1
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He T, Yin Q, Li X. Effects of Antibiotics on the DAMO Process and Microbes in Cattle Manure. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:3883-3894. [PMID: 38347804 DOI: 10.1021/acs.est.3c07135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Denitrifying anaerobic methane oxidation (DAMO) can mitigate methane emissions; however, this process has not been studied in cattle manure, an important source of methane emissions in animal agriculture. The objective of this study was to investigate the occurrence of DAMO microbes in cattle manure and examine the impacts of veterinary antibiotics on the DAMO process in cattle manure. Results show that DAMO archaea and bacteria consistently occur at high concentrations in beef cattle manure. During the long-term operation of a sequencing batch reactor seeded with beef cattle manure, the DAMO activities intensified, and DAMO microbial biomass increased. Exposure to chlortetracycline at initial concentrations up to 5000 μg L-1 did not inhibit DAMO activities or affect the concentrations of the 16S rRNA gene and functional genes of DAMO microbes. In contrast, exposure to tylosin at initial concentrations of 50 and 500 μg L-1 increased the activities of the DAMO microbes. An initial concentration of 5000 μg L-1 TYL almost entirely halted DAMO activities and reduced the concentrations of DAMO microbes. These results show the occurrence of DAMO microbes in cattle manure and reveal that elevated concentrations of dissolved antibiotics could inhibit the DAMO process, potentially affecting net methane emissions from cattle manure.
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Affiliation(s)
- Ting He
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
- Institute of Chemistry, Henan Academy of Sciences, Zheng Zhou 450002, Henan, P. R. China
| | - Qidong Yin
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Xu Li
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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2
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Li K, Wang Z, Xiang Q, Zhao X, Ji L, Xin Y, Sun J, Liu C, Shen X, Xu X, Chen Q. Coupling of soil methane emissions at different depths under typical coastal wetland vegetation types. CHEMOSPHERE 2023; 338:139505. [PMID: 37454988 DOI: 10.1016/j.chemosphere.2023.139505] [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: 04/30/2023] [Revised: 07/02/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
As an important source of atmospheric methane, methane emissions from coastal wetlands are affected by many factors. However, the methane emission process and interrelated coupling mechanisms in coastal wetland soils of a variety of environments remain unclear owing to complex interactions between intensified anthropogenic activities and climate change in recent years. In this study, we investigated methane cycling processes and the response mechanisms of environmental and microbial factors in soils at different depths under four typical coastal wetland vegetation types of the Yellow River Delta, China, using laboratory culture and molecular biology techniques. Our results show that methane generation pathways differed among the different soil layers, and that the methane emission process has a special response to soil N compounds (NO3-, NH4+). We found that nitrogen can indirectly affect methane emission by impacting key physicochemical properties (pH, oxidation reduction potential, etc.) and some functional communities (mcrA, ANME-2d, sulfate-reducing bacteria (SRB), narG, nosZII). Methane production processes in shallow soils compete closely with sulfate reduction processes, while methane emissions facilitated in deeper soils due to denitrification processes. We believe that our results provide a reference for future research and wetland management practices that seek to mitigate the global greenhouse effect and climate change.
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Affiliation(s)
- Kun Li
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Zihao Wang
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266100, PR China
| | - Qingyue Xiang
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Xinkun Zhao
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Linhui Ji
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Yu Xin
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Jingyu Sun
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Chenmiao Liu
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Xiaoyan Shen
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Xiaoya Xu
- 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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3
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Wang Z, Li K, Shen X, Yan F, Zhao X, Xin Y, Ji L, Xiang Q, Xu X, Li D, Ran J, Xu X, Chen Q. Soil nitrogen substances and denitrifying communities regulate the anaerobic oxidation of methane in wetlands of Yellow River Delta, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159439. [PMID: 36252671 DOI: 10.1016/j.scitotenv.2022.159439] [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: 07/25/2022] [Revised: 09/23/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Anaerobic oxidation of methane (AOM) in wetland soils is widely recognized as a key sink for the greenhouse gas methane (CH4). The occurrence of this reaction is influenced by several factors, but the exact process and related mechanism of this reaction remain unclear, due to the complex interactions between multiple influencing factors in nature. Therefore, we investigated how environmental and microbial factors affect AOM in wetlands using laboratory incubation methods combined with molecular biology techniques. The results showed that wetland AOM was associated with a variety of environmental factors and microbial factors. The environmental factors include such as vegetation, depth, hydrogen ion concentration (pH), oxidation-reduction potential (ORP), electrical conductivity (EC), total nitrogen (TN), nitrate (NO3-), sulfate (SO42-), and nitrous oxide (N2O) flux, among them, soil N substances (TN, NO3-, N2O) have essential regulatory roles in the AOM process, while NO3- and N2O may be the key electron acceptors driving the AOM process under the coexistence of multiple electron acceptors. Moreover, denitrification communities (narG, nirS, nirK, nosZI, nosZII) and anaerobic methanotrophic (ANME-2d) were identified as important functional microorganisms affecting the AOM process, which is largely regulated by the former. In the environmental context of growing global anthropogenic N inputs to wetlands, these findings imply that N cycle-mediated AOM processes are a more important CH4 sink for controlling global climate change. This studying contributes to the knowledge and prediction of wetland CH4 biogeochemical cycling and provides a microbial ecology viewpoint on the AOM response to global environmental change.
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Affiliation(s)
- Zihao Wang
- 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
| | - Xiaoyan Shen
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Feifei Yan
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, PR China
| | - Xinkun Zhao
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Yu Xin
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Linhui Ji
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Qingyue Xiang
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Xinyi Xu
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Daijia Li
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Junhao Ran
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Xiaoya Xu
- 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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4
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Wang J, Yao X, Jia Z, Zhu L, Zheng P, Kartal B, Hu B. Nitrogen input promotes denitrifying methanotrophs' abundance and contribution to methane emission reduction in coastal wetland and paddy soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 302:119090. [PMID: 35240269 DOI: 10.1016/j.envpol.2022.119090] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/11/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Denitrifying anaerobic methane oxidation (DAMO) microorganisms, using nitrate/nitrite to oxidize methane, have been proved to be an important microbial methane sink in natural habitats. Increasing nitrogen deposit around the globe brings increased availability of substrates for these microorganisms. However, how elevated nitrogen level affects denitrifying methanotrophs has not been elucidated. In this study, sediment/soil samples from coastal wetland with continuous nitrogen input and paddy field with periodic nitrogen input were collected to investigate the influence of nitrogen input on the abundance and activity of denitrifying methanotrophs. The results indicated that nitrogen input significantly promoted DAMO microorganisms' abundance and contribution to methane emission reduction. In the coastal wetland, the contribution rate of DAMO process to methane removal increased from 12.1% to 33.5% along with continuously elevated nitrogen level in the 3-year tracking study. In the paddy field, the DAMO process accounted for 71.9% of total methane removal when nitrogen fertilizer was applied during the growing season, exceeding the aerobic methane oxidation process. This work would help us better understand the microbial methane cycle and reduce uncertainties in the estimations of the global methane emission.
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Affiliation(s)
- Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, 310058, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Boran Kartal
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, 310058, China.
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Wang X, Xie GJ, Tian N, Dang CC, Cai C, Ding J, Liu BF, Xing DF, Ren NQ, Wang Q. Anaerobic microbial manganese oxidation and reduction: A critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153513. [PMID: 35101498 DOI: 10.1016/j.scitotenv.2022.153513] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Manganese is a vital heavy metal abundant in terrestrial and aquatic environments. Anaerobic manganese redox reactions mediated by microorganisms have been recognized for a long time, which promote elements mobility and bioavailability in the environment. Biological anaerobic redox of manganese serves two reactions, including Mn(II) oxidation and Mn(IV) reduction. This review provides a comprehensive analysis of manganese redox cycles in the environment, closely related to greenhouse gas mitigation, the fate of nutrients, microbial bioremediation, and global biogeochemical cycle, including nitrogen, sulfur, and carbon. The oxidation and reduction of manganese occur cyclically and simultaneously in the environment. Anaerobic reduction of Mn(IV) receives electrons from methane, ammonium and sulfide, while Mn(II) can function as an electron source for manganese-oxidizing microorganisms for autotrophic denitrification and photosynthesis. The anaerobic redox transition between Mn(II) and Mn(IV) promotes a dynamic biogeochemical cycle coupled to microorganisms in water, soil and sediment environments. The discussion of reaction mechanisms, microorganism diversity, environmental influence bioremediation and application identify the research gaps for future investigation, which provides promising opportunities for further development of biotechnological applications to remediate contaminated environments.
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Affiliation(s)
- Xuan Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Ning Tian
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Cheng-Cheng Dang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Chen Cai
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qilin Wang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
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6
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He B, Cai C, McCubbin T, Muriel JC, Sonnenschein N, Hu S, Yuan Z, Marcellin E. A Genome-Scale Metabolic Model of Methanoperedens nitroreducens: Assessing Bioenergetics and Thermodynamic Feasibility. Metabolites 2022; 12:metabo12040314. [PMID: 35448501 PMCID: PMC9024614 DOI: 10.3390/metabo12040314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/18/2022] [Accepted: 03/26/2022] [Indexed: 11/16/2022] Open
Abstract
Methane is an abundant low-carbon fuel that provides a valuable energy resource, but it is also a potent greenhouse gas. Therefore, anaerobic oxidation of methane (AOM) is an essential process with central features in controlling the carbon cycle. Candidatus ‘Methanoperedens nitroreducens’ (M. nitroreducens) is a recently discovered methanotrophic archaeon capable of performing AOM via a reverse methanogenesis pathway utilizing nitrate as the terminal electron acceptor. Recently, reverse methanogenic pathways and energy metabolism among anaerobic methane-oxidizing archaea (ANME) have gained significant interest. However, the energetics and the mechanism for electron transport in nitrate-dependent AOM performed by M. nitroreducens is unclear. This paper presents a genome-scale metabolic model of M. nitroreducens, iMN22HE, which contains 813 reactions and 684 metabolites. The model describes its cellular metabolism and can quantitatively predict its growth phenotypes. The essentiality of the cytoplasmic heterodisulfide reductase HdrABC in the reverse methanogenesis pathway is examined by modeling the electron transfer direction and the specific energy-coupling mechanism. Furthermore, based on better understanding electron transport by modeling, a new energy transfer mechanism is suggested. The new mechanism involves reactions capable of driving the endergonic reactions in nitrate-dependent AOM, including the step reactions in reverse canonical methanogenesis and the novel electron-confurcating reaction HdrABC. The genome metabolic model not only provides an in silico tool for understanding the fundamental metabolism of ANME but also helps to better understand the reverse methanogenesis energetics and its thermodynamic feasibility.
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Affiliation(s)
- Bingqing He
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia; (B.H.); (T.M.)
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, Brisbane, QLD 4072, Australia; (C.C.); (S.H.); (Z.Y.)
| | - Chen Cai
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, Brisbane, QLD 4072, Australia; (C.C.); (S.H.); (Z.Y.)
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia; (B.H.); (T.M.)
| | - Jorge Carrasco Muriel
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (J.C.M.); (N.S.)
| | - Nikolaus Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (J.C.M.); (N.S.)
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, Brisbane, QLD 4072, Australia; (C.C.); (S.H.); (Z.Y.)
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, Brisbane, QLD 4072, Australia; (C.C.); (S.H.); (Z.Y.)
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia; (B.H.); (T.M.)
- Correspondence:
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7
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Ding J, Zeng RJ. Fundamentals and potential environmental significance of denitrifying anaerobic methane oxidizing archaea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143928. [PMID: 33316511 DOI: 10.1016/j.scitotenv.2020.143928] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/01/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
Many properties of denitrifying anaerobic methane oxidation (DAMO) bacteria have been explored since their first discovery, while DAMO archaea have attracted less attention. Since nitrate is more abundant than nitrite not only in wastewater but also in the natural environment, in depth investigations of the nitrate-DAMO process should be conducted to determine its environmental significance in the global carbon and nitrogen cycles. This review summarizes the status of research on DAMO archaea and the catalyzed nitrate-dependent anaerobic methane oxidation, including such aspects as laboratory enrichment, environmental distribution, and metabolic mechanism. It is shown that appropriate inocula and enrichment parameters are important for the culture enrichment and thus the subsequent DAMO activity, but there are still relatively few studies on the environmental distribution and physiological metabolism of DAMO archaea. Finally, some hypotheses and directions for future research on DAMO archaea, anaerobic methanotrophic archaea, and even anaerobically metabolizing archaea are also discussed.
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Affiliation(s)
- Jing Ding
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, Jiangsu 215009, China; Jiangsu Provincial Key Laboratory of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, Jiangsu 215009, China
| | - Raymond Jianxiong Zeng
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; CAS Key Laboratory for Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, China.
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8
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Xie F, Ma A, Zhou H, Liang Y, Yin J, Ma K, Zhuang X, Zhuang G. Niche differentiation of denitrifying anaerobic methane oxidizing bacteria and archaea leads to effective methane filtration in a Tibetan alpine wetland. ENVIRONMENT INTERNATIONAL 2020; 140:105764. [PMID: 32371309 DOI: 10.1016/j.envint.2020.105764] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
Denitrifying anaerobic methane oxidation (DAMO) is a vital methane sink in wetlands. However, the interactions and niche partitioning of DAMO bacteria and archaea in freshwater wetland soils, in addition to the interactions among microorganisms that couple methane and nitrogen cycling is still unclear, despite that these factors may govern the fate of methane and nitrogen in wetlands. Here, we evaluated the vertical distribution of DAMO bacteria and archaea in soil layers along with the potential interactions among populations in the methane-coupled nitrogen cycling microbial community of Tibetan freshwater wetlands. A combination of molecular biology, stable isotope tracer technology, and microbial bioinformatics was used to evaluate these interrelated dynamics. The abundances and potential methane oxidation rates indicated that DAMO bacteria and archaea differentially occupy surface and subsurface soil layers, respectively. The inferred interactions between DAMO bacteria and nitrogen cycling microorganisms within their communities are complex, DAMO bacteria apparently achieve an advantage in the highly competitive environment of surface soils layers and occupy a specific niche in those environments. Conversely, the apparent relationships between DAMO archaea and nitrogen cycling microorganisms are relatively simple, wherein high levels of cooperation are inferred between DAMO archaea and nitrate-producing organisms in subsurface soils layers. These results suggest that the vertical distribution patterns of DAMO bacteria and archaea enable them to play significant roles in the methane oxidation activity of different soil layers and collectively form an effective methane filtration consortium.
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Affiliation(s)
- Fei Xie
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Anzhou Ma
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China.
| | - Hanchang Zhou
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yu Liang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jun Yin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Ke Ma
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China; Sino-Danish College of University of Chinese Academy of Sciences, 101400 Beijing, China
| | - Xuliang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Guoqiang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China.
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9
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Nie WB, Xie GJ, Ding J, Peng L, Lu Y, Tan X, Yue H, Liu BF, Xing DF, Meng J, Han HJ, Ren NQ. Operation strategies of n-DAMO and Anammox process based on microbial interactions for high rate nitrogen removal from landfill leachate. ENVIRONMENT INTERNATIONAL 2020; 139:105596. [PMID: 32259754 DOI: 10.1016/j.envint.2020.105596] [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: 11/26/2019] [Revised: 02/09/2020] [Accepted: 02/18/2020] [Indexed: 06/11/2023]
Abstract
Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) coupling to Anaerobic ammonium oxidation (Anammox) provides an opportunity for simultaneous nitrogen removal and methane emissions mitigation from wastewater. However, to achieve high nitrogen removal rate in such a process remains a critical challenge in practical application. This work investigated the interactions between n-DAMO and Anammox in membrane biofilm reactor (MBfR) and then developed operational strategies of MBfR for high rate nitrogen removal from landfill leachate. Initially, influent containing nitrate and ammonium facilitated the development of n-DAMO and Anammox microorganisms in MBfR, but nitrogen removal performance is hard to be further improved even deteriorated. Detailed investigations of interactions among n-DAMO and Anammox microorganisms confirmed that extra addition of nitrite into MBfR fed with nitrate and ammonium not only stimulated the activities of Anammox bacteria, but also enhanced the activities of n-DAMO archaea from 172.3 to 356.9 mg NO3--N L-1 d-1. Functional gene analysis also indicated that mcrA and hzsA genes increased after nitrite addition. Based on this finding, influent containing NO3-, NO2- and NH4+ enabled nitrogen removal rates of MBfR increase from 224.9 to 888.2 mg N L-1 d-1. Finally, nitrate in the influent was gradually replaced with nitrite to mimic the effluent from partial nitriation of landfill leachate, but maintain the nitrate availability for n-DAMO archaea through increasing nitrate production from Anammox. These operation strategies enabled MBfR achieve the steady state with a nitrogen removal rate of 6.1 kg N m-3 d-1. Microbial community analysis revealed n-DAMO archaea, n-DAMO bacteria and Anammox bacteria jointly dominated the biofilm, and their relative abundance dynamically shifted with feeding regime. This work provides promising operational strategies for high rate of nitrogen removal from landfill leachate through integrating n-DAMO and Anammox process.
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Affiliation(s)
- Wen-Bo Nie
- 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.
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Lai Peng
- School of Resources and Environmental Engineering, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Yang Lu
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore
| | - Xin Tan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Hao Yue
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - 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
| | - Jia Meng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China; Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - 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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10
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Lu P, Wang X, Tang Y, Ding A, Yang H, Guo J, Cui Y, Ling C. Granular activated carbon assisted nitrate-dependent anaerobic methane oxidation-membrane bioreactor: Strengthening effect and mechanisms. ENVIRONMENT INTERNATIONAL 2020; 138:105675. [PMID: 32213427 DOI: 10.1016/j.envint.2020.105675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/17/2020] [Accepted: 03/17/2020] [Indexed: 06/10/2023]
Abstract
Eutrophication and global warming are two main urgent environmental problems around the world. Nitrate-dependent Anaerobic Methane Oxidation (NdAMO) is a bioprocess coupling nitrate reduction with anaerobic methane oxidation, which could mitigate of these two environmental issues simultaneously. In this study, a newly granular active carbon-NdAMO-membrane bioreactor (GAC-NdAMO-MBR) system was established to evaluate its nitrogen removal efficiency, membrane fouling property and the probable strengthening mechanism was also uncovered. Results indicated that the nitrate removal rate in GAC-NdAMO-MBR reached 31.85 ± 3.19 mgN·L-1·d-1 while it was only 10.35 ± 2.02 mgN·L-1·d-1 in NdAMO-MBR system (lack of GAC), which was multiplied three-fold. The membrane flux decay rate of GAC- NdAMO -MBR was 0.15 L/m2·h·d while it was 0.49 L/m2·h·d without GAC, and the addition of GAC could extend membrane fouling time for 2.5 times. Notablely, the relative abundance of NdAMO bacteria sharply increased from 27.15% to 56.91% after GAC addition while the NdAMO archaea showed similar variation trend. The physicochemical property of GAC mainly contributed the strengthening effect. The porous structure of GAC absorbed methane and adhered by microorganism, which enhance microorganism amount and metabolic activity. The mechanical strength of GAC scoured membrane surface to mitigate external fouling and pores absorbed EPS to reduce internal fouling. The combined effects could improve NdAMO microorganism growth and metabolism activity and finally improved nitrogen removal performance and controlled membrane fouling. These findings could deep the knowledge of NdAMO process and help extend its application potential in environment science and engineering.
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Affiliation(s)
- Peili Lu
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Xuewen Wang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Yingshuang Tang
- Ecology and Environment Bureau of Bishan, Chongqing 400044, China
| | - Aqiang Ding
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing 400044, China.
| | - Han Yang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Junliang Guo
- Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Ying Cui
- Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Chuanxiang Ling
- Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing 400044, China
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11
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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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12
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Bai YN, Wang XN, Wu J, Lu YZ, Fu L, Zhang F, Lau TC, Zeng RJ. Humic substances as electron acceptors for anaerobic oxidation of methane driven by ANME-2d. WATER RESEARCH 2019; 164:114935. [PMID: 31387057 DOI: 10.1016/j.watres.2019.114935] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Humic substances (humics) are ubiquitous in terrestrial and aquatic environments where they can serve as electron acceptors for anaerobic oxidation of organic compounds. Methane is a powerful greenhouse gas, as well as the least reactive organic molecule. Anaerobic oxidation of methane (AOM) coupled to microbial reduction of various electron acceptors plays a crucial role in mitigating methane emissions. Here, we reported that humics could serve as terminal electron acceptors for AOM using enriched nitrate-reducing AOM microorganisms. AOM coupled to the reduction of humics was demonstrated based on the production of 13C-labelled carbon dioxide, and AOM activity was evaluated with different methane partial pressures and electron acceptor concentrations. After three-cycle reduction, both AOM activity and copy numbers of the archaea 16S rRNA and mcrA genes were the highest when anthraquinone-2,6-disulfonic acid and anthraquinone-2-sulfonic acid were electron acceptors. The high-throughput sequencing results suggested that ANME-2d were the dominant methane oxidation archaea after humics reduction, although the partner bacteria NC10 trended downward, other reported humics reduction bacteria (Geobactor and Anammox) appeared. The potential electron transfer models from ANME-2d to humics were proposed. These results enable a better understanding of available electron acceptors for AOM in natural environments and broaden our insight into the significant role of ANME-2d.
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Affiliation(s)
- Ya-Nan Bai
- Advanced Laboratory for Environmental Research and Technology, USTC-CityU, Suzhou, PR China; School of Life Sciences, University of Science and Technology of China, Hefei, 230026, PR China
| | - Xiu-Ning Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, PR China
| | - Jun Wu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, PR China
| | - Yong-Ze Lu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, PR China
| | - Liang Fu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, PR China
| | - Fang Zhang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
| | - Tai-Chu Lau
- Advanced Laboratory for Environmental Research and Technology, USTC-CityU, Suzhou, PR China; State Key Laboratory in Marine Pollution, Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | - Raymond J Zeng
- Advanced Laboratory for Environmental Research and Technology, USTC-CityU, Suzhou, PR China; School of Life Sciences, University of Science and Technology of China, Hefei, 230026, PR China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
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13
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Spatial-Temporal Pattern of Sulfate-Dependent Anaerobic Methane Oxidation in an Intertidal Zone of the East China Sea. Appl Environ Microbiol 2019; 85:AEM.02638-18. [PMID: 30709818 DOI: 10.1128/aem.02638-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/19/2019] [Indexed: 11/20/2022] Open
Abstract
Methane is a primary greenhouse gas which is responsible for global warming. The sulfate-dependent anaerobic methane oxidation (S-AOM) process catalyzed by anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB) is a vital link connecting the global carbon and sulfur cycles, and it is considered to be the overriding methane sink in marine ecosystem. However, there have been few studies regarding the role of S-AOM process and the distribution of ANME archaea in intertidal ecosystem. The intertidal zone is a buffer zone between sea and land and plays an important role in global geochemical cycle. In the present study, the abundance, potential methane oxidation rate, and community structure of ANME archaea in the intertidal zone were studied by quantitative PCR, stable isotope tracing method and high-throughput sequencing. The results showed that the potential S-AOM activity ranged from 0 to 0.77 nmol 13CO2 g-1 (dry sediment) day-1 The copy number of 16S rRNA gene of ANME archaea reached 106 ∼ 107 copies g-1 (dry sediment). The average contribution of S-AOM to total anaerobic methane oxidation was up to 34.5%, while denitrifying anaerobic methane oxidation accounted for the rest, which implied that S-AOM process was an essential methane sink that cannot be overlooked in intertidal ecosystem. The simulated column experiments also indicated that ANME archaea were sensitive to oxygen and preferred anaerobic environmental conditions. This study will help us gain a better understanding of the global carbon-sulfur cycle and greenhouse gas emission reduction and introduce a new perspective into the enrichment of ANME archaea.IMPORTANCE The sulfate-dependent anaerobic methane oxidation (S-AOM) process catalyzed by anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB) is a vital link connecting the global carbon and sulfur cycles. We conducted a research into the spatial-temporal pattern of S-AOM process and the distribution of ANME archaea in coastal sediments collected from the intertidal zone. The results implied that S-AOM process was a methane sink that cannot be overlooked in the intertidal ecosystem. We also found that ANME archaea were sensitive to oxygen and preferred anaerobic environmental conditions. This study will help us gain a better understanding of the global carbon-sulfur cycle and greenhouse gas emission reduction and introduce a new perspective into the enrichment of ANME archaea.
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14
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Fu L, Bai YN, Lu YZ, Ding J, Zhou D, Zeng RJ. Degradation of organic pollutants by anaerobic methane-oxidizing microorganisms using methyl orange as example. JOURNAL OF HAZARDOUS MATERIALS 2019; 364:264-271. [PMID: 30384235 DOI: 10.1016/j.jhazmat.2018.10.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 06/08/2023]
Abstract
Anaerobic oxidation of methane (AOM) microorganisms widespread in nature and they are able to utilize methane as electron donor to reduce sulfate, nitrate, nitrite, and high valence metals. However, whether persistent organic contaminants can also be degraded remains unknown. In this study, the organic pollutant methyl orange (MO) was used to address this open question. The initial concentration of MO affected its degradation efficiency and higher concentration (>100 mg/L) caused considerable inhibition. A 13CH4 isotope experiment indicated that methane oxidation was involved in MO degradation, which produced N, N-dimethyl-p-phenylenediamine, and 4-aminobenzenesulfonic acid corresponded stoichiometrically. During the long-term experiment, the maximum degradation rate was 47.91 mg/(L·d). The percentage of Candidatus Methanoperedens and Pseudoxanthomonas significantly increased after 30-d of MO degradation under CH4 conditions; moreover, Candidatus Methanoperedens dominated (46.83%) the microbial community. Candidatus Methanoperedens, either alone or in combination with Pseudoxanthomonas, utilized methane as the sole carbon source to degrade MO via direct interspecies electron transfer or the syntrophy pathway. This study will add to our understanding of the functions and applications of AOM microorganisms.
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Affiliation(s)
- Liang Fu
- School of Environment, Northeast Normal University, Changchun 130117, China; CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Ya-Nan Bai
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Yong-Ze Lu
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Jing Ding
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Dandan Zhou
- School of Environment, Northeast Normal University, Changchun 130117, China
| | - Raymond Jianxiong Zeng
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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15
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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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16
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He Z, Wang J, Hu J, Yu H, Jetten MSM, Liu H, Cai C, Liu Y, Ren H, Zhang X, Hua M, Xu X, Zheng P, Hu B. Regulation of coastal methane sinks by a structured gradient of microbial methane oxidizers. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 244:228-237. [PMID: 30342364 DOI: 10.1016/j.envpol.2018.10.057] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/29/2018] [Accepted: 10/11/2018] [Indexed: 06/08/2023]
Abstract
Coastal wetlands are widely recognized as atmospheric methane sources. However, recent field studies suggest that some coastal wetlands could also act as methane sinks, but the mechanism is not yet clear. Here, we investigated methane oxidation with different electron acceptors (i.e., oxygen, nitrate/nitrite, sulfate, Fe(III) and Mn(IV)) in four coastal wetlands in China using a combination of molecular biology methods and isotopic tracing technologies. The geochemical profiles and in situ Gibbs free energies suggest that there was significant nitrite-dependent anaerobic oxidation of methane (nitrite-AOM) in the sub-surface sediments; this was subsequently experimentally verified by both the microbial abundance and activity. Remarkably, the methanotrophic communities seemed to exist in the sediments as layered structures, and the surface aerobic methane-oxidizing bacteria were able to take up atmospheric methane at a rate of 0.10-0.18 nmol CH4 day-1 cm-2, while most, if not all, sedimentary methane was being completely consumed by anaerobic methanotrophs (23-58% by methane oxidizers in phylum NC10). These results suggest that coastal methane sinks might be governed by diverse microbial communities where NC10 methane oxidizers contributed significantly. This finding helps to better understand and predict the coastal methane cycle and reduce uncertainties in the estimations of the global methane flux.
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Affiliation(s)
- Zhanfei He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Hanqing Yu
- Department of Chemistry, University of Science & Technology of China, Hefei, China
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Huan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Chaoyang Cai
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Hongxing Ren
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Xu Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Miaolian Hua
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Xinhua Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou, China.
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17
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Li W, Lu P, Chai F, Zhang L, Han X, Zhang D. Long-term nitrate removal through methane-dependent denitrification microorganisms in sequencing batch reactors fed with only nitrate and methane. AMB Express 2018; 8:108. [PMID: 29961200 PMCID: PMC6026486 DOI: 10.1186/s13568-018-0637-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/25/2018] [Indexed: 11/25/2022] Open
Abstract
Denitrifying anaerobic methane oxidation (damo) bioprocesses can remove nitrate using methane as the electron donor, which gains great concern due to the current stringent discharge standard of nitrogen in wastewater treatment plants. To obtain an engineering acceptable nitrogen removal rate (NRR) and demonstrate the long-term stable ability of damo system under conditions of nitrate and methane, two sequencing batch reactors (SBRs) fed with only nitrate and methane were operated for more than 600 days at 30 °C. The NRR of 21.91 ± 0.73 mg NO3--N L-1 day-1 was obtained which is, to the best of our knowledge, the highest rate observed in the literatures under such conditions. The temperature was found to significantly affect the system performance. Furthermore, the microbial community was analyzed by using real-time PCR technique. The results showed that the microbial consortium contained damo archaea and bacteria. These two microbes cooperated to maintain the long-term stability. And the number of damo archaea was higher than that of damo bacteria with the ratio of 1.77. By using methane as the electron donor, damo archaea reduced nitrate to nitrite coupled to methane oxidation and damo bacteria reduce the generated nitrite to nitrogen gas. The first step of nitrate to nitrite taken by damo archaea might be the limiting step of this cooperation system. SBR could be a suitable reactor configuration to enrich slow-growing microbes like damo culture. These results demonstrated the potential application of damo processes for nitrogen removal of wastewater containing low C/N ratios.
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Affiliation(s)
- Weiwei Li
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044 People’s Republic of China
- Department of Environmental Science, Chongqing University, Chongqing, 400044 People’s Republic of China
| | - Peili Lu
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044 People’s Republic of China
- Department of Environmental Science, Chongqing University, Chongqing, 400044 People’s Republic of China
| | - Fengguang Chai
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044 People’s Republic of China
| | - Lilan Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044 People’s Republic of China
- Department of Environmental Science, Chongqing University, Chongqing, 400044 People’s Republic of China
| | - Xinkuan Han
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044 People’s Republic of China
| | - Daijun Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044 People’s Republic of China
- Department of Environmental Science, Chongqing University, Chongqing, 400044 People’s Republic of China
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18
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Xu S, Cai C, Guo J, Lu W, Yuan Z, Hu S. Different clusters of Candidatus 'Methanoperedens nitroreducens'-like archaea as revealed by high-throughput sequencing with new primers. Sci Rep 2018; 8:7695. [PMID: 29769540 PMCID: PMC5955947 DOI: 10.1038/s41598-018-24974-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/23/2018] [Indexed: 11/25/2022] Open
Abstract
The newly discovered Candidatus ‘Methanoperedens nitroreducens’ (M. nitroreducens), mediating nitrate-dependent anaerobic oxidation of methane, is an important microorganism in linking carbon and nitrogen cycles. In order to explore the diversity of M. nitroreducens-like archaea in various environmental niches with advanced high-throughput sequencing, new primers based on alpha subunit of methyl-coenzyme M reductase gene were designed. The PCR results demonstrated that the new primers could effectively detect M. nitroreducens-like archaea from an enrichment culture dominated by M. nitroreducens as well as samples collected from a natural freshwater lake and a full-scale wastewater treatment plant (WWTP). By high-throughput sequencing, more than 30,000 M. nitroreducens-like sequences were obtained. Phylogenetic analysis of these sequences along with published sequences showed that M. nitroreducens-like archaea could be divided into three sub-branches (named as Group A, Group B and Group C in this study). Clear geographical difference was observed, with Group A and Group B dominating samples in Queensland (Australia) and in European ecosystems, respectively. Further quantitative PCR revealed that the M. nitroreducens-like archaea were more abundant in WWTP than the freshwater lake. The study provided a large number of sequences for M. nitroreducens-like archaeal communities, thus expanded our understanding on the ecological diversity of M. nitroreducens-like archaea.
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Affiliation(s)
- Sai Xu
- Advanced Water Management Centre, The University of Queensland, Brisbane, 4072, Australia.,School of Environment, Tsinghua University, Beijing, 100084, China.,Key Laboratory for Solid Waste Management and Environment Safety (Tsinghua University), Ministry of Education of China, Tsinghua University, Beijing, 100084, China
| | - Chen Cai
- Advanced Water Management Centre, The University of Queensland, Brisbane, 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, Brisbane, 4072, Australia
| | - Wenjing Lu
- School of Environment, Tsinghua University, Beijing, 100084, China. .,Key Laboratory for Solid Waste Management and Environment Safety (Tsinghua University), Ministry of Education of China, Tsinghua University, Beijing, 100084, China.
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, Brisbane, 4072, Australia.,School of Environment, Tsinghua University, Beijing, 100084, China
| | - Shihu Hu
- Advanced Water Management Centre, The University of Queensland, Brisbane, 4072, Australia.
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19
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Lomakina AV, Mamaeva EV, Pogodaeva TV, Kalmychkov GV, Khal’zov IA, Zemskaya TI. Anaerobic Methane Oxidation in Enrichment Cultures from Deep Sediments of a Mud Volcano Peschanka (South Baikal). Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718030049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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20
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Xu S, Lu W, Muhammad FM, Liu Y, Guo H, Meng R, Wang H. New molecular method to detect denitrifying anaerobic methane oxidation bacteria from different environmental niches. J Environ Sci (China) 2018; 65:367-374. [PMID: 29548408 DOI: 10.1016/j.jes.2017.04.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 02/22/2017] [Accepted: 04/19/2017] [Indexed: 06/08/2023]
Abstract
The denitrifying anaerobic methane oxidation is an ecologically important process for reducing the potential methane emission into the atmosphere. The responsible bacterium for this process was Candidatus Methylomirabilis oxyfera belonging to the bacterial phylum of NC10. In this study, a new pair of primers targeting all the five groups of NC10 bacteria was designed to amplify NC10 bacteria from different environmental niches. The results showed that the group A was the dominant NC10 phylum bacteria from the sludges and food waste digestate while in paddy soil samples, group A and group B had nearly the same proportion. Our results also indicated that NC10 bacteria could exist in a high pH environment (pH9.24) from the food waste treatment facility. The Pearson relationship analysis showed that the pH had a significant positive relationship with the NC10 bacterial diversity (p<0.05). The redundancy analysis further revealed that the pH, volatile solid and nitrite nitrogen were the most important factors in shaping the NC10 bacterial structure (p=0.01) based on the variation inflation factors selection and Monte Carlo test (999 times). Results of this study extended the existing molecular tools for studying the NC10 bacterial community structures and provided new information on the ecological distributions of NC10 bacteria.
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Affiliation(s)
- Sai Xu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Wenjing Lu
- School of Environment, Tsinghua University, Beijing 100084, China; Key Laboratory for Solid Waste Management and Environment Safety (Tsinghua University), Ministry of Education of China, Tsinghua University, Beijing 100084, China.
| | | | - Yanting Liu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Hanwen Guo
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Ruihong Meng
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Hongtao Wang
- School of Environment, Tsinghua University, Beijing 100084, China; Key Laboratory for Solid Waste Management and Environment Safety (Tsinghua University), Ministry of Education of China, Tsinghua University, Beijing 100084, China
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Liu L, Xu X, Cao Y, Cai C, Cui H, Yao J. Nitrate decreases methane production also by increasing methane oxidation through stimulating NC10 population in ruminal culture. AMB Express 2017; 7:76. [PMID: 28378285 PMCID: PMC5380647 DOI: 10.1186/s13568-017-0377-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/28/2017] [Indexed: 01/26/2023] Open
Abstract
Studies proved that addition of nitrate in rumen could lead to reduction of methane emission. The mechanism of this function was involved in the competition effect of nitrate on hydrogen consumption and the inhibitory effect of generated nitrite on methanogen proliferation. The present study investigated an alternative mechanism that denitrifying anaerobic methane oxidizing (DAMO) bacteria, DAMO archaea and anammox bacteria may co-exist in rumen, therefore, more methane can be oxidized when addition of nitrate. Ruminal batch culture model was used to test the effects of addition of 5 mM NaNO3, 4 mM NH4Cl, or both into the culture substrate on methane production, fermentation patterns, and population of methanogens, NC10 and anaerobic methanotrophic-2d (ANME-2d). Our results showed that NC10 in the ruminal culture was detected by polymerase chain reaction (PCR) when using NC10 special primer sets, and addition of nitrate reduced methane production and the relative proportions of methanogen, whereas increased the relative proportion of NC10. A combined addition of ammonia salt and nitrate did not show further inhibitory effect on methane production but accelerated nitrate removal. We did not detect DAMO archaea in ruminal culture by real-time PCR when using ANME-2d special primer sets. The present study may encourage researchers to pay more attention to methane oxidation performed by anaerobic methanotroph when studying the strategies of inhibiting ruminal methane emission.
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Vaksmaa A, van Alen TA, Ettwig KF, Lupotto E, Valè G, Jetten MSM, Lüke C. Stratification of Diversity and Activity of Methanogenic and Methanotrophic Microorganisms in a Nitrogen-Fertilized Italian Paddy Soil. Front Microbiol 2017; 8:2127. [PMID: 29180985 PMCID: PMC5693880 DOI: 10.3389/fmicb.2017.02127] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/18/2017] [Indexed: 11/30/2022] Open
Abstract
Paddy fields are important ecosystems, as rice is the primary food source for about half of the world's population. Paddy fields are impacted by nitrogen fertilization and are a major anthropogenic source of methane. Microbial diversity and methane metabolism were investigated in the upper 60 cm of a paddy soil by qPCR, 16S rRNA gene amplicon sequencing and anoxic 13C-CH4 turnover with a suite of electron acceptors. The bacterial community consisted mainly of Acidobacteria, Chloroflexi, Proteobacteria, Planctomycetes, and Actinobacteria. Among archaea, Euryarchaeota and Bathyarchaeota dominated over Thaumarchaeota in the upper 30 cm of the soil. Bathyarchaeota constituted up to 45% of the total archaeal reads in the top 5 cm. In the methanogenic community, Methanosaeta were generally more abundant than the versatile Methanosarcina. The measured maximum methane production rate was 444 nmol gdwh-1, and the maximum rates of nitrate-, nitrite-, and iron-dependent anaerobic oxidation of methane (AOM) were 57 nmol, 55 nmol, and 56 nmol gdwh-1, respectively, at different depths. qPCR revealed a higher abundance of 'Candidatus Methanoperedens nitroreducens' than methanotrophic NC10 phylum bacteria at all depths, except at 60 cm. These results demonstrate that there is substantial potential for AOM in fertilized paddy fields, with 'Candidatus Methanoperedens nitroreducens' archaea as a potential important contributor.
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Affiliation(s)
- Annika Vaksmaa
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Theo A. van Alen
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Katharina F. Ettwig
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Elisabetta Lupotto
- Research Centre for Food and Nutrition, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Rome, Italy
| | - Giampiero Valè
- Research Centre for Cereal and Industrial Crops, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
| | - Mike S. M. Jetten
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Claudia Lüke
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
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Shen LD, Wu HS, Liu X, Li J. Cooccurrence and potential role of nitrite- and nitrate-dependent methanotrophs in freshwater marsh sediments. WATER RESEARCH 2017; 123:162-172. [PMID: 28668629 DOI: 10.1016/j.watres.2017.06.075] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 05/31/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
Nitrite- and nitrate-dependent anaerobic methane oxidation are mediated by the NC10 bacteria closely related to "Candidatus Methylomirabilis oxyfera" (M. oxyfera) and the ANME-2d archaea closely related to "Candidatus Methanoperedens nitroreducens" (M. nitroreducens), respectively. Here, we investigated the occurrence and activity of both M. oxyfera-like bacteria and M. nitroreducens-like archaea in the sediment of freshwater marshes in Eastern China. The presence of diverse M. oxyfera-like bacteria (>87% identity to M. oxyfera) and M. nitroreducens-like archaea (>96% identity to M. nitroreducens) was confirmed by using Illumina-based total bacterial and archaeal 16S rRNA gene sequencing, respectively. The recovered M. oxyfera-like bacterial sequences accounted for 1.6-4.3% of the total bacterial 16S rRNA pool, and M. nitroreducens-like archaeal sequences accounted for 0.2-1.8% of the total archaeal 16S rRNA pool. The detected numbers of OTUs of the 16S rRNA genes of M. oxyfera-like bacteria and M. nitroreducens-like archaea were 78 and 72, respectively, based on 3% sequence difference. Quantitative PCR showed that the 16S rRNA gene abundance of M. oxyfera-like bacteria (6.1 × 106-3.2 × 107 copies g-1 sediment) was 2-4 orders of magnitude higher than that of M. nitroreducens-like archaea (1.4 × 103-3.2 × 104 copies g-1 sediment). Stable isotope experiments showed that the addition of both nitrite and nitrate stimulated the anaerobic methane oxidation, while the stimulation by nitrite is more significant than nitrate. Our results provide the first evidence that the M. oxyfera-like bacteria play a more important role than the M. nitroreducens-like archaea in methane cycling in wetland systems.
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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, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China; Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China.
| | - Hong-Sheng Wu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China; Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Xu Liu
- Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Ji Li
- Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
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Ding J, Lu YZ, Fu L, Ding ZW, Mu Y, Cheng SH, Zeng RJ. Decoupling of DAMO archaea from DAMO bacteria in a methane-driven microbial fuel cell. WATER RESEARCH 2017; 110:112-119. [PMID: 27998783 DOI: 10.1016/j.watres.2016.12.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 11/30/2016] [Accepted: 12/07/2016] [Indexed: 06/06/2023]
Abstract
Anaerobic oxidation of methane (AOM) contributes significantly to the global methane sink. Previously, studies of anaerobic methanotrophic (ANME) archaea have been limited as they have not been separable from their bacterial partners during the AOM process because of their dependence on the bacteria. A microbial fuel cell (MFC) is a device capable of directly transforming chemical energy to electrical energy via electrochemical reactions involving biochemical pathways. In this study, decoupling of denitrifying anaerobic methane oxidation (DAMO) archaea and DAMO bacteria was investigated in an microbial fuel cell (MFC) using methane as the fuel. The DAMO fuel cell worked successfully but demonstrated weak electrogenic capability with around 25 mV production. After 45 days' enrichment, the sequencing and fluorescence in situ hybridization results showed the DAMO archaea percentage had increased from 26.96% (inoculum) to 65.77% (electrode biofilm), while the DAMO bacteria percentage decreased from 24.39% to 2.07%. Moreover, the amount of ANME-2d had doubled in the electrode biofilm compared with the inoculum. The sequencing results also showed substantial enrichment of the Ignavibacterium and Geobacter genera. The roles of Ignavibacterium and Geobacter in the MFC system need to be further investigated. Nevertheless, these results illustrate that an MFC device may provide a possible approach to separate DAMO archaea from DAMO bacteria.
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Affiliation(s)
- Jing Ding
- Advanced Laboratory for Environmental Research and Technology, USTC-CityU, Suzhou 215123, PR China
| | - Yong-Ze Lu
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, PR China
| | - Liang Fu
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, PR China
| | - Zhao-Wei Ding
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, PR China
| | - Yang Mu
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, PR China
| | - Shuk H Cheng
- Advanced Laboratory for Environmental Research and Technology, USTC-CityU, Suzhou 215123, PR China; State Key Laboratory in Marine Pollution, Department of Biomedical Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Raymond J Zeng
- Advanced Laboratory for Environmental Research and Technology, USTC-CityU, Suzhou 215123, PR China; CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, PR China.
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Nitrogen source effects on the denitrifying anaerobic methane oxidation culture and anaerobic ammonium oxidation bacteria enrichment process. Appl Microbiol Biotechnol 2017; 101:3895-3906. [DOI: 10.1007/s00253-017-8163-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/20/2017] [Accepted: 01/24/2017] [Indexed: 11/25/2022]
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Vaksmaa A, Jetten MSM, Ettwig KF, Lüke C. McrA primers for the detection and quantification of the anaerobic archaeal methanotroph 'Candidatus Methanoperedens nitroreducens'. Appl Microbiol Biotechnol 2017; 101:1631-1641. [PMID: 28084539 PMCID: PMC5266762 DOI: 10.1007/s00253-016-8065-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/05/2016] [Accepted: 12/07/2016] [Indexed: 12/31/2022]
Abstract
The nitrogen and methane cycles are important biogeochemical processes. Recently, ‘Candidatus Methanoperedens nitroreducens,’ archaea that catalyze nitrate-dependent anaerobic oxidation of methane (AOM), were enriched, and their genomes were analyzed. Diagnostic molecular tools for the sensitive detection of ‘Candidatus M. nitroreducens’ are not yet available. Here, we report the design of two novel mcrA primer combinations that specifically target the alpha sub-unit of the methyl-coenzyme M reductase (mcrA) gene of ‘Candidatus M. nitroreducens’. The first primer pair produces a fragment of 186-bp that can be used to quantify ‘Candidatus M. nitroreducens’ cells, whereas the second primer pair yields an 1191-bp amplicon that is with sufficient length and well suited for more detailed phylogenetic analyses. Six different environmental samples were evaluated with the new qPCR primer pair, and the abundances were compared with those determined using primers for the 16S rRNA gene. The qPCR results indicated that the number of copies of the ‘Candidatus M. nitroreducens’ mcrA gene was highest in rice field soil, with 5.6 ± 0.8 × 106 copies g−1 wet weight, whereas Indonesian river sediment had only 4.6 ± 2.7 × 102 copies g−1 wet weight. In addition to freshwater environments, sequences were also detected in marine sediment of the North Sea, which contained approximately 2.5 ± 0.7 × 104 copies g−1 wet weight. Phylogenetic analysis revealed that the amplified 1191-bp mcrA gene sequences from the different environments all clustered together with available genome sequences of mcrA from known ‘Candidatus M. nitroreducens’ archaea. Taken together, these results demonstrate the validity and utility of the new primers for the quantitative and sensitive detection of the mcrA gene sequences of these important nitrate-dependent AOM archaea. Furthermore, the newly obtained mcrA sequences will contribute to greater phylogenetic resolution of ‘Candidatus M. nitroreducens’ sequences, which have been only poorly captured by general methanogenic mcrA primers.
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Affiliation(s)
- Annika Vaksmaa
- 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
| | - Katharina F Ettwig
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Claudia Lüke
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands.
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Reverse Methanogenesis and Respiration in Methanotrophic Archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2017; 2017:1654237. [PMID: 28154498 PMCID: PMC5244752 DOI: 10.1155/2017/1654237] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/11/2016] [Accepted: 10/31/2016] [Indexed: 12/21/2022]
Abstract
Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., “trace methane oxidation”). In turn, ANME can produce methane, but only during net methane oxidation (i.e., enzymatic back flux). Net AOM is exergonic when coupled to an external electron acceptor such as sulfate (ANME-1, ANME-2abc, and ANME-3), nitrate (ANME-2d), or metal (oxides). In this review, the reversibility of the methanogenesis pathway and essential differences between ANME and methanogens are described by combining published information with domain based (meta)genome comparison of archaeal methanotrophs and selected archaea. These differences include abundances and special structure of methyl coenzyme M reductase and of multiheme cytochromes and the presence of menaquinones or methanophenazines. ANME-2a and ANME-2d can use electron acceptors other than sulfate or nitrate for AOM, respectively. Environmental studies suggest that ANME-2d are also involved in sulfate-dependent AOM. ANME-1 seem to use a different mechanism for disposal of electrons and possibly are less versatile in electron acceptors use than ANME-2. Future research will shed light on the molecular basis of reversal of the methanogenic pathway and electron transfer in different ANME types.
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Welte CU, Rasigraf O, Vaksmaa A, Versantvoort W, Arshad A, Op den Camp HJM, Jetten MSM, Lüke C, Reimann J. Nitrate- and nitrite-dependent anaerobic oxidation of methane. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:941-955. [PMID: 27753265 DOI: 10.1111/1758-2229.12487] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Microbial methane oxidation is an important process to reduce the emission of the greenhouse gas methane. Anaerobic microorganisms couple the oxidation of methane to the reduction of sulfate, nitrate and nitrite, and possibly oxidized iron and manganese minerals. In this article, we review the recent finding of the intriguing nitrate- and nitrite-dependent anaerobic oxidation of methane (AOM). Nitrate-dependent AOM is catalyzed by anaerobic archaea belonging to the ANME-2d clade closely related to Methanosarcina methanogens. They were named 'Candidatus Methanoperedens nitroreducens' and use reverse methanogenesis with the key enzyme methyl-coenzyme M (methyl-CoM) reductase for methane activation. Their major end product is nitrite which can be taken up by nitrite-dependent methanotrophs. Nitrite-dependent AOM is performed by the NC10 bacterium 'Candidatus Methylomirabilis oxyfera' that probably utilizes an intra-aerobic pathway through the dismutation of NO to N2 and O2 for aerobic methane activation by methane monooxygenase, yet being a strictly anaerobic microbe. Environmental distribution, physiological and biochemical aspects are discussed in this article as well as the cooperation of the microorganisms involved.
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Affiliation(s)
- Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Netherlands Earth Systems Science Center, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Arslan Arshad
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Netherlands Earth Systems Science Center, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Claudia Lüke
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
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Experimental evaluation of the metabolic reversibility of ANME-2d between anaerobic methane oxidation and methanogenesis. Appl Microbiol Biotechnol 2016; 100:6481-6490. [DOI: 10.1007/s00253-016-7475-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 03/13/2016] [Accepted: 03/15/2016] [Indexed: 01/26/2023]
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Environmental evaluation of coexistence of denitrifying anaerobic methane-oxidizing archaea and bacteria in a paddy field. Appl Microbiol Biotechnol 2015; 100:439-46. [DOI: 10.1007/s00253-015-6986-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 08/20/2015] [Accepted: 09/02/2015] [Indexed: 01/04/2023]
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