scholarly journals Description of two novel species, Sphingomonas abaci sp. nov. and Sphingomonas panni sp. nov.

2005 ◽  
Vol 55 (6) ◽  
pp. 2565-2569 ◽  
Author(s):  
Hans-Jürgen Busse ◽  
Elke Hauser ◽  
Peter Kämpfer
Keyword(s):  
Fatty Acid ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Sensu Stricto ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Genomic Fingerprinting ◽  
Protein Patterns ◽  
The University

Two Gram-negative, rod-shaped, non-spore-forming bacterial strains designated C42T and C52T were isolated in the Medical Clinic for Small Animals and Ungulates at the University for Veterinary Medicine Vienna, Austria. On the basis of 16S rRNA gene sequence similarity, both strains were shown to belong to the genus Sphingomonas. Strain C42T showed the greatest levels of sequence similarity with Sphingomonas melonis DSM 14444T and Sphingomonas aquatilis KCTC 2881T (both 97·7 %). Strain C52T showed the greatest levels of sequence similarity with Sphingomonas koreensis KCTC 2882T (97·2 %), Sphingomonas aquatilis KCTC 2881T (97·1 %) and S. melonis DSM 14444T (97·0 %). The presence of Q-10 as the main ubiquinone, the predominance of the compound sym-homospermidine in the polyamine patterns, the presence of a Sphingomonadaceae-specific sphingoglycolipid in the polar lipid patterns, the presence of the fatty acid 2-OH C14 : 0 and the lack of 3-hydroxy fatty acids supported the identification of the two novel strains as members of the genus Sphingomonas sensu stricto. Unique physiological characteristics, protein patterns, quantitative differences in their fatty acid profiles and the results of genomic fingerprinting and DNA–DNA hybridizations differentiated strains C42T and C52T from closely related Sphingomonas species. Hence, the two strains are described as novel species of the genus Sphingomonas sensu stricto. The names Sphingomonas abaci sp. nov. (type strain C42T=LMG 21978T=DSM 15867T) and Sphingomonas panni sp. nov. (type strain C52T=LMG 21979T=DSM 15761T) are proposed.

scholarly journals Pseudomonas psychrotolerans sp. nov.

2004 ◽  
Vol 54 (5) ◽  
pp. 1633-1637 ◽  
Author(s):  
Elke Hauser ◽  
Peter Kämpfer ◽  
Hans-Jürgen Busse
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Sensu Stricto ◽  
Rrna Gene ◽  
Pseudomonas Oleovorans ◽  
Bacterial Strains ◽  
Genomic Fingerprinting ◽  
Physiological And Biochemical Characteristics ◽  
The University ◽  
Physiological And Biochemical

Three yellow-pigmented, Gram-negative, rod-shaped, non-spore-forming bacterial strains, C36T, C37 and C39, were isolated in the Medical Clinic for Small Animals and Ungulates at the University for Veterinary Medicine in Vienna, Austria. On the basis of 16S rRNA gene sequence similarity, strain C36T was shown to belong to the genus Pseudomonas; Pseudomonas oleovorans DSM 1045T was the nearest relative (99·5 % sequence similarity). Other Pseudomonas species shared <97 % sequence similarity with strain C36T. The presence of Q-9 as the major ubiquinone, the predominance of putrescine and spermidine in its polyamine patterns and its fatty acid profile [i.e. the predominance of C16 : 0, summed feature 3 (C16 : 1 ω7c and/or 2-OH C15 : 0 iso), C18 : 1 ω7c and the presence of 3-OH C10 : 0, 3-OH C12 : 0 and 2-OH C12 : 0] were in agreement with identification of this strain as a member of the genus Pseudomonas. Physiological and biochemical characteristics and the results of genomic fingerprinting clearly differentiated strain C36T from its phylogenetic relative P. oleovorans DSM 1045T. Results from DNA–DNA hybridization showed that strain C36T represents a species that is distinct from P. oleovorans DSM 1045T. These data demonstrate that strain C36T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas psychrotolerans sp. nov. is proposed. The type strain is C36T (=LMG 21977T=DSM 15758T). Additionally, physiological, biochemical, chemotaxonomic and genomic fingerprints indicate that P. oleovorans ATCC 29347 may not be a member of the species P. oleovorans sensu stricto.

scholarly journals Thalassospira xiamenensis sp. nov. and Thalassospira profundimaris sp. nov.

2007 ◽  
Vol 57 (2) ◽  
pp. 316-320 ◽  
Author(s):  
Chenli Liu ◽  
Yehui Wu ◽  
Li Li ◽  
Yingfei Ma ◽  
Zongze Shao
Keyword(s):  
Fatty Acid ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Tween 80 ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Biochemical Tests ◽  
Deep Sea Sediment

Two bacterial strains, M-5T and WP0211T, were isolated from the surface water of a waste-oil pool in a coastal dock and from a deep-sea sediment sample from the West Pacific Ocean, respectively. Analysis of 16S rRNA gene sequences indicated that both strains belonged to the class Alphaproteobacteria and were closely related to Thalassospira lucentensis (96.1 and 96.2 %, gene sequence similarity, respectively). Based on the results of physiological and biochemical tests, as well as DNA–DNA hybridization experiments, it is suggested that these isolates represent two novel species of the genus Thalassospira. Various traits allow both novel strains to be differentiated from Thalassospira lucentensis, including oxygen requirement, nitrate reduction and denitrification abilities and major fatty acid profiles, as well as their ability to utilize six different carbon sources. Furthermore, the novel strains may be readily distinguished from each other by differences in their motility, flagellation, growth at 4 °C and 40 °C, their ability to hydrolyse Tween 40 and Tween 80, their utilization of 19 different carbon sources and by quantitative differences in their fatty acid contents. It is proposed that the isolates represent two novel species for which the names Thalassospira xiamenensis sp. nov. (type strain, M-5T=DSM 17429T=CGMCC 1.3998T) and Thalassospira profundimaris sp. nov. (type strain, WP0211T=DSM 17430T=CGMCC 1.3997T) are proposed.

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 Paenibacillus rhizosphaerae sp. nov., isolated from the rhizosphere of Cicer arietinum

2005 ◽  
Vol 55 (3) ◽  
pp. 1305-1309 ◽  
Author(s):  
Raúl Rivas ◽  
Carmen Gutiérrez ◽  
Adriana Abril ◽  
Pedro F. Mateos ◽  
Eustoquio Martínez-Molina ◽  
...  
Keyword(s):  
Cicer Arietinum ◽  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Gas Production ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Bacterial Strains ◽  
16S Rrna Gene Sequences

Two sporulating bacterial strains designated CECAP06T and CECAP16 were isolated from the rhizosphere of the legume Cicer arietinum in Argentina. Almost-complete 16S rRNA gene sequences identified the isolates as a Paenibacillus species. It was most closely related to Paenibacillus cineris LMG 18439T (99·6 % sequence similarity), Paenibacillus favisporus LMG 20987T (99·4 % sequence similarity) and Paenibacillus azoreducens DSM 13822T (97·7 % sequence similarity). The cells of this novel species were motile, sporulating, rod-shaped, Gram-positive and strictly aerobic. The predominant fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. The DNA G+C content of strains CECAP06T and CECAP16 was 51·3 and 50·9 mol%, respectively. Growth was observed from many carbohydrates, but gas production was not observed from glucose. Catalase and oxidase activities were present. The isolates produced β-galactosidase and hydrolysed aesculin. Gelatinase, caseinase and urease were not produced. The results of DNA–DNA hybridization showed that the strains from this study constitute a novel species of the genus Paenibacillus, for which the name Paenibacillus rhizosphaerae sp. nov. is proposed. The type strain is CECAP06T (=LMG 21955T=CECT 5831T).

scholarly journals Bacillus aerius sp. nov., Bacillus aerophilus sp. nov., Bacillus stratosphericus sp. nov. and Bacillus altitudinis sp. nov., isolated from cryogenic tubes used for collecting air samples from high altitudes

2006 ◽  
Vol 56 (7) ◽  
pp. 1465-1473 ◽  
Author(s):  
S. Shivaji ◽  
P. Chaturvedi ◽  
K. Suresh ◽  
G. S. N. Reddy ◽  
C. B. S. Dutt ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Air Samples ◽  
Bacillus Altitudinis ◽  
Bacillus Sonorensis

Four novel bacterial strains were isolated from cryogenic tubes used to collect air samples at altitudes of 24, 28 and 41 km. The four strains, 24KT, 28KT, 41KF2aT and 41KF2bT, were identified as members of the genus Bacillus. Phylogenetic analysis based on 16S rRNA gene sequences indicated that three of the strains, 24KT, 28KT and 41KF2aT, are very similar to one another (>98 % sequence similarity) and show a similarity of 98–99 % with Bacillus licheniformis and 98 % with Bacillus sonorensis. DNA–DNA hybridization studies showed that strains 24KT, 28KT and 41KF2aT exhibit <70 % similarity with each other and with B. licheniformis and B. sonorensis. Differences in phenotypic and chemotaxonomic characteristics between the novel strains and B. licheniformis and B. sonorensis further confirmed that these three isolates are representatives of three separate novel species. Strain 41KF2bT showed 100 % 16S rRNA gene sequence similarity to Bacillus pumilus, but differed from its nearest phylogenetic neighbour in a number of phenotypic and chemotaxonomic characteristics and showed only 55 % DNA–DNA relatedness. Therefore, the four isolates represent four novel species for which the names Bacillus aerius sp. nov. (type strain, 24KT=MTCC 7303T=JCM 13348T), Bacillus aerophilus sp. nov. (type strain, 28KT=MTCC 7304T=JCM 13347T), Bacillus stratosphericus sp. nov. (type strain, 41KF2aT=MTCC 7305T=JCM 13349T) and Bacillus altitudinis sp. nov. (type strain, 41KF2bT=MTCC 7306T=JCM 13350T) are proposed.

Reclassification of Herbaspirillum putei as a later heterotypic synonym of Herbaspirillum huttiense, with the description of H. huttiense subsp. huttiense subsp. nov. and H. huttiense subsp. putei subsp. nov., comb. nov., and description of Herbaspirillum aquaticum sp. nov.

2010 ◽  
Vol 60 (6) ◽  
pp. 1418-1426 ◽  
Author(s):  
Anatoly P. Dobritsa ◽  
M. C. S. Reddy ◽  
Mansour Samadpour
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Phenotypic Characteristics ◽  
Phylogenetic Relatedness ◽  
The 16S Rrna Gene

Resequencing of the 16S rRNA gene of the type strain of Herbaspirillum putei Ding and Yokota 2004 revealed 99.9 % sequence similarity to that of the type strain of Herbaspirillum huttiense (Leifson 1962) Ding and Yokota 2004. This high phylogenetic relatedness of H. putei and H. huttiense was confirmed by the results of DNA–DNA hybridization between H. huttiense DSM 10281T and H. putei ATCC BAA-806T (reassociation value 96 %). Therefore, it is proposed to reclassify the type strain of H. putei as a strain of H. huttiense. However, the genome of the type strain of H. putei is about 0.9 Mb larger than that of the H. huttiense type strain. This results in a decrease in the reassociation value in the reciprocal DNA–DNA hybridization to 72 %, a level slightly above the threshold for delineating bacterial species. These data and distinctive phenotypic characteristics indicate that the name Herbaspirillum putei is a later heterotypic synonym of Herbaspirillum huttiense and permit the description of two novel subspecies, Herbaspirillum huttiense subsp. huttiense subsp. nov. (type strain ATCC 14670T =JCM 21423T =DSM 10281T) and Herbaspirillum huttiense subsp. putei subsp. nov., comb. nov. (type strain 7-2T =JCM 21495T =ATCC BAA-806T). Three bacterial strains, IEH 4430T, IEH 4515 and IEH 8757, isolated from water were found to be the closest relatives of these strains. Strain IEH 8757 was classified as a strain of H. huttiense subsp. putei. Studies of genotypic and phenotypic features of strains IEH 4430T and IEH 4515 showed that the strains represent a novel species, which is most closely related to H. huttiense and for which the name Herbaspirillum aquaticum sp. nov. is proposed (type strain IEH 4430T =DSM 21191T =ATCC BAA-1628T).

scholarly journals Agromyces ulmi sp. nov., a xylanolytic bacterium isolated from Ulmus nigra in Spain

2004 ◽  
Vol 54 (6) ◽  
pp. 1987-1990 ◽  
Author(s):  
Raúl Rivas ◽  
Martha E. Trujillo ◽  
Pedro F. Mateos ◽  
Eustoquio Martínez-Molina ◽  
Encarna Velázquez
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Phylogenetic Cluster ◽  
Separate Branch ◽  
Gene Sequence Analysis

Two xylan-degrading bacterial strains were isolated from a decayed Ulmus nigra tree in Spain. The isolates were Gram-positive, non-motile, aerobic and formed substrate mycelium which fragmented into irregular rods. 16S rRNA gene sequence analysis indicated that the isolates form a separate branch within the genus Agromyces phylogenetic cluster, with Agromyces mediolanus DSM 20152T being their closest relative (97·7 and 97·6 % sequence similarity). Catalase, nitrate reduction and urease tests differentiated these strains from A. mediolanus. Cell-wall peptidoglycan composition, major menaquinone, predominant fatty acids and phospholipid pattern were typical of the genus Agromyces. The DNA G+C content determined for the type strain XIL01T was 72 mol%. Based on the data presented, a novel species Agromyces ulmi sp. nov. is proposed. The type strain is XIL01T (=LMG 21954T=DSM 15747T).

Mongoliicoccus alkaliphilus sp. nov. and Litoribacter alkaliphilus sp. nov., isolated from salt pans

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3457-3462 ◽  
Author(s):  
Y. Subhash ◽  
L. Tushar ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Coastal Region ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Content Type ◽  
Link Type

Four bacterial strains (JC165T, JC166T, JC169 and JC170) were isolated from salt pan soils from a coastal region of Tamilnadu, India. They were obligately aerobic, pink- to red-pigmented, mesophilic, haloalkaliphiles having chemoorganoheterotrophic growth on various carbon sources and were catalase- and oxidase-positive. Phototrophic growth and bacteriochlorophyll a were absent in all four strains. Major carotenoids present were β-carotene and rhodoxanthin. The main fatty acid in all strains was iso-C15 : 0. The main polar lipids were phosphatidylethanolamine (PE) and phosphatidylcholine (PC) as well as a few unidentified lipids. Bacterial hopane derivatives and diplopterol (DPL) were detected in all four strains. Based on the 16S rRNA gene sequences, all four strains belong to the family Cyclobacteriaceae in the phylum Bacteroidetes . Strains JC165T and JC169 had a sequence similarity of 97.2 % with Mongoliicoccus roseus MIM28T, while strains JC166T and JC170 had a sequence similarity of 99.5 % with Litoribacter ruber YIM CH208T. Strains JC165T/JC169 and JC166T/JC170 had genomic DNA reassociation values (based on DNA–DNA hybridization) of 21±2 % and 23±1 % with M. roseus KCTC 19808T ( = MIM28T) and L. ruber KCTC 22899T ( = YIM CH208T), respectively, suggesting that they represented novel species. The reassociation values of >85 % between strains JC165T and JC169, and JC166T and JC170 suggested they were strains of the same species. The genomic information was supported by phenotypic observations leading to the proposal of two novel species, Mongoliicoccus alkaliphilus sp. nov. (type strain, JC165T = KCTC 32210T = LMG 27255T) and Litoribacter alkaliphilus sp. nov. (type strain, JC166T = KCTC 32217T = LMG 27256T).

scholarly journals Mesonia hippocampi sp. nov., isolated from the brood pouch of a diseased Barbour's Seahorse (Hippocampus barbouri)

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2241-2247 ◽  
Author(s):  
Judy Kolberg ◽  
Hans-Jürgen Busse ◽  
Thomas Wilke ◽  
Patrick Schubert ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Type Strain ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Brood Pouch ◽  
Diaminopimelic Acid ◽  
Sugar Residue ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Monophyletic Cluster

An orange-pigmented, Gram-staining-negative, rod-shaped bacterium, designated 96_Hippo_TS_3/13T was isolated from the brood pouch of a diseased seahorse male of the species Hippocampus barbouri from the animal facility of the University of Giessen, Germany. Phylogenetic analyses based on the nearly full-length 16S rRNA gene sequence placed strain 96_Hippo_TS_3/13T into the monophyletic cluster of the genus Mesonia within the family Flavobacteriaceae. However, the strain shared only 92.2–93.8 % sequence similarity to type strains of species of the genus Mesonia, with highest sequence similarity to the type strain of Mesonia aquimarina. Cellular fatty acid analysis showed a Mesonia-typical fatty acid profile including several branched and hydroxyl fatty acids with highest amounts of iso-C15 : 0 (40.9 %) followed by iso-C17 : 0 3-OH (14.8 %). In the polyamine pattern, sym-homospermidine was predominant. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The quinone system contained exclusively menaquinone MK-6. The only identified compound in the polar lipid profile was phosphatidylethanolamine present in major amounts. Additionally, major amounts of an unidentified aminolipid and two unidentified lipids not containing a phosphate group, an amino group or a sugar residue were detected. The genomic G+C content of strain 96_Hippo_TS_3/13T was 30 mol%. Based on genotypic, chemotaxonomic and physiological characterizations we propose a novel species of the genus Mesonia, Mesonia hippocampi sp. nov., with strain 96_Hippo_TS_3/13T ( = CIP 110839T =  LMG 28572T = CCM 8557T) as the type strain. An emended description of the genus Mesonia is also provided.

scholarly journals Paenibacillus algorifonticola sp. nov., isolated from a cold spring

2011 ◽  
Vol 61 (9) ◽  
pp. 2167-2172 ◽  
Author(s):  
Qi-Yong Tang ◽  
Na Yang ◽  
Jian Wang ◽  
Yu-Qing Xie ◽  
Biao Ren ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Cold Spring ◽  
Xinjiang Uyghur Autonomous Region ◽  
The 16S Rrna Gene

A Gram-stain-positive, endospore-forming, rod-shaped bacterium, designated XJ259T, was isolated from a cold spring sample from Xinjiang Uyghur Autonomous Region, China. The isolate grew optimally at 20–30 °C and pH 7.3–7.8. Comparative analysis of the 16S rRNA gene sequence showed that isolate XJ259T belonged phylogenetically to the genus Paenibacillus, and was most closely related to Paenibacillus xinjiangensis B538T (with 96.6 % sequence similarity), Paenibacillus glycanilyticus DS-1T (96.3 %) and Paenibacillus castaneae Ch-32T (96.1 %), sharing less than 96.0 % sequence similarity with all other members of the genus Paenibacillus. Chemotaxonomic analysis revealing menaquinone-7 (MK-7) as the major isoprenoid quinone, diphosphatidylglycerol, phosphatidylethanolamine and two unknown phosphoglycolipids as the major cellular polar lipids, a DNA G+C content of 47.0 mol%, and anteiso-C15 : 0 and C16 : 0 as the major fatty acids supported affiliation of the new isolate to the genus Paenibacillus. Based on these data, isolate XJ259T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus algorifonticola sp. nov. is proposed. The type strain is XJ259T ( = CGMCC 1.10223T  = JCM 16598T).

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