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Datkhile KD, Gaikwad PS, Ghaskadbi SS, Mukhopadhyaya R, Nath BB. Chironomus ramosus larvae exhibit DNA damage control in response to gamma radiation. Int J Radiat Biol 2015; 91:742-8. [DOI: 10.3109/09553002.2015.1062572] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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52
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Chan CS, Chan KG, Tay YL, Chua YH, Goh KM. Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing. Front Microbiol 2015; 6:177. [PMID: 25798135 PMCID: PMC4350410 DOI: 10.3389/fmicb.2015.00177] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/17/2015] [Indexed: 02/04/2023] Open
Abstract
The Sungai Klah (SK) hot spring is the second hottest geothermal spring in Malaysia. This hot spring is a shallow, 150-m-long, fast-flowing stream, with temperatures varying from 50 to 110°C and a pH range of 7.0–9.0. Hidden within a wooded area, the SK hot spring is continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC). In this study, a sample taken from the middle of the stream was analyzed at the 16S rRNA V3-V4 region by amplicon metagenome sequencing. Over 35 phyla were detected by analyzing the 16S rRNA data. Firmicutes and Proteobacteria represented approximately 57% of the microbiome. Approximately 70% of the detected thermophiles were strict anaerobes; however, Hydrogenobacter spp., obligate chemolithotrophic thermophiles, represented one of the major taxa. Several thermophilic photosynthetic microorganisms and acidothermophiles were also detected. Most of the phyla identified by 16S rRNA were also found using the shotgun metagenome approaches. The carbon, sulfur, and nitrogen metabolism within the SK hot spring community were evaluated by shotgun metagenome sequencing, and the data revealed diversity in terms of metabolic activity and dynamics. This hot spring has a rich diversified phylogenetic community partly due to its natural environment (plant litter, high TOC, and a shallow stream) and geochemical parameters (broad temperature and pH range). It is speculated that symbiotic relationships occur between the members of the community.
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Affiliation(s)
- Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | | | | | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
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53
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Thermococcus eurythermalis sp. nov., a conditional piezophilic, hyperthermophilic archaeon with a wide temperature range for growth, isolated from an oil-immersed chimney in the Guaymas Basin. Int J Syst Evol Microbiol 2015; 65:30-35. [DOI: 10.1099/ijs.0.067942-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A conditional piezophilic, hyperthermophilic archaeon showing growth over a wide range of temperature, pH and pressure was isolated from an oil-immersed hydrothermal chimney at a depth of 2006.9 m in the Guaymas Basin. Enrichment and isolation of strain A501T were performed at 80 °C at 0.1 MPa. Cells of isolate A501T were irregular motile cocci with a polar tuft of flagella and generally 0.6–2.6 µm in diameter. Growth was detected over the range 50–100 °C (optimal growth at 85 °C) at atmospheric pressure and was observed at 102 °C at a pressure of 10 MPa. At 85 °C, growth was observed at a pressure of 0.1–70 MPa (optimum pressure 0.1 MPa–30 MPa), while at 95 °C, the pressure allowing growth ranged from 0.1 MPa to 50 MPa (optimum pressure 10 MPa). Cells of strain A501T grew at pH 4–9 (optimum pH 7.0) and a NaCl concentration of 1.0–5.0 % (w/v) (optimum concentration 2.5 % NaCl). This isolate was an anaerobic chemo-organoheterotroph and was able to utilize yeast extract, peptone, tryptone and starch as the single carbon source for growth. Elemental sulfur and cysteine stimulated growth; however, these molecules were not necessary. The DNA G+C content of the complete genome was 53.47 mol%. The results of 16S rRNA gene sequence analysis indicated that strain A501T belongs to the genus
Thermococcus
. There was no significant similarity between strain A501T and the phylogenetically related species of the genus
Thermococcus
based on complete genome sequence alignments and calculation of the average nucleotide identity and the tetranucleotide signature frequency correlation coefficient. These results indicate that strain A501T represents a novel species, Thermococcus eurythermalis sp. nov. The type strain is A501T ( = CGMCC 7834T = JCM 30233T).
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Yang YS, Fernandez B, Lagorce A, Aloin V, De Guillen KM, Boyer JB, Dedieu A, Confalonieri F, Armengaud J, Roumestand C. Prioritizing targets for structural biology through the lens of proteomics: the archaeal protein TGAM_1934 from Thermococcus gammatolerans. Proteomics 2015; 15:114-23. [PMID: 25359407 DOI: 10.1002/pmic.201300535] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 10/01/2014] [Accepted: 10/24/2014] [Indexed: 11/09/2022]
Abstract
ORFans are hypothetical proteins lacking any significant sequence similarity with other proteins. Here, we highlighted by quantitative proteomics the TGAM_1934 ORFan from the hyperradioresistant Thermococcus gammatolerans archaeon as one of the most abundant hypothetical proteins. This protein has been selected as a priority target for structure determination on the basis of its abundance in three cellular conditions. Its solution structure has been determined using multidimensional heteronuclear NMR spectroscopy. TGAM_1934 displays an original fold, although sharing some similarities with the 3D structure of the bacterial ortholog of frataxin, CyaY, a protein conserved in bacteria and eukaryotes and involved in iron-sulfur cluster biogenesis. These results highlight the potential of structural proteomics in prioritizing ORFan targets for structure determination based on quantitative proteomics data. The proteomic data and structure coordinates have been deposited to the ProteomeXchange with identifier PXD000402 (http://proteomecentral.proteomexchange.org/dataset/PXD000402) and Protein Data Bank under the accession number 2mcf, respectively.
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Affiliation(s)
- Yin-Shan Yang
- Centre de Biochimie Structurale, Universités de Montpellier, Montpellier, France
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55
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Zuo S, Xue D, Zhang T, Jiang B, Mu W. Biochemical characterization of an extremely thermostable l-asparaginase from Thermococcus gammatolerans EJ3. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.08.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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56
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Gorlas A, Croce O, Oberto J, Gauliard E, Forterre P, Marguet E. Thermococcus
nautili sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal deep-sea vent. Int J Syst Evol Microbiol 2014; 64:1802-1810. [DOI: 10.1099/ijs.0.060376-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thermococcus nautili, strain 30-1T (formerly reported as Thermococcus nautilus), was isolated from a hydrothermal chimney sample collected from the East Pacific Rise at a depth of 2633 m on the ‘La chainette PP57’ area. Cells were motile, irregular cocci with a polar tuft of flagella (0.8–1.5 µm) and divided by constriction. The micro-organism grew optimally at 87.5 °C (range 55–95 °C), at pH 7 (range pH 4–9) and with 2 % NaCl (range 1–4 %). Doubling time was 64 min in Zillig’s broth medium under optimal conditions. Growth was strictly anaerobic. It grew preferentially in the presence of elemental sulfur or cystine, which are reduced to H2S, on complex organic substrates such as yeast extract, tryptone, peptone, Casamino acids and casein. Slow growth was observed on starch and pyruvate. Strain 30-1T was resistant to chloramphenicol and tetracyclin (at 100 µg ml−1) but sensitive to kanamycin and rifampicin. The G+C content of the genomic DNA was 54 mol%. Strain 30-1T harboured three plasmids named pTN1, pTN2 and pTN3 and produced membrane vesicles that incorporate pTN1 and pTN3. As determined by 16S rRNA gene sequence analysis, strain 30-1T is related most closely to Thermococcus sp. AM4 (99.3 % similarity) and
Thermococcus gammatolerans
DSM 15229T (99.2 %). DNA–DNA hybridization values (in silico) with these two closest relatives were below the threshold value of 70 % (33 % with Thermococcus sp. AM4 and 32 % with
T. gammatolerans
DSM 15229T) and confirmed that strain 30-1 represents a novel species. On the basis of the data presented, strain 30-1T is considered to represent a novel species of the genus
Thermococcus
, for which the name Thermococcus nautili sp. nov. is proposed. The type strain is 30-1T ( = CNCM 4275 = JCM 19601).
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Affiliation(s)
- Aurore Gorlas
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS UMR8621, 91405 Orsay Cedex, France
| | - Olivier Croce
- Université Aix-Marseille, Faculté de médecine, CNRS UMR7278, Marseille, France
| | - Jacques Oberto
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS UMR8621, 91405 Orsay Cedex, France
| | - Emilie Gauliard
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS UMR8621, 91405 Orsay Cedex, France
| | - Patrick Forterre
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS UMR8621, 91405 Orsay Cedex, France
| | - Evelyne Marguet
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS UMR8621, 91405 Orsay Cedex, France
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57
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General Characteristics and Important Model Organisms. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014. [DOI: 10.1128/9781555815516.ch2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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58
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Egas C, Barroso C, Froufe HJC, Pacheco J, Albuquerque L, da Costa MS. Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4. Stand Genomic Sci 2014; 9:1062-75. [PMID: 25197483 PMCID: PMC4148983 DOI: 10.4056/sigs.5661021] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rubrobacter radiotolerans strain RSPS-4 is a slightly thermophilic member of the phylum “Actinobacteria” isolated from a hot spring in São Pedro do Sul, Portugal. This aerobic and halotolerant bacterium is also extremely resistant to gamma and UV radiation, which are the main reasons for the interest in sequencing its genome. Here, we present the complete genome sequence of strain RSPS-4 as well as its assembly and annotation. We also compare the gene sequence of this organism with that of the type strain of the species R. radiotolerans isolated from a hot spring in Japan. The genome of strain RSPS-4 comprises one circular chromosome of 2,875,491 bp with a G+C content of 66.91%, and 3 circular plasmids of 190,889 bp, 149,806 bp and 51,047 bp, harboring 3,214 predicted protein coding genes, 46 tRNA genes and a single rRNA operon.
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Affiliation(s)
- C Egas
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - C Barroso
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - H J C Froufe
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - J Pacheco
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - L Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - M S da Costa
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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59
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Gorlas A, Alain K, Bienvenu N, Geslin C. Thermococcus
prieurii sp. nov., a hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2013; 63:2920-2926. [DOI: 10.1099/ijs.0.026419-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel hyperthermophilic, anaerobic archaeon, strain Bio-pl-0405IT2T, was isolated from a hydrothermal chimney sample collected from the East Pacific Rise at 2700 m depth in the ‘Sarah Spring’ area (7° 25′ 24″ S 107° 47′ 66″ W). Cells were irregular, motile cocci (0.8–1.5 µm in diameter) and divided by constriction. Growth was observed at temperatures between 60 °C and 95 °C with an optimum at 80 °C. The pH range for growth was between pH 4.0 and pH 8.0 with an optimum around pH 7.0. Strain Bio-pl-0405IT2T grew at salt concentrations of 1–5 % (w/v) NaCl with an optimum at 2 %. The novel isolate grew by fermentation or sulphur respiration on a variety of organic compounds. It was a chemoorganoheterotrophic archaeon growing preferentially with yeast extract, peptone and tryptone as carbon and energy sources and sulphur and organic compounds as electron acceptors; it also grew on maltose and starch. Sulphur or l-cystine were required for growth and were reduced to hydrogen sulfide. The strain was resistant to rifampicin, chloramphenicol, vancomycin and kanamycin (all at 100 µg ml−1) but was sensitive to tetracycline. The G+C content of its genomic DNA was 53.6 mol%. Phylogenetic analysis of the almost complete 16S rRNA gene sequence (1450 bp) of strain Bio-pl-0405IT2T showed that the novel isolate belonged to the genus
Thermococcus
. DNA–DNA hybridization values with the two closest relatives
Thermococcus hydrothermalis
AL662T and
Thermococcus celer
JCM 8558T were below the threshold value of 70 %. On the basis of the physiological and genotypic distinctness, we propose a novel species,
Thermococcus
prieurii sp. nov. The type strain is Bio-pl-0405IT2T ( = CSUR P577T = JCM 16307T).
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Affiliation(s)
- Aurore Gorlas
- UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, IUEM, Technopôle Brest-Iroise, F-29280 Plouzané, France
| | - Karine Alain
- UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, IUEM, Technopôle Brest-Iroise, F-29280 Plouzané, France
| | - Nadège Bienvenu
- UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, IUEM, Technopôle Brest-Iroise, F-29280 Plouzané, France
| | - Claire Geslin
- UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, IUEM, Technopôle Brest-Iroise, F-29280 Plouzané, France
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60
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Archaeal DNA polymerase D but not DNA polymerase B is required for genome replication in Thermococcus kodakarensis. J Bacteriol 2013; 195:2322-8. [PMID: 23504010 DOI: 10.1128/jb.02037-12] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Three evolutionarily distinct families of replicative DNA polymerases, designated polymerase B (Pol B), Pol C, and Pol D, have been identified. Members of the Pol B family are present in all three domains of life, whereas Pol C exists only in Bacteria and Pol D exists only in Archaea. Pol B enzymes replicate eukaryotic chromosomal DNA, and as members of the Pol B family are present in all Archaea, it has been assumed that Pol B enzymes also replicate archaeal genomes. Here we report the construction of Thermococcus kodakarensis strains with mutations that delete or inactivate key functions of Pol B. T. kodakarensis strains lacking Pol B had no detectable loss in viability and no growth defects or changes in spontaneous mutation frequency but had increased sensitivity to UV irradiation. In contrast, we were unable to introduce mutations that inactivated either of the genes encoding the two subunits of Pol D. The results reported establish that Pol D is sufficient for viability and genome replication in T. kodakarensis and argue that Pol D rather than Pol B is likely the replicative DNA polymerase in this archaeon. The majority of Archaea contain Pol D, and, as discussed, if Pol D is the predominant replicative polymerase in Archaea, this profoundly impacts hypotheses for the origin(s), evolution, and distribution of the different DNA replication enzymes and systems now employed in the three domains of life.
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61
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A simple procedure to determine the infectivity and host range of viruses infecting anaerobic and hyperthermophilic microorganisms. Extremophiles 2013; 17:349-55. [PMID: 23340763 DOI: 10.1007/s00792-013-0513-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 01/04/2013] [Indexed: 10/27/2022]
Abstract
Plaque assay is the method traditionally used to isolate and purify lytic viruses, to determine the viral titer and host range. Whereas most bacterioviruses are either temperate or lytic, the majority of known archeoviruses are not lytic (i.e. they are temperate or chronic). In view of the widespread occurrence of such viruses in extreme environments, we designed an original method, called the inverted spot test, to determine the host range and infectivity of viruses isolated from anaerobic hyperthermophilic and sulfur-reducing microorganisms. Here, we used this approach to prove for the first time the infectivity of Pyrococcus abyssi virus 1 (PAV1) and to confirm the host range of Thermococcus prieurii virus 1 (TPV1), the only two viruses isolated so far from any of the described marine hyperthermophilic archaea (Euryarchaeota phylum, Thermococcales order).
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62
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Polyextremophiles and the Constraints for Terrestrial Habitability. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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63
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Radiation Resistance in Extremophiles: Fending Off Multiple Attacks. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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64
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Role of Mn2+ and compatible solutes in the radiation resistance of thermophilic bacteria and archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2012; 2012:845756. [PMID: 23209374 PMCID: PMC3505630 DOI: 10.1155/2012/845756] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/18/2012] [Accepted: 10/13/2012] [Indexed: 01/28/2023]
Abstract
Radiation-resistant bacteria have garnered a great deal of attention from scientists seeking to expose the mechanisms underlying their incredible survival abilities. Recent analyses showed that the resistance to ionizing radiation (IR) in the archaeon Halobacterium salinarum is dependent upon Mn-antioxidant complexes responsible for the scavenging of reactive oxygen species (ROS) generated by radiation. Here we examined the role of the compatible solutes trehalose, mannosylglycerate, and di-myo-inositol phosphate in the radiation resistance of aerobic and anaerobic thermophiles. We found that the IR resistance of the thermophilic bacteria Rubrobacter xylanophilus and Rubrobacter radiotolerans was highly correlated to the accumulation of high intracellular concentration of trehalose in association with Mn, supporting the model of Mn2+-dependent ROS scavenging in the aerobes. In contrast, the hyperthermophilic archaea Thermococcus gammatolerans and Pyrococcus furiosus did not contain significant amounts of intracellular Mn, and we found no significant antioxidant activity from mannosylglycerate and di-myo-inositol phosphate in vitro. We therefore propose that the low levels of IR-generated ROS under anaerobic conditions combined with highly constitutively expressed detoxification systems in these anaerobes are key to their radiation resistance and circumvent the need for the accumulation of Mn-antioxidant complexes in the cell.
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65
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Møller AP, Mousseau TA. The effects of natural variation in background radioactivity on humans, animals and other organisms. Biol Rev Camb Philos Soc 2012; 88:226-54. [DOI: 10.1111/j.1469-185x.2012.00249.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 09/26/2012] [Accepted: 10/05/2012] [Indexed: 01/23/2023]
Affiliation(s)
- Anders P. Møller
- Laboratoire d'Ecologie; Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud; Bâtiment 362; F-91405; Orsay Cedex; France
| | - Timothy A. Mousseau
- Department of Biological Sciences; University of South Carolina; Columbia; SC; 29208; USA
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66
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Genome-wide transcriptional response of the archaeon Thermococcus gammatolerans to cadmium. PLoS One 2012; 7:e41935. [PMID: 22848664 PMCID: PMC3407056 DOI: 10.1371/journal.pone.0041935] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 06/26/2012] [Indexed: 12/16/2022] Open
Abstract
Thermococcus gammatolerans, the most radioresistant archaeon known to date, is an anaerobic and hyperthermophilic sulfur-reducing organism living in deep-sea hydrothermal vents. Knowledge of mechanisms underlying archaeal metal tolerance in such metal-rich ecosystem is still poorly documented. We showed that T. gammatolerans exhibits high resistance to cadmium (Cd), cobalt (Co) and zinc (Zn), a weaker tolerance to nickel (Ni), copper (Cu) and arsenate (AsO4) and that cells exposed to 1 mM Cd exhibit a cellular Cd concentration of 67 µM. A time-dependent transcriptomic analysis using microarrays was performed at a non-toxic (100 µM) and a toxic (1 mM) Cd dose. The reliability of microarray data was strengthened by real time RT-PCR validations. Altogether, 114 Cd responsive genes were revealed and a substantial subset of genes is related to metal homeostasis, drug detoxification, re-oxidization of cofactors and ATP production. This first genome-wide expression profiling study of archaeal cells challenged with Cd showed that T. gammatolerans withstands induced stress through pathways observed in both prokaryotes and eukaryotes but also through new and original strategies. T. gammatolerans cells challenged with 1 mM Cd basically promote: 1) the induction of several transporter/permease encoding genes, probably to detoxify the cell; 2) the upregulation of Fe transporters encoding genes to likely compensate Cd damages in iron-containing proteins; 3) the induction of membrane-bound hydrogenase (Mbh) and membrane-bound hydrogenlyase (Mhy2) subunits encoding genes involved in recycling reduced cofactors and/or in proton translocation for energy production. By contrast to other organisms, redox homeostasis genes appear constitutively expressed and only a few genes encoding DNA repair proteins are regulated. We compared the expression of 27 Cd responsive genes in other stress conditions (Zn, Ni, heat shock, γ-rays), and showed that the Cd transcriptional pattern is comparable to other metal stress transcriptional responses (Cd, Zn, Ni) but not to a general stress response.
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67
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Complete genome sequence of the hyperthermophilic archaeon Thermococcus sp. strain AM4, capable of organotrophic growth and growth at the expense of hydrogenogenic or sulfidogenic oxidation of carbon monoxide. J Bacteriol 2012; 193:7019-20. [PMID: 22123768 DOI: 10.1128/jb.06259-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Analysis of the complete genome of Thermococcus sp. strain AM4, which was the first lithotrophic Thermococcales isolate described and the first archaeal isolate to exhibit a capacity for hydrogenogenic carboxydotrophy, reveals a proximity with Thermococcus gammatolerans, corresponding to close but distinct species that differ significantly in their lithotrophic capacities.
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68
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Anderson RE, Brazelton WJ, Baross JA. Is the genetic landscape of the deep subsurface biosphere affected by viruses? Front Microbiol 2011; 2:219. [PMID: 22084639 PMCID: PMC3211056 DOI: 10.3389/fmicb.2011.00219] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 10/14/2011] [Indexed: 12/26/2022] Open
Abstract
Viruses are powerful manipulators of microbial diversity, biogeochemistry, and evolution in the marine environment. Viruses can directly influence the genetic capabilities and the fitness of their hosts through the use of fitness factors and through horizontal gene transfer. However, the impact of viruses on microbial ecology and evolution is often overlooked in studies of the deep subsurface biosphere. Subsurface habitats connected to hydrothermal vent systems are characterized by constant fluid flux, dynamic environmental variability, and high microbial diversity. In such conditions, high adaptability would be an evolutionary asset, and the potential for frequent host-virus interactions would be high, increasing the likelihood that cellular hosts could acquire novel functions. Here, we review evidence supporting this hypothesis, including data indicating that microbial communities in subsurface hydrothermal fluids are exposed to a high rate of viral infection, as well as viral metagenomic data suggesting that the vent viral assemblage is particularly enriched in genes that facilitate horizontal gene transfer and host adaptability. Therefore, viruses are likely to play a crucial role in facilitating adaptability to the extreme conditions of these regions of the deep subsurface biosphere. We also discuss how these results might apply to other regions of the deep subsurface, where the nature of virus-host interactions would be altered, but possibly no less important, compared to more energetic hydrothermal systems.
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Affiliation(s)
- Rika E Anderson
- School of Oceanography and Astrobiology Program, University of Washington Seattle, WA, USA
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69
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Yun SH, Kwon SO, Park GW, Kim JY, Kang SG, Lee JH, Chung YH, Kim S, Choi JS, Kim SI. Proteome analysis of Thermococcus onnurineus NA1 reveals the expression of hydrogen gene cluster under carboxydotrophic growth. J Proteomics 2011; 74:1926-33. [DOI: 10.1016/j.jprot.2011.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 04/18/2011] [Accepted: 05/06/2011] [Indexed: 10/18/2022]
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70
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Ragon M, Restoux G, Moreira D, Møller AP, López-García P. Sunlight-exposed biofilm microbial communities are naturally resistant to chernobyl ionizing-radiation levels. PLoS One 2011; 6:e21764. [PMID: 21765911 PMCID: PMC3135598 DOI: 10.1371/journal.pone.0021764] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 06/06/2011] [Indexed: 02/06/2023] Open
Abstract
Background The Chernobyl accident represents a long-term experiment on the effects of exposure to ionizing radiation at the ecosystem level. Though studies of these effects on plants and animals are abundant, the study of how Chernobyl radiation levels affect prokaryotic and eukaryotic microbial communities is practically non-existent, except for a few reports on human pathogens or soil microorganisms. Environments enduring extreme desiccation and UV radiation, such as sunlight exposed biofilms could in principle select for organisms highly resistant to ionizing radiation as well. Methodology/Principal Findings To test this hypothesis, we explored the diversity of microorganisms belonging to the three domains of life by cultivation-independent approaches in biofilms developing on concrete walls or pillars in the Chernobyl area exposed to different levels of radiation, and we compared them with a similar biofilm from a non-irradiated site in Northern Ireland. Actinobacteria, Alphaproteobacteria, Bacteroidetes, Acidobacteria and Deinococcales were the most consistently detected bacterial groups, whereas green algae (Chlorophyta) and ascomycete fungi (Ascomycota) dominated within the eukaryotes. Close relatives to the most radio-resistant organisms known, including Rubrobacter species, Deinococcales and melanized ascomycete fungi were always detected. The diversity of bacteria and eukaryotes found in the most highly irradiated samples was comparable to that of less irradiated Chernobyl sites and Northern Ireland. However, the study of mutation frequencies in non-coding ITS regions versus SSU rRNA genes in members of a same actinobacterial operational taxonomic unit (OTU) present in Chernobyl samples and Northern Ireland showed a positive correlation between increased radiation and mutation rates. Conclusions/Significance Our results show that biofilm microbial communities in the most irradiated samples are comparable to non-irradiated samples in terms of general diversity patterns, despite increased mutation levels at the single-OTU level. Therefore, biofilm communities growing in sunlight exposed substrates are capable of coping with increased mutation rates and appear pre-adapted to levels of ionizing radiation in Chernobyl due to their natural adaptation to periodical desiccation and ambient UV radiation.
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Affiliation(s)
- Marie Ragon
- Unité d'Ecologie, Systématique et Evolution - CNRS UMR8079, Université Paris-Sud, Orsay, France
| | - Gwendal Restoux
- Unité d'Ecologie, Systématique et Evolution - CNRS UMR8079, Université Paris-Sud, Orsay, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution - CNRS UMR8079, Université Paris-Sud, Orsay, France
| | - Anders Pape Møller
- Unité d'Ecologie, Systématique et Evolution - CNRS UMR8079, Université Paris-Sud, Orsay, France
| | - Purificación López-García
- Unité d'Ecologie, Systématique et Evolution - CNRS UMR8079, Université Paris-Sud, Orsay, France
- * E-mail:
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Abstract
Ionizing radiation is a ubiquitous feature of the Cosmos, from exogenous cosmic rays (CR) to the intrinsic mineral radioactivity of a habitable world, and its influences on the emergence and persistence of life are wide-ranging and profound. Much attention has already been focused on the deleterious effects of ionizing radiation on organisms and the complex molecules of life, but ionizing radiation also performs many crucial functions in the generation of habitable planetary environments and the origins of life. This review surveys the role of CR and mineral radioactivity in star formation, generation of biogenic elements, and the synthesis of organic molecules and driving of prebiotic chemistry. Another major theme is the multiple layers of shielding of planetary surfaces from the flux of cosmic radiation and the various effects on a biosphere of violent but rare astrophysical events such as supernovae and gamma-ray bursts. The influences of CR can also be duplicitous, such as limiting the survival of surface life on Mars while potentially supporting a subsurface biosphere in the ocean of Europa. This review highlights the common thread that ionizing radiation forms between the disparate component disciplines of astrobiology.
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Affiliation(s)
- Lewis R Dartnell
- UCL Institute for Origins, University College London, London, UK.
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Abstract
Deinococcus radiodurans is a robust bacterium best known for its capacity to repair massive DNA damage efficiently and accurately. It is extremely resistant to many DNA-damaging agents, including ionizing radiation and UV radiation (100 to 295 nm), desiccation, and mitomycin C, which induce oxidative damage not only to DNA but also to all cellular macromolecules via the production of reactive oxygen species. The extreme resilience of D. radiodurans to oxidative stress is imparted synergistically by an efficient protection of proteins against oxidative stress and an efficient DNA repair mechanism, enhanced by functional redundancies in both systems. D. radiodurans assets for the prevention of and recovery from oxidative stress are extensively reviewed here. Radiation- and desiccation-resistant bacteria such as D. radiodurans have substantially lower protein oxidation levels than do sensitive bacteria but have similar yields of DNA double-strand breaks. These findings challenge the concept of DNA as the primary target of radiation toxicity while advancing protein damage, and the protection of proteins against oxidative damage, as a new paradigm of radiation toxicity and survival. The protection of DNA repair and other proteins against oxidative damage is imparted by enzymatic and nonenzymatic antioxidant defense systems dominated by divalent manganese complexes. Given that oxidative stress caused by the accumulation of reactive oxygen species is associated with aging and cancer, a comprehensive outlook on D. radiodurans strategies of combating oxidative stress may open new avenues for antiaging and anticancer treatments. The study of the antioxidation protection in D. radiodurans is therefore of considerable potential interest for medicine and public health.
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73
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Survival of thermophilic and hyperthermophilic microorganisms after exposure to UV-C, ionizing radiation and desiccation. Arch Microbiol 2011; 193:797-809. [DOI: 10.1007/s00203-011-0718-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 05/13/2011] [Accepted: 05/18/2011] [Indexed: 12/11/2022]
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74
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Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev 2011; 75:361-422. [PMID: 21646433 PMCID: PMC3122624 DOI: 10.1128/mmbr.00039-10] [Citation(s) in RCA: 338] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The majority of life on Earth--notably, microbial life--occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean-the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.-has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.
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Affiliation(s)
- Beth N. Orcutt
- Center for Geomicrobiology, Aarhus University, 8000 Aarhus, Denmark
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Jason B. Sylvan
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Nina J. Knab
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Katrina J. Edwards
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
- Department of Earth Sciences, University of Southern California, Los Angeles, California 90089
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75
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Edgcomb VP, Leadbetter ER, Bourland W, Beaudoin D, Bernhard JM. Structured multiple endosymbiosis of bacteria and archaea in a ciliate from marine sulfidic sediments: a survival mechanism in low oxygen, sulfidic sediments? Front Microbiol 2011; 2:55. [PMID: 21833311 PMCID: PMC3153031 DOI: 10.3389/fmicb.2011.00055] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 03/10/2011] [Indexed: 11/13/2022] Open
Abstract
Marine micro-oxic to sulfidic environments are sites of intensive biogeochemical cycling and elemental sequestration, where prokaryotes are major driving forces mediating carbon, nitrogen, sulfur, phosphorus, and metal cycles, important from both biogeochemical and evolutionary perspectives. Associations between single-celled eukaryotes and bacteria and/or archaea are common in such habitats. Here we describe a ciliate common in the micro-oxic to anoxic, typically sulfidic, sediments of Santa Barbara Basin (CA, USA). The ciliate is 95% similar to Parduzcia orbis (18S rRNA). Transmission electron micrographs reveal clusters of at least three different endobiont types organized within membrane-bound sub-cellular regions. Catalyzed reporter deposition-fluorescent in situ hybridization and 16S rRNA clone libraries confirm the symbionts include up to two sulfate reducers (Desulfobulbaceae, Desulfobacteraceae), a methanogen (Methanobacteriales), and possibly a Bacteroidete (Cytophaga) and a Type I methanotroph, suggesting synergistic metabolisms in this environment. This case study is discussed in terms of implications to biogeochemistry, and benthic ecology.
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Affiliation(s)
- Virginia P Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
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77
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Yakimov MM, Cono VL, Smedile F, DeLuca TH, Juárez S, Ciordia S, Fernández M, Albar JP, Ferrer M, Golyshin PN, Giuliano L. Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea). ISME JOURNAL 2011; 5:945-61. [PMID: 21209665 DOI: 10.1038/ismej.2010.197] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mesophilic Crenarchaeota have recently been thought to be significant contributors to nitrogen (N) and carbon (C) cycling. In this study, we examined the vertical distribution of ammonia-oxidizing Crenarchaeota at offshore site in Southern Tyrrhenian Sea. The median value of the crenachaeal cell to amoA gene ratio was close to one suggesting that virtually all deep-sea Crenarchaeota possess the capacity to oxidize ammonia. Crenarchaea-specific genes, nirK and ureC, for nitrite reductase and urease were identified and their affiliation demonstrated the presence of 'deep-sea' clades distinct from 'shallow' representatives. Measured deep-sea dark CO(2) fixation estimates were comparable to the median value of photosynthetic biomass production calculated for this area of Tyrrhenian Sea, pointing to the significance of this process in the C cycle of aphotic marine ecosystems. To elucidate the pivotal organisms in this process, we targeted known marine crenarchaeal autotrophy-related genes, coding for acetyl-CoA carboxylase (accA) and 4-hydroxybutyryl-CoA dehydratase (4-hbd). As in case of nirK and ureC, these genes are grouped with deep-sea sequences being distantly related to those retrieved from the epipelagic zone. To pair the molecular data with specific functional attributes we performed [(14)C]HCO(3) incorporation experiments followed by analyses of radiolabeled proteins using shotgun proteomics approach. More than 100 oligopeptides were attributed to 40 marine crenarchaeal-specific proteins that are involved in 10 different metabolic processes, including autotrophy. Obtained results provided a clear proof of chemolithoautotrophic physiology of bathypelagic crenarchaeota and indicated that this numerically predominant group of microorganisms facilitate a hitherto unrecognized sink for inorganic C of a global importance.
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Affiliation(s)
- Michail M Yakimov
- Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment, CNR, Messina, Italy.
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Houghton JL, Seyfried WE. An experimental and theoretical approach to determining linkages between geochemical variability and microbial biodiversity in seafloor hydrothermal chimneys. GEOBIOLOGY 2010; 8:457-470. [PMID: 20726900 DOI: 10.1111/j.1472-4669.2010.00255.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
New experimental results of fluid-mineral reactions at hydrothermal conditions relevant to life demonstrate that key redox reactions involving iron, sulfur, and hydrogen remain at disequilibrium at 100 °C, even in a heterogeneous system and thus are energetically favorable for microbial metabolism. Predictions from geochemical models utilizing the experimental results and specific to two contrasting case studies from the East Pacific Rise were statistically characterized and correlated to the energetics of redox reactions available for intra-chimney microbial populations. In general, predictions of available energy for autotrophic metabolism are largely similar between the mature and the nascent chimneys, although important differences still exist. Metabolic processes predicted by energetics exhibit the same trends observed in the field data for the mature chimney, but overestimate the diversity observed in the nascent chimney. Several combinations of redox reaction pairs are predicted to support mixed consortia, while some combinations appear to favor more versatile microbes capable of utilizing several reactions under rapidly changing environmental conditions within chimney walls. In addition, conditions favorable to elemental sulfur reduction and methanogenesis exhibit a negative control on the diversity of microbial populations within these chimney walls, whereas H₂S oxidation, elemental sulfur oxidation and the knallgas reaction are positively correlated with both abundance and diversity of micro-organisms. Coupling field observations of both microbial diversity and geochemical heterogeneity with lab-based experimental and theoretical modeling can facilitate translation of the observed genetic diversity into physiological diversity, thus enhancing understanding of linked phenomena of microbially induced biogeochemical transformations in complex heterogeneous systems.
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Affiliation(s)
- J L Houghton
- Department of Biology, Rhodes College, Memphis, TN, USA.
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80
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Fairén AG, Davila AF, Lim D, Bramall N, Bonaccorsi R, Zavaleta J, Uceda ER, Stoker C, Wierzchos J, Dohm JM, Amils R, Andersen D, McKay CP. Astrobiology through the ages of Mars: the study of terrestrial analogues to understand the habitability of Mars. ASTROBIOLOGY 2010; 10:821-843. [PMID: 21087162 DOI: 10.1089/ast.2009.0440] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Mars has undergone three main climatic stages throughout its geological history, beginning with a water-rich epoch, followed by a cold and semi-arid era, and transitioning into present-day arid and very cold desert conditions. These global climatic eras also represent three different stages of planetary habitability: an early, potentially habitable stage when the basic requisites for life as we know it were present (liquid water and energy); an intermediate extreme stage, when liquid solutions became scarce or very challenging for life; and the most recent stage during which conditions on the surface have been largely uninhabitable, except perhaps in some isolated niches. Our understanding of the evolution of Mars is now sufficient to assign specific terrestrial environments to each of these periods. Through the study of Mars terrestrial analogues, we have assessed and constrained the habitability conditions for each of these stages, the geochemistry of the surface, and the likelihood for the preservation of organic and inorganic biosignatures. The study of these analog environments provides important information to better understand past and current mission results as well as to support the design and selection of instruments and the planning for future exploratory missions to Mars.
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81
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Kimura H, Nashimoto H, Shimizu M, Hattori S, Yamada K, Koba K, Yoshida N, Kato K. Microbial methane production in deep aquifer associated with the accretionary prism in Southwest Japan. ISME JOURNAL 2009; 4:531-41. [DOI: 10.1038/ismej.2009.132] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Zivanovic Y, Armengaud J, Lagorce A, Leplat C, Guérin P, Dutertre M, Anthouard V, Forterre P, Wincker P, Confalonieri F. Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea. Genome Biol 2009; 10:R70. [PMID: 19558674 PMCID: PMC2718504 DOI: 10.1186/gb-2009-10-6-r70] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Revised: 05/29/2009] [Accepted: 06/26/2009] [Indexed: 11/15/2022] Open
Abstract
The genome sequence of Thermococcus gammatolerans, a radioresistant archaeon, is described; a proteomic analysis reveals that radioresistance may be due to unknown DNA repair enzymes. Background Thermococcus gammatolerans was isolated from samples collected from hydrothermal chimneys. It is one of the most radioresistant organisms known amongst the Archaea. We report the determination and annotation of its complete genome sequence, its comparison with other Thermococcales genomes, and a proteomic analysis. Results T. gammatolerans has a circular chromosome of 2.045 Mbp without any extra-chromosomal elements, coding for 2,157 proteins. A thorough comparative genomics analysis revealed important but unsuspected genome plasticity differences between sequenced Thermococcus and Pyrococcus species that could not be attributed to the presence of specific mobile elements. Two virus-related regions, tgv1 and tgv2, are the only mobile elements identified in this genome. A proteogenome analysis was performed by a shotgun liquid chromatography-tandem mass spectrometry approach, allowing the identification of 10,931 unique peptides corresponding to 951 proteins. This information concurrently validates the accuracy of the genome annotation. Semi-quantification of proteins by spectral count was done on exponential- and stationary-phase cells. Insights into general catabolism, hydrogenase complexes, detoxification systems, and the DNA repair toolbox of this archaeon are revealed through this genome and proteome analysis. Conclusions This work is the first archaeal proteome investigation done at the stage of primary genome annotation. This archaeon is shown to use a large variety of metabolic pathways even under a rich medium growth condition. This proteogenomic study also indicates that the high radiotolerance of T. gammatolerans is probably due to proteins that remain to be characterized rather than a larger arsenal of known DNA repair enzymes.
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Affiliation(s)
- Yvan Zivanovic
- Laboratoire de Génomique des Archae, Université Paris-Sud 11, CNRS, UMR8621, Bât400 F-91405 Orsay, France.
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83
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Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, Cary SC. Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genet 2009; 5:e1000362. [PMID: 19197347 PMCID: PMC2628731 DOI: 10.1371/journal.pgen.1000362] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Accepted: 12/31/2008] [Indexed: 11/19/2022] Open
Abstract
Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. Vents are typified by rapid fluctuations in temperature and redox potential that impose a strong selective pressure on resident microbial communities. Nautilia profundicola strain Am-H is a moderately thermophilic, deeply-branching Epsilonproteobacterium found free-living at hydrothermal vents and is a member of the microbial mass on the dorsal surface of vent polychaete, Alvinella pompejana. Analysis of the 1.7-Mbp genome of N. profundicola uncovered adaptations to the vent environment--some unique and some shared with other Epsilonproteobacterial genomes. The major findings included: (1) a diverse suite of hydrogenases coupled to a relatively simple electron transport chain, (2) numerous stress response systems, (3) a novel predicted nitrate assimilation pathway with hydroxylamine as a key intermediate, and (4) a gene (rgy) encoding the hallmark protein for hyperthermophilic growth, reverse gyrase. Additional experiments indicated that expression of rgy in strain Am-H was induced over 100-fold with a 20 degrees C increase above the optimal growth temperature of this bacterium and that closely related rgy genes are present and expressed in bacterial communities residing in geographically distinct thermophilic environments. N. profundicola, therefore, is a model Epsilonproteobacterium that contains all the genes necessary for life in the extreme conditions widely believed to reflect those in the Archaean biosphere--anaerobic, sulfur, H2- and CO2-rich, with fluctuating redox potentials and temperatures. In addition, reverse gyrase appears to be an important and common adaptation for mesophiles and moderate thermophiles that inhabit ecological niches characterized by rapid and frequent temperature fluctuations and, as such, can no longer be considered a unique feature of hyperthermophiles.
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84
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Recovery of ionizing-radiation damage after high doses of gamma ray in the hyperthermophilic archaeon Thermococcus gammatolerans. Extremophiles 2009; 13:333-43. [DOI: 10.1007/s00792-008-0221-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 12/12/2008] [Indexed: 10/21/2022]
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85
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Abstract
Thermophilic anaerobes are Archaea and Bacteria that grow optimally at temperatures of 50 degrees C or higher and do not require the use of O(2) as a terminal electron acceptor for growth. The prokaryotes with this type of physiology are studied for a variety of reasons, including (a) to understand how life can thrive under extreme conditions, (b) for their biotechnological potential, and (c) because anaerobic thermophiles are thought to share characteristics with the early evolutionary life forms on Earth. Over 300 species of thermophilic anaerobes have been described; most have been isolated from thermal environments, but some are from mesobiotic environments, and others are from environments with temperatures below 0 degrees C. In this overview, the authors outline the phylogenetic and physiological diversity of thermophilic anaerobes as currently known. The purpose of this overview is to convey the incredible diversity and breadth of metabolism within this subset of anaerobic microorganisms.
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Affiliation(s)
- Isaac D Wagner
- 212 Biological Sciences Building, 1000 Cedar Street, University of Georgia, Athens, GA 30602-2605, USA
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86
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Virus-like vesicles and extracellular DNA produced by hyperthermophilic archaea of the order Thermococcales. Res Microbiol 2008; 159:390-9. [DOI: 10.1016/j.resmic.2008.04.015] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 04/04/2008] [Accepted: 04/14/2008] [Indexed: 11/20/2022]
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Quaiser A, Constantinesco F, White MF, Forterre P, Elie C. The Mre11 protein interacts with both Rad50 and the HerA bipolar helicase and is recruited to DNA following gamma irradiation in the archaeon Sulfolobus acidocaldarius. BMC Mol Biol 2008; 9:25. [PMID: 18294364 PMCID: PMC2288612 DOI: 10.1186/1471-2199-9-25] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Accepted: 02/22/2008] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The ubiquitous Rad50 and Mre11 proteins play a key role in many processes involved in the maintenance of genome integrity in Bacteria and Eucarya, but their function in the Archaea is presently unknown. We showed previously that in most hyperthermophilic archaea, rad50-mre11 genes are linked to nurA encoding both a single-strand endonuclease and a 5' to 3' exonuclease, and herA, encoding a bipolar DNA helicase which suggests the involvement of the four proteins in common molecular pathway(s). Since genetic tools for hyperthermophilic archaea are just emerging, we utilized immuno-detection approaches to get the first in vivo data on the role(s) of these proteins in the hyperthermophilic crenarchaeon Sulfolobus acidocaldarius. RESULTS We first showed that S. acidocaldarius can repair DNA damage induced by high doses of gamma rays, and we performed a time course analysis of the total levels and sub-cellular partitioning of Rad50, Mre11, HerA and NurA along with the RadA recombinase in both control and irradiated cells. We found that during the exponential phase, all proteins are synthesized and display constant levels, but that all of them exhibit a different sub-cellular partitioning. Following gamma irradiation, both Mre11 and RadA are immediately recruited to DNA and remain DNA-bound in the course of DNA repair. Furthermore, we show by immuno-precipitation assays that Rad50, Mre11 and the HerA helicase interact altogether. CONCLUSION Our analyses strongly support that in Sulfolobus acidocaldarius, the Mre11 protein and the RadA recombinase might play an active role in the repair of DNA damage introduced by gamma rays and/or may act as DNA damage sensors. Moreover, our results demonstrate the functional interaction between Mre11, Rad50 and the HerA helicase and suggest that each protein play different roles when acting on its own or in association with its partners. This report provides the first in vivo evidence supporting the implication of the Mre11 protein in DNA repair processes in the Archaea and showing its interaction with both Rad50 and the HerA bipolar helicase. Further studies on the functional interactions between these proteins, the NurA nuclease and the RadA recombinase, will allow us to define their roles and mechanism of action.
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Affiliation(s)
- Achim Quaiser
- Univ Paris-Sud, Institut de Génétique et Microbiologie, CNRS UMR 8621, Bâtiment 409, F 91405 Orsay Cedex, France.
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Pikuta EV, Marsic D, Itoh T, Bej AK, Tang J, Whitman WB, Ng JD, Garriott OK, Hoover RB. Thermococcus thioreducens sp. nov., a novel hyperthermophilic, obligately sulfur-reducing archaeon from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2007; 57:1612-1618. [PMID: 17625204 DOI: 10.1099/ijs.0.65057-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A hyperthermophilic, sulfur-reducing, organo-heterotrophic archaeon, strain OGL-20P(T), was isolated from 'black smoker' chimney material from the Rainbow hydrothermal vent site on the Mid-Atlantic Ridge (36.2 degrees N, 33.9 degrees W). The cells of strain OGL-20P(T) have an irregular coccoid shape and are motile with a single flagellum. Growth was observed within a pH range of 5.0-8.5 (optimum pH 7.0), an NaCl concentration range of 1-5 % (w/v) (optimum 3 %) and a temperature range of 55-94 degrees C (optimum 83-85 degrees C). The novel isolate is strictly anaerobic and obligately dependent upon elemental sulfur as an electron acceptor, but it does not reduce sulfate, sulfite, thiosulfate, Fe(III) or nitrate. Proteolysis products (peptone, bacto-tryptone, Casamino acids and yeast extract) are utilized as substrates during sulfur reduction. Strain OGL-20P(T) is resistant to ampicillin, chloramphenicol, kanamycin and gentamicin, but sensitive to tetracycline and rifampicin. The G+C content of the DNA is 52.9 mol%. The 16S rRNA gene sequence analysis revealed that strain OGL-20P(T) is closely related to Thermococcus coalescens and related species, but no significant homology by DNA-DNA hybridization was observed between those species and the new isolate. On the basis of physiological and molecular properties of the new isolate, we conclude that strain OGL-20P(T) represents a new separate species within the genus Thermococcus, for which we propose the name Thermococcus thioreducens sp. nov. The type strain is OGL-20P(T) (=JCM 12859(T)=DSM 14981(T)=ATCC BAA-394(T)).
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MESH Headings
- Anaerobiosis
- Anti-Bacterial Agents/pharmacology
- Atlantic Ocean
- Base Composition
- DNA, Archaeal/chemistry
- DNA, Archaeal/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Ferric Compounds/metabolism
- Flagella
- Genes, rRNA
- Hot Springs/microbiology
- Hydrogen-Ion Concentration
- Locomotion
- Molecular Sequence Data
- Nitrates/metabolism
- Nucleic Acid Hybridization
- Oxidation-Reduction
- Peptones/metabolism
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Ribosomal, 16S/genetics
- Seawater/microbiology
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/metabolism
- Sulfur/metabolism
- Temperature
- Thermococcus/classification
- Thermococcus/drug effects
- Thermococcus/isolation & purification
- Thermococcus/physiology
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Affiliation(s)
- Elena V Pikuta
- Astrobiology Laboratory, NASA/NSSTC, VP62, 320 Sparkman Dr., Huntsville, AL 35805, USA
| | - Damien Marsic
- Laboratory for Structural Biology, Department of Biological Sciences, The University of Alabama in Huntsville, MSB 221, Huntsville, AL 35899, USA
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Asim K Bej
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jane Tang
- United States Department of Agriculture, Monitoring Programs Office, 8609 Sudley Rd., Suite 206, Manassas, VA 20110, USA
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605, USA
| | - Joseph D Ng
- Laboratory for Structural Biology, Department of Biological Sciences, The University of Alabama in Huntsville, MSB 221, Huntsville, AL 35899, USA
| | - Owen K Garriott
- Department of Biological Sciences, UAH, Huntsville, AL 35899, USA
| | - Richard B Hoover
- Astrobiology Laboratory, NASA/NSSTC, VP62, 320 Sparkman Dr., Huntsville, AL 35805, USA
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89
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Abstract
Prokaryotic extremophiles were the first representatives of life on Earth and they are responsible for the genesis of geological structures during the evolution and creation of all currently known ecosystems. Flexibility of the genome probably allowed life to adapt to a wide spectrum of extreme environments. As a result, modern prokaryotic diversity formed in a framework of physico-chemical factors, and it is composed of: thermophilic, psychrophilic, acidophilic, alkaliphilic, halophilic, barophilic, and radioresistant species. This artificial systematics cannot reflect the multiple actions of different environmental factors since one organism could unite characteristics of several extreme-groups. In this review we show the current status of studies in all fields of extremophiles and summarize the limits of life for different species of microbial extremophiles. We also discuss the finding of extremophiles from unusual places such as soils, and briefly review recent studies of microfossils in meteorites in the context of the significance of microbial extremophiles to Astrobiology.
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Affiliation(s)
- Elena V Pikuta
- National Space Sciences and Technology Center, NASA, Astrobiology Laboratory, Huntsville, Alabama 35805, USA.
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90
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Kuwabara T, Minaba M, Ogi N, Kamekura M. Thermococcus celericrescens sp. nov., a fast-growing and cell-fusing hyperthermophilic archaeon from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2007; 57:437-443. [PMID: 17329765 DOI: 10.1099/ijs.0.64597-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A fast-growing and cell-fusing hyperthermophilic archaeon was isolated from a hydrothermal vent at Suiyo Seamount, Izu-Bonin Arc, Western Pacific Ocean. Strain TS2T is an irregular, motile coccus that is generally 0.7–1.5 μm in diameter and possesses a polar tuft of flagella. In the mid-exponential phase of growth, cells that appeared black under phase-contrast microscopy fused at room temperature in the presence of a DNA-intercalating dye, as previously observed in Thermococcus coalescens. Cell fusion was not observed in later growth phases. Transmission electron microscopy revealed that the cells in the mid-exponential phase had a 5 nm-thick, electron-dense cell envelope that appeared to associate loosely with the cytoplasmic membrane. As the growth stage progressed, a surface layer developed on the membrane under the envelope and the envelope eventually peeled off. These observations suggest that the surface layer prevents the fusion of cells. Cells of strain TS2T grew at 50–85 °C, pH 5.6–8.3 and at NaCl concentrations of 1.0 to 4.5 %, with optimal growth occurring at 80 °C, pH 7.0 and 3.0 % NaCl. Under optimal growth conditions, strain TS2T grew very fast with an apparent doubling time of 20 min. It is suggested that the biosynthesis of the surface layer cannot catch up with cell multiplication in the mid-exponential phase and thus cells without the surface layer are generated. Strain TS2T was an anaerobic chemo-organotroph that grew on either yeast extract or tryptone as the sole growth substrate. The genomic DNA G+C content was 54.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the isolate belongs to the genus Thermococcus. However, no significant DNA–DNA hybridization was observed between the genomic DNA of strain TS2T and phylogenetically related Thermococcus species. On the basis of this evidence, strain TS2T is proposed to represent a novel species, Thermococcus celericrescens sp. nov., a name chosen to reflect the fast growth of the strain. The type strain is TS2T (=NBRC 101555T=JCM 13640T=DSM 17994T).
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Affiliation(s)
- Tomohiko Kuwabara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Masaomi Minaba
- Master's Program in Biosystem Studies, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Noriko Ogi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
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91
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Hamana K, Hosoya R, Itoh T. Polyamine analysis of methanogens, thermophiles and extreme halophiles belonging to the domain Archaea. ACTA ACUST UNITED AC 2007. [DOI: 10.3118/jjse.6.25] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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92
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Shukla M, Chaturvedi R, Tamhane D, Vyas P, Archana G, Apte S, Bandekar J, Desai A. Multiple-Stress Tolerance of Ionizing Radiation-Resistant Bacterial Isolates Obtained from Various Habitats: Correlation Between Stresses. Curr Microbiol 2006; 54:142-8. [PMID: 17180747 DOI: 10.1007/s00284-006-0311-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Accepted: 09/12/2006] [Indexed: 11/29/2022]
Abstract
Isolation of five ionizing radiation (IR)-resistant bacteria by screening of isolates from various habitats classified as common and stressed is reported. IR-resistant isolates exhibited varying degrees of resistance to gamma-radiation and were classified as highly and moderately radiation resistant. Resistance to ultraviolet (UV) radiation correlated well with gamma-radiation resistance, whereas a comparable desiccation resistance for all the highly and moderately radiation-resistant isolates was observed. However, salt tolerance failed to correlate with IR resistance, indicating a divergent evolution of the salt tolerance and radiation resistance. Characterization of isolates by the amplified rDNA restriction analysis profiling attested to the clustering of these isolates with their stress phenotype. 16S rRNA gene-based analysis of the isolates showed that the bacteria with similar-resistance physiologies clustered together and belonged to related genera. Hydrogen peroxide resistance and mitomycin survival patterns of the isolates indicated the roles of oxidative-stress tolerance in desiccation survival and recombination repair in higher radiation resistance, respectively.
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Affiliation(s)
- Manish Shukla
- Department of Microbiology, M.S. University of Baroda, Vadodara, 390 002, India
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93
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Pavlov AK, Kalinin VL, Konstantinov AN, Shelegedin VN, Pavlov AA. Was Earth ever infected by martian biota? Clues from radioresistant bacteria. ASTROBIOLOGY 2006; 6:911-8. [PMID: 17155889 DOI: 10.1089/ast.2006.6.911] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Here we propose that the radioresistance (tolerance to ionizing radiation) observed in several terrestrial bacteria has a martian origin. Multiple inconsistencies with the current view of radioresistance as an accidental side effect of tolerance to desiccation are discussed. Experiments carried out 25 years ago were reproduced to demonstrate that "ordinary" bacteria can develop high radioresistance ability after multiple cycles of exposure to high radiation dosages followed by cycles of recovery of the bacterial population. We argue that "natural" cycles of this kind could have taken place only on the martian surface, and we hypothesize that Mars microorganisms could have developed radioresistance in just several million years' time and, subsequently, have undergone transfer to Earth by way of martian meteorites. Our mechanism implies multiple and frequent exchanges of biota between Mars and Earth.
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Affiliation(s)
- Anatoly K Pavlov
- Laboratory of Nuclear and Space Physics, Ioffe Physico-Technical Institute of Russian Academy of Sciences, St. Petersburg, Russia
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94
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Kuwabara T, Minaba M, Iwayama Y, Inouye I, Nakashima M, Marumo K, Maruyama A, Sugai A, Itoh T, Ishibashi JI, Urabe T, Kamekura M. Thermococcus coalescens sp. nov., a cell-fusing hyperthermophilic archaeon from Suiyo Seamount. Int J Syst Evol Microbiol 2006; 55:2507-2514. [PMID: 16280518 DOI: 10.1099/ijs.0.63432-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A cell-fusing hyperthermophilic archaeon was isolated from hydrothermal fluid obtained from Suiyo Seamount of the Izu-Bonin Arc. The isolate, TS1(T), is an irregular coccus, usually 0.5-2 microm in diameter and motile with a polar tuft of flagella. Cells in the exponential phase of growth fused at room temperature in the presence of DNA-intercalating dye to become as large as 5 microm in diameter. Fused cells showed dark spots that moved along in the cytoplasm. Large cells with a similar appearance were also observed upon culture at 87 degrees C, suggesting the occurrence of similar cell fusions during growth. Transmission electron microscopy revealed that cells in the exponential phase possessed a thin and electron-lucent cell envelope that could be lost subsequently during culture. The fragile cell envelope must be related to cell fusion. The cells grew at 57-90 degrees C, pH 5.2-8.7 and at NaCl concentrations of 1.5-4.5 %, with the optima being 87 degrees C, pH 6.5 and 2.5 % NaCl. The isolate was an anaerobic chemo-organotroph that grew on either yeast extract or tryptone as the sole growth substrate. The genomic DNA G+C content was 53.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the isolate was closely related to Thermococcus species. However, no significant DNA-DNA hybridization was observed between genomic DNA of strain TS1(T) and phylogenetically related Thermococcus species. We propose that isolate TS1(T) represents a novel species, Thermococcus coalescens sp. nov., with the name reflecting the cell fusion activity observed in the strain. The type strain is TS1(T) (=JCM 12540T=DSM 16538T).
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Affiliation(s)
- Tomohiko Kuwabara
- Master's Program in Biosystem Studies, University of Tsukuba, Tsukuba 305-8572, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Masaomi Minaba
- Master's Program in Biosystem Studies, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Yukihiro Iwayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Isao Inouye
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Miwako Nakashima
- Institute for Marine Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan
| | - Katsumi Marumo
- Institute for Marine Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan
| | - Akihiko Maruyama
- Research Institute of Biological Resources, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
| | - Akihiko Sugai
- Division of Chemistry, Center for Natural Science, Kitasato University, Sagamihara 228-8555, Japan
| | - Toshihiro Itoh
- Division of Chemistry, Center for Natural Science, Kitasato University, Sagamihara 228-8555, Japan
| | - Jun-Ichiro Ishibashi
- Department of Earth and Planetary Science, Faculty of Science, Kyushu University, Fukuoka 812-8581, Japan
| | - Tetsuro Urabe
- Department of Earth & Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
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95
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Abstract
The domain Archaea represents a third line of evolutionary descent, separate from Bacteria and Eucarya. Initial studies seemed to limit archaea to various extreme environments. These included habitats at the extreme limits that allow life on earth, in terms of temperature, pH, salinity, and anaerobiosis, which were the homes to hyper thermo philes, extreme (thermo)acidophiles, extreme halophiles, and methanogens. Typical environments from which pure cultures of archaeal species have been isolated include hot springs, hydrothermal vents, solfataras, salt lakes, soda lakes, sewage digesters, and the rumen. Within the past two decades, the use of molecular techniques, including PCR-based amplification of 16S rRNA genes, has allowed a culture-independent assessment of microbial diversity. Remarkably, such techniques have indicated a wide distribution of mostly uncultured archaea in normal habitats, such as ocean waters, lake waters, and soil. This review discusses organisms from the domain Archaea in the context of the environments where they have been isolated or detected. For organizational purposes, the domain has been separated into the traditional groups of methanogens, extreme halophiles, thermoacidophiles, and hyperthermophiles, as well as the uncultured archaea detected by molecular means. Where possible, we have correlated known energy-yielding reactions and carbon sources of the archaeal types with available data on potential carbon sources and electron donors and acceptors present in the environments. From the broad distribution, metabolic diversity, and sheer numbers of archaea in environments from the extreme to the ordinary, the roles that the Archaea play in the ecosystems have been grossly underestimated and are worthy of much greater scrutiny.Key words: Archaea, methanogen, extreme halophile, hyperthermophile, thermoacidophile, uncultured archaea, habitats.
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Affiliation(s)
- Bonnie Chaban
- Department of Microbiology and Immunology, Queen's University, Kingston, ON, Canada
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96
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Slobodkin AI, Tourova TP, Kostrikina NA, Lysenko AM, German KE, Bonch-Osmolovskaya EA, Birkeland NK. Tepidimicrobium ferriphilum gen. nov., sp. nov., a novel moderately thermophilic, Fe(III)-reducing bacterium of the order Clostridiales. Int J Syst Evol Microbiol 2006; 56:369-372. [PMID: 16449442 DOI: 10.1099/ijs.0.63694-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A moderately thermophilic, anaerobic bacterium (strain SB91T) was isolated from a freshwater hot spring at Barguzin Valley, Buryatiya, Russia. Cells of strain SB91T were straight to slightly curved rods, 0·5–0·6 μm in diameter and 3·0–7·0 μm in length. Formation of endospores was not observed. The temperature range for growth was 26–62 °C, with an optimum at 50 °C. The pH range for growth was 5·5–9·5, with an optimum at pH 7·5–8·0. The substrates utilized by strain SB91T in the presence of 9,10-anthraquinone 2,6-disulfonate included peptone, tryptone, Casamino acids, yeast extract, beef extract, casein hydrolysate, alanine plus glycine, alanine plus proline, l-valine and n-propanol. Carbohydrates were not utilized. Strain SB91T reduced amorphous Fe(III) oxide, Fe(III) citrate, Fe(III) EDTA or Fe(III) nitrilotriacetate with peptone, l-valine or n-propanol as an electron donor. Strain SB91T reduced 9,10-anthraquinone 2,6-disulfonate, thiosulfate, elemental sulfur, fumarate and selenite. Strain SB91T survived after exposure to gamma-radiation at a dose of 5·4 kGy. The G+C content of the DNA of strain SB91T was 33 mol%. Analysis of the 16S rRNA gene sequence revealed that the isolated organism belonged to cluster XII of the clostridia. On the basis of its physiological properties and the results of phylogenetic analyses, it is proposed that strain SB91T represents the sole species of a novel genus, Tepidimicrobium; the name Tepidimicrobium ferriphilum gen. nov., sp. nov. is proposed, with strain SB91T (=DSM 16624T=VKM B-2348T) as the type strain.
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MESH Headings
- Bacteria, Anaerobic/classification
- Bacteria, Anaerobic/genetics
- Bacteria, Anaerobic/isolation & purification
- Bacteria, Anaerobic/physiology
- Bacterial Typing Techniques
- DNA, Bacterial/analysis
- DNA, Ribosomal/analysis
- Ferric Compounds/metabolism
- Genes, rRNA
- Gram-Positive Asporogenous Rods, Irregular/classification
- Gram-Positive Asporogenous Rods, Irregular/genetics
- Gram-Positive Asporogenous Rods, Irregular/isolation & purification
- Gram-Positive Asporogenous Rods, Irregular/physiology
- Hot Springs/microbiology
- Hot Temperature
- Iron/metabolism
- Molecular Sequence Data
- Oxidation-Reduction
- Phenotype
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Russia
- Sequence Analysis, DNA
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Affiliation(s)
- A I Slobodkin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117 312 Moscow, Russia
| | - T P Tourova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117 312 Moscow, Russia
| | - N A Kostrikina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117 312 Moscow, Russia
| | - A M Lysenko
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117 312 Moscow, Russia
| | - K E German
- Institute of Physical Chemistry, Russian Academy of Sciences, Leninskiy prospect 31, 119 991 Moscow, Russia
| | - E A Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117 312 Moscow, Russia
| | - N-K Birkeland
- Department of Biology, University of Bergen, PO Box 7800, N-5020 Bergen, Norway
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97
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Miroshnichenko ML, Bonch-Osmolovskaya EA. Recent developments in the thermophilic microbiology of deep-sea hydrothermal vents. Extremophiles 2006; 10:85-96. [PMID: 16418793 DOI: 10.1007/s00792-005-0489-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2005] [Accepted: 11/02/2005] [Indexed: 10/25/2022]
Abstract
The diversity of thermophilic prokaryotes inhabiting deep-sea hot vents was actively studied over the last two decades. The ever growing interest is reflected in the exponentially increasing number of novel thermophilic genera described. The goal of this paper is to survey the progress in this field made in the years 2000-2005. In this period, representatives of several new taxa of hyperthermophilic archaea were obtained from deep-sea environments. Two of these isolates had phenotypic features new for this group of organisms: the presence of an outer cell membrane (the genus Ignicoccus) and the ability to grow anaerobically with acetate and ferric iron (the genus Geoglobus). Also, our knowledge on the diversity of thermophilic bacteria from deep-sea thermal environments extended significantly. The new bacterial isolates represented diverse bacterial divisions: the phylum Aquificae, the subclass Epsilonproteobacteria, the order Thermotogales, the families Thermodesulfobacteriaceae, Deferribacteraceae, and Thermaceae, and a novel bacterial phylum represented by the genus Caldithrix. Most of these isolates are obligate or facultative lithotrophs, oxidizing molecular hydrogen in the course of different types of anaerobic respiration or microaerobic growth. The existence and significant ecological role of some of new bacterial thermophilic isolates was initially established by molecular methods.
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98
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99
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1 Extremophile Microorganisms and the Methods to Handle Them. METHODS IN MICROBIOLOGY 2006. [DOI: 10.1016/s0580-9517(08)70004-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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100
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Abstract
Relatively little is known about the biochemical basis of the capacity of Deinococcus radiodurans to endure the genetic insult that results from exposure to ionizing radiation and can include hundreds of DNA double-strand breaks. However, recent reports indicate that this species compensates for extensive DNA damage through adaptations that allow cells to avoid the potentially detrimental effects of DNA strand breaks. It seems that D. radiodurans uses mechanisms that limit DNA degradation and that restrict the diffusion of DNA fragments that are produced following irradiation, to preserve genetic integrity. These mechanisms also increase the efficiency of the DNA-repair proteins.
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Affiliation(s)
- Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706-1544, USA
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