bluuebunny/crossref_metadata_2025 huggingface dataset:
Mesorhizobium septentrionale sp. nov. and Mesorhizobium temperatum sp. nov., isolated from Astragalus adsurgens growing in the northern regions of China
Authors: Gao Jun-Lian , Turner Sarah Lea , Kan Feng Ling , Wang En Tao , Tan Zhi Yuan , Qiu Yu Hui , Gu Jun , Terefework Zewdu , Young J. Peter W. , Lindström Kristina , Chen Wen Xin
Published: November 2004

Ninety-five rhizobial strains isolated from Astragalus adsurgens growing in the northern regions of China were classified into three main groups, candidate species I, II and III, based on a polyphasic approach. Comparative analysis of full-length 16S rRNA gene sequences of representative strains showed that candidate species I and II were Mesorhizobium, while candidate species III, which consisted of non-nodulating strains, was closely related to Agrobacterium tumefaciens. The phylogenetic relationships of the three candidate species and some related strains were also confirmed by the sequencing of glnA genes, which were used as an alternative chromosomal marker. The DNA–DNA relatedness was between 11·3 and 47·1 % among representative strains of candidate species I and II and the type strains of defined Mesorhizobium species. Candidate III had DNA relatedness of between 4·3 and 25·2 % with type strains of Agrobacterium tumefaciens and Agrobacterium rubi. Two novel species are proposed to accommodate candidate species I and II, Mesorhizobium septentrionale sp. nov. (type strain, SDW014T=CCBAU 11014T=HAMBI 2582T) and Mesorhizobium temperatum sp. nov. (type strain, SDW018T=CCBAU 11018T=HAMBI 2583T), respectively. At least two distinct nodA sequences were identified among the strains. The numerically dominant nodA sequence type was most similar to that from the Mesorhizobium tianshanense type strain and was identified in strains belonging to the two novel species as well as other, as yet, undefined genome types. Host range studies indicate that the different nodA sequences correlate with different host ranges. Further comparative studies with the defined Agrobacterium species are needed to clarify the taxonomic identity of candidate species III.
Brevibacterium celere sp. nov., isolated from degraded thallus of a brown alga
Authors: Ivanova Elena P. , Christen Richard , Alexeeva Yulia V. , Zhukova Natalia V. , Gorshkova Natalia M. , Lysenko Anatoly M. , Mikhailov Valery V. , Nicolau Dan V.
Published: November 2004

Two whitish yellow, Gram-positive, non-motile, aerobic bacteria were isolated from enrichment culture during degradation of the thallus of the brown alga Fucus evanescens. The bacteria studied were chemo-organotrophic, mesophilic and grew well on nutrient media containing up to 15 % (w/v) NaCl. The DNA G+C content was 61 mol%. The two isolates exhibited a conspecific DNA–DNA relatedness value of 98 %, indicating that they belong to the same species. A comparative analysis of 16S rRNA gene sequences revealed that strain KMM 3637T formed a distinct phyletic lineage in the genus Brevibacterium (family Brevibacteriaceae, class Actinobacteria) and showed the highest sequence similarity (about 97 %) to Brevibacterium casei. DNA–DNA hybridization experiments demonstrated 45 % binding with the DNA of B. casei DSM 20657T. Physiological and chemotaxonomic characteristics (meso-diaminopimelic acid in the peptidoglycan, major cellular fatty acids 15 : 0ai and 17 : 0ai) of the bacteria studied were consistent with the genomic and phylogenetic data. On the basis of the results of this study, a novel species, Brevibacterium celere sp. nov., is proposed. The type strain is KMM 3637T (=DSM 15453T=ATCC BAA-809T).
Burkholderia tropica sp. nov., a novel nitrogen-fixing, plant-associated bacterium
Authors: Reis V. M. , Santos P. Estrada-de los , Tenorio-Salgado S. , Vogel J. , Stoffels M. , Guyon S. , Mavingui P. , Baldani V. L. D. , Schmid M. , Baldani J. I. , Balandreau J. , Hartmann A. , Caballero-Mellado J.
Published: November 2004

In an ecological survey of nitrogen-fixing bacteria isolated from the rhizosphere and as endophytes of sugarcane, maize and teosinte plants in Brazil, Mexico and South Africa, a new phylogenetically homogeneous group of N2-fixing bacteria was identified within the genus Burkholderia. This polyphasic taxonomic study included microscopic and colony morphology, API 20NE tests and growth on different culture media at different pH and temperatures, as well as carbon source assimilation tests and whole-cell protein pattern analysis. Analysis of 16S rRNA gene sequences showed 99·2–99·9 % similarity within the novel species and 97·2 % similarity to the closest related species, Burkholderia sacchari. The novel species was composed of four distinct amplified 16S rDNA restriction analysis groups. The DNA–DNA reassociation values within the novel species were greater than 70 % and less than 42 % for the closest related species, B. sacchari. Based on these results and on many phenotypic characteristics, a novel N2-fixing species is proposed for the genus Burkholderia, Burkholderia tropica sp. nov., with the type strain Ppe8T (=ATCC BAA-831T=LMG 22274T=DSM 15359T). B. tropica was isolated from plants grown in geographical regions with climates ranging from temperate subhumid to hot humid.
Mahella australiensis gen. nov., sp. nov., a moderately thermophilic anaerobic bacterium isolated from an Australian oil well
Authors: Bonilla Salinas Monica , Fardeau Marie-Laure , Thomas Pierre , Cayol Jean-Luc , Patel Bharat K. C. , Ollivier Bernard
Published: November 2004

A novel Gram-positive, anaerobic and moderately thermophilic bacterium, strain 50-1 BONT, was isolated from an Australian terrestrial oil reservoir. Cells were spore-forming straight rods, motile by peritrichous flagella. The optimum growth conditions were 50 °C, pH 7·5 and 0·1 % NaCl. Strain 50-1 BONT fermented arabinose, cellobiose, fructose, galactose, glucose, mannose, sucrose, xylose and yeast extract. Glucose was fermented mainly into lactate, formate, hydrogen and CO2. The major end product of pyruvate fermentation was acetate together with H2 and CO2. Thiosulfate, sulfate, elemental sulfur and nitrate were not used as terminal electron acceptors. The DNA G+C content was 55·5 mol%. The closest phylogenetic relative of strain 50-1 BONT was Thermoanaerobacterium thermosulfurigenes (16S rRNA gene sequence similarity of 85·7 %). As strain 50-1 BONT was physiologically and phylogenetically different from members of the order ‘Thermoanaerobacteriales’, it is proposed that strain 50-1 BONT (=DSM 15567T=CIP 107919T) be classified as the type strain of a novel species of a new genus, Mahella australiensis gen. nov., sp. nov.
Geobacillus gargensis sp. nov., a novel thermophile from a hot spring, and the reclassification of Bacillus vulcani as Geobacillus vulcani comb. nov.
Authors: Nazina Tamara N. , Lebedeva Elena V. , Poltaraus Andrei B. , Tourova Tatyana P. , Grigoryan Alexandre A. , Sokolova Diyana Sh. , Lysenko Anatoliy M. , Osipov George A.
Published: November 2004

A novel thermophilic spore-forming strain, GaT, was isolated from the Garga hot spring located in the northern part of the Transbaikal region (Russia). Strain GaTwas found to be an aerobic, Gram-positive, rod-shaped, thermophilic (optimum growth temperature is 60–65 °C), chemo-organotrophic bacterium that grows on various sugars, carboxylic acids and hydrocarbons. The G+C content of its DNA is 52·9 mol%. The 16S rRNA gene sequence similarity data show that strain GaTis closely related to members of the genusGeobacillus. Relevant chemotaxonomic data (in particular, the major fatty acid profile of strain GaT, which includes iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0 acids) support the assignment of this strain to the genusGeobacillus. The physiological, biochemical and DNA–DNA hybridization studies of strain GaTshowed that it differs both genotypically and phenotypically from the recognizedGeobacillusspecies. Based on these data, strain GaTbelongs to a novel species,Geobacillus gargensissp. nov. (type strain, GaT=VKM B-2300T=DSM 15378T). The analysis of the phenotypic characteristics (additional to those given in the original description) of the type strain ofBacillus vulcani(DSM 13174T) showed that they are very similar to the major phenotypic characteristics of the genusGeobacillus. The low DNA–DNA reassociation values of strain DSM 13174Twith various species of this genus (from 38 to 54 %) clearly demonstrate a sufficient genomic distinction of this strain and its taxonomic status as a species. The physiological characteristics, phylogenetic position and DNA–DNA reassociation values ofB. vulcaniallow this species to be reclassified asGeobacillus vulcanicomb. nov. The main properties that differentiateG. vulcanifrom the other species of the genus are its ability to produce acids from glycerol, lactose and ribose.
Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description)
Authors: Hugenholtz Philip , Stackebrandt Erko
Published: November 2004

Sphaerobacter thermophilus was originally classified as the deepest branching member of the phylum Actinobacteria (high-G+C, Gram-positive bacteria) based on 16S rRNA gene comparative analysis. However, the analysis lacked suitable outgroups, and additional 16S rRNA gene sequences indicate that it is most closely related to Thermomicrobium roseum, which it also resembles phenotypically. Furthermore, both species are reproducibly affiliated with the phylum Chloroflexi (green non-sulfur bacteria), despite T. roseum currently being classified in its own phylum, the Thermomicrobia. Transfer of Sphaerobacter to the class Thermomicrobia, and transfer of the class Thermomicrobia to the phylum Chloroflexi, are proposed. Descriptions for the phylum Chloroflexi and the class Thermomicrobia are emended to reflect the proposed changes in classification.
Hydrogenivirga caldilitoris gen. nov., sp. nov., a novel extremely thermophilic, hydrogen- and sulfur-oxidizing bacterium from a coastal hydrothermal field
Authors: Nakagawa Satoshi , Nakamura Sachiko , Inagaki Fumio , Takai Ken , Shirai Nobuaki , Sako Yoshihiko
Published: November 2004

A novel extremely thermophilic, hydrogen- and sulfur-oxidizing bacterium, designated strain IBSK3T, was isolated from a coastal hot spring in Ibusuki, Kagoshima Prefecture, Japan. The cells were motile, straight to slightly curved rods (1·2–3·0 μm long and 0·3–0·4 μm wide). Strain IBSK3T was an obligate chemolithoautotroph growing by respiratory nitrate reduction with H2, forming N2O as an end product. Low concentrations of O2 (0·4–7·7 %, v/v; optimum 2·0 %, v/v) could serve as an alternative electron acceptor to growth. In addition, strain IBSK3T was able to utilize elemental sulfur as a sole electron donor with either nitrate or low concentrations of O2 as an electron acceptor. Growth was observed between 55 and 77·5 °C (optimum 75 °C; 2 h doubling time), pH 5·5 and 8·3 (optimum pH 6·5–7·0), and in the presence of 0·5 and 4·0 % NaCl (optimum 2·0 %). The G+C content of the genomic DNA was 49·2 mol%. On the basis of 16S rRNA gene sequence analysis, strain IBSK3T belonged to the family Aquificaceae, but it only demonstrated a distant phylogenetic relationship with any recognized species within the family (sequence similarity was less than 92 %). On the basis of the physiological and molecular characteristics of the novel isolate, a new genus and novel species are proposed: the type strain of Hydrogenivirga caldilitoris gen. nov., sp. nov. is IBSK3T (=JCM 12173T=ATCC BAA-821T).
Agromyces ulmi sp. nov., a xylanolytic bacterium isolated from Ulmus nigra in Spain
Authors: Rivas Raúl , Trujillo Martha E. , Mateos Pedro F. , Martínez-Molina Eustoquio , Velázquez Encarna
Published: November 2004

Two xylan-degrading bacterial strains were isolated from a decayed Ulmus nigra tree in Spain. The isolates were Gram-positive, non-motile, aerobic and formed substrate mycelium which fragmented into irregular rods. 16S rRNA gene sequence analysis indicated that the isolates form a separate branch within the genus Agromyces phylogenetic cluster, with Agromyces mediolanus DSM 20152T being their closest relative (97·7 and 97·6 % sequence similarity). Catalase, nitrate reduction and urease tests differentiated these strains from A. mediolanus. Cell-wall peptidoglycan composition, major menaquinone, predominant fatty acids and phospholipid pattern were typical of the genus Agromyces. The DNA G+C content determined for the type strain XIL01T was 72 mol%. Based on the data presented, a novel species Agromyces ulmi sp. nov. is proposed. The type strain is XIL01T (=LMG 21954T=DSM 15747T).
Nocardia shimofusensis sp. nov., isolated from soil, and Nocardia higoensis sp. nov., isolated from a patient with lung nocardiosis in Japan
Authors: Kageyama Akiko , Yazawa Katsukiyo , Mukai Akira , Kinoshita Mari , Takata Nobukatsu , Nishimura Kazuko , Kroppenstedt Reiner M. , Mikami Yuzuru
Published: November 2004

Three actinomycete strains isolated from soils and one strain isolated from a patient with lung nocardiosis in 1999 and 2001 in Japan have been provisionally assigned to the genus Nocardia on the basis of morphological criteria. These isolates were further investigated to determine their specific taxonomic status. Detailed chemotaxonomic characterization and 16S rRNA gene sequence analysis of these isolates confirmed that they belong to the genus Nocardia. The 16S rRNA gene sequences of the four strains were most similar to that of Nocardia farcinica. However, the sequence similarity values between these four strains and N. farcinica were <98·9 %. These four strains were susceptible to 5-fluorouracil, and they have the ability to decompose urea, which is a very characteristic trait. Furthermore, DNA–DNA relatedness data revealed that IFM 10311T, IFM 10312 and IFM 10313 comprise a single novel species of Nocardia, that IFM 10084T represents another novel species of Nocardia and that these two novel species could be distinguished from N. farcinica. The names Nocardia shimofusensis sp. nov. and Nocardia higoensis sp. nov. are proposed, with IFM 10311T (=NBRC 100134T=JCM 12122T=DSM 44733T) and IFM 10084T (=NBRC 100133T=JCM 12121T=DSM 44732T) as the respective type strains.
Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. nov., K. gansuensis sp. nov., K. nipponensis sp. nov., K. paranensis sp. nov. and K. terrestris sp. nov.
Authors: Groth Ingrid , Rodríguez Carlos , Schütze Barbara , Schmitz Petra , Leistner Eckhard , Goodfellow Michael
Published: November 2004

A polyphasic study was carried out to establish the taxonomic positions of six strains isolated from diverse soil samples and provisionally assigned to the genus Kitasatospora. The isolates were found to have chemical and morphological properties consistent with their classification as Kitasatospora strains. Direct 16S rRNA gene sequence data confirmed the taxonomic position of the strains following the generation of phylogenetic trees by using three tree-making algorithms. Five of the isolates were considered to merit species status using complementary genotypic and phenotypic data. These organisms were designated Kitasatospora arboriphila sp. nov. (HKI 0189T=2291-120T=DSM 44785T=NCIMB 13973T), Kitasatospora gansuensis sp. nov. (HKI 0314T=2050-015T=DSM 44786T=NCIMB 13974T), Kitasatospora nipponensis sp. nov. (HKI 0315T=2148-013T=DSM 44787T=NCIMB 13975T), Kitasatospora paranensis sp. nov. (HKI 0190T=2292-041T=DSM 44788T=NCIMB 13976T) and Kitasatospora terrestris sp. nov. (HKI 0186T=2293-012T=DSM 44789T=NCIMB 13977T). The remaining organism, isolate HKI 0316 (=2122-022=DSM 44790=NCIMB 13978), was considered to be a strain of Kitasatospora kifunensis on the basis of 16S rRNA gene sequence, DNA–DNA relatedness and phenotypic data.
Nocardia araoensis sp. nov. and Nocardia pneumoniae sp. nov., isolated from patients in Japan
Authors: Kageyama Akiko , Yazawa Katsukiyo , Mukai Akira , Kohara Tadahiro , Nishimura Kazuko , Kroppenstedt Reiner M. , Mikami Yuzuru
Published: November 2004

Two actinomycete strains isolated from two patients with lung nocardiosis between 1995 and 1997 in Japan were assigned to novel species of the genus Nocardia based on morphological and chemical criteria. Comparative 16S rRNA gene sequence analysis of the two strains revealed that they belong to the genus Nocardia and are most closely related to the species Nocardia beijingensis. Determination of DNA–DNA relatedness indicated that these strains could be assigned to two novel species. Based on their phenotypic and phylogenetic characters, two novel species of the genus Nocardia are proposed: Nocardia araoensis sp. nov. for IFM 0575T (=NBRC 100135T=JCM 12118T=DSM 44729T) and Nocardia pneumoniae sp. nov. for IFM 0784T (=NBRC 100136T=JCM 12119T=DSM 44730T).
Emended description of the genus Glycomyces and description of Glycomyces algeriensis sp. nov., Glycomyces arizonensis sp. nov. and Glycomyces lechevalierae sp. nov.
Authors: Labeda David P. , Kroppenstedt Reiner M.
Published: November 2004

A polyphasic taxonomic evaluation of presumptive strains representative of the genus Glycomyces held within the Agricultural Research Service Culture Collection resulted in the discovery of three novel species. Analysis of the whole cell sugar content of these novel species, as well as of two species presently assigned to the genus, revealed that the whole cell sugar pattern was different from that reported in the formal description of the genus Glycomyces. The sugars present in all strains studied included ribose, xylose, mannose and galactose rather than xylose and arabinose as reported in the original description of the genus. Moreover, the menaquinone patterns observed for the novel species also deviated from the original genus description. The formal description of the genus Glycomyces is emended to reflect these new data. The novel species proposed and described are Glycomyces algeriensis sp. nov. (type strain NRRL B-16327T=DSM 44727T), Glycomyces arizonensis sp. nov. (type strain NRRL B-16153T=DSM 44726T) and Glycomyces lechevalierae sp. nov. (type strain NRRL B-16149T=DSM 44724T).
Erythrobacter aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea
Authors: Yoon Jung-Hoon , Kang Kook Hee , Oh Tae-Kwang , Park Yong-Ha
Published: November 2004

Three Gram-negative, non-motile, non-spore-forming, slightly halophilic rods (strains SW-110T, SW-116 and SW-140) were isolated from sea water of a tidal flat of the Yellow Sea in Korea and subjected to a polyphasic taxonomic study. The three isolates did not produce bacteriochlorophyllaand were characterized chemotaxonomically by having ubiquinone-10 as the predominant respiratory lipoquinone and C18 : 1ω7cand C17 : 1ω6cas the major fatty acids. The DNA G+C content of the three isolates was between 62·2 and 62·9 mol%. Strains SW-110T, SW-116 and SW-140 showed no difference in their 16S rRNA gene sequences, and their mean level of DNA–DNA relatedness was 94·8 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that the three strains form a distinct phylogenetic lineage within the cluster comprisingErythrobacterspecies. Similarities between the 16S rRNA gene sequences of strains SW-110T, SW-116 and SW-140 and the type strains ofErythrobacterspecies ranged from 98·4 % (withErythrobacter longus) to 97·7 % (withErythrobacter flavus). Levels of DNA–DNA relatedness between strains SW-110T, SW-116 and SW-140 and the type strains of all recognizedErythrobacterspecies were in the range 5·3–12·7 %. On the basis of polyphasic taxonomic data, strains SW-110T, SW-116 and SW-140 were classified as a novelErythrobacterspecies, for which the nameErythrobacter aquimarissp. nov. is proposed. The type strain is SW-110T(=KCCM 41818T=JCM 12189T).
Exiguobacterium oxidotolerans sp. nov., a novel alkaliphile exhibiting high catalase activity
Authors: Yumoto Isao , Hishinuma-Narisawa Megumi , Hirota Kikue , Shingyo Tomohiro , Takebe Fumihiko , Nodasaka Yoshinobu , Matsuyama Hidetoshi , Hara Isao
Published: November 2004

A novel alkaliphile was isolated from a drain of a fish processing plant. The isolate grew at a pH range of 7–10. Cells were Gram-positive, facultatively aerobic, motile rods with peritrichous flagella. Colonies were orange or yellow in colour. Catalase and oxidase reactions were positive. The isolate grew in 0–12 % NaCl but not above 15 % NaCl. Its cell extract exhibited 567 times higher catalase activity than an Escherichia coli cell extract. The major cellular fatty acids were iso-C13 : 0, anteiso-C13 : 0, iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, anteiso-C17 : 0 and iso-C17 : 1. Its DNA G+C content was 46·7 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing and chemotaxonomic data indicated that strain T-2-2T is a member of the genus Exiguobacterium. DNA–DNA hybridization revealed a low relatedness of the isolate to several phylogenetic neighbours (less than 25 %). On the basis of phenotypic characteristics, phylogenetic data and DNA–DNA relatedness data, the isolate merits classification as a novel species, for which the name Exiguobacterium oxidotolerans sp. nov. is proposed. The type strain is T-2-2T (=JCM 12280T=NCIMB 13980T).
Nocardia xishanensis sp. nov., a novel actinomycete isolated from soil
Authors: Zhang Jianli , Liu Zhiheng , Goodfellow Michael
Published: November 2004

The taxonomic position of a soil isolate, strain 276T, was established using a polyphasic approach. The organism showed a range of chemical and morphological properties consistent with its classification in the genusNocardia. An almost complete 16S rRNA gene sequence determined for the strain was aligned with corresponding sequences of representatives of the genusNocardiaand related taxa using three tree-making algorithms. The organism formed a distinct phyletic line within the evolutionary radiation occupied by the genusNocardiaand was most closely related to the type strain ofNocardia abscessus. However, the two strains shared a low DNA–DNA relatedness value and were readily distinguished using a combination of phenotypic properties. The combined genotypic and phenotypic data show that strain 276Tshould be assigned to the genusNocardiaas a novel species. The name proposed for this new taxon isNocardia xishanensissp. nov. The type strain is 276T(=CGMCC 4.1860T=JCM 12160T).
Nocardioides aestuarii sp. nov., isolated from tidal flat sediment
Authors: Yi Hana , Chun Jongsik
Published: November 2004

A strictly aerobic, non-motile, rod-shaped actinomycete, designated strain JC2056T, was isolated from a sediment sample of getbol, the tidal flat of Korea. Results of 16S rRNA gene sequence analysis indicated that the isolate belonged to the genus Nocardioides, with the highest similarity being to Nocardioides luteus KCTC 9575T (95·7 %). The major menaquinone was MK-8(H4), and predominant cellular fatty acids were iso-16 : 0 and iso-16 : 1 H. The DNA G+C content was 70 mol%. Based on the morphological, physiological, biochemical and chemotaxonomical data presented in this study, strain JC2056T should be classified as a novel species, for which the name Nocardioides aestuarii sp. nov. is proposed; the type strain is JC2056T (=IMSNU 14029T=KCTC 9921T=JCM 12125T).
Transfer of Bacillus halodenitrificans Denariaz et al. 1989 to the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov.
Authors: Yoon Jung-Hoon , Oh Tae-Kwang , Park Yong-Ha
Published: November 2004

A Gram-variable, endospore-forming moderately halophilic rod, strain SF-121, was isolated from a marine solar saltern of the Yellow Sea in Korea. The result of 16S rRNA gene sequence analysis showed that strain SF-121 has highest sequence similarity (99·7 %) with the type strain of Bacillus halodenitrificans. Phylogenetic analyses based on 16S rRNA gene sequences revealed that B. halodenitrificans DSM 10037T and strain SF-121 are more closely related to the genus Virgibacillus than to the genus Bacillus. Strain SF-121 and B. halodenitrificans DSM 10037T exhibited 16S rRNA gene similarity levels of 95·3–97·5 % with the type strains of Virgibacillus species and 94·0 % with the type strain of Bacillus subtilis. DNA–DNA relatedness and phenotypic data indicated that B. halodenitrificans DSM 10037T and strain SF-121 are members of the same species. B. halodenitrificans DSM 10037T and strain SF-121 exhibited DNA–DNA relatedness values of 9–11 % with the type strains of Virgibacillus carmonensis and Virgibacillus marismortui. On the basis of the phenotypic, chemotaxonomic, phylogenetic and genetic data, B. halodenitrificans should be reclassified in the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov.
Aeromonas molluscorum sp. nov., isolated from bivalve molluscs
Authors: Miñana-Galbis David , Farfán Maribel , Fusté M. Carme , Lorén J. Gaspar
Published: November 2004

FiveAeromonasstrains (848TT, 93M, 431E, 849T and 869N), which were isolated from bivalve molluscs and were recognized previously by numerical taxonomy as members of an unknownAeromonastaxon, were subjected to a polyphasic taxonomic study. DNA–DNA hybridization experiments showed that DNA of strain 848TTwas <70 % similar (27–45 %) to that of the type/reference strains of the currentAeromonashybridization groups (HGs), but 93 % similar to that of strain 93M. The DNA G+C content of the five strains ranged from 59·0 to 59·4 mol%. 16S rRNA gene sequence analysis confirmed that the strains belonged to the genusAeromonasand showed high similarity toAeromonas encheleia. Amplified fragment length polymorphism fingerprinting clustered the novel strains in a homogeneous group with low genotypic relatedness to otherAeromonasspecies. Useful phenotypic features for differentiating the five isolates from otherAeromonasspecies include their negative reactions in tests for indole production, lysine decarboxylase, gas from glucose and starch hydrolysis. From the results of this study, the nameAeromonas molluscorumsp. nov. is proposed for these strains, with the type strain 848TT(=CECT 5864T=LMG 22214T).
Classification of isolates from locations in Austria and Yellowstone National Park as Geobacillus tepidamans sp. nov.
Authors: Schäffer Christina , Franck William L. , Scheberl Andrea , Kosma Paul , McDermott Timothy R. , Messner Paul
Published: November 2004

Two moderately thermophilic, Gram-positive, spore-forming bacteria were isolated from different geographical locations and sources; strain GS5-97Tfrom a beet sugar factory in Leopoldsdorf, Lower Austria, and strain YNP10 from a geothermally heated soil, Yellowstone National Park, USA. The sequences of their 16S rRNA genes were found to be 99·8 % identical, and DNA–DNA hybridization experiments revealed that strains GS5-97Tand YNP10 share 89·9 mol% similarity to each other, but only 34·3 and 39·2 mol% similarity, respectively, toGeobacillus caldoxylosilyticusDSM 12041T, which is their closest related type strain. A polyphasic analysis showed that these two isolates were more similar to each other than to other characterized geobacilli. Their DNA G+C content was 43·2 and 42·4 mol%, respectively, and they were identical with respect to many phenotypic features (e.g. Topt55 °C; pHopt7·0). Both strains clearly displayed best growth when cultured aerobically. They differed slightly in their cellular fatty acid profiles and polar lipid pattern, and genotypically they could also be distinguished based on randomly amplified polymorphic DNA fingerprints and internal transcribed spacer analysis. Freeze-etching experiments revealed oblique surface layer (S-layer) lattices in both strains, and biochemical analyses of the purified S-layer proteins indicated the occurrence of glycosylation. Based on the properties of these organisms relative to those currently documented for the genusGeobacillusand for the various sister genera in theBacillusradiation, a novel species is proposed,Geobacillus tepidamanssp. nov., with GS5-97T(=ATCC BAA-942T=DSM 16325T) as the type strain. Strain YNP10 has been deposited in the American Type Culture Collection as ATCC BAA-943.
Geobacillus debilis sp. nov., a novel obligately thermophilic bacterium isolated from a cool soil environment, and reassignment of Bacillus pallidus to Geobacillus pallidus comb. nov.
Authors: Banat Ibrahim M. , Marchant Roger , Rahman Thahira J.
Published: November 2004

Several aerobic, motile, rod-shaped, thermophilic, spore-formingGeobacillusbacteria predominantly giving a Gram-positive staining reaction were isolated from a cool soil environment in Northern Ireland and taxonomically investigated. Two isolates, F10 and TfT, showed low 16S rRNA gene sequence similarity to recognized members of the genusGeobacillus. Phylogenetic tree investigation using neighbour-joining, maximum-likelihood and parsimony methods indicated that strains F10 and TfTrepresent a single novel species, for which the nameGeobacillus debilissp. nov. is proposed, with type strain TfT(=DSM 16016T=NCIMB 13995T) and which belongs to a subgroup of the genusGeobacilluscomprisingGeobacillus toebiiandGeobacillus caldoxylosilyticus. However,G. debilisshowed closest affinities toBacillus pallidus, which we propose should becomeGeobacillus palliduscomb. nov.
Vibrio crassostreae sp. nov., isolated from the haemolymph of oysters (Crassostrea gigas)
Authors: Faury N. , Saulnier D. , Thompson F. L. , Gay M. , Swings J. , Roux F. Le
Published: November 2004

Polyphasic analysis of five new Vibrio isolates originating from the haemolymph of diseased cultured oysters is described. The new isolates were closely related to Vibrio splendidus, having 98 % 16S rRNA gene sequence similarity. gyrB phylogenetic analysis, fluorescent amplified-fragment length polymorphism (FAFLP) fingerprinting and DNA–DNA hybridization experiments clearly showed that the new isolates form a tight genomic group that is different from the currently known Vibrio species. It is proposed to accommodate these isolates in a novel species, Vibrio crassostreae sp. nov. (type strain LGP 7T=LMG 22240T=CIP 108327T). Phenotypic and chemotaxonomic features that differentiate V. crassostreae from other known Vibrio species include arginine dihydrolase, utilization and fermentation of various carbon sources, β-galactosidase activity, NO2 production and the presence of the fatty acids 14 : 0 iso and 16 : 0 iso.
Expansion of the Candida tanzawaensis yeast clade: 16 novel Candida species from basidiocarp-feeding beetles
Authors: Suh Sung-Oui , McHugh Joseph V. , Blackwell Meredith
Published: November 2004

A major clade of new yeast taxa from the digestive tract of basidiocarp-feeding beetles is recognized based on rRNA gene sequence analyses. Almost 30 % of 650 gut isolates formed a statistically well-supported clade that included Candida tanzawaensis. The yeasts in the clade were isolated from 11 families of beetles, of which Tenebrionidae and Erotylidae were most commonly sampled. Repeated isolation of certain yeasts from the same beetle species at different times and places indicated strong host associations. Sexual reproduction was never observed in the yeasts. Based on comparisons of small- and large-subunit rRNA gene sequences and morphological and physiological traits, the yeasts were placed in Candida ambrosiae and in 16 other undescribed taxa. In this report, the novel species in the genus Candida are described and their relationships with other taxa in the Saccharomycetes are discussed. The novel species and their type strains are as follows: Candida guaymorum (NRRL Y-27568T=CBS 9823T), Candida bokatorum (NRRL Y-27571T=CBS 9824T), Candida kunorum (NRRL Y-27580T=CBS 9825T), Candida terraborum (NRRL Y-27573T=CBS 9826T), Candida emberorum (NRRL Y-27606T=CBS 9827T), Candida wounanorum (NRRL Y-27574T=CBS 9828T), Candida yuchorum (NRRL Y-27569T=CBS 9829T), Candida chickasaworum (NRRL Y-27566T=CBS 9830T), Candida choctaworum (NRRL Y-27584T=CBS 9831T), Candida bolitotheri (NRRL Y-27587T=CBS 9832T), Candida atakaporum (NRRL Y-27570T=CBS 9833T), Candida panamericana (NRRL Y-27567T=CBS 9834T), Candida bribrorum (NRRL Y-27572T=CBS 9835T), Candida maxii (NRRL Y-27588T=CBS 9836T), Candida anneliseae (NRRL Y-27563T=CBS 9837T) and Candida taliae (NRRL Y-27589T=CBS 9838T).
Loktanella hongkongensis sp. nov., a novel member of the α-Proteobacteria originating from marine biofilms in Hong Kong waters
Authors: Lau Stanley C. K. , Tsoi Mandy M. Y. , Li Xiancui , Plakhotnikova Ioulia , Wu Madeline , Wong Po-Keung , Qian Pei-Yuan
Published: November 2004

A Gram-negative, non-motile, non-spore-forming, short rod-shaped bacterium (UST950701-009PT) was isolated from a marine biofilm in Hong Kong waters. Colonies are pink in colour, convex with a smooth surface and entire edge. Brown diffusible pigment is produced. Whitish colonies, with otherwise identical morphology, emerge from every culture upon ageing. The white colonies can be maintained as separate cultures (UST950701-009W) without turning pink. UST950701-009PT and UST950701-009W have identical 16S rRNA gene sequences and similar G+C (65·9–66·2 mol%) and fatty acid (86·22–88·52 % 18 : 1ω7c) contents. Phylogenetic analysis of the 16S rRNA gene sequence places UST950701-009PT within the Rhodobacter group of the α-subclass of the Proteobacteria. The nearest neighbours belong to the genus Loktanella, with similarity values ranging from 94·5 to 95·5 %. Data on G+C and fatty acid contents support the affiliation to the genus Loktanella. UST950701-009PT and -009W are heterotrophic, strictly aerobic and require NaCl for growth (2·0–14·0 %). Both grow in pH 5·0–10·0 and at 8–44 °C. Both are positive in oxidase, catalase and β-galactosidase tests, but they differ in the pattern of carbohydrate oxidation and assimilation. Molecular evidence together with phenotypic characteristics shows that UST950701-009PT constitutes a novel species within the genus Loktanella. The name Loktanella hongkongensis sp. nov. is proposed; the type strain is UST950701-009PT (=NRRL B-41039T=JCM 12479T) and a morphovar is UST950701-009W (=NRRL B-41040=JCM 12480).
MIM/BEG4, a Sonic hedgehog-responsive gene that potentiates Gli-dependent transcription
Authors: Callahan Christopher A. , Ofstad Tyler , Horng Lily , Wang Jordon K. , Zhen Hanson H. , Coulombe Pierre A. , Oro Anthony E.
Published: November 2004

Sonic hedgehog (Shh) signaling plays a critical role during development and carcinogenesis. While Gli family members govern the transcriptional output of Shh signaling, little is known how Gli-mediated transcriptional activity is regulated. Here we identify the actin-binding protein Missing in Metastasis (MIM) as a new Shh-responsive gene. Together, Gli1 and MIM recapitulate Shh-mediated epidermal proliferation and invasion in regenerated human skin. MIM is part of a Gli/Suppressor of Fused complex and potentiates Gli-dependent transcription using domains distinct from those used for monomeric actin binding. These data define MIM as both a Shh-responsive gene and a new member of the pathway that modulates Gli responses during growth and tumorigenesis.
JNK potentiates TNF-stimulated necrosis by increasing the production of cytotoxic reactive oxygen species
Authors: Ventura Juan-Jose , Cogswell Patricia , Flavell Richard A. , Baldwin Albert S. , Davis Roger J.
Published: November 2004

The c-Jun NH2-terminal kinase (JNK) has been implicated in both cell death and survival responses to different stimuli. Here we reexamine the function of JNK in tumor necrosis factor (TNF)-stimulated cell death using fibroblasts isolated from wild-type, Mkk4-/-Mkk7-/-, and Jnk1-/-Jnk2-/- mice. We demonstrate that JNK can act to suppress TNF-stimulated apoptosis. However, we find that JNK can also potentiate TNF-stimulated necrosis by increasing the production of reactive oxygen species (ROS). Together, these data indicate that JNK can shift the balance of TNF-stimulated cell death from apoptosis to necrosis. Increased necrosis may represent a contributing factor in stress-induced inflammatory responses mediated by JNK.
The Photogrammetric Society: 1952–2001
Authors: Atkinson K. B. , Newton I.
Published: November 2004

A scholarly account of the formative discussions, the founding and the first 20 years of the Photogrammetric Society was published in 1971 and republished in 1974. This present review concentrates on the latter years of the life of the Photogrammetric Society prior to its merger with the Remote Sensing Society in 2001.

The authors joined the Photogrammetric Society in 1960 and were conspicuous in its affairs for many years. Although both occupied the Society's presidential chair, they also fulfilled several other roles in its efficient management. Atkinson's first contribution to the Photogrammetric Record was published in 1968 and Newton's in 1971.
Bundle Adjustment with Self–Calibration Using Straight Lines
Authors: Habib Ayman F. , Morgan Michel , Lee Young–Ran
Published: November 2004

Increased use of digital imagery has facilitated the opportunity to use features, in addition to points, in photogrammetric applications. Straight lines are often present in object space, and prior research has focused on incorporating straight–line constraints into bundle adjustment for frame imagery. In the research reported in this paper, object–space straight lines are used in a bundle adjustment with self–calibration. The perspective projection of straight lines in the object space produces straight lines in the image space in the absence of distortions. Any deviations from straightness in the image space are attributed to various distortion sources, such as radial and decentric lens distortions. Before incorporating straight lines into a bundle adjustment with self–calibration, the representation and perspective transformation of straight lines between image space and object space should be addressed. In this investigation, images of straight lines are represented as a sequence of points along the image line. Also, two points along the object–space straight line are used to represent that line. The perspective relationship between image– and object–space lines is incorporated in a mathematical constraint. The underlying principle in this constraint is that the vector from the perspective centre to an image point on a straight–line feature lies on the plane defined by the perspective centre and the two object points defining the straight line. This constraint has been embedded in a software application for bundle adjustment with self–calibration that can incorporate point as well as straight–line features. Experiments with simulated and real data have proved the feasibility and the efficiency of the algorithm proposed.
An Approach for Merging Plans Hierarchically in Decomposable Domains
Authors: Britanik J. , Marefat M.
Published: November 2004

Recent works in domain‐independent plan merging have shown that the optimal plan‐merging problem is NP‐hard, and heuristic algorithms have been proposed to generate near‐optimal solutions. These works have shown heuristic algorithms which assume that the mergeability of two actions can be determined by considering only the actions themselves. In this paper, we show that it is often that case that the surrounding actions in the plan must also be considered when determining the mergeability of two or more actions; therefore, the context in which the actions are used affects their mergeability. To address this problem, we have developed a plan‐merging methodology that merges partial‐order plans based on the the notion of plan fragments, which encapsulate actions with the context in which they are being utilized. This methodology applies to a class of planning domains, called decomposable domains, which consist of actions that follow all or some portion of a type sequence. Merging is performed hierarchically by action type. We also investigate the previously unexplored notion of alternative actions in domain‐independent plan merging, which can improve the quality of the resulting merged plan. A novel approach is presented for removing cyclic dependencies that may occur during the plan‐merging process.

A key part of the methodology is the computation of a minimum cost cover of plan fragments. We provide theoretical analyses of two optimal algorithms and a greedy‐based algorithm for computing the minimum cost cover. We support the theoretical analysis of these algorithms with experimental data to show that the greedy approach is near‐optimal and efficient.
Civil Society or the State?: Recent Approaches to the History of Voluntary Welfare
Authors: Kidd Alan
Published: November 2004

Since the 1970s a drift away from state corporatist solutions to social welfare problems has had its parallel in an academic rediscovery of the voluntary sector. Revived confidence in non–statutory approaches often assumes two things. Firstly, that voluntary action is a vital component in civil society and that civil society itself is an attribute of liberal democracy. These ideas are central to the perceived ‘crisis of the welfare state’. They are also related to debates about political culture and the future of democracy with the institutions of civil society cast positively as ‘schools of citizenship’. Secondly, it is frequently assumed that there is an opposition in principle between the voluntary and the statutory and in some quarters an assumption (reversing an earlier presumption about the rationality of state welfare) that voluntary action is the superior mechanism (at least morally). The purpose of this paper is threefold. First, I want to reflect on the revival of interest in the role of the institutions of civil society in the history of welfare provision. Second, I will survey some recent approaches to voluntary action and ‘civil society’. Third, in the process of this survey I discuss the relevance of these approaches to the study of past states of welfare.
“Engines Of Acculturation”: The Last Political Generation of Jewish Women in Interwar East Europe
Authors: Elazar Dahlia S.
Published: November 2004

This study explores the formation of a political generation of Jewish women in interwar East Europe. Based on questionnaire data obtained from the Survivors of the Ravensbrueck Concentration Camp for Women and on secondary historical materials, it applied Mannheim’s theory of political generations and the conditions for the formation of “generational units” under the impression of “fresh contact” in order to examine the role of class, education, and religiosity in the formation of political generations. Under the specific socio–historical circumstances analyzed, it is argued that Jewish women who came of age in interwar East Europe formed, perhaps for the first time a distinct political generation, as evidenced by high rates of political participation and assimilation into the thriving secular nationalistic culture of their time.
Third‐Degree Price Discrimination With Interdependent Demands
Authors: Layson Stephen K.
Published: November 2004

This paper analyzes the price, output, and welfare effects of third‐degree price discrimination for a monopolist who sells in two interdependent markets. The case where the two goods sold by the monopolist are complements is analyzed as well as the more typical case where the two goods are substitutes. The economic effects of price discrimination are shown to depend on the type and strength of demand interdependence, the curvature of the demands and the slope of marginal cost. The circumstances under which price discrimination causes both market prices to either rise or fall are also analyzed.
The Entry‐Inducing Effects of Horizontal Mergers: An Exploratory Analysis
Authors: Werden Gregory J. , Froeb Luke M.
Published: November 2004

Antitrust law presumes that entry normally prevents or reverses anticompetitive effects from horizontal mergers. But when sunk costs associated with entry are at levels suggested by prevailing market structure, the opportunity for entry created by an anticompetitive merger plausibly is too small to induce entry, even absent Stiglerian ‘barriers to entry.’ This is illustrated for Cournot and Bertrand models. Significant entry also makes otherwise profitable Bertrand mergers unprofitable, assuming no efficiency gains. Consequently, the entry issue can be collapsed into the efficiency issue: if a presumably profitable merger does not generate significant efficiencies, it cannot be expected to induce entry.
How to Set Minimum Acceptable Bids, with an Application to Real Estate Auctions
Authors: McAfee R. Preston , Quan Daniel C. , Vincent Daniel R.
Published: November 2004

In a general auction model with affiliated signals, common components to valuations and endogenous entry, we compute the equilibrium bidding strategies and outcomes, and derive a lower bound on the optimal reserve price. This lower bound can be computed using data on past auctions combined with information about the subsequent sales prices of unsold goods. We illustrate how to compute the lower bound using data from real estate auctions.
All–Pay Auctions with Variable Rewards
Authors: Kaplan Todd , Luski Israel , Sela Aner , Wettstein David
Published: November 2004

We study all–pay auctions with variable rewards under incomplete information. In standard models, a reward depends on a bidder’s privately known type; however, in our model it is also a function of his bid. We show that in such models there is a potential for paradoxical behavior where a reduction in the rewards or an increase in costs may increase the expected sum of bids or alternatively the expected highest bid.
Love or Money? The Effects of Owner Motivation in the California Wine Industry
Authors: Scott Morton Fiona M. , Podolny Joel M.
Published: November 2004

Models that assume only consumer tastes determine the characteristics of supply are restrictive; producers can gain utility from aspects of production and pay for deviating from demand by accepting lower financial returns. We model and measure motivations of California winery owners, and analyze their effects on quality and price. We find utility–maximizers are more likely to produce high quality and set higher quality–adjusted prices. Profit–oriented owners are less likely to produce high quality wines. These results suggest that the presence of hobbyists who enjoy producing high quality may lower financial returns in the segment and discourage profit–maximizers from locating there.
Pricing with Consumer Switching Costs: Evidence from the Credit Card Market
Authors: Stango Victor
Published: November 2004

The credit card market is a natural setting for investigating the relationship between pricing and consumer switching costs. I find, using a detailed panel of credit card issuers, that switching costs are an important influence on pricing for commercial banks. The results are stronger for commercial banks with risky customer bases, suggesting that there is a relationship between default and switching costs. Switching costs appear to have almost no influence on pricing for credit unions, a result that is consistent with their status as not–for–profit entities.
Science And Faith: New Books with the Same Scepticism
Authors: Anderson Owen
Published: November 2004

Books reviewed in this article:

Richard A. Lee Jr., Science, the Singular, and the Question of Theology

Andrew P. Porter, By the Waters of Naturalism: Theology Perplexed Among the Sciences

W. Mark Richardson, Robert John Russell, Philip Clayton, and Kirk Wegter–McNelly (eds), Science and the Spiritual Quest: New Essays by Leading Scientists

W. Mark Richardson and Gordy Slack (eds), Faith in Science: Scientists Search for Truth
Survey Evidence on Wage Rigidity and Unemployment: Sweden in the 1990s*
Authors: Agell Jonas , Lundborg Per
Published: November 2004

We document the results of a repeat survey, which updates Agell and Lundborg (1995), on wage rigidity in a sample of 159 Swedish manufacturing firms, conducted during the severe Swedish recession of the 1990s. It is found that not even a prolonged period of very high unemployment and quite low inflation softened workers’ resistance to wage cuts. We discuss possible reasons for this. In addition, we report new evidence on underbidding, efficiency‐wage mechanisms, and unemployment persistence.