bluuebunny/crossref_metadata_2025 huggingface dataset:
Tumour–host interactions: implications for developing anti-cancer therapies
Authors: Gadea Bedrick B. , Joyce Johanna A.
Published: December 2006

Cancers are a complex set of proliferative diseases that arise in most cases through multi-step pathways involving an accumulation of genetic and epigenetic changes. These steps include inactivation of tumour suppressor genes and activation of oncogenes. However, in addition to genetic mutations in the tumour cells themselves, the local host environment can act as a critical modulator of cancer progression, having either tumour-suppressive or tumour-promoting effects depending on the stage and site of cancer development. Because stromal cells can have these opposing functions during cancer development and progression, a recurring theme throughout this review will be that of balance: maintaining the normal functions of these co-opted cells, yet selectively inhibiting their pro-tumourigenic functions. To achieve this equilibrium, we need to understand the molecular mechanisms by which normal cells become modified by cancer cells before we can hope to target these functions selectively. Here, we will discuss recent efforts to address these key challenges and offer perspectives on the translation of discoveries made in model systems to the clinic.
Mechanisms of serpin dysfunction in disease
Authors: Kaiserman Dion , Whisstock James C. , Bird Phillip I.
Published: December 2006

The serpin superfamily encompasses hundreds of proteins, spread across all kingdoms of life, linked by a common tertiary fold. This review focuses on five diseases caused by serpin dysfunction: variants of antithrombin III lose their ability to interact with heparin; the α1-antitrypsin Pittsburgh mutation causes a change in target proteinase; the α1-antitrypsin Z mutation and neuroserpin, polymerisation of which lead to cellular cytotoxicity; and a loss of maspin expression resulting in cancer.
Organic field-effect inversion-mode transistors and single-component complementary inverters on charged electrets
Authors: Huang Cheng , Katz Howard E. , West James E.
Published: December 2006

We demonstrate that the electrostatic polarization of an organic semiconductor (OSC) by a gate dielectric with stored charges and electric fields enables the realization of both threshold voltage tuning and inversion process control of OSC thin-film field-effect transistors (OFETs). As a result, OFETs based on typically unipolar n-channel copper hexadecafluorophthalocyanine semiconductor thin films, deposited on a silicon dioxide quasipermanent charged electret as a gate insulator, show unipolar p-channel “inversion” operation in ambient air and form complementary monolithic, single-semiconductor inverter circuits. The field produced by patterned, grid-controlled negative corona charging and subsequent thermal annealing (before semiconductor deposition) electrostatically induces sufficient positive charges to provide significant hole mobility, ca. 0.011cm2V−1s−1, in response to moderate additional negative gate voltages.
Influence of layer microstructure on the double nucleation process in Cu∕Mg multilayers
Authors: Gonzalez-Silveira M. , Rodriguez-Viejo J. , Garcia G. , Pi F. , Ager F. J. , Lábár J. L. , Barna A. , Menyhárd M. , Kótis L.
Published: December 2006

We have investigated by differential scanning calorimetry the thermal evolution of Cu∕Mg multilayers with different modulation lengths, ranging from 7∕28to30∕120nm. The Cu and Mg layers were grown by sequential evaporation in an electron beam deposition system. The phase identification and layer microstructure were determined by cross-section transmission electron microscopy, Rutherford backscattering, and scanning electron microscopy with focused ion beam for sample preparation. Upon heating, the intermetallic CuMg2 forms at the interfaces until coalescence is reached and thickens through a diffusion-limited process. Cross-section transmission electron microscopy observations show a distinct microstructure at the top and bottom of the as-prepared Mg layers, while no significant differences were seen in the Cu layers. We show that this effect is responsible for the observed asymmetry in the nucleation process between the Cu on Mg and the Mg on Cu interfaces. By modeling the calorimetric data we determine the role of both interfaces in the nucleation and lateral growth stages. We also show that vertical growth proceeds by grain development of the product phase, increasing significantly the roughness of the interfaces.
From nanowires to nanoislands: Morphological evolutions of erbium silicide nanostructures formed on the vicinal Si(001) surface
Authors: Zhu Yan , Zhou Wei , Wang Shuhua , Ji Ting , Hou Xiaoyuan , Cai Qun
Published: December 2006

The growth behavior and morphology evolution of erbium silicide nanostructures are studied on the vicinal Si(001) surface with a 4° miscut angle towards the [110] direction as the functions of annealing temperature, annealing time, and Er coverage. Three kinds of nanostructures can be observed on the surface: nanowires, rectangular nanoislands and square nanoislands. The experimental results reveal that nanowires in AlB2-type structure and the nanoislands in ThSi2-type structure can be formed at 600–650 and 700–750°C, respectively. At the final growth stage, the nanowires of erbium silicide undergo Ostwald ripening. At high coverage of two monolayers, many AlB2-type nanoislands will appear in a rectangular shape on the sample surface. According to the AlB2-type crystalline structure of ErSi2 and the scanning tunneling microscopy results obtained on the flat and vicinal substrate surfaces, a model is suggested to describe the ErSi2∕Si(001) interfacial structure. This model explains the spatial orientation relationship between erbium silicide nanowire and Si dimer row, and is consistent with Er-induced (2×3) reconstruction at the initial stage of Er growth on the Si(001) surface.
Handel at Drury Lane: Ballad Opera and the Production of Kitty Clive
Authors: Joncus Berta
Published: December 2006

Handel's music was a key source for Drury Lane entertainments from 1728 to 1745. Ballad-opera writers regularly deployed Handel tunes, generating multiple performances of his music in low-style, native works that long preceded his oratorios. The soprano Kitty Clive, the biggest star of this genre, initially performed Handel airs both in ballad operas and as additional songs. From 1737, Handel compositions helped bolster Clive's ‘high-style’ reputation, while Handel benefited from Clive's audience-drawing power. In its politics, narratives and musical forms, the design of music Handel composed for Clive shows him adhering closely to the soprano's already established star persona.
In the ‘Twilight Zone’: Beethoven's Unfinished Piano Trio in F Minor
Authors: Marston Nicholas
Published: December 2006

Although it has long been known that Beethoven began composing a piano trio in F minor in 1816, scholarly examination of the extant sources for this unfinished project has only recently progressed beyond Nottebohm's brief remarks in the 1880s. The present article reveals the existence of numerous new sources evidently unknown to Nottebohm, including a leaf which forms the continuation of the draft score (Concept) of the first movement, the principal source for the trio. (Transcriptions of this score, including the new continuation, and of a newly identified draft which preceded it, accompany the article.) The trio project is contextualized in relation to other compositions, in particular the String Quartet in F minor, op. 95, the ‘Archduke’ Trio and the Piano Sonata in A, op. 101, and an attempt is made to understand the failure of the trio project in relation to Beethoven's limited compositional activity at this much-discussed point in his career.
Streptomyces turgidiscabies and Streptomyces reticuliscabiei: one genomic species, two pathogenic groups
Authors: Bouchek-Mechiche K. , Gardan L. , Andrivon D. , Normand P.
Published: December 2006

Three strains ofStreptomyces reticuliscabieiand two strains ofStreptomyces turgidiscabieswere analysed, together with reference and type strains of otherStreptomycesspecies, for phenotypic traits, DNA–DNA relatedness, comparison of 16S rRNA gene sequences and presence of necrotic protein gene (nec1) homologues in order to clarify their phylogenetic relationships. A numerical analysis of phenotypic characteristics showed thatS. reticuliscabieiandS. turgidiscabiesbelong to the same cluster and share almost all morphological and biochemical traits that are important in the identification ofStreptomycesspecies. DNA–DNA hybridization and phylogenetic comparisons of 16S rRNA gene sequences confirmed that the two species are genomically closely related. In contrast, pathological data showed thatS. turgidiscabiesandS. reticuliscabieicause two distinct diseases. Gene homologues ofnec1were detected inS. turgidiscabiesand other common scab species (Streptomyces scabiei,Streptomyces europaeiscabieiandStreptomyces stelliscabiei), but not inS. reticuliscabiei. To avoid confusion between agents causing separate diseases, it is proposed that the existing distinct species names are retained:S. turgidiscabiesinvolved in common scab andS. reticuliscabieiinvolved in netted scab.
Desulfosporosinus lacus sp. nov., a sulfate-reducing bacterium isolated from pristine freshwater lake sediments
Authors: Ramamoorthy S. , Sass H. , Langner H. , Schumann P. , Kroppenstedt R. M. , Spring S. , Overmann J. , Rosenzweig R. F.
Published: December 2006

A novel sulfate-reducing bacterium was isolated from pristine sediments of Lake Stechlin, Germany. This strain, STP12T, was found to contain predominantlyc-type cytochromes and to reduce sulfate, sulfite and thiosulfate using lactate as an electron donor. Although STP12Tcould not utilize elemental sulfur as an electron acceptor, it could support growth by dissimilatory Fe(III) reduction. In a comparison of 16S rRNA gene sequences, STP12Twas 96.7 % similar toDesulfosporosinus auripigmentiDSM 13351T, 96.5 % similar toDesulfosporosinus meridieiDSM 13257Tand 96.4 % similar toDesulfosporosinus orientisDSM 765T. DNA–DNA hybridization experiments revealed that strain STP12Tshows only 32 % reassociation with the type strain of the type species of the genus,D. orientisDSM 765T. These data, considered in conjunction with strain-specific differences in heavy metal tolerance, cell-wall chemotaxonomy and riboprint patterns, support recognition of strain STP12T(=DSM 15449T=JCM 12239T) as the type strain of a distinct and novel species within the genusDesulfosporosinus,Desulfosporosinus lacussp. nov.
Genetic relationships of Aeromonas strains inferred from 16S rRNA, gyrB and rpoB gene sequences
Authors: Küpfer Mara , Kuhnert Peter , Korczak Bożena M. , Peduzzi Raffaele , Demarta Antonella
Published: December 2006

Genetic relationships among bacterial strains belonging to the genusAeromonaswere inferred from 16S rRNA,gyrBandrpoBgene sequences. Twenty-eight type or collection strains of the recognized species or subspecies and 33Aeromonasstrains isolated from human and animal specimens as well as from environmental samples were included in the study. As reported previously, the 16S rRNA gene sequence is highly conserved within the genusAeromonas, having only limited resolution for this very tight group of species. Analysis of a 1.1 kbgyrBsequence confirmed that this gene has high resolving power, with maximal interspecies divergence of 15.2 %. Similar results were obtained by sequencing only 517 bp of therpoBgene, which showed maximal interspecies divergence of 13 %. The topologies of thegyrB- andrpoB-derived trees were similar. The results confirm the close relationship of species within the genusAeromonasand show that a phylogenetic approach including several genes is suitable for improving the complicated taxonomy of the genus.
Desulfurobacterium atlanticum sp. nov., Desulfurobacterium pacificum sp. nov. and Thermovibrio guaymasensis sp. nov., three thermophilic members of the Desulfurobacteriaceae fam. nov., a deep branching lineage within the Bacteria
Authors: L'Haridon S. , Reysenbach A.-L. , Tindall B. J. , Schönheit P. , Banta A. , Johnsen U. , Schumann P. , Gambacorta A. , Stackebrandt E. , Jeanthon C.
Published: December 2006

Three thermophilic, anaerobic, strictly chemolithoautotrophic, sulphur- and/or thiosulphate-reducing bacteria, designated SL17T, SL19Tand SL22T, were isolated from deep-sea hydrothermal samples collected at 13 °N (East Pacific Rise), Guaymas Basin (Gulf of California) and 23 °N (Mid-Atlantic Ridge), respectively. These strains differed in their morphology, temperature range and optimum for growth, energy substrates and 16S rRNA gene sequences. The G+C content of the genomic DNA was 41 mol% (SL22T), 42 mol% (SL17T) and 46 mol% (SL19T). Comparative analysis of phenotypic and phylogenetic traits indicated that strains SL17Tand SL22Trepresented two novel species of the genusDesulfurobacteriumand that strain SL19Tshould be considered as a novel species of the genusThermovibrio. The namesDesulfurobacterium pacificumsp. nov. (type strain SL17T=DSM 15522T=JCM 12127T),Desulfurobacterium atlanticumsp. nov. (type strain SL22T=DSM 15668T=JCM 12129T) andThermovibrio guaymasensissp. nov. (type strain SL19T=DSM 15521T=JCM 12128T) are proposed for these organisms. Furthermore, phylogenetic data based on 16S rRNA gene sequence analyses correlated with the significant phenotypic differences between members of the lineage encompassing the generaDesulfurobacterium,ThermovibrioandBalneariumand that of the familiesAquificaceaeandHydrogenothermaceae. It is therefore proposed that this lineage represents a new family,Desulfurobacteriaceaefam. nov., within the orderAquificales.
Erwinia tasmaniensis sp. nov., a non-phytopathogenic bacterium from apple and pear trees
Authors: Geider Klaus , Auling Georg , Du Zhiqiang , Jakovljevic Vladimir , Jock Susanne , Völksch Beate
Published: December 2006

Bacteria were isolated from flowers and bark of apple and pear trees at three places in Australia. In Victoria, Tasmania and Queensland, strains with white colonies on nutrient agar were screened for dome-shaped colony morphology on agar with sucrose and were found to be closely related by several criteria. The isolates were not pathogenic on apples or pears. They were characterized by a polyphasic approach including microbiological and API assays as well as fatty acid methyl ester analysis, DNA–DNA hybridization and DNA sequencing. For molecular classification, the 16S rRNA cistron and the conserved genes gpd and recA of these bacteria were investigated. Together with other taxonomic criteria, the results of these studies indicate that the bacteria belong to a novel separate species, which we propose to name Erwinia tasmaniensis sp. nov., with the type strain Et1/99T (=DSM 17950T=NCPPB 4357T). From DNA–DNA hybridization kinetics, microbiological characteristics and nucleotide sequence analyses, this species is related to pathogenic Erwinia species, but also to the epiphytic species Erwinia billingiae.
Bacillus taeanensis sp. nov., a halophilic Gram-positive bacterium from a solar saltern in Korea
Authors: Lim Jee-Min , Jeon Che Ok , Kim Chang-Jin
Published: December 2006

A halophilic bacterium, strain BH030017T, showing optimum growth at 2–5 % (w/v) NaCl was isolated from solar-saltern sediment from the Tae-An area of Korea and was characterized taxonomically. The cells of strain BH030017T were Gram-positive, motile, short rods containing cell-wall peptidoglycan based on meso-diaminopimelic acid. The major cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C content was 36 mol% and the predominant lipoquinone was MK-7. The major cellular phospholipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BH030017T formed a cluster with Bacillus clarkii DSM 8720T and Bacillus agaradhaerens DSM 8721T within the family Bacillaceae. 16S rRNA gene sequence similarities with respect to closely related type strains were less than 95.1 %. On the basis of its phylogenetic, phenotypic and chemotaxonomic properties, strain BH030017T represents a novel species within the genus Bacillus, for which the name Bacillus taeanensis sp. nov. is proposed. The type strain is BH030017T (=KCTC 3918T=DSM 16466T).
Methylotenera mobilis gen. nov., sp. nov., an obligately methylamine-utilizing bacterium within the family Methylophilaceae
Authors: Kalyuzhnaya Marina G. , Bowerman Sarah , Lara Jimmie C. , Lidstrom Mary E. , Chistoserdova Ludmila
Published: December 2006

A novel obligate methylamine utilizer (strain JLW8T), isolated from Lake Washington sediment, was characterized taxonomically. The isolate was an aerobic, Gram-negative bacterium. Cells were rod-shaped and motile by means of a single flagellum. Reproduction was by binary fission and no resting bodies were formed. Growth was observed within a pH range of 5–8.5, with optimum growth at pH 7.5. It utilized methylamine as a single source of energy, carbon and nitrogen. Methylamine was oxidized via methylamine dehydrogenase and formaldehyde was assimilated via the ribulose monophosphate cycle. The cellular fatty acid profile was dominated by C16 : 0
ω7c and C16 : 0 and the major phospholipid was phosphatidylethanolamine. The DNA G+C content was 54 mol%. 16S rRNA gene sequence analysis indicated that the new isolate was closely related (97–98 % similarity) to a broad group of sequences from uncultured or uncharacterized Betaproteobacteria, but only distantly related (93–96 % similarity) to known methylotrophs of the family Methylophilaceae. Strain JLW8T (=ATCC BAA-1282T=DSM 17540T) is proposed as the type strain of a novel species in a new genus within the family Methylophilaceae, Methylotenera mobilis gen. nov., sp. nov.
Mechercharimyces mesophilus gen. nov., sp. nov. and Mechercharimyces asporophorigenens sp. nov., antitumour substance-producing marine bacteria, and description of Thermoactinomycetaceae fam. nov.
Authors: Matsuo Yoshihide , Katsuta Atsuko , Matsuda Satoru , Shizuri Yoshikazu , Yokota Akira , Kasai Hiroaki
Published: December 2006

A study was carried out to clarify the taxonomy of four Gram-positive, heterotrophic mesophiles isolated from marine lakes in the Republic of Palau. The strains, designated YM3-251T, YM3-653, YM3-671 and YM11-542T, formed aerial and substrate mycelia. The cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine. The G+C content of their genomic DNA was approximately 45 mol%. The major fatty acid was iso-C15 : 0 and the major isoprenoid quinone was MK-9. The strains formed a distinct group in the 16S rRNA gene tree and shared a range of phenotypic properties that distinguished them from members of related genera in Thermoactinomycetaceae fam. nov. The name proposed to accommodate the new isolates is Mechercharimyces gen. nov., comprising two species based on genotypic and phenotypic criteria, including comparative gyrB and DNA–DNA relatedness data. The names proposed for these taxa are Mechercharimyces mesophilus sp. nov., the type species, and Mechercharimyces asporophorigenens sp. nov., with the type strains YM3-251T (=MBIC06230T=DSM 44894T) and YM11-542T (=MBIC06487T=DSM 44955T), respectively.
Analysis of bifidobacterial evolution using a multilocus approach
Authors: Ventura Marco , Canchaya Carlos , Casale Antonio Del , Dellaglio Franco , Neviani Erasmo , Fitzgerald Gerald F. , van Sinderen Douwe
Published: December 2006

Bifidobacteria represent one of the most numerous groups of bacteria found in the gastrointestinal tract of humans and animals. In man, gastrointestinal bifidobacteria are associated with health effects and for this reason they are often used as functional ingredients in food and pharmaceutical products. Such applications may benefit from or require a clear and reliable bifidobacterial species identification. The increasing number of available bacterial genome sequences has provided a large amount of housekeeping gene sequences that can be used both for identification of bifidobacterial species as well as for understanding bifidobacterial evolution. In order to assess their relative positions in the evolutionary process, fragments from seven conserved genes, clpC, dnaB, dnaG, dnaJ1, purF, rpoC and xfp, were sequenced from each of the currently described type strains of the genus Bifidobacterium. The results demonstrate that the concatenation of these seven gene sequences for phylogenetic purposes allows a significant increase in the discriminatory power between taxa.
Brevundimonas terrae sp. nov., isolated from an alkaline soil in Korea
Authors: Yoon Jung-Hoon , Kang So-Jung , Lee Jung-Sook , Oh Tae-Kwang
Published: December 2006

A Gram-negative, rod-shaped,Brevundimonas-like bacterial strain, KSL-145T, was isolated from an alkaline soil in Korea and subjected to a polyphasic taxonomic investigation. Strain KSL-145Tgrew optimally at pH 7.5–8.0 and 30 °C without NaCl. It was characterized chemotaxonomically as containing Q-10 as the predominant ubiquinone and C18 : 1ω7cand C16 : 0as the major fatty acids. The DNA G+C content was 61.8 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain KSL-145Tfell within the radiation of the cluster comprisingBrevundimonasspecies andMycoplana bullata. The levels of 16S rRNA gene sequence similarity between strain KSL-145Tand the type strains ofBrevundimonasspecies andM. bullataranged from 95.3 to 98.7 %. The mean DNA–DNA relatedness values between strain KSL-145Tand the type strains ofBrevundimonas diminutaandM. bullata, the closest phylogenetic relatives, were 26 and 15 %, respectively. Strain KSL-145Tcould be differentiated fromBrevundimonasspecies andM. bullataby differences in several phenotypic characteristics. On the basis of the phenotypic, phylogenetic and genetic data, strain KSL-145Trepresents a novel species in the genusBrevundimonas, for which the nameBrevundimonas terraesp. nov. is proposed. The type strain is KSL-145T(=KCTC 12481T=JCM 13476T).
New insight into diversity in the genus Xenorhabdus, including the description of ten novel species
Authors: Tailliez Patrick , Pagès Sylvie , Ginibre Nadège , Boemare Noël
Published: December 2006

We investigated the diversity of a collection of 76Xenorhabdusstrains, isolated from at least 27 species ofSteinernemanematodes and collected in 32 countries, using three complementary approaches: 16S rRNA gene sequencing, molecular typing and phenotypic characterization. The 16S rRNA gene sequences of theXenorhabdusstrains were highly conserved (similarity coefficient >95 %), suggesting that the common ancestor of the genus probably emerged between 250 and 500 million years ago. Based on comparisons of the 16S rRNA gene sequences, we identified 13 groups and seven unique sequences. This classification was confirmed by analysis of molecular typing profiles of the strains, leading to the classification of new isolates into theXenorhabdusspecies described previously and the description of ten novelXenorhabdusspecies:Xenorhabdus cabanillasiisp. nov. (type strain USTX62T=CIP 109066T=DSM 17905T),Xenorhabdus doucetiaesp. nov. (type strain FRM16T=CIP 109074T=DSM 17909T),Xenorhabdus griffiniaesp. nov. (type strain ID10T=CIP 109073T=DSM 17911T),Xenorhabdus hominickiisp. nov. (type strain KE01T=CIP 109072T=DSM 17903T),Xenorhabdus koppenhoeferisp. nov. (type strain USNJ01T=CIP 109199T=DSM 18168T),Xenorhabdus kozodoiisp. nov. (type strain SaVT=CIP 109068T=DSM 17907T),Xenorhabdus mauleoniisp. nov. (type strain VC01T=CIP 109075T=DSM 17908T),Xenorhabdus miraniensissp. nov. (type strain Q1T=CIP 109069T=DSM 17902T),Xenorhabdus romaniisp. nov. (type strain PR06-AT=CIP 109070T=DSM 17910T) andXenorhabdus stockiaesp. nov. (type strain TH01T=CIP 109067T=DSM 17904T). TheXenorhabdusstrains studied here had very similar phenotypic patterns, but phenotypic features nonetheless differentiated the following species:X. bovienii,X. cabanillasii,X. hominickii,X. kozodoii,X. nematophila,X. poinariiandX. szentirmaii. Based on phenotypic analysis, we identified two major groups of strains. Phenotypic group GAcomprised strains able to grow at temperatures of 35–42 °C, whereas phenotypic group GBcomprised strains that grew at temperatures below 35 °C, suggesting that someXenorhabdusspecies may be adapted to tropical or temperate regions and/or influenced by the growth and development temperature of their nematode host.
Desulfitibacter alkalitolerans gen. nov., sp. nov., an anaerobic, alkalitolerant, sulfite-reducing bacterium isolated from a district heating plant
Authors: Nielsen Marie Bank , Kjeldsen Kasper Urup , Ingvorsen Kjeld
Published: December 2006

A novel alkalitolerant, anaerobic bacterium, designated strain sk.kt5T, was isolated from a metal coupon retrieved from a corrosion-monitoring reactor of a Danish district heating plant (Skanderborg, Jutland). The cells of strain sk.kt5Twere motile, rod-shaped (0.4–0.6×2.5–9.6 μm), stained Gram-positive and formed endospores. Strain sk.kt5Tgrew at pH 7.6–10.5 (with optimum growth at pH 8.0–9.5), at temperatures in the range 23–44 °C (with optimum growth at 35–37 °C), at NaCl concentrations in the range 0–5 % (w/v) (with optimum growth at 0–0.5 %) and required yeast extract for growth. Only a limited number of substrates were utilized as electron donors, including betaine, formate, lactate, methanol, choline and pyruvate. Elemental sulfur, sulfite, thiosulfate, nitrate and nitrite, but not sulfate or Fe(III) citrate, were used as electron acceptors. The G+C content of the DNA was 41.6 mol%. Phylogenetic analyses of the sequence data for thedsrABgenes [encoding the major subunits of dissimilatory (bi)sulfite reductase] and the 16S rRNA gene placed strain sk.kt5Twithin a novel lineage in the classClostridiaof the phylumFirmicutes. Taken together, the physiological and genotypic data suggest that strain sk.kt5Trepresents a novel species within a novel genus, for which the nameDesulfitibacter alkalitoleransgen. nov., sp. nov. is proposed. The type strain ofDesulfitibacter alkalitoleransis sk.kt5T(=JCM 12761T=DSM 16504T).
Citreimonas salinaria gen. nov., sp. nov., a member of the Roseobacter clade isolated from a solar saltern
Authors: Choi Dong H. , Cho Byung C.
Published: December 2006

A lemon-shaped marine bacterium, strain CL-SP20T, isolated from hypersaline water from a solar saltern in Korea, was characterized in terms of its physiological and biochemical features, its fatty acid profile and its phylogenetic position based on 16S rRNA gene sequences. Analysis of the 16S rRNA gene sequence revealed a clear affiliation with the Roseobacter lineage (91.0–96.3 % similarity) of the family Rhodobacteraceae. However, strain CL-SP20T did not form a robust clade with any species of the Roseobacter clade, forming a distinct subline. Strain CL-SP20T is non-motile and forms beige colonies on marine agar. The strain is able to grow with sea salts at concentrations in the range 1–10 %, with optimal growth between 5 and 6 %. It grows at temperatures in the range 15–40 °C and at pH 6–10. The strain cannot oxidize thiosulfate. The fatty acids are dominated by 18 : 1ω7c (54.3 %) and 19 : 0 cyclo ω8c (20.4 %). The DNA G+C content is 67.3 mol%. According to the physiological data, fatty acid composition and phylogenetic analysis of the 16S rRNA gene sequence, strain CL-SP20T represents a novel species in a novel genus of the family Rhodobacteraceae, for which the name Citreimonas salinaria gen. nov., sp. nov. is proposed. The type strain of Citreimonas salinaria is CL-SP20T (=KCCM 42116T=JCM 13036T).
Variovorax soli sp. nov., isolated from greenhouse soil
Authors: Kim Byung-Yong , Weon Hang-Yeon , Yoo Seung-Hee , Lee Seon-Young , Kwon Soon-Wo , Go Seung-Joo , Stackebrandt Erko
Published: December 2006

A Gram-negative, rod-shaped, non-spore-forming bacterium, strain GH9-3T, isolated from greenhouse soil, was investigated in a polyphasic study. The novel organism grew at 10–35 °C, 0–3 % NaCl and pH 5–9. It had ubiquinone 8 (Q-8) as the predominant isoprenoid quinone and possessed C16 : 0, summed feature 3, C17 : 0 cyclo and C18 : 1
ω7c as the major fatty acids (together representing 87.4 % of the total). The DNA G+C content was 67.1 mol%. 16S rRNA gene sequence analysis of strain GH9-3T showed that it grouped within the Variovorax cluster, with highest sequence similarities to Variovorax paradoxus IAM 12373T (98.3 %) and Variovorax dokdonensis DS-43T (98.0 %). DNA–DNA hybridization values between strain GH9-3T and V. paradoxus DSM 30034T and V. dokdonensis DS-43T were 38 and 29 %, respectively. Based on phenotypic, chemotaxonomic and phylogenetic features, it is proposed that strain GH9-3T represents a novel species of the genus Variovorax with the name Variovorax soli sp. nov. The type strain is GH9-3T (=KACC 11579T=DSM 18216T).
Desulfoglaeba alkanexedens gen. nov., sp. nov., an n-alkane-degrading, sulfate-reducing bacterium
Authors: Davidova Irene A. , Duncan Kathleen E. , Choi Ok Kyoung , Suflita Joseph M.
Published: December 2006

Two novel sulfate-reducing bacteria, strains ALDCTand Lake, which were able to oxidize n-alkanes, were isolated from a naval oily wastewater-storage facility (VA, USA) and from oilfield production water (OK, USA), respectively. The type strain (ALDCT) had a narrow substrate specificity and could grow only with n-alkanes (from C6to C12), pyruvate, butyrate, hexanoic acid and 4-methyloctanoic acid. Cells of strain ALDCTstained Gram-negative and were slightly curved, short rods with oval ends (2.5–3.0×1.0–1.4 μm), often occurring in pairs. Cells tended to form aggregates or large clusters and were non-motile and did not form endospores. Optimum growth occurred between 31 and 37 °C and at pH 6.5–7.2. NaCl was not required for growth, but salt concentrations up to 55 g l−1could be tolerated. The DNA G+C content was 53.6 mol%. Phylogenetic analysis of the 16S rRNA genes revealed that strains ALDCTand Lake were closely related, but not identical (99.9 % similarity). The two strains were not closely related to other known alkane-degrading, sulfate-reducing bacteria or to other genera of theDeltaproteobacteria. Therefore, it is proposed that strain ALDCT(=JCM 13588T=ATCC BAA-1302T) represents the type strain of a novel species and genus, with the nameDesulfoglaeba alkanexedensgen. nov., sp. nov.
Bacillus panaciterrae sp. nov., isolated from soil of a ginseng field
Authors: Ten Leonid N. , Baek Sang-Hoon , Im Wan-Taek , Liu Qing-Mei , Aslam Zubair , Lee Sung-Taik
Published: December 2006

A Gram-positive, non-motile, endospore-forming bacterium, designated Gsoil 1517T, was isolated from soil of a ginseng field in Pocheon Province (South Korea) and was characterized in order to determine its taxonomic position, using a polyphasic approach. It was found to rod-shaped and aerobic or facultatively anaerobic. It grew optimally at 30 °C and at pH 6.5–7.0. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 1517Tforms a distinct phylogenetic lineage within the genusBacillus, being related toBacillus funiculusJCM 11201T(96.8 %). The strain showed less than 94.3 % sequence similarity with otherBacillusspecies. The G+C content of the genomic DNA was found to be 47.8 mol% and the predominant respiratory quinone was MK-7. The major fatty acids were iso-C15 : 0(42.4 %), anteiso-C15 : 0(17.4 %), iso-C14 : 0(9.7 %) and C16 : 0(6.0 %). On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 1517Trepresents a novel species of the genusBacillus, for which the nameBacillus panaciterraesp. nov. is proposed. The type strain is Gsoil 1517T(=KCTC 13929T=CCUG 52470T=LMG 23408T).
Glaciecola chathamensis sp. nov., a novel marine polysaccharide-producing bacterium
Authors: Matsuyama Hidetoshi , Hirabayashi Toshikazu , Kasahara Hirokazu , Minami Hideki , Hoshino Tamotsu , Yumoto Isao
Published: December 2006

Two novel exopolysaccharide-producing bacteria, strains S18K6T and S18K5, were isolated from Pacific Ocean sediment. The isolates were Gram-negative, motile, strictly aerobic chemoheterotrophic bacteria. The DNA G+C contents of strains S18K6T and S18K5 were 44.8 and 46.3 mol%, respectively. DNA–DNA relatedness between the two strains was 70 %. Major fatty acids were hexadecanoic acid (C16 : 0), hexadecenoic acid (C16 : 1
ω7c) and octadecenoic acid (C18 : 1
ω7c). 16S rRNA gene sequence, chemotaxonomic and morphological data indicated that these strains clearly belonged to the genus Glaciecola. Based on phenotypic properties and DNA–DNA hybridization data, strains S18K6T and S18K5 are considered to represent a novel species of the genus Glaciecola, for which the name Glaciecola chathamensis sp. nov. is proposed. The type strain is S18K6T (=JCM 13645T=NCIMB 14146T).
Isoptericola dokdonensis sp. nov., isolated from soil
Authors: Yoon Jung-Hoon , Schumann Peter , Kang So-Jung , Jung Seo-Youn , Oh Tae-Kwang
Published: December 2006

A Gram-positive, non-motile, rod- or coccoid-shapedIsoptericola-like bacterium, strain DS-3T, was isolated from a soil sample from Dokdo, Korea, and its taxonomic position was investigated by a polyphasic approach. The organism grew optimally at 30 °C and pH 7.0–8.0. Strain DS-3Thad the peptidoglycan type based onl-lys–d-Asp, and galactose, glucose, rhamnose and ribose as the whole-cell sugars. It contained MK-9(H4) as the predominant menaquinone and anteiso-C15 : 0and iso-C15 : 0as the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unidentified glycolipids. The DNA G+C content was 74.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-3Twas most closely related to members of the genusIsoptericola. Similarity values between the 16S rRNA gene sequences of strain DS-3Tand the type strains ofIsoptericolaspecies ranged from 98.0 to 98.4 %. DNA–DNA relatedness values (11–23 %) and differential phenotypic properties demonstrated that strain DS-3Twas distinguishable from recognizedIsoptericolaspecies. On the basis of phenotypic properties and phylogenetic and genetic distinctiveness, strain DS-3Trepresents a novel species in the genusIsoptericola, for which the nameIsoptericola dokdonensissp. nov. is proposed. The type strain is DS-3T(=KCTC 19128T=CIP 108921T).
Schlegelella aquatica sp. nov., a novel thermophilic bacterium isolated from a hot spring
Authors: Chou Yi-Ju , Sheu Shih-Yi , Sheu Der-Shyan , Wang Jih-Terng , Chen Wen-Ming
Published: December 2006

A moderately thermophilic bacterial strain designated wcf1T, isolated from a hot spring located in the Tainan area, southern Taiwan, was characterized using a polyphasic approach. The cells were Gram-negative, non-pigmented, rod-shaped, non-spore-forming and motile. Phylogenetic analysis using 16S rRNA gene sequences showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Schlegelella; its only close neighbour was the type strain of Schlegelella thermodepolymerans, K14T (97.8 %). The isolate was clearly distinguishable from other strains using phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics. It was evident from the genotypic and phenotypic data that strain wcf1T represents a novel species in the genus Schlegelella, for which the name Schlegelella aquatica sp. nov. is proposed, with the type strain wcf1T (=BCRC 17557T=LMG 23380T).
Rhodonellum psychrophilum gen. nov., sp. nov., a novel psychrophilic and alkaliphilic bacterium of the phylum Bacteroidetes isolated from Greenland
Authors: Schmidt Mariane , Priemé Anders , Stougaard Peter
Published: December 2006

A novel alkaliphilic and psychrophilic bacterium was isolated from the cold and alkaline ikaite tufa columns of the Ikka Fjord in south-west Greenland. According to 16S rRNA gene sequence analysis, strain GCM71T belonged to the family ‘Flexibacteraceae’ in the phylum Bacteroidetes. Strain GCM71T, together with five related isolates from ikaite columns, formed a separate cluster with 86–93 % gene sequence similarity to their closest relative, Belliella baltica. The G+C content of the DNA from strain GCM71T was 43.1 mol%, whereas that of B. baltica was reported to be 35 mol%. DNA–DNA hybridization between strain GCM71T and B. baltica was 9.5 %. The strain was red pigmented, Gram-negative, strictly aerobic with non-motile, rod-shaped cells. The optimal growth conditions for strain GCM71T were pH 9.2–10.0, 5 °C and 0.6 % NaCl. The fatty acid profile of the novel strain was dominated by branched and unsaturated fatty acids (90–97 %), with a high abundance of iso-C17 : 1
ω9c (17.5 %), iso-C17 : 0 3-OH (17.5 %) and summed feature 3, comprising iso-C15 : 0 2-OH and/or C16 : 1
ω7c (12.6 %). Phylogenetic, chemotaxonomic and physiological characteristics showed that the novel strain could not be affiliated to any known genus. A new genus, Rhodonellum gen. nov., is proposed to accommodate the novel strain. Strain GCM71T (=DSM 17998T=LMG 23454T) is proposed as the type strain of the type species, Rhodonellum psychrophilum sp. nov.
Isolation of aerobic, gliding, xylanolytic and laminarinolytic bacteria from acidic Sphagnum peatlands and emended description of Chitinophaga arvensicola Kämpfer et al. 2006
Authors: Pankratov Timofei A. , Kulichevskaya Irina S. , Liesack Werner , Dedysh Svetlana N.
Published: December 2006

Four aerobic, heterotrophic, yellow-pigmented and flexirubin-producing bacterial strains with gliding motility were isolated from acidic Sphagnum-dominated wetlands of Northern Russia. These bacteria are capable of degrading xylan, laminarin and some other polysaccharides, but not cellulose, pectin or chitin. The four strains possess almost identical 16S rRNA gene sequences and are most closely related (98.9–99.5 % sequence similarity) to the recently reclassified species of the phylum Bacteroidetes, Chitinophaga arvensicola Kämpfer et al. 2006, formerly known as [Cytophaga] arvensicola Oyaizu et al. 1983. However, the novel isolates from Sphagnum peat differed from C. arvensicola DSM 3695T in their ability to degrade xylan and starch, by greater tolerance of acidic pH and by their inability to reduce nitrate. An emended description of this species is proposed.
Runella limosa sp. nov., isolated from activated sludge
Authors: Ryu Seung Hyun , Nguyen Thi Thu Hien , Park Woojun , Kim Chang-Jin , Jeon Che Ok
Published: December 2006

A Gram-negative bacterium, designated strain EMB111T, was isolated from activated sludge performing enhanced biological phosphorus removal in a sequencing batch reactor. Cells were long and rod-shaped. The isolate was strictly aerobic and non-motile. The strain grew optimally at 25–30 °C and pH 7.5–8.0. The predominant fatty acids of strain EMB111Twere iso-C15 : 0, C16 : 1ω5c, iso-C17 : 03-OH, iso-C15 : 03-OH, C16 : 03-OH, C16 : 0and summed feature 3 (C16 : 1ω7cand/or iso-C15 : 02-OH). The strain contained a large amount of phosphatidylglycerol and small amounts of two unknown phospholipids (PL1, PL2) as the polar lipids. The major isoprenoid quinone was menaquinone-7. The G+C content of the genomic DNA was 42.7 mol%. Phylogenetic analysis showed that strain EMB111Tformed a phyletic cluster with members of the genusRunellawithin the familyFlexibacteraceaeand was most closely related toRunella slithyformisATCC 29530Twith a 16S rRNA gene sequence similarity of 94.8 %. On the basis of chemotaxonomic data and molecular properties, strain EMB111Trepresents a novel species within the genusRunella, for which the nameRunella limosasp. nov. is proposed. The type strain is EMB111T(=KCTC 12615T=DSM 17973T).
Paenibacillus cellulosilyticus sp. nov., a cellulolytic and xylanolytic bacterium isolated from the bract phyllosphere of Phoenix dactylifera
Authors: Rivas Raúl , García-Fraile Paula , Mateos Pedro F. , Martínez-Molina Eustoquio , Velázquez Encarna
Published: December 2006

A bacterial strain designated PALXIL08Twas isolated from the phyllosphere ofPhoenix dactyliferabracts. A phylogenetic analysis based on the 16S rRNA gene sequence placed the isolate within the genusPaenibacillusin the same subgroup asPaenibacillus kobensisandPaenibacillus curdlanolyticus(98.9 and 97.9 % sequence similarity, respectively). The DNA hybridization values between the isolate and the type strains ofPaenibacillus kobensisandPaenibacillus curdlanolyticuswere found to be 27.4 and 17.6 %, respectively. The isolate comprised Gram-variable, facultatively anaerobic, motile, sporulating rods. Catalase and oxidase were produced and cellulose, xylan, starch and aesculin were hydrolysed. Many carbohydrates served as carbon sources for growth. MK-7 was the predominant menaquinone, and anteiso-C15 : 0and iso-C16 : 0were the major fatty acids. The DNA G+C content was 51 mol%. DNA relatedness data and the results of phylogenetic and phenotypic analyses showed that strain PALXIL08Tshould be considered as the type strain of a novel species of the genusPaenibacillus, for which the namePaenibacillus cellulosilyticussp. nov. is proposed. The type strain is PALXIL08T(=LMG 22232T=CECT 5696T).
Aureispira marina gen. nov., sp. nov., a gliding, arachidonic acid-containing bacterium isolated from the southern coastline of Thailand
Authors: Hosoya Shoichi , Arunpairojana Vullapa , Suwannachart Chatrudee , Kanjana-Opas Akkharawit , Yokota Akira
Published: December 2006

Three strains of gliding bacteria, 24T, 62 and 71, isolated from a marine sponge and algae from the southern coastline of Thailand, were studied using a polyphasic approach to clarify their taxonomic positions. A phylogenetic analysis based on 16S rRNA gene sequences showed that the three isolates formed a distinct lineage within the family ‘Saprospiraceae’ of the phylum Bacteroidetes and were related to members of the genus Saprospira. The G+C contents of the isolates were in the range 38–39 mol%. The major respiratory quinone was MK-7. The predominant cellular fatty acids were 20 : 4ω6c (arachidonic acid), 16 : 0 and iso-17 : 0. On the basis of morphological, physiological and chemotaxonomic characteristics, together with DNA–DNA hybridization data and 16S rRNA gene sequences, the isolates represent a novel species of a novel genus, for which the name Aureispira marina gen. nov., sp. nov. is proposed. The type strain of Aureispira marina is 24T (=IAM 15389T=TISTR 1719T).
Exiguobacterium indicum sp. nov., a psychrophilic bacterium from the Hamta glacier of the Himalayan mountain ranges of India
Authors: Chaturvedi Preeti , Shivaji S.
Published: December 2006

Strain HHS 31T, a Gram-positive, motile, rod-shaped, non-spore-forming, alkaliphilic bacterium, was isolated from the melt water of a glacier. Phenotypic and chemotaxonomic characteristics indicate that strain HHS 31T is related to species of the genus Exiguobacterium. The 16S rRNA gene sequence similarities between HHS 31T and strains of known species confirm that it is closely related to members of the genus Exiguobacterium (93–99 %) and that it exhibits >97 % similarity with Exiguobacterium acetylicum DSM 20416T (98.9 %), Exiguobacterium antarcticum DSM 14480T (98.0 %), Exiguobacterium oxidotolerans JCM 12280T (97.9 %) and Exiguobacterium undae DSM 14481T (97.4 %). Phylogenetic analysis based on the 16S rRNA gene sequence further confirms the affiliation of HHS 31T with the genus Exiguobacterium. However, the levels of DNA–DNA relatedness between HHS 31T and E. oxidotolerans JCM 12280T, E. acetylicum DSM 20416T, E. undae DSM 14481T and E. antarcticum DSM 14480T are 50, 63, 67 and 28 %, respectively. Strain HHS 31T also differs from these four closely related species in terms of a number of phenotypic traits. The phenotypic, chemotaxonomic and phylogenetic data suggest that HHS 31T merits the status of a novel species, for which the name Exiguobacterium indicum sp. nov. is proposed. The type strain is HHS 31T (=LMG 23471T=IAM 15368T).
Cyclobacterium lianum sp. nov., a marine bacterium isolated from sediment of an oilfield in the South China Sea, and emended description of the genus Cyclobacterium
Authors: Ying Jiao-Yan , Wang Bao-Jun , Yang Su-Sheng , Liu Shuang-Jiang
Published: December 2006

The marine bacterial strain HY9Twas isolated from sediment from the South China Sea. Strain HY9Tis aerobic, heterotrophic and rose-pigmented. The cells are non-motile and curved, i.e. ring-like or horseshoe-shaped. The 16S rRNA gene sequence of strain HY9Twas determined andblastsearches revealed that it possessed significant sequence similarities with respect toCyclobacteriumspecies (92.8–93.6 %). Phylogenetic analysis confirmed that strain HY9Twas tightly clustered with members of the genusCyclobacterium. The cellular morphology and chemotaxonomic and phenotypic properties of strain HY9Tshowed that it should be classified as a member of the genusCyclobacterium. Significant evolutionary distances and a range of phenotypic features distinguished strain HY9Tfrom previously describedCyclobacteriumspecies. Hence, strain HY9Trepresents a novel species in the genusCyclobacterium, for which the nameCyclobacterium lianumsp. nov. is proposed. The type strain is HY9T(=CGMCC 1.6102T=JCM 14011T). On the basis of this study and previously described properties ofCyclobacteriumspecies, an emended description of the genusCyclobacteriumis proposed.
Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum
Authors: Lan Pham Thi Ngoc , Sakamoto Mitsuo , Sakata Shinji , Benno Yoshimi
Published: December 2006

Eight bacterial strains isolated from the caecum of chicken, BL2T, BL66, EG3, EG6, M27, BL78T, C35Tand C43, were characterized by determining their phenotypic characteristics, cellular fatty acid profiles, menaquinone profiles and phylogenetic positions based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that these isolates belonged to the genusBacteroides. One group of five strains (BL2T, BL66, EG3, EG6 and M27) was related most closely toBacteroides coprocolaJCM 12979T, with approximately 93 % 16S rRNA gene sequence similarity, and toBacteroides plebeiusJCM 12973T, with about 92 % similarity, and shared ⩾99.6 % similarity with each other. Strain BL78Texhibited 90.5 % similarity toB. plebeiusJCM 12973Tand 89.8 % similarity toB. coprocolaJCM 12979Tand differed from the above group of five strains at ⩾10 % sequence divergence. Strains C35Tand C43 were related most closely toBacteroides eggerthiiJCM 12986T, with 95.1 % sequence similarity, toBacteroides stercorisJCM 9496T, with 94.6 % similarity, and toBacteroides uniformisJCM 5828T, with 94.4 % similarity, and shared 100 % similarity with each other. From results of phenotypic examination, cellular fatty acid composition analysis, menaquinone composition analysis and DNA G+C contents, the group of five strains as well as strain BL78Twere shown to differ from the type strains ofB. coprocolaandB. plebeius. Strain BL78Tdiffered from the others based on its menaquinone composition, which included MK-11 and MK-12. Strains C35Tand C43 could also be differentiated from the type strains ofB. eggerthii,B. stercorisandB. uniformis. The group of five strains, strain BL78T,B. coprocolaJCM 12979TandB. plebeiusJCM 12973Tshowed low levels of DNA–DNA relatedness (<35 %) with each other. High levels of DNA–DNA relatedness were obtained within the group of five strains (>75 %). Strains C35Tand C43 exhibited a high level of DNA–DNA relatedness (>88 %) with each other, but low levels withB. eggerthiiJCM 12986T(<40 %),B. stercorisJCM 9496T(<37 %) andB. uniformisJCM 5828T(<16 %). On the basis of these data, three novelBacteroidesspecies are proposed:Bacteroides barnesiaesp. nov. (type strain BL2T=JCM 13652T=DSM 18169T),Bacteroides salanitronissp. nov. (type strain BL78T=JCM 13657T=DSM 18170T) andBacteroides gallinarumsp. nov. (type strain C35T=JCM 13658T=DSM 18171T).