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Emerson JB, Varner RK, Wik M, Parks DH, Neumann RB, Johnson JE, Singleton CM, Woodcroft BJ, Tollerson R, Owusu-Dommey A, Binder M, Freitas NL, Crill PM, Saleska SR, Tyson GW, Rich VI. Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes. Nat Commun 2021; 12:5815. [PMID: 34611153 PMCID: PMC8492752 DOI: 10.1038/s41467-021-25983-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/07/2021] [Indexed: 11/23/2022] Open
Abstract
Northern post-glacial lakes are significant, increasing sources of atmospheric carbon through ebullition (bubbling) of microbially-produced methane (CH4) from sediments. Ebullitive CH4 flux correlates strongly with temperature, reflecting that solar radiation drives emissions. However, here we show that the slope of the temperature-CH4 flux relationship differs spatially across two post-glacial lakes in Sweden. We compared these CH4 emission patterns with sediment microbial (metagenomic and amplicon), isotopic, and geochemical data. The temperature-associated increase in CH4 emissions was greater in lake middles—where methanogens were more abundant—than edges, and sediment communities were distinct between edges and middles. Microbial abundances, including those of CH4-cycling microorganisms and syntrophs, were predictive of porewater CH4 concentrations. Results suggest that deeper lake regions, which currently emit less CH4 than shallower edges, could add substantially to CH4 emissions in a warmer Arctic and that CH4 emission predictions may be improved by accounting for spatial variations in sediment microbiota. Arctic lakes are strong and increasing sources of atmospheric methane, but extreme conditions and limited observations hinder robust understanding. Here the authors show that microbes in the middle of Arctic lakes have elevated methane producing potential, and are poised to release even more in the future.
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Affiliation(s)
- Joanne B Emerson
- Department of Microbiology, The Ohio State University, 496W 12th Ave, Columbus, OH, 43210, USA. .,Department of Plant Pathology, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.
| | - Ruth K Varner
- Department of Earth Sciences, University of New Hampshire, 56 College Road, Durham, NH, 03824, USA. .,Earth Systems Research Center, Institute for the Study of Earth, Oceans and Space, University of New Hampshire, 8 College Road, Durham, NH, 03824, USA.
| | - Martin Wik
- Department of Geological Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Rebecca B Neumann
- Civil & Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA
| | - Joel E Johnson
- Department of Earth Sciences, University of New Hampshire, 56 College Road, Durham, NH, 03824, USA
| | - Caitlin M Singleton
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia.,Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, 9220, Denmark
| | - Ben J Woodcroft
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Rodney Tollerson
- Department of Microbiology, The Ohio State University, 496W 12th Ave, Columbus, OH, 43210, USA.,Department of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91106, USA
| | - Akosua Owusu-Dommey
- Department of Environmental Science, University of Arizona, Tucson, AZ, 85721, USA.,Parkland Hospital, 5200 Harry Hines Blvd., Dallas, TX, 75235, USA
| | - Morgan Binder
- Department of Environmental Science, University of Arizona, Tucson, AZ, 85721, USA.,John C. Lincoln Health Network, 34975N North Valley Pkwy Ste 100, Phoenix, AZ, 85086, USA
| | - Nancy L Freitas
- Department of Environmental Science, University of Arizona, Tucson, AZ, 85721, USA.,Energy and Resources Group, University of California, Berkeley, USA
| | - Patrick M Crill
- Department of Geological Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Scott R Saleska
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia.,Centre for Microbiome Research, Queensland University of Technology, 37 Kent St, Woolloongabba, QLD, 4102, Australia
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, 496W 12th Ave, Columbus, OH, 43210, USA.
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Microbial Communities in Methane Cycle: Modern Molecular Methods Gain Insights into Their Global Ecology. ENVIRONMENTS 2021. [DOI: 10.3390/environments8020016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The role of methane as a greenhouse gas in the concept of global climate changes is well known. Methanogens and methanotrophs are two microbial groups which contribute to the biogeochemical methane cycle in soil, so that the total emission of CH4 is the balance between its production and oxidation by microbial communities. Traditional identification techniques, such as selective enrichment and pure-culture isolation, have been used for a long time to study diversity of methanogens and methanotrophs. However, these techniques are characterized by significant limitations, since only a relatively small fraction of the microbial community could be cultured. Modern molecular methods for quantitative analysis of the microbial community such as real-time PCR (Polymerase chain reaction), DNA fingerprints and methods based on high-throughput sequencing together with different “omics” techniques overcome the limitations imposed by culture-dependent approaches and provide new insights into the diversity and ecology of microbial communities in the methane cycle. Here, we review available knowledge concerning the abundances, composition, and activity of methanogenic and methanotrophic communities in a wide range of natural and anthropogenic environments. We suggest that incorporation of microbial data could fill the existing microbiological gaps in methane flux modeling, and significantly increase the predictive power of models for different environments.
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Dyksma S, Jansen L, Gallert C. Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste. MICROBIOME 2020; 8:105. [PMID: 32620171 PMCID: PMC7334858 DOI: 10.1186/s40168-020-00862-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/11/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Anaerobic digestion (AD) is a globally important technology for effective waste and wastewater management. In AD, microorganisms interact in a complex food web for the production of biogas. Here, acetoclastic methanogens and syntrophic acetate-oxidizing bacteria (SAOB) compete for acetate, a major intermediate in the mineralization of organic matter. Although evidence is emerging that syntrophic acetate oxidation is an important pathway for methane production, knowledge about the SAOB is still very limited. RESULTS A metabolic reconstruction of metagenome-assembled genomes (MAGs) from a thermophilic solid state biowaste digester covered the basic functions of the biogas microbial community. Firmicutes was the most abundant phylum in the metagenome (53%) harboring species that take place in various functions ranging from the hydrolysis of polymers to syntrophic acetate oxidation. The Wood-Ljungdahl pathway for syntrophic acetate oxidation and corresponding genes for energy conservation were identified in a Dethiobacteraceae MAG that is phylogenetically related to known SAOB. 16S rRNA gene amplicon sequencing and enrichment cultivation consistently identified the uncultured Dethiobacteraceae together with Syntrophaceticus, Tepidanaerobacter, and unclassified Clostridia as members of a potential acetate-oxidizing core community in nine full-scare digesters, whereas acetoclastic methanogens were barely detected. CONCLUSIONS Results presented here provide new insights into a remarkable anaerobic digestion ecosystem where acetate catabolism is mainly realized by Bacteria. Metagenomics and enrichment cultivation revealed a core community of diverse and novel uncultured acetate-oxidizing bacteria and point to a particular niche for them in dry fermentation of biowaste. Their genomic repertoire suggests metabolic plasticity besides the potential for syntrophic acetate oxidation. Video Abstract.
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Affiliation(s)
- Stefan Dyksma
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany.
| | - Lukas Jansen
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany
| | - Claudia Gallert
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany
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Methane Production in Soil Environments-Anaerobic Biogeochemistry and Microbial Life between Flooding and Desiccation. Microorganisms 2020; 8:microorganisms8060881. [PMID: 32545191 PMCID: PMC7357154 DOI: 10.3390/microorganisms8060881] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 11/17/2022] Open
Abstract
Flooding and desiccation of soil environments mainly affect the availability of water and oxygen. While water is necessary for all life, oxygen is required for aerobic microorganisms. In the absence of O2, anaerobic processes such as CH4 production prevail. There is a substantial theoretical knowledge of the biogeochemistry and microbiology of processes in the absence of O2. Noteworthy are processes involved in the sequential degradation of organic matter coupled with the sequential reduction of electron acceptors, and, finally, the formation of CH4. These processes follow basic thermodynamic and kinetic principles, but also require the presence of microorganisms as catalysts. Meanwhile, there is a lot of empirical data that combines the observation of process function with the structure of microbial communities. While most of these observations confirmed existing theoretical knowledge, some resulted in new information. One important example was the observation that methanogens, which have been believed to be strictly anaerobic, can tolerate O2 to quite some extent and thus survive desiccation of flooded soil environments amazingly well. Another example is the strong indication of the importance of redox-active soil organic carbon compounds, which may affect the rates and pathways of CH4 production. It is noteworthy that drainage and aeration turns flooded soils, not generally, into sinks for atmospheric CH4, probably due to the peculiarities of the resident methanotrophic bacteria.
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Vavilin V, Lokshina L, Rytov S. Using kinetic isotope effect to evaluate the significance of the sequential and parallel steps: formation of microbial consortium during reversible anaerobic methane oxidation coupled with sulfate reduction. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2019; 79:2056-2067. [PMID: 31318343 DOI: 10.2166/wst.2019.201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The purpose of this study was to describe the dynamics of anaerobic oxidation of methane (AOM) coupled with sulfate reduction (SR) using experimental data from a continuous incubation experiments published earlier in order to show that formation of consortia of anaerobic archaea (ANME) and Desulfosarcina-like bacteria (DSS) may have a significant effect on sulfur isotope fractionation. The dynamic simulation of reversible AOM by ANME coupled with SR by DSS was performed. This simulation took into account biomass growth and fractionation of stable isotopes of sulfur. Two kinetic schemes with and without ANME + DSS consortium formation were tested. The respective models were applied at five influent methane concentrations. A good fit to experimental data was obtained only when assuming active ANME and DSS biomass accumulation. The assumption about incorporation of reversibility of anaerobic methane oxidation and sulfate reduction did not improve the model's fit to experimental data. In accordance with both the models, sulfur isotope fractionation was smallest for the highest influent methane concentration. The model considering the formation of consortia of ANME + DSS is proved to be more appropriate.
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Affiliation(s)
- Vasily Vavilin
- Water Problems Institute, Russian Academy of Sciences, 3 Gubkina str., Moscow 119333, Russian Federation E-mail:
| | - Lyudmila Lokshina
- Water Problems Institute, Russian Academy of Sciences, 3 Gubkina str., Moscow 119333, Russian Federation E-mail:
| | - Sergey Rytov
- Water Problems Institute, Russian Academy of Sciences, 3 Gubkina str., Moscow 119333, Russian Federation E-mail:
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Vavilin VA, Rytov SV, Lokshina LY. Modelling the specific pathway of CH 4 and CO 2 formation using carbon isotope fractionation: an example for a boreal mesotrophic fen. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2018; 54:475-493. [PMID: 29807459 DOI: 10.1080/10256016.2018.1478820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 03/17/2018] [Indexed: 06/08/2023]
Abstract
We described mathematically the process of peat methanization in a boreal mesotrophic fen. Gaseous and dissolved CH4 and CO2 as well as their δ13C signatures were considered in the dynamic equations for incubation bottles. In accordance with the model, acetate, H2, and CO2 were produced during cellulose hydrolysis and acidogenesis. 13C/12C in CO2 was a key variable reflecting dynamic changes in the rates of cellulose hydrolysis and acidogenesis, acetoclastic and hydrogenotrophic methanogenesis. As CO2 is the substrate in hydrogenotrophic methanogenesis, δ13C-CO2 increased from the start till the dissolved hydrogen concentration became very low. Thereafter, the rate of acetoclastic methanogenesis with the significant current acetate concentration dominated over the rate of hydrogenotrophic methanogenesis leading to the decreasing δ13C-CO2 and the increasing δ13C-CH4. The model was validated by describing the system's dynamics under strong and weak inhibition of acetoclastic and hydrogenotrophic methanogenesis by methyl fluoride, respectively. During peat methanization at the lowered temperature of 10 °C, the processes of hydrogenotrophic methanogenesis and homoacetogenesis competing for H2 may occur. However, based on dynamics of the carbon isotope signatures, especially on dynamics of δ13C-CO2, the model showed no significant contribution of homoacetogens in peat methanization.
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Affiliation(s)
- Vasily A Vavilin
- a Ecological Department , Water Problems Institute, Russian Academy of Sciences , Moscow , Russian Federation
| | - Sergey V Rytov
- a Ecological Department , Water Problems Institute, Russian Academy of Sciences , Moscow , Russian Federation
| | - Lyudmila Y Lokshina
- a Ecological Department , Water Problems Institute, Russian Academy of Sciences , Moscow , Russian Federation
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