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Sedlmayr VL, Luger M, Pittenauer E, Marchetti-Deschmann M, Kronlachner L, Limbeck A, Raunjak P, Quehenberger J, Spadiut O. Development of a defined medium for the heterotrophic cultivation of Metallosphaera sedula. Extremophiles 2024; 28:36. [PMID: 39060419 PMCID: PMC11282131 DOI: 10.1007/s00792-024-01348-0] [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: 03/25/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024]
Abstract
The heterotrophic cultivation of extremophilic archaea still heavily relies on complex media. However, complex media are associated with unknown composition, high batch-to-batch variability, potential inhibiting and interfering components, as well as regulatory challenges, hampering advancements of extremophilic archaea in genetic engineering and bioprocessing. For Metallosphaera sedula, a widely studied organism for biomining and bioremediation and a potential production host for archaeal ether lipids, efforts to find defined cultivation conditions have still been unsuccessful. This study describes the development of a novel chemically defined growth medium for M. sedula. Initial experiments with commonly used complex casein-derived media sources deciphered Casamino Acids as the most suitable foundation for further development. The imitation of the amino acid composition of Casamino Acids in basal Brock medium delivered the first chemically defined medium. We could further simplify the medium to 5 amino acids based on the respective specific substrate uptake rates. This first defined cultivation medium for M. sedula allows advanced genetic engineering and more controlled bioprocess development approaches for this highly interesting archaeon.
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Affiliation(s)
- Viktor Laurin Sedlmayr
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, 1060, Vienna, Austria
| | - Maximilian Luger
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, 1060, Vienna, Austria
| | - Ernst Pittenauer
- TU Wien, Institute of Chemical Technologies and Analytics, 1060, Vienna, Austria
| | | | - Laura Kronlachner
- TU Wien, Institute of Chemical Technologies and Analytics, 1060, Vienna, Austria
| | - Andreas Limbeck
- TU Wien, Institute of Chemical Technologies and Analytics, 1060, Vienna, Austria
| | - Philipp Raunjak
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, 1060, Vienna, Austria
| | - Julian Quehenberger
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, 1060, Vienna, Austria
| | - Oliver Spadiut
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, 1060, Vienna, Austria.
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Killelea T, Palud A, Akcha F, Lemor M, L'haridon S, Godfroy A, Henneke G. The interplay at the replisome mitigates the impact of oxidative damage on the genetic integrity of hyperthermophilic Archaea. eLife 2019; 8:45320. [PMID: 31184586 PMCID: PMC6559790 DOI: 10.7554/elife.45320] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022] Open
Abstract
8-oxodeoxyguanosine (8-oxodG), a major oxidised base modification, has been investigated to study its impact on DNA replication in hyperthermophilic Archaea. Here we show that 8-oxodG is formed in the genome of growing cells, with elevated levels following exposure to oxidative stress. Functional characterisation of cell-free extracts and the DNA polymerisation enzymes, PolB, PolD, and the p41/p46 complex, alone or in the presence of accessory factors (PCNA and RPA) indicates that translesion synthesis occurs under replicative conditions. One of the major polymerisation effects was stalling, but each of the individual proteins could insert and extend past 8-oxodG with differing efficiencies. The introduction of RPA and PCNA influenced PolB and PolD in similar ways, yet provided a cumulative enhancement to the polymerisation performance of p41/p46. Overall, 8-oxodG translesion synthesis was seen to be potentially mutagenic leading to errors that are reminiscent of dA:8-oxodG base pairing.
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Affiliation(s)
- Tom Killelea
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Adeline Palud
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Farida Akcha
- Laboratoire d'Ecotoxicologie, Ifremer, Nantes, France
| | - Mélanie Lemor
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Stephane L'haridon
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Anne Godfroy
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Ghislaine Henneke
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
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Topçuoğlu BD, Meydan C, Nguyen TB, Lang SQ, Holden JF. Growth Kinetics, Carbon Isotope Fractionation, and Gene Expression in the Hyperthermophile Methanocaldococcus jannaschii during Hydrogen-Limited Growth and Interspecies Hydrogen Transfer. Appl Environ Microbiol 2019; 85:e00180-19. [PMID: 30824444 PMCID: PMC6495749 DOI: 10.1128/aem.00180-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 02/15/2019] [Indexed: 11/20/2022] Open
Abstract
Hyperthermophilic methanogens are often H2 limited in hot subseafloor environments, and their survival may be due in part to physiological adaptations to low H2 conditions and interspecies H2 transfer. The hyperthermophilic methanogen Methanocaldococcus jannaschii was grown in monoculture at high (80 to 83 μM) and low (15 to 27 μM) aqueous H2 concentrations and in coculture with the hyperthermophilic H2 producer Thermococcus paralvinellae The purpose was to measure changes in growth and CH4 production kinetics, CH4 fractionation, and gene expression in M. jannaschii with changes in H2 flux. Growth and cell-specific CH4 production rates of M. jannaschii decreased with decreasing H2 availability and decreased further in coculture. However, cell yield (cells produced per mole of CH4 produced) increased 6-fold when M. jannaschii was grown in coculture rather than monoculture. Relative to high H2 concentrations, isotopic fractionation of CO2 to CH4 (εCO2-CH4) was 16‰ larger for cultures grown at low H2 concentrations and 45‰ and 56‰ larger for M. jannaschii growth in coculture on maltose and formate, respectively. Gene expression analyses showed H2-dependent methylene-tetrahydromethanopterin (H4MPT) dehydrogenase expression decreased and coenzyme F420-dependent methylene-H4MPT dehydrogenase expression increased with decreasing H2 availability and in coculture growth. In coculture, gene expression decreased for membrane-bound ATP synthase and hydrogenase. The results suggest that H2 availability significantly affects the CH4 and biomass production and CH4 fractionation by hyperthermophilic methanogens in their native habitats.IMPORTANCE Hyperthermophilic methanogens and H2-producing heterotrophs are collocated in high-temperature subseafloor environments, such as petroleum reservoirs, mid-ocean ridge flanks, and hydrothermal vents. Abiotic flux of H2 can be very low in these environments, and there is a gap in our knowledge about the origin of CH4 in these habitats. In the hyperthermophile Methanocaldococcus jannaschii, growth yields increased as H2 flux, growth rates, and CH4 production rates decreased. The same trend was observed increasingly with interspecies H2 transfer between M. jannaschii and the hyperthermophilic H2 producer Thermococcus paralvinellae With decreasing H2 availability, isotopic fractionation of carbon during methanogenesis increased, resulting in isotopically more negative CH4 with a concomitant decrease in H2-dependent methylene-tetrahydromethanopterin dehydrogenase gene expression and increase in F420-dependent methylene-tetrahydromethanopterin dehydrogenase gene expression. The significance of our research is in understanding the nature of hyperthermophilic interspecies H2 transfer and identifying biogeochemical and molecular markers for assessing the physiological state of methanogens and possible source of CH4 in natural environments.
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Affiliation(s)
- Begüm D Topçuoğlu
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Cem Meydan
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
| | - Tran B Nguyen
- School of the Earth, Ocean, and Environment, University of South Carolina, Columbia, South Carolina, USA
| | - Susan Q Lang
- School of the Earth, Ocean, and Environment, University of South Carolina, Columbia, South Carolina, USA
| | - James F Holden
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
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Kambourova M, Radchenkova N, Tomova I, Bojadjieva I. Thermophiles as a Promising Source of Exopolysaccharides with Interesting Properties. BIOTECHNOLOGY OF EXTREMOPHILES: 2016. [DOI: 10.1007/978-3-319-13521-2_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Deive FJ, López E, Rodríguez A, Longo MA, Sanromán MÁ. Targeting the Production of Biomolecules by Extremophiles at Bioreactor Scale. Chem Eng Technol 2012. [DOI: 10.1002/ceat.201100528] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Byrne N, Lesongeur F, Bienvenu N, Geslin C, Alain K, Prieur D, Godfroy A. Effect of variation of environmental conditions on the microbial communities of deep-sea vent chimneys, cultured in a bioreactor. Extremophiles 2009; 13:595-608. [DOI: 10.1007/s00792-009-0242-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Accepted: 03/30/2009] [Indexed: 10/20/2022]
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Postec A, Lesongeur F, Pignet P, Ollivier B, Querellou J, Godfroy A. Continuous enrichment cultures: insights into prokaryotic diversity and metabolic interactions in deep-sea vent chimneys. Extremophiles 2007; 11:747-57. [PMID: 17576518 DOI: 10.1007/s00792-007-0092-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Accepted: 05/15/2007] [Indexed: 10/23/2022]
Abstract
The prokaryotic diversity of culturable thermophilic communities of deep-sea hydrothermal chimneys was analysed using a continuous enrichment culture performed in a gas-lift bioreactor, and compared to classical batch enrichment cultures in vials. Cultures were conducted at 60 degrees C and pH 6.5 using a complex medium containing carbohydrates, peptides and sulphur, and inoculated with a sample of a hydrothermal black chimney collected at the Rainbow field, Mid-Atlantic Ridge, at 2,275 m depth. To assess the relevance of both culture methods, bacterial and archaeal diversity was studied using cloning and sequencing, DGGE, and whole-cell hybridisation of 16S rRNA genes. Sequences of heterotrophic microorganisms belonging to the genera Marinitoga, Thermosipho, Caminicella (Bacteria) and Thermococcus (Archaea) were obtained from both batch and continuous enrichment cultures while sequences of the autotrophic bacterial genera Deferribacter and Thermodesulfatator were only detected in the continuous bioreactor culture. It is presumed that over time constant metabolite exchanges will have occurred in the continuous enrichment culture enabling the development of a more diverse prokaryotic community. In particular, CO(2) and H(2) produced by the heterotrophic population would support the growth of autotrophic populations. Therefore, continuous enrichment culture is a useful technique to grow over time environmentally representative microbial communities and obtain insights into prokaryotic species interactions that play a crucial role in deep hydrothermal environments.
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Affiliation(s)
- Anne Postec
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, IFREMER, Centre de Brest, BP 70, 29280, Plouzané, France.
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Godfroy A, Postec A, Raven N. 4 Growth of Hyperthermophilic Microorganisms for Physiological and Nutritional Studies. METHODS IN MICROBIOLOGY 2006. [DOI: 10.1016/s0580-9517(08)70007-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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