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  • 1
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    The phylogeny of prokaryotes (1980)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1980-07-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fox, G E -- Stackebrandt, E -- Hespell, R B -- Gibson, J -- Maniloff, J -- Dyer, T A -- Wolfe, R S -- Balch, W E -- Tanner, R S -- Magrum, L J -- Zablen, L B -- Blakemore, R -- Gupta, R -- Bonen, L -- Lewis, B J -- Stahl, D A -- Luehrsen, K R -- Chen, K N -- Woese, C R -- New York, N.Y. -- Science. 1980 Jul 25;209(4455):457-63.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6771870" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/*classification ; Base Sequence ; Biological Evolution ; Chloroplasts/analysis ; Clostridium/classification ; Cyanobacteria/classification ; DNA/analysis ; *Phylogeny ; RNA, Ribosomal/*analysis ; Species Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Gram-positive bacteria: possible photosynthetic ancestry (1985)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1985-01-01
    Description: A 16S ribosomal RNA gene has been sequenced from Heliobacterium chlorum, the recently discovered photosynthetic bacterium that contains a novel form of chlorophyll. Comparisons with other 16S ribosomal RNA sequences show that the organism belongs to the Gram-positive bacteria (one of ten eubacterial "phyla")--more precisely to the so-called low G + C (G, guanine; C, cytosine) subdivision thereof. This brings to five the number of such phyla that contain photosynthetic species, the other four being the purple bacteria and relatives, the green sulfur bacteria, the green nonsulfur bacteria, and the cyanobacteria. The finding suggests that Gram-positive bacteria may be of photosynthetic ancestry, and it strengthens the case for a common photosynthetic ancestry for all eubacteria.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Woese, C R -- Debrunner-Vossbrinck, B A -- Oyaizu, H -- Stackebrandt, E -- Ludwig, W -- New York, N.Y. -- Science. 1985;229:762-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics and Development, University of Illinois, Urbana 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11539659" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria ; Base Sequence ; *Biological Evolution ; Chlorobi ; Chlorophyll/analysis ; Cyanobacteria ; Cytosine/analysis ; DNA, Bacterial/analysis/chemistry/genetics ; Gram-Positive Bacteria/*classification/genetics/physiology ; Guanine/analysis ; Molecular Sequence Data ; Oligonucleotides/analysis/chemistry/genetics ; Photosynthesis/*genetics/physiology ; RNA, Bacterial/analysis/chemistry/genetics ; RNA, Ribosomal, 16S/analysis/chemistry/*genetics ; *Sequence Homology, Nucleic Acid
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
    Electronic Resource
    Electronic Resource
    Methodological developments in nucleic acid diagnosis (1994)
    Springer
    Cellular and molecular life sciences 50 (1994), S. 789-789 
    Details
    ISSN: 1420-9071
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01956433
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  • 4
    Electronic Resource
    Electronic Resource
    Response to Althoff et al. (Mar Biol 130: 529–536). Deriving taxonomic decisions from 16S rDNA: a case study (1999)
    Springer
    Marine biology 133 (1999), S. 159-161 
    Details
    ISSN: 1432-1793
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002270050454
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  • 5
    Electronic Resource
    Electronic Resource
    Phylogenetic Analysis of Bacterial Communities Associated with Leaves of the Seagrass Halophila stipulacea by a Culture-Independent Small-Subunit rRNA Gene Approach (2000)
    Springer
    Microbial ecology 39 (2000), S. 22-31 
    Details
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The phylogenetic diversity of the bacterial community associated with leaves of the marine plant Halophila stipulacea in the northern Gulf of Elat was examined by 16S rRNA gene (rDNA) sequence analyses of a clone library. For 59 clones corresponding to 51 ARDRA (amplified rDNA restriction analysis) groups, the sequence of ∼1 kb was determined, and the fraction of the corresponding ARDRA groups of the leaf library was calculated. The class Proteobacteria was represented by 62.6% of the clone sequences. Most sequences originated from members of the γ-subclass (27.3%), affiliated with members of the genera Pseudomonas, Vibrio, Marinomonas, Oceanospirillum, and other marine groups. Affiliation to the α-subclass was determined for 24.2% of the sequences. They were related to the genera Hyphomonas, Roseobacter, Ruegeria, and Rhizobiaceae. Several α-proteobacterial sequences were distantly related to known sequences. Only 4% of the clone sequences were related to β-Proteobacteria. Additionally, 7.1% of the sequences possibly belonged to the class Proteobacteria, but branched deeply from known subclasses. Several sequences were affiliated to members of the orders Verrucomicrobiales and Planctomycetales, the Holophaga/Acidobacterium phylum, and chloroplasts of marine diatoms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002489900194
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  • 6
    Electronic Resource
    Electronic Resource
    What are mycoplasmas: The relationship of tempo and mode in bacterial evolution (1985)
    Springer
    Journal of molecular evolution 21 (1985), S. 305-316 
    Details
    ISSN: 1432-1432
    Keywords: Bacterial evolution ; Mycoplasma ; 16S rRNA ; Phylogeny ; Tachytely
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary In phenotype the mycoplasmas are very different from ordinary bacteria. However, genotypically (i.e., phylogenetically) they are not. On the basis of ribosomal RNA homologies the mycoplasmas belong with the clostridia, and indeed havespecific clostridial relatives. Mycoplasmas are, however, unlike almost all other bacteria in the evolutionary characteristics of their ribosomal RNAs. These RNAs contain relatively few of the highly conserved oligonucleotide sequences characteristic of normal eubacterial ribosomal RNAs. This is interpreted to be a reflection of an elevated mutation rate in mycoplasma lines of descent. A general consequence of this would be that the variation associated with a mycoplasma population is augmented both in number and kind, which in turn would lead to an unusual evolutionary course, one unique in all respects. Mycoplasmas, then, are actually tachytelic bacteria. The unusual evolutionary characteristics of their ribosomal RNAs are the imprints of their rapid evolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02115648
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  • 7
    Electronic Resource
    Electronic Resource
    DNA-DNA homology studies among strains of Arthrobacter and Brevibacterium (1979)
    Springer
    Archives of microbiology 120 (1979), S. 289-295 
    Details
    ISSN: 1432-072X
    Keywords: Coryneform bacteria ; Arthrobacter ; Brevibacterium ; Taxonomy ; DNA-DNA homology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Sixteen named strains of Arthrobacter and two strains of Brevibacterium were investigated by nucleic acid hybridisation. The Arthrobacter strains show homology values ranging between 11 and 55% to the type strain A. globiformis DSM 20124 (ATCC 8010), indicating only a low to moderate relationship. Two strains of A. globiformis, DSM 20124 and DSM 20125, exhibit only poor relationship to one another (30%). Among all the Arthrobacter strains the homology data range between 10 to 70% demonstrating separate status of almost all species. Only A. polychromogenes DSM 20136 was found to be a subspecies of A. oxydans DSM 20119. The type strain of A. citreus, DSM 20133 shows a remarkable lack of homology to four other strains of A. citreus, deposited as ATCC 15170, ATCC 17775, ATCC 21040 and ATCC 21348 (11–13%) which themselves can be separated into two groups according to the homology data (24–31%). Each of the two strains of Brevibacterium share high genetic relatedness with one of these A. citreus groups (71 and 73%, respectively). According to the DNA-DNA homology data, most of the species of Arthrobacter can actually be ranged taxonomically as species.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00423078
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  • 8
    Electronic Resource
    Electronic Resource
    Methanocorpusculaceae fam. nov., represented by Methanocorpusculum parvum, Methanocorpusculum sinense spec. nov. and Methanocorpusculum bavaricum spec. nov. (1989)
    Springer
    Archives of microbiology 151 (1989), S. 381-390 
    Details
    ISSN: 1432-072X
    Keywords: Archaebacteria ; Methanocorpusculaceae ; Methanocorpusculum sinense spec. nov., Methanocorpusculum bavaricum spec. nov. ; Methanocorpusculum parvum ; 16 S rRNA ; Secondary alcohols ; Lipids ; Polyamines ; S-layer ; Glycoproteins ; Physiology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Two new methanogenic bacteria, Methanocorpusculum sinense spec. nov. strain DSM 4274 from a pilot plant for treatment of distillery wastewater in Chengdu (Province Sichuan, China), and Methanocorpusculum bavaricum spec. nov. strain DSM 4179, from a wastewater pond of the sugar factory in Regensburg (Bavaria, FRG) are described. Methanocorpusculum strains are weakly motile and form irregularly coccoid cells, about 1 μm in diameter. The cell envelope consists of a cytoplasmic membrane and a S-layer, composed of hexagonally arranged glycoprotein subunits with molecular weights of 90000 (Methanocorpusculum parvum), 92000 (M. sinense), and 94000 (M. bavaricum). The center-to-center spacings are 14.3 nm, 15.8 nm and 16.0 nm, respectively. Optimal growth of strains is obtained in the mesophilic temperature range and at a pH around 7. Methane is produced from H2/CO2, formate, 2-propanol/CO2 and 2-butanol/CO2 by M. parvum and M. bavaricum, whereas M. sinense can only utilize H2/CO2 and formate. Growth of M. sinense and M. bavaricum is dependent on the presence of clarified rumen fluid. The G+C content of the DNA of the three strains is ranging from 47.7–53.6 mol% as determined by different methods. A similar, but distinct polar lipid pattern indicates a close relationship between the three Methanocorpusculum species. The polyamine patterns of M. parvum, M. sinense and M. bavaricum are similar, but distinct from those of other methanogens and are characterized by a high concentration of the otherwise rare 1,3-diaminopropane. Quantitative comparison of the antigenic fingerprint of members of Methanocorpusculum revealed no antigenic relationship with any one of the reference methanogens tested. On the basis of the distant phylogenetic position of M. parvum and the data presented in this paper a new family, the Methanocorpusculaceae fam. nov., is defined.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00416595
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  • 9
    Electronic Resource
    Electronic Resource
    Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds (1994)
    Springer
    Archives of microbiology 162 (1994), S. 85-90 
    Details
    ISSN: 1432-072X
    Keywords: Key words     Holophaga foetida ; Sulfide-methylation ; Homoacetogenic bacterium ; Pelobacter ; Acetobacterium ; 16S rRNA analysis ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract      A polyphasic approach was used in which genotypic and phenotypic properties of a gram-negative, obligately anaerobic, rod-shaped bacterium isolated from a black anoxic freshwater mud sample were determined. Based on these results, the name Holophaga foetida gen. nov., sp. nov. is proposed. This microorganism produced dimethylsulfide and methanethiol during growth on trimethoxybenzoate or syringate. The only oth er compounds utilized were pyruvate and trihydroxybenzenes such as gallate, phloroglucinol, or pyrogallol. The aromatic compounds were degraded to acetate. Although comparison of the signature nucleotide pattern of the five established subclasses of Proteobacteria with the 16S rDNA sequence of Holophaga foetida revealed a relationship to members of the δ-subclass, the phylogenetic position within the radiation of this class is so deep and dependent upon the number and selection of reference seq uences that its affiliation to the Proteobacteria must be considered tentative. The type strain is H. foetida strain TMBS4 (DSM 6591).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00264378
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  • 10
    Electronic Resource
    Electronic Resource
    Concurrent evolution of nitrogenase genes and 16S rRNA in Rhizobium species and other nitrogen fixing bacteria (1985)
    Springer
    Archives of microbiology 142 (1985), S. 342-348 
    Details
    ISSN: 1432-072X
    Keywords: Evolution ; Nif genes ; Nitrogen fixation ; Nitrogenase ; Nucleotide sequence ; Phylogeny ; Rhizobium ; 16S rRNA cataloguing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract It was known that nitrogenase genes and proteins are well conserved even though they are present in a large variety of phylogenetically diverse nitrogen fixing bacteria. This has lead to the speculation, among others, that nitrogen fixation (nif) genes were spread by lateral gene transfer relatively late in evolution. Here we report an attempt to test this hypothesis. We had previously established the complete nucleotide sequences of the three nitrogenase genes from Bradyrhizobium japonicum, and have now analyzed their homologies (or the amino acid sequence homologies of their gene products) with corresponding genes (and proteins) from other nitrogen fixing bacteria. There was a considerable sequence conservation which certainly reflects the strict structural requirements of the nitrogenase iron-sulfur proteins for catalytic functioning. Despite this, the sequences were divergent enough to classify them into an evolutionary scheme that was conceptually not different from the phylogenetic positions, based on 16S rRNA homology, of the species or genera harboring these genes. Only the relation of nif genes of slow-growing rhizobia (to which B. japonicum belongs) and fast-growing rhizobia was unexpectedly distant. We have, therefore, performed oligonucleotide cataloguing of their 16S rRNA, and found that there was indeed only a similarity of S AB=0.53 between fast- and slowgrowing rhizobia. In conclusion, the results suggest that nif genes may have evolved to a large degree in a similar fashion as the bacteria which carry them. This interpretation would speak against the idea of a recent lateral distribution of nif genes among microorganisms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00491901
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