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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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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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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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Zuo Z, Xing Y, Liu T, Zheng M, Lu X, Chen Y, Jiang G, Liang P, Huang X, Liu Y. Methane mitigation via the nitrite-DAMO process induced by nitrate dosing in sewers. WATER RESEARCH 2024; 257:121701. [PMID: 38733962 DOI: 10.1016/j.watres.2024.121701] [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: 12/07/2023] [Revised: 04/21/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
Nitrate or nitrite-dependent anaerobic methane oxidation (n-DAMO) is a microbial process that links carbon and nitrogen cycles as a methane sink in many natural environments. This study demonstrates, for the first time, that the nitrite-dependent anaerobic methane oxidation (nitrite-DAMO) process can be stimulated in sewer systems under continuous nitrate dosing for sulfide control. In a laboratory sewer system, continuous nitrate dosing not only achieved complete sulfide removal, but also significantly decreased dissolved methane concentration by ∼50 %. Independent batch tests confirmed the coupling of methane oxidation with nitrate and nitrite reduction, revealing similar methane oxidation rates of 3.68 ± 0.5 mg CH4 L-1 h-1 (with nitrate as electron acceptor) and 3.57 ± 0.4 mg CH4 L-1 h-1 (with nitrite as electron acceptor). Comprehensive microbial analysis unveiled the presence of a subgroup of the NC10 phylum, namely Candidatus Methylomirabilis (n-DAMO bacteria that couples nitrite reduction with methane oxidation), growing in sewer biofilms and surface sediments with relative abundances of 1.9 % and 1.6 %, respectively. In contrast, n-DAMO archaea that couple methane oxidation solely to nitrate reduction were not detected. Together these results indicated the successful enrichment of n-DAMO bacteria in sewerage systems, contributing to approx. 64 % of nitrite reduction and around 50 % of dissolved methane removal through the nitrite-DAMO process, as estimated by mass balance analysis. The occurrence of the nitrite-DAMO process in sewer systems opens a new path to sewer methane emissions.
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Affiliation(s)
- Zhiqiang Zuo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia; National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China
| | - Yaxin Xing
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Tao Liu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia; Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia; Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Xi Lu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Yan Chen
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Peng Liang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yanchen Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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Li X, Yu R, Wang J, Sun H, Liu X, Ren X, Zhuang S, Guo Z, Lu X. Greenhouse gas emissions from Daihai Lake, China: Should eutrophication and salinity promote carbon emission dynamics? J Environ Sci (China) 2024; 135:407-423. [PMID: 37778815 DOI: 10.1016/j.jes.2022.12.021] [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: 09/08/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 10/03/2023]
Abstract
Greenhouse gases (GHGs) emitted or absorbed by lakes are an important component of the global carbon cycle. However, few studies have focused on the GHG dynamics of eutrophic saline lakes, thus preventing a comprehensive understanding of the carbon cycle. Here, we conducted four sampling analyses using a floating chamber in Daihai Lake, a eutrophication saline lake in Inner Mongolia Autonomous Region, China, to explore its carbon dioxide (CO2) and methane (CH4) emissions. The mean CO2 emission flux (FCO2) and CH4 emission flux (FCH4) were 17.54 ± 14.54 mmol/m2/day and 0.50 ± 0.50 mmol/m2/day, respectively. The results indicated that Daihai Lake was a source of CO2 and CH4, and GHG emissions exhibited temporal variability. The mean CO2 partial pressure (pCO2) and CH4 partial pressure (pCH4) were 561.35 ± 109.59 µatm and 17.02 ± 13.45 µatm, which were supersaturated relative to the atmosphere. The regression and correlation analysis showed that the main influencing factors of pCO2 were wind speed, dissolved oxygen (DO), total nitrogen (TN) and Chlorophyll a (Chl.a), whereas the main influencing factors of pCH4 were water temperature (WT), Chl.a, nitrate nitrogen (NO3--N), TN, dissolved organic carbon (DOC) and water depth. Salinity regulated carbon mineralization and organic matter decomposition, and it was an important influencing factor of pCO2 and pCH4. Additionally, the trophic level index (TLI) significantly increased pCH4. Our study elucidated that salinity and eutrophication play an important role in the dynamic changes of GHG emissions. However, research on eutrophic saline lakes needs to be strengthened.
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Affiliation(s)
- Xiangwei Li
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010070, China
| | - Ruihong Yu
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010070, China; Key Laboratory of Mongolian Plateau Ecology and Resource Utilization, Ministry of Education, Hohhot 010070, China; Autonomous Region Collaborative Innovation Center for Integrated Management of Water Resources and Water Environment in the Inner Mongolia Reaches of the Yellow River, Hohhot 010018, China.
| | - Jun Wang
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010070, China
| | - Heyang Sun
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010070, China
| | - Xinyu Liu
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010070, China
| | - Xiaohui Ren
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010070, China
| | - Shuai Zhuang
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010070, China
| | - Zhiwei Guo
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010070, China
| | - Xixi Lu
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010070, China; Department of Geography, National University of Singapore, 117570, Singapore
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Fenibo EO, Selvarajan R, Wang H, Wang Y, Abia ALK. Untapped talents: insight into the ecological significance of methanotrophs and its prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166145. [PMID: 37579801 DOI: 10.1016/j.scitotenv.2023.166145] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/06/2023] [Accepted: 08/06/2023] [Indexed: 08/16/2023]
Abstract
The deep ocean is a rich reservoir of unique organisms with great potential for bioprospecting, ecosystem services, and the discovery of novel materials. These organisms thrive in harsh environments characterized by high hydrostatic pressure, low temperature, and limited nutrients. Hydrothermal vents and cold seeps, prominent features of the deep ocean, provide a habitat for microorganisms involved in the production and filtration of methane, a potent greenhouse gas. Methanotrophs, comprising archaea and bacteria, play a crucial role in these processes. This review examines the intricate relationship between the roles, responses, and niche specialization of methanotrophs in the deep ocean ecosystem. Our findings reveal that different types of methanotrophs dominate specific zones depending on prevailing conditions. Type I methanotrophs thrive in oxygen-rich zones, while Type II methanotrophs display adaptability to diverse conditions. Verrumicrobiota and NC10 flourish in hypoxic and extreme environments. In addition to their essential role in methane regulation, methanotrophs contribute to various ecosystem functions. They participate in the degradation of foreign compounds and play a crucial role in cycling biogeochemical elements like metals, sulfur, and nitrogen. Methanotrophs also serve as a significant energy source for the oceanic food chain and drive chemosynthesis in the deep ocean. Moreover, their presence offers promising prospects for biotechnological applications, including the production of valuable compounds such as polyhydroxyalkanoates, methanobactin, exopolysaccharides, ecotines, methanol, putrescine, and biofuels. In conclusion, this review highlights the multifaceted roles of methanotrophs in the deep ocean ecosystem, underscoring their ecological significance and their potential for advancements in biotechnology. A comprehensive understanding of their niche specialization and responses will contribute to harnessing their full potential in various domains.
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Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence, Centre for Oilfield Chemical Research, University of Port Harcourt, Port Harcourt 500272, Nigeria
| | - Ramganesh Selvarajan
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China; Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa
| | - Huiqi Wang
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China
| | - Yue Wang
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China
| | - Akebe Luther King Abia
- Environmental Research Foundation, Westville 3630, South Africa; Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
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Li X, Yu R, Wang J, Sun H, Lu C, Liu X, Ren X, Zhuang S, Guo Z, Lu X. Fluxes in CO 2 and CH 4 and influencing factors at the sediment-water interface in a eutrophic saline lake. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118314. [PMID: 37343475 DOI: 10.1016/j.jenvman.2023.118314] [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: 02/15/2023] [Revised: 05/06/2023] [Accepted: 05/30/2023] [Indexed: 06/23/2023]
Abstract
Although saline aquatic ecosystems are significant emitters of greenhouse gases (GHGs), dynamic changes in GHGs at the sediment-water interface remain unclear. The present investigation carried out a total of four sampling campaigns in Daihai Lake, which is a eutrophic saline lake situated in a semi-arid area of northern China. The aim of this study was to investigate the spatio-temporal dynamics of carbon dioxide (CO2) and methane (CH4) fluxes at the sediment-water interface and the influencing factors. The mean concentrations of porewater CO2 and CH4 were 44.98 ± 117.99 μmol L-1 and 124.36 ± 97.00 μmol L-1, far exceeding those in water column of 11.14 ± 2.16 μmol L-1 and 0.33 ± 0.23 μmol L-1, respectively. The CO2 and CH4 fluxes at the sediment-water interface (FS-WCO2 and FS-WCH4) exhibited significant spatial and temporal variations, with mean values of 9.24 ± 13.84 μmol m-2 d-1 and 3.53 ± 4.36 μmol m-2 d-1, respectively, indicating that sediment is the source of CO2 and CH4 in the water column. However, CO2 and CH4 fluxes were much lower than those measured at the water-air interface in a companion study (17.54 ± 14.54 mmol m-2d-1 and 0.50 ± 0.50 mmol m-2d-1, respectively), indicating that the diffusive flux of gases at the sediment-water interface was not the primary source of CO2 and CH4 emissions to the atmosphere. Regression and correlation analyses revealed that salinity (Sal) and nutrients were the most influential factors on porewater gas concentrations, and that gas fluxes increased with increasing gas concentrations and porosity. The microbial activity of sediment is greatly affected by nutrients and Sal. Additionally, Sal has the ability to regulate biogeochemical processes, thereby regulating GHG emissions. The present investigation addresses the research gap concerning GHG emissions from sediments of eutrophic saline lakes. The study suggests that controlling the eutrophication and salinization of lakes could be a viable strategy for reducing carbon emissions from lakes. However, further investigations are required to establish more conclusive results.
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Affiliation(s)
- Xiangwei Li
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Ruihong Yu
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China; Key Laboratory of Mongolian Plateau Ecology and Resource Utilization, Ministry of Education, Hohhot, 010070, China; Autonomous Region Collaborative Innovation Center for Integrated Management of Water Resources and Water Environment in the Inner Mongolia Reaches of the Yellow River, Hohhot, 010018, China.
| | - Jun Wang
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Heyang Sun
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Changwei Lu
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Xinyu Liu
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Xiaohui Ren
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Shuai Zhuang
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Zhiwei Guo
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Xixi Lu
- Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China; Department of Geography, National University of Singapore, 17570, Singapore
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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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9
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Li B, Tao Y, Mao Z, Gu Q, Han Y, Hu B, Wang H, Lai A, Xing P, Wu QL. Iron oxides act as an alternative electron acceptor for aerobic methanotrophs in anoxic lake sediments. WATER RESEARCH 2023; 234:119833. [PMID: 36889095 DOI: 10.1016/j.watres.2023.119833] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/13/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Conventional aerobic CH4-oxidizing bacteria (MOB) are frequently detected in anoxic environments, but their survival strategy and ecological contribution are still enigmatic. Here we explore the role of MOB in enrichment cultures under O2 gradients and an iron-rich lake sediment in situ by combining microbiological and geochemical techniques. We found that enriched MOB consortium used ferric oxides as alternative electron acceptors for oxidizing CH4 with the help of riboflavin when O2 was unavailable. Within the MOB consortium, MOB transformed CH4 to low molecular weight organic matter such as acetate for consortium bacteria as a carbon source, while the latter secrete riboflavin to facilitate extracellular electron transfer (EET). Iron reduction coupled to CH4 oxidation mediated by the MOB consortium was also demonstrated in situ, reducing 40.3% of the CH4 emission in the studied lake sediment. Our study indicates how MOBs survive under anoxia and expands the knowledge of this previously overlooked CH4 sink in iron-rich sediments.
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Affiliation(s)
- Biao Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ye Tao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhendu Mao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Qiujin Gu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yixuan Han
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Hongwei Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Anxing Lai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
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10
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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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11
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Seasonal Hypoxia Enhances Benthic Nitrogen Fixation and Shapes Specific Diazotrophic Community in the Eutrophic Marine Ranch. Processes (Basel) 2023. [DOI: 10.3390/pr11010138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Recently, a growing number of studies have confirmed that biological nitrogen fixation is also an important reactive nitrogen source in coastal regions. However, how benthic nitrogen fixation and diazotrophic community in coastal regions respond to seasonal hypoxia remains largely unknown. In this study, we investigated the spatiotemporal pattern of potential nitrogen fixation rate and diazotrophic abundance and community in sediments of a eutrophic marine ranch experiencing summer hypoxia using 15N tracing and high throughput sequencing techniques. The results showed that potential nitrogen fixation rates ranged from 0.013 to 10.199 μmol kg−1 h−1, and were significantly enhanced by summer hypoxia (ANOVA, p < 0.05). However, nifH gene abundance peaked in June. The diazotrophic community was dominated by Geobacteraceae (>60%), followed by Desulfobulbaceae (13.61%). Bottom water oxygen, pH, Chl-a concentration, and sediment NH4+ significantly regulated benthic nitrogen fixation, while the variation of diazotrophic community was explained by sediment TOC, TN, and Fe content (p < 0.05). This study highlighted that hypoxia stimulated benthic nitrogen fixation, which counteracted the nitrogen removal by denitrification and anammox, and could further aggregate eutrophication of the coastal marine ranch. Moreover, the result emphasized the importance of nitrogen fixation in coastal regions for the global N budget.
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12
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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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13
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Lv K, Guo X, Wang C, Su Q, Liu D, Xiao S, Yang Z. Sediment nitrogen contents controlled by microbial community in a eutrophic tributary in Three Gorges Reservoir, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120312. [PMID: 36183874 DOI: 10.1016/j.envpol.2022.120312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 06/16/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen pollution caused serious environmental problems in reservoir ecosystems. Reducing nitrogen pollution by enhancing nitrogen removal in river sediments deserved intensive research. Distributions of nitrogen contents in sediment-water interface were characterized along the Xiangxi bay (XXB), a eutrophic tributary in Three Gorges Reservoir, China. More than 47% of total Kjeldahl nitrogen (TKN) and 67% of total organic nitrogen (TON) were degraded during burial. Higher TN, TON and NH4+ consuming at downstream sites indicated stronger nitrogen mineralization and release due to higher turbulence of the overlying density currents. Nitrifying bacteria, denitrifying bacteria, anaerobic ammonium oxidizing (anammox) bacteria and nitrite/nitrate-dependent anaerobic methane oxidation (N-DAMO) bacteria were detected in nitrate-ammonium transition zone. Nitrogen contents transitions were responded to microbial stakeholders indicated microbially mediated nitrogen cycling in sediments. The dissolved oxygen and nitrate availabilities were the key limits of denitrification and associated reactions. These results suggested microbial mediated nitrogen cycling processes in sediments were critical for nitrogen removal in aquatic ecosystems, and replenishing dissolved oxygen and nitrate was expected to enhance sediment denitrification and strengthen potential environmental self-purification.
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Affiliation(s)
- Kun Lv
- Engineering Research Center of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, Yichang, China
| | - Xiaojuan Guo
- Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang, China
| | - Congfeng Wang
- Engineering Research Center of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, Yichang, China; Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang, China
| | - Qingqing Su
- Engineering Research Center of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, Yichang, China; Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang, China
| | - Defu Liu
- Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang, China
| | - Shangbin Xiao
- Engineering Research Center of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, Yichang, China
| | - Zhengjian Yang
- Engineering Research Center of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, Yichang, China.
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14
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Shi LD, Zhou YJ, Tang XJ, Kappler A, Chistoserdova L, Zhu LZ, Zhao HP. Coupled Aerobic Methane Oxidation and Arsenate Reduction Contributes to Soil-Arsenic Mobilization in Agricultural Fields. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11845-11856. [PMID: 35920083 DOI: 10.1021/acs.est.2c01878] [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] [Indexed: 06/15/2023]
Abstract
Microbial oxidation of organic compounds can promote arsenic release by reducing soil-associated arsenate to the more mobile form arsenite. While anaerobic oxidation of methane has been demonstrated to reduce arsenate, it remains elusive whether and to what extent aerobic methane oxidation (aeMO) can contribute to reductive arsenic mobilization. To fill this knowledge gap, we performed incubations of both microbial laboratory cultures and soil samples from arsenic-contaminated agricultural fields in China. Incubations with laboratory cultures showed that aeMO could couple to arsenate reduction, wherein the former bioprocess was carried out by aerobic methanotrophs and the latter by a non-methanotrophic bacterium belonging to a novel and uncultivated representative of Burkholderiaceae. Metagenomic analyses combined with metabolite measurements suggested that formate served as the interspecies electron carrier linking aeMO to arsenate reduction. Such coupled bioprocesses also take place in the real world, supported by a similar stoichiometry and gene activity in the incubations with natural paddy soils, and contribute up to 76.2% of soil-arsenic mobilization into pore waters in the top layer of the soils where oxygen was present. Overall, this study reveals a previously overlooked yet significant contribution of aeMO to reductive arsenic mobilization.
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Affiliation(s)
- Ling-Dong Shi
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yu-Jie Zhou
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xian-Jin Tang
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Andreas Kappler
- Center for Applied Geosciences, University of Tübingen, Tübingen 72074, Germany
| | - Ludmila Chistoserdova
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-0005, United States
| | - Li-Zhong Zhu
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
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15
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Steinsdóttir HGR, Gómez Ramírez E, Mhatre S, Schauberger C, Bertagnolli AD, Pratte ZA, Stewart FJ, Thamdrup B, Bristow LA. Anaerobic methane oxidation in a coastal oxygen minimum zone: spatial and temporal dynamics. Environ Microbiol 2022; 24:2361-2379. [PMID: 35415879 PMCID: PMC9323439 DOI: 10.1111/1462-2920.16003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 11/28/2022]
Abstract
Coastal waters are a major source of marine methane to the atmosphere. Particularly high concentrations of this potent greenhouse gas are found in anoxic waters, but it remains unclear if and to what extent anaerobic methanotrophs mitigate the methane flux. Here we investigate the long-term dynamics in methanotrophic activity and the methanotroph community in the coastal oxygen minimum zone (OMZ) of Golfo Dulce, Costa Rica, combining biogeochemical analyses, experimental incubations, and 16S rRNA gene sequencing over three consecutive years. Our results demonstrate a stable redox zonation across the years with high concentrations of methane (up to 1.7 μmol L-1 ) in anoxic bottom waters. However, we also measured high activities of anaerobic methane oxidation in the OMZ core (rate constant, k, averaging 30 yr-1 in 2018 and 8 yr-1 in 2019-2020). The OPU3 and Deep Sea-1 clades of the Methylococcales were implicated as conveyors of the activity, peaking in relative abundance 5-25 m below the oxic-anoxic interface and in the deep anoxic water, respectively. Although their genetic capacity for anaerobic methane oxidation remains unexplored, their sustained high relative abundance indicates an adaptation of these clades to the anoxic, methane-rich OMZ environment, allowing them to play major roles in mitigating methane fluxes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Eddy Gómez Ramírez
- CIMAR, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Snehit Mhatre
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | | | - Anthony D Bertagnolli
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana
| | - Zoe A Pratte
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana
| | - Frank J Stewart
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana.,School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA
| | - Bo Thamdrup
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Laura A Bristow
- Department of Biology, University of Southern Denmark, Odense, Denmark
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16
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Cerbin S, Pérez G, Rybak M, Wejnerowski Ł, Konowalczyk A, Helmsing N, Naus-Wiezer S, Meima-Franke M, Pytlak Ł, Raaijmakers C, Nowak W, Bodelier PLE. Methane-Derived Carbon as a Driver for Cyanobacterial Growth. Front Microbiol 2022; 13:837198. [PMID: 35432228 PMCID: PMC9010870 DOI: 10.3389/fmicb.2022.837198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/23/2022] [Indexed: 11/23/2022] Open
Abstract
Methane, a potent greenhouse gas produced in freshwater ecosystems, can be used by methane-oxidizing bacteria (MOB) and can therefore subsidize the pelagic food web with energy and carbon. Consortia of MOB and photoautotrophs have been described in aquatic ecosystems and MOB can benefit from photoautotrophs which produce oxygen, thereby enhancing CH4 oxidation. Methane oxidation can account for accumulation of inorganic carbon (i.e., CO2) and the release of exometabolites that may both be important factors influencing the structure of phytoplankton communities. The consortium of MOB and phototroph has been mainly studied for methane-removing biotechnologies, but there is still little information on the role of these interactions in freshwater ecosystems especially in the context of cyanobacterial growth and bloom development. We hypothesized that MOB could be an alternative C source to support cyanobacterial growth in freshwater systems. We detected low δ13C values in cyanobacterial blooms (the lowest detected value −59.97‰ for Planktothrix rubescens) what could be the result of the use of methane-derived carbon by cyanobacteria and/or MOB attached to their cells. We further proved the presence of metabolically active MOB on cyanobacterial filaments using the fluorescein isothiocyanate (FITC) based activity assay. The PCR results also proved the presence of the pmoA gene in several non-axenic cultures of cyanobacteria. Finally, experiments comprising the co-culture of the cyanobacterium Aphanizomenon gracile with the methanotroph Methylosinus sporium proved that cyanobacterial growth was significantly improved in the presence of MOB, presumably through utilizing CO2 released by MOB. On the other hand, 13C-CH4 labeled incubations showed the uptake and assimilation of MOB-derived metabolites by the cyanobacterium. We also observed a higher growth of MOB in the presence of cyanobacteria under a higher irradiance regime, then when grown alone, underpinning the bidirectional influence with as of yet unknown environmental consequences.
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Affiliation(s)
- Slawek Cerbin
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
- *Correspondence: Slawek Cerbin,
| | - Germán Pérez
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Michał Rybak
- Department of Water Protection, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Łukasz Wejnerowski
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Adam Konowalczyk
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Nico Helmsing
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Suzanne Naus-Wiezer
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Łukasz Pytlak
- Montanuniversität Leoben, Applied Geosciences and Geophysics, Leoben, Austria
| | - Ciska Raaijmakers
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Witold Nowak
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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17
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Shi J, Zhang B, Liu J, Fang Y, Wang A. Spatiotemporal dynamics in microbial communities mediating biogeochemical cycling of nutrients across the Xiaowan Reservoir in Lancang River. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:151862. [PMID: 34826492 DOI: 10.1016/j.scitotenv.2021.151862] [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: 09/09/2021] [Revised: 10/27/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Microbes drive biogeochemical cycles of nutrients controlling water quality in freshwater ecosystems, yet little is known regarding how spatiotemporal variation in the microbial community affects this ecosystem-level functional processes to resist perturbations. Here we examined spatiotemporal dynamics of microbial communities in paired stratified water columns and sediments collected from the Xiaowan Reservoir of Lancang-Mekong River over a year long period. Results highlighted distinctive spatiotemporal patterns of microbial communities in water columns mainly driven by sulfate, dissolved oxygen, nitrate and temperature, whilst sediment communities only showed a seasonal variation pattern governed by pH, reduced inorganic sulfur, sulfate, organic matter and total nitrogen. Microbial co-occurrence networks revealed the succession of keystone taxa in both water columns and sediments, reflecting core ecological functions in response to altered environmental conditions. Specifically, in shallow water, keystone nitrogen fixers and denitrifiers were responsible for providing nitrogen nutrients in summer, while recalcitrant substance degraders likely supplied microbially available organic matters to maintain ecosystem stability in winter. But in deep water, methane oxidation was the critical process linked to microbial-mediated cycle of carbon, nitrogen and sulfur. In addition, carbon metabolism and mercury methylation mediated by sulfate reducers, denitrifiers and nitrogen fixers were core functioning features of sediments in summer and winter, respectively. This work expands our knowledge of the importance of keystone taxa in maintaining stability of reservoir ecosystems under changing environments, providing new perspectives for water resource conservation and management.
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Affiliation(s)
- Jiaxin Shi
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Baogang Zhang
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Jun Liu
- State Key Laboratory of Agricultural Microbiology, State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yun Fang
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resources and Environments, Harbin Institute of Technology, Harbin 150090, China
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18
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Niu Y, Zheng Y, Hou L, Gao D, Chen F, Pei C, Dong H, Liang X, Liu M. Microbial dynamics and activity of denitrifying anaerobic methane oxidizers in China's estuarine and coastal wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150425. [PMID: 34560448 DOI: 10.1016/j.scitotenv.2021.150425] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Estuarine and coastal wetlands, which act as large sources of methane (CH4) and undergo substantial loading of anthropogenic nitrogen (N), provide ideal conditions for denitrifying anaerobic methane oxidation (DAMO) to occur. Yet the microbial mechanisms governing DAMO and the main driving factors in estuarine and coastal ecosystems remain unclear. This study investigated the spatiotemporal distribution and associated activity of DAMO microorganisms along a wide swath of China's coastline (latitudinal range: 22-41°N) using molecular assays and isotope tracing techniques. We uncovered significant spatial and seasonal variation in DAMO bacterial community structure, whereas DAMO archaeal community structure exhibited no seasonal differences. The abundance of DAMO bacterial pmoA gene (2.2 × 105-1.0 × 107 copies g-1) was almost one order of magnitude higher than that of DAMO archaeal mcrA gene (8.7 × 104 -1.8 × 106 copies g-1). A significant positive correlation between pmoA and mcrA gene abundances (p < 0.01) was observed, indicating that DAMO bacteria and archaea may cooperate closely and thus complete nitrate elimination. Potential DAMO rates, in the range of 0.09-23.4 nmol 13CO2 g-1 day-1 for nitrite-DAMO and 0.03-43.7 nmol 13CO2 g-1 day-1 for nitrate-DAMO, tended to be greater in the relatively warmer low-latitudes. Potential DAMO rates were weakly positively correlated with gene abundances, suggesting that DAMO microbial activity could not be predicted directly by gene abundance alone. The heterogeneous variability of DAMO was shaped by interactions among key environmental characteristics (sediment texture, N availability, TOC, Fe3+, salinity of water, and temperature). On a broader continental scale, potential N removal rates of 0.1-11.2 g N m-2 yr-1 were estimated via nitrite-DAMO activity in China's coastal wetlands. Overall, our results highlight the widespread distribution of DAMO microbes and their potential role in eliminating excess N inputs and reducing CH4 emissions in estuarine and coastal ecosystems, which could help mitigate global warming.
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Affiliation(s)
- Yuhui Niu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Dengzhou Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Feiyang Chen
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Chenya Pei
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
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19
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Shenoy DM, Kurian S, Shirodkar G, Uskaikar H, Gauns M, Naqvi SWA. Impact of physical processes on oxygen loss and production of hydrogen sulphide and methane in a tropical freshwater reservoir. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:39655-39667. [PMID: 33761073 DOI: 10.1007/s11356-021-13472-x] [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: 10/01/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Carbon neutrality of tropical reservoirs is a big concern in recent years as some estimates project high methane emission from these reservoirs. While there are studies available on the impact of physical processes (stratification and mixing) on the biogeochemistry of tropical reservoirs, not much information is available on the inter-annual variability in the low-oxygen conditions and production/accumulation of hydrogen sulphide (H2S) and methane (CH4) during summer. This paper presents time series data based on monthly in situ observations from a tropical reservoir (Tillari, Maharashtra) situated in the Western Ghats in India. Sampling was carried out for temperature, dissolved oxygen (DO), H2S, and CH4 at a fixed location from March 2010 until June 2014. The reservoir experiences stable stratification during summer (March to June) with complete loss of oxygen and production of H2S (max. ~ 9 μM) and CH4 (max. ~ 185 μM) in the profundal zone. During the summer stratification, the hypolimnion acted as a pool of CH4 with integrated values ranging between 3502 and 41,632 mg m-2. However, the intensity and duration of anoxia varied during different years, influencing H2S and CH4 production. Mixing in the reservoir was observed between July and September in association with the monsoonal runoff, which increased the DO concentrations in the sub-surface layers. Besides, complete mixing was observed between December and February due to winter convection. This, however, was found to play an important role, as weaker mixing in the preceding year was associated with severe oxygen loss in the profundal zone during the following summer with a production of H2S and CH4. In contrast, more robust mixing during winter led to moderate low-oxygen conditions with less production of these gases in the subsequent summer. Based on our observations and considering a large number of reservoirs in the tropics, we hypothesise that with the present trends of global warming and less cold winters, low-oxygen conditions in the profundal zone may become more severe in the future with positive feedback on H2S and CH4 production during summer.
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Affiliation(s)
- Damodar M Shenoy
- Chemical Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403004, India.
| | - Siby Kurian
- Chemical Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403004, India
| | - Gayatri Shirodkar
- Chemical Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403004, India
| | - Hema Uskaikar
- Chemical Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403004, India
| | - Mangesh Gauns
- Chemical Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403004, India
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20
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Pierangeli GMF, Domingues MR, de Jesus TA, Coelho LHG, Hanisch WS, Pompêo MLM, Saia FT, Gregoracci GB, Benassi RF. Higher Abundance of Sediment Methanogens and Methanotrophs Do Not Predict the Atmospheric Methane and Carbon Dioxide Flows in Eutrophic Tropical Freshwater Reservoirs. Front Microbiol 2021; 12:647921. [PMID: 33815337 PMCID: PMC8010658 DOI: 10.3389/fmicb.2021.647921] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/23/2021] [Indexed: 12/02/2022] Open
Abstract
Freshwater reservoirs emit greenhouse gases (GHGs) such as methane (CH4) and carbon dioxide (CO2), contributing to global warming, mainly when impacted by untreated sewage and other anthropogenic sources. These gases can be produced by microbial organic carbon decomposition, but little is known about the microbiota and its participation in GHG production and consumption in these environments. In this paper we analyzed the sediment microbiota of three eutrophic tropical urban freshwater reservoirs, in different seasons and evaluated the correlations between microorganisms and the atmospheric CH4 and CO2 flows, also correlating them to limnological variables. Our results showed that deeper water columns promote high methanogen abundance, with predominance of acetoclastic Methanosaeta spp. and hydrogenotrophs Methanoregula spp. and Methanolinea spp. The aerobic methanotrophic community was affected by dissolved total carbon (DTC) and was dominated by Crenothrix spp. However, both relative abundance of the total methanogenic and aerobic methanotrophic communities in sediments were uncoupled to CH4 and CO2 flows. Network based approach showed that fermentative microbiota, including Leptolinea spp. and Longilinea spp., which produces substrates for methanogenesis, influence CH4 flows and was favored by anthropogenic pollution, such as untreated sewage loads. Additionally, less polluted conditions favored probable anaerobic methanotrophs such as Candidatus Bathyarchaeota, Sva0485, NC10, and MBG-D/DHVEG-1, which promoted lower gaseous flows, confirming the importance of sanitation improvement to reduce these flows in tropical urban freshwater reservoirs and their local and global warming impact.
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Affiliation(s)
| | - Mercia Regina Domingues
- Center of Engineering, Modeling and Applied Social Sciences, Federal University of ABC, Santo André, Brazil
| | - Tatiane Araujo de Jesus
- Center of Engineering, Modeling and Applied Social Sciences, Federal University of ABC, Santo André, Brazil
| | - Lúcia Helena Gomes Coelho
- Center of Engineering, Modeling and Applied Social Sciences, Federal University of ABC, Santo André, Brazil
| | | | | | | | | | - Roseli Frederigi Benassi
- Center of Engineering, Modeling and Applied Social Sciences, Federal University of ABC, Santo André, Brazil
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Zhang S, Zhang Z, Xia S, Ding N, Long X, Wang J, Chen M, Ye C, Chen S. Combined genome-centric metagenomics and stable isotope probing unveils the microbial pathways of aerobic methane oxidation coupled to denitrification process under hypoxic conditions. BIORESOURCE TECHNOLOGY 2020; 318:124043. [PMID: 32911364 DOI: 10.1016/j.biortech.2020.124043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Obligate aerobic methanotrophs have been proven to oxidize methane and participate in denitrification under hypoxic conditions. However, this phenomenon and its metabolic mechanism have not been investigated in detail in aerobic methane oxidation coupled to denitrification (AME-D) process. In this study, a type of hypoxic AME-D consortium was enriched and operated for a long time in a CH4-cycling bioreactor with strict anaerobic control and the nitrite removal rate reached approximately 50 mg N/L/d. Metagenomics combined with DNA stable-isotope probing demonstrated that the genus Methylomonas, which constitutes type I aerobic methanotrophs, was the dominant member and contributed to methane oxidation and partial denitrification. Metagenomic binning recovered a near-complete (98%) draft genome affiliated with the family Methylococcaceae containing essential genes that encode nitrite reductase (nirK), nitric oxide reductase (norBC) and hydroxylamine dehydrogenase (hao). Metabolic reconstruction of the selected Methylococcaceae genomes also revealed a potential link between methanotrophy and partial denitrification.
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Affiliation(s)
- Shici Zhang
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, China; Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Zhaoji Zhang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Shibin Xia
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, China
| | - Ningning Ding
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xien Long
- School of Geographic Sciences, Nantong University, No. 999 Tongjing Road, Nantong 226007, China
| | - Jinsong Wang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Minquan Chen
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Chengsong Ye
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Shaohua Chen
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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22
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Shi LD, Lv PL, Wang M, Lai CY, Zhao HP. A mixed consortium of methanotrophic archaea and bacteria boosts methane-dependent selenate reduction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 732:139310. [PMID: 32442771 DOI: 10.1016/j.scitotenv.2020.139310] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Though methane-based selenate reduction has been reported, neither the selenate load nor the removal rate could satisfy practical applications, thus limiting this technique to bio-remediate selenate pollution. In the present study, using a membrane biofilm batch reactor (MBBR), we successfully enriched a consortium performing methane-dependent selenate reduction, with enhanced reduction rates from 16.1 to 28.9 μM-day-1 under a comparable Se concentration to industrial wastewaters (i.e., ~500 μM). During active reduction, 16S rRNA gene copies of Archaea and Bacteria were both increased more than one order of magnitude. Clone library construction and high-throughput sequencing indicated that Methanosarcina and Methylocystis were the only methane-oxidizing microorganisms. The presence of 20 mM bromoethanesulphonate or 0.15 mM acetylene both significantly, but not completely, inhibited methane-dependent selenate reduction, indicating the concurrent contributions of methanotrophic archaea and bacteria. Fluorescence in situ hybridization (FISH) revealed that archaea directly adhered to the surface of the membrane while bacteria were in the outer layer, together forming the mature biofilm. This study highlights the crucial role of both methanotrophic archaea and bacteria in methane-dependent selenate reduction, and lays foundations in applying methane to bio-remediate practical selenate pollution.
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Affiliation(s)
- Ling-Dong Shi
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Prov Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China
| | - Pan-Long Lv
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Prov Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China
| | - Min Wang
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Chun-Yu Lai
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Prov Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China.
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23
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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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24
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Lundie D, Secco A. Breakthrough instruments and products Hiden Analytical, pQA: A new portable mass spectrometer system for environmental applications. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:079501. [PMID: 32752789 DOI: 10.1063/5.0017811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 06/13/2020] [Indexed: 06/11/2023]
Abstract
The Hiden pQA portable gas analyzer is a versatile mass spectrometer suitable for broad application ranges where analysis of dissolved species in liquid samples is required. The system's gas analysis breakthrough features are its ability to handle small sample volumes and in environmental applications where detection of low concentration levels is required. In this article, the system's instrumental characteristics and a few high-impact applications are described.
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Affiliation(s)
- David Lundie
- Hiden Analytical Ltd., 420 Europa Blvd., Warrington WA57UN, United Kingdom
| | - Andrea Secco
- Hiden Analytical Ltd., 420 Europa Blvd., Warrington WA57UN, United Kingdom
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25
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Shi LD, Wang M, Han YL, Lai CY, Shapleigh JP, Zhao HP. Multi-omics reveal various potential antimonate reductases from phylogenetically diverse microorganisms. Appl Microbiol Biotechnol 2019; 103:9119-9129. [DOI: 10.1007/s00253-019-10111-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/23/2019] [Accepted: 08/28/2019] [Indexed: 12/11/2022]
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Qin Y, Ding B, Li Z, Chen S. Variation of Feammox following ammonium fertilizer migration in a wheat-rice rotation area, Taihu Lake, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:119-127. [PMID: 31146225 DOI: 10.1016/j.envpol.2019.05.055] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 05/10/2019] [Accepted: 05/12/2019] [Indexed: 06/09/2023]
Abstract
Feammox is a newly discovered and important anaerobic nitrogen (N) loss pathway, and its variation and role in removing N following the application of N fertilizer and its migration from paddies to other land use types and from surface soils to deep soils have not been thoroughly elucidated to date. In this study, field sampling and slurry incubation experiments were performed to evaluate the Feammox rate between different land use types (paddy, irrigation ditch, riparian zone and lake, 0-10 cm) and different paddy soil depths (0-70 cm) in a wheat-rice rotation area in China. Based on a 15N-labelled isotope-tracing technique and analysis of microbial communities, it was estimated that the potential Feammox rate ranged from 0.031 to 0.42 mg N kg-1 d-1 in this area. In the soil profile of the paddy, the depth of 20-30 cm was the active region of Feammox, with a value of 0.37 ± 0.057 mg N kg-1 d-1. Compared with the surface soil (0-10 cm) of the paddy (0.18 ± 0.031 mg N kg-1 d-1), the potential Feammox rate of the irrigation ditch soil was not significantly different, but that of the lake riparian soil and lake sediment were decreased by 27.27% and 32.11%, respectively (p < 0.01). Fe(III) content was the best predictor of the Feammox rate and explained the variation of the Feammox rate by 36.00% in the surface soil. At the genus level, the paddy soil at a depth of 20-30 cm had the greatest abundance of the genera in which the Fe reduction bacteria were distributed; and where Bacillus, Geobacter and Anaeromyxobacter had higher proportions. It was estimated that the potential N loss by Feammox was in the range of 7.36 (the lake) ∼43.35 (the paddy) kg N ha-1 year-1 in the surface soil of this area. Considering denitrification and the Feammox rate as a whole, we found that denitrification remained to be the main contributor to N loss in the surface soil (94.72-96.89% of N loss), although Feammox dominated N loss in the deep soil (below 0-10 cm).
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Affiliation(s)
- Yunbin Qin
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, 210023, China; School of the Environment, Nanjing University, Jiangsu, Nanjing, 210023, China
| | - Bangjing Ding
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, 210023, China; School of the Environment, Nanjing University, Jiangsu, Nanjing, 210023, China
| | - Zhengkui Li
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, 210023, China; School of the Environment, Nanjing University, Jiangsu, Nanjing, 210023, China.
| | - Shi Chen
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, 210023, China; School of the Environment, Nanjing University, Jiangsu, Nanjing, 210023, China
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Palacin-Lizarbe C, Camarero L, Hallin S, Jones CM, Cáliz J, Casamayor EO, Catalan J. The DNRA-Denitrification Dichotomy Differentiates Nitrogen Transformation Pathways in Mountain Lake Benthic Habitats. Front Microbiol 2019; 10:1229. [PMID: 31214153 PMCID: PMC6558203 DOI: 10.3389/fmicb.2019.01229] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/16/2019] [Indexed: 01/04/2023] Open
Abstract
Effects of nitrogen (N) deposition on microbially-driven processes in oligotrophic freshwater ecosystems are poorly understood. We quantified guilds in the main N-transformation pathways in benthic habitats of 11 mountain lakes along a dissolved inorganic nitrogen gradient. The genes involved in denitrification (nirS, nirK, nosZ), nitrification (archaeal and bacterial amoA), dissimilatory nitrate reduction to ammonium (DNRA, nrfA) and anaerobic ammonium oxidation (anammox, hdh) were quantified, and the bacterial 16S rRNA gene was sequenced. The dominant pathways and associated bacterial communities defined four main N-transforming clusters that differed across habitat types. DNRA dominated in the sediments, except in the upper layers of more productive lakes where nirS denitrifiers prevailed with potential N2O release. Loss as N2 was more likely in lithic biofilms, as indicated by the higher hdh and nosZ abundances. Archaeal ammonia oxidisers predominated in the isoetid rhizosphere and rocky littoral sediments, suggesting nitrifying hotspots. Overall, we observed a change in potential for reactive N recycling via DNRA to N losses via denitrification as lake productivity increases in oligotrophic mountain lakes. Thus, N deposition results in a shift in genetic potential from an internal N accumulation to an atmospheric release in the respective lake systems, with increased risk for N2O emissions from productive lakes.
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Affiliation(s)
- Carlos Palacin-Lizarbe
- Centro de Investigación Ecológica y Aplicaciones Forestales, Cerdanyola del Vallès, Spain
| | - Lluís Camarero
- Center for Advanced Studies of Blanes, (CEAB-CSIC), Girona, Spain
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christopher M Jones
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Joan Cáliz
- Center for Advanced Studies of Blanes, (CEAB-CSIC), Girona, Spain
| | | | - Jordi Catalan
- Centro de Investigación Ecológica y Aplicaciones Forestales, Cerdanyola del Vallès, Spain.,Consejo Superior de Investigaciones Científicas, Cerdanyola del Vallès, Spain
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Bodelier PLE, Pérez G, Veraart AJ, Krause SMB. Methanotroph Ecology, Environmental Distribution and Functioning. METHANOTROPHS 2019. [DOI: 10.1007/978-3-030-23261-0_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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29
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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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Lai CY, Dong QY, Rittmann BE, Zhao HP. Bioreduction of Antimonate by Anaerobic Methane Oxidation in a Membrane Biofilm Batch Reactor. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:8693-8700. [PMID: 30001126 DOI: 10.1021/acs.est.8b02035] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Employing a special anaerobic membrane biofilm batch reactor (MBBR), we demonstrated antimonate (Sb(V)) reduction using methane (CH4) as the sole electron donor. Scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), and Raman and photoluminescence (PL) spectra identified that Sb2O3 microcrystals were the main reduced products. The Sb(V) reduction rate increased continually over the 111-day experiment, which supports the enrichment of the microorganisms responsible for Sb(V) reduction to Sb(III). Copy numbers of the mcrA gene and archaeal and bacterial 16 S rRNA genes increased in parallel. Clone library and Illumina sequencing of 16S rRNA gene demonstrated that Methanosarcina became the dominant archaea in the biofilm, suggesting that Methanosarcina might play an important role in Sb(V) reduction in the CH4-based MBBR.
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Affiliation(s)
- Chun-Yu Lai
- College of Environmental and Resource Science , Zhejiang University , Hangzhou , Zhejiang 310058 , China
- Advanced Water Management Centre , The University of Queensland , St Lucia , Queensland 4072 , Australia
| | - Qiu-Yi Dong
- College of Environmental and Resource Science , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology , Arizona State University , P.O. Box 875701, Tempe , Arizona 85287-5701 , United States
| | - He-Ping Zhao
- College of Environmental and Resource Science , Zhejiang University , Hangzhou , Zhejiang 310058 , China
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety , Zhejiang University , Hangzhou , Zhejiang 310058 , China
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science , Zhejiang University , Hangzhou , Zhejiang 310058 , China
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