scholarly journals Polynucleobacter difficilis sp. nov., a planktonic freshwater bacterium affiliated with subcluster B1 of the genus Polynucleobacter

2012 ◽  
Vol 62 (2) ◽  
pp. 376-383 ◽  
Author(s):  
Martin W. Hahn ◽  
Arevik Minasyan ◽  
Elke Lang ◽  
Ulrike Koll ◽  
Catrin Spröer
Keyword(s):  
Fatty Acids ◽  
Dna Hybridization ◽  
Novel Species ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
The Novel ◽  
Free Living ◽  
Phenotypic Differences ◽  
Hydroxylated Fatty Acids ◽  
Gene Similarity

Strain AM-8B5T, isolated from Lake Sevan in Armenia, was characterized phenotypically, chemotaxonomically and phylogenetically. This chemo-organoheterotrophic, aerobic, facultatively anaerobic, catalase- and oxidase-positive, non-motile strain grew on NSY medium at NaCl concentrations of 0.0–0.2 % (w/v) and at 4–30 °C. Whole-cell fatty acids were dominated by summed feature 3 (including C16 : 1ω7c and iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. C12 : 0 2-OH and C16 : 1 2-OH were the only hydroxylated fatty acids detected. Phylogenetic analysis as well as phenotypic and chemotaxonomic similarities indicated that the novel isolate was affiliated with the genus Polynucleobacter. 16S rRNA gene similarity values with the four previously described Polynucleobacter species ranged from 96.2 to 98.7 %. DNA–DNA hybridization experiments showed that the isolate did not belong to any of the previously described Polynucleobacter species. The isolate could be distinguished from all previously established Polynucleobacter species based on chemotaxonomic and phenotypic traits. The bacterium possessed a free-living lifestyle and represents a group of bacteria inhabiting the water column of many freshwater lakes. Based on the revealed phylogeny, and chemotaxonomic and phenotypic differences to previously described Polynucleobacter species, it is proposed that the isolate represents a novel species, Polynucleobacter difficilis sp. nov.; the type strain is AM-8B5T ( = DSM 22349T = CIP 110078T).

scholarly journals Polynucleobacter acidiphobus sp. nov., a representative of an abundant group of planktonic freshwater bacteria

2011 ◽  
Vol 61 (4) ◽  
pp. 788-794 ◽  
Author(s):  
Martin W. Hahn ◽  
Elke Lang ◽  
Ulrike Brandt ◽  
Cathrin Spröer
Keyword(s):  
Dna Hybridization ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
The Novel ◽  
Straight Chain ◽  
Free Living ◽  
Phenotypic Differences ◽  
Freshwater Bacteria ◽  
Gene Similarity ◽  
Established Species

The heterotrophic, aerobic, facultatively anaerobic, catalase- and oxidase-positive, non-motile strain MWH-PoolGreenA3T, isolated from a rock pool filled with freshwater, was characterized. The strain grew on NSY medium over a NaCl range of 0.0–0.3 % (w/v). Whole-cell fatty acids were dominated by C16 : 1ω7c (feature 3), C18 : 1ω7c and straight-chain C16 : 0; furthermore, the components C12 : 0 and C14 : 0 2-OH were present. The DNA G+C content was 48.3 mol%. Phylogenetic analysis as well as strong similarities in phenotypic and chemotaxonomic traits indicated the affiliation with the genus Polynucleobacter. 16S rRNA gene similarity values with the three described species of the genus Polynucleobacter ranged from 96.7 to 97.8 %. DNA–DNA hybridization experiments did not reveal that the strain belongs to a previously described species of the genus Polynucleobacter. The strain can be discriminated from previously established species of the genus Polynucleobacter by chemotaxonomic and phenotypic traits. The bacterium possesses a free-living lifestyle and represents a group of planktonic freshwater bacteria occurring with high cell numbers in many freshwater lakes. Based on the phylogeny revealed and the chemotaxonomic and phenotypic differences from previously described species of the genus Polynucleobacter, we propose to establish the novel species Polynucleobacter acidiphobus sp. nov. with the type strain MWH-PoolGreenA3T ( = DSM 21994T  = CIP 110079T).

scholarly journals Polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lake

2011 ◽  
Vol 61 (4) ◽  
pp. 781-787 ◽  
Author(s):  
Martin W. Hahn ◽  
Elke Lang ◽  
Mitsunori Tarao ◽  
Ulrike Brandt
Keyword(s):  
Fatty Acids ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Free Living ◽  
Acidic Lake ◽  
Phenotypic Differences ◽  
Freshwater Habitats

The heterotrophic, aerobic, facultatively anaerobic under denitrifying conditions, catalase- and oxidase-positive, non-motile strain MT-CBb6A5T, which was isolated from an acidic lake located in Wisconsin (USA), was characterized. The strain grew on NSY medium over a temperature range of 15–30 °C and a NaCl range of 0.0–0.3 % (w/v). The predominant fatty acids were C16 : 0, C18 : 1ω7c, 11-methyl C18 : 1ω7c, feature 3 (including C16 : 1ω7c), and feature 2 (including C14 : 0 3-OH). The DNA G+C content of the strain was 40.3 mol%. Phylogenetic analysis as well as strong similarities in phenotypic and chemotaxonomic traits indicated the affiliation with the genus Polynucleobacter. 16S rRNA gene sequence similarity values with the two described species of the genus Polynucleobacter ranged from 95.6 to 96.0 %. The strain differs from the two described species of the genus Polynucleobacter in the ability to assimilate oxalic and glycolic acids, and in the presence of the fatty acids C15 : 1ω8c and C16 : 0 3-OH as well as in quantitative differences in fatty acid composition. It has to be assumed that the strain shares with other free-living bacteria of the genus Polynucleobacter a planktonic lifestyle in the water column of freshwater habitats. Based on the phylogeny revealed and the chemotaxonomic and phenotypic differences from Polynucleobacter necessarius and Polynucleobacter cosmopolitanus, we propose to establish the novel species Polynucleobacter rarus sp. nov. with the type strain MT-CBb6A5T ( = DSM 21648T  = CIP 109928T).

Bradyrhizobium cytisi sp. nov., isolated from effective nodules of Cytisus villosus

2011 ◽  
Vol 61 (12) ◽  
pp. 2922-2927 ◽  
Author(s):  
Rajaa Chahboune ◽  
Lorena Carro ◽  
Alvaro Peix ◽  
Said Barrijal ◽  
Encarna Velázquez ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Nitrogen Sources ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Phenotypic Differences ◽  
Carbon And Nitrogen ◽  
Gene Sequence Analysis

Several strains isolated from Cytisus villosus nodules have been characterized based on their diverse genetic, phenotypic and symbiotic characteristics. According to 16S rRNA gene sequence analysis, the isolates formed a group that was closely related to Bradyrhizobium canariense BTA-1T with 99.4 % similarity. Analysis of three housekeeping genes, recA, atpD and glnII, suggested that the C. villosus strains represent a novel Bradyrhizobium species most closely related to B. canariense BTA-1T with similarities of 94.2, 96.7 and 94.5 %, respectively. All these differences were congruent with DNA–DNA hybridization analysis, which revealed 31 % relatedness between a representative strain (CTAW11T) isolated from C. villosus nodules and B. canariense BTA-1T. Phenotypic differences among the strains isolated from C. villosus and B. canariense were based on assimilation of carbon and nitrogen sources. The nodC and nifH genes of strain CTAW11T were phylogenetically related to those of strains belonging to bv. genistearum and divergent from those of bv. glycinearum and, accordingly, they do not nodulate soybean. Based on the genotypic and phenotypic data obtained in this study, our strains should be classified as representatives of a novel species for which the name Bradyrhizobium cytisi sp. nov. is proposed; the type strain is CTAW11T ( = LMG 25866T = CECT 7749T).

scholarly journals Flammeovirga kamogawensis sp. nov., isolated from coastal seawater in Japan

2007 ◽  
Vol 57 (6) ◽  
pp. 1327-1330 ◽  
Author(s):  
Shoichi Hosoya ◽  
Akira Yokota
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Threshold Values ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Coastal Seawater ◽  
Definition Of ◽  
Type Strains

Two strains of gliding, agarolytic bacteria, strains YS10T and YML5, were isolated from coastal seawater off Kamogawa, Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel isolates represent a separate lineage within the genus Flammeovirga. DNA–DNA hybridization values between these isolates and the type strains of species of the genus Flammeovirga were significantly lower than those accepted as threshold values for the phylogenetic definition of a species. Furthermore, some of the phenotypic characteristics indicate that the isolates differ from other Flammeovirga species. Based on these differences, it is suggested that the isolates represent a novel species, for which the name Flammeovirga kamogawensis sp. nov. is proposed. The type strain is YS10T (=IAM 15451T=NCIMB 14281T).

scholarly journals Staphylococcus pettenkoferi sp. nov., a novel coagulase-negative staphylococcal species isolated from human clinical specimens

2007 ◽  
Vol 57 (7) ◽  
pp. 1543-1548 ◽  
Author(s):  
Konrad Trülzsch ◽  
Béatrice Grabein ◽  
Peter Schumann ◽  
Alexander Mellmann ◽  
Uladzimir Antonenka ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Cellular Fatty Acids ◽  
Hybridization Data ◽  
Staphylococcus Capitis ◽  
Medical Facilities ◽  
Physiological Tests ◽  
Human Blood Cultures

Five coagulase-negative, novobiocin-susceptible staphylococcal strains were isolated from human blood cultures in different German and Belgian medical facilities. A novel species, ‘Staphylococcus pettenkoferi’ was proposed recently to accommodate two of these strains (B3117T and A6664), although the name was not validly published. All five strains belonged to the genus Staphylococcus because they were non-motile, Gram-positive, catalase-positive cocci with peptidoglycan type (A3α type l-lys–gly2–4–l-Ser–Gly), menaquinone pattern (MK-7, MK-6 and MK-8) and major cellular fatty acids (ai-C15 : 0, ai-C17 : 0 and i-C15 : 0) that corresponded to those of staphylococci. Phenotypically, the isolates most closely resembled Staphylococcus capitis subsp. capitis and Staphylococcus auricularis, but they could be distinguished from these species by physiological tests and chemotaxonomic investigations. The results of DNA–DNA hybridization, chemotaxonomic investigations and 16S rRNA gene and RNA polymerase B gene (rpoB) sequence analysis enabled strains B3117T, K6999, 229 and 230 to be differentiated genotypically and phenotypically from known Staphylococcus species, indicating that these isolates are representatives of a novel species. The name Staphylococcus pettenkoferi sp. nov. is proposed for this novel species, with strain B3117T (=CIP 107711T=CCUG 51270T) as the type strain. Due to differences in the results of physiological and chemotaxonomic investigations and DNA–DNA hybridization data, strain A6664 was not included in the description of the novel species.

scholarly journals Polynucleobacter cosmopolitanus sp. nov., free-living planktonic bacteria inhabiting freshwater lakes and rivers

2010 ◽  
Vol 60 (1) ◽  
pp. 166-173 ◽  
Author(s):  
Martin W. Hahn ◽  
Elke Lang ◽  
Ulrike Brandt ◽  
Heinrich Lünsdorf ◽  
Qinglong L. Wu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Natural Environments ◽  
The Novel ◽  
Free Living ◽  
Monophyletic Cluster ◽  
Freshwater Habitats

Five heterotrophic, aerobic, catalase- and oxidase-positive, non-motile strains were characterized from freshwater habitats located in Austria, France, Uganda, P. R. China and New Zealand. The strains shared 16S rRNA gene similarities of ≥99.3 %. The novel strains grew on NSY medium over a temperature range of 10–35 °C (two strains also grew at 5 °C and one strain grew at 38 °C) and a NaCl tolerance range of 0.0–0.3 % (four strains grew up to 0.5 % NaCl). The predominant fatty acids were C16 : 0, C18 : 1 ω7c, C12 : 0 3-OH, and summed feature 3 (including C16 : 1 ω7c). The DNA G+C content of strain MWH-MoIso2T was 44.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the five new strains formed a monophyletic cluster closely related to Polynucleobacter necessarius (96–97 % sequence similarity). This cluster also harboured other isolates as well as environmental sequences which have been obtained from several habitats. Investigations with taxon-specific FISH probes demonstrated that the novel bacteria dwell as free-living, planktonic cells in freshwater systems. Based on the revealed phylogeny and pronounced chemotaxonomic differences to P. necessarius (presence of >7 % C12 : 0 3-OH and absence of C12 : 0 and C12 : 0 2-OH), the new strains are suggested to represent a novel species, for which the name Polynucleobacter cosmopolitanus sp. nov. is proposed. The type strain is MWH-MoIso2T (=DSM 21490T=CIP 109840T=LMG 25212T). The novel species belongs to the minority of described species of free-living bacteria for which both in situ data from their natural environments and culture-based knowledge are available.

scholarly journals Lewinella xylanilytica sp. nov., a member of the family Saprospiraceae isolated from coastal seawater

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3433-3438 ◽  
Author(s):  
Hye-Ri Sung ◽  
Jin-Man Lee ◽  
Mibang Kim ◽  
Kee-Sun Shin
Keyword(s):  
Fatty Acids ◽  
Phylogenetic Analysis ◽  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Unidentified Phospholipid ◽  
Gram Staining ◽  
The Family

An orange-pigmented bacterium, designated strain 13-9-B8T, was isolated from a seawater sample collected at Marado, Jeju Island, South Korea. The novel strain was Gram-staining-negative, non-motile, non-gliding, rod-shaped and aerobic. A phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain clustered with members of the genus Lewinella of the family Saprospiraceae in the phylum Bacteroidetes and was most closely related to the species Lewinella marina (95.6 % similarity to the type strain). Strain 13-9-B8T grew optimally at 30 °C, pH 7.0 and with 2 % (w/v) NaCl. Strain 13-9-B8T contained MK-7 as the predominant menquinone and summed feature 3, iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The polar lipids detected in strain 13-9-B8T were phosphatidylethanolamine, one unidentified aminolipid, one unidentified phospholipid and eight unidentified lipids. The DNA G+C content of strain 13-9-B8T was 59.1 mol%. Based on phenotypic, chemotaxonomic and phylogenetic data presented, strain 13-9-B8T is considered to represent a novel species of the genus Lewinella, for which the name Lewinella xylanilytica sp. nov. is proposed. The type strain is 13-9-B8T ( = DSM 29526T = KCTC 32663T).

scholarly journals Carnobacterium pleistocenium sp. nov., a novel psychrotolerant, facultative anaerobe isolated from permafrost of the Fox Tunnel in Alaska

2005 ◽  
Vol 55 (1) ◽  
pp. 473-478 ◽  
Author(s):  
Elena V. Pikuta ◽  
Damien Marsic ◽  
Asim Bej ◽  
Jane Tang ◽  
Paul Krader ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Optimum Growth ◽  
Facultative Anaerobe ◽  
Phenotypic Characteristics ◽  
Gene Sequence Analysis ◽  
Ph Range

A novel, psychrotolerant, facultative anaerobe, strain FTR1T, was isolated from Pleistocene ice from the permafrost tunnel in Fox, Alaska. Gram-positive, motile, rod-shaped cells were observed with sizes 0·6–0·7×0·9–1·5 μm. Growth occurred within the pH range 6·5–9·5 with optimum growth at pH 7·3–7·5. The temperature range for growth of the novel isolate was 0–28 °C and optimum growth occurred at 24 °C. The novel isolate does not require NaCl; growth was observed between 0 and 5 % NaCl with optimum growth at 0·5 % (w/v). The novel isolate was a catalase-negative chemoorganoheterotroph that used as substrates sugars and some products of proteolysis. The metabolic end products were acetate, ethanol and CO2. Strain FTR1T was sensitive to ampicillin, tetracycline, chloramphenicol, rifampicin, kanamycin and gentamicin. 16S rRNA gene sequence analysis showed 99·8 % similarity between strain FTR1T and Carnobacterium alterfunditum, but DNA–DNA hybridization between them demonstrated 39±1·5 % relatedness. On the basis of genotypic and phenotypic characteristics, it is proposed that strain FTR1T (=ATCC BAA-754T=JCM 12174T=CIP 108033T) be assigned to the novel species Carnobacterium pleistocenium sp. nov.

scholarly journals Donghicola eburneus gen. nov., sp. nov., isolated from seawater of the East Sea in Korea

2007 ◽  
Vol 57 (1) ◽  
pp. 73-76 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
New Genus ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Differences ◽  
Gene Similarity

A Gram-negative, aerobic, slightly halophilic, non-motile and coccoid- or rod-shaped bacterial strain, SW-277T, was isolated from seawater, Korea, and subjected to a polyphasic taxonomic study. Strain SW-277T was catalase- and oxidase-positive and grew optimally at pH 7.0–8.0 and 37 °C in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SW-277T belongs to the Alphaproteobacteria as part of the clade comprising the genera Roseivivax and Salipiger with a bootstrap resampling value of 72.5 %. 16S rRNA gene sequence similarity values between strain SW-277T and members of the genera Roseivivax and Salipiger were between 93.8 and 94.7 %. Strain SW-277T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and C16 : 0 as the major fatty acids. The DNA G+C content was 59.7 mol%. Strain SW-277T could be distinguished from members of the phylogenetically related genera Salipiger and Roseivivax by phenotypic differences and low 16S rRNA gene similarity values. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, strain SW-277T (=KCTC 12735T=JCM 13604T) should be classified as a representative of a novel species in a new genus, Donghicola eburneus gen. nov., sp. nov.

scholarly journals Variovorax soli sp. nov., isolated from greenhouse soil

2006 ◽  
Vol 56 (12) ◽  
pp. 2899-2901 ◽  
Author(s):  
Byung-Yong Kim ◽  
Hang-Yeon Weon ◽  
Seung-Hee Yoo ◽  
Seon-Young Lee ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Greenhouse Soil ◽  
Variovorax Paradoxus ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Sequence Similarities

A Gram-negative, rod-shaped, non-spore-forming bacterium, strain GH9-3T, isolated from greenhouse soil, was investigated in a polyphasic study. The novel organism grew at 10–35 °C, 0–3 % NaCl and pH 5–9. It had ubiquinone 8 (Q-8) as the predominant isoprenoid quinone and possessed C16 : 0, summed feature 3, C17 : 0 cyclo and C18 : 1 ω7c as the major fatty acids (together representing 87.4 % of the total). The DNA G+C content was 67.1 mol%. 16S rRNA gene sequence analysis of strain GH9-3T showed that it grouped within the Variovorax cluster, with highest sequence similarities to Variovorax paradoxus IAM 12373T (98.3 %) and Variovorax dokdonensis DS-43T (98.0 %). DNA–DNA hybridization values between strain GH9-3T and V. paradoxus DSM 30034T and V. dokdonensis DS-43T were 38 and 29 %, respectively. Based on phenotypic, chemotaxonomic and phylogenetic features, it is proposed that strain GH9-3T represents a novel species of the genus Variovorax with the name Variovorax soli sp. nov. The type strain is GH9-3T (=KACC 11579T=DSM 18216T).

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