bluuebunny/crossref_metadata_2025 huggingface dataset:
Streptomyces scabrisporus sp. nov.
Authors: Ping Xu , Takahashi Yōko , Seino Akio , Iwai Yuzuru , Ōmura Satoshi
Published: March 2004

The taxonomic position was determined for a soil actinomycete, isolate KM-4927T, that produced the antibiotic hitachimycin. The strain was assigned to the genus Streptomyces on the basis of 16S rDNA analysis, where it formed a separate clade. The strain is characterized by grey aerial cell mass, spiral spore chains and a rugose spore surface, menaquinones of the MK-9(H4, H2, H6) types and cell-wall chemotype I. DNA–DNA reassociation with 21 phylogenetically neighbouring Streptomyces type strains showing similar morphological characteristics to strain KM-4927T indicated that this isolate is only moderately related to other Streptomyces species. On the basis of genomic and physiological properties, the novel species Streptomyces scabrisporus sp. nov. is proposed; the type strain is strain KM-4927T (=JCM 11712T=NRRL B-24202T).
Isolation from oil reservoirs of novel thermophilic anaerobes phylogenetically related to Thermoanaerobacter subterraneus: reassignment of T. subterraneus, Thermoanaerobacter yonseiensis, Thermoanaerobacter tengcongensis and Carboxydibrachium pacificum to Caldanaerobacter subterraneus gen. nov., sp. nov., comb. nov. as four novel subspecies
Authors: Fardeau Marie-Laure , Salinas Monica Bonilla , L'Haridon Stéphane , Jeanthon Christian , Verhé Frédéric , Cayol Jean-Luc , Patel Bharat K. C. , Garcia Jean-Louis , Ollivier Bernard
Published: March 2004

Novel thermophilic, anaerobic, Gram-positive, rod-shaped bacteria, strains SL9 and OCA1, were isolated from oilfields in France and Australia, respectively. Both strains, together with Thermoanaerobacter yonseiensis KB-1T (=DSM 13777T), Thermoanaerobacter tengcongensis MB4T (=DSM 15242T) and Carboxydibrachium pacificum JMT (=DSM 12653T), possessed genomic (DNA–DNA hybridization studies) and phylogenetic similarities with Thermoanaerobacter subterraneus SEBR 7858T (=DSM 13054T), which was isolated recently from an oilfield reservoir in south-west France. Marked phenotypic differences exist between the three oilfield isolates (T. subterraneus, strain OCA1 and strain SL9): they include temperature range for growth and substrates used. Differences were also observed in the DNA G+C contents of all organisms. Similarly to T. subterraneus, strains SL9 and OCA1, and also T. yonseiensis, T. tengcongensis and Carboxydibrachium pacificum, produced acetate and l-alanine as major end products of glucose metabolism [0·8–1·0 mol l-alanine produced (mol glucose consumed)−1] and reduced thiosulfate, but not sulfate, to sulfide. Because of these significant metabolic and phylogenetic differences between the oilfield isolates (T. subterraneus, strain OCA1 and strain SL9), T. yonseiensis, T. tengcongensis and Carboxydibrachium pacificum and other Thermoanaerobacter species, it is proposed to reassign them as a novel genus and species, Caldanaerobacter subterraneus gen. nov., sp. nov., comb. nov., with the creation of four novel subspecies, Caldanaerobacter subterraneus subsp. subterraneus subsp. nov., comb. nov., Caldanaerobacter subterraneus subsp. yonseiensis subsp. nov., comb. nov., Caldanaerobacter subterraneus subsp. tengcongensis subsp. nov., comb. nov. and Caldanaerobacter subterraneus subsp. pacificus subsp. nov., comb. nov.
Shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in Korea
Authors: Yoon Jung-Hoon , Kang Kook Hee , Oh Tae-Kwang , Park Yong-Ha
Published: March 2004

A Gram-negative, motile, non-spore-forming, rod-shaped strain, TF-27T (=KCCM 41648T=JCM 11814T), was isolated from a tidal flat in Korea. This organism grew well at 25–35 °C, with optimum growth at 30 °C. Strain TF-27T grew optimally in the presence of 2 % NaCl; it did not grow without NaCl or in the presence of >8 % NaCl. Strain TF-27T simultaneously contained both menaquinones and ubiquinones as isoprenoid quinones. The predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The major fatty acids in strain TF-27T were iso-C15 : 0 (20·6 %) and iso-C15 : 0 2-OH and/or C16 : 1
ω7c (21·1 %). The DNA G+C content of strain TF-27T was 42 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-27T falls within the radiation of the cluster that is encompassed by the genus Shewanella. Levels of 16S rDNA sequence similarity between strain TF-27T and the type strains of Shewanella species were 93·2–96·8 %. On the basis of phenotypic properties and phylogenetic data, strain TF-27T should be placed in the genus Shewanella as a novel species, for which the name Shewanella gaetbuli sp. nov. is proposed.
Polyphyly of true branching cyanobacteria (Stigonematales)
Authors: Gugger Muriel F. , Hoffmann Lucien
Published: March 2004

Cyanobacteria with true branching are classified in Subsection V (formerly order Stigonematales) in the phylumCyanobacteria. They exhibit a high degree of morphological complexity and are known from particular biotopes. Only a few stigonematalean morphotypes have been cultured, and therefore the high variability of morphotypes found in nature is under-represented in culture. Axenic cultures ofChlorogloeopsisandFischerella sensuRippkaet al. were, to date, the only representatives of this Subsection in phylogenetic studies. The 16S rDNA sequence analysis data in this report confirm that heterocyst-forming cyanobacteria are a monophyletic group. However, unlike previous studies have suggested, these 16S rDNA data on new Stigonematales strains show that the true branching cyanobacteria are polyphyletic and can be separated into at least two major groups defined by their branching type, the first group being characterized by T-branching and the second group by Y-branching. Cyanobacteria with intercalary heterocysts and either no branching or false-branching also formed separate clusters. In consequence, our phylogenetic data do not correlate with the bacteriological and traditional classifications, which distinguish filamentous heterocystous cyanobacteria with or without true branching (Nostocales/Stigonematales).
Rhodococcus gordoniae sp. nov., an actinomycete isolated from clinical material and phenol-contaminated soil
Authors: Jones Amanda L. , Brown June M. , Mishra Vachaspati , Perry John D. , Steigerwalt Arnold G. , Goodfellow Michael
Published: March 2004

The taxonomic relationships of two actinomycetes provisionally assigned to the genusRhodococcuswere determined using a polyphasic taxonomic approach. The generic assignment was confirmed by 16S rRNA gene similarity data, as the organisms, strains MTCC 1534 and W 4937T, were shown to belong to theRhodococcus rhodochroussubclade. These organisms had phenotypic properties typical of rhodococci; they were aerobic, Gram-positive, weakly acid-fast actinomycetes that showed an elementary branching-rod–coccus growth cycle and containedmeso-diaminopimelic acid, arabinose and galactose in whole-organism hydrolysates,N-glycolated muramic acid residues, dehydrogenated menaquinones with eight isoprene units as the predominant isoprenologue and mycolic acids that co-migrated with those extracted from the type strain ofR. rhodochrous. The strains had identical phenotypic profiles and belong to the same genomic species, albeit one distinguished fromRhodococcus pyridinivorans, with which they formed a distinct phyletic line. They were also distinguished from representatives of all of the species classified in theR. rhodochrous16S rRNA gene tree using a set of phenotypic features. The genotypic and phenotypic data show that the strains merit recognition as a novel species ofRhodococcus. The name proposed isRhodococcus gordoniaesp. nov., with the type strain W 4937T(=DSM 44689T=NCTC 13296T).
Deinococcus indicus sp. nov., an arsenic-resistant bacterium from an aquifer in West Bengal, India
Authors: Suresh K. , Reddy G. S. N. , Sengupta S. , Shivaji S.
Published: March 2004

An arsenic- and radiation-resistant bacterium, strain Wt/1aT, was isolated from water from an arsenic-contaminated aquifer located in the Chakdah district of West Bengal, India. The bacterium stains Gram-negative and is rod-shaped, non-motile, non-sporulating and red-pigmented. Cell-wall peptidoglycan contains ornithine as the diamino acid, MK-8 is the major menaquinone, C15 : 1and C16 : 1are the major fatty acids and the DNA G+C content of the organism is 65·8 mol%. Based on these phenotypic and chemotaxonomic characteristics, strain Wt/1aTwas identified as a member of the genusDeinococcus. Strain Wt/1aTexhibited maximum 16S rRNA gene sequence similarity (95 %) withDeinococcus grandis; however, strain Wt/1aTexhibited only 14 % similarity toD. grandisIAM 13005Tat the DNA–DNA level. Furthermore, strain Wt/1aT(compared toD. grandisIAM 13005T) is more resistant to arsenate and arsenite, is positive for arginine dihydrolase, utilizes a number of carbon sources and exhibits quantitative differences in fatty acid composition and qualitative differences in lipid composition. Strain Wt/1aTis identified as a novel species of the genusDeinococcus, for which the nameDeinococcus indicussp. nov. is proposed. The type strain ofDeinococcus indicusis Wt/1aT(=MTCC 4913T=DSM 15307T).
Genetic evidence that Weissella kimchii Choi et al. 2002 is a later heterotypic synonym of Weissella cibaria Björkroth et al. 2002
Authors: Ennahar Saïd , Cai Yimin
Published: March 2004

The taxonomic positions ofWeissella kimchiiandWeissella cibariawere examined using phenotypic tests, 16S rRNA gene sequencing and DNA–DNA hybridization. The two species displayed very similar sugar-fermentation patterns and produced thed-form of lactic acid. Phylogenetic analysis showed thatW. cibariais the closest neighbour ofW. kimchii, sharing about 99·7 % similarity in the 16S rRNA gene sequence. DNA–DNA hybridization experiments further reinforced these results, demonstrating a 98·2 % reassociation level betweenW. cibariaLMG 17699TandW. kimchiiDSM 14295T. On the other hand, strain RO5, an isolate from paddy rice silage, exhibited 99·4 % 16S rRNA gene sequence similarity and a DNA reassociation level of more than 97 % with both type strains. Therefore, it is proposed that the speciesW. kimchiishould be reclassified asW. cibaria.
Aeromonas simiae sp. nov., isolated from monkey faeces
Authors: Harf-Monteil Colette , Flèche Anne Le , Riegel Philippe , Prévost Gilles , Bermond Delphine , Grimont Patrick A. D. , Monteil Henri
Published: March 2004

TwoAeromonasstrains, IBS S6874Tand IBS S6652, were isolated from the faeces of two healthy monkeys (Macaca fascicularis) from Mauritius that were kept in quarantine in the Centre for Primatology, Strasbourg, France. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two isolates formed an unknown genetic lineage within the genusAeromonas. The two isolates had nearly identical sequences (0·1 % nucleotide substitution) that were related closely to those of recognizedAeromonasspecies (1·7–3·5 % nucleotide substitution). DNA–DNA hybridization showed that strains IBS S6874Tand IBS S6652 had high DNA–DNA similarity (89 %) to each other and a low level of DNA–DNA similarity to closely related taxa (18 % relatedness toAeromonas trotaand 16 % relatedness toAeromonas schubertii). Phenotypically, the two monkey isolates differed from most previously described mesophilicAeromonasspecies by their lack of haemolysis on sheep-blood agar and inability to produce indole, gas from glucose or acid from mannitol. They differed from the most closely related species,A. schubertii, by their ability to produce acid fromd-cellobiose andd-sucrose and by their pyrazinamidase activity. The nameAeromonas simiaesp. nov. is proposed for these isolates; strain IBS S6874T(=CIP 107798T=CCUG 47378T) is the type strain.
Nocardia inohanensis sp. nov., Nocardia yamanashiensis sp. nov. and Nocardia niigatensis sp. nov., isolated from clinical specimens
Authors: Kageyama Akiko , Yazawa Katsukiyo , Nishimura Kazuko , Mikami Yuzuru
Published: March 2004

Comparative 16S rDNA studies on six strains of actinomycete isolated from clinical specimens revealed that they belong to the genus Nocardia and are closely related to Nocardia seriolae, Nocardia otitidiscaviarum, Nocardia uniformis, Nocardia pseudobrasiliensis and Nocardia crassostreae. However, the novel organisms consistently formed a clade distinct from that of the five latter species. Determination of DNA–DNA relatedness indicated that these strains could be classified under three novel species. Based on their phenotypic and phylogenetic characters, three novel species of the genus Nocardia are established: Nocardia inohanensis sp. nov. for IFM 0092T (=NBRC 100128T=JCM 11891T=DSM 44667T), Nocardia yamanashiensis sp. nov. for IFM 0265T (=NBRC 100130T=JCM 11893T=DSM 44669T) and Nocardia niigatensis sp. nov. for IFM 0330T (=NBRC 100131T=JCM 11894T=DSM 44670T), IFM 0260, IFM 0636 and IFM 0833.
Aestuariibacter salexigens gen. nov., sp. nov. and Aestuariibacter halophilus sp. nov., isolated from tidal flat sediment, and emended description of Alteromonas macleodii
Authors: Yi Hana , Bae Kyung Sook , Chun Jongsik
Published: March 2004

Two strictly aerobic, halophilic strains of the γ-Proteobacteria, designated JC2042T and JC2043T, were obtained from a sediment sample of getbol, the Korean tidal flat. Comparative 16S rDNA sequence studies revealed that the test strains were related most closely to the type strains of the genera Alteromonas (93·5–95·5 %) and Glaciecola (91·1–93·3 %). Phylogenetic analyses demonstrated that strains JC2042T and JC2043T formed a distinct monophyletic clade within the family Alteromonadaceae and clustered distantly with the genera Alteromonas and Glaciecola. Physiological, biochemical and chemotaxonomic data also indicated that the two getbol isolates were significantly different from members of these two genera and others with validly published names. Cells were rod-shaped and motile with a polar flagellum. The major isoprenoid quinone was Q8. The predominant cellular fatty acids were C16 : 0, C18 : 1
ω7c and a mixture of C16 : 1
ω7c and iso-C15 : 0 2-OH. DNA G+C contents were 48–54 mol%. On the basis of this polyphasic study, Aestuariibacter gen. nov. is proposed with two novel species, Aestuariibacter salexigens sp. nov. (type strain, JC2042T=IMSNU 14006T=KCTC 12042T=DSM 15300T) and Aestuariibacter halophilus sp. nov. (type strain, JC2043T=IMSNU 14007T=KCTC 12043T=DSM 15266T). Aestuariibacter salexigens is the type species of the genus. In addition, an emended description of Alteromonas macleodii is proposed.
‘Candidatus Rhabdochlamydia porcellionis’, an intracellular bacterium from the hepatopancreas of the terrestrial isopod Porcellio scaber (Crustacea: Isopoda)
Authors: Kostanjšek Rok , Štrus Jasna , Drobne Damjana , Avguštin Gorazd
Published: March 2004

Intracellular bacteria were observed in the hepatopancreas of the terrestrial isopod Porcellio scaber. Comparative 16S rRNA gene sequence analysis and electron microscopic observations were used to determine the taxonomic position of these intracellular bacteria. Phylogenetic analysis and a complex developmental cycle affiliate these bacteria to the order Chlamydiales, within which they form a distinctive lineage, close to the family Simkaniaceae. They share <92 % 16S rRNA gene sequence similarity with their closest relative and <88 % similarity with other members of the order Chlamydiales. A specific signature oligonucleotide sequence was identified and used as a probe, enabling the identification of intracellular bacteria in infected hepatopancreatic tissue. According to the distinctive morphology of their elementary bodies, which are rod-shaped rather than spherical and contain translucent oblong structures, their genomic properties and their crustacean host, the name ‘Candidatus Rhabdochlamydia porcellionis' is proposed for intracellular bacteria in the hepatopancreas of P. scaber.
Nocardiopsis aegyptia sp. nov., isolated from marine sediment
Authors: Sabry Soraya A. , Ghanem Nevine B. , Abu-Ella Gehan A. , Schumann Peter , Stackebrandt Erko , Kroppenstedt Reiner M.
Published: March 2004

An actinomycete, strain SNG49T, was isolated from marine sediment of Abu Qir Bay, on the western seashore of Alexandria, Egypt. The bacterium was aerobic and Gram-positive. It produced beige to light-yellow aerial mycelium, brown substrate mycelium and straight to flexuous hyphae, but no specific spore chains. 16S rDNA sequence analysis and chemotaxonomic markers were consistent with classification of strain SNG49Tin the genusNocardiopsis, i.e.meso-diaminopimelic acid; no diagnostic sugars; phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylinositol, phosphatidylglycerol and diphosphatidylglycerol as polar lipids; menaquinones of the MK-10 series from MK-10(H0) to MK-10(H8); and iso/anteiso-branched and 10-methyl-branched fatty acids, the principal fatty acids being anteiso-17 : 0 and tuberculostearic acid.Nocardiopsis lucentensisandNocardiopsis albaare the phylogenetic neighbours of strain SNG49T, respectively showing 98·8 and 98·7 % 16S rRNA gene sequence similarity; however, moderate DNA–DNA reassociation values between these two species and strain SNG49T(44 and 60 %, respectively) showed that strain SNG49Tcould be clearly separated from them. These data, together with distinct physiological traits, led to the conclusion that this isolate represents a novel species within the genusNocardiopsis, for which the nameNocardiopsis aegyptiais proposed. The type strain is SNG49T(=DSM 44442T=NRRL B-24244T).
Bacillus galactosidilyticus sp. nov., an alkali-tolerant β-galactosidase producer
Authors: Heyndrickx Marc , Logan Niall A. , Lebbe Liesbeth , Rodríguez-Díaz Marina , Forsyth Gillian , Goris Johan , Scheldeman Patsy , De Vos Paul
Published: March 2004

A novelBacillusisolate from raw milk and four strains from diverse origins that were identified previously asBacillus lentus,Bacillus firmusandBacillus circulansshowed a high degree of similarity in amplified rDNA restriction analysis, SDS-PAGE and routine phenotypic tests, whilst 16S rDNA sequence comparisons and DNA relatedness data showed that this taxon was different from relatedBacillusspecies. On the basis of these data,Bacillus galactosidilyticussp. nov. is proposed, with the type strain LMG 17892T(=DSM 15595T=Logan B2188T=MB 800T).
Streptococcus minor sp. nov., from faecal samples and tonsils of domestic animals
Authors: Vancanneyt M. , Devriese L. A. , De Graef E. M. , Baele M. , Lefebvre K. , Snauwaert C. , Vandamme P. , Swings J. , Haesebrouck F.
Published: March 2004

Nine isolates, which were obtained from tonsils, anal swabs and faeces of dogs and from tonsils of a cat and a calf, constituted a homogeneous but unidentified taxon after screening with tRNA intergenic length polymorphism analysis and whole-cell protein fingerprinting. 16S rDNA sequence analysis classified representative strains in the genus Streptococcus. Highest sequence similarity (95·9 %) was obtained with Streptococcus ovis. Growth characteristics, biochemical features, DNA–DNA hybridization and DNA G+C contents of selected strains demonstrated that they represent a single, novel streptococcal species. The name Streptococcus minor sp. nov. is proposed for the novel species; the type strain (ON59T=LMG 21734T=CCUG 47487T) was isolated from a dog tonsil.
Genetic diversity of Leptotrichia and description of Leptotrichia goodfellowii sp. nov., Leptotrichia hofstadii sp. nov., Leptotrichia shahii sp. nov. and Leptotrichia wadei sp. nov.
Authors: Eribe Emenike R. K. , Paster Bruce J. , Caugant Dominique A. , Dewhirst Floyd E. , Stromberg Verlyn K. , Lacy George H. , Olsen Ingar
Published: March 2004

Sixty strains of Gram-negative, anaerobic, rod-shaped bacteria from human sources initially assigned to Leptotrichia buccalis (n=58) and ‘Leptotrichia pseudobuccalis’ (n=2) have been subjected to polyphasic taxonomy. Full-length 16S rDNA sequencing, DNA–DNA hybridization, RAPD, SDS-PAGE of whole-cell proteins, cellular fatty acid analysis and enzymic/biochemical tests supported the establishment of four novel Leptotrichia species from this collection, Leptotrichia goodfellowii sp. nov. (type strain LB 57T=CCUG 32286T=CIP 107915T), Leptotrichia hofstadii sp. nov. (type strain LB 23T=CCUG 47504T=CIP 107917T), Leptotrichia shahii sp. nov. (type strain LB 37T=CCUG 47503T=CIP 107916T) and Leptotrichia wadei sp. nov. (type strain LB 16T=CCUG 47505T=CIP 107918T). Light and electron microscopy showed that the four novel species were Gram-negative, non-spore-forming and non-motile rods. L. goodfellowii produced arginine dihydrolase, β-galactosidase, N-acetyl-β-glucosaminidase, arginine arylamidase, leucine arylamidase and histidine arylamidase. L. shahii produced α-arabinosidase. L. buccalis and L. goodfellowii fermented mannose and were β-galactosidase-6-phosphate positive. L. goodfellowii, L. hofstadii and L. wadei were β-haemolytic. L. buccalis fermented raffinose. With L. buccalis, L. goodfellowii showed 3·8–5·5 % DNA–DNA relatedness, L. shahii showed 24·5–34·1 % relatedness, L. hofstadii showed 27·3–36·3 % relatedness and L. wadei showed 24·1–35·9 % relatedness. 16S rDNA sequencing demonstrated that L. hofstadii, L. shahii, L. wadei and L. goodfellowii each formed individual clusters with 97, 96, 94 and 92 % similarity, respectively, to L. buccalis.
Characterization of the marine propionate-degrading, sulfate-reducing bacterium Desulfofaba fastidiosa sp. nov. and reclassification of Desulfomusa hansenii as Desulfofaba hansenii comb. nov.
Authors: Abildgaard Lone , Ramsing Niels Birger , Finster Kai
Published: March 2004

A rod-shaped, slightly curved sulfate reducer, designated strain P2T, was isolated from the sulfate–methane transition zone of a marine sediment. Cells were motile by means of a single polar flagellum. The strain reduced sulfate, thiosulfate and sulfite to sulfide and used propionate, lactate and 1-propanol as electron donors. Strain P2T also grew by fermentation of lactate. Propionate was oxidized incompletely to acetate and CO2. The DNA G+C content was 48·8mol%. Sequence analysis of the small-subunit rDNA and the dissimilatory sulfite reductase gene revealed that strain P2T was related to the genera Desulfonema, Desulfococcus, Desulfosarcina, ‘Desulfobotulus’, Desulfofaba, Desulfomusa and Desulfofrigus. These genera include incomplete as well as complete oxidizers of substrates. Strain P2T shared important morphological and physiological traits with Desulfofaba gelida and Desulfomusa hansenii, including the ability to oxidize propionate incompletely to acetate. The 16S rRNA gene similarities of P2T to Desulfofaba gelida and Desulfomusa hansenii were respectively 92·9 and 91·5%. Combining phenotypic and genotypic traits, we propose strain P2T to be a member of the genus Desulfofaba. The name Desulfofaba fastidiosa sp. nov. (type strain P2T=DSM 15249T=ATCC BAA-815T) is proposed, reflecting the limited number of substrates consumed by the strain. In addition, the reclassification of Desulfomusa hansenii as a member of the genus Desulfofaba, Desulfofaba hansenii comb. nov., is proposed. A common line of descent and a number of shared phenotypic traits support this reclassification.
Molecular phylogeny of the heterocystous cyanobacteria (subsections IV and V) based on nifD
Authors: Henson Brian J. , Hesselbrock Sharon M. , Watson Linda E. , Barnum Susan R.
Published: March 2004

The heterocystous cyanobacteria are currently placed in subsections IV and V, which are distinguished by cellular division in one plane (false branching) and in more than one plane (true branching), respectively. Published phylogenies of 16S rRNA gene sequence data support the monophyly of the heterocystous cyanobacteria, with members of subsection V embedded within subsection IV. It has been postulated that members of subsection V arose from within subsection IV. Therefore, phylogenetic analysis of nucleotide sequences of the nitrogen-fixation gene nifD from representatives of subsections IV and V was performed by using maximum-likelihood criteria. The heterocystous cyanobacteria are supported as being monophyletic, with the non-heterocystous cyanobacteria as their closest relative. However, neither subsection IV nor subsection V is monophyletic, with representatives of both subsections intermixed in two sister clades. Analysis of nifD does not support recognition of two distinct subsections.
Aeropyrum camini sp. nov., a strictly aerobic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney
Authors: Nakagawa Satoshi , Takai Ken , Horikoshi Koki , Sako Yoshihiko
Published: March 2004

A novel hyperthermophilic archaeon, designated strain SY1T, was isolated from a deep-sea hydrothermal vent chimney sample collected from the Suiyo Seamount in the Izu-Bonin Arc, Japan, at a depth of 1385 m. The cells were irregular cocci (1·2 to 2·1 μm in diameter), occurring singly or in pairs, and stained Gram-negative. Growth was observed between 70 and 97 °C (optimum, 85 °C; 220 min doubling time), pH 6·5 and 8·8 (optimum, pH 8·0), and salinity of 2·2 and 5·3 % (optimum, 3·5 %). It was a strictly aerobic heterotroph capable of growing on complex proteinaceous substrates such as yeast extract and tryptone. The G+C content of the genomic DNA was 54·4 mol%. Phylogenetic analysis based on the 16S rDNA sequence of the isolate indicated that the isolate was closely related toAeropyrum pernixstrain K1T. However, no significant genetic relatedness was observed between them by DNA–DNA hybridization. On the basis of the molecular and physiological traits of the new isolate, the nameAeropyrum caminisp. nov. is proposed, with the type strain SY1T(=JCM 12091T=ATCC BAA-758T).
Tepidibacter formicigenes sp. nov., a novel spore-forming bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent
Authors: Urios Laurent , Cueff Valérie , Pignet Patricia , Barbier Georges
Published: March 2004

A novel anaerobic, Gram-positive, sporulating and strictly chemoorganoheterotrophic bacterium, designated strain DV1184T, was isolated from a deep-sea hydrothermal vent sample from the Mid-Atlantic Ridge. The cells were short, straight rods (4 μm long and 0·8 μm wide) and were motile with peritrichous flagella. They grew between 35 and 55 °C (optimum, 45 °C), between pH 5·0 and 8·0 (optimum, 6·0) and at 20–60 g sea salts l−1(optimum sea salts concentration, 30 g l−1). Strain DV1184Twas able to ferment yeast extract, tryptone, peptone, glucose, sucrose, maltose and pyruvate. The main fermentation products from glucose were (in decreasing order) formate, acetate and ethanol. The genomic DNA G+C content was 29 mol%. Phylogenetic analysis of the 16S rRNA gene located the strain within cluster XI of the lineage that encompasses the genusClostridiumand related genera in the bacterial domain. On the basis of 16S rDNA sequence comparison and physiological and biochemical characteristics, it is proposed that the isolate should be described as a novel species,Tepidibacter formicigenessp. nov. The type strain is DV1184T(=CIP 107893T=DSM 15518T).
Nocardia tenerifensis sp. nov.
Authors: Kämpfer Peter , Buczolits Sandra , Jäckel Udo , Grün-Wollny Iris , Busse Hans-Jürgen
Published: March 2004

A Gram-positive, non-spore-forming bacterium (GW39-1573T) was isolated from soil of the Spanish island of Tenerife. 16S rRNA gene sequence similarity studies showed that strain GW39-1573T belonged to the genus Nocardia and was most closely related to Nocardia brasiliensis (98·0 %), Nocardia beijingensis (97·3 %), Nocardia transvalensis (97·5 %), Nocardia asteroides (97·2 %) and Nocardia farcinica (97·0 %). Strain GW39-1573T could be distinguished from all other validly described Nocardia species by sequence similarity values of less than 97 %. Chemotaxonomic data [major menaquinone: MK-8(H4, ω-cycl); major polar lipids: diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and an unknown glycolipid and an unknown phospholipid; major fatty acids: C16 : 0, C18 : 1
ω9c and 10 methyl C16 : 0] and the presence of mycolic acids supported the affiliation of strain GW39-1573T to the genus Nocardia. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW39-1573T from those related species that showed 16S rRNA gene sequence similarity values of greater than 97 %. Strain GW39-1573T merits species status, and the name Nocardia tenerifensis is proposed with the type strain GW39-1573T (=DSM 44704T=CIP 107929T).
Mycoplasma ovis comb. nov. (formerly Eperythrozoon ovis), an epierythrocytic agent of haemolytic anaemia in sheep and goats
Authors: Neimark Harold , Hoff Brent , Ganter Martin
Published: March 2004

Eperythrozoon ovis, an erythrocytic agent that causes haemolytic anaemia in sheep and goats, occurs worldwide and is currently thought to be a rickettsia. To determine the relationship between this agent and other haemotrophic bacterial parasites, the 16S rRNA gene of this organism was sequenced. Phylogenetic analysis revealed that this wall-less bacterium is not a rickettsia, but a mycoplasma. This mycoplasma is related closely to several other uncultivated, epierythrocytic mycoplasmas that comprise a recently identified group, the haemotrophic mycoplasmas (haemoplasmas). The haemoplasma group is composed of former Eperythrozoon and Haemobartonella species, as well as newly identified epierythrocytic mycoplasmas. Haemoplasmas parasitize the surface of erythrocytes of a wide variety of vertebrate animal hosts and are transmitted mainly by blood-feeding arthropod vectors. Recognition that E. ovis is a mycoplasma provides a new approach to dealing with this bacterium. It is proposed that E. ovis should be reclassified as Mycoplasma ovis comb. nov.
Cellulomonas xylanilytica sp. nov., a cellulolytic and xylanolytic bacterium isolated from a decayed elm tree
Authors: Rivas Raúl , Trujillo Martha E. , Mateos P. F. , Martínez-Molina E. , Velázquez Encarna
Published: March 2004

A Gram-positive, aerobic, non-motile bacterium was isolated from a decayed elm tree. Phylogenetic analysis based on 16S rDNA sequences revealed 99·0 % similarity toCellulomonas humilata. Chemotaxonomic data that were determined for this isolate included cell-wall composition, fatty acid profiles and polar lipids; the results supported the placement of strain XIL11Tin the genusCellulomonas. The DNA G+C content was 73 mol%. The results of DNA–DNA hybridization withC. humilataATCC 25174T, in combination with chemotaxonomic and physiological data, demonstrated that isolate XIL11Tshould be classified as a novelCellulomonasspecies. The nameCellulomonas xylanilyticasp. nov. is proposed, with strain XIL11T(=LMG 21723T=CECT 5729T) as the type strain.
Yania halotolerans gen. nov., sp. nov., a novel member of the suborder Micrococcineae from saline soil in China
Authors: Li Wen-Jun , Chen Hua-Hong , Xu Ping , Zhang Yu-Qin , Schumann Peter , Tang Shu-Kun , Xu Li-Hua , Jiang Cheng-Lin
Published: March 2004

A novel coccoid, halotolerant actinobacterium, designated strain YIM 70085T, was isolated from a soil sample that was collected in Xinjiang Province, China, and characterized by using a polyphasic approach. Optimum growth temperature was 28 °C and growth occurred optimally in culture media that contained 10 % KCl. The peptidoglycan type was A4α,l-lys–gly–l-Glu. Whole-cell sugars consisted of xylose, mannose and galactose. Phospholipids were diphosphatidylglycerol, phosphatidylglycerol, one unknown phospholipid, one unknown glycolipid and traces of phosphatidylinositol. Menaquinones were MK-8 (83 %), MK-7 (12 %) and MK-9 (15 %). Predominant fatty acids were i-C15 : 0(44·29 %), ai-C15 : 0(35·60 %) and ai-C17 : 0(9·74 %). The DNA G+C content was 53·5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 70085Toccupies a branch that is distinct from, although very close to, the familyMicrococcaceaein the suborderMicrococcineae. Based on its phenotypic characteristics, phylogenetic position (as determined by 16S rRNA gene sequence analysis) and 16S rDNA signature nucleotide data, it is concluded that the isolate represents a novel member of the suborderMicrococcineae, for which the nameYania halotoleransgen. nov., sp. nov. is proposed. The type strain is YIM 70085T(=CCTCC AA001023T=DSM 15476T).
Nocardia neocaledoniensis sp. nov., a novel actinomycete isolated from a New-Caledonian brown hypermagnesian ultramafic soil
Authors: Saintpierre-Bonaccio Danielle , Maldonado Luis A. , Amir Hamid , Pineau René , Goodfellow Michael
Published: March 2004

The taxonomic position of an actinomycete isolated from a hypermagnesian ultramafic soil was examined using a polyphasic approach. The strain, designated SBHR OA6T, was shown to have chemical and morphological properties typical of members of the genus Nocardia. The organism was most closely associated with Nocardia asteroides using 16S rRNA gene sequence data. It showed a distinctive set of phenotypic properties that distinguished it from representatives of all species with validly published names classified in the genus Nocardia. The combined genotypic and phenotypic data show that strain SBHR OA6T (=DSM 44717T=NCIMB 13955T) merits description as the type strain of a novel Nocardia species, Nocardia neocaledoniensis sp. nov.
Reclassification of Brevibacillus brevis strains NCIMB 13288 and DSM 6472 (=NRRL NRS-887) as Aneurinibacillus danicus sp. nov. and Brevibacillus limnophilus sp. nov.
Authors: Goto Keiichi , Fujita Rieko , Kato Yuko , Asahara Mika , Yokota Akira
Published: March 2004

Comparison of the hypervariable region (269–279 bases in length) at the 5′ end of the 16S rDNA sequences of 29 bacterial strains that were identified previously asBrevibacillus brevisshowed that 13 strains clustered withAneurinibacillusspecies, eight strains clustered withBacillusspecies and eight strains clustered withBrevibacillusspecies. Based on DNA–DNA hybridization results, 27 strains, not including [Brevibacillus brevis] NCIMB 13288 and [Brevibacillus brevis] DSM 6472, were reidentified asAneurinibacillus migulanus,Aneurinibacillus thermoaerophilus,Bacillus methanolicus,Bacillus oleronius,Brevibacillus agri,Brevibacillus brevisandBrevibacillus parabrevis. [Brevibacillus brevis] NCIMB 13288, which was located in theAneurinibacilluscluster, showed low DNA–DNA relatedness (<14 %) and low 16S rDNA sequence similarity (96·8–97·9 %) to otherAneurinibacillusspecies. [Brevibacillus brevis] DSM 6472, which was located in theBrevibacilluscluster, also showed low DNA–DNA relatedness (<12 %) and low 16S rDNA sequence similarity (95·4–98·8 %) to otherBrevibacillusspecies. These genotypic and phylogenetic data, plus phenotypic and chemotaxonomic characteristics, suggest that [Brevibacillus brevis] NCIMB 13288 (=IAM 15048) and [Brevibacillus brevis] DSM 6472 (=NRRL NRS-887) represent novel species of the generaAneurinibacillusandBrevibacillus, respectively, for which the namesAneurinibacillus danicussp. nov. andBrevibacillus limnophilussp. nov. are proposed.
Reclassification of Lactobacillus kefirgranum Takizawa et al. 1994 as Lactobacillus kefiranofaciens subsp. kefirgranum subsp. nov. and emended description of L. kefiranofaciens Fujisawa et al. 1988
Authors: Vancanneyt M. , Mengaud J. , Cleenwerck I. , Vanhonacker K. , Hoste B. , Dawyndt P. , Degivry M. C. , Ringuet D. , Janssens D. , Swings J.
Published: March 2004

Fourteen homofermentative lactic acid bacteria that were isolated from kefir grains and kefir fermented milks were assigned to either Lactobacillus kefiranofaciens or Lactobacillus kefirgranum, based on their characteristic morphotypes, phenotypic features and SDS-PAGE profiles of whole-cell proteins. Further genotypic analyses on representative strains from both taxa demonstrated that L. kefiranofaciens and L. kefirgranum share 100 % 16S rDNA sequence similarity and belong phylogenetically to the Lactobacillus acidophilus species group. DNA–DNA binding values of >79 % and analogous DNA G+C contents of 37–38 mol% showed that the strains studied belonged to one species: L. kefirgranum is a later synonym of L. kefiranofaciens. An emended description is proposed for L. kefiranofaciens. Due to the specific morphological and biochemical characteristics of these taxa in kefir grain formation, it is proposed that L. kefirgranum should be reclassified as L. kefiranofaciens subsp. kefirgranum subsp. nov.
Gillisia limnaea gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from a microbial mat in Lake Fryxell, Antarctica
Authors: Van Trappen Stefanie , Vandecandelaere Ilse , Mergaert Joris , Swings Jean
Published: March 2004

A taxonomic study was performed on three strains isolated from microbial mats in Lake Fryxell, McMurdo Dry Valleys, Antarctica. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belong to the familyFlavobacteriaceae, in which they form a distinct lineage. The isolates are Gram-negative, chemoheterotrophic, aerobic, rod-shaped cells. They are psychrophilic and yellow-pigmented, with DNA G+C contents in the range 37·8–38·9 mol%. Whole-cell fatty acid profiles revealed mainly branched fatty acids and 17 : 0 2-OH. On the basis of genotypic, phenotypic, chemotaxonomic and phylogenetic results, it is proposed that the isolates represent a novel species in a new genus,Gillisia limnaeagen. nov., sp. nov. The type strain is LMG 21470T(=DSM 15749T).
Developing competencies, critical analysis and personal transferable skills in future information professionals
Authors: Ashcroft Linda
Published: March 2004

New technologies mean library and information science is currently characterised by fast‐paced change, with staff needing to be flexible in adapting and adopting new skills and levels of awareness. New developments need to be marketed and evaluated, and these are additional skills for information professionals to adopt. Findings of a research project carried out at Liverpool John Moores University into the marketing and management of e‐journals demonstrate the need for LIS professionals to develop marketing and evaluation skills and strategies for new technologies. Other emerging skills in the electronic information environment are communication, negotiation and collaboration, with information professionals being called upon to teach new skills.
The implementation of the European Credit Transfer system as a curriculum evaluation tool
Authors: Espelt Constança
Published: March 2004

This paper gives an overview of library and information science provision in Spain, describing the first and second cycle courses open to students wishing to study LIS, and the constraints of the current system. It describes in detail the provision of LIS courses at the University of Barcelona, in particular the University of Barcelona's financial backing for teaching innovation, resulting in funding for specific activities related to the transition to the European system of credits. Also analyses and evaluates pilot projects regarding this transition carried out in the LIS Faculty at the University of Barcelona.
The challenge of developing a competence‐oriented curriculum: an integrative framework
Authors: Roggema‐van Heusden Marijke
Published: March 2004

This paper discusses developments in society that have called for a rethinking of LIS education and subsequent widening of the curriculum of the LIS schools in the Netherlands that has been taking place to meet the demands of organizations for a different professional contribution. The focus has changed from the acquisition of “factual” knowledge to teaching students how to solve problems, to respond aptly to changeable professional situations, to interact within a team, and to acquire new knowledge and skills continuously, throughout life. In order to keep up with these developments the Dutch national council for higher vocational education has demanded a remodelling of courses from the LIS schools in Holland. The purpose of this study is to describe the framework and to show how it functions in current education.
Bridging gaps – pedagogical investment
Authors: Rafste Elisabeth T. , Sætre Tove P.
Published: March 2004

This paper has four main parts. In Part 1 we look into the broad perspectives pedagogy can give to library and information science. In the following parts we limit the presentation to our main focus for this paper: pedagogy for school librarians. In Part 2 we give a very short description of the role of the school library in the 13 school years of the Norwegian national curriculum. In Part 3, we go deeper into crucial and basic fundamentals in didactics: learning theories. Part 4 gives examples on how two University Colleges in Norway, Agder and Bergen have invested in their education of school librarians and librarians and on how these investments are meant to bridge gaps between institutions, professionals, and professionals and users.
Library and information studies in Malta: challenges and opportunities
Authors: Paris Martes
Published: March 2004

The Maltese Islands strive to keep abreast with the developments taking place within the realm of Information and Communication Technology (ICT). The University of Malta appointed its first full‐time lecturer in Library Studies in 1992, within the Centre for Communication Technology (CCT), in response to an increase in the number of libraries and a need felt by librarians for professional training. Growing need for professional training from library professionals has led to the University appointing a second full‐time academic and seriously considering offering Library and Information Studies at degree level, as of October 2003. This paper discusses in detail the challenges faced by the Division of Library and Information Studies at the University of Malta, in the context of a small island state.
Theory of grey systems: capturing uncertainties of grey information
Authors: Lin Yi , Chen Mian‐yun , Liu Sifeng
Published: March 2004

In this paper, we take a look at the state‐of‐the‐art of the theory and applications of the so‐called grey systems theory founded in the 1980s. After a brief historical review of the development history of this theory, we look at the main blocks of the theory followed by several successful applications. It is our hope that a reader who does not know anything about this branch of scientific exploration will gain a firm understanding of the basics so that the rest of this special issue becomes possible to comprehend.
SCGM‐model and grey control of “poor” information systems
Authors: Chen Mian‐Yun , Li Zhijun , Zhou Long , Xiong Hejing , An Xianjie
Published: March 2004

“Poor” information systems are found everywhere. In this paper, a control approach to “poor” information systems, such as social economic systems, is proposed. First, “poor” information processing and SCGM‐model will be discussed. Secondly, we will develop an optimal controller of “poor” information systems.
The GM models that x(n) be taken as initial value
Authors: Yaoguo Dang , Sifeng Liu , Kejia Chen
Published: March 2004

In this paper, the starting conditions of GM model group are studied. By choosing the nth component of X(1) as the starting conditions of the grey differential model, improvements are made on the models. As the new information is fully used, the accuracy of prediction is improved greatly. Therefore, it has high theoretical and practical value.
Improved absolute grey incidence degree and its application
Authors: Xin Gao , Maoxing Shen
Published: March 2004

On the basis of the given absolute incidence degree, a new absolute incidence degree is defined. It not only possesses the characteristic of invariant translational transformation, but also can describe the incidence property between every two sequences exactly.
Dynamically updating UIDB to implement personalized service
Authors: Jiang Xue‐Feng
Published: March 2004

User interests in electronic commerce reflect the behavior set of users acting on certain impulse. Electronic commerce web stations (ECWS) might make full use of intelligent IT to create and refine user interests database (UIDB) to make services personalized. In this paper, the issues about how to implement such kind of services are investigated, the concepts of user interests and their transitions are defined; the structure of UIDB and how to create it are explored, and the analysis and mining of the data in server log files to help dynamically updating UIDB are discussed in detail. Then, ECWS can actively recommend suitable series of pre‐sent web pages for different users and flexibly deal with transitions of users' interests. The dynamic structure may make the system perfect after a period of use to help ECWS to offer their users with personalized service.
A dynamic method of air temperature forecast
Authors: Kong Fanliang , Sun MingSong , Zhu Lianxing , Zhou Liyao
Published: March 2004

According to the air temperature change and concerning some information from a region and a large city over the years, this paper delves into a dynamic method of air temperature forecast. A mathematical model and a set of recursive estimate formulas are used for the forecast of air temperature change. By these formulas, the recent information can be fully applied, a forecast with satisfactory accuracy is obtained. The calculation is simplified, and the forecast effect is better than that by ordinary least square estimate method.
Synthetic utility index method and venturous capital decision‐making
Authors: Liu Sifeng , Dang Yaoguo , Lin Yi
Published: March 2004

A new risk investment decision‐making method, the synthetic utility index method, based on the whitenization weight function of grey numbers and the capital assets pricing model is proposed in this paper. The new method overcomes the shortcomings of the expectation‐variance method and Sharpe's index method and avoids the inconvenience of constructing utility function to a certain extent as well.
Technical change and funds for science and technology
Authors: Liu Sifeng , Lin Yi , Dang Yaoguo , Li Bingjun
Published: March 2004

In this paper, first a new model, the G‐C‐D model, which is used to measure the technological advance, is built. The progress with non‐technical elements in Solow's “remaining value” is removed by using the idea, method and modeling technique of grey system theory. So the difficult technical problem in measurement of technological advance has been solved to a certain extent. Secondly, another new model, the G‐E model, which combines the Grey model with the econometrics model, is built. Using the principle of grey incidence to analyse and cluster system factors, adopting the GM(1,1) simulated values of system's variables to build the econometrics model and confirming the predicted values with grey models, some difficult techniques in econometrics model building have been solved. Thirdly, the periodic G‐C‐D model of Henan Province is built in four different periods and the contribution rate of the periodic technological advance of Henan Province is measured. Lastly, the technical change and the relation between the technical change and the funds for science and technology of Henan Province are analysed with the grey production function (the G‐C‐D) and the grey‐econometrics combined model (the G‐E), and some useful outcome for policy‐making body are obtained.
The G‐C‐D model and technical change
Authors: Sifeng Liu , Liang Zhao , Yaoguo Dang , Bingjun Li
Published: March 2004

A new model called the G‐C‐D model, which is used to measure the technological advance, is built in this paper. The progress in non‐technical elements in Solow's “remaining value” is removed by using the idea, method and modeling technique of grey system theory. So, the difficult technical problem in the measurement of technological advance has been solved to a certain extent. The periodic G‐C‐D model of Henan Province is built in four different periods and the contribution rate of periodic technological advance of Henan Province is measured.