scholarly journals Dyadobacter crusticola sp. nov., from biological soil crusts in the Colorado Plateau, USA, and an emended description of the genus Dyadobacter Chelius and Triplett 2000

2005 ◽  
Vol 55 (3) ◽  
pp. 1295-1299 ◽  
Author(s):  
Gundlapally S. N. Reddy ◽  
Ferran Garcia-Pichel
Keyword(s):  
Type Strain ◽  
Colorado Plateau ◽  
Sequence Similarity ◽  
Stationary Growth Phase ◽  
Biological Soil Crusts ◽  
Rrna Gene ◽  
Stationary Growth ◽  
Soil Crusts ◽  
Gene Sequence Analysis ◽  
Emended Description

Bacterial strain CP183-8T was isolated from biological soil crusts collected in the Colorado Plateau, USA. Cells of this strain were aerobic, non-motile, Gram-negative, psychrotolerant and formed beaded chains in the stationary growth phase. They contained C16 : 1 ω5c and C16 : 1 ω7c as major fatty acids. 16S rRNA gene sequence analysis assigned the strain to the genus Dyadobacter. However, it shared a sequence similarity of only 95·88 % with the type strain of Dyadobacter fermentans, NS114T. Because it also exhibited a significant number of phenotypic and chemotaxonomic differences from D. fermentans, it is described as a novel second species in the genus Dyadobacter, with the name Dyadobacter crusticola sp. nov. The type strain is CP183-8T (=DSM 16708T=ATCC BAA-1036T).

scholarly journals Sphingomonas mucosissima sp. nov. and Sphingomonas desiccabilis sp. nov., from biological soil crusts in the Colorado Plateau, USA

2007 ◽  
Vol 57 (5) ◽  
pp. 1028-1034 ◽  
Author(s):  
G. S. N. Reddy ◽  
Ferran Garcia-Pichel
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Colorado Plateau ◽  
Sequence Similarity ◽  
Biological Soil Crusts ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Dna Relatedness ◽  
Soil Crusts

Two bacterial strains, CP173-2T and CP1DT, were isolated from biological soil crusts (BSCs) collected in the Colorado Plateau, USA. Both strains were pigmented, Gram-negative, non-motile rods and produced abundant mucus. They contained C16 : 0, C18 : 1 ω7c and C14 : 0 2-OH as the predominant cellular fatty acids, ubiquinone-10 as the isoprenoid quinone and sphingoglycolipid. Based on the above characteristics, the isolates were assigned to the family Sphingomonadaceae; 16 rRNA gene signature nucleotides placed them within the genus Sphingomonas. Strains CP173-2T and CP1DT had a 16S rRNA gene sequence similarity of 96.7 % with each other and 91.6–98.9 % sequence similarity with other species in the genus, indicating that they represent two separate, and possibly novel, species. The closest species to strains CP173-2T and CP1DT were, respectively, Sphingomonas dokdonensis (98.9 % gene sequence similarity) and Sphingomonas panni (97.9 %). However, strain CP173-2T exhibited a DNA–DNA relatedness of only 32.5 % with the type strain of S. dokdonensis. Similarly, the DNA–DNA relatedness between strain CP1DT and the type strain of S. panni was only 18 %. Phenotypic characterization supported this low relatedness. On the basis of this evidence, we propose that the new strains represent two novel species, for which the names Sphingomonas mucosissima sp. nov. (with type strain CP173-2T=ATCC BAA-1239T=DSM 17494T) and Sphingomonas desiccabilis sp. nov. (with type strain CP1DT=ATCC BAA-1041T=DSM 16792T) are proposed.

scholarly journals Pseudomonas moraviensis sp. nov. and Pseudomonas vranovensis sp. nov., soil bacteria isolated on nitroaromatic compounds, and emended description of Pseudomonas asplenii

2006 ◽  
Vol 56 (11) ◽  
pp. 2657-2663 ◽  
Author(s):  
Ludmila Tvrzová ◽  
Peter Schumann ◽  
Cathrin Spröer ◽  
Ivo Sedláček ◽  
Zdena Páčová ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Additional Data ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Negative Bacteria ◽  
Selective Enrichment ◽  
Gene Sequence Analysis ◽  
Emended Description ◽  
Pseudomonas Jessenii

Two strains of Gram-negative bacteria isolated from soil by selective enrichment with nitroaromatics were subjected to a polyphasic taxonomic study. On the basis of 16S rRNA gene sequence analysis, the two strains were found to belong to the genus Pseudomonas, within the Gammaproteobacteria. Strain 1B4T shared the highest sequence similarity with Pseudomonas koreensis DSM 16610T (99.5 %) and Pseudomonas jessenii CCM 4840T (99.3 %), and strain 2B2T with Pseudomonas asplenii DSM 17133T (98.9 %), Pseudomonas fuscovaginae DSM 7231T (98.9 %) and Pseudomonas putida DSM 291T (98.7 %). On the basis of phylogenetic analysis, DNA–DNA hybridization and phenotype, including chemotaxonomic characteristics, two novel species, Pseudomonas moraviensis sp. nov. with the type strain 1B4T (=CCM 7280T=DSM 16007T) and Pseudomonas vranovensis sp. nov. with the type strain 2B2T (=CCM 7279T=DSM 16006T), are proposed. The description of P. asplenii was emended on the basis of additional data obtained in this study.

scholarly journals Vitellibacter aestuarii sp. nov., isolated from tidal-flat sediment, and an emended description of the genus Vitellibacter

2010 ◽  
Vol 60 (9) ◽  
pp. 1989-1992 ◽  
Author(s):  
Bong-Soo Kim ◽  
Ok-Sun Kim ◽  
Eun Young Moon ◽  
Jongsik Chun
Keyword(s):  
Tidal Flat ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Tidal Flat Sediment ◽  
Gene Sequence Analysis ◽  
Emended Description ◽  
Study Support ◽  
Yellowish Orange

A Gram-reaction-negative, aerobic, yellowish-orange-pigmented bacterial strain, designated JC2436T, was isolated from tidal-flat sediment of Oi Island in Korea. Comparative 16S rRNA gene sequence analysis indicated its close affiliation to Vitellibacter vladivostokensis, with 96 % sequence similarity to the type strain. Cells grew with 2–6 % NaCl and at 10–41 °C. Orange flexirubin pigments were present. The major isoprenoid quinone was MK-6, the DNA G+C content was 48.7 mol% and the predominant fatty acids (>10 %) were iso-C15 : 0 and iso-C17 : 0 3-OH. The data obtained from this polyphasic study support the classification of this isolate within a novel species in the genus Vitellibacter, for which the name Vitellibacter aestuarii sp. nov. is proposed. The type strain is JC2436T (=IMSNU 14137T =KACC 13727T =KCTC 22361T =JCM 15496T).

scholarly journals Description of Microvirga aerophila sp. nov. and Microvirga aerilata sp. nov., isolated from air, reclassification of Balneimonas flocculans Takeda et al. 2004 as Microvirga flocculans comb. nov. and emended description of the genus Microvirga

2010 ◽  
Vol 60 (11) ◽  
pp. 2596-2600 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Soon-Wo Kwon ◽  
Jung-A Son ◽  
Eun-Hye Jo ◽  
Soo-Jin Kim ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Phenotypic Data ◽  
Gene Sequence Analysis ◽  
Emended Description

Two bacterial strains, 5420S-12T and 5420S-16T, isolated from air samples, were characterized using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain 5420S-12T was related phylogenetically to Microvirga subterranea FaiI4T (97.4 % sequence similarity) and Microvirga guangxiensis 25BT (97.1 %) and that strain 5420S-16T was closely related to Balneimonas flocculans TFBT (98.0 %) and Microvirga guangxiensis 25BT (97.2 %). The G+C content of the genomic DNA was 62.2 mol% for strain 5420S-12T and 61.5 mol% for strain 5420S-16T. The major fatty acid was C18 : 1 ω7c. The results of DNA–DNA hybridization and the phenotypic data showed that strains 5420S-12T and 5420S-16T could be distinguished from phylogenetically related species and represent two novel species within the genus Microvirga, for which the names Microvirga aerophila sp. nov. (type strain 5420S-12T =KACC 12743T =NBRC 106136T) and Microvirga aerilata sp. nov. (type strain 5420S-16T =KACC 12744T =NBRC 106137T) are proposed. Furthermore, the reclassification of Balneimonas flocculans as Microvirga flocculans comb. nov. (type strain TFBT =JCM 11936T =KCTC 12101T =IAM 15034T =ATCC BAA-817T) is proposed and an emended description of the genus Microvirga is provided.

scholarly journals Bacillus thermolactis sp. nov., isolated from dairy farms, and emended description of Bacillus thermoamylovorans

2011 ◽  
Vol 61 (8) ◽  
pp. 1954-1961 ◽  
Author(s):  
An Coorevits ◽  
Niall A. Logan ◽  
Anna E. Dinsdale ◽  
Gillian Halket ◽  
Patsy Scheldeman ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Emended Description

A polyphasic taxonomic study was performed on 22 thermotolerant, aerobic, endospore-forming bacteria from dairy environments. Seventeen isolates were retrieved from raw milk, one from a filter cloth and four from grass, straw or milking equipment. These latter four isolates (R-6546, R-7499, R-7764 and R-7440) were identified as Bacillus thermoamylovorans based on DNA–DNA hybridizations (values above 70 % with Bacillus thermoamylovorans LMG 18084T) but showed discrepancies in characteristics with the original species description, so an emended description of this species is given. According to 16S rRNA gene sequence analysis and DNA–DNA hybridization experiments, the remaining 18 isolates (R-6488T, R-28193, R-6491, R-6492, R-7336, R-33367, R-6486, R-6770, R-31288, R-28160, R-26358, R-7632, R-26955, R-26950, R-33520, R-6484, R-26954 and R-7165) represented one single species, most closely related to Bacillus thermoamylovorans (93.9 % 16S rRNA gene sequence similarity), for which the name Bacillus thermolactis is proposed. Cells were Gram-stain-positive, facultatively anaerobic, endospore-forming rods that grew optimally at 40–50 °C. The cell wall peptidoglycan type of strain R-6488T, the proposed type strain, was A1γ based on meso-diaminopimelic acid. Major fatty acids of the strains were C16 : 0 (28.0 %), iso-C16 : 0 (12.1 %) and iso-C15 : 0 (12.0 %). MK-7 was the predominant menaquinone, and major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and some unidentified phospholipids. DNA G+C content was 35.0 mol%. Phenotypic properties allowed discrimination from other thermotolerant species of the genus Bacillus and supported the description of the novel species Bacillus thermolactis, with strain R-6488T ( = LMG 25569T  = DSM 23332T) as the proposed type strain.

scholarly journals Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea

2007 ◽  
Vol 57 (3) ◽  
pp. 548-551 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Min-Kyeong Kim ◽  
Seung-Hee Yoo ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Bacterial Strains ◽  
Lysobacter Enzymogenes ◽  
Gene Sequence Analysis ◽  
Greenhouse Soils

Two bacterial strains, designated GH34-4T and GH41-7T, were isolated from greenhouse soil cultivated with cucumber. The bacteria were strictly aerobic, Gram-negative, rod-shaped and oxidase- and catalase-positive. 16S rRNA gene sequence analysis indicated that these strains belong to the genus Lysobacter within the Gammaproteobacteria. Strain GH34-4T showed highest sequence similarity to Lysobacter yangpyeongensis GH19-3T (97.5 %) and Lysobacter koreensis Dae16T (96.4 %), and strain GH41-7T showed highest sequence similarity to Lysobacter antibioticus DSM 2044T (97.5 %), Lysobacter enzymogenes DSM 2043T (97.5 %) and Lysobacter gummosus ATCC 29489T (97.4 %). Levels of DNA–DNA relatedness indicated that strains GH34-4T and GH41-7T represented species clearly different from L. yangpyeongensis, L. antibioticus, L. enzymogenes and L. gummosus. The major cellular fatty acids of strains GH34-4T and GH41-7T were iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1 ω9c, and the major isoprenoid quinone was Q-8. The DNA G+C contents of GH34-4T and GH41-7T were 62.5 and 66.6 mol%, respectively. On the basis of the polyphasic taxonomic data presented, it is evident that each of these strains represents a novel species of the genus Lysobacter, for which the names Lysobacter niabensis sp. nov. (type strain GH34-4T=KACC 11587T=DSM 18244T) and Lysobacter niastensis sp. nov. (type strain GH41-7T=KACC 11588T=DSM 18481T) are proposed.

scholarly journals Description of Sulfitobacter donghicola sp. nov., isolated from seawater of the East Sea in Korea, transfer of Staleya guttiformis Labrenz et al. 2000 to the genus Sulfitobacter as Sulfitobacter guttiformis comb. nov. and emended description of the genus Sulfitobacter

2007 ◽  
Vol 57 (8) ◽  
pp. 1788-1792 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
East Sea ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Unidentified Phospholipid ◽  
Emended Description

A Gram-negative, non-motile and rod-, oval- or coccoid-shaped bacterial strain, DSW-25T, which is phylogenetically closely related to the genera Staleya and Sulfitobacter, was isolated from seawater of the East Sea, Korea, and subjected to a polyphasic taxonomic study. Strain DSW-25T grew optimally at pH 7.0–8.0 and at 25 °C. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. Major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The DNA G+C content was 56.9 mol%. Strain DSW-25T exhibited 16S rRNA gene sequence similarity values of 98.4 % to the type strain of Staleya guttiformis and of 96.6–97.6 % to Sulfitobacter species. There were no distinct phenotypic, particularly chemotaxonomic, properties to differentiate Staleya guttiformis and strain DSW-25T from the genus Sulfitobacter. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain DSW-25T differs from recognized Sulfitobacter species and Staleya guttiformis. On the basis of phenotypic, chemotaxonomic, phylogenetic and genetic data, strain DSW-25T was classified in the genus Sulfitobacter as a member of a novel species, for which the name Sulfitobacter donghicola sp. nov. is proposed. The type strain is strain DSW-25T (=KCTC 12864T =JCM 14565T). It is also proposed that Staleya guttiformis be transferred to the genus Sulfitobacter as Sulfitobacter guttiformis comb. nov.

Imtechella halotolerans gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from estuarine water

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2624-2630 ◽  
Author(s):  
Vikram Surendra ◽  
Pant Bhawana ◽  
Korpole Suresh ◽  
T. N. R. Srinivas ◽  
Pinnaka Anil Kumar
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Estuarine Water ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Pairwise Sequence Similarity

A novel Gram-negative, rod-shaped, non-motile, non-sporulating bacterium, designated strain K1T, was isolated from an estuarine water sample collected from Kochi, Kerala, India. Colonies on marine agar were circular, 2.0–2.5 mm in diameter, shiny, yellow, translucent and convex with entire margins. Strain K1T was negative for ornithine decarboxylase, lysine decarboxylase, nitrate reduction and H2S production. The fatty acids were dominated by iso-branched components with a high abundance of iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH; MK-6 (64 %) and MK-7 (34 %) were found as major respiratory quinones; and phosphatidylethanolamine, two unidentified aminolipids, four unidentified phospholipids and two unidentified lipids were major polar lipids. The DNA G+C content of strain K1T was 46.1 mol%. 16S rRNA gene sequence analysis indicated that strain K1T was related most closely to the type strain of Zhouia amylolytica (pairwise sequence similarity of 93.0 %). Phylogenetic analysis showed that strain K1T formed a distinct branch within the family Flavobacteriaceae and clustered with the clade comprising species of the genera Zhouia , Coenonia and Capnocytophaga , being phylogenetically most closely related to the type strain of Zhouia amylolytica at a distance of 9.2 % (90.8 % similarity). Other species of the genera within the same clade were related to strain K1T at distances of 15.0–23.1 %. Based on phenotypic and chemotaxonomic characteristics and on phylogenetic inference, strain K1T is considered to represent a novel species of a new genus in the family Flavobacteriaceae , for which the name Imtechella halotolerans gen. nov., sp. nov. is proposed. The type strain of Imtechella halotolerans is K1T ( = MTCC 11055T = JCM 17677T).

scholarly journals Thermogymnomonas acidicola gen. nov., sp. nov., a novel thermoacidophilic, cell wall-less archaeon in the order Thermoplasmatales, isolated from a solfataric soil in Hakone, Japan

2007 ◽  
Vol 57 (11) ◽  
pp. 2557-2561 ◽  
Author(s):  
Takashi Itoh ◽  
Naoto Yoshikawa ◽  
Tomonori Takashina
Keyword(s):  
Cell Wall ◽  
Yeast Extract ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Total Dna

A novel thermoacidophilic, cell wall-less archaeon, strain IC-189T, was isolated from a solfataric field in Ohwaku-dani, Hakone, Japan. The cells were irregular cocci, sometimes lobed, club-shaped or catenated, and were highly variable in size, ranging from 0.8 to 8.0 μm in diameter. The strain grew at temperatures in the range 38–68 °C (optimally at 60 °C) and at pH 1.8–4.0 (optimally at around pH 3.0). Strain IC-189T was obligately aerobic and heterotrophic, requiring yeast extract for growth. Yeast extract, glucose and mannose served as carbon and energy sources. The polar lipids consisted mainly of cyclic or acyclic glycerol-bisdiphytanyl-glycerol tetraethers, and the predominant quinone was a menaquinone with seven isoprenoid units (MK-7). The G+C content of total DNA was 56.1 mol%. 16S rRNA gene sequence analysis revealed that strain IC-189T was a member of the order Thermoplasmatales, but diverged from the hitherto known species of the genera Thermoplasma, Picrophilus and Ferroplasma (86.2–91.0 % sequence similarity). These phenotypic and phylogenetic properties clearly support a separate taxonomic status for this strain. Therefore, strain IC-189T represents a novel genus (order Thermoplasmatales) and species, for which the name Thermogymnomonas acidicola gen. nov., sp. nov. is proposed, with type strain IC-189T (=JCM 13583T=DSM 18835T).

Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil

2010 ◽  
Vol 60 (11) ◽  
pp. 2577-2582 ◽  
Author(s):  
Myungjin Lee ◽  
Sung-Geun Woo ◽  
Joonhong Park ◽  
Soon-Ae Yoo
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Low Levels

A Gram-negative, non-motile, aerobic bacterial strain, designated MJ20T, was isolated from farm soil near Daejeon (South Korea) and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ20T belongs to the family Cytophagaceae, class Sphingobacteria, and was related most closely to Dyadobacter fermentans DSM 18053T (98.9 % sequence similarity), Dyadobacter beijingensis JCM 14200T (98.0 %) and Dyadobacter ginsengisoli KCTC 12589T (96.4 %). The G+C content of the genomic DNA of strain MJ20T was 48.5 mol%. The detection of MK-7 as the predominant menaquinone and a fatty acid profile with summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 0 and C16 : 1 ω5c as major components supported the affiliation of strain MJ20T to the genus Dyadobacter. The new isolate exhibited relatively low levels of DNA–DNA relatedness with respect to D. fermentans DSM 18053T (mean±sd of three determinations, 47±7 %) and D. beijingensis JCM 14200T (38±8 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain MJ20T (=KCTC 22481T =JCM 16232T) should be classified in the genus Dyadobacter as the type strain of a novel species, for which the name Dyadobacter soli sp. nov. is proposed.

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