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Vreeland RH, Sun YP, Wang BB, Hou J, Cui HL. Halorubrum hochsteinianum sp. nov., an ancient haloarchaeon from a natural experiment. Extremophiles 2023; 28:1. [PMID: 37906310 DOI: 10.1007/s00792-023-01320-4] [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] [Received: 01/16/2023] [Accepted: 10/06/2023] [Indexed: 11/02/2023]
Abstract
A single extremely halophilic strain was isolated from salt brine produced when a fresh water lake flooded a large salt mine located beneath the lake. The water that entered this mine contained less than 0.34 M NaCl, but over time, this sealed brine became saturated by Cenozoic age salt (121-125 million-year BCE). The isolated strain requires at least 1.7 M NaCl for survival and grows optimally in 3.1 M NaCl. Therefore, it could not have survived or been present in the waters that flooded this salt mine. The strain grows at a pH range from 6.5 to 9.0 and has a wide tolerance to temperatures from 25 ℃ to at least 60 ℃. The comparison of 16S rRNA and rpoB' genes revealed that strain 1-13-28T is related to Halorubrum tebenquichense DSM 14210T showing 98.6% and 98.1% similarities, respectively. Phylogenetic analyses based on 16S rRNA, rpoB' genes and 122 concatenated archaeal genes show that the strain 1-13-28T consistently forms a cluster with Halorubrum tebenquichense of the genus Halorubrum. Strain 1-13-28T contained sulfated mannosyl glucosyl diether, and the polar lipid profile was identical to those of most Halorubrum species. Based on the overall combination of physiological, phylogenetic, polar lipids and phylogenomic characteristics, strain 1-13-28T (= ATCC 700083T = CGMCC 1.62627T) represents a newly identified species within the genus Halorubrum for which the name Halorubrum hochsteinianum is proposed.
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Affiliation(s)
- Russell H Vreeland
- Eastern Shore Microbes, 15397 Merry Cat Lane; Post Office Box 216, Belle Haven, VA, 23306, USA.
| | - Ya-Ping Sun
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Bei-Bei Wang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China.
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2
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Experimental evolution of extremophile resistance to ionizing radiation. Trends Genet 2021; 37:830-845. [PMID: 34088512 DOI: 10.1016/j.tig.2021.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 11/22/2022]
Abstract
A growing number of known species possess a remarkable characteristic - extreme resistance to the effects of ionizing radiation (IR). This review examines our current understanding of how organisms can adapt to and survive exposure to IR, one of the most toxic stressors known. The study of natural extremophiles such as Deinococcus radiodurans has revealed much. However, the evolution of Deinococcus was not driven by IR. Another approach, pioneered by Evelyn Witkin in 1946, is to utilize experimental evolution. Contributions to the IR-resistance phenotype affect multiple aspects of cell physiology, including DNA repair, removal of reactive oxygen species, the structure and packaging of DNA and the cell itself, and repair of iron-sulfur centers. Based on progress to date, we overview the diversity of mechanisms that can contribute to biological IR resistance arising as a result of either natural or experimental evolution.
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Najjari A, Stathopoulou P, Elmnasri K, Hasnaoui F, Zidi I, Sghaier H, Ouzari HI, Cherif A, Tsiamis G. Assessment of 16S rRNA Gene-Based Phylogenetic Diversity of Archaeal Communities in Halite-Crystal Salts Processed from Natural Saharan Saline Systems of Southern Tunisia. BIOLOGY 2021; 10:biology10050397. [PMID: 34064384 PMCID: PMC8147861 DOI: 10.3390/biology10050397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/27/2022]
Abstract
A thorough assessment of the phylogenetic diversity and community structure of halophilic archaea from three halite-crystal salts, processed from two separated saline systems of Southern Tunisia has been performed using culture dependent and independent methods targeting different regions of 16S rRNA gene sequences including DGGE, 16S rRNA clone libraries and Illumina Miseq sequencing. Two samples, CDR (red halite-crystal salts) and CDW (white halite-crystal salts), were collected from Chott-Eljerid and one sample CDZ (white halite-crystal salts) from Chott Douz. Fourteen isolates were identified as Halorubrum, Haloferax, Haloarcula, and Halogeometricum genera members. Culture-independent approach revealed a high diversity of archaeal members present in all samples, represented by the Euryarchaeal phylum and the dominance of the Halobacteria class. Nanohaloarchaea were also identified only in white halite samples based on metagenomic analysis. In fact, a total of 61 genera were identified with members of the Halorhabdus, Halonotius, Halorubrum, Haloarcula, and unclassified. Halobacteriaceae were shared among all samples. Unexpected diversity profiles between samples was observed where the red halite crust sample was considered as the most diverse one. The highest diversity was observed with Miseq approach, nevertheless, some genera were detected only with 16S rRNA clone libraries and cultured approaches.
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Affiliation(s)
- Afef Najjari
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia; (F.H.); (I.Z.); (H.I.O.)
- Correspondence:
| | - Panagiota Stathopoulou
- Department of Environmental Engineering, Laboratory of Systems Microbiology and Applied Genomics, University of Patras, 2 Seferi Str., 30100 Agrinio, Greece; (P.S.); (G.T.)
| | - Khaled Elmnasri
- Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia; (K.E.); (H.S.); (A.C.)
| | - Faten Hasnaoui
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia; (F.H.); (I.Z.); (H.I.O.)
| | - Ines Zidi
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia; (F.H.); (I.Z.); (H.I.O.)
| | - Haitham Sghaier
- Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia; (K.E.); (H.S.); (A.C.)
- Laboratory “Energy and Matter for Development of Nuclear Sciences” (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), 2020 Sidi Thabet, Tunisia
| | - Hadda Imene Ouzari
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia; (F.H.); (I.Z.); (H.I.O.)
| | - Ameur Cherif
- Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia; (K.E.); (H.S.); (A.C.)
| | - George Tsiamis
- Department of Environmental Engineering, Laboratory of Systems Microbiology and Applied Genomics, University of Patras, 2 Seferi Str., 30100 Agrinio, Greece; (P.S.); (G.T.)
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16S rRNA Gene Diversity in Ancient Gray and Pink Salt from San Simón Salt Mines in Tarija, Bolivia. Microbiol Resour Announc 2020; 9:9/41/e00820-20. [PMID: 33033125 PMCID: PMC7545279 DOI: 10.1128/mra.00820-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
DNA from 250 million-year-old pink and gray salts from mines in Tarija, Bolivia, subjected to 16S rRNA gene amplicon sequencing and analysis provided evidence for similar but distinct prokaryotic communities. The results constitute a snapshot of archaeal and bacterial microorganisms in these remote and ancient salt deposits. DNA from 250 million-year-old pink and gray salts from mines in Tarija, Bolivia, subjected to 16S rRNA gene amplicon sequencing and analysis provided evidence for similar but distinct prokaryotic communities. The results constitute a snapshot of archaeal and bacterial microorganisms in these remote and ancient salt deposits.
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Afouda P, Dubourg G, Raoult D. Archeomicrobiology applied to environmental samples. Microb Pathog 2020; 143:104140. [DOI: 10.1016/j.micpath.2020.104140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
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The Biogeography of Great Salt Lake Halophilic Archaea: Testing the Hypothesis of Avian Mechanical Carriers. DIVERSITY 2018. [DOI: 10.3390/d10040124] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Halophilic archaea inhabit hypersaline ecosystems globally, and genetically similar strains have been found in locales that are geographically isolated from one another. We sought to test the hypothesis that small salt crystals harboring halophilic archaea could be carried on bird feathers and that bird migration is a driving force of these distributions. In this study, we discovered that the American White Pelicans (AWPE) at Great Salt Lake soak in the hypersaline brine and accumulate salt crystals (halite) on their feathers. We cultured halophilic archaea from AWPE feathers and halite crystals. The microorganisms isolated from the lakeshore crystals were restricted to two genera: Halorubrum and Haloarcula, however, archaea from the feathers were strictly Haloarcula. We compared partial DNA sequence of the 16S rRNA gene from our cultivars with that of similar strains in the GenBank database. To understand the biogeography of genetically similar halophilic archaea, we studied the geographical locations of the sampling sites of the closest-matched species. An analysis of the environmental factors of each site pointed to salinity as the most important factor for selection. The geography of the sites was consistent with the location of the sub-tropical jet stream where birds typically migrate, supporting the avian dispersal hypothesis.
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Cheng Z, Xiao L, Wang H, Yang H, Li J, Huang T, Xu Y, Ma N. Bacterial and Archaeal Lipids Recovered from Subsurface Evaporites of Dalangtan Playa on the Tibetan Plateau and Their Astrobiological Implications. ASTROBIOLOGY 2017; 17:1112-1122. [PMID: 28926282 DOI: 10.1089/ast.2016.1526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Qaidam Basin (Tibetan Plateau) is considered an applicable analogue to Mars with regard to sustained extreme aridity and abundant evaporites. To investigate the possibility of the preservation of microbial lipids under these Mars analog conditions, we conducted a mineralogical and organic geochemistry study on samples collected from two Quaternary sections in Dalangtan Playa, northwestern Qaidam Basin, which will enhance our understanding of the potential preservation of molecular biomarkers on Mars. Two sedimentary units were identified along two profiles: one salt unit characterized by a predominance of gypsum and halite, and one detrital unit with a decrease of gypsum and halite and enrichment in siliciclastic minerals. Bacterial fatty acids and archaeal acyclic diether and tetraether membrane lipids were detected, and they varied throughout the sections in concentration and abundance. Bacterial and archaeal biomolecules indicate a dominance of Gram-positive bacteria and halophilic archaea in this hypersaline ecosystem that is similar to those in other hypersaline environments. Furthermore, the abundance of bacterial lipids decreases with the increase of salinity, whereas archaeal lipids showed a reverse trend. The detection of microbial lipids in hypersaline environments would indicate, for example on Mars, a high potential for the detection of microbial biomarkers in evaporites over geological timescales. Key Words: Dalangtan playa-The Qaidam Basin-Subsurface evaporites-Lipid biomarkers-Mars. Astrobiology 17, 1112-1122.
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Affiliation(s)
- Ziye Cheng
- 1 State Key Laboratory of Geological Processes and Mineral Resources, Planetary Science Institute, School of Earth Sciences, China University of Geosciences , Wuhan, China
| | - Long Xiao
- 1 State Key Laboratory of Geological Processes and Mineral Resources, Planetary Science Institute, School of Earth Sciences, China University of Geosciences , Wuhan, China
- 2 Macau University of Science and Technology , Macau, China
| | - Hongmei Wang
- 3 State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan, China
| | - Huan Yang
- 3 State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan, China
| | - Jingjing Li
- 4 State Key Laboratory of Lake Sciences and Environment, Nanjing Institute of Geography and Limnology , Chinese Academy of Sciences, Nanjing, China
| | - Ting Huang
- 1 State Key Laboratory of Geological Processes and Mineral Resources, Planetary Science Institute, School of Earth Sciences, China University of Geosciences , Wuhan, China
| | - Yi Xu
- 2 Macau University of Science and Technology , Macau, China
| | - Nina Ma
- 5 Key Laboratory of Saline Lake Resources and Environments, Chinese Academy of Geological Sciences , Beijing, China
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8
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Gales G, Tsesmetzis N, Neria I, Alazard D, Coulon S, Lomans BP, Morin D, Ollivier B, Borgomano J, Joulian C. Preservation of ancestral Cretaceous microflora recovered from a hypersaline oil reservoir. Sci Rep 2016; 6:22960. [PMID: 26965360 PMCID: PMC4786803 DOI: 10.1038/srep22960] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 02/19/2016] [Indexed: 11/16/2022] Open
Abstract
Microbiology of a hypersaline oil reservoir located in Central Africa was investigated with molecular and culture methods applied to preserved core samples. Here we show that the community structure was partially acquired during sedimentation, as many prokaryotic 16S rRNA gene sequences retrieved from the extracted DNA are phylogenetically related to actual Archaea inhabiting surface evaporitic environments, similar to the Cretaceous sediment paleoenvironment. Results are discussed in term of microorganisms and/or DNA preservation in such hypersaline and Mg-rich solutions. High salt concentrations together with anaerobic conditions could have preserved microbial/molecular diversity originating from the ancient sediment basin wherein organic matter was deposited.
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Affiliation(s)
- Grégoire Gales
- Aix-Marseille Université, CEREGE, Centre St Charles, Case 67, 3 Place Victor Hugo, 13331 Marseille, France.,Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
| | - Nicolas Tsesmetzis
- Shell International Exploration and Production Inc., 3333 Highway 6 South, Houston, Texas 77082, USA
| | - Isabel Neria
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
| | - Didier Alazard
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
| | - Stéphanie Coulon
- BRGM, Unité BioGéochimie Environnementale, 3 Avenue Claude Guillemin, BP 36009, 45060 ORLEANS cedex 2, France
| | - Bart P Lomans
- Emerging Technologies - Subsurface, Projects &Technologies, Shell Global Solutions International B.V., Kessler Park 1, 2288 GS Rijswijk, The Netherlands
| | - Dominique Morin
- BRGM, Unité BioGéochimie Environnementale, 3 Avenue Claude Guillemin, BP 36009, 45060 ORLEANS cedex 2, France
| | - Bernard Ollivier
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
| | - Jean Borgomano
- Aix-Marseille Université, CEREGE, Centre St Charles, Case 67, 3 Place Victor Hugo, 13331 Marseille, France
| | - Catherine Joulian
- BRGM, Unité BioGéochimie Environnementale, 3 Avenue Claude Guillemin, BP 36009, 45060 ORLEANS cedex 2, France
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9
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Buried Alive: Microbes from Ancient Halite. Trends Microbiol 2016; 24:148-160. [DOI: 10.1016/j.tim.2015.12.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/26/2015] [Accepted: 12/08/2015] [Indexed: 11/20/2022]
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10
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Abstract
Global microbial cell numbers in the seabed exceed those in the overlying water column, yet these organisms receive less than 1% of the energy fixed as organic matter in the ocean. The microorganisms of this marine deep biosphere subsist as stable and diverse communities with extremely low energy availability. Growth is exceedingly slow, possibly regulated by virus-induced mortality, and the mean generation times are tens to thousands of years. Intermediate substrates such as acetate are maintained at low micromolar concentrations, yet their turnover time may be several hundred years. Owing to slow growth, a cell community may go through only 10,000 generations from the time it is buried beneath the mixed surface layer until it reaches a depth of tens of meters several million years later. We discuss the efficiency of the energy-conserving machinery of subsurface microorganisms and how they may minimize energy consumption through necessary maintenance, repair, and growth.
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Affiliation(s)
- Bo Barker Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark; ,
| | - Ian P G Marshall
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark; ,
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11
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Chen S, Liu HC, Zhao D, Yang J, Zhou J, Xiang H. Halorubrum yunnanense sp. nov., isolated from a subterranean salt mine. Int J Syst Evol Microbiol 2015; 65:4526-4532. [DOI: 10.1099/ijsem.0.000605] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two halophilic archaeal strains, Q85T and Q86, were isolated from a subterranean salt mine in Yunnan, China. Cells were rod-shaped, Gram-stain-negative and motile. Colonies were red, smooth, convex and round (1.0–2.0 mm in diameter). The orthologous 16S rRNA and rpoB′ gene sequences of these two strains were almost identical (99.5 and 99.7 % similarities). Their closest relatives were Halorubrum kocurii BG-1T (98.0–98.1 % 16S rRNA gene sequence similarity), Halorubrum aidingense 31-hongT (97.6–97.7 %) and Halorubrum lipolyticum 9-3T (97.5–97.6 %). The level of DNA–DNA relatedness between strains Q85T and Q86 was 90 %, while that between Q85T and other related Halorubrum strains was less than 30 % (29 % for H. kocurii BG-1T, 25 % for H. aidingense 31-hongT and 22 % for H. lipolyticum 9-3T). Optimal growth of the two novel strains was observed with 20 % (w/v) NaCl and at 42–45 °C under aerobic conditions, with a slight difference in optimum Mg2+ concentration (0.7 M for Q85T, 0.5 M for Q86) and a notable difference in optimum pH (pH 7.5 for Q85T, pH 6.6 for Q86). Anaerobic growth occurred with nitrate, but not with l-arginine or DMSO. The major polar lipids of the two strains were identical, including phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and sulfated diglycosyl diether, which are the major lipids of the genus Halorubrum. The G+C contents of strains Q85T and Q86 were 66.3 and 66.8 %, respectively. Based on the phenotypic, chemotaxonomic and phylogenetic properties of strains Q85T and Q86, a novel species, Halorubrum yunnanense sp. nov., is proposed. The type strain is Q85T ( = CGMCC 1.15057T = JCM 30665T).
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Affiliation(s)
- Shaoxing Chen
- University Key Laboratory of Crop High Quality and High Effective Cultivation and Safety Control in Yunnan Province, Honghe University, Mengzi 66110, Yunnan, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jian Yang
- University Key Laboratory of Crop High Quality and High Effective Cultivation and Safety Control in Yunnan Province, Honghe University, Mengzi 66110, Yunnan, PR China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Abstract
Halophilic archaebacteria (Haloarchaea) can survive extreme desiccation, starvation and radiation, sometimes apparently for millions of years. Several of the strategies that are involved appear specific for Haloarchaea (for example, the formation of halomucin, survival in fluid inclusions of halite), and some are known from other prokaryotes (dwarfing of cells, reduction of ATP). Several newly-discovered haloarchaeal strategies that were inferred to possibly promote long-term survival—halomucin, polyploidy, usage of DNA as a phosphate storage polymer, production of spherical dormant stages—remain to be characterized in detail. More information on potential strategies is desirable, since evidence for the presence of halite on Mars and on several moons in the solar system increased interest in halophiles with respect to the search for extraterrestrial life. This review deals in particular with novel findings and hypotheses on haloarchaeal long-term survival.
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Soppa J. Polyploidy in archaea and bacteria: about desiccation resistance, giant cell size, long-term survival, enforcement by a eukaryotic host and additional aspects. J Mol Microbiol Biotechnol 2015; 24:409-19. [PMID: 25732342 DOI: 10.1159/000368855] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
During recent years, it has become clear that many species of archaea and bacteria are polyploid and contain more than 10 copies of their chromosome. In this contribution, eight examples are discussed to highlight different aspects of polyploidy in prokaryotes. The species discussed are the bacteria Azotobacter vinelandii, Deinococcus radiodurans, Sinorhizobium meliloti, and Epulopiscium as well as the archaea Methanocaldococcus jannaschii, Methanococcus maripaludis, Haloferax volcanii, and haloarchaeal isolates from salt deposits. The topics include possible laboratory artifacts, resistance against double-strand breaks, long-term survival, relaxation of DNA segregation and septum formation, enforced polyploidy by a eukaryotic host, genome equalization by gene conversion, and the nongenetic usage of genomic DNA as a phosphate storage polymer. Together, the selected topics give an overview of the biodiversity of polyploidy in archaea and bacteria.
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Affiliation(s)
- Jörg Soppa
- Biocentre, Institute for Molecular Biosciences, Goethe University, Frankfurt, Germany
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Sankaranarayanan K, Lowenstein TK, Timofeeff MN, Schubert BA, Lum JK. Characterization of ancient DNA supports long-term survival of Haloarchaea. ASTROBIOLOGY 2014; 14:553-560. [PMID: 24977469 PMCID: PMC4094027 DOI: 10.1089/ast.2014.1173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 05/14/2014] [Indexed: 06/01/2023]
Abstract
Bacteria and archaea isolated from crystals of halite 10(4) to 10(8) years old suggest long-term survival of halophilic microorganisms, but the results are controversial. Independent verification of the authenticity of reputed living prokaryotes in ancient salt is required because of the high potential for environmental and laboratory contamination. Low success rates of prokaryote cultivation from ancient halite, however, hamper direct replication experiments. In such cases, culture-independent approaches that use the polymerase chain reaction (PCR) and sequencing of 16S ribosomal DNA are a robust alternative. Here, we use amplification, cloning, and sequencing of 16S ribosomal DNA to investigate the authenticity of halophilic archaea cultured from subsurface halite, Death Valley, California, 22,000 to 34,000 years old. We recovered 16S ribosomal DNA sequences that are identical, or nearly so (>99%), to two strains, Natronomonas DV462A and Halorubrum DV427, which were previously isolated from the same halite interval. These results provide the best independent support to date for the long-term survival of halophilic archaea in ancient halite. PCR-based approaches are sensitive to small amounts of DNA and could allow investigation of even older halites, 10(6) to 10(8) years old, from which microbial cultures have been reported. Such studies of microbial life in ancient salt are particularly important as we search for microbial signatures in similar deposits on Mars and elsewhere in the Solar System.
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Affiliation(s)
- Krithivasan Sankaranarayanan
- Department of Biological Sciences, State University of New York, Binghamton, New York
- Laboratory of Evolutionary Anthropology and Health, State University of New York, Binghamton, New York
| | - Tim K. Lowenstein
- Department of Geological Sciences and Environmental Studies, State University of New York, Binghamton, New York
| | - Michael N. Timofeeff
- Department of Geological Sciences and Environmental Studies, State University of New York, Binghamton, New York
| | - Brian A. Schubert
- School of Geosciences, University of Louisiana, Lafayette, Louisiana
| | - J. Koji Lum
- Department of Biological Sciences, State University of New York, Binghamton, New York
- Laboratory of Evolutionary Anthropology and Health, State University of New York, Binghamton, New York
- Department of Anthropology, State University of New York, Binghamton, New York
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15
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Self-assembly: from amphiphiles to chromophores and beyond. Molecules 2014; 19:8589-609. [PMID: 24959684 PMCID: PMC6271149 DOI: 10.3390/molecules19068589] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/17/2014] [Accepted: 06/17/2014] [Indexed: 11/17/2022] Open
Abstract
Self-assembly has been recognised as a ubiquitous aspect of modern chemistry. Our understanding and applications of self-assembly are substantially based on what has been learned from biochemical systems. In this review, we describe various aspects of self-assembly commencing with an account of the soft structures that are available by assembly of surfactant amphiphiles, which are important scientific and industrial materials. Variation of molecular design using rules defined by surfactant self-assembly permits synthesis of functional nanostructures in solution and at surfaces while increasing the strength of intermolecular interactions through π-π stacking, metal cation coordination and/or hydrogen bonding leads to formation of highly complex bespoke nanostructured materials exemplified by DNA assemblies. We describe the origins of self-assembly involving aggregation of lipid amphiphiles and how this subject has been expanded to include other highly advanced chemical systems.
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16
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Zerulla K, Soppa J. Polyploidy in haloarchaea: advantages for growth and survival. Front Microbiol 2014; 5:274. [PMID: 24982654 PMCID: PMC4056108 DOI: 10.3389/fmicb.2014.00274] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 05/19/2014] [Indexed: 02/02/2023] Open
Abstract
The investigated haloarchaeal species, Halobacterium salinarum, Haloferax mediterranei, and H. volcanii, have all been shown to be polyploid. They contain several replicons that have independent copy number regulation, and most have a higher copy number during exponential growth phase than in stationary phase. The possible evolutionary advantages of polyploidy for haloarchaea, most of which have experimental support for at least one species, are discussed. These advantages include a low mutation rate and high resistance toward X-ray irradiation and desiccation, which depend on homologous recombination. For H. volcanii, it has been shown that gene conversion operates in the absence of selection, which leads to the equalization of genome copies. On the other hand, selective forces might lead to heterozygous cells, which have been verified in the laboratory. Additional advantages of polyploidy are survival over geological times in halite deposits as well as at extreme conditions on earth and at simulated Mars conditions. Recently, it was found that H. volcanii uses genomic DNA as genetic material and as a storage polymer for phosphate. In the absence of phosphate, H. volcanii dramatically decreases its genome copy number, thereby enabling cell multiplication, but diminishing the genetic advantages of polyploidy. Stable storage of phosphate is proposed as an alternative driving force for the emergence of DNA in early evolution. Several additional potential advantages of polyploidy are discussed that have not been addressed experimentally for haloarchaea. An outlook summarizes selected current trends and possible future developments.
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Affiliation(s)
- Karolin Zerulla
- Biocentre, Institute for Molecular Biosciences, Department of Biological Sciences, Goethe University Frankfurt Frankfurt, Germany
| | - Jörg Soppa
- Biocentre, Institute for Molecular Biosciences, Department of Biological Sciences, Goethe University Frankfurt Frankfurt, Germany
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Abstract
Several species of haloarchaea have been shown to be polyploid and thus this trait might be typical for and widespread in haloarchaea. In the present paper, nine different possible evolutionary advantages of polyploidy for haloarchaea are discussed, including low mutation rate, radiation/desiccation resistance, gene redundancy and survival over geological times and at extraterrestrial sites. Experimental indications exist for all but one of these evolutionary advantages. Several of the advantages require gene conversion, which has been shown to be present and active in haloarchaea.
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Xiao W, Wang ZG, Wang YX, Schneegurt MA, Li ZY, Lai YH, Zhang SY, Wen ML, Cui XL. Comparative molecular analysis of the prokaryotic diversity of two salt mine soils in southwest China. J Basic Microbiol 2013; 53:942-52. [PMID: 23457089 DOI: 10.1002/jobm.201200200] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 08/25/2012] [Indexed: 11/09/2022]
Abstract
While much is known about the microbial diversity in some hypersaline environments, little is known about those of salt mine tunnel soils. The objective of this study was to conduct a comprehensive phylogenetic comparison of the archaeal and bacterial communities present in Yipinglang salt mine (YPL) and Qiaohou salt mine (QH) tunnels differing in salinity and salt composition using 16S rRNA gene clone libraries. Two hundred twenty-eight sequences for QH and 182 sequences for YPL were analyzed by amplified ribosomal DNA-restriction analysis. Libraries revealed 44 bacterial and 57 archaeal different operational taxonomic units belonging to at least 8 bacterial and 3 archaeal divisions, but not all divisions were observed in both salt mines. The bacterial community affiliated with the Bacteroidetes was the most abundant (60% of clones) in QH, while the community in YPL was dominated by δ-Proteobacteria (45% of clones). All archaeal clones from QH were affiliated with Halobacteriaceae. In contrast, in the YPL library, 49% of clones belonged to Halobacteriaceae, 31% of clones related to unclassified archaea, and 21% of clones belonged to Crenarchaeota. Bioinformatic analysis and comparisons showed that the clone libraries were significantly different between two salt mines.
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Affiliation(s)
- Wei Xiao
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, P.R. China
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Properties of Halococcus salifodinae, an Isolate from Permian Rock Salt Deposits, Compared with Halococci from Surface Waters. Life (Basel) 2013; 3:244-59. [PMID: 25371342 PMCID: PMC4187196 DOI: 10.3390/life3010244] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 02/07/2013] [Accepted: 02/14/2013] [Indexed: 11/17/2022] Open
Abstract
Halococcus salifodinae BIpT DSM 8989T, an extremely halophilic archaeal isolate from an Austrian salt deposit (Bad Ischl), whose origin was dated to the Permian period, was described in 1994. Subsequently, several strains of the species have been isolated, some from similar but geographically separated salt deposits. Hcc. salifodinae may be regarded as one of the most ancient culturable species which existed already about 250 million years ago. Since its habitat probably did not change during this long period, its properties were presumably not subjected to the needs of mutational adaptation. Hcc. salifodinae and other isolates from ancient deposits would be suitable candidates for testing hypotheses on prokaryotic evolution, such as the molecular clock concept, or the net-like history of genome evolution. A comparison of available taxonomic characteristics from strains of Hcc. salifodinae and other Halococcus species, most of them originating from surface waters, is presented. The cell wall polymer of Hcc. salifodinae was examined and found to be a heteropolysaccharide, similar to that of Hcc. morrhuae. Polyhydroxyalkanoate granules were present in Hcc. salifodinae, suggesting a possible lateral gene transfer before Permian times.
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Fendrihan S, Dornmayr-Pfaffenhuemer M, Gerbl FW, Holzinger A, Grösbacher M, Briza P, Erler A, Gruber C, Plätzer K, Stan-Lotter H. Spherical particles of halophilic archaea correlate with exposure to low water activity--implications for microbial survival in fluid inclusions of ancient halite. GEOBIOLOGY 2012; 10:424-33. [PMID: 22804926 PMCID: PMC3495301 DOI: 10.1111/j.1472-4669.2012.00337.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 06/05/2012] [Accepted: 06/05/2012] [Indexed: 05/23/2023]
Abstract
Viable extremely halophilic archaea (haloarchaea) have been isolated from million-year-old salt deposits around the world; however, an explanation of their supposed longevity remains a fundamental challenge. Recently small roundish particles in fluid inclusions of 22 000- to 34 000-year-old halite were identified as haloarchaea capable of proliferation (Schubert BA, Lowenstein TK, Timofeeff MN, Parker MA, 2010, Environmental Microbiology, 12, 440-454). Searching for a method to produce such particles in the laboratory, we exposed rod-shaped cells of Halobacterium species to reduced external water activity (a(w)). Gradual formation of spheres of about 0.4 μm diameter occurred in 4 M NaCl buffer of a(w) ≤ 0.75, but exposure to buffered 4 M LiCl (a(w) ≤ 0.73) split cells into spheres within seconds, with concomitant release of several proteins. From one rod, three or four spheres emerged, which re-grew to normal rods in nutrient media. Biochemical properties of rods and spheres were similar, except for a markedly reduced ATP content (about 50-fold) and an increased lag phase of spheres, as is known from dormant bacteria. The presence of viable particles of similar sizes in ancient fluid inclusions suggested that spheres might represent dormant states of haloarchaea. The easy production of spheres by lowering a(w) should facilitate their investigation and could help to understand the mechanisms for microbial survival over geological times.
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Affiliation(s)
- S Fendrihan
- Romanian Bioresource Centre and Advanced Research Association, Bucharest, Romania
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Ancient microbes from halite fluid inclusions: optimized surface sterilization and DNA extraction. PLoS One 2011; 6:e20683. [PMID: 21694765 PMCID: PMC3111412 DOI: 10.1371/journal.pone.0020683] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 05/07/2011] [Indexed: 11/20/2022] Open
Abstract
Fluid inclusions in evaporite minerals (halite, gypsum, etc.) potentially preserve genetic records of microbial diversity and changing environmental conditions of Earth's hydrosphere for nearly one billion years. Here we describe a robust protocol for surface sterilization and retrieval of DNA from fluid inclusions in halite that, unlike previously published methods, guarantees removal of potentially contaminating surface-bound DNA. The protocol involves microscopic visualization of cell structures, deliberate surface contamination followed by surface sterilization with acid and bleach washes, and DNA extraction using Amicon centrifugal filters. Methods were verified on halite crystals of four different ages from Saline Valley, California (modern, 36 ka, 64 ka, and 150 ka), with retrieval of algal and archaeal DNA, and characterization of the algal community using ITS1 sequences. The protocol we developed opens up new avenues for study of ancient microbial ecosystems in fluid inclusions, understanding microbial evolution across geological time, and investigating the antiquity of life on earth and other parts of the solar system.
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Lange C, Zerulla K, Breuert S, Soppa J. Gene conversion results in the equalization of genome copies in the polyploid haloarchaeon Haloferax volcanii. Mol Microbiol 2011; 80:666-77. [PMID: 21338422 DOI: 10.1111/j.1365-2958.2011.07600.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Haloferax volcanii is highly polyploid and contains about 20 copies of the major chromosome. A heterozygous strain was constructed that contained two different types of genomes: the leuB locus contained either the wild-type leuB gene or a leuB:trpA gene introduced by gene replacement. As the trpA locus is devoid of the wild-type trpA gene, growth in the absence of both amino acids is only possible when both types of genomes are simultaneously present, exemplifying gene redundancy and the potential to form heterozygous cells as one possible evolutionary advantage of polyploidy. The heterozygous strain was grown (i) in the presence of tryptophan, selecting for the presence of leuB, (ii) in the presence of leucine selecting for leuB:trpA and (iii) in the absence of selection. Both types of genomes were quantified with real-time PCR. The first condition led to a complete loss of leuB:trpA-containing genomes, while under the second condition leuB-containing genomes were lost. Also in the absence of selection gene conversion led to a fast equalization of genomes and resulted in homozygous leuB-containing cells. Gene conversion leading to genome equalization can explain the escape from 'Muller's ratchet' as well as the ease of mutant construction using polyploid haloarchaea.
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Affiliation(s)
- Christian Lange
- Johann Wolfgang Goethe University, Institute for Molecular Biosciences, Max-von-Laue-Strasse 9, 60438 Frankfurt a.M., Germany
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Gramain A, Díaz GC, Demergasso C, Lowenstein TK, McGenity TJ. Archaeal diversity along a subterranean salt core from the Salar Grande (Chile). Environ Microbiol 2011; 13:2105-21. [DOI: 10.1111/j.1462-2920.2011.02435.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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A major role for nonenzymatic antioxidant processes in the radioresistance of Halobacterium salinarum. J Bacteriol 2011; 193:1653-62. [PMID: 21278285 DOI: 10.1128/jb.01310-10] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Oxidative stress occurs when the generation of reactive oxygen species (ROS) exceeds the capacity of the cell's endogenous systems to neutralize them. Our analyses of the cellular damage and oxidative stress responses of the archaeon Halobacterium salinarum exposed to ionizing radiation (IR) revealed a critical role played by nonenzymatic antioxidant processes in the resistance of H. salinarum to IR. ROS-scavenging enzymes were essential for resistance to chemical oxidants, yet those enzymes were not necessary for H. salinarum's resistance to IR. We found that protein-free cell extracts from H. salinarum provided a high level of protection for protein activity against IR in vitro but did not protect DNA significantly. Compared with cell extracts of radiation-sensitive bacteria, H. salinarum extracts were enriched in manganese, amino acids, and peptides, supporting an essential role in ROS scavenging for those small molecules in vivo. With regard to chemical oxidants, we showed that the damage caused by gamma irradiation was mechanistically different than that produced by hydrogen peroxide or by the superoxide-generating redox-cycling drug paraquat. The data presented support the idea that IR resistance is most likely achieved by a "metabolic route," with a combination of tightly coordinated physiological processes.
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