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  • 11
    Electronic Resource
    Electronic Resource
    Retrieval of first genome data for rice cluster I methanogens by a combination of cultivation and molecular techniques (2005)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 53 (2005), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: We report first insights into a representative genome of rice cluster I (RC-I), a major group of as-yet uncultured methanogens. The starting point of our study was the methanogenic consortium MRE50 that had been stably maintained for 3 years by consecutive transfers to fresh medium and anaerobic incubation at 50 °C. Process-oriented measurements provided evidence for hydrogenotrophic CO2-reducing methanogenesis. Assessment of the diversity of consortium MRE50 suggested members of the families Thermoanaerobacteriaceae and Clostridiaceae to constitute the major bacterial component, while the archaeal population was represented entirely by RC-I. The RC-I population amounted to more than 50% of total cells, as concluded from fluorescence in situ hybridization using specific probes for either Bacteria or Archaea. The high enrichment status of RC-I prompted construction of a large insert fosmid library from consortium MRE50. Comparative sequence analysis of internal transcribed spacer (ITS) regions revealed that three different RC-I rrn operon variants were present in the fosmid library. Three, approximately 40-kb genomic fragments, each representative for one of the three different rrn operon variants, were recovered and sequenced. Computational analysis of the sequence data resulted in two major findings: (i) consortium MRE50 most likely harbours only a single RC-I genotype, which is characterized by multiple rrn operon copies; (ii) seven genes were identified to possess a strong phylogenetic signal (eIF2a, dnaG, priA, pcrA, gatD, gatE, and a gene encoding a putative RNA-binding protein). Trees exemplarily computed for the deduced amino acid sequences of eIF2a, dnaG, and priA corroborated a specific phylogenetic association of RC-I with the Methanosarcinales.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsec.2004.12.004
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  • 12
    Electronic Resource
    Electronic Resource
    Comparative analysis of gene sequences encoding ammonia monooxygenase of Nitrosospira sp. AHB1 and Nitrosolobus multiformis C-71 (1995)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 133 (1995), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract DNA encoding ammonia monooxygenase from two phylogenetically related autotrophic nitrifying bacteria, Nitrosospira sp. AHB1 and Nitrosolobus multiformis C-71, was amplified by PCR. The resulting products were cloned into the vector pCR-Script. A continuous region of DNA of about 1.5 kb for strain AHB1 and 1.24 kb for N. multiformis C-71 was analysed. These comprised the major part of the gene amoA encoding the active site polypeptide and, directly downstream, the 5′ portion of the amoB gene. The identity values for these sequences at the amino acid level were 93.0% for amoA and 96.1% for amoB. The corresponding values for the nucleic acid sequences were 86.7% and 88.8%, respectively. The identity of the 16S rRNA gene of strain AHB1 to that of N. multiformis C-71 was at least 98.5%. The different degree of sequence conservation between the 16S rDNA and the genes encoding for ammonia monooxygenase facilitates the application of the latter as a molecular tool for a fine-scale differentiation of autotrophic nitrifying bacteria, at the species or strain level, in both environmental and cultivation studies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1995.tb07873.x
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  • 13
    Electronic Resource
    Electronic Resource
    16S ribosomal RNA- and cell wall analysis of Gemmata obscuriglobus, a new member of the order Planctomycetales (1986)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 37 (1986), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract Gemmata obscuriglobus UQM2246 was investigated by the 16S ribosomal RNA cataloguing approach in order to determine its phylogenetic position. This budding organism is a member of the order Planctomycetales, displaying a remote and equidistant relationship to representatives of the genera Planctomyces and Pirella. Like the other members of this order, G. obscuriglobus lacks peptidoglycan, possessing a proteinaceous cell wall instead.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1986.tb01810.x
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  • 14
    Electronic Resource
    Electronic Resource
    Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia (2007)
    [s.l.] : Nature Publishing Group
    Nature 450 (2007), S. 879-882 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Aerobic methanotrophic bacteria consume methane as it diffuses away from methanogenic zones of soil and sediment. They act as a biofilter to reduce methane emissions to the atmosphere, and they are therefore targets in strategies to combat global climate change. No cultured methanotroph grows ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature06411
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  • 15
    Electronic Resource
    Electronic Resource
    Clostridium viride sp. nov., a strictly anaerobic bacterium using 5-aminovalerate as growth substrate, previously assigned to Clostridium aminovalericum (1994)
    Springer
    Archives of microbiology 162 (1994), S. 387-394 
    Details
    ISSN: 1432-072X
    Keywords: Clostridium viride sp. nov. ; Clostridium aminovalericum ; 5-Aminovalerate ; Sulphur reduction ; Anacrobic degradation ; 2,4-Pentadienoyl-CoA reductase ; 5-Hydroxyvaleryl-CoA dehydratase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Strain T2–7, a 5-aminovalerate-fermenting bacterium previously classified as Clostridium aminovalericum, was further characterized, both physiologically and phylogenetically. Comparative sequencing analysis of the almost complete 16S rDNA revealed that strain T2–7 forms a distinct lineage within a phylogenetically coherent cluster of gram-positive bacteria currently assigned to the genus Clostridium. Strain T2–7 grew with 5-aminovalerate, 5-hydroxyvalerate, 4-hydroxybutyrate, vinylacetate, and crotonate, and required yeast extract and l-cysteine for growth. Other substrates were not utilized. The fermentation products, depending on the growth substrate, were ammonia, acetate, propionate, butyrate, and valerate. Sulphur was reduced by a mechanism not linked to energy conservation. Other acceptors were not utilized. Cells were gram-positive pointed-ended ovals, motile by means of two subpolar flagella, and possessed a gram-positive cell wall structure with an S-layer of hexagonally arranged subunits of 18.5 nm diameter. The DNA mol% G+C was 41.5. Strain T2–7 (DSM 6836) is proposed as the type strain of a new species, Clostridium viride sp. nov.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00282102
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  • 16
    Electronic Resource
    Electronic Resource
    Succinate decarboxylation by Propionigenium maris sp. nov., a new anaerobic bacterium from an estuarine sediment (1995)
    Springer
    Archives of microbiology 164 (1995), S. 29-35 
    Details
    ISSN: 1432-072X
    Keywords: Key wordsPropionigenium maris sp. nov. ; Anaerobic degradation ; Succinate ; Propionate ; Decarboxylation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Enrichments on succinate plus yeast extract under anoxic conditions from intertidal mud-flat sediments yielded cultures dominated by oval to round-ended rod-shaped cells. Strain 10succ1, obtained in pure culture, was characterized in detail. The non-motile cells possessed a gram-negative cell wall and did not form spores. Carbohydrates were fermented to formate, acetate, ethanol, and lactate. Succinate was decarboxylated to propionate. Other organic and amino acids were variously fermented to formate, acetate, propionate, and butyrate. Sulfur, sulfate, thiosulfate, and nitrate were not used as electron acceptors. Growth required the presence of yeast extract and at least 5 g/l NaCl, and was possible only in the absence of oxygen. No cytochromes were detected. The DNA base ratio was 40 mol% G+C. Phylogenetically, strain 10succ1 is closely related to Propionigenium modestum, as revealed by 16S rDNA analysis, but is physiologically distinct. Accordingly, strain 10succ1 (DSM 9537) is described as the type strain of a new species of the genus Propionigenium, P. maris sp. nov.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002030050232
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  • 17
    Electronic Resource
    Electronic Resource
    Tetramethylammonium:coenzyme M methyltransferase system from Methanococcoides sp. (1998)
    Springer
    Archives of microbiology 170 (1998), S. 220-226 
    Details
    ISSN: 1432-072X
    Keywords: Key words Methylamine metabolism ; Methyltransferases ; Corrinoid proteins ; Methanogenic ; archaea ; Methanosarcina ; Methanococcoides
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A methanogen (strain NaT1) that belongs to the family of Methanosarcinaceae and that can grow on tetramethylammonium as the sole energy source has recently been isolated. We report here that cell extracts of the archaeon catalyze the formation of methyl-coenzyme M from coenzyme M and tetramethylammonium. The activity was dependent on the presence of Ti(III) citrate and ATP, and was rapidly lost under oxic conditions. Anoxic chromatography on DEAE-Sepharose revealed that two fractions, fractions 3 and 4, were required for activity. A 50-kDa protein that together with fraction 3 catalyzed methyl-coenzyme M formation from tetramethylammonium and coenzyme M was purified from fraction 4. From fraction 3, a 22-kDa corrinoid protein and a 40-kDa protein exhibiting methylcobalamin:coenzyme M methyltransferase (MT2) activity were purified. The N-terminal amino acid sequences of these purified proteins were determined. The 40-kDa protein showed sequence similarity to MT2 isoenzymes from Methanosarcina barkeri. Cell extract of strain NaT1 grown on trimethylamine rather than on tetramethylammonium did not exhibit tetramethylammonium:coenzyme M methyltransferase activity. The strain was identified as belonging to the genus of Methanococcoides, its closest relative being Methanococcoides methylutens.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002030050636
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  • 18
    Electronic Resource
    Electronic Resource
    Phenotype variability of identical genotypes: the need for a combined approach in cyanobacterial taxonomy demonstrated on Merismopedia-like isolates (1996)
    Springer
    Archives of microbiology 166 (1996), S. 224-233 
    Details
    ISSN: 1432-072X
    Keywords: Key words Cyanobacteria ; Merismopedia ; Synechococcus ; Synechocystis ; Eucapsis ; 16S rDNA ; sequencing ; SDS-PAGE ; Taxonomy ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Five Merismopedia-like cyanobacterial strains were collected from microbial mats at Norderney Island, subcultured in the laboratory, and finally grown as unicyanobacterial cultures. As a sixth strain, Merismopedia glauca from the „Sammlung von Algenkulturen“ at Göttingen (SAG) was used for comparisons. According to morphological and physiological characteristics initially observed in the field and during initial subculturing, the five strains were assigned to the species Merismopedia glauca, Merismopedia punctata, or Merismopedia elegans. However, after prolonged maintenance under laboratory conditions, the formation of platelet-like colonies stopped, whereas cell sizes, production of extracellular polymeric substances, and division patterns were stably maintained. These physiological and morphological parameters allowed us to divide the six strains into two clusters. This division was further supported by the profiling of total cell protein and phycobilisomes using SDS-PAGE. The nearly complete 16S rDNA sequence of three of the six isolates was determined. The comparative sequencing analysis revealed an almost 100% identity of these three Merismopedia-like strains. The evolutionary distance dendrogram constructed placed this Merismopedia cluster into a common line of descent with Synechocystis sp. strain PCC6906. Based on the analysis of common stretches of 1,050 nucleotides, the overall similarity between the sequence types of „Merismopedia“ and „Synechocystis“ is 96–97%. The values of the different methods for taxonomic classification of unicyanobacterial strains, the relationship of the cyanobacterial genera Merismopedia, Synechococcus, Synechocystis, and Eucapsis sp., and the functional role of different Merismopedia morphologies within microbial mats are discussed. It is suggested that all analyzed Merismopedia strains be combined into one species, namely Merismopedia punctata Meyen (1839).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002030050378
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  • 19
    Electronic Resource
    Electronic Resource
    Thiorhodococcus minus, gen. nov., sp. nov., a new purple sulfur bacterium isolated from coastal lagoon sediments (1997)
    Springer
    Archives of microbiology 168 (1997), S. 16-23 
    Details
    ISSN: 1432-072X
    Keywords: Key words Chromatiaceae ; Thiorhodococcus ; Thiocystis ; Thiocapsa ; Coastal lagoon ; Bacteriochlorophyll a ; Rhodopin ; Phylogenetic ; relationships
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A new marine phototrophic purple sulfur bacterium (strain CE2203) was isolated in pure culture from a man-made coastal lagoon located on the Atlantic coast (Arcachon Bay, France). Single cells were coccus-shaped, did not contain gas vesicles, and were highly motile. Intracellular photosynthetic membranes were of the vesicular type. Bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series were present as photosynthetic pigments. Hydrogen sulfide, thiosulfate, elemental sulfur, and molecular hydrogen were used as electron donors during photolithotrophic growth under anoxic conditions, while carbon dioxide was utilized as carbon source. Acetate, propionate, lactate, glycolate, pyruvate, fumarate, succinate, fructose, sucrose, ethanol, and propanol were photoassimilated in the presence of hydrogen sulfide. During growth on sulfide, elemental sulfur globules were stored inside the cells. Chemotrophic growth under microoxic conditions in the dark was possible. The DNA base composition was 66.9 mol% G+C. Comparative sequence analysis of the 16S rRNA gene confirmed the membership of strain CE2203 in the family Chromatiaceae. Morphological characteristics of strain CE2203 indicated a close affiliation to the genera Thiocystis and Thiocapsa. However, the phylogenetic treeing revealed no closer relationship to Thiocystis spp. than to Thiocapsa roseopersicina or other known members of the Chromatiaceae. Consequently, strain CE2203 is proposed as the type strain of a new genus and species, Thiorhodococcus minus gen. nov., sp. nov.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002030050464
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  • 20
    Electronic Resource
    Electronic Resource
    Ribotyping of 16S and 23S rRNA genes and organization of rrn operons in members of the bacterial genera Gemmata, Planctomyces, Thermotoga, Thermus, and Verrucomicrobium (1991)
    Springer
    Archives of microbiology 155 (1991), S. 263-271 
    Details
    ISSN: 1432-072X
    Keywords: Planctomyces limnophilus ; Gemmata obscuriglobus ; Thermus aquaticus ; Thermotoga maritima ; Verrucomicrobium spinosum ; rRNA gene organization ; Ribotyping
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The number of organization of rrn genes of two members of the order Planctomycetales, Planctomyces limnophilus and Gemmata obscuriglobus, as well as three species from other bacterial phyla, namely Thermotoga maritima, Thermus aquaticus and Verrucomicrobium spinosum were examined by Southern blot hybridization analysis of restricted DNA with labeled 16S- and 23S rRNAs. Ribotyping analysis revealed that two species contain unlinked 16S- and 23S rRNA genes. Planctomyces limnophilus possessed two unlinked rrn genes which were separated from each other by at least 4.3 kb, and Thermus aquaticus had to unlinked 16S and 23S rRNA genes, separated from each other by at least 2.5 kb. Gemmata obscuriglobus exhibited five genes for which the organization could as yet not be determined because of the complex hybridization patterns. In the other two species, rrn genes clustered in operons. Thermotoga maritima had a single gene for each rRNA species which were separated by not more than 1.5 kb, while Verrucomicrobium spinosum had four copies of probably linked 16S and 23S rRNA genes with a maximal distance between 16S and 23S rRNA genes of 1.3 kb.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00252210
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