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Trischler R, Poehlein A, Daniel R, Müller V. Ethanologenesis from glycerol by the gut acetogen Blautia schinkii. Environ Microbiol 2023; 25:3577-3591. [PMID: 37807918 DOI: 10.1111/1462-2920.16517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023]
Abstract
The human gut is an anoxic environment that harbours a multitude of microorganisms that not only contribute to food digestion. The microbiome is also involved in malfunctions such as diseases, inflammation processes or development of obesity, but it is also involved in processes that increase the human well-being. Both, the good and the bad, are mediated by fermentation end products of bacterial metabolism, among others. However, despite a steadily growing knowledge of 'who lives out there', little in known of 'what do they do out there'. The genus Blautia is commonly found in the gut and associated with human well-being, but the exploration of their metabolic potential has just started. We demonstrate that B. schinkii grows on glycerol by producing acetate and ethanol. Transcriptome studies and biochemical analyses revealed a glycerol dehydrogenase and dihydroxyacetone kinase that funnel the substrate into glycolysis. Consequently, cells also grew on dihydroxyacetone. Cells could be adapted to grow at high (up to 1.5 M) glycerol concentrations but then only ethanol was formed. Ethanol production from glycerol is not only of relevance for the human host but also for potential bioindustrial production of bioethanol from waste glycerol.
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Affiliation(s)
- Raphael Trischler
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - A Poehlein
- Georg August University Göttingen, Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Göttingen, Germany
| | - R Daniel
- Georg August University Göttingen, Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Göttingen, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
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2
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Povedano-Priego C, Jroundi F, Solari PL, Guerra-Tschuschke I, Abad-Ortega MDM, Link A, Vilchez-Vargas R, Merroun ML. Unlocking the bentonite microbial diversity and its implications in selenium bioreduction and biotransformation: Advances in deep geological repositories. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130557. [PMID: 36502723 DOI: 10.1016/j.jhazmat.2022.130557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Selenium, 79Se, is one of the most critical radionuclides in radioactive waste disposed in future deep geological repositories (DGRs). Here, we investigate the impact of bentonite microbial communities on the allotropic transformation of Se(IV) bioreduction products under DGR relevant conditions. In addition, Se amendment-dependent shifts in the bentonite microbial populations are assessed. Microcosms of water-saturated bentonites were spiked with a bacterial consortium, treated with selenite and incubated anaerobically for six months. A combination of X-Ray Absorption Spectroscopy, Electron Microscopy, and Raman Spectroscopy was used to track the allotropic changes of the Se bioreduction products. Interestingly, the color of bentonite shifted from orange to black in the selenite-treated microcosms. In the orange layers, amorphous or monoclinic Se(0) were identified, whilst black precipitates consisted of stable trigonal Se(0) form. Illumina DNA sequencing indicated the distribution of strains with Se(IV) reducing and Se(0) allotropic biotransformation potential, like Pseudomonas, Stenotrophomonas, Desulfosporosinus, and unclassified-Desulfuromonadaceae. The archaea Methanosarcina decreased its abundance in the presence of Se(IV), probably caused by this oxyanion toxicity. These findings provide an understanding of the bentonite microbial strategies involved in the immobilization of Se(IV) by reduction processes, and prove their implication in the allotropic biotransformation from amorphous to trigonal Se(0) under DGR relevant conditions.
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Affiliation(s)
| | - Fadwa Jroundi
- Department of Microbiology, Faculty of Sciences, University of Granada, Granada, Spain.
| | - Pier L Solari
- MARS Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, Gif-sur-Yvette Cedex, France.
| | | | | | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, University of Magdeburg, Magdeburg, Germany.
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, University of Magdeburg, Magdeburg, Germany.
| | - Mohamed L Merroun
- Department of Microbiology, Faculty of Sciences, University of Granada, Granada, Spain.
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3
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Mao Z, Gräßle F, Frey J, Franchini P, Schleheck D, Müller N, Schink B. Phosphitispora fastidiosa gen. nov. sp. nov., a new dissimilatory phosphite-oxidizing anaerobic bacterium isolated from anaerobic sewage sludge. Int J Syst Evol Microbiol 2021; 71. [PMID: 34878375 DOI: 10.1099/ijsem.0.005142] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new strictly anaerobic bacterium, strain DYL19T, was enriched and isolated with phosphite as the sole electron donor and CO2 as a single carbon source and electron acceptor from anaerobic sewage sludge sampled at a sewage treatment plant in Constance, Germany. It is a Gram-positive, spore-forming, slightly curved, rod-shaped bacterium which oxidizes phosphite to phosphate while reducing CO2 to biomass and small amounts of acetate. Optimal growth is observed at 30 °C, pH 7.2, with a doubling time of 3 days. Beyond phosphite, no further inorganic or organic electron donor can be used, and no other electron acceptor than CO2 is reduced. Sulphate inhibits growth with phosphite and CO2. The G+C content is 45.95 mol%, and dimethylmenaquinone-7 is the only quinone detectable in the cells. On the basis of 16S rRNA gene sequence analysis and other chemotaxonomic properties, strain DYL19T is described as the type strain of a new genus and species, Phosphitispora fastidiosa gen. nov., sp. nov.
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Affiliation(s)
- Zhuqing Mao
- Department of Biology, University of Konstanz, Constance, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | - Fabian Gräßle
- Department of Biology, University of Konstanz, Constance, Germany
| | - Jasmin Frey
- Department of Biology, University of Konstanz, Constance, Germany
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Constance, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, Constance, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | - Nicolai Müller
- Department of Biology, University of Konstanz, Constance, Germany
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Constance, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
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4
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Gräßle F, Plugge C, Franchini P, Schink B, Schleheck D, Müller N. Pelorhabdus rhamnosifermentans gen. nov., sp. nov., a strictly anaerobic rhamnose degrader from freshwater lake sediment. Syst Appl Microbiol 2021; 44:126225. [PMID: 34198168 DOI: 10.1016/j.syapm.2021.126225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/14/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022]
Abstract
A rhamnose-degrading bacterium, strain BoRhaAT, was isolated from profundal sediment of Lake Constance in agar dilution series with l-rhamnose as substrate and with a background lawn of Methanospirillum hungatei. The isolated strain was a motile rod that stained Gram positive. Growth was observed within a pH range of 4.0-7.5 and a temperature range of 15-30°C. Fermentation products of rhamnose or glucose were acetate, propionate, ethanol, butyrate, and 1-propanol. The G+C content was 40.6% G+C. The dominant fatty acids are C16:1ω9c, i-C13:03OH, C16:0 and C17:1ω8c with 8-21% relative abundance. Polar lipids were glycolipids, phosphatidylethanolamine, phosphoaminolipid and other lipids, of which phosphatidylethanolamine was most abundant. The sequence of the 16S rRNA gene of the new isolate matches the sequence of its closest relative Anaerosporomusa subterranea to 92.4%. A comparison of the genome with this strain showed 60.2% genome-wide average amino acid identity (AAI), comparisons with other type strains showed a maximum of 62.7% AAI. Thus, the definition of a new genus is justified for which we propose the name Pelorhabdus. For strain BoRhaAT, we propose the name Pelorhabdus rhamnosifermentans gen. nov., sp. nov., with strain BoRhaAT (DSM 111565T = JCM 39158T) as the type strain.
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Affiliation(s)
- Fabian Gräßle
- Department of Biology, University of Konstanz, Konstanz, Germany; Research Training Group R3 - Resilience of Lake Ecosystems, University of Konstanz, Konstanz, Germany
| | - Caroline Plugge
- Research Training Group R3 - Resilience of Lake Ecosystems, University of Konstanz, Konstanz, Germany; Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Konstanz, Germany; Research Training Group R3 - Resilience of Lake Ecosystems, University of Konstanz, Konstanz, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, Konstanz, Germany; Research Training Group R3 - Resilience of Lake Ecosystems, University of Konstanz, Konstanz, Germany
| | - Nicolai Müller
- Department of Biology, University of Konstanz, Konstanz, Germany; Research Training Group R3 - Resilience of Lake Ecosystems, University of Konstanz, Konstanz, Germany.
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The Role of Glycerol and Its Derivatives in the Biochemistry of Living Organisms, and Their Prebiotic Origin and Significance in the Evolution of Life. Catalysts 2021. [DOI: 10.3390/catal11010086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The emergence and evolution of prebiotic biomolecules on the early Earth remain a question that is considered crucial to understanding the chemistry of the origin of life. Amongst prebiotic molecules, glycerol is significant due to its ubiquity in biochemistry. In this review, we discuss the significance of glycerol and its various derivatives in biochemistry, their plausible roles in the origin and evolution of early cell membranes, and significance in the biochemistry of extremophiles, followed by their prebiotic origin on the early Earth and associated catalytic processes that led to the origin of these compounds. We also discuss various scenarios for the prebiotic syntheses of glycerol and its derivates and evaluate these to determine their relevance to early Earth biochemistry and geochemistry, and recapitulate the utilization of various minerals (including clays), condensation agents, and solvents that could have led to the successful prebiotic genesis of these biomolecules. Furthermore, important prebiotic events such as meteoritic delivery and prebiotic synthesis reactions under astrophysical conditions are also discussed. Finally, we have also highlighted some novel features of glycerol, including glycerol nucleic acid (GNA), in the origin and evolution of the life.
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Liu B, Popp D, Müller N, Sträuber H, Harms H, Kleinsteuber S. Three Novel Clostridia Isolates Produce n-Caproate and iso-Butyrate from Lactate: Comparative Genomics of Chain-Elongating Bacteria. Microorganisms 2020; 8:microorganisms8121970. [PMID: 33322390 PMCID: PMC7764203 DOI: 10.3390/microorganisms8121970] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 02/07/2023] Open
Abstract
The platform chemicals n-caproate and iso-butyrate can be produced by anaerobic fermentation from agro-industrial residues in a process known as microbial chain elongation. Few lactate-consuming chain-elongating species have been isolated and knowledge on their shared genetic features is still limited. Recently we isolated three novel clostridial strains (BL-3, BL-4, and BL-6) that convert lactate to n-caproate and iso-butyrate. Here, we analyzed the genetic background of lactate-based chain elongation in these isolates and other chain-elongating species by comparative genomics. The three strains produced n-caproate, n-butyrate, iso-butyrate, and acetate from lactate, with the highest proportions of n-caproate (18%) for BL-6 and of iso-butyrate (23%) for BL-4 in batch cultivation at pH 5.5. They show high genomic heterogeneity and a relatively small core-genome size. The genomes contain highly conserved genes involved in lactate oxidation, reverse β-oxidation, hydrogen formation and either of two types of energy conservation systems (Rnf and Ech). Including genomes of another eleven experimentally validated chain-elongating strains, we found that the chain elongation-specific core-genome encodes the pathways for reverse β-oxidation, hydrogen formation and energy conservation, while displaying substantial genome heterogeneity. Metabolic features of these isolates are important for biotechnological applications in n-caproate and iso-butyrate production.
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Affiliation(s)
- Bin Liu
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (B.L.); (D.P.); (H.S.); (H.H.)
| | - Denny Popp
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (B.L.); (D.P.); (H.S.); (H.H.)
| | - Nicolai Müller
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany;
| | - Heike Sträuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (B.L.); (D.P.); (H.S.); (H.H.)
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (B.L.); (D.P.); (H.S.); (H.H.)
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (B.L.); (D.P.); (H.S.); (H.H.)
- Correspondence: ; Tel.: +49-341-235-1325
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7
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Hidalgo M, Puerta-Fernández E. Fermentation of glycerol by a newly discovered anaerobic bacterium: adding value to biodiesel production. Microb Biotechnol 2017; 10:528-530. [PMID: 28332326 PMCID: PMC5404201 DOI: 10.1111/1751-7915.12709] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 03/06/2017] [Indexed: 11/27/2022] Open
Affiliation(s)
- María Hidalgo
- Departamento de Genética, Universidad de Sevilla, Avda. Reina Mercedes, 6, 41012, Sevilla, Spain
| | - Elena Puerta-Fernández
- Departamento de Genética, Universidad de Sevilla, Avda. Reina Mercedes, 6, 41012, Sevilla, Spain
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8
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Patil Y, Müller N, Schink B, Whitman WB, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Junghare M. High-quality-draft genome sequence of the fermenting bacterium Anaerobium acetethylicum type strain GluBS11 T (DSM 29698). Stand Genomic Sci 2017; 12:24. [PMID: 28250895 PMCID: PMC5322786 DOI: 10.1186/s40793-017-0236-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 01/26/2017] [Indexed: 11/10/2022] Open
Abstract
Anaerobium acetethylicum strain GluBS11T belongs to the family Lachnospiraceae within the order Clostridiales. It is a Gram-positive, non-motile and strictly anaerobic bacterium isolated from biogas slurry that was originally enriched with gluconate as carbon source (Patil, et al., Int J Syst Evol Microbiol 65:3289-3296, 2015). Here we describe the draft genome sequence of strain GluBS11T and provide a detailed insight into its physiological and metabolic features. The draft genome sequence generated 4,609,043 bp, distributed among 105 scaffolds assembled using the SPAdes genome assembler method. It comprises in total 4,132 genes, of which 4,008 were predicted to be protein coding genes, 124 RNA genes and 867 pseudogenes. The G + C content was 43.51 mol %. The annotated genome of strain GluBS11T contains putative genes coding for the pentose phosphate pathway, the Embden-Meyerhoff-Parnas pathway, the Entner-Doudoroff pathway and the tricarboxylic acid cycle. The genome revealed the presence of most of the necessary genes required for the fermentation of glucose and gluconate to acetate, ethanol, and hydrogen gas. However, a candidate gene for production of formate was not identified.
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Affiliation(s)
- Yogita Patil
- Department of Biology, Microbial Ecology, University of Konstanz, D-78457 Konstanz, Germany
| | - Nicolai Müller
- Department of Biology, Microbial Ecology, University of Konstanz, D-78457 Konstanz, Germany
| | - Bernhard Schink
- Department of Biology, Microbial Ecology, University of Konstanz, D-78457 Konstanz, Germany
| | | | | | - Alicia Clum
- DOE-Joint Genome Institute, Walnut Creek, CA USA
| | - Manoj Pillay
- DOE-Joint Genome Institute, Walnut Creek, CA USA
| | | | | | | | | | | | - Chris Daum
- DOE-Joint Genome Institute, Walnut Creek, CA USA
| | | | | | | | - Tanja Woyke
- DOE-Joint Genome Institute, Walnut Creek, CA USA
| | - Madan Junghare
- Department of Biology, Microbial Ecology, University of Konstanz, D-78457 Konstanz, Germany
- Konstanz Research School of Chemical Biology, University of Konstanz, D-78457 Konstanz, Germany
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9
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Patil Y, Junghare M, Müller N. Fermentation of glycerol by Anaerobium acetethylicum and its potential use in biofuel production. Microb Biotechnol 2016; 10:203-217. [PMID: 28004884 PMCID: PMC5270724 DOI: 10.1111/1751-7915.12484] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/27/2016] [Accepted: 11/10/2016] [Indexed: 11/29/2022] Open
Abstract
Growth of biodiesel industries resulted in increased coproduction of crude glycerol which is therefore becoming a waste product instead of a valuable 'coproduct'. Glycerol can be used for the production of valuable chemicals, e.g. biofuels, to reduce glycerol waste disposal. In this study, a novel bacterial strain is described which converts glycerol mainly to ethanol and hydrogen with very little amounts of acetate, formate and 1,2-propanediol as coproducts. The bacterium offers certain advantages over previously studied glycerol-fermenting microorganisms. Anaerobium acetethylicum during growth with glycerol produces very little side products and grows in the presence of maximum glycerol concentrations up to 1500 mM and in the complete absence of complex organic supplements such as yeast extract or tryptone. The highest observed growth rate of 0.116 h-1 is similar to that of other glycerol degraders, and the maximum concentration of ethanol that can be tolerated was found to be about 60 mM (2.8 g l-1 ) and further growth was likely inhibited due to ethanol toxicity. Proteome analysis as well as enzyme assays performed in cell-free extracts demonstrated that glycerol is degraded via glyceraldehyde-3-phosphate, which is further metabolized through the lower part of glycolysis leading to formation of mainly ethanol and hydrogen. In conclusion, fermentation of glycerol to ethanol and hydrogen by this bacterium represents a remarkable option to add value to the biodiesel industries by utilization of surplus glycerol.
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Affiliation(s)
- Yogita Patil
- Department of Biology, Microbial Ecology, University of Konstanz, Konstanz, D-78457, Germany
| | - Madan Junghare
- Department of Biology, Microbial Ecology, University of Konstanz, Konstanz, D-78457, Germany.,Konstanz Research School of Chemical Biology, University of Konstanz, Konstanz, D-78457, Germany
| | - Nicolai Müller
- Department of Biology, Microbial Ecology, University of Konstanz, Konstanz, D-78457, Germany
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