bluuebunny/crossref_metadata_2025 huggingface dataset:
Altering the interaction between σ
70
and RNA polymerase generates complexes with distinct transcription-elongation properties
Authors: Berghöfer-Hochheimer Yvonne , Lu Chi Zen , Gross Carol A.
Published: January 2005

We compare the elongation behavior of native
Escherichia coli
RNA polymerase holoenzyme assembled
in vivo
, holoenzyme reconstituted from σ
70
and RNA polymerase
in vitro
, and holoenzyme with a specific alteration in the interface between σ
70
and RNA polymerase. Elongating RNA polymerase from each holoenzyme has distinguishable properties, some of which cannot be explained by differential retention or rebinding of σ
70
during elongation, or by differential presence of elongation factors. We suggest that interactions between RNA polymerase and σ
70
may influence the ensemble of conformational states adopted by RNA polymerase during initiation. These states, in turn, may affect the conformational states adopted by the elongating enzyme, thereby physically and functionally imprinting RNA polymerase.
Expression of Cry1Ac protein in cry1Ac/CpTI transgenic rice and its resistance in different developmental stages to Chilo suppressalis
Authors: Yong-Jun Zhang , Hong-Ying Zhao , Kong-Ming Wu , Kui-Jun Zhao , Yu-Fa Peng , Yu-Yuan Guo
Published: January 2005

The expression patterns of Cry1Ac protein and the resistance to striped stem borer Chilo suppressalis (Walker) of cry1Ac/CpTI transgenic rice (Oryza sativa L.) were investigated by ELISA and laboratory bioassay. ELISA results showed that Cry1Ac protein could be detected in all organs during the development process of cry1Ac/CpTI transgenic rice. The content of Cry1Ac protein varied markedly in different tissues at different stages: it was higher in the earlier stage than in the later stage. The highest level of Cry1Ac protein in terminal leaves of the main stem was found at the jointing stage. Thereafter, it decreased at the booting stage, and a gradual reduction to the lowest level was recorded from the flowering to the filling stage, before a slight increase was shown at the maturing stage. In addition, higher concentrations of this protein were detected in the main stem at the seedling, jointing and flowering stages than at other stages. Relatively lower levels of Cry1Ac protein were found in seeds. The results from laboratory bioassay showed high resistance of terminal leaves of the main stem in all developmental stages to C. suppressalis larvae. Corrected mortality values of C. suppressalis at 4 days after feeding on the detached leaves of cry1Ac/CpTI transgenic rice reached 90% before the filling stage and decreased to nearly 60% after the filling stage. Interestingly, results of whole plant bioassay coincided with those obtained in the detached leaf bioassay. The tendency of larval morality in the detached leaf bioassay and whole plant bioassay was consistent with that of Cry1Ac protein content in the different growing periods and organs.
Relationship between calcium and ABA in ethylene synthesis in tomato fruit
Authors: Ben-Zhong Zhu , Shao-Chong Wei , Yun-Bo Luo
Published: January 2005

The influence of calcium and ABA on ethylene biosynthesis was investigated at different stages and patterns of tomato (Lycopersicon esculentumcv. Lichun) fruit to analyse the relationship between calcium and ABA in relation to the ethylene biosynthesis system. The ethylene production of discs excised from mature green tomato fruits increased rapidly with 100 μmol/l ABA or 100 mmol/l calcium treatment. The increase with the two treatments combined was more than that after application of a single chemical, which suggests that these two chemicals could play synergistic roles in the ethylene synthesis of mature green tomato fruits. It was also found that application of the calcium chelator EGTA inhibited ethylene synthesis, and the production of ethylene after application of EGTA plus ABA was higher than that after treatment with EGTA alone. However, the effect changed when immature fruits were treated with these chemicals. ABA inhibited ethylene synthesis obviously and calcium still promoted it. When we treated immature fruit discs with both calcium and ABA simultaneously, ethylene production was more than that of ABA and less than that of calcium, which indicates that ABA and calcium play agonistic roles in ethylene biosynthesis of the immature tomato fruit discs. Furthermore, ethylene release from transgenic antisense ACS immature tomato fruit discs with application of both calcium and ABA was inhibited markedly, but was stimulated when the mature fruits were treated with ABA and calcium. All of these data suggest that there are different relationships between calcium and ABA in the ethylene synthesis system in different patterns and stages of tomato fruit ripening.
Isolation and regeneration of protoplasts fromPenicillium digitatum
Authors: Ai-Huan Song , Hong-Ye Li , Xiao-Hong Liu
Published: January 2005

The effects of some factors on the isolation of protoplasts fromPenicillium digitatumwere studied, including the appropriate material (young mycelia and generating spores), the concentrations of enzyme and osmotic pressure stabilizers, reaction time and reaction temperature. Results demonstrated that germinating spores were an ideal material resource for the isolation ofP. digitatumprotoplasts. Highest yield and quality ofP. digitatumprotoplasts were obtained by shaking germinating spores suspended in a solution of 10 mg/ml Lywallzyme™ dissolved in 0.7 M NaCl as osmotic pressure stabilizer at 80 rev/min and 30°C for 3.0–3.5 h. The regeneration rate of the isolated protoplasts was as high as 24.9% on double-layer Czapek medium containing 0.7 M NaCl. Additionally, observation of the protoplast release pattern showed that the protoplasts ofP. digitatumwere released primarily from the hyphal apex and occasionally from the subapical or original sites of germinating tubes. The protoplasts ofP. digitatumwere regenerated in a direct manner of either yeast-like cell development or mycelium formation.
Computing periodic solutions of linear differential-algebraic equations by waveform relaxation
Authors: Jiang Yao-Lin , Chen Richard
Published: January 2005

We propose an algorithm, which is based on the waveform relaxation (WR) approach, to compute the periodic solutions of a linear system described by differential-algebraic equations. For this kind of two-point boundary problems, we derive an analytic expression of the spectral set for the periodic WR operator. We show that the periodic WR algorithm is convergent if the supremum value of the spectral radii for a series of matrices derived from the system is less than 1. Numerical examples, where discrete waveforms are computed with a backward-difference formula, further illustrate the correctness of the theoretical work in this paper.
Conjugate gradient predictor corrector method for solving large scale problems
Authors: Syam Muhammed
Published: January 2005

In this paper, we give a new method for solving large scale problems. The basic idea of this method depends on implementing the conjugate gradient as a corrector into a continuation method. We use the Euler method as a predictor. Adaptive steplength control is used during the tracing of the solution curve. We present some of our experimental examples to demonstrate the efficiency of the method.
Data-sparse approximation to a class of operator-valued functions
Authors: Gavrilyuk Ivan , Hackbusch Wolfgang , Khoromskij Boris
Published: January 2005

In earlier papers we developed a method for the data-sparse approximation of the solution operators for elliptic, parabolic, and hyperbolic PDEs based on the Dunford-Cauchy representation to the operator-valued functions of interest combined with the hierarchical matrix approximation of the operator resolvents. In the present paper, we discuss how these techniques can be applied to approximate a hierarchy of the operator-valued functions generated by an elliptic operatorL\mathcal {L}.
Sobolev bounds on functions with scattered zeros, with applications to radial basis function surface fitting
Authors: Narcowich Francis , Ward Joseph , Wendland Holger
Published: January 2005

In this paper we discuss Sobolev bounds on functions that vanish at scattered points in a bounded, Lipschitz domain that satisfies a uniform interior cone condition. The Sobolev spaces involved may have fractional as well as integer order. We then apply these results to obtain estimates for continuous and discrete least squares surface fits via radial basis functions (RBFs). These estimates include situations in which the target function does not belong to the native space of the RBF.
Subdivision schemes with nonnegative masks
Authors: Zhou Xinlong
Published: January 2005

The conjecture concerning the characterization of a convergent univariate subdivision algorithm with nonnegative finite mask is confirmed.
Tame kernels of cubic cyclic fields
Authors: Browkin Jerzy
Published: January 2005

There are many results describing the structure of the tame kernels of algebraic number fields and relating them to the class numbers of appropriate fields. In the present paper we give some explicit results on tame kernels of cubic cyclic fields. Table 1 collects the results of computations of the structure of the tame kernel for all cubic fields with only one ramified prime

p
,

p,

7
≤
p
>
5
,
000.

7\le p>5,000.

In particular, we investigate the structure of the 7-primary and 13-primary parts of the tame kernels. The theoretical tools we develop, based on reflection theorems and singular primary units, enable the determination of the structure even of 7-primary and 13-primary parts of the tame kernels for all fields as above. The results are given in Tables 2 and 3.
Spiroplasma atrichopogonis sp. nov., from a ceratopogonid biting midge
Authors: Koerber R. Thomas , Gasparich Gail E. , Frana Mark F. , Grogan William L.
Published: January 2005

Spiroplasma sp. strain GNAT3597T was isolated from the biting midge genus Atrichopogon (Diptera: Ceratopogonidae). It was serologically distinct from other Spiroplasma species, groups or subgroups. Dark-field microscopy of the cells revealed the classical helical shape and subsequent transmission electron microscopy revealed cells surrounded by only a cell membrane (i.e. lacking a cell wall). Growth of strain GNAT3597T occurred in M1D medium at 30 °C. Strain GNAT3597T catabolized both glucose and arginine, but did not hydrolyse urea. The DNA G+C content of strain GNAT3597T was 29±1 mol%. Only one strain, SMCAT (Spiroplasma mirum), is serologically related to strain GNAT3597T, although the relationship is weak (positive reaction to only a 1 : 80 dilution). It is therefore proposed that strain GNAT3597T (=ATCC BAA-520T=NBRC 100390T) represents a novel species, Spiroplasma atrichopogonis sp. nov. (class Mollicutes: order Entomoplasmatales: family Spiroplasmataceae).
Cryptanaerobacter phenolicus gen. nov., sp. nov., an anaerobe that transforms phenol into benzoate via 4-hydroxybenzoate
Authors: Juteau Pierre , Côté Valérie , Duckett Marie-France , Beaudet Réjean , Lépine François , Villemur Richard , Bisaillon Jean-Guy
Published: January 2005

An anaerobic bacterium that transforms phenol and 4-hydroxybenzoate (4-OHB) into benzoate, strain LR7.2T, was isolated from a culture originating from a mixture of swamp water, sewage sludge, swine waste and soil. Cells of strain LR7.2Tare Gram-positive short rods (1×2 μm) that are electron-dense when observed by electron microscopy. The optimum pH and temperature for growth and transformation activity of 4-OHB are 7·5–8·0 and 30–37 °C, respectively. The bacterium does not use sulphate, thiosulphate, nitrate, nitrite, FeCl3, fumarate or arsenate as an electron acceptor. It does not normally use sulphite, although stimulation of growth and 4-OHB transformation activity at a low concentration (up to 2 mM) has been reported previously under different culture conditions. The presence of 4-OHB or phenol is essential for growth; transformation of 4-OHB or phenol into benzoate is used to produce energy for growth. Using [6D]-phenol, 4-OHB was shown to be an intermediate in the transformation of phenol into benzoate. No spore was observed. The bacterium has a DNA G+C content of 51 mol% and its major membrane fatty acid is anteiso-C15 : 0. The 16S rRNA gene sequence of strain LR7.2Tshows only 90 % similarity to its closest relative (Pelotomaculum thermopropionicum). From these results, a new taxon is proposed:Cryptanaerobacter phenolicusgen. nov., sp. nov. The type strain is LR7.2T(=ATCC BAA-820T=DSM 15808T).
Chryseobacterium daecheongense sp. nov., isolated from freshwater lake sediment
Authors: Kim Kwang Kyu , Bae Hee-Sung , Schumann Peter , Lee Sung-Taik
Published: January 2005

A novel nitrate-reducing bacterium, CPW406T, was isolated from the sediment of a shallow, freshwater lake. The strain was a Gram-negative, non-motile, non-spore-forming rod, which formed yellow-pigmented colonies on nutrient agar and contained a polyamine pattern with sym-homospermidine as the major compound, MK-6 as the predominant menaquinone, 15 : 0 iso and 17 : 0 iso 3-OH as the major fatty acids and phosphatidylethanolamine and several unknown lipids in the polar lipid profile. The 16S rRNA gene sequence of strain CPW406T was found to be most similar to that of the type strain of Chryseobacterium defluvii (DSM 14219T; 97·9 % similarity). However, DNA–DNA relatedness data and its phenotypic properties showed that strain CPW406T could be distinguished from all known Chryseobacterium species and thus represented a novel species, for which the name Chryseobacterium daecheongense sp. nov. is proposed; the type strain is CPW406T (=DSM 15235T=KCTC 12088T).
Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov., isolated from activated sludge
Authors: Kämpfer Peter , Schulze Renate , Jäckel Udo , Malik Khursheed A. , Amann Rudolf , Spring Stefan
Published: January 2005

Two Gram-negative, oxidase-positive rods (strains BSB 9.5T and BSB 41.8T) isolated from wastewater were studied using a polyphasic approach. 16S rRNA gene sequence comparisons demonstrated that both strains cluster phylogenetically within the family Comamonadaceae: the two strains shared 99·9 % 16S rRNA gene sequence similarity and were most closely related to the type strains of Hydrogenophaga palleronii (98·5 %) and Hydrogenophaga taeniospiralis (98·0 %). The fatty acid patterns and substrate-utilization profiles displayed similarity to the those of the five Hydrogenophaga species with validly published names, although clear differentiating characteristics were also observed. The two strains showed DNA–DNA hybridization values of 51 % with respect to each other. No close similarities to any other Hydrogenophaga species were detected in hybridization experiments with the genomic DNAs. On the basis of these results, two novel Hydrogenophaga species, Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov. are proposed, with BSB 9.5T (=DSM 15341T=CIP 108119T) and BSB 41.8T (=DSM 15342T=CIP 108118T) as the respective type strains.
Lactobacillus rossii sp. nov., isolated from wheat sourdough
Authors: Corsetti Aldo , Settanni Luca , van Sinderen Douwe , Felis Giovanna E. , Dellaglio Franco , Gobbetti Marco
Published: January 2005

Screening of sourdough lactic acid bacteria for bacteriocin production resulted in the isolation of a Gram-positive, catalase-negative, non-spore-forming, non-motile rod bacterium (strain CS1T) that could not be associated with any previously described species. Comparative 16S rRNA gene sequence analysis recognized strain CS1Tas a distinct member of the genusLactobacillus. By a species-specific PCR strategy, five additional strains previously isolated from sourdoughs were found to belong to the same species as strain CS1T, as confirmed by 16S rRNA gene sequence analysis. The closest related species wereLactobacillus durianis,Lactobacillus malefermentansandLactobacillus suebicus, with which strain CS1Tshared 93 % sequence similarity. For a further characterization of strain CS1T, physiological (growth temperature, CO2production, hydrolysis of arginine, isomeric type of lactate, sugar fermentation) and chemotaxonomic (G+C content and peptidoglycan structure) properties were determined. Phenotypic characterization showed that strain CS1Twas a member of the obligately heterofermentative group of the genusLactobacillus. The DNA G+C content was 44·6 mol%. The peptidoglycan was of the A3α(l-lys–l-ser–l-Ala2) type. Physiological, biochemical and genotypic data, as well as results of DNA–DNA hybridization of genomic DNA with one of the closest phylogenetic relatives,L. durianis(34·3 %), indicated that strain CS1Trepresents a novel species of the genusLactobacillusfor which the nameLactobacillus rossiisp. nov. is proposed. The type strain of this species is CS1T(=ATCC BAA-822T=DSM 15814T).
Lactobacillus gastricus sp. nov., Lactobacillus antri sp. nov., Lactobacillus kalixensis sp. nov. and Lactobacillus ultunensis sp. nov., isolated from human stomach mucosa
Authors: Roos Stefan , Engstrand Lars , Jonsson Hans
Published: January 2005

In an attempt to study the composition of the Lactobacillus flora from mucosa of human stomach, 16S rRNA gene sequences of 129 isolates were analysed. For 15 of these, the results differed significantly from known sequences, and additional tests were performed to determine whether these isolates represented as yet unrecognized species. Phenotypic and genetic characteristics revealed that these isolates represented four novel Lactobacillus species. Two belong to the Lactobacillus reuteri and the other two to the Lactobacillus delbrueckii subgroup of Lactobacillus. The names Lactobacillus gastricus sp. nov., Lactobacillus antri sp. nov., Lactobacillus kalixensis sp. nov. and Lactobacillus ultunensis sp. nov. are proposed, with the respective type strains Kx156A7T (=LMG 22113T=DSM 16045T=CCUG 48454T), Kx146A4T (=LMG 22111T=DSM 16041T=CCUG 48456T), Kx127A2T (=LMG 22115T=DSM 16043T=CCUG 48459T) and Kx146C1T (=LMG 22117T=DSM 16047T=CCUG 48460T).
Psychrobacter alimentarius sp. nov., isolated from squid jeotgal, a traditional Korean fermented seafood
Authors: Yoon Jung-Hoon , Yeo Soo-Hwan , Oh Tae-Kwang , Park Yong-Ha
Published: January 2005

Two Gram-negative, non-motile, non-spore-forming, moderately halophilic strains, JG-100Tand JG-102, were isolated from squid jeotgal, a traditional Korean fermented seafood. The two strains grew optimally at 30 °C and in the presence of 2–3 % (v/w) NaCl. Strains JG-100Tand JG-102 were characterized chemotaxonomically; they both had ubiquinone-8 as the predominant respiratory lipoquinone and C18 : 1ω9cas the major fatty acid. Their DNA G+C content was 44 mol%. Strains JG-100Tand JG-102 showed 1 bp difference in their 16S rRNA gene sequences and a mean DNA–DNA relatedness level of 88 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains JG-100Tand JG-102 form a distinct phylogenetic lineage within the cluster comprisingPsychrobacterspecies. The 16S rRNA gene sequences of strains JG-100Tand JG-102 had similarity levels of 95·2–98·4 % to sequences of the type strains of recognizedPsychrobacterspecies. Levels of DNA–DNA relatedness between strains JG-100Tand JG-102 and the type strains of some phylogenetically relatedPsychrobacterspecies were 6–24 %. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains JG-100Tand JG-102 should be placed in the genusPsychrobacteras a novel species, for which the namePsychrobacter alimentariussp. nov. (type strain, JG-100T=KCTC 12186T=DSM 16065T) is proposed.
Shewanella decolorationis sp. nov., a dye-decolorizing bacterium isolated from activated sludge of a waste-water treatment plant
Authors: Xu Meiying , Guo Jun , Cen Yinghua , Zhong Xiaoyan , Cao Wei , Sun Guoping
Published: January 2005

A highly efficient dye-decolorizing bacterium, strain S12T, was isolated from activated sludge of a textile-printing waste-water treatment plant in Guangzhou, China. The cells were Gram-negative and motile by means of a single polar flagellum. The strain was capable of anaerobic growth either by fermentation of glucose or by anaerobic respiration and utilized a variety of electron acceptors, including nitrate, iron oxide and thiosulfate. The physiological properties, tested by using the Biolog GN2 system, were similar to those of the genus ofShewanella. Analysis of the nearly complete 16S rRNA gene sequence of strain S12Tshowed the highest similarity (98 and 97 %, respectively) toShewanella balticaandShewanella putrefaciens. However, the level ofgyrBsimilarity between strain S12TandS. putrefacienswas 87 %. DNA from strain S12Tshowed 41·8 and 41·9 % DNA relatedness, respectively, to the DNA ofS. balticaDSM 9439TandS. putrefaciensDSM 6067T. The DNA G+C content of strain S12Twas 49·3 mol%. The predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The dominant fatty acids were 15 : 0, 16 : 0, iso-15 : 0 and 16 : 1ω7c, similar to the profiles of otherShewanellaspecies. On the basis of its physiological and molecular properties, strain S12Tappears to represent a novel species of the genusShewanella, for which the nameShewanella decolorationissp. nov. is proposed. The type strain is S12T(=CCTCC M 203093T=IAM 15094T).
Tenuibacillus multivorans gen. nov., sp. nov., a moderately halophilic bacterium isolated from saline soil in Xin-Jiang, China
Authors: Ren Pei-Gen , Zhou Pei-Jin
Published: January 2005

Two Gram-positive, rod-shaped, spore-forming and moderately halophilic bacteria (strains 28-1T, 28-4), isolated from a soil sample from a neutral salt lake in Xin-Jiang, China, were characterized polyphasically. On the basis offasta(ungapped) analyses of 16S rRNA gene sequences, strains 28-1Tand 28-4 were shown to belong to theBacillaceaeand to be closely related toFilobacillus milensisDSM 13259T(97·0 %) andBacillus haloalkaliphilusDSM 5271T(95·7 %). 16S rRNA gene sequence similarity with other recognized species was not more than 94·1 %. Phylogenetic, chemotaxonomic, physiological and biochemical data supported the differentiation of these novel strains fromF. milensisandB. haloalkaliphilus. Therefore these two previously unidentified strains are considered to represent a new genus and species, for which the nameTenuibacillus multivoransgen. nov., sp. nov. is proposed. The type strain is 28-1T(=AS 1.3442T=NBRC 100370T).
Geotrichum silvicola sp. nov., a novel asexual arthroconidial yeast species related to the genus Galactomyces
Authors: Pimenta Raphael S. , Alves Priscila D. D. , Corrêa Ary , Lachance Marc-André , Prasad G. S. , Rajaram  , Sinha B. R. R. P. , Rosa Carlos A.
Published: January 2005

Four strains of an asexual arthroconidial yeast species were isolated from Drosophila flies in two Atlantic rain forest sites in Brazil and two strains from oak tasar silkworm larvae (Antheraea proylei) in India. Analysis of the sequences of the D1/D2 large subunit rRNA gene showed that this yeast represented a novel species of the genus Geotrichum, described as Geotrichum silvicola sp. nov. The novel species was related to the ascogenous genus Galactomyces. The closest relatives of Geotrichum silvicola were Galactomyces sp. strain NRRL Y-6418 and Galactomyces geotrichum. The type culture of Geotrichum silvicola is UFMG-354-2T (=CBS 9194T=NRRL Y-27641T).
Nocardia takedensis sp. nov., isolated from moat sediment and scumming activated sludge
Authors: Yamamura Hideki , Hayakawa Masayuki , Nakagawa Youji , Tamura Tomohiko , Kohno Tetsuro , Komatsu Fumio , Iimura Yuzuru
Published: January 2005

Chemotaxonomic and morphological characterization of two actinomycete strains, MS1-3T and AS4-2, respectively isolated from moat sediment and scumming activated sludge, was carried out. This characterization clearly demonstrated that strains MS1-3T and AS4-2 belong to the genus Nocardia. 16S rRNA gene sequencing studies showed that these isolates are most closely related to Nocardia beijingensis (98·1–98·3 % similarity), Nocardia brasiliensis (97·9–98·0 %) and Nocardia tenerifensis (97·8–97·9 %). However, the results of DNA–DNA hybridizations and physiological and biochemical tests showed that strains MS1-3T and AS4-2 could be differentiated from their closest phylogenetic relatives both genotypically and phenotypically. It is proposed that the two isolates be classified as representatives of a novel species of Nocardia, Nocardia takedensis sp. nov. The type strain is MS1-3T (=NBRC 100417T=DSM 44801T); AS4-2 (=NBRC 100418=DSM 44802) is a reference strain.
Sphingopyxis flavimaris sp. nov., isolated from sea water of the Yellow Sea in Korea
Authors: Yoon Jung-Hoon , Oh Tae-Kwang
Published: January 2005

A Gram-negative, motile, yellow-pigmented, slightly halophilic bacterial strain, SW-151T, was isolated from sea water of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. The isolate grew optimally at 30 °C and in the presence of 2–3 % NaCl. Strain SW-151Twas characterized chemotaxonomically as having Q-10 as the predominant respiratory lipoquinone and C18 : 1ω7c, C16 : 1ω7cand/or iso-C15 : 02-OH and C17 : 1ω6cas the major fatty acids. Sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids. The DNA G+C content was 58 mol%. 16S rRNA gene sequence analysis showed that strain SW-151Tjoins the evolutionary radiation enclosed by the genusSphingopyxis. Similarities between the 16S rRNA gene sequences of strain SW-151Tand the type strains ofSphingopyxisspecies ranged from 92·3 to 94·3 %, which is low enough to categorize strain SW-151Tas a species distinct from previously describedSphingopyxisspecies. On the basis of phenotypic properties and phylogenetic distinctiveness, strain SW-151T(=KCTC 12232T=DSM 16223T) should be classified as a novelSphingopyxisspecies, for which the nameSphingopyxis flavimarissp. nov. is proposed.
Marinilactibacillus piezotolerans sp. nov., a novel marine lactic acid bacterium isolated from deep sub-seafloor sediment of the Nankai Trough
Authors: Toffin Laurent , Zink Klaus , Kato Chiaki , Pignet Patricia , Bidault Adeline , Bienvenu Nadège , Birrien Jean-Louis , Prieur Daniel
Published: January 2005

A piezotolerant, mesophilic, marine lactic acid bacterium (strain LT20T) was isolated from a deep sub-seafloor sediment core collected at Nankai Trough, off the coast of Japan. Cells were Gram-positive, rod-shaped, non-sporulating and non-motile. The NaCl concentration range for growth was 0–120 g l−1, with the optimum at 10–20 g l−1. The temperature range for growth at pH 7·0 was 4–50 °C, with the optimum at 37–40 °C. The optimum pH for growth was 7·0–8·0. The optimum pressure for growth was 0·1 MPa with tolerance up to 30 MPa. The main cellular phospholipids were phosphatidylglycerols (25 %), diphosphatidylglycerols (34 %) and a group of compounds tentatively identified as ammonium-containing phosphatidylserines (32 %); phosphatidylethanolamines (9 %) were minor components. The fatty acid composition was dominated by side chains of 16 : 0, 14 : 0 and 16 : 1. The G+C content of the genomic DNA was 42 mol%. On the basis of 16S rRNA gene sequence analysis and the secondary structure of the V6 region, this organism was found to belong to the genusMarinilactibacillusand was closely related toMarinilactibacillus psychrotoleransM13-2T(99 %),Marinilactibacillussp. strain MJYP.25.24 (99 %) andAlkalibacterium olivapovliticusstrain ww2-SN4C (97 %). Despite the high similarity between their 16S rRNA gene sequences (99 %), the DNA–DNA hybridization levels were less than 20 %. On the basis of physiological and genetic characteristics, it is proposed that this organism be classified as a novel species,Marinilactibacillus piezotoleranssp. nov. The type strain is LT20T(=DSM 16108T=JCM 12337T).
Citricoccus alkalitolerans sp. nov., a novel actinobacterium isolated from a desert soil in Egypt
Authors: Li Wen-Jun , Chen Hua-Hong , Zhang Yu-Qin , Kim Chang-Jin , Park Dong-Jin , Lee Jae-Chan , Xu Li-Hua , Jiang Cheng-Lin
Published: January 2005

An actinobacterium, strain YIM 70010T, which was isolated from a desert soil sample collected in Egypt, was subjected to a polyphasic taxonomy study. The organism was alkalitolerant and its optimum growth occurred at pH 8·0–9·0. The isolate contained chemotaxonomic markers that were characteristic of the genusCitricoccus, i.e. the peptidoglycan type Lys–Gly–Glu (variation A4α), the predominant menaquinone MK-9(H2) and a polar lipid profile consisting of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unknown glycolipids. The major fatty acids were anteiso-C15 : 0and iso-C15 : 0. The G+C content of the genomic DNA was 63·8 mol%. Strain YIM 70010Texhibited a 16S rRNA gene sequence similarity of 99·6 % and DNA–DNA relatedness value of 56 % withCitricoccus muralisDSM 14442T. The phenotypic characteristics and DNA–DNA relatedness data indicate that strain YIM 70010Tcan be distinguished fromC. muralis(DSM 14442T). Therefore, on the basis of the polyphasic taxonomic data presented, a novel species of the genusCitricoccus,Citricoccus alkalitoleranssp. nov. (type strain, YIM 70010T=CCTCC AA 203008T=DSM 15665T=KCTC 19012T) is proposed.
Transfer of the misnamed [Alysiella] sp. IAM 14971 (=ATCC 29468) to the genus Moraxella as Moraxella oblonga sp. nov.
Authors: Xie Cheng-Hui , Yokota Akira
Published: January 2005

Phylogenetic analysis based on 16S rRNA gene sequences revealed that [Alysiella] sp. IAM 14971 (=ATCC 29468) is closely related to the genus Moraxella of the γ-Proteobacteria (96–97 % similarity). The newly obtained phenotypic data also indicate that [Alysiella] sp. IAM 14971 is distinct from the genus Alysiella and similar to the genus Moraxella. On the basis of these results, the strain should be classified in the genus Moraxella, as Moraxella oblonga sp. nov. The type strain is IAM 14971T (=ATCC 29468T).
Pibocella ponti gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi
Authors: Nedashkovskaya Olga I. , Kim Seung Bum , Lee Kang Hyun , Bae Kyung Sook , Frolova Galina M. , Mikhailov Valery V. , Kim In Seop
Published: January 2005

A marine, heterotrophic, Gram-negative, aerobic, yellow-pigmented, bacterium that was motile by gliding, isolated from the green algaAcrosiphonia sonderi, was studied by polyphasic taxonomic methods. 16S rRNA gene sequence analysis indicated that strain KMM 6031Tformed a distinct lineage within the familyFlavobacteriaceae. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses, the novel bacterium was classified asPibocella pontigen. nov., sp. nov. The type strain is KMM 6031T(=KCTC 12262T=NBRC 100591T=LMG 22573T).
Gillisia mitskevichiae sp. nov., a novel bacterium of the family Flavobacteriaceae, isolated from sea water
Authors: Nedashkovskaya Olga I. , Kim Seung Bum , Lee Kang Hyun , Mikhailov Valery V. , Bae Kyung Sook
Published: January 2005

The taxonomic position of a novel marine, heterotrophic, aerobic, pigmented bacterium, non-motile by gliding, that was isolated from a sea-water sample collected in the Sea of Japan, was determined. 16S rRNA gene sequence analysis revealed that strain KMM 6034T is a member of the genus Gillisia. The phenotypic and chemotaxonomic data showed that the isolate represents a novel species of the genus Gillisia, for which the name Gillisia mitskevichiae sp. nov. is proposed. The type strain is KMM 6034T (=KCTC 12261T=NBRC 100590T=LMG 22575T).
Advenella incenata gen. nov., sp. nov., a novel member of the Alcaligenaceae, isolated from various clinical samples
Authors: Coenye Tom , Vanlaere Elke , Samyn Emly , Falsen Enevold , Larsson Peter , Vandamme Peter
Published: January 2005

A polyphasic taxonomic study of 14 isolates recovered from various human and veterinary clinical samples was performed. Phenotypically these isolates shared several characteristics with members of the Alcaligenaceae and related genera. Random amplified polymorphic DNA fingerprinting and whole-cell protein analysis suggested the presence of multiple genomic groups, which was confirmed by DNA–DNA hybridization experiments. 16S rRNA gene sequence analysis indicated that these isolates were related to the genera Pelistega, Taylorella, Oligella, Pigmentiphaga, Alcaligenes, Kerstersia, Achromobacter and Bordetella and belonged to the family Alcaligenaceae. Based on the results of the present study the organisms were classified in a novel genus, Advenella gen. nov. This genus comprises one named species, Advenella incenata sp. nov. (type strain LMG 22250T=CCUG 45225T) and five currently unnamed genomic species. The DNA G+C content of members of the novel genus Advenella is between 54·0 and 57·7 mol%.
Sejongia antarctica gen. nov., sp. nov. and Sejongia jeonii sp. nov., isolated from the Antarctic
Authors: Yi Hana , Yoon Ho Il , Chun Jongsik
Published: January 2005

Two yellow-pigmented, Gram-negative and aerobic bacterial strains, designated AT1013T and AT1047T, were isolated from terrestrial samples of the Antarctic. On the basis of 16S rRNA gene sequence analyses, the two Antarctic strains shared 97·7 % sequence similarity and showed moderate relationships to the genera Chryseobacterium (92·5–95·3 %), Riemerella (92·3–93·5 %), Bergeyella (92·5–92·6 %) and Kaistella (92·5–93·3 %). In phylogenetic analyses, the two isolates formed a robust monophyletic clade and represented a distinct phyletic line that equated to novel generic status. Cells were non-motile, non-gliding and psychrotolerant with an optimum growth temperature of about 20 °C. Flexirubins were absent. The major isoprenoid quinone was MK-6. The predominant cellular fatty acids were 15 : 0 iso, 15 : 0 anteiso and 17 : 1 iso ω9c. DNA G+C contents were 34–36 mol%. The two isolates shared low genomic relatedness (27 %) and were differentiated from each other by several phenotypic characteristics. The polyphasic data presented in this study indicated that these isolates should be recognized as two separate novel species in a novel genus within the family Flavobacteriaceae. The name Sejongia gen. nov. is therefore proposed for the Antarctic isolates, with the type species Sejongia antarctica sp. nov. (type strain AT1013T=IMSNU 14040T=KCTC 12225T=JCM 12381T) and Sejongia jeonii sp. nov. (type strain AT1047T=IMSNU 14049T=KCTC 12226T=JCM 12382T).
Thalassobacter stenotrophicus gen. nov., sp. nov., a novel marine α-proteobacterium isolated from Mediterranean sea water
Authors: Macián M. C. , Arahal D. R. , Garay E. , Ludwig W. , Schleifer K. H. , Pujalte M. J.
Published: January 2005

A Gram-negative, slightly halophilic, strictly aerobic, chemo-organotrophic bacterium was isolated from Mediterranean sea water near Valencia (Spain). 16S rRNA gene sequence comparisons showed that the isolate represented a separate branch within the α-3 subclass of the Proteobacteria, now included within the order ‘Rhodobacterales’. Jannaschia helgolandensis was the closest relative, but their low sequence similarity and other features indicated that they were not related at the genus level. Isolate 5SM22T produced bacteriochlorophyll a and grew on solid media as regular salmon-pink colonies. Cells are motile rods, with polar flagella. The DNA G+C content is 59·1 mol%. Morphological, physiological and genotypic differences from related, thus far known genera support the description of Thalassobacter stenotrophicus gen. nov., sp. nov. with strain 5SM22T (=CECT 5294T=DSM 16310T) as the type strain.
Nesterenkonia sandarakina sp. nov. and Nesterenkonia lutea sp. nov., novel actinobacteria, and emended description of the genus Nesterenkonia
Authors: Li Wen-Jun , Chen Hua-Hong , Kim Chang-Jin , Zhang Yu-Qin , Park Dong-Jin , Lee Jae-Chan , Xu Li-Hua , Jiang Cheng-Lin
Published: January 2005

Two novel actinobacteria isolates, designated YIM 70009Tand YIM 70081T, were characterized in order to determine their taxonomic position. Cells of strains YIM 70009Tand YIM 70081Twere cocci, although only the latter were motile. The G+C contents of their DNAs were 64·0 and 64·5 mol%, respectively. On the basis of chemotaxonomic characteristics and 16S rRNA gene sequence analysis, the two isolates were classified in the genusNesterenkonia. DNA–DNA hybridization and comparison of phenotypic characteristics revealed that strains YIM 70009Tand YIM 70081Tdiffered from each other and from known species. Therefore, it is proposed that they represent two separate novel species of the genusNesterenkonia:Nesterenkonia sandarakinasp. nov. (type strain, YIM 70009T=CCTCC AA 203007T=DSM 15664T=KCTC 19011T) andNesterenkonia luteasp. nov. (type strain, YIM 70081T=CCTCC AA 203010T=DSM 15666T=KCTC 19013T).
Planococcus stackebrandtii sp. nov., isolated from a cold desert of the Himalayas, India
Authors: Mayilraj S. , Prasad G. S. , Suresh K. , Saini H. S. , Shivaji S. , Chakrabarti T.
Published: January 2005

The taxonomic position of a bacterium isolated from a cold desert of the Himalayas, India, was analysed by using a polyphasic approach. The isolated strain, designated K22-03T, had phenotypic characteristics that matched those of the genusPlanococcusand it represents a novel species. The almost-complete 16S rRNA gene sequence (1464 bases) of the novel strain was compared with those of previously studiedPlanococcustype strains and confirmed that the strain belongs to the genusPlanococcus. 16S rRNA gene sequence analysis indicated that strain K22-03Tdiffers from all other species ofPlanococcusby at least 2·5 %. DNA–DNA hybridization showed that it had low genomic relatedness withPlanomicrobium mcmeekinii(MTCC 3704T, 23 %),Planococcus psychrophilus(MTCC 3812T, 61 %),Planococcus antarcticus(MTCC 3854T, 45 %) andPlanomicrobium okeanokoites(MTCC 3703T, 51 %), the four species with which it was most closely related based on 16S rRNA gene sequence analysis (97–97·5 % similarity). Therefore, strain K22-03Tshould be recognized as a novel species, for which the namePlanococcus stackebrandtiisp. nov. is proposed. The type strain is K22-03T(=MTCC 6226T=DSM 16419T=JCM 12481T).
Salegentibacter mishustinae sp. nov., isolated from the sea urchin Strongylocentrotus intermedius
Authors: Nedashkovskaya Olga I. , Kim Seung Bum , Lysenko Anatoly M. , Mikhailov Valery V. , Bae Kyung Sook , Kim In Seop
Published: January 2005

A bacterial strain, designated KMM 6049T, was isolated from the sea urchin Strongylocentrotus intermedius inhabiting the Sea of Japan. The bacterium studied was strictly aerobic, heterotrophic, yellow-pigmented, non-motile, Gram-negative and oxidase-, catalase-, β-galactosidase- and alkaline phosphatase-positive. 16S rRNA gene sequence analysis indicated that strain KMM 3524T was closely related to Salegentibacter holothuriorum and Salegentibacter salegens (sharing 97·7 and 98 % sequence similarity, respectively). DNA–DNA relatedness levels between strains KMM 6049T and S. holothuriorum KMM 3524T and S. salegens DSM 5424T were 24 and 45 %, respectively, indicating that KMM 6049T belongs to a novel species of the genus Salegentibacter, for which the name Salegentibacter mishustinae sp. nov. is proposed. The type strain is KMM 6049T (=KCTC 12263T=LMG 22584T=NBRC 100592T).
Reclassification of strain CCM 132, previously classified as Kocuria varians, as Kocuria carniphila sp. nov.
Authors: Tvrzová Ludmila , Schumann Peter , Sedláček Ivo , Páčová Zdena , Spröer Cathrin , Verbarg Susanne , Kroppenstedt Reiner M.
Published: January 2005

A Gram-positive actinobacterium, previously classified as Kocuria varians, was subjected to a polyphasic taxonomic study. The bacterium showed the peptidoglycan type Lys–Ala3 (variation A3α), MK-7(H2) was the major menaquinone and anteiso-C15 : 0 and anteiso-C17 : 0 were the major fatty acids. On the basis of the phylogenetic and phenotypic characteristics of the actinobacterium, a novel species, Kocuria carniphila sp. nov. (type strain, CCM 132T=DSM 16004T), is proposed.
Pontibacillus chungwhensis gen. nov., sp. nov., a moderately halophilic Gram-positive bacterium from a solar saltern in Korea
Authors: Lim Jee-Min , Jeon Che Ok , Song Sung Min , Kim Chang-Jin
Published: January 2005

Three moderately halophilic, spore-forming strains, designated BH030062T, BH030049 and BH030080, were isolated from a solar saltern in Korea. Phylogenetic analyses and comparative 16S rRNA gene sequence studies revealed that the isolates represent a novel distinct monophyletic lineage within the phyletic group classically defined as the genusBacillusand are most closely related to members of the generaGracilibacillus(93·7–95·1 % similarity),Virgibacillus(93·5–94·8 %),Halobacillus(94·8–95·9 %),Filobacillus(94·4–94·8 %) andLentibacillus(93·3–93·7 %). Strain BH030062Twas strictly aerobic, rod-shaped, Gram-positive and motile by means of peritrichous flagella. It grew in the presence of 1–15 % (w/v) NaCl and at temperatures of 15–45 °C. The cell wall peptidoglycan contained A1γ-meso-diaminopimelic acid as the diagnostic diamino acid. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0and iso-C16 : 0. DNA G+C content was about 41 mol% and the major isoprenoid quinone was MK-7. On the basis of their physiological and molecular properties, the isolates represent a new genus,Pontibacillusgen. nov., and novel species,Pontibacillus chungwhensissp. nov. The type strain is BH030062T(=KCTC 3890T=DSM 16287T).
Methylobacterium hispanicum sp. nov. and Methylobacterium aquaticum sp. nov., isolated from drinking water
Authors: Gallego Virginia , García María Teresa , Ventosa Antonio
Published: January 2005

Members of the genusMethylobacteriumare ubiquitous in nature and can be isolated from almost any freshwater environment where dissolved oxygen exists. This genus is composed of a variety of pink-pigmented, facultatively methylotrophic (PPFM) bacteria. During a screening programme to monitor the bacterial population present in the drinking water of a municipal water supply in Seville (Spain) during the year 2003, five strains of PPFM bacteria were isolated and characterized. Analysis of their complete 16S rRNA gene sequences revealed that they constituted two separate phylogenetic groups (strains GP34Tand GR18, and strains GR16T, GP22 and GP32, respectively) showing highest similarity to members of the genusMethylobacterium. The highest 16S rRNA sequence similarities of strain GP34Twere found with respect to the type strains ofMethylobacterium radiotolerans(96·6 %) andMethylobacterium fujisawaense(96·4 %) and the highest 16S rRNA sequence similarities of strain GR16Twere to the type strains ofMethylobacterium extorquens(96·0 %) andMethylobacterium rhodesianum(95·8 %). The G+C content of their DNA ranged from 66·5 to 67·8 mol%. DNA–DNA hybridization studies confirmed that they constituted two separate genospecies. On the basis of this phenotypic, phylogenetic and genotypic study, two novel species of the genusMethylobacteriumare proposed:Methylobacterium hispanicumsp. nov., with type strain GP34T(CECT 5997T=CCM 7219T=DSM 16372T=CIP 108332T), andMethylobacterium aquaticumsp. nov., with type strain GR16T(CECT 5998T=CCM 7218T=DSM 16371T=CIP 108333T).
Multilocus sequence phylogenetic study of the genus Haemophilus with description of Haemophilus pittmaniae sp. nov.
Authors: Nørskov-Lauritsen Niels , Bruun Brita , Kilian Mogens
Published: January 2005

The phylogeny of human isolates of Haemophilus species was estimated based on partial sequences of four separate housekeeping genes. The clustering of each set of sequences was in accordance with speciation of the strains with few exceptions: of 108 gene fragments examined, only three appeared to have been subject to recombination events across the species barrier. Housekeeping gene similarity supported previous DNA–DNA hybridization data for the genus rather than the phylogeny inferred from 16S rRNA gene sequence comparison. The similarity of sequences of Haemophilus parainfluenzae with those of Haemophilus influenzae suggested preservation of the former species in the genus Haemophilus. Three strains representing a novel taxon were unique with respect to the four investigated gene loci. 16S rRNA gene sequence analysis suggested that this taxon belonged to the Parainfluenzae cluster. DNA–DNA hybridization data supported this generic placement. Nine strains of the novel taxon were available for analysis. They were distinct from representatives of all current species of the genus Haemophilus by conventional phenotypic characterization. Genotypic and phenotypic data show that the strains merit recognition as a novel species of Haemophilus. The name Haemophilus pittmaniae sp. nov. is proposed, with HK 85T (=CCUG 48703T=NCTC 13334T) as the type strain.
Silanimonas lenta gen. nov., sp. nov., a slightly thermophilic and alkaliphilic gammaproteobacterium isolated from a hot spring
Authors: Lee Eun Mi , Jeon Che Ok , Choi Inpyo , Chang Kyu-Seob , Kim Chang-Jin
Published: January 2005

A moderately thermophilic aerobic bacterium, strain 25-4T, was isolated from a hot spring at Baekdoo Mountain in Korea. The cells were Gram-negative, motile rods each having a polar flagellum. Analysis of the 16S rRNA gene sequence indicated that the strain represented a new lineage within the family ‘Xanthomonadaceae’ of the ‘Gammaproteobacteria’, being most closely related to the generaThermomonas,Xanthomonas,Luteimonas,Pseudoxanthomonas,StenotrophomonasandXylellaand having 16S rRNA gene sequence similarities to the most related species of the genera of between 92·9 and 94·4 %. The strain contained Q-8 as the major isoprenoid quinone and had a fatty acid profile with predominant iso-branched fatty acids. Growth occurred at pH 6·0–10, with an optimum at pH 9·0, and at 25–53 °C, with an optimum at 47 °C. The G+C content of the genomic DNA was 50·7 mol%. On the basis of phylogenetic analyses and its phenotypic characteristics, strain 25-4Tbelongs to a new genus,Silanimonasgen. nov., within the ‘Gammaproteobacteria’. The sole species of this genus isSilanimonas lentasp. nov. (type strain, 25-4T=DSM 16282T=KCTC 12236T).
Lebetimonas acidiphila gen. nov., sp. nov., a novel thermophilic, acidophilic, hydrogen-oxidizing chemolithoautotroph within the ‘Epsilonproteobacteria’, isolated from a deep-sea hydrothermal fumarole in the Mariana Arc
Authors: Takai Ken , Hirayama Hisako , Nakagawa Tatsunori , Suzuki Yohey , Nealson Kenneth H. , Horikoshi Koki
Published: January 2005

A novel thermophilic, acidophilic bacterium, designated strain Pd55T, was isolated from a self-temperature-recordingin situcolonization system deployed in a hydrothermal diffusing flow (maximum temperature of 78 °C) at the TOTO caldera in the Mariana Arc. Cells of strain Pd55Twere motile, short rods with a single polar flagellum. Growth was observed between 30 and 68 °C (optimum growth at 50 °C; 120 min doubling time) and between (initial) pH 4·2 and 7·0 (optimum at pH 5·2). The isolate was a strictly anaerobic chemolithoautotroph capable of using molecular hydrogen as sole energy source and carbon dioxide as sole carbon source. Elemental sulfur served as the sole electron acceptor to support growth. The G+C content of the genomic DNA was 34·0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate was related to members of the generaNautiliaandCaminibacter, although it appeared to be a novel lineage prior to the divergence betweenNautiliaandCaminibacter. Strain Pd55Tcould also be differentiated fromNautiliaandCaminibacterspecies on the basis of its physiological properties. It is, therefore, proposed that strain Pd55T(=JCM 12420T=DSM 16356T) represents the type strain of a novel species in a new genus,Lebetimonas acidiphilagen. nov., sp. nov.