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Robinson A, Ulrich SM. Haloferax volcanii Remains Viable and Shows Morphological Changes under Anoxic (CO 2-Enriched) and Hypobaric (2.4 kPa) Atmospheric Conditions. ASTROBIOLOGY 2022; 22:829-837. [PMID: 35325555 DOI: 10.1089/ast.2021.0076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Potentially habitable zones have been discovered on Mars today in underground areas containing perchlorate brines. Understanding the low-pressure adaptations of microorganisms is essential in learning more about what life could potentially be found on Mars today or could have existed in the distant past. Many studies have looked at low-pressure adaptations in bacteria; however, studies aimed at understanding these adaptations in archaea are scarcer. Haloferax volcanii is a species of halophilic archaea documented to tolerate high concentrations of oxidizing agents present on Mars (i.e., perchlorates and nitrates). In this study, we expose H. volcanii to a hypobaric (2.4 kPa) and an anoxic CO2-enriched atmosphere in the presence of perchlorate, chlorate, and nitrate. While no growth was observed during incubation in these conditions, survivability was increased in cultures incubated in low-pressure atmospheric conditions compared to ambient Earth atmospheric pressures. Scanning electron microscopy observations showed morphological changes in low-pressure conditions not observed at ambient Earth atmospheric pressures. Results suggest that previously undocumented low-pressure adaptations in H. volcanii increase survivability in simulated subsurface martian conditions. Future experiments to understand the changes in gene expression under these conditions may be valuable to understand more about low-pressure adaptations in archaea.
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Affiliation(s)
- Adam Robinson
- Department of Natural Science, St. Petersburg College, Clearwater, Florida, USA
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Favreau C, Tribondeau A, Marugan M, Guyot F, Alpha-Bazin B, Marie A, Puppo R, Dufour T, Huguet A, Zirah S, Kish A. Molecular acclimation of Halobacterium salinarum to halite brine inclusions. Front Microbiol 2022; 13:1075274. [PMID: 36875534 PMCID: PMC9976938 DOI: 10.3389/fmicb.2022.1075274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/22/2022] [Indexed: 01/27/2023] Open
Abstract
Halophilic microorganisms have long been known to survive within the brine inclusions of salt crystals, as evidenced by the change in color for salt crystals containing pigmented halophiles. However, the molecular mechanisms allowing this survival has remained an open question for decades. While protocols for the surface sterilization of halite (NaCl) have enabled isolation of cells and DNA from within halite brine inclusions, "-omics" based approaches have faced two main technical challenges: (1) removal of all contaminating organic biomolecules (including proteins) from halite surfaces, and (2) performing selective biomolecule extractions directly from cells contained within halite brine inclusions with sufficient speed to avoid modifications in gene expression during extraction. In this study, we tested different methods to resolve these two technical challenges. Following this method development, we then applied the optimized methods to perform the first examination of the early acclimation of a model haloarchaeon (Halobacterium salinarum NRC-1) to halite brine inclusions. Examinations of the proteome of Halobacterium cells two months post-evaporation revealed a high degree of similarity with stationary phase liquid cultures, but with a sharp down-regulation of ribosomal proteins. While proteins for central metabolism were part of the shared proteome between liquid cultures and halite brine inclusions, proteins involved in cell mobility (archaellum, gas vesicles) were either absent or less abundant in halite samples. Proteins unique to cells within brine inclusions included transporters, suggesting modified interactions between cells and the surrounding brine inclusion microenvironment. The methods and hypotheses presented here enable future studies of the survival of halophiles in both culture model and natural halite systems.
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Affiliation(s)
- Charly Favreau
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS, Paris, France
| | - Alicia Tribondeau
- Unité Physiologie Moléculaire et Adaptation (PhyMA), MNHN, CNRS, Paris, France
| | - Marie Marugan
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS, Paris, France
| | - François Guyot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), MNHN, Sorbonne Université, CNRS, IRD, Paris, France
| | - Beatrice Alpha-Bazin
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, Bagnols-sur-Cèze, France
| | - Arul Marie
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS, Paris, France
| | - Remy Puppo
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS, Paris, France
| | - Thierry Dufour
- Laboratoire de Physique des Plasma (LPP), Sorbonne Université, CNRS, École Polytechnique, Université Paris-Sud, Observatoire de Paris, Paris, France
| | - Arnaud Huguet
- Unité Milieux Environnementaux Transferts et Interactions dans les hydrosystèmes et les Sols (METIS), Sorbonne Université, CNRS, EPHE, PSL, Paris, France
| | - Séverine Zirah
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS, Paris, France
| | - Adrienne Kish
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS, Paris, France
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Hazan R, Schoemann M, Klutstein M. Endurance of extremely prolonged nutrient prevention across kingdoms of life. iScience 2021; 24:102745. [PMID: 34258566 PMCID: PMC8258982 DOI: 10.1016/j.isci.2021.102745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Numerous observations demonstrate that microorganisms can survive very long periods of nutrient deprivation and starvation. Moreover, it is evident that prolonged periods of starvation are a feature of many habitats, and many cells in all kingdoms of life are found in prolonged starvation conditions. Bacteria exhibit a range of responses to long-term starvation. These include genetic adaptations such as the long-term stationary phase and the growth advantage in stationary phase phenotypes characterized by mutations in stress-signaling genes and elevated mutation rates. Here, we suggest using the term "endurance of prolonged nutrient prevention" (EPNP phase), to describe this phase, which was also recently described in eukaryotes. Here, we review this literature and describe the current knowledge about the adaptations to very long-term starvation conditions in bacteria and eukaryotes, its conceptual and structural conservation across all kingdoms of life, and point out possible directions that merit further research.
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Affiliation(s)
- Ronen Hazan
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel
| | - Miriam Schoemann
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel
| | - Michael Klutstein
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel
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Huby TJC, Clark DR, McKew BA, McGenity TJ. Extremely halophilic archaeal communities are resilient to short-term entombment in halite. Environ Microbiol 2021; 23:3370-3383. [PMID: 31919959 PMCID: PMC8359394 DOI: 10.1111/1462-2920.14913] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/06/2020] [Accepted: 01/06/2020] [Indexed: 11/28/2022]
Abstract
Some haloarchaea avoid the harsh conditions present in evaporating brines by entombment in brine inclusions within forming halite crystals, where a subset of haloarchaea survives over geological time. However, shifts in the community structure of halite-entombed archaeal communities remain poorly understood. Therefore, we analysed archaeal communities from in situ hypersaline brines collected from Trapani saltern (Sicily) and their successional changes in brines versus laboratory-grown halite over 21 weeks, using high-throughput sequencing. Haloarchaea were dominant, comprising >95% of the archaeal community. Unexpectedly, the OTU richness of the communities after 21 weeks was indistinguishable from the parent brine and overall archaeal abundance in halite showed no clear temporal trends. Furthermore, the duration of entombment was less important than the parent brine from which the halite derived in determining the community composition and relative abundances of most genera in halite-entombed communities. These results show that halite-entombed archaeal communities are resilient to entombment durations of up to 21 weeks, and that entombment in halite may be an effective survival strategy for near complete communities of haloarchaea. Additionally, the dominance of 'halite specialists' observed in ancient halite must occur over periods of years, rather than months, hinting at long-term successional dynamics in this environment.
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Affiliation(s)
- Tom J. C. Huby
- School of Life SciencesUniversity of EssexColchesterEssexUK
| | - Dave R. Clark
- School of Life SciencesUniversity of EssexColchesterEssexUK
| | - Boyd A. McKew
- School of Life SciencesUniversity of EssexColchesterEssexUK
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Verma DK, Vasudeva G, Sidhu C, Pinnaka AK, Prasad SE, Thakur KG. Biochemical and Taxonomic Characterization of Novel Haloarchaeal Strains and Purification of the Recombinant Halotolerant α-Amylase Discovered in the Isolate. Front Microbiol 2020; 11:2082. [PMID: 32983058 PMCID: PMC7490331 DOI: 10.3389/fmicb.2020.02082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/07/2020] [Indexed: 11/13/2022] Open
Abstract
Haloarchaea are salt-loving archaea and potential source of industrially relevant halotolerant enzymes. In the present study, three reddish-pink, extremely halophilic archaeal strains, namely wsp1 (wsp-water sample Pondicherry), wsp3, and wsp4, were isolated from the Indian Solar saltern. The phylogenetic analysis based on 16S rRNA gene sequences suggests that both wsp3 and wsp4 strains belong to Halogeometricum borinquense while wsp1 is closely related to Haloferax volcanii species. The comparative genomics revealed an open pangenome for both genera investigated here. Whole-genome sequence analysis revealed that these isolates have multiple copies of industrially/biotechnologically important unique genes and enzymes. Among these unique enzymes, for recombinant expression and purification, we selected four putative α-amylases identified in these three isolates. We successfully purified functional halotolerant recombinant Amy2, from wsp1 using pelB signal sequence-based secretion strategy using Escherichia coli as an expression host. This method may prove useful to produce functional haloarchaeal secretory recombinant proteins suitable for commercial or research applications. Biochemical analysis of Amy2 suggests the halotolerant nature of the enzyme having maximum enzymatic activity observed at 1 M NaCl. We also report the isolation and characterization of carotenoids purified from these isolates. This study highlights the presence of several industrially important enzymes in the haloarchaeal strains which may potentially have improved features like stability and salt tolerance suitable for industrial applications.
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Affiliation(s)
- Dipesh Kumar Verma
- G. N. Ramachandran Protein Centre, Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Gunjan Vasudeva
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Chandni Sidhu
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Anil K Pinnaka
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Senthil E Prasad
- Biochemical Engineering Research and Process Development Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Krishan Gopal Thakur
- G. N. Ramachandran Protein Centre, Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
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Maslov I, Bogorodskiy A, Mishin A, Okhrimenko I, Gushchin I, Kalenov S, Dencher NA, Fahlke C, Büldt G, Gordeliy V, Gensch T, Borshchevskiy V. Efficient non-cytotoxic fluorescent staining of halophiles. Sci Rep 2018; 8:2549. [PMID: 29416075 PMCID: PMC5803262 DOI: 10.1038/s41598-018-20839-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 01/19/2018] [Indexed: 11/09/2022] Open
Abstract
Research on halophilic microorganisms is important due to their relation to fundamental questions of survival of living organisms in a hostile environment. Here we introduce a novel method to stain halophiles with MitoTracker fluorescent dyes in their growth medium. The method is based on membrane-potential sensitive dyes, which were originally used to label mitochondria in eukaryotic cells. We demonstrate that these fluorescent dyes provide high staining efficiency and are beneficial for multi-staining purposes due to the spectral range covered (from orange to deep red). In contrast with other fluorescent dyes used so far, MitoTracker does not affect growth rate, and remains in cells after several washing steps and several generations in cell culture. The suggested dyes were tested on three archaeal (Hbt. salinarum, Haloferax sp., Halorubrum sp.) and two bacterial (Salicola sp., Halomonas sp.) strains of halophilic microorganisms. The new staining approach provides new insights into biology of Hbt. salinarum. We demonstrated the interconversion of rod-shaped cells of Hbt. salinarium to spheroplasts and submicron-sized spheres, as well as the cytoplasmic integrity of giant rod Hbt. salinarum species. By expanding the variety of tools available for halophile detection, MitoTracker dyes overcome long-standing limitations in fluorescence microscopy studies of halophiles.
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Affiliation(s)
- Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Ivan Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Sergei Kalenov
- Mendeleyev University of Chemical Technology of Russia, 125047, Moscow, Russia
| | - Norbert A Dencher
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
- CSI Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287, Darmstadt, Germany
| | - Christoph Fahlke
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
- Institute of Complex Systems (ICS), ICS-4: Cellular Biophysics, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Georg Büldt
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Thomas Gensch
- Institute of Complex Systems (ICS), ICS-4: Cellular Biophysics, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia.
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Wang J, Lowenstein TK, Fang X. Microbial Habitability and Pleistocene Aridification of the Asian Interior. ASTROBIOLOGY 2016; 16:379-388. [PMID: 27159080 DOI: 10.1089/ast.2015.1397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
UNLABELLED Fluid inclusions trapped in ancient halite can contain a community of halophilic prokaryotes and eukaryotes that inhabited the surface brines from which the halite formed. Long-term survival of bacteria and archaea and preservation of DNA have been reported from halite, but little is known about the distribution of microbes in buried evaporites. Here we report the discovery of prokaryotes and single-celled algae in fluid inclusions in Pleistocene halite, up to 2.26 Ma in age, from the Qaidam Basin, China. We show that water activity (aw), a measure of water availability and an environmental control on biological habitability in surface brines, is also related to microbe entrapment in fluid inclusions. The aw of Qaidam Basin brines progressively decreased over the last ∼1 million years, driven by aridification of the Asian interior, which led to decreased precipitation and water inflow and heightened evaporation rates. These changes in water balance produced highly concentrated brines, which reduced the habitability of surface lakes and decreased the number of microbes trapped in halite. By 0.13 Ma, the aw of surface brines approached the limits tolerated by halophilic prokaryotes and algae. These results show the response of microbial ecosystems to climate change in an extreme environment, which will guide future studies exploring deep life on Earth and elsewhere in the Solar System. KEY WORDS Halite fluid inclusions-Ancient microbes-Water activity-Qaidam Basin-Pleistocene aridification. Astrobiology 16, 379-388.
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Affiliation(s)
- Jiuyi Wang
- 1 CAS Center for Excellence in Tibetan Plateau Earth Sciences and Key Laboratory of Continental Collision and Plateau Uplift, Institute of Tibetan Plateau Research , Chinese Academy of Sciences, Beijing, China
- 2 Department of Geological Sciences and Environmental Studies, State University of New York , Binghamton, New York, USA
| | - Tim K Lowenstein
- 2 Department of Geological Sciences and Environmental Studies, State University of New York , Binghamton, New York, USA
| | - Xiaomin Fang
- 1 CAS Center for Excellence in Tibetan Plateau Earth Sciences and Key Laboratory of Continental Collision and Plateau Uplift, Institute of Tibetan Plateau Research , Chinese Academy of Sciences, Beijing, China
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