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Liu XY, Ma JY, Wang Y, Duan JL, Feng LJ, Zhu FP, Sun XD, Yan Z, Yuan XZ. Chemical Dynamics of Selenium Nanoparticles in Archaeal Systems. ACS NANO 2024; 18:15661-15670. [PMID: 38841753 DOI: 10.1021/acsnano.4c01596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Methanogenic archaea, characterized by their cell membrane lipid molecules consisting of isoprenoid chains linked to glycerol-1-phosphate via ether bonds, exhibit exceptional adaptability to extreme environments. However, this distinct lipid architecture also complicates the interactions between methanogenic archaea and nanoparticles. This study addresses this challenge by exploring the interaction and transformation of selenium nanoparticles (SeNPs) within archaeal Methanosarcina acetivorans C2A. We demonstrated that the effects of SeNPs are highly concentration-dependent, with chemical stimulation of cellular processes at lower SeNPs concentrations as well as oxidative stress and metabolic disruption at higher concentrations. Notably, we observed the formation of a protein corona on SeNPs, characterized by the selective adsorption of enzymes critical for methylotrophic methanogenesis and those involved in selenium methylation, suggesting potential alterations in protein function and metabolic pathways. Furthermore, the intracellular transformation of SeNPs into both inorganic and organic selenium species highlighted their bioavailability and dynamic transformation within archaea. These findings provide vital insights into the nano-bio interface in archaeal systems, contributing to our understanding of archaeal catalysis and its broader applications.
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Affiliation(s)
- Xiao-Yu Liu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Jing-Ya Ma
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Yue Wang
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Jian-Lu Duan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Li-Juan Feng
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
- College of Geography and Environment, Shandong Normal University, Jinan, Shandong 250014, P. R. China
| | - Fan-Ping Zhu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Xiao-Dong Sun
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Zhen Yan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Xian-Zheng Yuan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
- Sino-French Research Institute for Ecology and Environment, Shandong University, Qingdao, Shandong 266237, P. R. China
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Cowan DA, Albers SV, Antranikian G, Atomi H, Averhoff B, Basen M, Driessen AJM, Jebbar M, Kelman Z, Kerou M, Littlechild J, Müller V, Schönheit P, Siebers B, Vorgias K. Extremophiles in a changing world. Extremophiles 2024; 28:26. [PMID: 38683238 PMCID: PMC11058618 DOI: 10.1007/s00792-024-01341-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Extremophiles and their products have been a major focus of research interest for over 40 years. Through this period, studies of these organisms have contributed hugely to many aspects of the fundamental and applied sciences, and to wider and more philosophical issues such as the origins of life and astrobiology. Our understanding of the cellular adaptations to extreme conditions (such as acid, temperature, pressure and more), of the mechanisms underpinning the stability of macromolecules, and of the subtleties, complexities and limits of fundamental biochemical processes has been informed by research on extremophiles. Extremophiles have also contributed numerous products and processes to the many fields of biotechnology, from diagnostics to bioremediation. Yet, after 40 years of dedicated research, there remains much to be discovered in this field. Fortunately, extremophiles remain an active and vibrant area of research. In the third decade of the twenty-first century, with decreasing global resources and a steadily increasing human population, the world's attention has turned with increasing urgency to issues of sustainability. These global concerns were encapsulated and formalized by the United Nations with the adoption of the 2030 Agenda for Sustainable Development and the presentation of the seventeen Sustainable Development Goals (SDGs) in 2015. In the run-up to 2030, we consider the contributions that extremophiles have made, and will in the future make, to the SDGs.
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Affiliation(s)
- D A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa.
| | - S V Albers
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - G Antranikian
- Institute of Technical Biocatalysis, Hamburg University of Technology, 21073, Hamburg, Germany
| | - H Atomi
- Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - B Averhoff
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt Am Main, Germany
| | - M Basen
- Department of Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - A J M Driessen
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - M Jebbar
- Univ. Brest, CNRS, Ifremer, Laboratoire de Biologie Et d'Écologie Des Écosystèmes Marins Profonds (BEEP), IUEM, Rue Dumont d'Urville, 29280, Plouzané, France
| | - Z Kelman
- Institute for Bioscience and Biotechnology Research and the National Institute of Standards and Technology, Rockville, MD, USA
| | - M Kerou
- Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - J Littlechild
- Henry Wellcome Building for Biocatalysis, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - V Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt Am Main, Germany
| | - P Schönheit
- Institute of General Microbiology, Christian Albrechts University, Kiel, Germany
| | - B Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, 45117, Essen, Germany
| | - K Vorgias
- Biology Department and RI-Bio3, National and Kapodistrian University of Athens, Athens, Greece
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3
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Hanišáková N, Vítězová M, Vítěz T, Kushkevych I, Kotrlová E, Novák D, Lochman J, Zavada R. Microbiological insight into various underground gas storages in Vienna Basin focusing on methanogenic Archaea. Front Microbiol 2023; 14:1293506. [PMID: 38188570 PMCID: PMC10771303 DOI: 10.3389/fmicb.2023.1293506] [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: 09/13/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024] Open
Abstract
In recent years, there has been a growing interest in extending the potential of underground gas storage (UGS) facilities to hydrogen and carbon dioxide storage. However, this transition to hydrogen storage raises concerns regarding potential microbial reactions, which could convert hydrogen into methane. It is crucial to gain a comprehensive understanding of the microbial communities within any UGS facilities designated for hydrogen storage. In this study, underground water samples and water samples from surface technologies from 7 different UGS objects located in the Vienna Basin were studied using both molecular biology methods and cultivation methods. Results from 16S rRNA sequencing revealed that the proportion of archaea in the groundwater samples ranged from 20 to 58%, with methanogens being the predominant. Some water samples collected from surface technologies contained up to 87% of methanogens. Various species of methanogens were isolated from individual wells, including Methanobacterium sp., Methanocalculus sp., Methanolobus sp. or Methanosarcina sp. We also examined water samples for the presence of sulfate-reducing bacteria known to be involved in microbially induced corrosion and identified species of the genus Desulfovibrio in the samples. In the second part of our study, we contextualized our data by comparing it to available sequencing data from terrestrial subsurface environments worldwide. This allowed us to discern patterns and correlations between different types of underground samples based on environmental conditions. Our findings reveal presence of methanogens in all analyzed groups of underground samples, which suggests the possibility of unintended microbial hydrogen-to-methane conversion and the associated financial losses. Nevertheless, the prevalence of methanogens in our results also highlights the potential of the UGS environment, which can be effectively leveraged as a bioreactor for the conversion of hydrogen into methane, particularly in the context of Power-to-Methane technology.
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Affiliation(s)
- Nikola Hanišáková
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Monika Vítězová
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Tomáš Vítěz
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
- Department of Agricultural, Food and Environmental Engineering, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Ivan Kushkevych
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Eva Kotrlová
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - David Novák
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Lochman
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Roman Zavada
- Innovation Unit, NAFTA a.s., Bratislava, Slovakia
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Thapa A, Jo H, Han U, Cho SK. Ex-situ biomethanation for CO 2 valorization: State of the art, recent advances, challenges, and future prospective. Biotechnol Adv 2023; 68:108218. [PMID: 37481094 DOI: 10.1016/j.biotechadv.2023.108218] [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: 01/18/2023] [Revised: 06/21/2023] [Accepted: 07/17/2023] [Indexed: 07/24/2023]
Abstract
Ex-situ biomethanation is an emerging technology that facilitates the use of surplus renewable electricity and valorizes carbon dioxide (CO2) for biomethane production by hydrogenotrophic methanogens. This review offers an up-to-date overview of the current state of ex-situ biomethanation and thoroughly analyzes key operational parameters affecting hydrogen (H2) gas-liquid mass transfer and biomethanation performance, along with an in-depth discussion of the technical challenges. To the best of our knowledge, this is the first review article to discuss microbial community structure in liquid and biofilm phases and their responses after exposure to H2 starvation during ex-situ biomethanation. In addition, future research in areas such as reactor configuration and optimization of operational parameters for improving the H2 mass transfer rate, inhibiting opportunistic homoacetogens, integration of membrane technology, and use of conductive packing material is recommended to overcome challenges and improve the efficiency of ex-situ biomethanation. Furthermore, this review presents a techno-economic analysis for the future development and facilitation of industrial implementation. The insights presented in this review will offer useful information to identify state-of-the-art research trends and realize the full potential of this emerging technology for CO2 utilization and biomethane production.
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Affiliation(s)
- Ajay Thapa
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, IIsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Hongmok Jo
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, IIsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Uijeong Han
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, IIsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Si-Kyung Cho
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, IIsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea.
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Feickert Fenske C, Strübing D, Koch K. Biological methanation in trickle bed reactors - a critical review. BIORESOURCE TECHNOLOGY 2023:129383. [PMID: 37355141 DOI: 10.1016/j.biortech.2023.129383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/08/2023] [Accepted: 06/20/2023] [Indexed: 06/26/2023]
Abstract
Biological methanation of H2 and CO2 in trickle bed reactors is a promising energy conversion and storage approach that can support the energy transition towards a renewable-based system. Research in trickle bed reactor design and operation has significantly increased in recent years, but most studies were performed at laboratory scale and conditions. This review provides a comprehensive overview of the trickle bed reactor concept and current developments to support the decision-making process for future projects. In particular, the key design and operational parameters, such as trickling or nutrient provision, are presented, introducing the most recent advances. Furthermore, reactor operation, including the inoculation, long-term and dynamic operation, is described. To better assess the reactor upscaling, several parameters that enable reactor comparison are discussed. On the basis of this review, suitable operational strategies and further research needs were identified that will improve the overall trickle bed reactor performance.
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Affiliation(s)
- Carolina Feickert Fenske
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Dietmar Strübing
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Konrad Koch
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany.
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Fuchs W, Rachbauer L, Rittmann SKMR, Bochmann G, Ribitsch D, Steger F. Eight Up-Coming Biotech Tools to Combat Climate Crisis. Microorganisms 2023; 11:1514. [PMID: 37375016 DOI: 10.3390/microorganisms11061514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Biotechnology has a high potential to substantially contribute to a low-carbon society. Several green processes are already well established, utilizing the unique capacity of living cells or their instruments. Beyond that, the authors believe that there are new biotechnological procedures in the pipeline which have the momentum to add to this ongoing change in our economy. Eight promising biotechnology tools were selected by the authors as potentially impactful game changers: (i) the Wood-Ljungdahl pathway, (ii) carbonic anhydrase, (iii) cutinase, (iv) methanogens, (v) electro-microbiology, (vi) hydrogenase, (vii) cellulosome and, (viii) nitrogenase. Some of them are fairly new and are explored predominantly in science labs. Others have been around for decades, however, with new scientific groundwork that may rigorously expand their roles. In the current paper, the authors summarize the latest state of research on these eight selected tools and the status of their practical implementation. We bring forward our arguments on why we consider these processes real game changers.
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Affiliation(s)
- Werner Fuchs
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
| | - Lydia Rachbauer
- Lawrence Berkeley National Laboratory, Deconstruction Division at the Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Djerassiplatz 1, 1030 Wien, Austria
| | - Günther Bochmann
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
| | - Doris Ribitsch
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria
| | - Franziska Steger
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
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Lipidomics and Comparative Metabolite Excretion Analysis of Methanogenic Archaea Reveal Organism-Specific Adaptations to Varying Temperatures and Substrate Concentrations. mSystems 2023; 8:e0115922. [PMID: 36880756 PMCID: PMC10134847 DOI: 10.1128/msystems.01159-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Methanogenic archaea possess diverse metabolic characteristics and are an ecologically and biotechnologically important group of anaerobic microorganisms. Although the scientific and biotechnological value of methanogens is evident with regard to their methane-producing physiology, little is known about their amino acid excretion, and virtually nothing is known about the lipidome at different substrate concentrations and temperatures on a quantitative comparative basis. Here, we present the lipidome and a comprehensive quantitative analysis of proteinogenic amino acid excretion as well as methane, water, and biomass production of the three autotrophic, hydrogenotrophic methanogens Methanothermobacter marburgensis, Methanothermococcus okinawensis, and Methanocaldococcus villosus under varying temperatures and nutrient supplies. The patterns and rates of production of excreted amino acids and the lipidome are unique for each tested methanogen and can be modulated by varying the incubation temperature and substrate concentration, respectively. Furthermore, the temperature had a significant influence on the lipidomes of the different archaea. The water production rate was much higher, as anticipated from the rate of methane production for all studied methanogens. Our results demonstrate the need for quantitative comparative physiological studies connecting intracellular and extracellular constraints of organisms to holistically investigate microbial responses to environmental conditions. IMPORTANCE Biological methane production by methanogenic archaea has been well studied for biotechnological purposes. This study reveals that methanogenic archaea actively modulate their lipid inventory and proteinogenic amino acid excretion pattern in response to environmental changes and the possible utilization of methanogenic archaea as microbial cell factories for the targeted production of lipids and amino acids.
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8
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Palabikyan H, Ruddyard A, Pomper L, Novak D, Reischl B, Rittmann SKMR. Scale-up of biomass production by Methanococcus maripaludis. Front Microbiol 2022; 13:1031131. [PMID: 36504798 PMCID: PMC9727139 DOI: 10.3389/fmicb.2022.1031131] [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: 08/29/2022] [Accepted: 10/13/2022] [Indexed: 11/24/2022] Open
Abstract
The development of a sustainable energy economy is one of the great challenges in the current times of climate crisis and growing energy demands. Industrial production of the fifth-generation biofuel methane by microorganisms has the potential to become a crucial biotechnological milestone of the post fossil fuel era. Therefore, reproducible cultivation and scale-up of methanogenic archaea (methanogens) is essential for enabling biomass generation for fundamental studies and for defining peak performance conditions for bioprocess development. This study provides a comprehensive revision of established and optimization of novel methods for the cultivation of the model organism Methanococcus maripaludis S0001. In closed batch mode, 0.05 L serum bottles cultures were gradually replaced by 0.4 L Schott bottle cultures for regular biomass generation, and the time for reaching peak optical density (OD578) values was reduced in half. In 1.5 L reactor cultures, various agitation, harvesting and transfer methods were compared resulting in a specific growth rate of 0.16 h-1 and the highest recorded OD578 of 3.4. Finally, a 300-fold scale-up from serum bottles was achieved by growing M. maripaludis for the first time in a 22 L stainless steel bioreactor with 15 L working volume. Altogether, the experimental approaches described in this study contribute to establishing methanogens as essential organisms in large-scale biotechnology applications, a crucial stage of an urgently needed industrial evolution toward sustainable biosynthesis of energy and high value products.
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Affiliation(s)
- Hayk Palabikyan
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria
| | - Aquilla Ruddyard
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria,Arkeon GmbH, Tulln a.d. Donau, Austria
| | - Lara Pomper
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria
| | - David Novak
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Barbara Reischl
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria,Arkeon GmbH, Tulln a.d. Donau, Austria
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria,Arkeon GmbH, Tulln a.d. Donau, Austria,*Correspondence: Simon K.-M. R. Rittmann,
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9
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Lyu Z, Rotaru AE, Pimentel M, Zhang CJ, Rittmann SKMR. Editorial: The methane moment - Cross-boundary significance of methanogens: Preface. Front Microbiol 2022; 13:1055494. [PMID: 36504803 PMCID: PMC9731359 DOI: 10.3389/fmicb.2022.1055494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Zhe Lyu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States,Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States,*Correspondence: Zhe Lyu
| | - Amelia-Elena Rotaru
- Nordic Center for Earth Evolution (NORDCEE), University of Southern Denmark, Odense, Denmark,Amelia-Elena Rotaru
| | - Mark Pimentel
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, United States,Mark Pimentel
| | - Cui-Jing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China,Cui-Jing Zhang
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria,Arkeon GmbH, Tulln a.d. Donau, Austria,Simon K.-M. R. Rittmann
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Li J, Akinyemi TS, Shao N, Chen C, Dong X, Liu Y, Whitman WB. Genetic and Metabolic Engineering of Methanococcus spp. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Ebrahimian F, De Bernardini N, Tsapekos P, Treu L, Zhu X, Campanaro S, Karimi K, Angelidaki I. Effect of pressure on biomethanation process and spatial stratification of microbial communities in trickle bed reactors under decreasing gas retention time. BIORESOURCE TECHNOLOGY 2022; 361:127701. [PMID: 35905873 DOI: 10.1016/j.biortech.2022.127701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
The current study investigated the effect of elevating gas pressure on biomethanation in trickle-bed reactors (TBRs). The increased pressure led to successful biomethanation (CH4 > 90 %) at a gas retention time (GRT) of 21 min, due to the improved transfer rates of H2 and CO2. On the contrary, the non-pressurized TBR performance was reduced at GRTs shorter than 40 min. Metagenomic analysis revealed that the microbial populations collected from the lower and middle parts of the reactor under the same GRT were more homogeneous compared with those developed in the upper layer. Comparison with previous experiments suggest that microbial stratification is mainly driven by the nutrient provision strategy. Methanobacterium species was the most dominant methanogen and it was mainly associated with the bottom and middle parts of TBRs. Overall, the increased pressure did not affect markedly the microbial composition, while the GRT was the most important parameter shaping the microbiomes.
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Affiliation(s)
- Farinaz Ebrahimian
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark; Department of Chemical Engineering, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Nicola De Bernardini
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121 Padova, Italy
| | - Panagiotis Tsapekos
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
| | - Laura Treu
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121 Padova, Italy
| | - Xinyu Zhu
- School of Engineering, Westlake University, No.18, Shilongshan Road, Cloud Town, Xihu District, Hangzhou, Zhejiang Province, China
| | - Stefano Campanaro
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121 Padova, Italy
| | - Keikhosro Karimi
- Department of Chemical Engineering, Isfahan University of Technology, Isfahan 84156-83111, Iran; Department of Chemical Engineering, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Irini Angelidaki
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
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Li J, Zhang L, Xu Q, Zhang W, Li Z, Chen L, Dong X. CRISPR-Cas9 Toolkit for Genome Editing in an Autotrophic CO 2-Fixing Methanogenic Archaeon. Microbiol Spectr 2022; 10:e0116522. [PMID: 35766512 PMCID: PMC9430280 DOI: 10.1128/spectrum.01165-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/04/2022] [Indexed: 11/23/2022] Open
Abstract
The CRISPR-Cas9 system is a robust genome editing tool that is widely applied in eukaryotes and bacteria. However, use of this technique has only been developed for one species of Archaea, a domain of life ranking in parallel with Eukarya and Bacteria. In this study, we applied the CRISPR-Cas9 genome editing technique to Methanococcus maripaludis, an autotrophic and hydrogenotrophic methanogenic archaeon with a remarkably polyploid genome comprising up to ~55 chromosomal copies per cell. An editing plasmid was designed that encodes small guide RNA (sgRNA), Cas9 protein and an ~1-kb repair template (donor). Highly efficient (75% to 100%) and precise genome editing was achieved following one-step transformation. Significantly, the Cas9-based system efficiently deleted one or two genes and a large DNA fragment (~9 kb) and even synchronously deleted 13 genes located at three loci in all chromosomal copies of M. maripaludis. Moreover, precise in situ genome modifications, such as gene tagging and multiple- and even single-nucleotide mutagenesis, were also introduced with high efficiency. Further, as a proof of concept, precise mutagenesis at the nucleotide level allowed the engineering of both transcriptional and translational activities. Mutations were introduced into an archaeal promoter BRE (transcription factor B [TFB] recognition element), a terminator U-tract region, and a gene coding region. Stop codon introduction into a gene through single-nucleotide substitution shut down its expression, providing an alternative strategy for gene inactivation. In conclusion, the robust CRISPR-Cas9 genetic toolkit developed in this investigation greatly facilitates the application of M. maripaludis as a model system in the study of archaeal biology and biotechnology development, particularly CO2-based biotechnologies. IMPORTANCE Archaea are prokaryotes with intriguing biological characteristics. They possess bacterial cell structures but eukaryotic homologous information processing machinery and eukaryotic featured proteins. Archaea also display excellent adaptability to extreme environments and play pivotal roles in ecological processes, thus exhibiting valuable biotechnological potential. However, the in-depth understanding and practical application of archaea are much lagging, because only a minority of pure cultures are available, and even worse, very few can be genetically manipulated. This work developed CRISPR-Cas9-based genome editing technology in Methanococcus maripaludis, a CO2-fixing methanogenic archaeon. The CRISPR-Cas9 approach developed in this study provides an elegant and efficient genome editing toolkit that can be applied in the knockout of single or multiple genes, in situ gene tagging, multiple- or single-nucleotide mutagenesis, and inactivation of gene expression by introduction of stop codons. The successful development of the CRISPR-Cas9 toolkit will facilitate the application of M. maripaludis in archaeal biology research and biotechnology development, particularly CO2-derived biotechnologies.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liuyang Zhang
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Qing Xu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China
| | - Wenting Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhihua Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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Biological Aspects, Advancements and Techno-Economical Evaluation of Biological Methanation for the Recycling and Valorization of CO2. ENERGIES 2022. [DOI: 10.3390/en15114064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Nowadays, sustainable and renewable energy production is a global priority. Over the past decade, several Power-to-X (PtX) technologies have been proposed to store and convert the surplus of renewable energies into chemical bonds of chemicals produced by different processes. CO2 is a major contributor to climate change, yet it is also an undervalued source of carbon that could be recycled and represents an opportunity to generate renewable energy. In this context, PtX technologies would allow for CO2 valorization into renewable fuels while reducing greenhouse gas (GHG) emissions. With this work we want to provide an up-to-date overview of biomethanation as a PtX technology by considering the biological aspects and the main parameters affecting its application and scalability at an industrial level. Particular attention will be paid to the concept of CO2-streams valorization and to the integration of the process with renewable energies. Aspects related to new promising technologies such as in situ, ex situ, hybrid biomethanation and the concept of underground methanation will be discussed, also in connection with recent application cases. Furthermore, the technical and economic feasibility will be critically analyzed to highlight current options and limitations for implementing a sustainable process.
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14
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Baumann LMF, Taubner RS, Oláh K, Rohrweber AC, Schuster B, Birgel D, Rittmann SKMR. Quantitative Analysis of Core Lipid Production in Methanothermobacter marburgensis at Different Scales. Bioengineering (Basel) 2022; 9:169. [PMID: 35447729 PMCID: PMC9027985 DOI: 10.3390/bioengineering9040169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/06/2022] [Indexed: 11/17/2022] Open
Abstract
Archaeal lipids have a high biotechnological potential, caused by their high resistance to oxidative stress, extreme pH values and temperatures, as well as their ability to withstand phospholipases. Further, methanogens, a specific group of archaea, are already well-established in the field of biotechnology because of their ability to use carbon dioxide and molecular hydrogen or organic substrates. In this study, we show the potential of the model organism Methanothermobacter marburgensis to act both as a carbon dioxide based biological methane producer and as a potential supplier of archaeal lipids. Different cultivation settings were tested to gain an insight into the optimal conditions to produce specific core lipids. The study shows that up-scaling at a constant particle number (n/n = const.) seems to be a promising approach. Further optimizations regarding the length and number of the incubation periods and the ratio of the interaction area to the total liquid volume are necessary for scaling these settings for industrial purposes.
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Affiliation(s)
- Lydia M. F. Baumann
- Institute for Geology, Center for Earth System Research and Sustainability, Universität Hamburg, Bundesstraße 55, 20146 Hamburg, Germany; (L.M.F.B.); (A.-C.R.); (D.B.)
| | - Ruth-Sophie Taubner
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Djerassiplatz 1, 1030 Wien, Austria;
- Institute for Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria; (K.O.); (B.S.)
- Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, Altenbergerstraße 69, 4040 Linz, Austria
| | - Kinga Oláh
- Institute for Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria; (K.O.); (B.S.)
| | - Ann-Cathrin Rohrweber
- Institute for Geology, Center for Earth System Research and Sustainability, Universität Hamburg, Bundesstraße 55, 20146 Hamburg, Germany; (L.M.F.B.); (A.-C.R.); (D.B.)
| | - Bernhard Schuster
- Institute for Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria; (K.O.); (B.S.)
| | - Daniel Birgel
- Institute for Geology, Center for Earth System Research and Sustainability, Universität Hamburg, Bundesstraße 55, 20146 Hamburg, Germany; (L.M.F.B.); (A.-C.R.); (D.B.)
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Djerassiplatz 1, 1030 Wien, Austria;
- Arkeon GmbH, Technopark 1, 3430 Tulln an der Donau, Austria
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15
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The Historical Development of Cultivation Techniques for Methanogens and Other Strict Anaerobes and Their Application in Modern Microbiology. Microorganisms 2022; 10:microorganisms10020412. [PMID: 35208865 PMCID: PMC8879435 DOI: 10.3390/microorganisms10020412] [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: 01/20/2022] [Revised: 02/03/2022] [Accepted: 02/09/2022] [Indexed: 02/06/2023] Open
Abstract
The cultivation and investigation of strictly anaerobic microorganisms belong to the fields of anaerobic microbial physiology, microbiology, and biotechnology. Anaerobic cultivation methods differ from classic microbiological techniques in several aspects. The requirement for special instruments, which are designed to prevent the contact of the specimen with air/molecular oxygen by different means of manipulation, makes this field more challenging for general research compared to working with aerobic microorganisms. Anaerobic microbiological methods are required for many purposes, such as for the isolation and characterization of new species and their physiological examination, as well as for anaerobic biotechnological applications or medical indications. This review presents the historical development of methods for the cultivation of strictly anaerobic microorganisms focusing on methanogenic archaea, anaerobic cultivation methods that are still widely used today, novel methods for anaerobic cultivation, and almost forgotten, but still relevant, techniques.
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16
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Bio-Fermentation Improved Rumen Fermentation and Decreased Methane Concentration of Rice Straw by Altering the Particle-Attached Microbial Community. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8020072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Bio-fermentation technology has been successfully developed for ensiling rice straw; however, its effects on the particle-attached microbial community remains unknown. Therefore, rice straw (RS) and bio-fermented rice straw (BFRS) were used as substrates for in vitro rumen fermentation to investigate the effect of bio-fermentation on particle-attached microbial community, as well as their effects on gas and methane production, fermentation products, and fiber degradation. Our results have shown that total gas production, fiber degradation, and in vitro fermentation products were significantly higher (p < 0.05) for the BFRS than the RS, while methane concentration in total gas volume was significantly lower (p < 0.05) for the BFRS than RS. Linear discriminant effect size (LefSe) analysis revealed that the relative abundance of the phyla Bacteroidetes, Fibrobacteres, Proteobacteria, and Lantisphaerae, as well as the genera Fibrobacter, Saccharofermentans, and [Eubacterium] ruminantium groups in the tightly attached bacterial community, was significantly higher (p < 0.05) for the BFRS than the RS, whereas other microbial communities did not change. Thus, bio-fermentation altered the tightly attached bacterial community, thereby improving gas production, fiber degradation, and fermentation products. Furthermore, bio-fermentation reduced methane concentration in total gas volume without affecting the archaeal community.
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17
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Logroño W, Nikolausz M, Harms H, Kleinsteuber S. Physiological Effects of 2-Bromoethanesulfonate on Hydrogenotrophic Pure and Mixed Cultures. Microorganisms 2022; 10:microorganisms10020355. [PMID: 35208809 PMCID: PMC8877471 DOI: 10.3390/microorganisms10020355] [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: 12/17/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 01/27/2023] Open
Abstract
Mixed or pure cultures can be used for biomethanation of hydrogen. Sodium 2-bromoethanesulfonate (BES) is an inhibitor of methanogenesis used to investigate competing reactions like homoacetogenesis in mixed cultures. To understand the effect of BES on the hydrogenotrophic metabolism in a biomethanation process, anaerobic granules from a wastewater treatment plant, a hydrogenotrophic enrichment culture, and pure cultures of Methanococcus maripaludis and Methanobacterium formicicum were incubated under H2/CO2 headspace in the presence or absence of BES, and the turnover of H2, CO2, CH4, formate and acetate was analyzed. Anaerobic granules produced the highest amount of formate after 24 h of incubation in the presence of BES. Treating the enrichment culture with BES led to the accumulation of formate. M. maripaludis produced more formate than M. formicicum when treated with BES. The non-inhibited methanogenic communities produced small amounts of formate whereas the pure cultures did not. The highest amount of acetate was produced by the anaerobic granules concomitantly with formate consumption. These results indicate that formate is an important intermediate of hydrogenotrophic metabolism accumulating upon methanogenesis inhibition.
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18
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Haloarchaea as emerging big players in future polyhydroxyalkanoate bioproduction: Review of trends and perspectives. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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19
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Abstract
Climate neutral and sustainable energy sources will play a key role in future energy production. Biomethanation by gas to gas conversion of flue gases is one option with regard to renewable energy production. Here, we performed the conversion of synthetic carbon monoxide (CO)-containing flue gases to methane (CH4) by artificial hyperthermophilic archaeal co-cultures, consisting of Thermococcus onnurineus and Methanocaldococcus jannaschii, Methanocaldococcus vulcanius, or Methanocaldococcus villosus. Experiments using both chemically defined and complex media were performed in closed batch setups. Up to 10 mol% CH4 was produced by converting pure CO or synthetic CO-containing industrial waste gases at a high rate using a co-culture of T. onnurineus and M. villosus. These findings are a proof of principle and advance the fields of Archaea Biotechnology, artificial microbial ecosystem design and engineering, industrial waste-gas recycling, and biomethanation.
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20
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Design and engineering of artificial microbial consortia for biohydrogen production. Curr Opin Biotechnol 2021; 73:74-80. [PMID: 34340187 DOI: 10.1016/j.copbio.2021.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 12/24/2022]
Abstract
In natural microbial ecosystems the metabolic diversity of the organisms enables interaction among the community members and allows them to engage in syntrophic interactions. With regard to biotechnology, artificial microbial consortium engineering is used to improve productivities and yields of bioprocesses. However, to achieve supreme productivity or efficiency at industrial scale, defined ecosystems must be physiologically well-selected to meet eco-biotechnological demands. Here, we present an artificial microbial consortia design and engineering pipeline for developing dark fermentative biohydrogen production processes. The proposed pipeline might be considered as a blue-print for enhancing other bioprocesses that fundamentally face metabolic restrictions or kinetic limitations.
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21
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Methanogenesis at High Temperature, High Ionic Strength and Low pH in the Volcanic Area of Dallol, Ethiopia. Microorganisms 2021; 9:microorganisms9061231. [PMID: 34204110 PMCID: PMC8228321 DOI: 10.3390/microorganisms9061231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 11/17/2022] Open
Abstract
The Dallol geothermal area originated as a result of seismic activity and the presence of a shallow underground volcano, both due to the divergence of two tectonic plates. In its ascent, hot water dissolves and drags away the subsurface salts. The temperature of the water that comes out of the chimneys is higher than 100 °C, with a pH close to zero and high mineral concentration. These factors make Dallol a polyextreme environment. So far, nanohaloarchaeas, present in the salts that form the walls of the chimneys, have been the only living beings reported in this extreme environment. Through the use of complementary techniques: culture in microcosms, methane stable isotope signature and hybridization with specific probes, the methanogenic activity in the Dallol area has been assessed. Methane production in microcosms, positive hybridization with the Methanosarcinales probe and the δ13CCH4-values measured, show the existence of extensive methanogenic activity in the hydrogeothermic Dallol system. A methylotrophic pathway, carried out by Methanohalobium and Methanosarcina-like genera, could be the dominant pathway for methane production in this environment.
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