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Wang J, Qu YN, Evans PN, Guo Q, Zhou F, Nie M, Jin Q, Zhang Y, Zhai X, Zhou M, Yu Z, Fu QL, Xie YG, Hedlund BP, Li WJ, Hua ZS, Wang Z, Wang Y. Evidence for nontraditional mcr-containing archaea contributing to biological methanogenesis in geothermal springs. SCIENCE ADVANCES 2023; 9:eadg6004. [PMID: 37379385 DOI: 10.1126/sciadv.adg6004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/24/2023] [Indexed: 06/30/2023]
Abstract
Recent discoveries of methyl-coenzyme M reductase-encoding genes (mcr) in uncultured archaea beyond traditional euryarchaeotal methanogens have reshaped our view of methanogenesis. However, whether any of these nontraditional archaea perform methanogenesis remains elusive. Here, we report field and microcosm experiments based on 13C-tracer labeling and genome-resolved metagenomics and metatranscriptomics, revealing that nontraditional archaea are predominant active methane producers in two geothermal springs. Archaeoglobales performed methanogenesis from methanol and may exhibit adaptability in using methylotrophic and hydrogenotrophic pathways based on temperature/substrate availability. A five-year field survey found Candidatus Nezhaarchaeota to be the predominant mcr-containing archaea inhabiting the springs; genomic inference and mcr expression under methanogenic conditions strongly suggested that this lineage mediated hydrogenotrophic methanogenesis in situ. Methanogenesis was temperature-sensitive , with a preference for methylotrophic over hydrogenotrophic pathways when incubation temperatures increased from 65° to 75°C. This study demonstrates an anoxic ecosystem wherein methanogenesis is primarily driven by archaea beyond known methanogens, highlighting diverse nontraditional mcr-containing archaea as previously unrecognized methane sources.
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Affiliation(s)
- Jiajia Wang
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Yan-Ni Qu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Paul N Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, QLD, Australia
| | - Qinghai Guo
- MOE Key Laboratory of Groundwater Quality and Health, State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Fengwu Zhou
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
- College of Geography Science, Nanjing Normal University, Nanjing 210023, China
| | - Ming Nie
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Fudan University, Shanghai 200433, China
| | - Qusheng Jin
- Department of Earth Sciences, University of Oregon, Eugene, OR 97403, USA
| | - Yan Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiangmei Zhai
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Ming Zhou
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Zhiguo Yu
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Qing-Long Fu
- MOE Key Laboratory of Groundwater Quality and Health, State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Yuan-Guo Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Zimeng Wang
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Fudan University, Shanghai 200433, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Yanxin Wang
- MOE Key Laboratory of Groundwater Quality and Health, State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
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2
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Separating natural from human enhanced methane emissions in headwater streams. Nat Commun 2022; 13:3810. [PMID: 35778387 PMCID: PMC9249869 DOI: 10.1038/s41467-022-31559-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/22/2022] [Indexed: 12/05/2022] Open
Abstract
Headwater streams are natural sources of methane but are suffering severe anthropogenic disturbance, particularly land use change and climate warming. The widespread intensification of agriculture since the 1940s has increased the export of fine sediments from land to streams, but systematic assessment of their effects on stream methane is lacking. Here we show that excess fine sediment delivery is widespread in UK streams (n = 236) and, set against a pre-1940s baseline, has markedly increased streambed organic matter (23 to 100 g m−2), amplified streambed methane production and ultimately tripled methane emissions (0.2 to 0.7 mmol CH4 m−2 d−1, n = 29). While streambed methane production responds strongly to organic matter, we estimate the effect of the approximate 0.7 °C of warming since the 1940s to be comparatively modest. By separating natural from human enhanced methane emissions we highlight how catchment management targeting the delivery of excess fine sediment could mitigate stream methane emissions by some 70%. The effects of fertiliser from intensive agriculture are well recognised, but not so well for fine-sediment. Here we show how widespread ingress of agriculturally derived fine-sediment since the 1940s markedly amplifies methane emissions from streams.
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Pierangeli GMF, Domingues MR, Choueri RB, Hanisch WS, Gregoracci GB, Benassi RF. Spatial Variation and Environmental Parameters Affecting the Abundant and Rare Communities of Bacteria and Archaea in the Sediments of Tropical Urban Reservoirs. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02047-z. [PMID: 35610383 DOI: 10.1007/s00248-022-02047-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Microbial communities in freshwater sediments play an important role in organic matter remineralization, contributing to biogeochemical cycles, nutrient release, and greenhouse gases emissions. Bacterial and archaeal communities might show spatial or seasonal patterns and were shown to be influenced by distinct environmental parameters and anthropogenic activities, including pollution and damming. Here, we determined the spatial variation and the environmental variables influencing the abundant and rare bacterial and archaeal communities in the sediments of eutrophic-hypereutrophic reservoirs from a tropical urban area in Brazil. The most abundant microbes included mainly Anaerolineae and Deltaproteobacteria genera from the Bacteria domain, and Methanomicrobia genera from the Archaea domain. Microbial communities differed spatially in each reservoir, reflecting the establishment of specific environmental conditions. Locations with better or worst water quality, or close to a dam, showed more distinct microbial communities. Besides the water column depth, microbial communities were affected by some pollution indicators, including total phosphorus, orthophosphate, electrical conductivity, and biochemical oxygen demand. Distinct proportions of variation were explained by spatial and environmental parameters for each microbial community. Furthermore, spatial variations in environmental parameters affecting these communities, especially the most distinct ones, contributed to microbial variations mediated by spatial and environmental properties together. Finally, our study showed that different pressures in each reservoir affected the sediment microbiota, promoting different responses and possible adaptations of abundant and rare bacterial and archaeal communities.
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Affiliation(s)
- Gabrielle Maria Fonseca Pierangeli
- Marine Biotechnology Lab (Room 505), Institute of Marine Sciences, Federal University of São Paulo, Campus Baixada Santista, Rua Dr. Carvalho de Mendonça, 144 - Vila Belmiro, Santos, SP, 11070-100, Brazil
| | - Mercia Regina Domingues
- Center of Engineering, Modeling and Applied Social Sciences, Federal University of ABC, Santo André, SP, Brazil
| | - Rodrigo Brasil Choueri
- Marine Biotechnology Lab (Room 505), Institute of Marine Sciences, Federal University of São Paulo, Campus Baixada Santista, Rua Dr. Carvalho de Mendonça, 144 - Vila Belmiro, Santos, SP, 11070-100, Brazil
| | | | - Gustavo Bueno Gregoracci
- Marine Biotechnology Lab (Room 505), Institute of Marine Sciences, Federal University of São Paulo, Campus Baixada Santista, Rua Dr. Carvalho de Mendonça, 144 - Vila Belmiro, Santos, SP, 11070-100, Brazil.
| | - Roseli Frederigi Benassi
- Center of Engineering, Modeling and Applied Social Sciences, Federal University of ABC, Santo André, SP, Brazil
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4
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DelVecchia AG, Shanafield M, Zimmer MA, Busch MH, Krabbenhoft CA, Stubbington R, Kaiser KE, Burrows RM, Hosen J, Datry T, Kampf SK, Zipper SC, Fritz K, Costigan K, Allen DC. Reconceptualizing the hyporheic zone for nonperennial rivers and streams. FRESHWATER SCIENCE (PRINT) 2022; 41:167-182. [PMID: 35846249 PMCID: PMC9280706 DOI: 10.1086/720071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nonperennial streams dominate global river networks and are increasing in occurrence across space and time. When surface flow ceases or the surface water dries, flow or moisture can be retained in the subsurface sediments of the hyporheic zone, supporting aquatic communities and ecosystem processes. However, hydrological and ecological definitions of the hyporheic zone have been developed in perennial rivers and emphasize the mixing of water and organisms, respectively, from both the surface stream and groundwater. The adaptation of such definitions to include both humid and dry unsaturated conditions could promote characterization of how hydrological and biogeochemical variability shape ecological communities within nonperennial hyporheic zones, advancing our understanding of both ecosystem structure and function in these habitats. To conceptualize hyporheic zones for nonperennial streams, we review how water sources and surface and subsurface structure influence hydrological and physicochemical conditions. We consider the extent of this zone and how biogeochemistry and ecology might vary with surface states. We then link these components to the composition of nonperennial stream communities. Next, we examine literature to identify priorities for hydrological and ecological research exploring nonperennial hyporheic zones. Lastly, by integrating hydrology, biogeochemistry, and ecology, we recommend a multidisciplinary conceptualization of the nonperennial hyporheic zone as the porous subsurface streambed sediments that shift between lotic, lentic, humid, and dry conditions in space and time to support aquatic-terrestrial biodiversity. As river drying increases in extent because of global change, we call for holistic, interdisciplinary research across the terrestrial and aquatic sciences to apply this conceptualization to characterize hyporheic zone structure and function across the full spectrum of hydrological states.
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Affiliation(s)
- Amanda G. DelVecchia
- Department of Biology, Duke University, 130 Science Drive, Durham, North Carolina 27708 USA
| | - Margaret Shanafield
- College of Science and Engineering, Flinders University, Ring Road, Bedford Park, South Australia 5042 Australia
| | - Margaret A. Zimmer
- Department of Earth and Planetary Sciences, 1156 High Street, University of California, Santa Cruz, California 95064 USA
| | - Michelle H. Busch
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, Oklahoma 73019 USA
| | - Corey A. Krabbenhoft
- Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, 2003 Upper Buford Circle, St Paul, Minnesota 55108 USA
| | - Rachel Stubbington
- School of Science and Technology, Nottingham Trent University, Clifton Campus, Clifton Lane, Nottingham NG11 8NS United Kingdom
| | - Kendra E. Kaiser
- Geosciences Department, Boise State University, 1295 University Drive, Boise, Idaho 83725 USA
| | - Ryan M. Burrows
- School of Ecosystem and Forest Sciences, University of Melbourne, 500 Yarra Boulevard, Burnley, Victoria 3121 Australia
| | - Jake Hosen
- Department of Forestry and Natural Resources, Purdue University, 195 Marsteller Street, West Lafayette, Indiana 47906 USA
| | - Thibault Datry
- French National Institute for Agriculture, Food, and the Environment, UR-RiverLy, Centre de Lyon-Villeurbanne, Centre Lyon-Grenoble Auvergne-Rhône-Alpes, 5 rue de la Doua CS70077, 69626 Villeurbanne CEDEX France
| | - Stephanie K. Kampf
- Department of Ecosystem Science and Sustainability, Colorado State University, 1476 Campus Delivery, Fort Collins, Colorado 80521 USA
| | - Samuel C. Zipper
- Kansas Geological Survey, 1930 Constant Avenue, Lawrence, Kansas 66047 USA
| | - Ken Fritz
- Office of Research and Development, United States Environmental Protection Agency, 26 West Martin Luther King Drive, Mailstop 585, Cincinnati, Ohio 45268 USA
| | - Katie Costigan
- School of Geosciences, University of Louisiana, 611 McKinley Street, Hamilton Hall 323, P.O. Box 43717, Lafayette, Louisiana 70504USA
| | - Daniel C. Allen
- Department of Ecosystem Science and Management, The Pennsylvania State University, 311 Forestry Resources Building, University Park, Pennsylvania 16802 USA
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5
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Booth MT, Urbanic M, Wang X, Beaulieu JJ. Bioturbation frequency alters methane emissions from reservoir sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:148033. [PMID: 34323816 PMCID: PMC10825729 DOI: 10.1016/j.scitotenv.2021.148033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/09/2021] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
Inland aquatic systems are major global contributors to the atmospheric carbon budget through greenhouse gas (GHG) emissions, although the amount and form of carbon released varies widely across and within systems. Bioturbation of aquatic sediments can impact biogeochemical conditions and physically release sediment-bound bubbles containing GHGs, but variation in the frequency of such disturbance may modify the rate and composition of resulting GHG emissions. We hypothesized that an intermediate bioturbation frequency would result in the greatest methane (CH4) releases due to mechanical release of trapped bubbles, while frequent disturbance would result in greater diffusive carbon dioxide (CO2) releases relative to CH4, due to increased aeration of the sediment. We tested this bioturbation frequency hypothesis using laboratory mesocosms containing homogenized reservoir sediment. We used mechanical disturbance to simulate bioturbation at 3, 7, 14, or 21-day intervals; a control treatment was undisturbed for the duration of the experiment. We measured GHG emission (ebullition and diffusion) rates. An intermediate frequency of disturbance (7 days) produced the highest total GHG emission rate, while the most frequent disturbance interval (3 days) and least frequent interval (0 days) reduced overall GHG emissions relative to weekly disturbance by 24% and 15%, respectively. These patterns were primarily driven by differences in CH4 ebullition. Contrary to our hypothesis, there was no relationship between disturbance frequency and diffusive CO2 emissions. For all disturbance treatments, the majority of ebullition occurred during disturbance events, suggesting mechanical release of entrapped bubbles is an important emission mechanism. The frequency of disturbance has variable effects on GHG emissions and may explain conflicting results in prior studies of bioturbation. Our study provides insight into bioturbation as a driver of within-system variation in GHG emissions and highlights that variable bioturbation frequency results in non-linear responses in CH4 emissions, a globally important GHG, from reservoir sediments.
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Affiliation(s)
- Michael T Booth
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, United States of America.
| | - Megan Urbanic
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, United States of America
| | - Xia Wang
- Division of Statistics and Data Science, Department of Mathematical Sciences, University of Cincinnati, Cincinnati, OH 45221, United States of America.
| | - Jake J Beaulieu
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, United States of America.
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6
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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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7
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Chen C, Yang X, Luo H, Zeng D, Sima M, Huang S. Linking microbial community and biological functions to redox potential during black-odor river sediment remediation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:40392-40404. [PMID: 32666451 DOI: 10.1007/s11356-020-09805-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
The black-odor phenomenon in polluted urban rivers is a serious environmental problem that has received increasing attention in the recent years. The low redox potential (less than - 100 mV) in the sediment is considered to be the key factor causing the occurrence of black-odor phenomenon. Here, we studied the structure and function of the microbial community during the remediation of urban rivers. Results showed a clear improvement in water quality after undergoing river remediation processes. The on-site treatments showed a succession in the microbial composition and their predicted functions. The primary iron- and sulfur-reducing bacteria (Thiobacillus, Sulfuricurvum, and Sulfursoma) and the related reactions rapidly decreased after the dredging treatment but reappeared after a year. The structure and abundance of nitrogen and methane participants were also affected by river remediation process. These results indicated that although the water quality temporarily improved shortly after a dredging process, a recurrence of the black-odor phenomenon may occur as a result of the rebound in the microbial communities.
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Affiliation(s)
- Chen Chen
- State Environmental Protection Key Laboratory of Urban Ecological Environment Simulation and Protection, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Guangzhou, 510535, China
| | - Xunan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, 510070, China
| | - Hailin Luo
- State Environmental Protection Key Laboratory of Urban Ecological Environment Simulation and Protection, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Guangzhou, 510535, China
| | - Dong Zeng
- State Environmental Protection Key Laboratory of Urban Ecological Environment Simulation and Protection, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Guangzhou, 510535, China
| | - Matthew Sima
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Shan Huang
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, 08544, USA.
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.
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8
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Zamanpour MK, Kaliappan RS, Rockne KJ. Gas ebullition from petroleum hydrocarbons in aquatic sediments: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 271:110997. [PMID: 32778285 DOI: 10.1016/j.jenvman.2020.110997] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/19/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023]
Abstract
Gas ebullition in sediment results from biogenic gas production by mixtures of bacteria and archaea. It often occurs in organic-rich sediments that have been impacted by petroleum hydrocarbon (PHC) and other anthropogenic pollution. Ebullition occurs under a relatively narrow set of biological, chemical, and sediment geomechanical conditions. This process occurs in three phases: I) biogenic production of primarily methane and dissolved phase transport of the gases in the pore water to a bubble nucleation site, II) bubble growth and sediment fracture, and III) bubble rise to the surface. The rate of biogenic gas production in phase I and the resistance of the sediment to gas fracture in phase II play the most significant roles in ebullition kinetics. What is less understood is the role that substrate structure plays in the rate of methanogenesis that drives gas ebullition. It is well established that methanogens have a very restricted set of compounds that can serve as substrates, so any complex organic molecule must first be broken down to fermentable compounds. Given that most ebullition-active sediments are completely anaerobic, the well-known difficulty in degrading PHCs under anaerobic conditions suggests potential limitations on PHC-derived gas ebullition. To date, there are no studies that conclusively demonstrate that weathered PHCs can alone drive gas ebullition. This review consists of an overview of the factors affecting gas ebullition and the biochemistry of anaerobic PHC biodegradation and methanogenesis in sediment systems. We next compile results from the scholarly literature on PHCs serving as a source of methanogenesis. We combine these results to assess the potential for PHC-driven gas ebullition using energetics, kinetics, and sediment geomechanics analyses. The results suggest that short chain <C10 alkanes are the only PHC class that alone may have the potential to drive ebullition, and that PHC-derived methanogenesis likely plays a minor part in driving gas ebullition in contaminated sediments compared to natural organic matter.
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Affiliation(s)
| | - Raja Shankar Kaliappan
- Department of Civil and Materials Engineering, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Karl John Rockne
- Department of Civil and Materials Engineering, University of Illinois at Chicago, Chicago, IL, 60607, USA.
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9
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Bagnoud A, Pramateftaki P, Bogard MJ, Battin TJ, Peter H. Microbial Ecology of Methanotrophy in Streams Along a Gradient of CH 4 Availability. Front Microbiol 2020; 11:771. [PMID: 32477286 PMCID: PMC7241049 DOI: 10.3389/fmicb.2020.00771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Abstract
Despite the recognition of streams and rivers as sources of methane (CH4) to the atmosphere, the role of CH4 oxidation (MOX) in these ecosystems remains poorly understood to date. Here, we measured the kinetics of MOX in stream sediments of 14 sites to resolve the ecophysiology of CH4 oxidizing bacteria (MOB) communities. The streams cover a gradient of land cover and associated physicochemical parameter and differed in stream- and porewater CH4 concentrations. Michealis–Menten kinetic parameter of MOX, maximum reaction velocity (Vmax), and CH4 concentration at half Vmax (KS) increased with CH4 supply. KS values in the micromolar range matched the CH4 concentrations measured in shallow stream sediments and indicate that MOX is mostly driven by low-affinity MOB. 16S rRNA gene sequencing identified MOB classified as Methylococcaceae and particularly Crenothrix. Their relative abundance correlated with pmoA gene counts and MOX rates, underscoring their pivotal role as CH4 oxidizers in stream sediments. Building on the concept of enterotypes, we identify two distinct groups of co-occurring MOB. While there was no taxonomic difference among the members of each cluster, one cluster contained abundant and common MOB, whereas the other cluster contained rare operational taxonomic units (OTUs) specific to a subset of streams. These integrated analyses of changes in MOB community structure, gene abundance, and the corresponding ecosystem process contribute to a better understanding of the distal controls on MOX in streams.
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Affiliation(s)
- Alexandre Bagnoud
- Stream Biofilm and Ecosystem Research Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Paraskevi Pramateftaki
- Stream Biofilm and Ecosystem Research Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matthew J Bogard
- Groupe de recherche interuniversitaire en limnologie, Département des sciences biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Tom J Battin
- Stream Biofilm and Ecosystem Research Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Hannes Peter
- Stream Biofilm and Ecosystem Research Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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10
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Pedron R, Esposito A, Bianconi I, Pasolli E, Tett A, Asnicar F, Cristofolini M, Segata N, Jousson O. Genomic and metagenomic insights into the microbial community of a thermal spring. MICROBIOME 2019; 7:8. [PMID: 30674352 PMCID: PMC6343286 DOI: 10.1186/s40168-019-0625-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/14/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Water springs provide important ecosystem services including drinking water supply, recreation, and balneotherapy, but their microbial communities remain largely unknown. In this study, we characterized the spring water microbiome of Comano Terme (Italy) at four sampling points of the thermal spa, including natural (spring and well) and human-built (storage tank, bathtubs) environments. We integrated large-scale culturing and metagenomic approaches, with the aim of comprehensively determining the spring water taxonomic composition and functional potential. RESULTS The groundwater feeding the spring hosted the most atypical microbiome, including many taxa known to be recalcitrant to cultivation. The core microbiome included the orders Sphingomonadales, Rhizobiales, and Caulobacterales, and the families Bradyrhizobiaceae and Moraxellaceae. A comparative genomic analysis of 72 isolates and 30 metagenome-assembled genomes (MAGs) revealed that most isolates and MAGs belonged to new species or higher taxonomic ranks widely distributed in the microbial tree of life. Average nucleotide identity (ANI) values calculated for each isolated or assembled genome showed that 10 genomes belonged to known bacterial species (> 95% ANI), 36 genomes (including 1 MAG) had ANI values ranging 85-92.5% and could be assigned as undescribed species belonging to known genera, while the remaining 55 genomes had lower ANI values (< 85%). A number of functional features were significantly over- or underrepresented in genomes derived from the four sampling sites. Functional specialization was found between sites, with for example methanogenesis being unique to groundwater whereas methanotrophy was found in all samples. CONCLUSIONS Current knowledge on aquatic microbiomes is essentially based on surface or human-associated environments. We started uncovering the spring water microbiome, highlighting an unexpected diversity that should be further investigated. This study confirms that groundwater environments host highly adapted, stable microbial communities composed of many unknown taxa, even among the culturable fraction.
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Affiliation(s)
- Renato Pedron
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Alfonso Esposito
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Irene Bianconi
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Edoardo Pasolli
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Adrian Tett
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesco Asnicar
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | | | - Nicola Segata
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Olivier Jousson
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
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11
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Ulrich N, Kirchner V, Drucker R, Wright JR, McLimans CJ, Hazen TC, Campa MF, Grant CJ, Lamendella R. Response of Aquatic Bacterial Communities to Hydraulic Fracturing in Northwestern Pennsylvania: A Five-Year Study. Sci Rep 2018; 8:5683. [PMID: 29632304 PMCID: PMC5890257 DOI: 10.1038/s41598-018-23679-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 03/08/2018] [Indexed: 01/09/2023] Open
Abstract
Horizontal drilling and hydraulic fracturing extraction procedures have become increasingly present in Pennsylvania where the Marcellus Shale play is largely located. The potential for long-term environmental impacts to nearby headwater stream ecosystems and aquatic bacterial assemblages is still incompletely understood. Here, we perform high-throughput sequencing of the 16 S rRNA gene to characterize the bacterial community structure of water, sediment, and other environmental samples (n = 189) from 31 headwater stream sites exhibiting different histories of fracking activity in northwestern Pennsylvania over five years (2012-2016). Stream pH was identified as a main driver of bacterial changes within the streams and fracking activity acted as an environmental selector for certain members at lower taxonomic levels within stream sediment. Methanotrophic and methanogenic bacteria (i.e. Methylocystaceae, Beijerinckiaceae, and Methanobacterium) were significantly enriched in sites exhibiting Marcellus shale activity (MSA+) compared to MSA- streams. This study highlighted potential sentinel taxa associated with nascent Marcellus shale activity and some of these taxa remained as stable biomarkers across this five-year study. Identifying the presence and functionality of specific microbial consortia within fracking-impacted streams will provide a clearer understanding of the natural microbial community's response to fracking and inform in situ remediation strategies.
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Affiliation(s)
- Nikea Ulrich
- Juniata College, Department of Biology, Huntingdon, 16652, USA
| | | | - Rebecca Drucker
- Juniata College, Department of Biology, Huntingdon, 16652, USA
| | | | | | - Terry C Hazen
- University of Tennessee, Department of Civil and Environmental Engineering, Knoxville, 37996, USA
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, 37831, USA
| | - Maria F Campa
- University of Tennessee, Department of Civil and Environmental Engineering, Knoxville, 37996, USA
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, 37831, USA
| | | | - Regina Lamendella
- Juniata College, Department of Biology, Huntingdon, 16652, USA.
- Wright Labs LLC, Huntingdon, 16652, USA.
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12
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Methanogens in humans: potentially beneficial or harmful for health. Appl Microbiol Biotechnol 2018; 102:3095-3104. [DOI: 10.1007/s00253-018-8871-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/13/2018] [Accepted: 02/14/2018] [Indexed: 12/18/2022]
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13
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Zhang J, Xia X, Li S, Ran W. Response of methane production via propionate oxidation to carboxylated multiwalled carbon nanotubes in paddy soil enrichments. PeerJ 2018; 6:e4267. [PMID: 29340254 PMCID: PMC5768162 DOI: 10.7717/peerj.4267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/25/2017] [Indexed: 01/18/2023] Open
Abstract
Carboxylated multiwalled carbon nanotubes (MWCNTs-COOH) have become a growing concern in terms of their fate and toxicity in aqueous environments. Methane (CH4) is a major product of organic matter degradation in waterlogged environments. In this study, we determined the effect of MWCNTs-COOH on the production of CH4 from propionate oxidation in paddy soil enrichments. The results showed that the methanogenesis from propionate degradation was accelerated in the presence of MWCNTs-COOH. In addition, the rates of CH4 production and propionate degradation increased with increasing concentrations of MWCNTs-COOH. Scanning electron microscopy (SEM) observations showed that the cells were intact and maintained their structure in the presence of MWCNTs-COOH. In addition, SEM and fluorescence in situ hybridization (FISH) images revealed that the cells were in direct contact with the MWCNTs and formed cell-MWCNTs aggregates that contained both bacteria and archaea. On the other hand, nontoxic magnetite nanoparticles (Fe3O4) had similar effects on the CH4 production and cell integrity as the MWCNTs-COOH. Compared with no nanomaterial addition, the relative abundances of Geobacter and Methanosarcina species increased in the presence of MWCNTs-COOH. This study suggests that MWCNTs-COOH exerted positive rather than cytotoxic effects on the syntrophic oxidation of propionate in paddy soil enrichments and affected the bacterial and archaeal community structure at the test concentrations. These findings provide novel insight into the consequences of nanomaterial release into anoxic natural environments.
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Affiliation(s)
- Jianchao Zhang
- Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
| | - Xingxuan Xia
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Siliang Li
- Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
| | - Wei Ran
- Jiangsu Provincial Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
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14
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Laskar F, Das Purkayastha S, Sen A, Bhattacharya MK, Misra BB. Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems. J Basic Microbiol 2017; 58:101-119. [PMID: 29083035 DOI: 10.1002/jobm.201700341] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 12/15/2022]
Abstract
About half of the global methane (CH4 ) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH4 emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea.
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Affiliation(s)
- Folguni Laskar
- Advance Institutional Biotech Hub, Karimganj College, Karimganj, Assam, India
| | | | - Aniruddha Sen
- Advance Institutional Biotech Hub, Karimganj College, Karimganj, Assam, India
| | | | - Biswapriya B Misra
- Department of Genetics, Texas Biomedical Research Institute, San Antonio 78227, Texas, USA
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15
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Li F, Zheng F, Wang Y, Liu W, Zhang CL. Thermoplasmatales and Methanogens: Potential Association with the Crenarchaeol Production in Chinese Soils. Front Microbiol 2017; 8:1200. [PMID: 28717356 PMCID: PMC5494375 DOI: 10.3389/fmicb.2017.01200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 06/12/2017] [Indexed: 11/13/2022] Open
Abstract
Crenarchaeol is a unique isoprenoid glycerol dibiphytanyl glycerol tetraether (iGDGT) lipid, which is only identified in cultures of ammonia-oxidizing Thaumarchaeota. However, the taxonomic origins of crenarchaeol have been debated recently. The archaeal populations, other than Thaumarchaeota, may have associations with the production of crenarchaeol in ecosystems characterized by non-thaumarchaeotal microorganisms. To this end, we investigated 47 surface soils from upland and wetland soils and rice fields and another three surface sediments from river banks. The goal was to examine the archaeal community compositions in comparison with patterns of iGDGTs in four fractional forms (intact polar-, core-, monoglycosidic- and diglycosidic-lipid fractions) along gradients of environments. The DistLM analysis identified that Group I.1b Thaumarchaeota were mainly responsible for changes in crenarchaeol in the overall soil samples; however, Thermoplasmatales may also contribute to it. This is further supported by the comparison of crenarchaeol between samples characterized by methanogens, Thermoplasmatales or Group I.1b Thaumarchaeota, which suggests that the former two may contribute to the crenarchaeol pool. Last, when samples containing enhanced abundance of Thermoplasmatales and methanogens were considered, crenarchaeol was observed to correlate positively with Thermoplasmatales and archaeol, respectively. Collectively, our data suggest that the crenarchaeol production is mainly derived from Thaumarchaeota and partly associated with uncultured representatives of Thermoplasmatales and archaeol-producing methanogens in soil environments that may be in favor of their growth. Our finding supports the notion that Thaumarchaeota may not be the sole source of crenarchaeol in the natural environment, which may have implication for the evolution of lipid synthesis among different types of archaea.
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Affiliation(s)
- Fuyan Li
- Department of Ocean Science and Engineering, Southern University of Science and TechnologyShenzhen, China.,College of Life Sciences, Wuhan UniversityWuhan, China.,Division of Geological and Planetary Sciences, California Institute of Technology, PasadenaCA, United States.,State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Fengfeng Zheng
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Yongli Wang
- Key Laboratory of Petroleum Resources Research, Institute of Geology and Geophysics, Chinese Academy of SciencesLanzhou, China
| | - Weiguo Liu
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of SciencesXi'an, China.,School of Human Settlement and Civil Engineering, Xi'an Jiaotong UniversityXi'an, China
| | - Chuanlun L Zhang
- Department of Ocean Science and Engineering, Southern University of Science and TechnologyShenzhen, China
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16
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Bednařík A, Blaser M, Matoušů A, Hekera P, Rulík M. Effect of weir impoundments on methane dynamics in a river. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 584-585:164-174. [PMID: 28147296 DOI: 10.1016/j.scitotenv.2017.01.163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/21/2017] [Accepted: 01/24/2017] [Indexed: 06/06/2023]
Abstract
We measured CH4 concentration, CH4 oxidation in the water column and total CH4 emissions to the atmosphere (diffusion and ebullition) in three weir impoundments and river reaches between them, in order to understand their role in river methane (CH4) dynamics. Sediment samples were also collected to determine CH4 consumption and production potentials together with the contribution of individual methanogenic pathways. The CH4 surface water concentration increased 7.5 times in the 16km long river stretch. Microbial CH4 oxidation in the water column reached values ranging from 51 to 403nmoll-1d-1 and substantially contributed to the CH4 removal from surface water, together with CH4 emissions. The total CH4 emissions to the atmosphere varied between 0.8 and 207.1mmolCH4m-2d-1 with the highest values observed upstream of the weirs (mean 68.5±29.9mmolCH4m-2d-1). Most of the CH4 was transported through the air-water interface by ebullition upstream of the weirs, while the ebullition accounted for 95.8±2.0% of the total CH4 emissions. Both CH4 production and oxidation potential of sediments were higher upstream of the weirs compared to downstream of the weirs. The contribution of hydrogenotrophic methanogenesis to total CH4 sediment production was 36.7-89.4% and prevailed upstream of the weirs. Our findings indicate that weirs might influence river CH4 dynamics, especially by increased CH4 production and consumption by sediments, followed by increasing CH4 emissions to the atmosphere.
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Affiliation(s)
- Adam Bednařík
- Department of Ecology and Environmental Sciences, Laboratory of Aquatic Microbial Ecology, Faculty of Science, Palacky University in Olomouc, Olomouc, Czech Republic.
| | - Martin Blaser
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Anna Matoušů
- Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic; Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Hydrobiology, České Budějovice, Czech Republic
| | - Petr Hekera
- Department of Ecology and Environmental Sciences, Laboratory of Aquatic Microbial Ecology, Faculty of Science, Palacky University in Olomouc, Olomouc, Czech Republic
| | - Martin Rulík
- Department of Ecology and Environmental Sciences, Laboratory of Aquatic Microbial Ecology, Faculty of Science, Palacky University in Olomouc, Olomouc, Czech Republic
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17
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Chaudhary PP, Rulík M, Blaser M. Is the methanogenic community reflecting the methane emissions of river sediments?-comparison of two study sites. Microbiologyopen 2017; 6. [PMID: 28303666 PMCID: PMC5552910 DOI: 10.1002/mbo3.454] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/22/2016] [Accepted: 01/04/2017] [Indexed: 11/24/2022] Open
Abstract
Studies on methanogenesis from freshwater sediments have so far primarily focused on lake sediments. To expand our knowledge on the community composition of methanogenic archaea in river sediments, we studied the abundance and diversity of methanogenic archaea at two localities along a vertical profile (top 50 cm) obtained from sediment samples from Sitka stream (the Czech Republic). In this study, we compare two sites which previously have been shown to have a 10‐fold different methane emission. Archaeal and methanogen abundance were analyzed by real‐time PCR and T‐RFLP. Our results show that the absolute numbers for the methanogenic community (qPCR) are relatively stable along a vertical profile as well as for both study sites. This was also true for the archaeal community and for the three major methanogenic orders in our samples (Methanosarcinales, Methanomicrobiales, and Methanobacteriales). However, the underlying community structure (T‐RFLP) reveals different community compositions of the methanogens for both locations as well as for different depth layers and over different sampling times. In general, our data confirm that Methanosarcinales together with Methanomicrobiales are the two dominant methanogenic orders in river sediments, while members of Methanobacteriales contribute a smaller community and Methanocellales are only rarely present in this sediment. Our results show that the previously observed 10‐fold difference in methane emission of the two sites could not be explained by molecular methods alone.
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Affiliation(s)
| | - Martin Rulík
- Department of Ecology and Environmental Sciences, Faculty of Science, Laboratory of Aquatic Microbial Ecology, Palacky University, Olomouc, Czech Republic
| | - Martin Blaser
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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18
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McGinnis DF, Bilsley N, Schmidt M, Fietzek P, Bodmer P, Premke K, Lorke A, Flury S. Deconstructing Methane Emissions from a Small Northern European River: Hydrodynamics and Temperature as Key Drivers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:11680-11687. [PMID: 27696829 DOI: 10.1021/acs.est.6b03268] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Methane (CH4) emissions from small rivers and streams, particularly via ebullition, are currently under-represented in the literature. Here, we quantify the methane effluxes and drivers in a small, Northern European river. Methane fluxes are comparable to those from tropical aquatic systems, with average emissions of 320 mg CH4 m-2 d-1. Two important drivers of methane flux variations were identified in the studied system: 1) temperature-driven sediment methane ebullition and 2) flow-dependent contribution suspected to be hydraulic exchange with adjacent wetlands and small side-bays. This flow-dependent contribution to river methane loading is shown to be negligible for flows less than 4 m3 s-1 and greater than 50% as flows exceed 7 m3 s-1. While the temperature-ebullition relationship is comparable to other systems, the flow rate dependency has not been previously demonstrated. In general, we found that about 80% of the total emissions were due to methane bubbles. Applying ebullition rates to global estimates for fluvial systems, which currently are not considered, could dramatically increase emission rates to ranges from lakes or wetlands. This work illustrates that small rivers can emit significant methane and highlights the need for further studies on the link between hydrodynamics and connected wetlands.
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Affiliation(s)
- Daniel F McGinnis
- Aquatic Physics, Department F.-A. Forel, Section of Earth and Environment Sciences, Faculty of Science, University of Geneva , CH-1211 Geneva 4, Switzerland
- Chemical Analytics and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB) , 12587 Berlin, Germany
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD2 Marine Biogeochemistry, 24148 Kiel, Germany
| | - Nicole Bilsley
- Scripps Institution of Oceanography, La Jolla, California 92093, United States
| | - Mark Schmidt
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD2 Marine Biogeochemistry, 24148 Kiel, Germany
| | - Peer Fietzek
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD2 Marine Biogeochemistry, 24148 Kiel, Germany
- Kongsberg Maritime Contros GmbH, 24148 Kiel, Germany
| | - Pascal Bodmer
- Chemical Analytics and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB) , 12587 Berlin, Germany
- Institute of Biology, Freie Universität Berlin , 14195 Berlin, Germany
| | - Katrin Premke
- Chemical Analytics and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB) , 12587 Berlin, Germany
| | - Andreas Lorke
- Institute for Environmental Sciences, Environmental Physics, University of Koblenz-Landau , 76829 Landau, Germany
| | - Sabine Flury
- Chemical Analytics and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB) , 12587 Berlin, Germany
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19
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Blaser M, Conrad R. Stable carbon isotope fractionation as tracer of carbon cycling in anoxic soil ecosystems. Curr Opin Biotechnol 2016; 41:122-129. [DOI: 10.1016/j.copbio.2016.07.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 06/29/2016] [Accepted: 07/04/2016] [Indexed: 01/16/2023]
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20
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Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:563414. [PMID: 26568700 PMCID: PMC4623359 DOI: 10.1155/2015/563414] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/26/2015] [Accepted: 08/30/2015] [Indexed: 11/17/2022]
Abstract
Methanogens, a key contributor in global carbon cycling, methane emission, and alternative energy production, generate methane gas via anaerobic digestion of organic matter. The methane emission potential depends upon methanogenic diversity and activity. Since they are anaerobes and difficult to isolate and culture, their diversity present in the landfill sites of Delhi and marshlands of Southern Assam, India, was analyzed using molecular techniques like 16S rDNA sequencing, DGGE, and qPCR. The sequencing results indicated the presence of methanogens belonging to the seventh order and also the order Methanomicrobiales in the Ghazipur and Bhalsawa landfill sites of Delhi. Sequences, related to the phyla Crenarchaeota (thermophilic) and Thaumarchaeota (mesophilic), were detected from marshland sites of Southern Assam, India. Jaccard analysis of DGGE gel using Gel2K showed three main clusters depending on the number and similarity of band patterns. The copy number analysis of hydrogenotrophic methanogens using qPCR indicates higher abundance in landfill sites of Delhi as compared to the marshlands of Southern Assam. The knowledge about "methanogenic archaea composition" and "abundance" in the contrasting ecosystems like "landfill" and "marshland" may reorient our understanding of the Archaea inhabitants. This study could shed light on the relationship between methane-dynamics and the global warming process.
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21
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Zheng S, Zhang H, Li Y, Zhang H, Wang O, Zhang J, Liu F. Co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture. Front Microbiol 2015; 6:941. [PMID: 26441876 PMCID: PMC4562271 DOI: 10.3389/fmicb.2015.00941] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 08/24/2015] [Indexed: 01/06/2023] Open
Abstract
Methanosaeta harundinacea and Methanosarcina barkeri, known as classic acetoclastic methanogens, are capable of directly accepting electrons from Geobacter metallireducens for the reduction of carbon dioxide to methane, having been revealed as direct interspecies electron transfer (DIET) in the laboratory co-cultures. However, whether their co-occurrences are ubiquitous in the iron (III)-reducing environments and the other species of acetoclastic methanogens such as Methanosarcina mazei are capable of DIET are still unknown. Instead of initiating the co-cultures with pure cultures, two-step cultivation was employed to selectively enrich iron (III)-reducing microorganisms in a coastal gold mining river, Jiehe River, with rich iron content in the sediments. First, iron (III) reducers including Geobacteraceae were successfully enriched by 3-months successive culture on amorphous Fe(III) oxides as electron acceptor and acetate as electron donor. High-throughput Illumina sequencing, terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis based on 16S rRNA genes revealed that the enrichment cultures actively contained the bacteria belong to Geobacteraceae and Bacilli, exclusively dominated by the archaea belong to Methanosarcinaceae. Second, the enrichment cultures including methanogens and Geobacteraceae were transferred with ethanol as alternative electron donor. Remarkably, aggregates were successively formed in the enrichments after three transfers. The results revealed by RNA-based analysis demonstrate that the co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture. Furthermore, the aggregates, as close physical contact, formed in the enrichment culture, indicate that DIET could be a possible option for interspecies electron transfer in the aggregates.
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Affiliation(s)
- Shiling Zheng
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
| | - Hongxia Zhang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; University of Chinese Academy of Sciences Beijing, China
| | - Ying Li
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; University of Chinese Academy of Sciences Beijing, China
| | - Hua Zhang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
| | - Oumei Wang
- Key Laboratory for Genetic Hearing Disorders in Shandong, Binzhou Medical University Yantai, China
| | - Jun Zhang
- The College of Life Sciences, Northwest University Xi'an, China
| | - Fanghua Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
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22
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Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions. Appl Microbiol Biotechnol 2015; 99:5801-15. [DOI: 10.1007/s00253-015-6739-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/23/2015] [Accepted: 05/29/2015] [Indexed: 12/11/2022]
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