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  • 1
    Digitale Medien
    Digitale Medien
    An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi (2003)
    Oxford, UK : Blackwell Science, Ltd
    Molecular microbiology 47 (2003), S. 0 
    Details
    ISSN: 1365-2958
    Quelle: Blackwell Publishing Journal Backfiles 1879-2005
    Thema: Biologie , Medizin
    Notizen: The hyperthermophilic euryarchaeon Pyrococcus abyssi and the related species Pyrococcus furiosus and Pyrococcus horikoshii, whose genomes have been completely sequenced, are presently used as model organisms in different laboratories to study archaeal DNA replication and gene expression and to develop genetic tools for hyperthermophiles. We have performed an extensive re-annotation of the genome of P. abyssi to obtain an integrated view of its phylogeny, molecular biology and physiology. Many new functions are predicted for both informational and operational proteins. Moreover, several candidate genes have been identified that might encode missing links in key metabolic pathways, some of which have unique biochemical features. The great majority of Pyrococcus proteins are typical archaeal proteins and their phylogenetic pattern agrees with its position near the root of the archaeal tree. However, proteins probably from bacterial origin, including some from mesophilic bacteria, are also present in the P. abyssi genome.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1046/j.1365-2958.2003.03381.x
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  • 2
    Digitale Medien
    Digitale Medien
    ?-Proteobacterial diversity from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge (2001)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 205 (2001), S. 0 
    Details
    ISSN: 1574-6968
    Quelle: Blackwell Publishing Journal Backfiles 1879-2005
    Thema: Biologie
    Notizen: The prokaryotic phylogenetic diversity was determined for a sample associated with an in situ growth chamber deployed for 5 days on a Mid-Atlantic Ridge hydrothermal vent (23°22′N, 44°57′W). The DNA was extracted from the sample and the 16S rDNA amplified by PCR. No Archaea were detected in the sample. Eighty-seven clones containing bacterial 16S rDNA inserts were selected. Based on restriction fragment length polymorphism analysis, 47 clones were unique, however, based on comparative sequence analysis some of these were very similar, and thus only 22 clones were selected for full sequence and phylogenetic analysis. The phylotypes were dominated by ?-Proteobacteria (66%). The remainder formed a novel lineage within the Proteobacteria (33%). One clone formed a distinct deeply branching lineage, and was a distant relative of the Aquificales. This report further expands the growing evidence that ?-Proteobacteria are important members in biogeochemical cycling at deep-sea hydrothermal ecosystems, participating as epibionts and free living bacteria.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1111/j.1574-6968.2001.tb10968.x
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  • 3
    Digitale Medien
    Digitale Medien
    General vectors for archaeal hyperthermophiles: Strategies based on a mobile intron and a plasmid (1996)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology reviews 18 (1996), S. 0 
    Details
    ISSN: 1574-6976
    Quelle: Blackwell Publishing Journal Backfiles 1879-2005
    Thema: Biologie
    Notizen: Abstract: Although there are currently no cloning and expression vectors available for archaeal hyperthermophiles, small cryptic plasmids have been characterized for these organisms as well as viruses and introns capable of spreading between cells. Below, we review the recent progress in adapting these genetic elements as vectors for Pyrococcus furiosus and Sulfolobus acidocaldarius. An efficient and reliable transformation procedure is described for both organisms. The potential of the mobile intron from Desulfurococcus mobilis, inserted into the bacterial vector pUC18 to generate a new type of vector, was investigated in S. acidocaldarius. A polylinker was inserted upstream from the open reading frame encoding the homing enzyme I-DmoI. Both the polylinker and a 276 bp fragment of the tetracycline gene from pBR322 could be inserted into the intron-plasmid construct and spreading still occurred in the culture of S. acidocaldarius. Experiments are in progress to test the co-mobility of the alcohol dehydrogenase and β-galactosidase genes from Sulfolobus species with the intron. A shuttle vector pCSV1 was also produced by fusing the pGT5 plasmid from Pyrococcus abyssi and the bacterial vector pUC19 which, on transformation, is stable in both organisms without selection. Growth inhibition studies indicate that both P. furiosus and S. acidocaldarius are sensitive to the antibiotics carbomycin, celesticetin, chloramphenicol and thiostrepton as well as butanol and butylic alcohol. Spontaneous mutants resistant to these drugs have been isolated carrying single site mutations in their 23S rRNA gene; they include mutants of S. acidocaldarius resistant to chloramphenicol, carbomycin and celesticetin with the mutation C2452U and thiostrepton-resistant mutants of P. furiosus carrying the mutation A1067G (both numbers corresponding to Escherichia coli 23S rRNA). These mutated genes are being developed as selective markers. Moreover, two β-galactosidase genes from P. furiosus have been cloned as possible phenotypic markers; one of these exhibits maximum activity at 95°C with O-nitrophenyl β-d-galactopyranoside as substrate.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1111/j.1574-6976.1996.tb00229.x
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  • 4
    Digitale Medien
    Digitale Medien
    Numerical taxonomic study of thermophilic Bacillus isolated from three geographically separated deep-sea hydrothermal vents (1996)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 21 (1996), S. 0 
    Details
    ISSN: 1574-6941
    Quelle: Blackwell Publishing Journal Backfiles 1879-2005
    Thema: Biologie
    Notizen: Abstract: A numerical taxonomic study has been carried out with 80 strains, newly isolated, from three geographically separated deep-sea hydrothermal vents (Mid-Atlantic Ridge, Guaymas Basin and Lau Basin) and eleven thermophilic reference strains representing 11 Bacillus species. The deep-sea isolates were all halotolerant spore-forming rods and grew aerobically above 65°C. Results from unweighted average linkage cluster analysis of a similarity matrix derived from the simple matching coefficient, showed formation of nine major phena, which were defined at the 83% similarity level or above. Seven phena were composed exclusively of strains isolated from the same site (4 from Mid-Atlantic Ridge, 1 from Guaymas Basin and 2 from Lau Basin). The majority of the Lau Basin isolates clustered with 6 of the reference strains in one phenon, while isolates from Mid-Atlantic Ridge and Guaymas Basin were found separated from this phenon at the 69% similarity level. The other reference strains showed less than 69% similarity with the deep-sea isolates.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1111/j.1574-6941.1996.tb00122.x
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  • 5
    Digitale Medien
    Digitale Medien
    First isolation of thermophilic aerobic non-sporulating heterotrophic bacteria from deep-sea hydrothermal vents (1995)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 18 (1995), S. 0 
    Details
    ISSN: 1574-6941
    Quelle: Blackwell Publishing Journal Backfiles 1879-2005
    Thema: Biologie
    Notizen: Abstract: Thermophilic aerobic non-sporulating heterotrophic bacteria were isolated for the first time from deep-sea hydrothermal vents. Samples were taken at Snakepit (Mid-Atlantic Ridge) and Guaymas Basin (Gulf of California). Isolates consisting of pleomorphic rods, single cells or pairs, formed filaments of variable length, and grew at 70°C or some up to 80°C. They were halotolerant and unable to grow anaerobically, except some strains in the presence of nitrate. A numerical classification based on phenotypic features was performed on the isolates, including three reference strains Rhodothermus marinus (R-10), Thermus aquaticus (YT-1) and Thermus scotoductus (X-1) and one yellow pigmented Thermus strain. Results from unweighted average linkage (UPGMA) clustering applied to a similarity matrix derived from the simple matching (SSM) coefficient showed the formation of five main clusters which were defined for at least 80% similarity, whereas only three isolates remained outside of the clusters. One reference strain (X-1) clustered with one isolate at a level of 83% and between 76–78% with other clusters. The other reference strains showed less than 55% similarity with the deep-sea isolates.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1111/j.1574-6941.1995.tb00174.x
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  • 6
    Digitale Medien
    Digitale Medien
    Molecular monitoring of culturable bacteria from deep-sea sediment of the Nankai Trough, Leg 190 Ocean Drilling Program (2004)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 48 (2004), S. 0 
    Details
    ISSN: 1574-6941
    Quelle: Blackwell Publishing Journal Backfiles 1879-2005
    Thema: Biologie
    Notizen: Culturable bacteria were detected in deep-sea sediment samples collected from the Nankai Trough site 1173 (Ocean Drilling Program, ODP, Leg 190) at 4.15 m below the seafloor with 4791 m of overlying water. In this deep ocean near surface sediment, mainly fermentative heterotrophs, autotrophic acetogens and sulfate-reducing bacteria were enriched by using two different non-selective enrichment culture media. Culturable bacterial population shifts within the deep marine sediment enrichments were monitored by using denaturating gradient gel electrophoresis (DGGE). DGGE analysis revealed a decrease in the number of 16S rRNA gene fragments from high to low carbon concentrations, and from low to high dilution of inoculum, suggesting that fast-growing bacteria were numerically dominant in enrichment culture samples. The dominant 16S rRNA fragments observed in DGGE gels were assigned to the Firmicutes, Proteobacteria (γ and δ subgroups) and Spirochaeta phyla. Continual sub-culture and purification resulted in two isolates which were phylogenetically identified as members of the genera Acetobacterium and Marinilactibacillus. Our results, which combine enrichment culturing with DGGE analysis, indicated that enrichment cultures derived from inoculum dilution and media with various concentrations of carbon could facilitate the detection and isolation of a greater number of environmentally relevant bacterial species than when using traditional enrichment techniques alone.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1016/j.femsec.2004.02.009
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  • 7
    Digitale Medien
    Digitale Medien
    Thermotoga subterranea sp. nov., a new thermophilic bacterium isolated from a continental oil reservoir (1995)
    Springer
    Archives of microbiology 164 (1995), S. 91-97 
    Details
    ISSN: 1432-072X
    Schlagwort(e): Key words Thermophile ; Anaerobic bacterium ; Thermotogales ; Thermotoga subterranea
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Biologie
    Notizen: Abstract A thermophilic, strictly anaerobic bacterium, designated strain SL1, was isolated from a deep, continental oil reservoir in the East Paris Basin (France). This organism grew between 50 and 75°C, with an optimum at 70°C. It was inhibited by elemental sulfur and was able to reduce cystine and thiosulfate to hydrogen sulfide. The G+C content (40 mol%), the presence of a lipid structure unique to the genus Thermotoga, and the 16S rRNA sequence of strain SL1 indicated that the isolate belongs to the genus Thermotoga. Based on DNA-DNA hybridization, isolate SL1 does not show species-level similarity with the recognized species T. maritima, T. neapolitana, and T. thermarum. Based on this description of strain SL1, we propose the recognition of a new species: Thermotoga subterranea.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1007/s002030050239
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  • 8
    Digitale Medien
    Digitale Medien
    Pyrococcus abyssi sp. nov., a new hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent (1993)
    Springer
    Archives of microbiology 160 (1993), S. 338-349 
    Details
    ISSN: 1432-072X
    Schlagwort(e): Archaea ; Hyperthermophile ; Hydrostatic pressure ; Pyrococcus ; Deep-sea vent
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Biologie
    Notizen: Abstract A novel, hyperthermophilic, anaerobic, sulfurmetabolizing archaeon was isolated from a fluid sample from recently discovered hydrothermal vents in the North Fiji basin (SW Pacific), at 2000 m depth. The new organism, strain GE5, is a gram-negative, highly motile coccus. It grows between 67° and 102°C under atmospheric pressure, with an optimum at 96°C (doubling time 33 min). The upper growth temperature is extended by at least 3°C when cells are cultivated under in situ hydrostatic pressures (20 MPa). Strain GE5 is an obligate heterotroph, fermenting peptides, or mixtures of amino acids to acetate, isovalerate, isobutyrate, propionate, H2 and CO2. Hydrogen inhibits growth unless sulfur is present. In the presence of sulfur, H2S is then produced. Phylogenetic analyses of the 16 S rRNA sequence of strain GE5 places the new isolate within the Thermococcales. By its high growth temperature and physiological features the new isolate ressembles Pyrococcus sp. However it deffers by a 7% mol upper G+C-content and shows low level of DNA similarity with the two previously described species. Based on these differences the description of strain GE5 as a new species Pyrococcus abyssi (CNCM I-1302) is proposed.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1007/BF00252219
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  • 9
    Digitale Medien
    Digitale Medien
    Isolation and characterization of Thiobacillus hydrothermalis sp. nov., a mesophilic obligately chemolithotrophic bacterium isolated from a deep-sea hydrothermal vent in Fiji Basin (1993)
    Springer
    Archives of microbiology 159 (1993), S. 39-44 
    Details
    ISSN: 1432-072X
    Schlagwort(e): Thiobacillus hydrothermalis ; Obligate chemolithoautotroph ; Hydrothermal vent ; Ubiquinone ; Q-8 ; 16S rRNA
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Biologie
    Notizen: Abstract A novel obligately chemolithotrophic Thiobacillus species isolated from a deep-sea hydrothermal vent is described. This organism grows lithoautotrophically on thiosulphate, tetrathionate, sulphide and sulphur which are oxidized to sulphate. The isolate is slightly halophilic and markedly halotolerant, showing optimum growth at pH 7.5 and at 35°C. The G+C content of the DNA is 67.1 mol%. The 16S rRNA sequence is distinct from any other Thiobacilli sequences. Phylogenetic analysis shows the organism to be a representative of the γ-group of proteobacteria and a specific relative of Thiobacillus neapolitanus. The ubiquinone is ubiquinone-8. These characters distinguish the isolate from any other Thiobacillus or Thiomicrospira species previously reported and is a new species described as Thiobacillus hydrothermalis. The type strain is isolate R3, DSM7121.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1007/BF00244261
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  • 10
    Digitale Medien
    Digitale Medien
    Susceptibility to Heavy Metals and Cadmium Accumulation in Aerobic and Anaerobic Thermophilic Microorganisms Isolated from Deep-Sea Hydrothermal Vents (2000)
    Springer
    Current microbiology 41 (2000), S. 201-205 
    Details
    ISSN: 1432-0991
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Biologie , Medizin
    Notizen: Abstract Thirty thermophilic strains isolated from heavy metal-rich hydrothermal vent sites at Lau Basin were tested for their susceptibility to cadmium, zinc, cobalt, and nickel. The 14 aerobic spore formers belonging to the genus Bacillus, 6 anaerobic fermenters from the order Thermotogales, and 10 anaerobic sulfur reducers from the order Thermococcales could be clearly distinguished according to their metal susceptibilities. The Thermococcales were found to exhibit the highest resistance to cadmium and zinc, whereas Thermotogales were highly sensitive to these metals. In contrast, the Thermotogales displayed the highest resistance to cobalt ions. No clear distinction could be established between the metal susceptibilities of these strains and seven reference organisms used for comparative studies. Cadmium resistance, slightly inducible in some cadmium-resistant bacilli, was not plasmid mediated. The amount of cadmium immobilized by the Thermotogales was related to their level of resistance to this metal.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1007/s00284431056
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