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Matthews A, Lima-Zaloumis J, Debes Ii RV, Boyer G, Trembath-Reichert E. Heterotrophic Growth Dominates in the Most Extremotolerant Extremophile Cultures. ASTROBIOLOGY 2023; 23:446-459. [PMID: 36723486 DOI: 10.1089/ast.2022.0100] [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] [Indexed: 06/18/2023]
Abstract
Due to their ability to withstand "extreme" conditions, Earth's extremophilic organisms can constrain habitability windows for other planetary systems. However, there are many other considerations to microbial growth requirements beyond environmental extremes, such as nutrient availability. Here, we conduct a literature review of the most extremotolerant extremophiles in culture, since working with cultured organisms allows environmental and nutrient variables to be constrained with a high level of specificity. We generated a database that includes the isolation environment, carbon source(s) used, and growth preferences across temperature, pressure, salinity, and pH extremes. We found that the "most extreme" conditions were primarily sustained by heterotrophs, except for hyperthermophiles. These results highlight the importance of considering organic carbon availability when using extremophiles for habitability constraints. We also interrogated polyextreme potential across temperature, pressure, salinity, and pH conditions. Our findings suggest that the investigation of growth tolerance rather than growth optimum may reveal wider habitability parameters. Overall, these results highlight the potential polyextremes, environments, nutrient requirements, and additional analyses that could improve the application of cultured investigations to astrobiology questions.
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Affiliation(s)
- Adrianna Matthews
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | | | - R Vincent Debes Ii
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Grayson Boyer
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
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Moalic Y, Hartunians J, Dalmasso C, Courtine D, Georges M, Oger P, Shao Z, Jebbar M, Alain K. The Piezo-Hyperthermophilic Archaeon Thermococcus piezophilus Regulates Its Energy Efficiency System to Cope With Large Hydrostatic Pressure Variations. Front Microbiol 2021; 12:730231. [PMID: 34803948 PMCID: PMC8595942 DOI: 10.3389/fmicb.2021.730231] [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: 06/24/2021] [Accepted: 10/13/2021] [Indexed: 11/23/2022] Open
Abstract
Deep-sea ecosystems share a common physical parameter, namely high hydrostatic pressure (HHP). Some of the microorganisms isolated at great depths have a high physiological plasticity to face pressure variations. The adaptive strategies by which deep-sea microorganisms cope with HHP variations remain to be elucidated, especially considering the extent of their biotopes on Earth. Herein, we investigated the gene expression patterns of Thermococcus piezophilus, a piezohyperthermophilic archaeon isolated from the deepest hydrothermal vent known to date, under sub-optimal, optimal and supra-optimal pressures (0.1, 50, and 90 MPa, respectively). At stressful pressures [sub-optimal (0.1 MPa) and supra-optimal (90 MPa) conditions], no classical stress response was observed. Instead, we observed an unexpected transcriptional modulation of more than a hundred gene clusters, under the putative control of the master transcriptional regulator SurR, some of which are described as being involved in energy metabolism. This suggests a fine-tuning effect of HHP on the SurR regulon. Pressure could act on gene regulation, in addition to modulating their expression.
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Affiliation(s)
- Yann Moalic
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Jordan Hartunians
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Cécile Dalmasso
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Damien Courtine
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Myriam Georges
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Philippe Oger
- Université de Lyon, INSA Lyon, CNRS UMR 5240, Villeurbanne, France
| | - Zongze Shao
- IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France.,Key Laboratory of Marine Biogenetic Resources, The Third Institute of Oceanography SOA, Xiamen, China
| | - Mohamed Jebbar
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Karine Alain
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
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Abstract
Mobile genetic elements (MGEs) often encode integrases which catalyze the site-specific insertion of their genetic information into the host genome and the reverse reaction of excision. Hyperthermophilic archaea harbor integrases belonging to the SSV-family which carry the MGE recombination site within their open reading frame. Upon integration into the host genome, SSV integrases disrupt their own gene into two inactive pseudogenes and are termed suicidal for this reason. The evolutionary maintenance of suicidal integrases, concurring with the high prevalence and multiples recruitments of these recombinases by archaeal MGEs, is highly paradoxical. To elucidate this phenomenon, we analyzed the wide phylogenomic distribution of a prominent class of suicidal integrases which revealed a highly variable integration site specificity. Our results highlighted the remarkable hybrid nature of these enzymes encoded from the assembly of inactive pseudogenes of different origins. The characterization of the biological properties of one of these integrases, IntpT26-2 showed that this enzyme was active over a wide range of temperatures up to 99 °C and displayed a less-stringent site specificity requirement than comparable integrases. These observations concurred in explaining the pervasiveness of these suicidal integrases in the most hyperthermophilic organisms. The biochemical and phylogenomic data presented here revealed a target site switching system operating on highly thermostable integrases and suggested a new model for split gene reconstitution. By generating fast-evolving pseudogenes at high frequency, suicidal integrases constitute a powerful model to approach the molecular mechanisms involved in the generation of active genes variants by the recombination of proto-genes.
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Affiliation(s)
- Catherine Badel
- Microbiology Department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Violette Da Cunha
- Microbiology Department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Patrick Forterre
- Microbiology Department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France.,Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France
| | - Jacques Oberto
- Microbiology Department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
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LoRicco JG, Salvador-Castell M, Demé B, Peters J, Oger PM. Apolar Polyisoprenoids Located in the Midplane of the Bilayer Regulate the Response of an Archaeal-Like Membrane to High Temperature and Pressure. Front Chem 2020; 8:594039. [PMID: 33282836 PMCID: PMC7689154 DOI: 10.3389/fchem.2020.594039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/13/2020] [Indexed: 01/02/2023] Open
Abstract
Archaea are known to inhabit some of the most extreme environments on Earth. The ability of archaea possessing membrane bilayers to adapt to high temperature (>85°C) and high pressure (>1,000 bar) environments is proposed to be due to the presence of apolar polyisoprenoids at the midplane of the bilayer. In this work, we study the response of this novel membrane architecture to both high temperature and high hydrostatic pressure using neutron diffraction. A mixture of two diether, phytanyl chain lipids (DoPhPC and DoPhPE) and squalane was used to model this novel architecture. Diffraction data indicate that at high temperatures a stable coexistence of fluid lamellar phases exists within the membrane and that stable coexistence of these phases is also possible at high pressure. Increasing the amount of squalane in the membrane regulates the phase separation with respect to both temperature and pressure, and also leads to an increase in the lamellar repeat spacing. The ability of squalane to regulate the ultrastructure of an archaea-like membrane at high pressure and temperature supports the hypothesis that archaea can use apolar lipids as an adaptive mechanism to extreme conditions.
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Affiliation(s)
| | | | - Bruno Demé
- Department of Large Scale Structures, Institut Laue-Langevin, Grenoble, France
| | - Judith Peters
- Department of Large Scale Structures, Institut Laue-Langevin, Grenoble, France
- Department of Spectroscopy, Université Grenoble Alpes, LiPhy, Grenoble, France
| | - Philippe M. Oger
- Univ Lyon, INSA de Lyon, CNRS, MAP UMR 5240, Villeurbanne, France
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Siliakus MF, van der Oost J, Kengen SWM. Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure. Extremophiles 2017; 21:651-670. [PMID: 28508135 PMCID: PMC5487899 DOI: 10.1007/s00792-017-0939-x] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 04/29/2017] [Indexed: 12/30/2022]
Abstract
The cytoplasmic membrane of a prokaryotic cell consists of a lipid bilayer or a monolayer that shields the cellular content from the environment. In addition, the membrane contains proteins that are responsible for transport of proteins and metabolites as well as for signalling and energy transduction. Maintenance of the functionality of the membrane during changing environmental conditions relies on the cell's potential to rapidly adjust the lipid composition of its membrane. Despite the fundamental chemical differences between bacterial ester lipids and archaeal ether lipids, both types are functional under a wide range of environmental conditions. We here provide an overview of archaeal and bacterial strategies of changing the lipid compositions of their membranes. Some molecular adjustments are unique for archaea or bacteria, whereas others are shared between the two domains. Strikingly, shared adjustments were predominantly observed near the growth boundaries of bacteria. Here, we demonstrate that the presence of membrane spanning ether-lipids and methyl branches shows a striking relationship with the growth boundaries of archaea and bacteria.
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Affiliation(s)
- Melvin F Siliakus
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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