,ETH Zurich, Institute of Biogeochemistry and Pollutant Dynamics, Zürich, Switzerland
| | - Carsten J Schubert
- Eawag, Surface Waters-Research and Management, Kastanienbaum, Switzerland
| | - Marcel M M Kuypers
- Max-Planck-Institute for Marine Microbiology, Department of Biogeochemistry, Bremen, Germany
| | - Jana Milucka
- Max-Planck-Institute for Marine Microbiology, Department of Biogeochemistry, Bremen, Germany
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