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Casini I, McCubbin T, Esquivel-Elizondo S, Luque GG, Evseeva D, Fink C, Beblawy S, Youngblut ND, Aristilde L, Huson DH, Dräger A, Ley RE, Marcellin E, Angenent LT, Molitor B. An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter. iScience 2023; 26:108016. [PMID: 37854702 PMCID: PMC10579436 DOI: 10.1016/j.isci.2023.108016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/29/2023] [Accepted: 09/19/2023] [Indexed: 10/20/2023] Open
Abstract
Methanogenesis allows methanogenic archaea to generate cellular energy for their growth while producing methane. Thermophilic hydrogenotrophic species of the genus Methanothermobacter have been recognized as robust biocatalysts for a circular carbon economy and are already applied in power-to-gas technology with biomethanation, which is a platform to store renewable energy and utilize captured carbon dioxide. Here, we generated curated genome-scale metabolic reconstructions for three Methanothermobacter strains and investigated differences in the growth performance of these same strains in chemostat bioreactor experiments with hydrogen and carbon dioxide or formate as substrates. Using an integrated systems biology approach, we identified differences in formate anabolism between the strains and revealed that formate anabolism influences the diversion of carbon between biomass and methane. This finding, together with the omics datasets and the metabolic models we generated, can be implemented for biotechnological applications of Methanothermobacter in power-to-gas technology, and as a perspective, for value-added chemical production.
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Affiliation(s)
- Isabella Casini
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Synthetic Biology (COESB), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sofia Esquivel-Elizondo
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Guillermo G. Luque
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Daria Evseeva
- Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
| | - Christian Fink
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Sebastian Beblawy
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Nicholas D. Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Daniel H. Huson
- Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Andreas Dräger
- Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Synthetic Biology (COESB), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Largus T. Angenent
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- AG Angenent, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10D, 8000 Aarhus C, Denmark
- The Novo Nordisk Foundation CO2 Research Center (CORC), Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Bastian Molitor
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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2
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Gu W, Müller AL, Deutzmann JS, Williamson JR, Spormann AM. Growth rate-dependent coordination of catabolism and anabolism in the archaeon Methanococcus maripaludis under phosphate limitation. THE ISME JOURNAL 2022; 16:2313-2319. [PMID: 35780255 PMCID: PMC9478154 DOI: 10.1038/s41396-022-01278-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Catabolic and anabolic processes are finely coordinated in microorganisms to provide optimized fitness under varying environmental conditions. Understanding this coordination and the resulting physiological traits reveals fundamental strategies of microbial acclimation. Here, we characterized the system-level physiology of Methanococcus maripaludis, a niche-specialized methanogenic archaeon, at different dilution rates ranging from 0.09 to 0.003 h-1 in chemostat experiments under phosphate (i.e., anabolic) limitation. Phosphate was supplied as the limiting nutrient, while formate was supplied in excess as the catabolic substrate and carbon source. We observed a decoupling of catabolism and anabolism resulting in lower biomass yield relative to catabolically limited cells at the same dilution rates. In addition, the mass abundance of several coarse-grained proteome sectors (i.e., combined abundance of proteins grouped based on their function) exhibited a linear relationship with growth rate, mostly ribosomes and their biogenesis. Accordingly, cellular RNA content also correlated with growth rate. Although the methanogenesis proteome sector was invariant, the metabolic capacity for methanogenesis, measured as methane production rates immediately after transfer to batch culture, correlated with growth rate suggesting translationally independent regulation that allows cells to only increase catabolic activity under growth-permissible conditions. These observations are in stark contrast to the physiology of M. maripaludis under formate (i.e., catabolic) limitation, where cells keep an invariant proteome including ribosomal content and a high methanogenesis capacity across a wide range of growth rates. Our findings reveal that M. maripaludis employs fundamentally different strategies to coordinate global physiology during anabolic phosphate and catabolic formate limitation.
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Affiliation(s)
- Wenyu Gu
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Albert L Müller
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Jörg S Deutzmann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
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3
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Churio MS, Cerletti M, De Castro RE. Carotenoids from Haloarchaea: Extraction, Fractionation, and Characterization. Methods Mol Biol 2022; 2522:331-343. [PMID: 36125760 DOI: 10.1007/978-1-0716-2445-6_21] [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] [Indexed: 06/15/2023]
Abstract
Carotenoids are bioactive molecules known to promote human health. Many extreme halophilic archaea synthesize carotenoids, mainly represented by C50 bacterioruberin (BR) and its derivatives. BR has a potent antioxidant capacity, even higher than that of β-carotene, thus, there is an increasing interest to advance the study of its biological properties as well as to extend its current applications. Here, we describe a procedure to extract and characterize carotenoids (enriched in BR) from haloarchaea using a "hyperpigmented" genetically modified strain of Haloferax volcanii.
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Affiliation(s)
- María Sandra Churio
- Departamento de Química y Bioquímica, FCEyN (UNMDP), Mar del Plata, Argentina.
- IFIMAR, Instituto de Investigaciones Físicas de Mar del Plata (CONICET-UNMDP), Mar del Plata, Argentina.
| | - Micaela Cerletti
- Instituto de Investigaciones Biológicas, FCEyN, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
| | - Rosana Esther De Castro
- Instituto de Investigaciones Biológicas, FCEyN, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina.
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4
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Development of Stable Mixed Microbiota for High Yield Power to Methane Conversion. ENERGIES 2021. [DOI: 10.3390/en14217336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The performance of a mixed microbial community was tested in lab-scale power-to-methane reactors at 55 °C. The main aim was to uncover the responses of the community to starvation and stoichiometric H2/CO2 supply as the sole substrate. Fed-batch reactors were inoculated with the fermentation effluent of a thermophilic biogas plant. Various volumes of pure H2/CO2 gas mixtures were injected into the headspace daily and the process parameters were followed. Gas volumes and composition were measured by gas-chromatography, the headspace was replaced with N2 prior to the daily H2/CO2 injection. Total DNA samples, collected at the beginning and end (day 71), were analyzed by metagenome sequencing. Low levels of H2 triggered immediate CH4 evolution utilizing CO2/HCO3− dissolved in the fermentation effluent. Biomethanation continued when H2/CO2 was supplied. On the contrary, biomethane formation was inhibited at higher initial H2 doses and concomitant acetate formation indicated homoacetogenesis. Biomethane production started upon daily delivery of stoichiometric H2/CO2. The fed-batch operational mode allowed high H2 injection and consumption rates albeit intermittent operation conditions. Methane was enriched up to 95% CH4 content and the H2 consumption rate attained a remarkable 1000 mL·L−1·d−1. The microbial community spontaneously selected the genus Methanothermobacter in the enriched cultures.
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5
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Methanothermobacter thermautotrophicus strain ΔH as a potential microorganism for bioconversion of CO2 to methane. J CO2 UTIL 2020. [DOI: 10.1016/j.jcou.2020.101210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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6
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Zhang L, Loh KC, Sarvanantharajah S, Tong YW, Wang CH, Dai Y. Mesophilic and thermophilic anaerobic digestion of soybean curd residue for methane production: Characterizing bacterial and methanogen communities and their correlations with organic loading rate and operating temperature. BIORESOURCE TECHNOLOGY 2019; 288:121597. [PMID: 31176202 DOI: 10.1016/j.biortech.2019.121597] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 05/28/2023]
Abstract
To find the optimal operation parameters and provide an explanation of methanogenic pathway for methane production in mesophilic (35 °C) and thermophilic (55 °C) anaerobic digestion (MAD, TAD) of soybean curd residue (SCR), MAD and MAD were contrastively investigated for 95 days. The maximum available OLR was identified as 3.3 gVS/L for both MAD and TAD. Compared to MAD, TAD exhibited a 20% higher average methane yield (0.591 L/gVS) and a 7.5% higher volatile solids removal efficiency (74.1 ± 10.4%). Bacterial phyla Bacteroidetes, Firmicutes and Proteobacteria dominated in MAD digesters while genus Defluviitoga was selectively enriched in TAD digesters due to higher temperature and organic loading pressure. Principal coordinates analysis of methanogen community showed that both temperature and OLR were crucial environmental variables shifting the taxonomic patterns of the methanogens. The enriched methanogen genus Methanothermobacter (93%) with a hydrogenotrophic methanogenic pathway had a close correlation with the TAD performance.
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Affiliation(s)
- Le Zhang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore
| | - Kai-Chee Loh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore; NUS Environmental Research Institute, National University of Singapore, 1 Create Way, Create Tower #15-02, Singapore 138602, Singapore.
| | | | - Yen Wah Tong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore; NUS Environmental Research Institute, National University of Singapore, 1 Create Way, Create Tower #15-02, Singapore 138602, Singapore
| | - Chi-Hwa Wang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore; NUS Environmental Research Institute, National University of Singapore, 1 Create Way, Create Tower #15-02, Singapore 138602, Singapore
| | - Yanjun Dai
- School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai, China
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7
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Zalazar L, Pagola P, Miró M, Churio M, Cerletti M, Martínez C, Iniesta-Cuerda M, Soler A, Cesari A, De Castro R. Bacterioruberin extracts from a genetically modified hyperpigmented Haloferax volcanii
strain: antioxidant activity and bioactive properties on sperm cells. J Appl Microbiol 2019; 126:796-810. [DOI: 10.1111/jam.14160] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022]
Affiliation(s)
- L. Zalazar
- Instituto de Investigaciones Biológicas; FCEyN; Universidad Nacional de Mar del Plata (UNMDP); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Mar del Plata Argentina
| | - P. Pagola
- Departamento de Química; FCEyN (UNMDP); Mar del Plata Argentina
| | - M.V. Miró
- Instituto de Investigaciones Biológicas; FCEyN; Universidad Nacional de Mar del Plata (UNMDP); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Mar del Plata Argentina
| | - M.S. Churio
- Departamento de Química; FCEyN (UNMDP); Mar del Plata Argentina
- IFIMAR; Instituto de Investigaciones Físicas de Mar del Plata (CONICET-UNMDP); Mar del Plata Argentina
| | - M. Cerletti
- Instituto de Investigaciones Biológicas; FCEyN; Universidad Nacional de Mar del Plata (UNMDP); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Mar del Plata Argentina
| | - C. Martínez
- Instituto de Investigaciones Biológicas; FCEyN; Universidad Nacional de Mar del Plata (UNMDP); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Mar del Plata Argentina
| | - M. Iniesta-Cuerda
- SaBio IREC (CSIC-UCLM-JCCM). ETSIAM. Campus Universitario; Albacete Spain
| | - A.J. Soler
- SaBio IREC (CSIC-UCLM-JCCM). ETSIAM. Campus Universitario; Albacete Spain
| | - A. Cesari
- Instituto de Investigaciones Biológicas; FCEyN; Universidad Nacional de Mar del Plata (UNMDP); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Mar del Plata Argentina
| | - R. De Castro
- Instituto de Investigaciones Biológicas; FCEyN; Universidad Nacional de Mar del Plata (UNMDP); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Mar del Plata Argentina
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8
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Straub CT, Counts JA, Nguyen DMN, Wu CH, Zeldes BM, Crosby JR, Conway JM, Otten JK, Lipscomb GL, Schut GJ, Adams MWW, Kelly RM. Biotechnology of extremely thermophilic archaea. FEMS Microbiol Rev 2018; 42:543-578. [PMID: 29945179 DOI: 10.1093/femsre/fuy012] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 06/23/2018] [Indexed: 12/26/2022] Open
Abstract
Although the extremely thermophilic archaea (Topt ≥ 70°C) may be the most primitive extant forms of life, they have been studied to a limited extent relative to mesophilic microorganisms. Many of these organisms have unique biochemical and physiological characteristics with important biotechnological implications. These include methanogens that generate methane, fermentative anaerobes that produce hydrogen gas with high efficiency, and acidophiles that can mobilize base, precious and strategic metals from mineral ores. Extremely thermophilic archaea have also been a valuable source of thermoactive, thermostable biocatalysts, but their use as cellular systems has been limited because of the general lack of facile genetics tools. This situation has changed recently, however, thereby providing an important avenue for understanding their metabolic and physiological details and also opening up opportunities for metabolic engineering efforts. Along these lines, extremely thermophilic archaea have recently been engineered to produce a variety of alcohols and industrial chemicals, in some cases incorporating CO2 into the final product. There are barriers and challenges to these organisms reaching their full potential as industrial microorganisms but, if these can be overcome, a new dimension for biotechnology will be forthcoming that strategically exploits biology at high temperatures.
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Affiliation(s)
- Christopher T Straub
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - James A Counts
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Diep M N Nguyen
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Chang-Hao Wu
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - James R Crosby
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Jonathan M Conway
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Jonathan K Otten
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Gina L Lipscomb
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
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9
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Dong N, Bu F, Zhou Q, Khanal SK, Xie L. Performance and microbial community of hydrogenotrophic methanogenesis under thermophilic and extreme-thermophilic conditions. BIORESOURCE TECHNOLOGY 2018; 266:454-462. [PMID: 30005412 DOI: 10.1016/j.biortech.2018.05.105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 06/08/2023]
Abstract
In this study, hydrogenotrophic methanogenesis with respect to methanogenic activity and microbial structures under extreme-thermophilic conditions were examined, and compared with the conventional thermophilic condition. The hydrogenotrophic methanogens were successfully acclimated to the temperatures of 55, 65 and 70 °C. Although acclimation was slower at 65 and 70 °C, hydrogenotrophic methanogenesis remained fairly stable. High-throughput sequencing using 16S rRNA analysis showed that the higher temperatures resulted in single archaea community dominated by hydrogenotrophic Methanothermobacter. Moreover, the syntrophic bacteria changed from Coprothermobacter and Thermodesulfovibrio at 55 °C to Thermodesulfovibrio at 70 °C. Specific hydrogenotrophic methanogenic rate at 70 °C was 98.6 ± 4.2 Nml CH4/g VS/hr, which was over 4-folds higher than that 8at 55 °C. The lag phase under extreme-thermophilic conditions was longer than thermophilic condition, which was probably due to the archaeal structure with low diversity. Extreme-thermophilic condition resulted in a shift in methanogenesis pathway from acetoclastic methanogenesis to hydrogenotrophic methanogenesis with the enrichment of Methanothermobacter thermautotrophicus.
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Affiliation(s)
- Nanshi Dong
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze River Water Environment, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Fan Bu
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze River Water Environment, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Qi Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze River Water Environment, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Samir Kumar Khanal
- Department of Molecular Biosciences and Bioengineering (MBBE), University of Hawai'i at Mānoa, 1955 East-West Road, Agricultural Science Building 218, Honolulu, HI 96822, USA
| | - Li Xie
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze River Water Environment, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
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10
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Mauerhofer LM, Reischl B, Schmider T, Schupp B, Nagy K, Pappenreiter P, Zwirtmayr S, Schuster B, Bernacchi S, Seifert AH, Paulik C, Rittmann SKMR. Physiology and methane productivity of Methanobacterium thermaggregans. Appl Microbiol Biotechnol 2018; 102:7643-7656. [PMID: 29959465 PMCID: PMC6097776 DOI: 10.1007/s00253-018-9183-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/13/2018] [Accepted: 06/13/2018] [Indexed: 11/29/2022]
Abstract
Accumulation of carbon dioxide (CO2), associated with global temperature rise, and drastically decreasing fossil fuels necessitate the development of improved renewable and sustainable energy production processes. A possible route for CO2 recycling is to employ autotrophic and hydrogenotrophic methanogens for CO2-based biological methane (CH4) production (CO2-BMP). In this study, the physiology and productivity of Methanobacterium thermaggregans was investigated in fed-batch cultivation mode. It is shown that M. thermaggregans can be reproducibly adapted to high agitation speeds for an improved CH4 productivity. Moreover, inoculum size, sulfide feeding, pH, and temperature were optimized. Optimization of growth and CH4 productivity revealed that M. thermaggregans is a slightly alkaliphilic and thermophilic methanogen. Hitherto, it was only possible to grow seven autotrophic, hydrogenotrophic methanogenic strains in fed-batch cultivation mode. Here, we show that after a series of optimization and growth improvement attempts another methanogen, M. thermaggregas could be adapted to be grown in fed-batch cultivation mode to cell densities of up to 1.56 g L-1. Moreover, the CH4 evolution rate (MER) of M. thermaggregans was compared to Methanothermobacter marburgensis, the CO2-BMP model organism. Under optimized cultivation conditions, a maximum MER of 96.1 ± 10.9 mmol L-1 h-1 was obtained with M. thermaggregans-97% of the maximum MER that was obtained utilizing M. marburgensis in a reference experiment. Therefore, M. thermaggregans can be regarded as a CH4 cell factory highly suited to be applicable for CO2-BMP.
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Affiliation(s)
- Lisa-Maria Mauerhofer
- Archaea Physiology & Biotechnology Group, Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Althanstraße 14, 1090, Wien, Austria
| | - Barbara Reischl
- Archaea Physiology & Biotechnology Group, Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Althanstraße 14, 1090, Wien, Austria
- Krajete GmbH, Linz, Austria
| | - Tilman Schmider
- Archaea Physiology & Biotechnology Group, Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Althanstraße 14, 1090, Wien, Austria
| | - Benjamin Schupp
- Archaea Physiology & Biotechnology Group, Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Althanstraße 14, 1090, Wien, Austria
| | - Kinga Nagy
- Archaea Physiology & Biotechnology Group, Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Althanstraße 14, 1090, Wien, Austria
- Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Institute of Synthetic Bioarchitectures, Wien, Austria
| | - Patricia Pappenreiter
- Johannes Kepler Universität Linz, Institute for Chemical Technology of Organic Materials, Linz, Austria
| | - Sara Zwirtmayr
- Johannes Kepler Universität Linz, Institute for Chemical Technology of Organic Materials, Linz, Austria
| | - Bernhard Schuster
- Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Institute of Synthetic Bioarchitectures, Wien, Austria
| | | | | | - Christian Paulik
- Johannes Kepler Universität Linz, Institute for Chemical Technology of Organic Materials, Linz, Austria
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Althanstraße 14, 1090, Wien, Austria.
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11
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Lecker B, Illi L, Lemmer A, Oechsner H. Biological hydrogen methanation - A review. BIORESOURCE TECHNOLOGY 2017; 245:1220-1228. [PMID: 28893503 DOI: 10.1016/j.biortech.2017.08.176] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 05/07/2023]
Abstract
Surplus energy out of fluctuating energy sources like wind and solar energy is strongly increasing. Biological hydrogen (H2) methanation (BHM) is a highly promising approach to move the type of energy from electricity to natural gas via electrolysis and the subsequent step of the Sabatier-reaction. This review provides an overview of the numerous studies concerning the topic of BHM. The technical and biological parameters regarding the research results of these studies are compared and analyzed hereafter. A holistic view on how to overcome physical limitations of the fermentation process, such as gas-liquid mass transfer or a rise of the pH value, and on the enhancement of environmental circumstances for the bacterial biomass are delivered within. With regards to ex-situ methanation, the evaluated studies show a distinct connection between methane production and the methane percentage in the off-gas.
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Affiliation(s)
- Bernhard Lecker
- University of Hohenheim, State Institute of Agricultural Engineering and Bioenergy, Garbenstraße 9, 70599 Stuttgart, Germany.
| | - Lukas Illi
- University of Hohenheim, State Institute of Agricultural Engineering and Bioenergy, Garbenstraße 9, 70599 Stuttgart, Germany
| | - Andreas Lemmer
- University of Hohenheim, State Institute of Agricultural Engineering and Bioenergy, Garbenstraße 9, 70599 Stuttgart, Germany
| | - Hans Oechsner
- University of Hohenheim, State Institute of Agricultural Engineering and Bioenergy, Garbenstraße 9, 70599 Stuttgart, Germany
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12
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Abdel Azim A, Pruckner C, Kolar P, Taubner RS, Fino D, Saracco G, Sousa FL, Rittmann SKMR. The physiology of trace elements in biological methane production. BIORESOURCE TECHNOLOGY 2017. [PMID: 28628982 DOI: 10.1016/j.biortech.2017.05.211] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Trace element (TE) requirements of Methanothermobacter okinawensis and Methanothermobacter marburgensis were examined in silico, and using closed batch and fed-batch cultivation experiments. In silico analysis revealed genomic differences among the transport systems and enzymes related to the archaeal Wood-Ljungdahl pathway of these two methanogens. M. okinawensis responded to rising concentrations of TE by increasing specific growth rate (µ) and volumetric productivity (MER) during closed batch cultivation, and can grow and produce methane (CH4) during fed-batch cultivation. M. marburgensis showed higher µ and MER during fed-batch cultivation and was therefore prioritized for subsequent optimization of CO2-based biological CH4 production. Multiple-parameter cultivation dependency on growth and productivity of M. marburgensis was finally examined using exponential fed-batch cultivation at different medium-, TE- and sulphide dilution rates, and different gas inflow rates. MER of 476mmolL-1h-1 and µ of 0.69h-1 were eventually obtained during exponential fed-batch cultivations employing M. marburgensis.
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Affiliation(s)
- Annalisa Abdel Azim
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Vienna, Austria; Department of Applied Science and Technology (DISAT), Politecnico di Torino, Turin, Italy
| | - Christian Pruckner
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Vienna, Austria
| | - Philipp Kolar
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Vienna, Austria
| | - Ruth-Sophie Taubner
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Vienna, Austria; Institute of Astrophysics, Universität Wien, Vienna, Austria
| | - Debora Fino
- Department of Applied Science and Technology (DISAT), Politecnico di Torino, Turin, Italy
| | - Guido Saracco
- Department of Applied Science and Technology (DISAT), Politecnico di Torino, Turin, Italy; Centre for Sustainable Future Technologies (CSF@PoliTo), Istituto Italiano di Tecnologia (IIT), Turin, Italy
| | - Filipa L Sousa
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Vienna, Austria
| | - Simon K-M R Rittmann
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Vienna, Austria.
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13
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Savvas S, Donnelly J, Patterson TP, Dinsdale R, Esteves SR. Closed nutrient recycling via microbial catabolism in an eco-engineered self regenerating mixed anaerobic microbiome for hydrogenotrophic methanogenesis. BIORESOURCE TECHNOLOGY 2017; 227:93-101. [PMID: 28013141 DOI: 10.1016/j.biortech.2016.12.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/11/2016] [Accepted: 12/12/2016] [Indexed: 06/06/2023]
Abstract
A novel eco-engineered mixed anaerobic culture was successfully demonstrated for the first time to be capable of continuous regeneration in nutrient limiting conditions. Microbial catabolism has been found to support a closed system of nutrients able to enrich a culture of lithotrophic methanogens and provide microbial cell recycling. After enrichment, the hydrogenotrophic species was the dominating methanogens while a bacterial substratum was responsible for the redistribution of nutrients. q-PCR results indicated that 7% of the total population was responsible for the direct conversion of the gases. The efficiency of H2/CO2 conversion to CH4 reached 100% at a gassing rate of above 60v/v/d. The pH of the culture media was effectively sustained at optimal levels (pH 7-8) through a buffering system created by the dissolved CO2. The novel approach can reduce the process nutrient/metal requirement and enhance the environmental and financial performance of hydrogenotrophic methanogenesis for renewable energy storage.
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Affiliation(s)
- Savvas Savvas
- Wales Centre of Excellence for Anaerobic Digestion, University of South Wales, Pontypridd CF37 1DL, Wales, UK; Sustainable Environment Research Centre, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd CF37 1DL, Wales, UK.
| | - Joanne Donnelly
- Wales Centre of Excellence for Anaerobic Digestion, University of South Wales, Pontypridd CF37 1DL, Wales, UK; Sustainable Environment Research Centre, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd CF37 1DL, Wales, UK
| | - Tim P Patterson
- Wales Centre of Excellence for Anaerobic Digestion, University of South Wales, Pontypridd CF37 1DL, Wales, UK; Sustainable Environment Research Centre, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd CF37 1DL, Wales, UK
| | - Richard Dinsdale
- Sustainable Environment Research Centre, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd CF37 1DL, Wales, UK
| | - Sandra R Esteves
- Wales Centre of Excellence for Anaerobic Digestion, University of South Wales, Pontypridd CF37 1DL, Wales, UK; Sustainable Environment Research Centre, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd CF37 1DL, Wales, UK
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14
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Bernacchi S, Krajete A, Herwig C. Experimental workflow for developing a feed forward strategy to control biomass growth and exploit maximum specific methane productivity of Methanothermobacter marburgensis in a biological methane production process (BMPP). AIMS Microbiol 2016. [DOI: 10.3934/microbiol.2016.3.262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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15
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Pump J, Pratscher J, Conrad R. Colonization of rice roots with methanogenic archaea controls photosynthesis-derived methane emission. Environ Microbiol 2015; 17:2254-60. [PMID: 25367104 DOI: 10.1111/1462-2920.12675] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 11/28/2022]
Abstract
The methane emitted from rice fields originates to a large part (up to 60%) from plant photosynthesis and is formed on the rice roots by methanogenic archaea. To investigate to which extent root colonization controls methane (CH4 ) emission, we pulse-labeled rice microcosms with (13) CO2 to determine the rates of (13) CH4 emission exclusively derived from photosynthates. We also measured emission of total CH4 ((12+13) CH4 ), which was largely produced in the soil. The total abundances of archaea and methanogens on the roots and in the soil were analysed by quantitative polymerase chain reaction of the archaeal 16S rRNA gene and the mcrA gene coding for a subunit of the methyl coenzyme M reductase respectively. The composition of archaeal and methanogenic communities was determined with terminal restriction fragment length polymorphism (T-RFLP). During the vegetative growth stages, emission rates of (13) CH4 linearly increased with the abundance of methanogenic archaea on the roots and then decreased during the last plant growth stage. Rates of (13) CH4 emission and the abundance of methanogenic archaea were lower when the rice was grown in quartz-vermiculite with only 10% rice soil. Rates of total CH4 emission were not systematically related to the abundance of methanogenic archaea in soil plus roots. The composition of the archaeal communities was similar under all conditions; however, the analysis of mcrA genes indicated that the methanogens differed between the soil and root. Our results support the hypothesis that rates of photosynthesis-driven CH4 emission are limited by the abundance of methanogens on the roots.
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Affiliation(s)
- Judith Pump
- Department of Biogeochemistry, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Jennifer Pratscher
- Department of Biogeochemistry, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Ralf Conrad
- Department of Biogeochemistry, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
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16
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17
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Bernacchi S, Weissgram M, Wukovits W, Herwig C. Process efficiency simulation for key process parameters in biological methanogenesis. AIMS BIOENGINEERING 2014. [DOI: 10.3934/bioeng.2014.1.53] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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18
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Bernacchi S, Rittmann S, H. Seifert A, Krajete A, Herwig C. Experimental methods for screening parameters influencing the growth to product yield (Y (x/CH4)) of a biological methane production (BMP) process performed with Methanothermobacter marburgensis. AIMS BIOENGINEERING 2014. [DOI: 10.3934/bioeng.2014.2.72] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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19
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Meyer B, Kuehl JV, Deutschbauer AM, Arkin AP, Stahl DA. Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes. J Bacteriol 2013; 195:4900-14. [PMID: 23974031 PMCID: PMC3807489 DOI: 10.1128/jb.00504-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 08/20/2013] [Indexed: 12/31/2022] Open
Abstract
The mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers obligately linked by interspecies metabolite exchange in syntrophic consortia that may include sulfate reducing species such as Desulfovibrio. To evaluate the metabolic flexibility of syntrophic Desulfovibrio to adapt to naturally fluctuating methanogenic environments, we studied Desulfovibrio alaskensis strain G20 grown in chemostats under respiratory and syntrophic conditions with alternative methanogenic partners, Methanococcus maripaludis and Methanospirillum hungatei, at different growth rates. Comparative whole-genome transcriptional analyses, complemented by G20 mutant strain growth experiments and physiological data, revealed a significant influence of both energy source availability (as controlled by dilution rate) and methanogen on the electron transfer systems, ratios of interspecies electron carriers, energy generating systems, and interspecies physical associations. A total of 68 genes were commonly differentially expressed under syntrophic versus respiratory lifestyle. Under low-energy (low-growth-rate) conditions, strain G20 further had the capacity to adapt to the metabolism of its methanogenic partners, as shown by its differing gene expression of enzymes involved in the direct metabolic interactions (e.g., periplasmic hydrogenases) and the ratio shift in electron carriers used for interspecies metabolite exchange (hydrogen/formate). A putative monomeric [Fe-Fe] hydrogenase and Hmc (high-molecular-weight-cytochrome c3) complex-linked reverse menaquinone (MQ) redox loop become increasingly important for the reoxidation of the lactate-/pyruvate oxidation-derived redox pair, DsrC(red) and Fd(red), relative to the Qmo-MQ-Qrc (quinone-interacting membrane-bound oxidoreductase; quinone-reducing complex) loop. Together, these data underscore the high enzymatic and metabolic adaptive flexibility that likely sustains Desulfovibrio in naturally fluctuating methanogenic environments.
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Affiliation(s)
- Birte Meyer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Jennifer V. Kuehl
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam M. Deutschbauer
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam P. Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - David A. Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
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20
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Rittmann S, Seifert A, Herwig C. Essential prerequisites for successful bioprocess development of biological CH4production from CO2and H2. Crit Rev Biotechnol 2013; 35:141-51. [DOI: 10.3109/07388551.2013.820685] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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21
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Effects of H2 and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludis. J Bacteriol 2013; 195:1456-62. [PMID: 23335420 DOI: 10.1128/jb.02141-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hydrogenotrophic methanogenic Archaea are defined by an H2 requirement for growth. Despite this requirement, many hydrogenotrophs are also capable of growth with formate as an electron donor for methanogenesis. While certain responses of these organisms to hydrogen availability have been characterized, responses to formate starvation have not been reported. Here we report that during continuous culture of Methanococcus maripaludis under defined nutrient conditions, growth yields relative to methane production decreased markedly with either H2 excess or formate excess. Analysis of the growth yields of several mutants suggests that this phenomenon occurs independently of the storage of intracellular carbon or a transcriptional response to methanogenesis. Using microarray analysis, we found that the expression of genes encoding coenzyme F420-dependent steps of methanogenesis, including one of two formate dehydrogenases, increased with H2 starvation but with formate occurred at high levels regardless of limitation or excess. One gene, encoding H2-dependent methylene-tetrahydromethanopterin dehydrogenase, decreased in expression with either H2 limitation or formate limitation. Expression of genes for the second formate dehydrogenase, molybdenum-dependent formylmethanofuran dehydrogenase, and molybdenum transport increased specifically with formate limitation. Of the two formate dehydrogenases, only the first could support growth on formate in batch culture where formate was in excess.
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22
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Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase. Proc Natl Acad Sci U S A 2010; 107:11050-5. [PMID: 20534465 DOI: 10.1073/pnas.1003653107] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In methanogenic Archaea, the final step of methanogenesis generates methane and a heterodisulfide of coenzyme M and coenzyme B (CoM-S-S-CoB). Reduction of this heterodisulfide by heterodisulfide reductase to regenerate HS-CoM and HS-CoB is an exergonic process. Thauer et al. [Thauer, et al. 2008 Nat Rev Microbiol 6:579-591] recently suggested that in hydrogenotrophic methanogens the energy of heterodisulfide reduction powers the most endergonic reaction in the pathway, catalyzed by the formylmethanofuran dehydrogenase, via flavin-based electron bifurcation. Here we present evidence that these two steps in methanogenesis are physically linked. We identify a protein complex from the hydrogenotrophic methanogen, Methanococcus maripaludis, that contains heterodisulfide reductase, formylmethanofuran dehydrogenase, F(420)-nonreducing hydrogenase, and formate dehydrogenase. In addition to establishing a physical basis for the electron-bifurcation model of energy conservation, the composition of the complex also suggests that either H(2) or formate (two alternative electron donors for methanogenesis) can donate electrons to the heterodisulfide-H(2) via F(420)-nonreducing hydrogenase or formate via formate dehydrogenase. Electron flow from formate to the heterodisulfide rather than the use of H(2) as an intermediate represents a previously unknown path of electron flow in methanogenesis. We further tested whether this path occurs by constructing a mutant lacking F(420)-nonreducing hydrogenase. The mutant displayed growth equal to wild-type with formate but markedly slower growth with hydrogen. The results support the model of electron bifurcation and suggest that formate, like H(2), is closely integrated into the methanogenic pathway.
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Gray ND, Sherry A, Larter SR, Erdmann M, Leyris J, Liengen T, Beeder J, Head IM. Biogenic methane production in formation waters from a large gas field in the North Sea. Extremophiles 2009; 13:511-9. [DOI: 10.1007/s00792-009-0237-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2008] [Accepted: 03/03/2009] [Indexed: 11/29/2022]
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