Altererythrobacter troitsensis sp. nov., isolated from the sea urchin Strongylocentrotus intermedius

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 93-97 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Sung-Heun Cho ◽  
Yochan Joung ◽  
Kiseong Joh ◽  
Mi Na Kim ◽  
...  

An aerobic, halotolerant, Gram-negative bacterium was isolated from the sea urchin Strongylocentrotus intermedius and subjected to taxonomic characterization. The strain, designated KMM 6042T, was rod-shaped, motile and yellow-pigmented. Phylogenetic analysis indicated that the strain was most closely related to the type strain of Altererythrobacter dongtanensis , and the level of 16S rRNA gene sequence similarity between the two was 99.0 %. However, the DNA–DNA relatedness between the two strains was 34.4±7.6 %. Physiological and chemotaxonomic properties clearly distinguished the novel strain from other species of the genus Altererythrobacter . It is thus evident from the phylogenetic and phenotypic analyses that strain KMM 6042T merits recognition as a novel species of the genus Altererythrobacter , for which the name Altererythrobacter troitsensis sp. nov. (type strain, KMM 6042T = KCTC 12303T = JCM 17037T) is proposed.

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 288-297 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Vassilii I. Svetashev ◽  
Enevold Falsen

A group of five Gram-negative, aerobic, halotolerant, non-pigmented bacteria isolated from shallow sediment samples and invertebrate specimens collected from the Gulf of Alaska and the Sea of Japan was subjected to taxonomic study. On the basis of 16S rRNA gene sequence analysis, the novel isolates were affiliated to the genus Cobetia , sharing the highest sequence similarity of 99.3–99.9 % with Cobetia marina DSM 4741T. DNA–DNA hybridization experiments between and among the novel strains and C. marina DSM 4741T and Cobetia crustatorum JCM 15644T revealed that the five strains represent three separate genospecies, which could be differentiated in their morphological, physiological and biochemical characteristics. Halomonas halodurans NBRC 15607T was included in this study as it has recently been reported to exhibit high 16S rRNA gene sequence similarity to C. marina DSM 4741T, and it showed a high DNA relatedness value of 96 % with C. marina DSM 4741T, indicating that they belong to the same species. On the basis of phylogenetic analysis, DNA–DNA hybridization and phenotypic characterization, three novel species are proposed, named Cobetia amphilecti sp. nov. (type strain KMM 1561T  = NRIC 0815T  = CCUG 49560T), Cobetia litoralis sp. nov. (type strain KMM 3880T  = NRIC 0814T  = CCUG 49563T) and Cobetia pacifica sp. nov. (type strain KMM 3879T  = NRIC 0813T  = CCUG 49562T). It is also proposed that Halomonas halodurans is a later heterotypic synonym of Cobetia marina , and emended descriptions of the genus Cobetia and the species Cobetia marina are provided.


Author(s):  
Selma Vieira ◽  
Katharina J. Huber ◽  
Meina Neumann-Schaal ◽  
Alicia Geppert ◽  
Manja Luckner ◽  
...  

Members of the metabolically diverse order Nitrosomonadales inhabit a wide range of environments. Two strains affiliated with this order were isolated from soils in Germany and characterized by a polyphasic approach. Cells of strains 0125_3T and Swamp67T are Gram-negative rods, non-motile, non-spore-forming, non-capsulated and divide by binary fission. They tested catalase-negative, but positive for cytochrome c-oxidase. Both strains form small white colonies on agar plates and grow aerobically and chemoorganotrophically on SSE/HD 1 : 10 medium, preferably utilizing organic acids and proteinaceous substrates. Strains 0125_3T and Swamp67T are mesophilic and grow optimally without NaCl addition at slightly alkaline conditions. Major fatty acids are C16 : 1  ω7c, C16 : 0 and C14 : 0. The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyglycerol. The predominant respiratory quinone is Q-8. The G+C content for 0125_3T and Swamp67T was 67 and 66.1 %, respectively. The 16S rRNA gene analysis indicated that the closest relatives (<91 % sequence similarity) of strain 0125_3T were Nitrosospira multiformis ATCC 25196T, Methyloversatilis universalis FAM5T and Denitratisoma oestradiolicum AcBE2-1T, while Nitrosospira multiformis ATCC 25196T, Nitrosospira tenuis Nv1T and Nitrosospira lacus APG3T were closest to strain Swamp67T. The two novel strains shared 97.4 % 16S rRNA gene sequence similarity with one another and show low average nucleotide identity of their genomes (83.8 %). Based on the phenotypic, chemotaxonomic, genomic and phylogenetic analysis, we propose the two novel species Usitatibacter rugosus sp. nov (type strain 0125_3T=DSM 104443T=LMG 29998T=CECT 9241T) and Usitatibacter palustris sp. nov. (type strain Swamp67T=DSM 104440T=LMG 29997T=CECT 9242T) of the novel genus Usitatibacter gen. nov., within the novel family Usitatibacteraceae fam. nov.


Author(s):  
Soon Dong Lee ◽  
In Seop Kim

Two novel actinobacterial strains, designated C9-5T and C3-43, were isolated from soil samples of a cave in Jeju Island, Republic of Korea, and subjected to taxonomic study by a polyphasic approach. The organisms exhibited a typical rod–coccus developmental cycle during growth and grew at 10–30 °C, pH 5–9 and 0–3 % (w/v) NaCl. In 92 single-copy core gene sequence analysis, strain C9-5T was loosely associated with Rhodococcus tukisamuensis , albeit sharing low 16S rRNA gene sequence similarity (97.4 %). A combination of morphological and chemotaxonomic characteristics supported assignment with the genus Rhodococcus . With respect to 16S rRNA gene sequence similarity, the novel isolates showed the highest identity to the type strain of Rhodococcus subtropicus (98.7 % sequence similarity), followed by Rhodococcus olei (98.5 %) and Rhodococcus pedocola (98.4 %).The average nucleotide identity and digital DNA–DNA hybridization values between strain C9-5T and members of the genus Rhodococcus were ≤81.5 and ≤37.1 %, respectively. A set of physiological and chemotaxonomic properties together with overall genomic relatedness differentiated the novel isolates from members of the genus Rhodococcus , for which the name Rhodococcus spelaei sp. nov. is proposed. The type strain is C9-5T (=KACC 19822T=DSM 107558T). Based on genome analysis performed here, it is also proposed that Rhodococcus biphenylivorans Su et al. 2015 is a later heterotypic synonym of Rhodococcus pyridinivorans Yoon et al. 2000, Rhodococcus qingshengii Xu et al. 2007 and Rhodococcus baikonurensis Li et al. 2004 are later heterotypic synonyms of Rhodococcus erythropolis (Gray and Thornton 1928) Goodfellow and Alderson 1979 (Approved Lists 1980), and Rhodococcus percolatus Briglia et al. 1996 and Rhodococcus imtechensis Ghosh et al. 2006 are later heterotypic synonyms of Rhodococcus opacus Klatte et al. 1995.


Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Dominique Clermont ◽  
Alexis Criscuolo ◽  
...  

A Gram-stain-positive, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays, was studied for its detailed taxonomic allocation. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-447T was shown to be a member of the genus Paenibacillus , most closely related to the type strain of Paenibacillus solanacearum (97.8 %). The 16S rRNA gene sequence similarity values to all other Paenibacillus species were below 97.0 %. DNA–DNA hybridization (DDH) values with the type strain of P. solanacearum were 35.9 % (reciprocal 27%), respectively. The average nucleotide identity and in silico DDH values with the type strain of P. solanacearum were 84.86 and 28.9 %, respectively. The quinone system of strain JJ-447T consisted exclusively of menaquinones and the major component was MK-7 (96.4 %) but minor amounts of MK–6 (3.6 %) were detected as well. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. Major fatty acids were iso- and anteiso-branched with the major compounds anteiso-C15 : 0 and iso-C15 : 0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-447T from the most closely related species on the basis of d-glucose, l-arabinose and d-mannose assimilation and other physiological tests. Thus, JJ-447T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus allorhizosphaerae sp. nov. is proposed, with JJ-447T (=LMG 31601T=CCM 9021T=CIP 111802T) as the type strain.


2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1323-1328 ◽  
Author(s):  
William J. Wolfgang ◽  
Teresa V. Passaretti ◽  
Reashma Jose ◽  
Jocelyn Cole ◽  
An Coorevits ◽  
...  

A polyphasic analysis was undertaken of seven independent isolates of Gram-negative cocci collected from pathological clinical samples from New York, Louisiana, Florida and Illinois and healthy subgingival plaque from a patient in Virginia, USA. The 16S rRNA gene sequence similarity among these isolates was 99.7–100 %, and the closest species with a validly published name was Neisseria lactamica (96.9 % similarity to the type strain). DNA–DNA hybridization confirmed that these isolates are of the same species and are distinct from their nearest phylogenetic neighbour, N. lactamica . Phylogenetic analysis of 16S and 23S rRNA gene sequences indicated that the novel species belongs in the genus Neisseria . The predominant cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C18 : 1ω7c. The cellular fatty acid profile, together with other phenotypic characters, further supports the inclusion of the novel species in the genus Neisseria . The name Neisseria oralis sp. nov. (type strain 6332T  = DSM 25276T  = LMG 26725T) is proposed.


2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 3024-3029 ◽  
Author(s):  
Keun Sik Baik ◽  
Seong Chan Park ◽  
Han Na Choe ◽  
Se Na Kim ◽  
Jae-Hak Moon ◽  
...  

A non-motile, coccobacillus-shaped and pink pigmented bacterium, designated strain 03SU10-PT, was isolated from wetland freshwater (Woopo wetland, Republic of Korea). Cells were Gram reaction-negative and catalase- and oxidase-positive. The major fatty acids (>10 % of total) were C18 : 1ω7c and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). The predominant respiratory lipoquinone was Q-10. The DNA G+C content was 68 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine and an unknown aminolipid. Spermidine, putrescine and 1,3-diaminopropane were the major polyamines. A phylogenetic tree based on 16S rRNA gene sequence comparisons showed that strain 03SU10-PT formed an evolutionary lineage within the radiation enclosing the members of the genus Roseomonas . The nearest neighbour to the novel strain was Roseomonas stagni HS-69T (96.3 % gene sequence similarity). The evidence provided by the polyphasic taxonomic approach used in this study indicated that strain 03SU10-PT could not be assigned to any recognized species; therefore a novel species is proposed, Roseomonas riguiloci sp. nov., with 03SU10-PT ( = KCTC 23339T = JCM 17520T) as the type strain.


Author(s):  
Tobias Eisenberg ◽  
Sabine Gronow ◽  
Jane Falgenhauer ◽  
Can Imirzalioglu ◽  
Kristin Mühldorfer ◽  
...  

Members of the genus Sneathia are fastidious bacteria that predominantly colonise the female genital tract and are significantly associated with reproductive disorders and genital and neonatal disease. From a taxonomical perspective, the genus only comprises the species Sneathia sanguinegens . Numerous reports on a second species, ‘Sneathia amnii’, have been published, but the name has never been validated. The same is the case for ‘Leptotrichia amnionii’, which was previously shown to belong to the same species as ‘Sneathia amnii’. We studied strains DSM 16631T and DSM 16630, which have been identified and deposited as ‘Leptotrichia amnionii’ previously. At the time of isolation, these strains were found to be most closely related to, but clearly different from, Sneathia sanguinegens based on 16S rRNA gene sequence similarities. Both strains proved to be almost indistinguishable from ‘Sneathia amnii’ based on molecular, morphological and physiological traits. The 16S rRNA gene sequence analysis revealed that strain DSM 16631T was assigned to the genus Sneathia with a sequence similarity of 95.47 % to Sneathia sanguinegens CCUG 41628T, followed by type strains of Caviibacter abscessus (93.03 %), Oceanivirga salmonicida (92.68 %) and Oceanivirga miroungae (91.97 %) as the next closely related members of the Leptotrichiaceae . The novel species was also clearly differentiated from other related taxa by core genome phylogeny, average nucleotide and amino acid identities, in silico DNA–DNA hybridization and MALDI-TOF MS. With respect to chemotaxonomic and physiological patterns, strains DSM 16631T and DSM 16630 were again highly similar to Sneathia sanguinegens . On the basis of these data, we propose the novel species Sneathia vaginalis sp. nov. with the type strain DSM 16631T (=CCUG 52977T=CCUG 52889AT) and a second strain DSM 16630 (=CCUG 52976=CCUG 52888) that were both isolated from bloodstream infections in women with puerperal fever in France. The G+C content of the DNA of the type strain is 28.4 mol% and the genome size is 1.28 Mbp. Based on the observed extremely high similarities of genotypic and phenotypic traits of the novel proposed species to those reported for ‘Sneathia amnii’, we recommend using this new name in all further publications on this taxon.


2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1307-1313 ◽  
Author(s):  
Heng-Lin Cui ◽  
Xin Yang ◽  
Yu-Guang Zhou ◽  
Hong-Can Liu ◽  
Pei-Jin Zhou ◽  
...  

Two halophilic archaea, strains TBN53T and CSW2.24.4T, were characterized to elucidate their taxonomic status. Strain TBN53T was isolated from the Taibei marine solar saltern near Lianyungang city, Jiangsu province, China, whereas strain CSW2.24.4T was isolated from a saltern crystallizer in Victoria, Australia. Cells of the two strains were pleomorphic, stained Gram-negative and produced red-pigmented colonies. Strain TBN53T was able to grow at 25–55 °C (optimum 45 °C), with 1.4–5.1 M NaCl (optimum 2.6–3.9 M NaCl), with 0–1.0 M MgCl2 (optimum 0–0.1 M MgCl2) and at pH 5.5–9.5 (optimum pH 7.0), whereas strain CSW2.24.4T was able to grow at 25–45 °C (optimum 37 °C), with 2.6–5.1 M NaCl (optimum 3.4 M NaCl), with 0.01–0.7 M MgCl2 (optimum 0.05 M MgCl2) and at pH 5.5–9.5 (optimum pH 7.0–7.5). Cells of the two isolates lysed in distilled water. The minimum NaCl concentrations that prevented cell lysis were 8 % (w/v) for strain TBN53T and 12 % (w/v) for strain CSW2.24.4T. The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate, with two glycolipids chromatographically identical to sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively. Trace amounts of other unidentified lipids were also detected. On the basis of 16S rRNA gene sequence analysis, strains TBN53T and CSW2.24.4T showed 94.1 % similarity to each other and were closely related to Halobellus clavatus TNN18T (95.0 and 94.7 % similarity, respectively). Levels of rpoB′ gene sequence similarity between strains TBN53T and CSW2.24.4T, and between these strains and Halobellus clavatus TNN18T were 88.5, 88.5 and 88.1 %, respectively. The DNA G+C contents of strains TBN53T and CSW2.24.4T were 69.2 and 67.0 mol%, respectively. The level of DNA–DNA relatedness between strain TBN53T and strain CSW2.24.4T was 25 %, and these two strains showed low levels of DNA–DNA relatedness with Halobellus clavatus TNN18T (30 and 29 % relatedness, respectively). Based on these phenotypic, chemotaxonomic and phylogenetic properties, two novel species of the genus Halobellus are proposed to accommodate these two strains, Halobellus limi sp. nov. (type strain TBN53T = CGMCC 1.10331T = JCM 16811T) and Halobellus salinus sp. nov. (type strain CSW2.24.4T = DSM 18730T = CGMCC 1.10710T = JCM 14359T).


Author(s):  
Maik Hilgarth ◽  
Johannes Redwitz ◽  
Matthias A. Ehrmann ◽  
Rudi F. Vogel ◽  
Frank Jakob

As part of a study investigating the microbiome of bee hives and honey, two novel strains (TMW 2.1880T and TMW 2.1889T) of acetic acid bacteria were isolated and subsequently taxonomically characterized by a polyphasic approach, which revealed that they cannot be assigned to known species. The isolates are Gram-stain-negative, aerobic, pellicle-forming, catalase-positive and oxidase-negative. Cells of TMW 2.1880T are non-motile, thin/short rods, and cells of TMW 2.1889T are motile and occur as rods and long filaments. Morphological, physiological and phylogenetic analyses revealed a distinct lineage within the genus Bombella . Strain TMW 2.1880T is most closely related to the type strain of Bombella intestini with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 94.16 and 56.3 %, respectively. The genome of TMW 2.1880T has a size of 1.98 Mb and a G+C content of 55.3 mol%. Strain TMW 2.1889T is most closely related to the type strain of Bombella apis with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 85.12 and 29.5 %, respectively. The genome of TMW 2.1889T has a size of 2.07 Mb and a G+C content of 60.4 mol%. Ubiquinone analysis revealed that both strains contained Q-10 as the main respiratory quinone. Major fatty acids for both strains were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8, respectively, and additionally C14 : 0 2-OH only for TMW 2.1880T and C14 : 0 only for TMW 2.1889T. Based on polyphasic evidence, the two isolates from honeycombs of Apis mellifera represent two novel species of the genus Bombella , for which the names Bombella favorum sp. nov and Bombella mellum sp. nov. are proposed. The designated respective type strains are TMW 2.1880T (=LMG 31882T=CECT 30114T) and TMW 2.1889T (=LMG 31883T=CECT 30113T).


2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2828-2834 ◽  
Author(s):  
S. Kalyana Chakravarthy ◽  
E. V. V. Ramaprasad ◽  
E. Shobha ◽  
Ch. Sasikala ◽  
Ch. V. Ramana

Two strains (JA266T and JA333) of Gram-negative, rod-shaped, phototrophic, purple non-sulfur bacteria were isolated from a freshwater fish pond and an industrial effluent. Both strains were capable of phototrophic and chemotrophic growth. Bacteriochlorophyll a and carotenoids of the spirilloxanthin series were present as photosynthetic pigments. The major fatty acid for both strains was C18 : 1ω7c (>65 %), with minor amounts of 11-methyl C18 : 1ω7c, C16 : 0, C16 : 1ω7c and C18 : 0 also present. Both strains have the lamellar type of intracellular photosynthetic membranes. Ubiquinone-10 (Q10) and rhodoquinone-10 (RQ10) were present as primary quinone components. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine were the major polar lipids, while minor amounts of amino lipids (AL1, AL2) and an unidentified lipid (L1) were common to both strains. The DNA G+C contents of strains JA266T and JA333 were 71.3 and 69.9 mol%, respectively. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that both strains clustered with members of the genus Rhodoplanes in the class Alphaproteobacteria . Strains JA266T and JA333 had gene sequence similarity of 98.7 and 98.9 % with Rhodoplanes serenus TUT3530T, 96.4 and 96.5 % with Rhodoplanes elegans AS130T, respectively, and less than 96 % with other members of the genus Rhodoplanes . 16S rRNA gene sequence similarity between the two strains was 99.3 % and they exhibited high (84.7 %) relatedness based on DNA–DNA hybridization. Furthermore, both strains had less than 65 % DNA–DNA relatedness with the type strain R. serenus TUT3530T. On the basis of phenotypic and genotypic data, it is proposed that strain JA266T be classified as a novel species of the genus Rhodoplanes , with the species name Rhodoplanes piscinae sp. nov. The type strain of the proposed novel species is JA266T ( = JCM 14934T = KCTC 5627T), while strain JA333 ( = NBRC 107574 = KCTC 5962) is an additional strain.


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