101
|
Kulichevskaya IS, Guzev VS, Gorlenko VM, Liesack W, Dedysh SN. Rhodoblastus sphagnicola sp. nov., a novel acidophilic purple non-sulfur bacterium from Sphagnum peat bog. Int J Syst Evol Microbiol 2006; 56:1397-1402. [PMID: 16738120 DOI: 10.1099/ijs.0.63962-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An isolate of purple non-sulfur bacteria was obtained from an acidicSphagnumpeat bog and designated strain RST. The colour of cell suspensions of this bacterium growing in the light under anaerobic conditions is purplish red. Cells of strain RSTare rod-shaped, 0.8–1.0 μm wide and 2.0–6.0 μm long, motile by means of polar flagella, reproduce by budding and have a tendency to form rosette-like clusters in older cultures. The cells contain lamellar intracytoplasmic membranes underlying, and parallel to, the cytoplasmic membrane. The photosynthetic pigments are bacteriochlorophyllaand carotenoids; the absorption spectrum of living cells shows maxima at 377, 463, 492, 527, 592, 806 and 867 nm. The cells grow photoheterotrophically under anaerobic or microaerobic conditions with various organic carbon sources or grow photolithoautotrophically with H2and CO2. Strain RSTis a moderately acidophilic organism exhibiting growth at pH values between 4.8 and 7.0 (with an optimum at pH 5.2–5.5). The major fatty acids are 16 : 1ω7cand 18 : 1ω7c; the major quinones are Q-10 and Q-9. The DNA G+C content of strain RSTis 62.6 mol%. Analysis of the 16S rRNA gene sequence revealed that the novel isolate is most closely related (97.3 % sequence similarity) to the type strain ATCC 25092Tof the moderately acidophilic purple non-sulfur bacteriumRhodoblastus acidophilus, formerly namedRhodopseudomonas acidophila. However, in contrast toRbl. acidophilus, strain RSTis not capable of aerobic growth in the dark, has no spirilloxanthin among the carotenoids and differs in the pattern of substrate utilization. The value for DNA–DNA hybridization between strain RSTandRbl. acidophilusATCC 25092Tis only 22 %. Thus, strain RSTrepresents a novel species of the genusRhodoblastus, for which the nameRhodoblastus sphagnicolasp. nov. is proposed. Strain RST(=DSM 16996T=VKM B-2361T) is the type strain.
Collapse
Affiliation(s)
- Irina S Kulichevskaya
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | - Vladimir S Guzev
- M. V. Lomonosov Moscow State University, Faculty of Soil Science, GSP-2, Leninskie Gory, Moscow 119992, Russia
| | - Vladimir M Gorlenko
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | - Werner Liesack
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Svetlana N Dedysh
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| |
Collapse
|
102
|
Bogdanova TI, Tsaplina IA, Kondrat'eva TF, Duda VI, Suzina NE, Melamud VS, Tourova TP, Karavaiko GI. Sulfobacillus thermotolerans sp. nov., a thermotolerant, chemolithotrophic bacterium. Int J Syst Evol Microbiol 2006; 56:1039-1042. [PMID: 16627651 DOI: 10.1099/ijs.0.64106-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermotolerant, Gram-positive, aerobic, endospore-forming, acidophilic bacterium (strain Kr1T) was isolated from the pulp of a gold-containing sulfide concentrate processed at 40 °C in a gold-recovery plant (Siberia). Cells of strain Kr1T were straight to slightly curved rods, 0.8–1.2 μm in diameter and 1.5–4.5 μm in length. Strain Kr1T formed spherical and oval, refractile, subterminally located endospores. The temperature range for growth was 20–60 °C, with an optimum at 40 °C. The pH range for growth on medium containing ferrous iron was 1.2–2.4, with an optimum at pH 2.0; the pH range for growth on medium containing S0 was 2.0–5.0, with an optimum at pH 2.5. Strain Kr1T was mixotrophic, oxidizing ferrous iron, S0, tetrathionate or sulfide minerals as energy sources in the presence of 0.02 % yeast extract or other organic substrates. The G+C content of the DNA of strain Kr1T was 48.2±0.5 mol%. Strain Kr1T showed a low level of DNA–DNA reassociation with the known Sulfobacillus species (11–44 %). 16S rRNA gene sequence analysis revealed that Kr1T formed a separate phylogenetic group with a high degree of similarity between the nucleotide sequences (98.3–99.6 %) and 100 % bootstrap support within the phylogenetic Sulfobacillus cluster. On the basis of its physiological properties and the results of phylogenetic analyses, strain Kr1T can be affiliated to a novel species of the genus Sulfobacillus, for which the name Sulfobacillus thermotolerans sp. nov. is proposed. The type strain is Kr1T (=VKM B-2339T=DSM 17362T).
Collapse
Affiliation(s)
- Tat'yana I Bogdanova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow, 117312 Russia
| | - Iraida A Tsaplina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow, 117312 Russia
| | - Tamara F Kondrat'eva
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow, 117312 Russia
| | - Vitalii I Duda
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pr. Nauki 5, Pushchino, Moscow Region, 142290 Russia
| | - Natalya E Suzina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pr. Nauki 5, Pushchino, Moscow Region, 142290 Russia
| | - Vitalii S Melamud
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow, 117312 Russia
| | - Tat'yana P Tourova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow, 117312 Russia
| | - Grigorii I Karavaiko
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow, 117312 Russia
| |
Collapse
|
103
|
Jiang B, Parshina SN, van Doesburg W, Lomans BP, Stams AJM. Methanomethylovorans thermophila sp. nov., a thermophilic, methylotrophic methanogen from an anaerobic reactor fed with methanol. Int J Syst Evol Microbiol 2005; 55:2465-2470. [PMID: 16280511 DOI: 10.1099/ijs.0.63818-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
A novel thermophilic, obligately methylotrophic, methanogenic archaeon, strain L2FAWT, was isolated from a thermophilic laboratory-scale upflow anaerobic sludge blanket reactor fed with methanol as the carbon and energy source. Cells of strain L2FAWT were non-motile, irregular cocci, 0·7–1·5 μm in diameter and usually occurred singly (sometimes forming clusters of two or four cells). The cells stained Gram-negative and lysed immediately in 0·1 % (w/v) SDS. Growth was inhibited by chloramphenicol and tetracycline, but not by penicillin, bacitracin, spectinomycin, vancomycin or kanamycin. Methanol and mono-, di- and trimethylamine were used as substrates, but H2/CO2, formate, acetate, propanol, dimethyl sulfide and methanethiol were not. The temperature range for growth was 42–58 °C, with an optimum at 50 °C. The fastest growth was observed at a salinity below 100 mM NaCl; no growth occurred above 300 mM NaCl. The optimal pH for growth was 6·5; growth was observed from pH 5 to pH 7·5. The G+C content of the genomic DNA was 37·6 mol%. Analysis of the 16S rRNA gene sequence and the partial methyl-CoM reductase gene sequence revealed that the organism was phylogenetically closely related to Methanomethylovorans hollandica DMS1T (98 % similarity for the 16S rRNA gene sequence and 91 % similarity for the methyl-CoM reductase gene sequence). The DNA–DNA relatedness between L2FAWT and Methanomethylovorans hollandica DMS1T was 46 %. On the basis of these results, strain L2FAWT (=DSM 17232T=ATCC BAA-1173T) represents the type strain of a novel species, for which the name Methanomethylovorans thermophila sp. nov. is proposed.
Collapse
Affiliation(s)
- B Jiang
- Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
| | - S N Parshina
- Laboratory of Microbiology of Anthropogenic Environments, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
- Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
| | - W van Doesburg
- Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
| | - B P Lomans
- Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
| | - A J M Stams
- Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
| |
Collapse
|
104
|
Romanenko LA, Uchino M, Falsen E, Frolova GM, Zhukova NV, Mikhailov VV. Pseudomonas pachastrellae sp. nov., isolated from a marine sponge. Int J Syst Evol Microbiol 2005; 55:919-924. [PMID: 15774686 DOI: 10.1099/ijs.0.63176-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-negative, non-fermentative, non-denitrifying, non-pigmented, rod-shaped bacteria that were motile by means of polar flagella, designated strains KMM 330(T) and KMM 331, were isolated from a deep-sea sponge specimen and subjected to a polyphasic taxonomic study. The new isolates exhibited 16S rRNA gene sequence similarity of 99.9 %, and their mean level of DNA-DNA relatedness was 82 %. Phylogenetic analysis based on their 16S rRNA gene sequences placed the strains within the genus Pseudomonas as an independent deep clade. Strain KMM 330(T) shared highest sequence similarity (96.3 %) with each of Pseudomonas fulva NRIC 0180(T), Pseudomonas parafulva AJ 2129(T) and Pseudomonas luteola IAM 13000(T); sequence similarity to other recognized species of the genus Pseudomonas was below 95.7 %. The marine sponge isolates KMM 330(T) and KMM 331 could be distinguished from the other recognized Pseudomonas species based on a unique combination of their phenotypic characteristics, including growth in 8 or 10 % NaCl, the absence of pigments, the inability to denitrify and lack of carbohydrate utilization. On the basis of phylogenetic analysis, physiological and biochemical characterization, strains KMM 330(T) and KMM 331 should be classified as a novel species of the genus Pseudomonas, for which the name Pseudomonas pachastrellae sp. nov. is proposed. The type strain is KMM 330(T) (=JCM 12285(T)=NRIC 0583(T)=CCUG 46540(T)).
Collapse
Affiliation(s)
- Lyudmila A Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
| | - Masataka Uchino
- Laboratory of Food Science and Technology, Department of Applied Biology and Chemistry, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Enevold Falsen
- CCUG Culture Collection, Department of Clinical Bacteriology, University of Göteborg, Guldhedsgatan 10, S-413 46 Göteborg, Sweden
| | - Galina M Frolova
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
| | - Natalia V Zhukova
- Institute of Marine Biology, Far-Eastern Branch, Russian Academy of Sciences, 690041, Vladivostok, Russia
| | - Valery V Mikhailov
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
| |
Collapse
|
105
|
Karavaiko GI, Bogdanova TI, Tourova TP, Kondrat'eva TF, Tsaplina IA, Egorova MA, Krasil'nikova EN, Zakharchuk LM. Reclassification of 'Sulfobacillus thermosulfidooxidans subsp. thermotolerans' strain K1 as Alicyclobacillus tolerans sp. nov. and Sulfobacillus disulfidooxidans Dufresne et al. 1996 as Alicyclobacillus disulfidooxidans comb. nov., and emended description of the genus Alicyclobacillus. Int J Syst Evol Microbiol 2005; 55:941-947. [PMID: 15774689 DOI: 10.1099/ijs.0.63300-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparative analysis of 16S rRNA gene sequences, DNA-DNA hybridization data and phenotypic properties revealed that 'Sulfobacillus thermosulfidooxidans subsp. thermotolerans' strain K1 is not a member of the genus Sulfobacillus. Phylogenetically, strain K1 is closely related to unclassified strains of the genus Alicyclobacillus: the 16S rRNA gene sequence of strain K1 is similar to that of Alicyclobacillus sp. AGC-2 (99.6 %), Alicyclobacillus sp. 5C (98.9 %) and Alicyclobacillus sp. CLG (98.6 %) and bacterium GSM (99.1 %). The 16S rRNA gene sequence similarity values for strain K1 and species of the genus Alicyclobacillus with validly published names were in the range 92.1-94.6 %, and for S. thermosulfidooxidans VKM B-1269(T) the value was 87.7 %. Sulfobacillus disulfidooxidans SD-11(T) was also phylogenetically related to strain K1 (92.6 % sequence similarity) and thus belonged to the genus Alicyclobacillus. Chemotaxonomic data, such as the major cell-membrane lipid components of strains K1 and SD-11(T) (omega-alicyclic fatty acids) and the major isoprenoid quinone (menaquinone MK-7) of strain K1, supported the affiliation of strains K1 and SD-11(T) to the genus Alicyclobacillus. Physiological and molecular biological tests allowed genotypic and phenotypic differentiation of strains K1 and SD-11(T) from the nine Alicyclobacillus species with validly published names. The G+C content of the DNA of strain K1 was 48.7+/-0.6 mol%; that of strain SD-11(T) was 53+/-1 mol%. DNA-DNA reassociation studies showed low relatedness (22 %) between strains K1 and SD-11(T), and even lower relatedness (3-5 %) between these strains and Alicyclobacillus acidocaldarius subsp. acidocaldarius ATCC 27009(T), DSM 446(T). DNA reassociation of strains K1 and SD-11(T) with Alicyclobacillus cycloheptanicus DSM 4006(T) gave values of 15 and 21, respectively. Based on the phenotypic and phylogenetic characteristics of strains K1 and SD-11(T), Alicyclobacillus tolerans sp. nov. (type strain, K1(T)=VKM B-2304(T)=DSM 16297(T)) and Alicyclobacillus disulfidooxidans comb. nov. (type strain, SD-11(T)=ATCC 51911(T)=DSM 12064(T)) are proposed.
Collapse
Affiliation(s)
- Grigorii I Karavaiko
- Winogradsky-Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-letiya Oktyabrya 7/2, Moscow, 117811 Russia
| | - Tat'yana I Bogdanova
- Winogradsky-Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-letiya Oktyabrya 7/2, Moscow, 117811 Russia
| | - Tat'yana P Tourova
- Winogradsky-Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-letiya Oktyabrya 7/2, Moscow, 117811 Russia
| | - Tamara F Kondrat'eva
- Winogradsky-Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-letiya Oktyabrya 7/2, Moscow, 117811 Russia
| | - Iraida A Tsaplina
- Winogradsky-Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-letiya Oktyabrya 7/2, Moscow, 117811 Russia
| | - Marya A Egorova
- Moscow State University, Biological Faculty, Department of Microbiology, Vorob'evy Gory, Moscow, 119992 Russia
| | - Elena N Krasil'nikova
- Moscow State University, Biological Faculty, Department of Microbiology, Vorob'evy Gory, Moscow, 119992 Russia
| | - Leonid M Zakharchuk
- Moscow State University, Biological Faculty, Department of Microbiology, Vorob'evy Gory, Moscow, 119992 Russia
| |
Collapse
|
106
|
The Phylogenetic Diversity of Aerobic Organotrophic Bacteria from the Dagang High-Temperature Oil Field. Microbiology (Reading) 2005. [DOI: 10.1007/s11021-005-0073-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
107
|
Zhilina TN, Zavarzina DG, Kuever J, Lysenko AM, Zavarzin GA. Desulfonatronum cooperativum sp. nov., a novel hydrogenotrophic, alkaliphilic, sulfate-reducing bacterium, from a syntrophic culture growing on acetate. Int J Syst Evol Microbiol 2005; 55:1001-1006. [PMID: 15879225 DOI: 10.1099/ijs.0.63490-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel alkaliphilic, sulfate-reducing bacterium was isolated from a syntrophic acetate-decomposing community enriched from samples of the soda lake Khadin, Tuva, Russia; the isolate was designated strain Z-7999T. Cells of strain Z-7999T were vibrioid, Gram-negative, 0·4–0·5×1·0–2·5 μm and motile by means of a polar flagellum. The temperature range for growth was 15–40 °C, with an optimum of 35–38 °C. The pH range for growth was 6·7–10·3, with an optimum of pH 8·0–9·0. The NaCl concentration range for growth was 1–80 g l−1. The novel isolate was obligately anaerobic, was alkaliphilic with a broad pH range and had an obligate requirement for carbonate ions in the growth medium. In the presence of sulfate as electron acceptor, it grew with hydrogen, formate and lactate. It was not able to ferment sugars, organic acids, amino acids or peptides. During growth on formate, strain Z-7999T reduced sulfite and thiosulfate to sulfide. It was able to grow lithoheterotrophically with sulfate and formate when acetate was added as a carbon source for biosynthesis of biomass. The G+C content of the genomic DNA of strain Z-7999T was 56·5 mol%. Results of comparative 16S rRNA gene sequence analyses revealed that strain Z-7999T was part of the δ-Proteobacteria and clustered with other members of the genus Desulfonatronum (similarity values of 95·2 and 95·3 % to Desulfonatronum lacustre and Desulfonatronum thiodismutans, respectively). DNA–DNA hybridization with D. lacustre was 37 %. On the basis of physiological and phylogenetic data, it is proposed that strain Z-7999T (=DSM 16749T=VKM B-2329T) should be placed in the genus Desulfonatronum as a representative of a novel species, Desulfonatronum cooperativum sp. nov.
Collapse
Affiliation(s)
- Tatjana N Zhilina
- S. N. Winogradsky-Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312, Moscow, Russia
| | - Daria G Zavarzina
- S. N. Winogradsky-Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312, Moscow, Russia
| | - Jan Kuever
- Bremen Institute for Materials Testing, Department of Microbiology, Paul-Feller Str. 1, Bremen, D-28199, Germany
| | - Anatoly M Lysenko
- S. N. Winogradsky-Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312, Moscow, Russia
| | - Georgy A Zavarzin
- S. N. Winogradsky-Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312, Moscow, Russia
| |
Collapse
|
108
|
Romanenko LA, Uchino M, Falsen E, Lysenko AM, Zhukova NV, Mikhailov VV. Pseudomonas xanthomarina sp. nov., a novel bacterium isolated from marine ascidian. J GEN APPL MICROBIOL 2005; 51:65-71. [PMID: 15942867 DOI: 10.2323/jgam.51.65] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Two Pseudomonas-like yellow-orange-pigmented non-fluorescent denitrifying strains KMM 235 and KMM 1447T were isolated from marine ascidian specimens and investigated by a polyphasic approach to clarify their taxonomic status. On the basis of 16S rDNA gene sequence data the new isolates clustered with the Pseudomonas stutzeri species group with sequence similarities of >98%. The results of DNA-DNA hybridization and biochemical characterization showed genetic and phenotypic distinction between strains KMM 235 and KMM 1447T and from the other validly described Pseudomonas species. Strain KMM 235 was found to be closely related to the type strain of Pseudomonas stutzeri in their phenotypic and genetic characteristics and represented, probably, a new P. stutzeri genomovar. It is proposed that strain KMM 1447T be classified as a new species of the genus Pseudomonas, Pseudomonas xanthomarina sp. nov., with the type strain KMM 1447T (=JCM 12468T=NRIC 0617T=CCUG 46543T).
Collapse
Affiliation(s)
- Lyudmila A Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia.
| | | | | | | | | | | |
Collapse
|
109
|
Romanenko LA, Schumann P, Rohde M, Zhukova NV, Mikhailov VV, Stackebrandt E. Marinobacter bryozoorum sp. nov. and Marinobacter sediminum sp. nov., novel bacteria from the marine environment. Int J Syst Evol Microbiol 2005; 55:143-148. [PMID: 15653867 DOI: 10.1099/ijs.0.63258-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two marine, Gram-negative, aerobic, halophilic strains, designated KMM 3657T and KMM 3840T, were isolated and found to be phylogenetically closely related to each other, showing 96·6 % 16S rRNA gene sequence similarity. Both strains are members of the genus Marinobacter in the γ-Proteobacteria (94·7–98·0 % 16S rRNA gene sequence similarity). Strain KMM 3657T and Marinobacter lipolyticus SM19T were closely related, with 98·0 % sequence similarity. The novel strains shared generic physiological and chemotaxonomic properties with Marinobacter species, but differed in their temperature range for growth, inability to grow in 20 % NaCl and at >43 °C, metabolic properties and fatty acid composition. On the basis of phenotypic and phylogenetic analysis data, it is proposed that the strains represent two novel species, Marinobacter bryozoorum sp. nov., with the type strain KMM 3840T (=50-11T=DSM 15401T), and Marinobacter sediminum sp. nov., with the type strain KMM 3657T (=R65T=DSM 15400T).
Collapse
Affiliation(s)
- Lyudmila A Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospekt 100 Let Vladivostoku, 159, Russia
| | - Peter Schumann
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
| | - Manfred Rohde
- GBF - Gesellschaft für Biotechnologische Forschung GmbH, D-38124 Braunschweig, Germany
| | - Natalia V Zhukova
- Institute of Marine Biology, Far-Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Valery V Mikhailov
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospekt 100 Let Vladivostoku, 159, Russia
| | - Erko Stackebrandt
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
| |
Collapse
|
110
|
Romanenko LA, Lysenko AM, Rohde M, Mikhailov VV, Stackebrandt E. Psychrobacter maritimus sp. nov. and Psychrobacter arenosus sp. nov., isolated from coastal sea ice and sediments of the Sea of Japan. Int J Syst Evol Microbiol 2004; 54:1741-1745. [PMID: 15388738 DOI: 10.1099/ijs.0.63096-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four strains of Gram-negative, aerobic, psychrotolerant, non-motile, non-pigmented bacteria were isolated from coastal sea-ice and sediment samples. These strains displayed the general chemotaxonomic and phenotypic features of members of the genus Psychrobacter. 16S rRNA gene sequencing positioned the three isolates KMM 3646T, KMM 3643 and KMM 3645 and isolate KMM 3659T in two distinct lineages within the genus Psychrobacter, displaying less than 98·5 % sequence similarity to the type strains of other Psychrobacter species. Genomic distinctness was supported by phenotypic differences in growth temperatures, salinity range for growth and metabolic properties. Based on a combination of phenotypic and biochemical characteristics and phylogenetic position, it is proposed that the members of these two distinct lineages represent two novel species, for which the names Psychrobacter maritimus sp. nov. (type strain Pi2-20T=KMM 3646T=DSM 15387T) and Psychrobacter arenosus sp. nov. (type strain R7T=KMM 3659T=DSM 15389T) are proposed.
Collapse
MESH Headings
- Anti-Bacterial Agents/pharmacology
- Bacterial Typing Techniques
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Fatty Acids/analysis
- Genes, rRNA
- Geologic Sediments/microbiology
- Ice
- Japan
- Molecular Sequence Data
- Movement
- Phylogeny
- Pigments, Biological/biosynthesis
- Psychrobacter/classification
- Psychrobacter/cytology
- Psychrobacter/isolation & purification
- Psychrobacter/physiology
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Saline Solution, Hypertonic/pharmacology
- Sequence Analysis, DNA
- Temperature
- Water Microbiology
Collapse
Affiliation(s)
- Lyudmila A Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospekt 100 Let Vladivostoku, 159, Russia
| | - Anatoly M Lysenko
- Institute of Microbiology, Russian Academy of Sciences, 117811 Moscow, Russia
| | - Manfred Rohde
- GBF - Gesellschaft für Biotechnologische Forschung GmbH, D-38124 Braunschweig, Germany
| | - Valery V Mikhailov
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospekt 100 Let Vladivostoku, 159, Russia
| | - Erko Stackebrandt
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, D-38124 Braunschweig, Germany
| |
Collapse
|
111
|
Caumette P, Guyoneaud R, Imhoff JF, Süling J, Gorlenko V. Thiocapsa marina sp. nov., a novel, okenone-containing, purple sulfur bacterium isolated from brackish coastal and marine environments. Int J Syst Evol Microbiol 2004; 54:1031-1036. [PMID: 15280266 DOI: 10.1099/ijs.0.02964-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four marine, phototrophic, purple sulfur bacteria (strains 5811T, 5812, BM-3 and BS-1) were isolated in pure culture from different brackish to marine sediments in the Mediterranean Sea, the White Sea and the Black Sea. Single cells of these strains were coccus-shaped, non-motile and did not contain gas vesicles. The colour of cell suspensions that were grown in the light was purple–red. Bacteriochlorophyll a and carotenoids of the okenone series were present as photosynthetic pigments. Photosynthetic membrane systems were of the vesicular type. Hydrogen sulfide, thiosulfate, elemental sulfur and molecular hydrogen were used as electron donors during photolithotrophic growth under anoxic conditions; carbon dioxide was utilized as the carbon source. During growth on sulfide, elemental sulfur globules were stored inside the cells. In the presence of hydrogen sulfide, several organic substances could be photoassimilated. Comparative 16S rDNA sequence analysis revealed an affiliation of these four strains to the genus Thiocapsa. Both phylogenetic analysis and the results of DNA–DNA hybridization studies revealed that these strains formed a separate cluster within the genus Thiocapsa. Thus, according to phenotypic characteristics and mainly the carotenoid composition, 16S rDNA sequence analysis and DNA–DNA hybridization data, it is proposed that these strains should be classified as a novel species, Thiocapsa marina sp. nov., with strain 5811T (=DSM 5653T=ATCC 43172T) as the type strain.
Collapse
Affiliation(s)
- Pierre Caumette
- Laboratoire d'Ecologie Moléculaire, EA 3525, IBEAS, Université de Pau et des Pays de l'Adour, BP1155, F-64013 Pau Cedex, France
| | - Remy Guyoneaud
- Laboratoire d'Ecologie Moléculaire, EA 3525, IBEAS, Université de Pau et des Pays de l'Adour, BP1155, F-64013 Pau Cedex, France
| | - Johannes F Imhoff
- Institut für Meereskunde an der Universität Kiel, Abteilung Marine Mikrobiologie, Düsternbrooker Weg 20, D-24105 Kiel, Germany
| | - Jörg Süling
- Institut für Meereskunde an der Universität Kiel, Abteilung Marine Mikrobiologie, Düsternbrooker Weg 20, D-24105 Kiel, Germany
| | - Vladimir Gorlenko
- Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7 k. 2, 117312 Moscow, Russia
| |
Collapse
|
112
|
Denizci AA, Kazan D, Abeln ECA, Erarslan A. Newly isolated Bacillus clausii GMBAE 42: an alkaline protease producer capable to grow under higly alkaline conditions. J Appl Microbiol 2004; 96:320-7. [PMID: 14723693 DOI: 10.1046/j.1365-2672.2003.02153.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS The isolation and identification of new Bacillus sp. capable of growing under highly alkaline conditions as alkaline protease producers. METHODS AND RESULTS A Bacillus strain capable of growing under highly alkaline conditions was isolated from compost. The strain is a Gram-positive, spore-forming, motile, aerobic, catalase- and oxidase-positive, alkaliphilic bacterium and designated as GMBAE 42. Good growth of the strain was observed at pH 10. The strain was identified as Bacillus clausii according to the physiological properties, cellular fatty acid composition, G + C content of genomic DNA and 16S rRNA gene sequence analyses. The result of 16S rRNA sequence analyses placed this bacterium in a cluster with B. clausii. The G + C content of the genomic DNA of the isolate GMBAE 42 was found to be 49 mol%. The crude extracellular alkaline protease produced by the isolate showed maximal activity at pH 11.0 and 60 degrees C. CONCLUSIONS The results suggest that isolated strain GMBAE 42 is a new type of B. clausii capable of growing at pH 10.0 and produce extracellular alkaline protease very active at pH 11.0. SIGNIFICANCE AND IMPACT OF THE STUDY Isolated strain could be used in commercial alkaline protease production and its enzyme can be considered as a candidate as an additive for commercial detergents.
Collapse
Affiliation(s)
- A A Denizci
- Research Institute for Genetic Engineering and Biotechnology, Marmara Research Center Campus, The Scientific and Technical Research Council of Turkey, Gebze, Kocaeli, Turkey.
| | | | | | | |
Collapse
|
113
|
Dedysh SN, Berestovskaya YY, Vasylieva LV, Belova SE, Khmelenina VN, Suzina NE, Trotsenko YA, Liesack W, Zavarzin GA. Methylocella tundrae sp. nov., a novel methanotrophic bacterium from acidic tundra peatlands. Int J Syst Evol Microbiol 2004; 54:151-156. [PMID: 14742473 DOI: 10.1099/ijs.0.02805-0] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel species, Methylocella tundrae, is proposed for three methanotrophic strains (T4T, TCh1 and TY1) isolated from acidic Sphagnum tundra peatlands. These strains are aerobic, Gram-negative, non-motile, dinitrogen-fixing rods that possess a soluble methane monooxygenase and utilize the serine pathway for carbon assimilation. Strains T4T, TCh1 and TY1 are moderately acidophilic organisms capable of growth between pH 4·2 and 7·5 (optimum 5·5–6·0) and between 5 and 30 °C (optimum 15 °C). The major phospholipid fatty acid is 18 : 1ω7c. The DNA G+C content of strain T4T is 63·3 mol%. The three strains possess almost identical 16S rRNA gene sequences and are most closely related to two previously identified species of Methylocella, Methylocella palustris (97 % similarity) and Methylocella silvestris (97·5 % similarity). DNA–DNA hybridization values of strain T4T with Methylocella palustris KT and Methylocella silvestris BL2T were respectively 27 and 36 %. Thus, the tundra strains represent a novel species, for which the name Methylocella tundrae sp. nov. is proposed. Strain T4T (=DSM 15673T=NCIMB 13949T) is the type strain.
Collapse
Affiliation(s)
- Svetlana N Dedysh
- Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | | | - Lina V Vasylieva
- Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Svetlana E Belova
- Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Valentina N Khmelenina
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region 142292, Russia
| | - Natalia E Suzina
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region 142292, Russia
| | - Yuri A Trotsenko
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region 142292, Russia
| | - Werner Liesack
- Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - George A Zavarzin
- Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| |
Collapse
|
114
|
Goorissen HP, Boschker HTS, Stams AJM, Hansen TA. Isolation of thermophilic Desulfotomaculum strains with methanol and sulfite from solfataric mud pools, and characterization of Desulfotomaculum solfataricum sp. nov. Int J Syst Evol Microbiol 2003; 53:1223-1229. [PMID: 13129999 DOI: 10.1099/ijs.0.02476-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four strains of thermophilic, endospore-forming, sulfate-reducing bacteria were enriched and isolated from hot solfataric fields in the Krafla area of north-east Iceland, using methanol and sulfite as substrates. Morphologically, these strains resembled thermophilic Desulfotomaculum species. The strains grew with alcohols, including methanol, with glucose and fructose as electron donors, and with sulfate, sulfite or thiosulfate as electron acceptors. For all four strains, the optimum temperature and pH for growth were 60 degrees C and pH 7.3, respectively; no added NaCl was required. Phylogenetic analysis based on partial 16S rRNA gene sequence comparisons showed high levels of similarity of the novel strains (>92 %) with Desulfotomaculum kuznetsovii and Desulfotomaculum luciae. However, DNA-DNA hybridization studies with D. kuznetsovii revealed that the four strains belonged to one novel species. A representative of this group of isolates, strain V21(T), is proposed as the type strain of a novel species of the spore-forming, sulfate-reducing genus Desulfotomaculum, namely Desulfotomaculum solfataricum (type strain V21(T)=DSM 14956(T)=CIP 107984(T)).
Collapse
Affiliation(s)
- Heleen P Goorissen
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen (GBB), Kerklaan 30, 9751 NN Haren, The Netherlands
| | - Henricus T S Boschker
- Netherlands Institute of Ecology (NIOO-KNAW), Postbus 140, 4400 AC Yerseke, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
| | - Theo A Hansen
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen (GBB), Kerklaan 30, 9751 NN Haren, The Netherlands
| |
Collapse
|
115
|
Giménez-Jurado G, Kurtzman CP, Starmer WT, Spencer-Martins I. Metschnikowia vanudenii sp. nov. and Metschnikowia lachancei sp. nov., from flowers and associated insects in North America. Int J Syst Evol Microbiol 2003; 53:1665-1670. [PMID: 13130066 DOI: 10.1099/ijs.0.02470-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two new species of the ascosporic yeast genus Metschnikowia were isolated from nectaries and associated muscoid flies of flowers from the common milkweed (Asclepias syriaca) in North America, and are described as Metschnikowia vanudenii [type strain=PYCC 4650(T)=CBS 9134(T)=NRRL Y-27243(T)=UWO(PS) 86A4.1(T)] and Metschnikowia lachancei [type strain=PYCC 4605(T)=CBS 9131(T)=NRRL Y-27242(T)=UWO(PS) 7ASB2.3(T)]. As with the previously described Metschnikowia gruessii, M. vanudenii has vegetative cells with an 'aeroplane' or cross-like configuration, produces ovoid chlamydospores and forms ellipsoidopedunculate asci with two acicular ascospores. Metschnikowia lachancei is distinguished from other Metschnikowia species by formation of club-shaped asci with 1-2 thick clavate ascospores. The phylogenetic positions of the proposed new species within Metschnikowia were determined from sequence analysis of the D1/D2 domain of 26S rDNA. The new species show low nuclear DNA relatedness with neighbouring taxa.
Collapse
Affiliation(s)
- Gabriella Giménez-Jurado
- Centro de Recursos Microbiológicos (CREM), Biotechnology Unit, Faculty of Sciences and Technology, New University of Lisbon, 2829-516 Caparica, Portugal
| | - Cletus P Kurtzman
- National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA
| | | | - Isabel Spencer-Martins
- Centro de Recursos Microbiológicos (CREM), Biotechnology Unit, Faculty of Sciences and Technology, New University of Lisbon, 2829-516 Caparica, Portugal
| |
Collapse
|
116
|
Romanenko LA, Zhukova NV, Lysenko AM, Mikhailov VV, Stackebrandt E. Assignment of 'Alteromonas marinoglutinosa' NCIMB 1770 to Pseudoalteromonas mariniglutinosa sp. nov., nom. rev., comb. nov. Int J Syst Evol Microbiol 2003; 53:1105-1109. [PMID: 12892134 DOI: 10.1099/ijs.0.02564-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of the marine bacterium 'Alteromonas marinoglutinosa' NCIMB 1770 was investigated in a polyphasic study. Analysis of 16S rDNA sequence and DNA-DNA reassociation values confirmed the phylogenetic position of strain NCIMB 1770 within the genus Pseudoalteromonas as a separate species, distinct from all Pseudoalteromonas species with validly described names. On the basis of physiological and molecular properties, it is proposed that strain NCIMB 1770 is classified as Pseudoalteromonas mariniglutinosa sp. nov., nom. rev., comb. nov., with the type strain NCIMB 1770T (=KMM 3635T).
Collapse
Affiliation(s)
- Lyudmila A Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospekt 100 Let Vladivostoku, 159, Russia
| | - Natalia V Zhukova
- Institute of Marine Biology, Far-Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Anatoly M Lysenko
- Institute of Microbiology, Russian Academy of Sciences, 117811 Moscow, Russia
| | - Valery V Mikhailov
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospekt 100 Let Vladivostoku, 159, Russia
| | - Erko Stackebrandt
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
| |
Collapse
|
117
|
Balk M, Weijma J, Friedrich MW, Stams AJM. Methanol utilization by a novel thermophilic homoacetogenic bacterium, Moorella mulderi sp. nov., isolated from a bioreactor. Arch Microbiol 2003; 179:315-20. [PMID: 12637975 DOI: 10.1007/s00203-003-0523-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2002] [Revised: 01/13/2003] [Accepted: 01/22/2003] [Indexed: 11/25/2022]
Abstract
A thermophilic, anaerobic, spore-forming bacterium (strain TMS) was isolated from a thermophilic bioreactor operated at 65 degrees C with methanol as the energy source. Cells were gram-positive straight rods, 0.4-0.6 microm x 2-8 microm, growing as single cells or in pairs. The temperature range for growth was 40-70 degrees C with an optimum at 65 degrees C. Growth was observed from pH 5.5 to 8.5, and the optimum pH was around 7. The salinity range for growth was 0-45 g NaCl l(-1 )with an optimum at 10 g l(-1). The isolate was able to grow on methanol, H(2)-CO(2 )(80/20%, v/v), formate, lactate, pyruvate, glucose, fructose, cellobiose and pectin. The bacterium reduced thiosulfate to sulfide. The G+C content of the DNA was 53 mol%. Comparison of 16S rRNA genes revealed that strain TMS is related to Moorella glycerini (96%, sequence similarity), Moorella thermoacetica (92%) and Moorella thermoautotrophica (92%). On the basis of physiological and phylogenetic differences, strain TMS is proposed as a new species within the genus Moorella, Moorella mulderi sp. nov. (=DSM 14980, =ATCC BAA-608).
Collapse
Affiliation(s)
- Melike Balk
- Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT, Wageningen, The Netherlands.
| | | | | | | |
Collapse
|
118
|
Romanenko LA, Uchino M, Mikhailov VV, Zhukova NV, Uchimura T. Marinomonas primoryensis sp. nov., a novel psychrophile isolated from coastal sea-ice in the Sea of Japan. Int J Syst Evol Microbiol 2003; 53:829-832. [PMID: 12807208 DOI: 10.1099/ijs.0.02280-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains (KMM 3633(T) and KMM 3634) were isolated from marine coastal sea-ice and characterized by using phenotypic and molecular methods. The isolates were aerobic, Gram-negative, psychrophilic, halophilic and motile by means of a single polar flagellum. The DNA G + C content was 45.3-45.6 mol%. The major cellular fatty acids were C(16 :0), C(16 : 1)omega9c and C(18 : 1)omega7c. Comparison of almost-complete 16S rDNA sequences demonstrated that the strains were phylogenetically closely related to each other (99.5% sequence identity), and related to Marinomonas species (94.4-96.4% identity). DNA-DNA reassociation between KMM 3633(T) and KMM 3634 occurred at a level of 92%. Based on phenotypic, chemotaxonomic and phylogenetic properties, the name Marinomonas primoryensis sp. nov. is proposed for strains KMM 3633(T) and KMM 3634; the type strain is KMM 3633(T) (= JCM 11775(T) = NRIC 523(T)).
Collapse
Affiliation(s)
- Lyudmila A Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, Vladivostok 690022, Prospect 100 Let Vladivostoku 159, Russia
| | - Masataka Uchino
- Tokyo University of Agriculture, Department of Applied Biology and Chemistry, Faculty of Applied Bioscience, Laboratory of Food Science and Technology, Sakuragaoka 1-1-1, Setagaya-ku, Tokyo 156-8502, Japan
| | - Valery V Mikhailov
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, Vladivostok 690022, Prospect 100 Let Vladivostoku 159, Russia
| | - Natalia V Zhukova
- Institute of Marine Biology, Far-Eastern Branch, Russian Academy of Sciences, Vladivostok 690041, Russia
| | - Tai Uchimura
- Tokyo University of Agriculture, Department of Applied Biology and Chemistry, Faculty of Applied Bioscience, Laboratory of Food Science and Technology, Sakuragaoka 1-1-1, Setagaya-ku, Tokyo 156-8502, Japan
| |
Collapse
|
119
|
Romanenko LA, Zhukova NV, Rohde M, Lysenko AM, Mikhailov VV, Stackebrandt E. Glaciecola mesophila sp. nov., a novel marine agar-digesting bacterium. Int J Syst Evol Microbiol 2003; 53:647-651. [PMID: 12807181 DOI: 10.1099/ijs.0.02469-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Alteromonas-like strains KMM 241(T) and KMM 642, isolated from marine invertebrate specimens, were investigated to clarify their taxonomic position. The novel isolates were aerobic, Gram-negative, motile, slightly halophilic and heterotrophic and hydrolysed polysaccharides. They did not hydrolyse urea, gelatin or casein and produced acid weakly from carbohydrates. The DNA G + C content ranged between 44.6 and 44.8 mol%. DNA-DNA similarity between the two strains was 71%. Comparison of the 16S rRNA gene sequence of strain KMM 241(T) revealed 94.5-94.8% similarity to Glaciecola species. The novel strains shared several phenotypic and physiological properties with members of Glaciecola, but they differed in their lack of pigment production, their minimal and maximal growth temperatures and their ability to hydrolyse agar and carrageenan and in the utilization of organic compounds. On the basis of phenotypic and physiological characteristics as well as phylogenetic analysis, the isolates should be assigned to a novel species, Glaciecola mesophila sp. nov. The type strain is strain KMM 241(T) (=DSM 15026(T)).
Collapse
Affiliation(s)
- Lyudmila A Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospekt 100 Let Vladivostoku, 159, Russia
| | - Natalia V Zhukova
- Institute of Marine Biology, Far-Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Manfred Rohde
- GBF - Gesellschaft für Biotechnologische Forschung, D-38124 Braunschweig, Germany
| | - Anatoly M Lysenko
- Institute of Microbiology, Russian Academy of Sciences, 117811 Moscow, Russia
| | - Valery V Mikhailov
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospekt 100 Let Vladivostoku, 159, Russia
| | - Erko Stackebrandt
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
| |
Collapse
|
120
|
Romanenko LA, Zhukova NV, Rohde M, Lysenko AM, Mikhailov VV, Stackebrandt E. Pseudoalteromonas agarivorans sp. nov., a novel marine agarolytic bacterium. Int J Syst Evol Microbiol 2003; 53:125-131. [PMID: 12656163 DOI: 10.1099/ijs.0.02234-0] [Citation(s) in RCA: 46] [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
The phenotypic, genomic and phylogenetic characteristics of four aerobic, Gram-negative, non-fermentative, motile, non-pigmented, agarolytic Pseudoalteromonas-like bacteria, isolated from marine environments, have been investigated. These bacteria share DNA-DNA similarities above 86%. Comparative 16S rDNA sequence analysis of strain KMM 255T revealed its membership of the genus Pseudoalteromonas; it shares 99.9% sequence similarity with Pseudoalteromonas distincta, Pseudoalteromonas elyakovii, Pseudoalteromonas atlantica and Pseudoalteromonas espejiana. DNA-DNA reassociation levels obtained for strain KMM 255T and type strains of these four species and other Pseudoalteromonas species were below 45%. The marine isolates differed from known species of the genus by the fact that the cells are motile by means of a single flagellum or two to four polar unsheathed flagella and by an inability to utilize most organic compounds. On the basis of phenotypic, DNA-DNA hybridization and phylogenetic data, it is concluded that the isolates represent a novel species within the genus Pseudoalteromonas, for which the name Pseudoalteromonas agarivorans sp. nov. is proposed. The type strain is strain KMM 255T (= DSM 14585T).
Collapse
Affiliation(s)
- Lyudmila A Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospekt 100 Let Vladivostoku, 159, Russia
| | - Natalia V Zhukova
- Institute of Marine Biology, Far-Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Manfred Rohde
- GBF - Gesellschaft für Biotechnologische Forschung GmbH, D-38124 Braunschweig, Germany
| | - Anatoly M Lysenko
- Institute of Microbiology, Russian Academy of Sciences, 117811 Moscow, Russia
| | - Valery V Mikhailov
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospekt 100 Let Vladivostoku, 159, Russia
| | - Erko Stackebrandt
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
| |
Collapse
|
121
|
von Ahsen N, Wittwer CT, Schütz E. Oligonucleotide Melting Temperatures under PCR Conditions: Nearest-Neighbor Corrections for Mg2+, Deoxynucleotide Triphosphate, and Dimethyl Sulfoxide Concentrations with Comparison to Alternative Empirical Formulas. Clin Chem 2001. [DOI: 10.1093/clinchem/47.11.1956] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Background: Many techniques in molecular biology depend on the oligonucleotide melting temperature (Tm), and several formulas have been developed to estimate Tm. Nearest-neighbor (N-N) models provide the highest accuracy for Tm prediction, but it is not clear how to adjust these models for the effects of reagents commonly used in PCR, such as Mg2+, deoxynucleotide triphosphates (dNTPs), and dimethyl sulfoxide (DMSO).
Methods: The experimental Tms of 475 matched or mismatched target/probe duplexes were obtained in our laboratories or were compiled from the literature based on studies using the same real-time PCR platform. This data set was used to evaluate the contributions of [Mg2+], [dNTPs], and [DMSO] in N-N calculations. In addition, best-fit coefficients for common empirical formulas based on GC content, length, and the equivalent sodium ion concentration of cations [Na+eq] were obtained by multiple regression.
Results: When we used [Na+eq] = [Monovalent cations] + 120($\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\sqrt{{[}Mg^{2{+}}{]}\ {-}\ {[}dNTPs{]}}\) \end{document}$) (the concentrations in this formula are mmol/L) to correct ΔS0 and a DMSO term of 0.75 °C (%DMSO), the SE of the N-N Tm estimate was 1.76 °C for perfectly matched duplexes (n = 217). Alternatively, the empirical formula Tm (°C) = 77.1 °C + 11.7 × log[Na+eq] + 0.41(%GC) − 528/bp − 0.75 °C(%DMSO) gave a slightly higher SE of 1.87 °C. When all duplexes (matched and mismatched; n = 475) were included in N-N calculations, the SE was 2.06 °C.
Conclusions: This robust model, accounting for the effects of Mg2+, DMSO, and dNTPs on oligonucleotide Tm in PCR, gives reliable Tm predictions using thermodynamic N-N calculations or empirical formulas.
Collapse
Affiliation(s)
- Nicolas von Ahsen
- Department of Clinical Chemistry, Georg-August University, Robert Koch Strasse 40, 37075 Goettingen, Germany
| | - Carl T Wittwer
- Department of Pathology, University of Utah Medical School, Salt Lake City, UT 84132
| | - Ekkehard Schütz
- Department of Clinical Chemistry, Georg-August University, Robert Koch Strasse 40, 37075 Goettingen, Germany
- Chronic Illness Research Foundation, San Francisco, CA 94107
| |
Collapse
|
122
|
Affiliation(s)
- K Kuratomi
- Department of Biochemistry, Tokyo Medical College, 1-412, Higashi-okubo, Shinjuku-ku, Tokyo, Japan
| | | |
Collapse
|
123
|
Bryantseva IA, Gorlenko VM, Tourova TP, Kuznetsov BB, Lysenko AM, Bykova SA, Gal’chenko VF, Mityushina LL, Osipov GA. Heliobacterium sulfidophilum sp. nov. andHeliobacterium undosum sp. nov.: Sulfideoxidizing heliobacteria from thermal sulfidic springs. Microbiology (Reading) 2000. [DOI: 10.1007/bf02756742] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
124
|
Nazina TN, Tourova TP, Poltaraus AB, Novikova EV, Ivanova AE, Grigoryan AA, Lysenko AM, Belyaev SS. Physiological and phylogenetic diversity of thermophilic spore-forming hydrocarbon-oxidizing bacteria from oil fields. Microbiology (Reading) 2000. [DOI: 10.1007/bf02757264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
|
125
|
Kosako Y, Tamura K, Sakazaki R, Miki K. Enterobacter kobei sp. nov., a new species of the family Enterobacteriaceae resembling Enterobacter cloacae. Curr Microbiol 1996; 33:261-5. [PMID: 8824173 DOI: 10.1007/s002849900110] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The name Enterobacter kobei sp. nov. is proposed for a group of organisms referred to as NIH Group 21 at the National Institute of Health, Tokyo. The members of this species are Gram-negative, motile rods conforming to the definition of the family Enterobacteriaceae. The DNA relatedness of 23 strains of NIH Group 21 to the representative proposed as the type strain of this species averaged 82% at 70 degrees C, whereas the relatedness to other species within the family Enterobacteriaceae was less than 42%. Because the phenotypic resemblance to Enterobacter cloacae is very close and the DNA relatedness (12-42%) is closer to species of the genus Enterobacter than to other species of the family, the members of NIH Group 21 were placed in the genus Enterobacter. Close phenotypic and genetic relationships were also found between NIH Group 21 and a member of a group of organisms referred to as Enteric Group 69 at the Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA. It is suggested that the latter could be regarded as a subspecific rank of E. kobei, though this is subject to study of further strains. The majority of strains of E. kobei were isolated from clinical specimens. A culture of the type strain (NIH 1485-79) has been deposited in the Japan Collection of Microorganisms as JCM 8580.
Collapse
Affiliation(s)
- Y Kosako
- Japan Collection of Microorganisms, The Institute of Physical and Chemical Research (RIKEN), Wako, Saitama 35101, Japan
| | | | | | | |
Collapse
|
126
|
Separation of Candida fermentati comb. nov. from Candida guilliermondii by DNA base composition and electrophoretic karyotyping. Syst Appl Microbiol 1996. [DOI: 10.1016/s0723-2020(96)80043-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
127
|
Leptographium costaricense sp. nov., a new species from roots of Talauma sambuensis from Costa Rica. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s0953-7562(96)80206-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
128
|
Benight AS, Gallo FJ, Paner TM, Bishop KD, Faldasz BD, Lane MJ. Sequence context and DNA reactivity. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s1057-8943(96)80003-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
|
129
|
Girard PM, Bonnet-Mathonière B, Muriaux D, Paoletti J. A short autocomplementary sequence in the 5' leader region is responsible for dimerization of MoMuLV genomic RNA. Biochemistry 1995; 34:9785-94. [PMID: 7626648 DOI: 10.1021/bi00030a016] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Previous work has shown that a region of Moloney murine leukemia virus (MoMuLV) RNA located between nucleotides 280 and 330 in the PSI region (nt 215-565) is implicated in the dimerization process. We show with a deletion from nucleotides 290-299 in PSI RNA transcripts and through an antisense oligonucleotide complementary to nucleotides 275-291 that the 283-298 region is involved in RNA dimer formation in vitro. In an attempt to further characterize the mechanism of dimer formation, a series of short RNA transcripts was synthesized which overlapps the PSI region of MoMuLV RNA. The dimerization of these RNAs is temperature dependent. The predicted secondary structure of the 278-303 region, as a function of temperature, reveals that this sequence is able to adopt two conformations: (1) the U288 AGCUA293 sequence in a loop; (2) part of the same nucleotides implicated in a stem. These results, together with thermodynamic analysis, strongly suggest that (1) the loop conformation of the UAGCUA sequence modulates the relative amount of RNA dimer and (2) a 16 bp long Watson-Crick base pairing is involved in RNA dimer formation. We propose that loop-loop recognition via the U288 AGCUA293 sequence leads to a stable structure induced by a stem-loop opening. Furthermore, our results do not support purine quartet formation as necessary for the dimerization of the 5' leader MoMuLV RNA.
Collapse
Affiliation(s)
- P M Girard
- Unité de Biochimie, URA 147 CNRS, Institut Gustave Roussy, Villejuif, France
| | | | | | | |
Collapse
|
130
|
Steger G. Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction. Nucleic Acids Res 1994; 22:2760-8. [PMID: 8052531 PMCID: PMC308245 DOI: 10.1093/nar/22.14.2760] [Citation(s) in RCA: 154] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A program is described which calculates the thermal stability and the denaturation behaviour of double-stranded DNAs and RNAs up to a length of 1000 base pairs. The algorithm is based on recursive generation of conditional and a priori probabilities for base stacking. Output of the program may be compared directly to experimental results; thus the program may be used to optimize the nucleic acid fragments, the primers and the experimental conditions prior to experiments like polymerase chain reactions, temperature-gradient gel electrophoresis, denaturing-gradient gel electrophoresis and hybridizations. The program is available in three versions; the first version runs interactively on VAXstations producing graphics output directly, the second is implemented as part of the HUSAR package at GENIUSnet, the third runs on any computer producing text output which serves as input to available graphics programs.
Collapse
Affiliation(s)
- G Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany
| |
Collapse
|
131
|
Ticogloea, a new genus of hyphomycetes from roots of Ticodendron incognitum from Costa Rica. ACTA ACUST UNITED AC 1994. [DOI: 10.1016/s0953-7562(09)80413-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
132
|
|
133
|
Spaaij F, Weber G, Smith MT. Myxozyma vanderwaltii sp. nov. (Candidaceae), a new yeast species isolated from a flower of Protea repens (L.) L. Antonie Van Leeuwenhoek 1993; 63:17-21. [PMID: 8480988 DOI: 10.1007/bf00871726] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Three strains of an undescribed species of the genus Myxozyma were recovered. The new species differs from other accepted species of the genus in its assimilation pattern of carbon sources, mol% G + C and low DNA-DNA homology. A description of the new species, Myxozyma vanderwaltii, and a key to the species accepted in the genus are given.
Collapse
Affiliation(s)
- F Spaaij
- Lehrstuhl für Spezielle Botanik/Mykologie, Universität Tübingen, Germany
| | | | | |
Collapse
|
134
|
Yabuuchi E, Kosako Y, Arakawa M, Hotta H, Yano I. Identification of Oklahoma isolate as a strain of Pseudomonas pseudomallei. Microbiol Immunol 1992; 36:1239-49. [PMID: 1283773 DOI: 10.1111/j.1348-0421.1992.tb02128.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Based on the morphological, physiological, biochemical and nutritional characteristics, cellular fatty acid and lipid composition, ubiquinone-8 as the major respiratory quinone, guanine-plus-cytosine content of DNA, DNA-DNA homology value, and sequence alignment of 16S rRNA nucleotides, Oklahoma isolate was reidentified as a strain of Pseudomonas pseudomallei.
Collapse
Affiliation(s)
- E Yabuuchi
- Department of Bacteriology, Osaka City University Medical School, Japan
| | | | | | | | | |
Collapse
|
135
|
Spaaij F, Weber G, van der Walt JP, Oberwinkler F. Myxozyma neotropica sp. nov. (Candidaceae)--a new yeast species from Costa Rica. Antonie Van Leeuwenhoek 1992; 62:261-5. [PMID: 1285642 DOI: 10.1007/bf00572593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Two strains of an undescribed, soil-borne species of the genus Myxozyma were recovered. They differ from other accepted species of this genus in their carbon assimilation pattern, mol% G+C and low extent of DNA complementary. A description of the new species, Myxozyma neotropica, and a key to the species accepted in the genus are given.
Collapse
Affiliation(s)
- F Spaaij
- Lehrstuhl für Spezielle Botanik/Mykologie, Universität Tübingen, Germany
| | | | | | | |
Collapse
|
136
|
Weber G, Spaaij F, van der Walt JP. Kluyveromyces piceae sp. nov., a new yeast species isolated from the rhizosphere of Picea abies (L.) Karst. Antonie Van Leeuwenhoek 1992; 62:239-44. [PMID: 1416920 DOI: 10.1007/bf00582585] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Two strains of an undescribed species of the genus Kluyveromyces were recovered from the rhizosphere of spruce. A description of the new species, Kluyveromyces piceae, is given and its classification on basis of ascospore shape, substrate utilization, G+C-content, DNA-DNA-reassociation data and habitat specificity is discussed.
Collapse
Affiliation(s)
- G Weber
- Lehrstuhl Spezielle Botanik/Mykologie, Universität Tübingen, Germany
| | | | | |
Collapse
|
137
|
Myxozyma sirexii sp.nov. (Candidaceae), a New Yeast Isolated from Frass of the Woodwasp Sirex juvencus L. Syst Appl Microbiol 1992. [DOI: 10.1016/s0723-2020(11)80217-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
138
|
Spaaij F, Weber G, Roeijmans HJ, van Eijk GW, Oberwinkler F. Fellomyces horovitziae sp. nov., a new basidiomycetous yeast species isolated from a Xenasmatella basidiocarp. Antonie Van Leeuwenhoek 1991; 59:293-8. [PMID: 1883232 DOI: 10.1007/bf00583682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A new species of the genus Fellomyces, F. horovitziae, was isolated from a Xenasmatella basidiocarp. It differs from other accepted species in its carbon assimilation pattern, mol% G + C and low DNA-DNA homology. The delimiting characters are discussed and a key to the genus is provided.
Collapse
Affiliation(s)
- F Spaaij
- Institut f. Biologie l, Lehrstuhl f. Spezielle Botanik/Mykologie, Tübingen, Germany
| | | | | | | | | |
Collapse
|
139
|
Bogdanova E, Mindlin S. Occurrence of two structural types of mercury reductases among Gram-positive bacteria. FEMS Microbiol Lett 1991. [DOI: 10.1111/j.1574-6968.1991.tb04455.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
140
|
Roy C, Tounekti N, Mougel M, Darlix JL, Paoletti C, Ehresmann C, Ehresmann B, Paoletti J. An analytical study of the dimerization of in vitro generated RNA of Moloney murine leukemia virus MoMuLV. Nucleic Acids Res 1990; 18:7287-92. [PMID: 2259624 PMCID: PMC332864 DOI: 10.1093/nar/18.24.7287] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The genome of Moloney murine leukemia virus(MoMuLV) is composed of two identical RNA molecules joined at their 5' ends by the dimer linkage structure (DLS). Recently it was shown that in vitro generated MuLV RNA formed dimeric molecules and that dimerization sequences are located within the Psi encapsidation domain between positions 215 and 420. Conditions for the spontaneous dimerization of a MuLV RNA fragment encompassing the Psi domain have been investigated. The rate of spontaneous MuLV RNA dimer formation is dependent upon RNA, NaCl and MgCl2 concentrations as well as temperature. Thermal denaturation of in vitro generated dimer RNA of 350 nt, from positions 215 to 565, gave a Tm of about 58 degrees C in 100 mM NaCl. This Tm value is very close to that found for RNA corresponding to the 5' 755 nt and to the genomic 70 S RNA isolated from virions. According to thrermodynamic parameters derived from denaturation curves of MuLV dimer RNA generated in vitro, the dimer linkage structure probably involves short sequences.
Collapse
Affiliation(s)
- C Roy
- Unité de Biochimie, URA 158, CNRS and U 140 INSERM, Institut Gustave Roussy, Villejuif, France
| | | | | | | | | | | | | | | |
Collapse
|
141
|
van der Walt JP, Wingfield MJ, Yamada Y. Zygozyma smithiae sp.n. (Lipomycetaceae), a new ambrosia yeast from southern Africa. Antonie Van Leeuwenhoek 1990; 58:95-8. [PMID: 2264728 DOI: 10.1007/bf00422723] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A new species of the genus Zygozyma, Z. smithiae, was recovered from frass of the ambrosia beetle, Crossotarsus externedentatus in Northern Natal. A description of the new species and key to the genus are given.
Collapse
Affiliation(s)
- J P van der Walt
- Department of Microbiology & Biochemistry, University of the Orange Free State, Bloemfontein, South Africa
| | | | | |
Collapse
|
142
|
Spaaij F, Weber G, Van Der Walt J, Oberwinkler F. Myxozyma udenii sp. nov. (Candidaceae), a New Yeast Isolated from the Rhizosphere of Mangifera indica. Syst Appl Microbiol 1990. [DOI: 10.1016/s0723-2020(11)80166-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
143
|
Van Der Walt J, Smith M, Yamada Y, Richards P. Zygozyma arxii sp.n. (Lipomycetaceae), a New Species from Southern Africa. Syst Appl Microbiol 1989. [DOI: 10.1016/s0723-2020(89)80076-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
144
|
Khammas KM, Ageron E, Grimont PA, Kaiser P. Azospirillum irakense sp. nov., a nitrogen-fixing bacterium associated with rice roots and rhizosphere soil. Res Microbiol 1989; 140:679-93. [PMID: 2626596 DOI: 10.1016/0923-2508(89)90199-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A new species of nitrogen-fixing bacteria, Azospirillum irakense, was found associated with roots and the rhizosphere of rice in the region of Diwaniyah (Qadisya), Iraq. The seven isolates, on which the species description is based, have vibrioid to S-shaped cells with one polar flagellum in liquid medium. Additional lateral flagella are seen on cells grown on nutrient agar. Poly-beta-hydroxybutyrate granules are present in cells. Nitrogen fixation occurs in microaerobic conditions. The phenotypic characters were found to be very close to those of A. amazonense with the following differences: growth occurred in the presence of 3% NaCl, and at pH 5.5 and 8.5, myo-inositol was not utilized as sole source of carbon and energy and pectin was slowly (6 to 9 days) hydrolysed. The seven studied strains formed a DNA-relatedness group distinct from other Azospirillum and Herbaspirillum species. The G + C content of the DNA was 64 to 67 mol %. The type strain is KBC1 (CIP 103311).
Collapse
Affiliation(s)
- K M Khammas
- Laboratoire de Microbiologie, Institut National Agronomique, Paris
| | | | | | | |
Collapse
|
145
|
Van der Walt JP, Smith MT, Yamada Y. Debaryomyces udenii, sp. nov. (Saccharomycetaceae), a new species from soil. Antonie Van Leeuwenhoek 1989; 56:233-9. [PMID: 2589851 DOI: 10.1007/bf00418935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A new, soil-associated species of the genus Debaryomyces, D. udenii, is described. The species is characterized by pusticulate rather than verrucate ascospores, and slowly lytic asci.
Collapse
Affiliation(s)
- J P Van der Walt
- Division of Food Science & Technology, Council for Scientific and Industrial Research, Pretoria, South Africa
| | | | | |
Collapse
|
146
|
Peyret M, Freney J, Meugnier H, Fleurette J. Determination of G + C content of DNA using high-performance liquid chromatography for the identification of staphylococci and micrococci. Res Microbiol 1989; 140:467-75. [PMID: 2623365 DOI: 10.1016/0923-2508(89)90068-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The guanine-plus-cytosine (G + C) content of different species of Staphylococcus and Micrococcus was determined by high-performance liquid chromatography. Purified bacterial DNA was hydrolysed by nuclease P1. The nucleotides were separated by chromatography and quantified by measurement of the optical density at 260 nm. The G + C content of staphylococci ranged from 31.5 to 37.9 moles %, and that of micrococci from 68.7 to 75.2. Most of our results were comparable to those obtained with the thermal method.
Collapse
Affiliation(s)
- M Peyret
- Centre National de Référence des Staphylocoques, Laboratoire de Bactériologie, Faculté de Médecine Alexis Carrel, Lyon, France
| | | | | | | |
Collapse
|
147
|
Bernardet JF, Kerouault B. Phenotypic and genomic studies of "Cytophaga psychrophila" isolated from diseased rainbow trout (Oncorhynchus mykiss) in France. Appl Environ Microbiol 1989; 55:1796-800. [PMID: 2764577 PMCID: PMC202952 DOI: 10.1128/aem.55.7.1796-1800.1989] [Citation(s) in RCA: 101] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Five strains of gliding bacteria were isolated in France from farmed diseased rainbow trouts reared at low water temperature. The resemblance of these bacteria to the known fish pathogen "Cytophaga psychrophila" led to their comparative study with reference strain NCMB 1947 and with an American isolate. Morphological, physiological, and biochemical characteristics of the seven strains proved to be similar. Comparison of their DNA by the S1 nuclease DNA-DNA hybridization method showed that the seven strains formed a tight genomic species with DNA relatedness above 90%. This is the first identification of this fish pathogen in a European country. The main phenotypic characteristics differentiating this bacterium from other nonpathogenic gliding bacteria of fish origin include a poor gliding movement, yellow compact or weakly rhizoid colonies on solid media, and the presence of flexirubin-type pigments. The inability to metabolize any carbohydrates, the strong proteolytic activity, the absence of growth in more than 0.5% NaCl, and the tolerance to a maximum temperature of 25 degrees C are also useful characteristics of this group of bacteria.
Collapse
Affiliation(s)
- J F Bernardet
- Institut National de la Recherche Agronomique, Laboratoire dhIchtyopathologie, Jouy-en-Josas, France
| | | |
Collapse
|
148
|
Van der Walt J, Smith M, Yamada Y, Nakase T, Richards P. Lipomyces japonicus sp. nov. from Japanese Soil. Syst Appl Microbiol 1989. [DOI: 10.1016/s0723-2020(89)80028-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
|
149
|
Sakazaki R, Tamura K, Kosako Y, Yoshizaki E. Klebsiella ornithinolytica sp. nov., formerly known as ornithine-positiveKlebsiella oxytoca. Curr Microbiol 1989. [DOI: 10.1007/bf01570291] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
150
|
Golubev WI, Smith MT, Poot GA, Kock JL. Species delineation in the genus Nadsonia Sydow. Antonie Van Leeuwenhoek 1989; 55:369-82. [PMID: 2486058 DOI: 10.1007/bf00398515] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The genus Nadsonia Sydow is revised on the basis of morphology, physiology, amino acid and fatty acid composition, electrophoretic patterns of some enzymes and DNA relatedness. Two species, N. commutata (type CBS 6640) and N. fulvescens, with two varieties, N. fulvescens var. fulvescens (type CBS 2596) and N. fulvescens var. elongata (type CBS 2594) nov. comb. are recognized. A modified diagnosis of the genus and a key are given.
Collapse
Affiliation(s)
- W I Golubev
- All Union Collection of Microorganisms, Institute of Biochemistry and Physiology of Microorganisms, Pushchino, USSR
| | | | | | | |
Collapse
|