bluuebunny/crossref_metadata_2025 huggingface dataset:
The Organization of the Core Proteins of the Yeast Spindle Pole Body
Authors: Muller Eric G.D. , Snydsman Brian E. , Novik Isabella , Hailey Dale W. , Gestaut Daniel R. , Niemann Christine A. , O'Toole Eileen T. , Giddings Tom H. , Sundin Bryan A. , Davis Trisha N.
Published: May 2005

The spindle pole body (SPB) is the microtubule organizing center of Saccharomyces cerevisiae. Its core includes the proteins Spc42, Spc110 (kendrin/pericentrin ortholog), calmodulin (Cmd1), Spc29, and Cnm67. Each was tagged with CFP and YFP and their proximity to each other was determined by fluorescence resonance energy transfer (FRET). FRET was measured by a new metric that accurately reflected the relative extent of energy transfer. The FRET values established the topology of the core proteins within the architecture of SPB. The N-termini of Spc42 and Spc29, and the C-termini of all the core proteins face the gap between the IL2 layer and the central plaque. Spc110 traverses the central plaque and Cnm67 spans the IL2 layer. Spc42 is a central component of the central plaque where its N-terminus is closely associated with the C-termini of Spc29, Cmd1, and Spc110. When the donor-acceptor pairs were ordered into five broad categories of increasing FRET, the ranking of the pairs specified a unique geometry for the positions of the core proteins, as shown by a mathematical proof. The geometry was integrated with prior cryoelectron tomography to create a model of the interwoven network of proteins within the central plaque. One prediction of the model, the dimerization of the calmodulin-binding domains of Spc110, was confirmed by in vitro analysis.
From “Ward of the State” to “Revolutionary Without a Movement”: The Political Development of William C. Norris and Control Data Corporation, 1957–1986
Authors: Hart David M.
Published: May 2005

This article traces the political development of the Control Data Corporation (CDC) and its founder and chief executive officer, William C. Norris, from the firm’s formation in 1957 until his departure from its leadership in 1986. Norris was entrepreneurial in his political strategy, taking large risks to pursue what he perceived to be large opportunities in such areas as antitrust, trade policy, and poverty alleviation. Indeed, his perceptions of these opportunities often diverged substantially from those of others in the computer industry and the broader corporate and policy communities. The article links these differences to Norris’s personal circumstances, the business situation of CDC, and the broader political currents of the times. The experiences of Norris and CDC suggest that business historians need a more expansive and flexible conception of the political attitudes and behavior of business leaders and of the business-government relationship in the United States.
Continuity and Change in the Employment and Promotion of Japanese White-Collar Employees: The Case of the House of Mitsui
Authors: Kasuya Makoto
Published: May 2005

Lifetime employment is one of the most conspicuous features of contemporary large Japanese corporations. The employment practices of merchant houses in the Edo period (1603–1868) are sometimes proposed as one origin of such lifetime commitment. Little attention has been paid, however, to the connections between long-term employment in the Edo period and its practice in the twentieth century. This article examines how Edo employment practices were adapted to the environment of the early twentieth century within a new context of modern educational institutions and the need for professional managers.
An Efficient Pursuit? Independent Shopkeeping in 1930s Britain
Authors: Phillips Simon , Alexander Andrew
Published: May 2005

During the 1930s, the small-scale retailer was regarded by many commentators as being responsible for the apparent inefficiencies of the retail trade in Britain. Using a range of documentary evidence from the period, this article draws attention to debate on the merits of large- and small-scale retailers, highlighting a concern for the latter’s contribution to wider community well-being and to developments in retail trade practices. The relative inefficiency of the small trader was frequently explained in relation to a lack of awareness of sound shop management. Consequently, emphasis was placed by commentators on the need for small traders to enhance their knowledge of retail management practices in order to improve their own competitive position and efficiency in the retail trade more widely. Both the popular and trade press offered small traders a range of advice that was intended to improve their fortunes. This article considers the form and content of such advice.
Muricauda flavescens sp. nov. and Muricauda aquimarina sp. nov., isolated from a salt lake near Hwajinpo Beach of the East Sea in Korea, and emended description of the genus Muricauda
Authors: Yoon Jung-Hoon , Lee Mi-Hwa , Oh Tae-Kwang , Park Yong-Ha
Published: May 2005

Four Gram-negative, non-spore-forming, slightly halophilic rods (strains SW-62T, SW-74, SW-63T and SW-72) with appendages were isolated from a salt lake near Hwajinpo Beach on the East Sea in Korea, and subjected to a polyphasic taxonomic analysis. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SW-62T, SW-74, SW-63T and SW-72 formed a coherent cluster with Muricauda ruestringensis. Strains SW-62T and SW-74 had the same 16S rRNA gene sequence, as did strains SW-63T and SW-72. The level of 16S rRNA gene sequence similarity between strains SW-62T and SW-63T was 97·0 %. Strains SW-62T and SW-63T exhibited 16S rRNA gene similarity levels of 96·5 and 98·3 %, respectively, with respect to M. ruestringensis DSM 13258T. The predominant isoprenoid quinone found in the four isolates and M. ruestringensis DSM 13258T was MK-6. The four strains contained iso-C17 : 0 3-OH, iso-C15 : 1 and iso-C15 : 0 as the major fatty acids. Their DNA G+C contents were 44·1–45·4 mol%. The levels of DNA–DNA relatedness indicated that strains SW-62T and SW-74 and strains SW-63T and SW-72 were members of two species that were different from M. ruestringensis. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains SW-62T and SW-74 and strains SW-63T and SW-72 were placed in the genus Muricauda as two distinct novel species, for which the names Muricauda flavescens sp. nov. (type strain, SW-62T=KCCM 41645T=JCM 11812T) and Muricauda aquimarina sp. nov. (type strain, SW-63T=KCCM 41646T=JCM 11811T), respectively, are proposed.
Burkholderia phytofirmans sp. nov., a novel plant-associated bacterium with plant-beneficial properties
Authors: Sessitsch A. , Coenye T. , Sturz A. V. , Vandamme P. , Barka E. Ait , Salles J. F. , Van Elsas J. D. , Faure D. , Reiter B. , Glick B. R. , Wang-Pruski G. , Nowak J.
Published: May 2005

A Gram-negative, non-sporulating, rod-shaped, motile bacterium, with a single polar flagellum, designated strain PsJNT, was isolated from surface-sterilized onion roots. This isolate proved to be a highly effective plant-beneficial bacterium, and was able to establish rhizosphere and endophytic populations associated with various plants. Seven related strains were recovered from Dutch soils. Based on 16S rRNA gene sequence data, strain PsJNT and the Dutch strains were identified as representing a member of the genus Burkholderia, as they were closely related to Burkholderia fungorum (98·7 %) and Burkholderia phenazinium (98·5 %). Analysis of whole-cell protein profiles and DNA–DNA hybridization experiments confirmed that all eight strains belonged to a single species. Strain PsJNT had a DNA G+C content of 61·0 mol%. Only low levels of DNA–DNA hybridization to closely related species were found. Qualitative and quantitative differences in fatty acid composition between strain PsJNT and closely related species were identified. The predominant fatty acids in strain PsJNT were 16 : 0, 18 : 1ω7c and summed feature 3 (comprising 16 : 1ω7c and/or iso-15 : 0 2-OH). Isolate PsJNT showed high 1-aminocyclopropane-1-carboxylate deaminase activity and is therefore able to lower the ethylene level in a developing or stressed plant. Production of the quorum-sensing signal compound 3-hydroxy-C8-homoserine lactone was detected. Based on the results of this polyphasic taxonomic study, strain PsJNT and the seven Dutch isolates are considered to represent a single, novel species, for which the name Burkholderia phytofirmans sp. nov. is proposed. The type strain is strain PsJNT (=LMG 22146T=CCUG 49060T).
Owenweeksia hongkongensis gen. nov., sp. nov., a novel marine bacterium of the phylum ‘Bacteroidetes’
Authors: Lau Ken W. K. , Ng Connie Y. M. , Ren Jianping , Lau Simon C. L. , Qian Pei-Yuan , Wong Po-Keung , Lau T. C. , Wu Madeline
Published: May 2005

An aerobic, Gram-negative, non-fermentative, rod-shaped, motile, orange-pigmented bacterium, UST20020801T, was isolated from sea-water samples collected from Port Shelter, Hong Kong, S.A.R., China, in August 2002. The full 16S rRNA gene sequence of this strain shared only 87·5 % similarity with its nearest relative, Crocinitomix catalasitica, a species of the family Cryomorphaceae. However, strain UST20020801T possessed menaquinone-6, a major respiratory quinone of members of the family Flavobacteriaceae. This strain contains unique fatty acids such as i15 : 1G, i17 : 1ω9c, 2-OH 15 : 0, 15 : 1ω6c and three unknown fatty acids of equivalent chain-length of 11·543, 13·565 and 16·582. Further analysis of its ecophysiology and biochemistry suggests that this strain represents a new genus in the phylum ‘Bacteroidetes’. The name Owenweeksia hongkongensis gen. nov., sp. nov. is proposed. The type strain is UST20020801T (=NRRL B-23963T=JCM 12287T).
Reclassification of Agrobacterium ferrugineum LMG 128 as Hoeflea marina gen. nov., sp. nov.
Authors: Peix Alvaro , Rivas Raúl , Trujillo Martha E. , Vancanneyt Marc , Velázquez Encarna , Willems Anne
Published: May 2005

Members of the species Agrobacterium ferrugineum were isolated from marine environments. The type strain of this species (=LMG 22047T=ATCC 25652T) was recently reclassified in the new genus Pseudorhodobacter, in the order ‘Rhodobacterales’ of the class ‘Alphaproteobacteria’. Strain LMG 128 (=ATCC 25654) was also initially classified as belonging to the species Agrobacterium ferrugineum; however, the nearly complete 16S rRNA gene sequence of this strain indicated that it does not belong within the genus Agrobacterium or within the genus Pseudorhodobacter. The closest related organism, with 95·5 % 16S rRNA gene similarity, was Aquamicrobium defluvii from the family ‘Phyllobacteriaceae’ in the order ‘Rhizobiales’. The remaining genera from this order had 16S rRNA gene sequence similarities that were lower than 95·1 % with respect to strain LMG 128. These phylogenetic distances suggested that strain LMG 128 belonged to a different genus. The major fatty acid present in strain LMG 128 was mono-unsaturated straight chain 18 : 1ω7c. The G+C content of the DNA was 53·1 mol%. Strain LMG 128 grew at 4 °C but not at 40 °C, and tolerated up to 5 % NaCl. The pH range for growth was 6–8. It produced urease and β-galactosidase, and hydrolysed aesculin. Denitrification was negative. Growth was observed with many carbohydrates as the only carbon source. The data from this polyphasic study indicate that this strain belongs to a new genus of the family ‘Phyllobacteriaceae’, and therefore it is proposed that strain LMG 128T should be reclassified as representing a novel species within the new genus Hoeflea gen. nov., for which the name Hoeflea marina sp. nov. is proposed.
Bacteroides massiliensis sp. nov., isolated from blood culture of a newborn
Authors: Fenner Lukas , Roux Véronique , Mallet Marie-Noëlle , Raoult Didier
Published: May 2005

Gram-negative anaerobic rods were isolated from blood culture of a healthy baby born at term. Based on phylogenetic analysis and specific phenotypic characteristics, this strain was included within the Bacteroides cluster. The novel bile-resistant anaerobic species was designated Bacteroides massiliensis and it has 92·8 % 16S rRNA similarity to Bacteroides vulgatus and a DNA G+C content of 49 mol%. The major cellular fatty acid is anteiso-branched C15 : 0. The type strain of B. massiliensis sp. nov. is B84634T (=CIP 107942T=CCUG 48901T).
Lysobacter concretionis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor
Authors: Bae Hee-Sung , Im Wan-Taek , Lee Sung-Taik
Published: May 2005

The taxonomic positions of Lysobacter species with validly published names and a novel strain Ko07T, which was newly isolated from an upflow anaerobic sludge blanket reactor treating wastewater from a brewery, were (re)estimated on the basis of results obtained by using a polyphasic taxonomy approach. Phylogenetic inference based on 16S rRNA gene sequences showed that strain Ko07T and all Lysobacter species with validly published names clustered together in a phylogenetic branch within the class ‘Gammaproteobacteria’. The sequence similarity of strain Ko07T to the type strains of established Lysobacter species was in the range 94·9–96·7 %. Ubiquinone Q-8 and branched fatty acids, C11 : 0 iso, C15 : 0 iso, C16 : 0 iso, iso C17 : 1
ω9c and C11 : 0 iso 3OH, predominantly appeared in strain Ko07T as well as in all type strains of the recognized Lysobacter species. The DNA–DNA hybridization values of strain Ko07T with those of recognized Lysobacter species were estimated to be 2–20 %. Despite sharing common taxonomic features in important phenotypic characteristics, such as gliding movement, long-rod shape and proteolytic activity, strain Ko07T could be distinguished from the Lysobacter species with validly published names by its low DNA–DNA hybridization value, a comparatively low DNA G+C content (63·8 mol%), substrate utilization and some physiochemical characteristics. On the basis of the results obtained in this study, it is proposed that strain Ko07T should be classified as representing a novel member of the genus Lysobacter, for which the name Lysobacter concretionis sp. nov. is proposed. The type strain is Ko07T (=KCTC 12205T=DSM 16239T).
Thioclava pacifica gen. nov., sp. nov., a novel facultatively autotrophic, marine, sulfur-oxidizing bacterium from a near-shore sulfidic hydrothermal area
Authors: Sorokin Dimitry Yu. , Tourova Tatjana P. , Spiridonova Elizaveta M. , Rainey Fred A. , Muyzer Gerard
Published: May 2005

Strain TL 2T was isolated on mineral medium with thiosulfate from a near-shore sulfidic hydrothermal area in Matupi Harbour on the island of New Britain, Papua New Guinea. The cells varied from long filaments with swollen ends, often aggregated, to short rods, depending on the growth conditions. The bacterium was obligately aerobic and grew autotrophically with thiosulfate as energy source or heterotrophically with organic acids and sugars. In thiosulfate-limited continuous culture, μ
max and Y
max for autotrophic growth were 0·1 h−1 and 3 g protein mol−1, respectively. From the various reduced sulfur compounds tested, only thiosulfate and sulfide supported active respiration. Inorganic carbon was assimilated via the Calvin cycle. Presence of the ‘green’-type of form I RubisCO gene was detected. Growth was possible from 15 to 47 °C with an optimum at 35 °C, pH 6·5–8·5 with an optimum at pH 8·0, and between 10 and 90 g NaCl l−1 with an optimum at 35 g l−1. Phylogenetic analysis based on 16S rRNA and cbbL gene sequences demonstrated that strain TL 2T forms a separate lineage within the alpha-3 subdivision of the Proteobacteria, distantly related to the genera Rhodovulum and Rhodobacter. On the basis of these results, a novel genus and species, Thioclava pacifica gen. nov., sp. nov., is proposed to accommodate strain TL 2T (=DSM 10166T=UNIQEM 229T).
Petrimonas sulfuriphila gen. nov., sp. nov., a mesophilic fermentative bacterium isolated from a biodegraded oil reservoir
Authors: Grabowski Agnès , Tindall Brian J. , Bardin Véronique , Blanchet Denis , Jeanthon Christian
Published: May 2005

A mesophilic, anaerobic, fermentative bacterium, strain BN3T, was isolated from a producing well of a biodegraded oil reservoir in Canada. Cells were Gram-negative, non-motile rods that did not form spores. The temperature range for growth was 15–40 °C, with optimum growth at 37–40 °C. The strain grew with up 4 % NaCl, with optimum growth in the absence of NaCl. Tryptone was required for growth. Yeast extract and elemental sulfur stimulated growth. Growth was also enhanced during fermentation of glucose, arabinose, galactose, maltose, mannose, rhamnose, lactose, ribose, fructose, sucrose, cellobiose, lactate, mannitol and glycerol. Acetate, hydrogen and CO2were produced during glucose fermentation. Elemental sulfur and nitrate were used as electron acceptors and were reduced to sulfide and ammonium, respectively. The G+C content of the genomic DNA was 40·8 mol%. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the strain was a member of the phylum ‘Bacteroidetes’, distantly related to the generaBacteroidesandTannerella(similarity values of less than 90 %). The chemotaxonomic data (fatty acids, polar lipids and quinones composition) also indicated that strain BN3Tcould be clearly distinguished from its closest cultivated relatives. This novel organism possesses phenotypic, chemotaxonomic and phylogenetic traits that do not allow its classification as a member of any previously described genus; therefore, it is proposed that this isolate should be described as a member of a novel species of a new genus,Petrimonasgen. nov., of whichPetrimonas sulfuriphilasp. nov. is the type species. The type strain is BN3T(=DSM 16547T=JCM 12565T).
Leuconostoc durionis sp. nov., a heterofermenter with no detectable gas production from glucose
Authors: Leisner J. J. , Vancanneyt M. , Van der Meulen R. , Lefebvre K. , Engelbeen K. , Hoste B. , Laursen B. G. , Bay L. , Rusul G. , De Vuyst L. , Swings J.
Published: May 2005

Three lactic acid bacterial (LAB) strains obtained from a Malaysian acid-fermented condiment, tempoyak (made from pulp of the durian fruit), showed analogous but distinct patterns after screening by SDS-PAGE of whole-cell proteins and comparison with profiles of all recognized LAB species. 16S rRNA gene sequencing of one representative strain showed that the taxon belongs phylogenetically to the genus Leuconostoc, with its nearest neighbour being Leuconostoc fructosum (98 % sequence similarity). Biochemical characteristics and DNA–DNA hybridization experiments demonstrated that the strains differ from Leuconostoc fructosum and represent a single, novel Leuconostoc species for which the name Leuconostoc durionis sp. nov. is proposed. The type strain is LMG 22556T (=LAB 1679T=D-24T=CCUG 49949T).
Phylogenetic analysis and description of Eperythrozoon coccoides, proposal to transfer to the genus Mycoplasma as Mycoplasma coccoides comb. nov. and Request for an Opinion
Authors: Neimark Harold , Peters Wallace , Robinson Brian L. , Stewart Lindsay B.
Published: May 2005

Eperythrozoon coccoides, an epierythrocytic organism that causes a mild haemolytic anaemia in laboratory and wild mice, currently is thought to be a rickettsia. To determine the relationship of this agent to other haemotrophic bacterial parasites, the 16S rRNA gene of this organism has been sequenced and it is shown by phylogenetic analysis that this wall-less bacterium is not a rickettsia but actually is a mycoplasma. This mycoplasma shares properties with and is closely related to the other uncultivated mycoplasmas that comprise a recently identified group, the haemotrophic mycoplasmas (haemoplasmas). The haemoplasma group is composed of formerEperythrozoonandHaemobartonellaspecies as well as newly identified haemotrophic mycoplasmas. Haemoplasmas parasitize the surface of erythrocytes of a wide variety of vertebrate animal hosts and are transmitted mainly by blood-feeding arthropod vectors. Because both primary infections and chronic latent infections caused by this bacterium have been observed in many laboratories and this bacterium has been the subject of much experimental work, considerable information exists about this haemotrophic mycoplasma that may be applicable to other haemoplasmas. It is proposed thatEperythrozoon coccoidesbe reclassified asMycoplasma coccoidescomb. nov. A Request for an Opinion is submitted to the Judicial Commission of the International Committee on Systematics of Prokaryotes regarding this reclassification.
Cryptococcus taeanensis sp. nov., a new anamorphic basidiomycetous yeast isolated from a salt farm
Authors: Shin Kee-Sun , Park Yong-Ha , Park Dong-Jin , Kim Chang-Jin
Published: May 2005

Cryptococcus taeanensis, a new anamorphic yeast species originating from a salt farm on the Taean peninsula in Korea, is described. Strain 3-12T grew by budding, contained ubiquinone Q-10 and xylose in cell hydrolysates, utilized d-glucuronate and did not ferment d-glucose. A molecular phylogenetic analysis based on the large-subunit rRNA D1/D2 domain and ITS region sequences placed C. taeanensis near Auriculibuller fuscus and Bullera japonica, recently proposed taxa of the Tremellales. However, these species were distinguishable based on standard physiological tests used for yeast identification, with characteristics including the assimilation of l-sorbose, absence of ballistoconidia, no arbutin hydrolysis and no growth in the presence of 0·01 % cycloheximide. The isolate exhibited the typical physiology of the genus Cryptococcus Vuillemin, but its large-subunit rRNA D1/D2 domain sequence was clearly distinct from previously described species in the genus. Therefore, on the basis of these results, Cryptococcus taeanensis sp. nov. is proposed; the type strain is 3-12T (=KCTC 17149T=CBS 9742T).
Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment
Authors: Liu Chenli , Shao Zongze
Published: May 2005

Two bacterial strains, B-5T and NO1A, were isolated from the surface water of the Bohai Sea and deep-sea sediment of the east Pacific Ocean, respectively. Both strains were halophilic, aerobic, Gram-negative, non-spore-forming, catalase- and oxidase-positive motile rods. They grew on a restricted spectrum of organic compounds, including some organic acids and alkanes. On the basis of 16S rRNA gene sequence similarity, strains B-5T and NO1A were shown to belong to the γ-Proteobacteria. Highest similarity values were found with Alcanivorax venustensis (95·2 %), Alcanivorax jadensis (94·6 %) and Alcanivorax borkumensis (94·1 %). Principal fatty acids of both strains were C16 : 0, C16 : 1
ω7c and C18 : 1
ω7c. The chemotaxonomically characteristic fatty acid C19 : 0 cyclo ω8c was also detected. On the basis of the above, together with results of physiological and biochemical tests, DNA–DNA hybridization, comparisons of 16S–23S internal transcribed spacer sequences and comparisons of the partial deduced amino acid sequence of alkane hydroxylase, both strains were affiliated to the genus Alcanivorax but were differentiated from recognized Alcanivorax species. Therefore, a novel species, Alcanivorax dieselolei sp. nov., represented by strains B-5T and NO1A is proposed, with the type strain B-5T (=DSM 16502T=CGMCC 1.3690T).
Pseudomonas argentinensis sp. nov., a novel yellow pigment-producing bacterial species, isolated from rhizospheric soil in Córdoba, Argentina
Authors: Peix Alvaro , Berge Odile , Rivas Raúl , Abril Adriana , Velázquez Encarna
Published: May 2005

During a study in the Argentinian region of Chaco (Córdoba), some strains were isolated from the rhizosphere of grasses growing in semi-desertic arid soils. Two of these strains, one isolated from the rhizospheric soil of Chloris ciliata (strain CH01T) and the other from Pappophorum caespitosum (strain PA01), were Gram-negative, strictly aerobic rods, which formed yellow round colonies on nutrient agar. They produced a water-insoluble yellow pigment, and a fluorescent pigment was also detected. A polyphasic taxonomic approach was used to characterize the strains. Comparison of the 16S rRNA gene sequences showed a similarity of 99·3 % between them, and phylogenetic analysis revealed that the strains belong to the genus Pseudomonas, within the γ-subclass of the Proteobacteria. The closest related species is Pseudomonas straminea IAM 1598T (similarity of 99·0 % to strain CH01T and 98·8 % to strain PA01), clustering in a separate branch with the various methods of tree building used. Strains CH01T and PA01 both had a single polar flagellum, like other yellow pigment-producing pseudomonads related to them. Both strains produced catalase and oxidase. Similar to P. straminea, they did not hydrolyse gelatin or casein. The G+C DNA contents determined were 57·5 mol% for CH01T and 58·0 mol% for PA01. DNA–DNA hybridization results showed 81 % relatedness between them, and only 40–44 % relatedness with respect to the type strain of P. straminea. These results, together with other phenotypic characteristics, support the conclusion that both isolates belong to the same species, and should be described as representing a novel species within the genus Pseudomonas, for which the name Pseudomonas argentinensis sp. nov. is proposed. The type strain is CH01T (=LMG 22563T=CECT 7010T).
Comparative study of overlapping genes in bacteria, with special reference to Rickettsia prowazekii and Rickettsia conorii
Authors: Sakharkar Kishore R. , Sakharkar Meena K. , Verma Chandra , Chow Vincent T. K.
Published: May 2005

Overlapping genes have been proposed as a means of achieving genome reduction by compressing the maximum amount of information in limited sequence space. In this report, comparative analyses of the overlapping genes of genomes of nine bacteria with different lifestyles were performed. The results clearly suggest that overlapping genes may be a result of evolutionary pressure to minimize genome size. The genomes of two closely related obligatory intracellular parasites –Rickettsia prowazekiiandRickettsia conorii– were investigated further. Detailed analyses of these two genomes revealed that mutations at the ends of coding regions and elimination of intergenic DNA are the main forces that determine overlapping of genes.
Psychrobacter aquimaris sp. nov. and Psychrobacter namhaensis sp. nov., isolated from sea water of the South Sea in Korea
Authors: Yoon Jung-Hoon , Lee Choong-Hwan , Yeo Soo-Hwan , Oh Tae-Kwang
Published: May 2005

Two Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strains, SW-210Tand SW-242T, were isolated from sea water of the South Sea in Korea, and were characterized taxonomically by means of a polyphasic approach. The two isolates grew optimally at 25–30 °C and in the presence of 2–3 % (w/v) NaCl. Strains SW-210Tand SW-242Tcontained Q-8 as the predominant respiratory lipoquinone and C18 : 1ω9cas the major fatty acid. The DNA G+C contents of strains SW-210Tand SW-242Twere 43·2 and 45·3 mol%, respectively. The 16S rRNA gene sequences of strains SW-210Tand SW-242Twere 98·9 % similar, and the mean DNA–DNA relatedness value between them was 24 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains SW-210Tand SW-242Tform distinct phylogenetic lineages within the radiation of the cluster comprisingPsychrobacterspecies, having 16S rRNA gene sequence similarity levels of 95·9–99·2 % with respect to the type strains ofPsychrobacterspecies. The levels of DNA–DNA relatedness between the two isolates and the type strains of 15 phylogenetically relatedPsychrobacterspecies were well below 70 %. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains SW-210Tand SW-242Twere classified in the genusPsychrobacteras representing two distinct novel species, for which the namesPsychrobacter aquimarissp. nov. (type strain, SW-210T=KCTC 12254T=DSM 16329T) andPsychrobacter namhaensissp. nov. (type strain, SW-242T=KCTC 12255T=DSM 16330T) are proposed, respectively.
Pusillimonas noertemannii gen. nov., sp. nov., a new member of the family Alcaligenaceae that degrades substituted salicylates
Authors: Stolz Andreas , Bürger Sibylle , Kuhm Andrea , Kämpfer Peter , Busse Hans-Jürgen
Published: May 2005

The taxonomic position of a Pseudomonas-like strain, designated BN9T, was investigated. This strain had previously been isolated as a 5-aminosalicylate-degrading organism from a 6-aminonaphthalene-2-sulphonate-degrading mixed bacterial culture. Previously, detection of ubiquinone Q-8, a polyamine pattern with putrescine, spermidine and 2-hydroxyputrescine as the major polyamines, and partial 16S rRNA gene sequencing had suggested that strain BN9T belongs to the ‘Betaproteobacteria’. This was supported by sequencing the 16S rRNA gene, which demonstrated 94–96 % sequence similarity to different species of the genera Achromobacter, Alcaligenes and Bordetella, and suggested that strain BN9T represents a member of the family Alcaligenaceae. Different methods for the construction of phylogenetic dendrograms placed the strain separately from all other genera within the Alcaligenaceae. Fatty acid analysis demonstrated the presence of high concentrations of C19 : 0 cyclo ω8c. On the basis of low 16S rRNA gene sequence similarity to other members of the Alcaligenaceae, fatty acid and polar lipid profiles, and other unique phenotypic properties of strain BN9T, the creation of a new genus and species with the name Pusillimonas noertemannii gen. nov., sp. nov. is proposed. The type strain is BN9T (=DSM 10065T=NCIMB 14020T).
Desulfonatronum cooperativum sp. nov., a novel hydrogenotrophic, alkaliphilic, sulfate-reducing bacterium, from a syntrophic culture growing on acetate
Authors: Zhilina Tatjana N. , Zavarzina Daria G. , Kuever Jan , Lysenko Anatoly M. , Zavarzin Georgy A.
Published: May 2005

A novel alkaliphilic, sulfate-reducing bacterium was isolated from a syntrophic acetate-decomposing community enriched from samples of the soda lake Khadin, Tuva, Russia; the isolate was designated strain Z-7999T. Cells of strain Z-7999T were vibrioid, Gram-negative, 0·4–0·5×1·0–2·5 μm and motile by means of a polar flagellum. The temperature range for growth was 15–40 °C, with an optimum of 35–38 °C. The pH range for growth was 6·7–10·3, with an optimum of pH 8·0–9·0. The NaCl concentration range for growth was 1–80 g l−1. The novel isolate was obligately anaerobic, was alkaliphilic with a broad pH range and had an obligate requirement for carbonate ions in the growth medium. In the presence of sulfate as electron acceptor, it grew with hydrogen, formate and lactate. It was not able to ferment sugars, organic acids, amino acids or peptides. During growth on formate, strain Z-7999T reduced sulfite and thiosulfate to sulfide. It was able to grow lithoheterotrophically with sulfate and formate when acetate was added as a carbon source for biosynthesis of biomass. The G+C content of the genomic DNA of strain Z-7999T was 56·5 mol%. Results of comparative 16S rRNA gene sequence analyses revealed that strain Z-7999T was part of the δ-Proteobacteria and clustered with other members of the genus Desulfonatronum (similarity values of 95·2 and 95·3 % to Desulfonatronum lacustre and Desulfonatronum thiodismutans, respectively). DNA–DNA hybridization with D. lacustre was 37 %. On the basis of physiological and phylogenetic data, it is proposed that strain Z-7999T (=DSM 16749T=VKM B-2329T) should be placed in the genus Desulfonatronum as a representative of a novel species, Desulfonatronum cooperativum sp. nov.
Dyadobacter crusticola sp. nov., from biological soil crusts in the Colorado Plateau, USA, and an emended description of the genus Dyadobacter Chelius and Triplett 2000
Authors: Reddy Gundlapally S. N. , Garcia-Pichel Ferran
Published: May 2005

Bacterial strain CP183-8Twas isolated from biological soil crusts collected in the Colorado Plateau, USA. Cells of this strain were aerobic, non-motile, Gram-negative, psychrotolerant and formed beaded chains in the stationary growth phase. They contained C16 : 1ω5cand C16 : 1ω7cas major fatty acids. 16S rRNA gene sequence analysis assigned the strain to the genusDyadobacter. However, it shared a sequence similarity of only 95·88 % with the type strain ofDyadobacter fermentans, NS114T. Because it also exhibited a significant number of phenotypic and chemotaxonomic differences fromD. fermentans, it is described as a novel second species in the genusDyadobacter, with the nameDyadobacter crusticolasp. nov. The type strain is CP183-8T(=DSM 16708T=ATCC BAA-1036T).
Chryseobacterium taichungense sp. nov., isolated from contaminated soil
Authors: Shen Fo-Ting , Kämpfer Peter , Young Chiu-Chung , Lai Wei-An , Arun A. B.
Published: May 2005

A bacterial strain (CC-TWGS1-8T) isolated from a tar-contaminated soil in Taiwan was studied in a detailed taxonomic study. The cells were Gram-negative, rod-shaped and non-spore-forming. Phylogenetic analyses using the 16S rRNA gene sequence of the strain clearly revealed an affiliation to the genus Chryseobacterium, the highest sequence similarities being to the type strain of Chryseobacterium indologenes (96·8 %), to Chryseobacterium gleum (96·8 %) and to Chryseobacterium joostei (96·4 %). The 16S rRNA gene sequence similarities to all other Chryseobacterium species were below 96 %. The major whole-cell fatty acids were 15 : 0 iso (35·4 %) and 17 : 0 iso 3OH (22·5 %). DNA–DNA hybridization values and the biochemical and chemotaxonomic properties demonstrate that strain CC-TWGS1-8T represents a novel species, for which the name Chryseobacterium taichungense sp. nov. is proposed. The type strain is CC-TWGS1-8T (=CCUG 50001T=CIP 108519T).
Reclassification of Nocardia corynebacterioides Serrano et al. 1972 (Approved Lists 1980) as Rhodococcus corynebacterioides comb. nov.
Authors: Yassin A. F. , Schaal K. P.
Published: May 2005

The type strain of Nocardia corynebacterioides was the subject of a polyphasic taxonomic study. The 16S rRNA gene sequence was aligned with the sequences of representatives of the genera Corynebacterium, Dietzia, Gordonia, Mycobacterium, Nocardia, Rhodococcus, Skermania, Tsukamurella and Williamsia, and phylogenetic trees were constructed by using maximum-parsimony, maximum-likelihood and neighbour-joining methods. It was evident from the phylogenetic analysis that N. corynebacterioides represents a distinct phyletic line within the genus Rhodococcus. Menaquinone analysis showed that the organism contained dihydrogenated menaquinone with eight isoprene units, MK-8(H2), as the major isoprenologue. The genealogical evidence, together with chemotaxonomic and phenotypic data from this and previous studies, indicates that N. corynebacterioides DSM 20151T (=CIP 104510T) should be reclassified in the genus Rhodococcus as Rhodococcus corynebacterioides comb. nov.
Slackia faecicanis sp. nov., isolated from canine faeces
Authors: Lawson Paul A. , Greetham Hazel L. , Gibson Glenn R. , Giffard Catriona , Falsen Enevold , Collins Matthew D.
Published: May 2005

Morphological, biochemical and molecular genetic studies were carried out on an unknown non-spore-forming, Gram-positive, rod-shaped bacterium that was isolated from dog faeces. The bacterium grew under strictly anaerobic conditions, was asaccharolytic, and possessed a relatively high G+C content of 61 mol%. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that the unidentified bacterium was a member of the family Coriobacteriaceae and represents a hitherto unknown subline within the genus Slackia. Based on the presented findings, a novel species, Slackia faecicanis sp. nov., is described. The type strain of Slackia faecicanis is 5WC12T (=CCUG 48399T=CIP 108281T).
Pedobacter himalayensis sp. nov., from the Hamta glacier located in the Himalayan mountain ranges of India
Authors: Shivaji S. , Chaturvedi P. , Reddy G. S. N. , Suresh K.
Published: May 2005

Strain HHS 22T was isolated from a glacial water sample from the snout of the Hamta glacier located in the Himalayan mountain ranges of India. Phenotypic, chemotaxonomic and phylogenetic analyses established the affiliation of the isolate to the genus Pedobacter. HHS 22T exhibits high 16S rRNA gene sequence similarity with Pedobacter cryoconitis (98 %). However, the level of DNA–DNA relatedness between HHS 22T and P. cryoconitis is only 42 %. Furthermore, HHS 22T differs from P. cryoconitis and the four other recognized species of Pedobacter in a number of phenotypic characteristics. These data suggest that HHS 22T represents a novel species of the genus Pedobacter, for which the name Pedobacter himalayensis sp. nov. is proposed. The type strain is HHS 22T (=JCM 12171T=MTCC 6384T).
Pichia myanmarensis sp. nov., a novel cation-tolerant yeast isolated from palm sugar in Myanmar
Authors: Nagatsuka Yuka , Kawasaki Hiroko , Seki Tatsuji
Published: May 2005

Four halotolerant yeast strains, M21T, M34-1, HS054 and D41, were isolated from various foods in South-East Asia. These isolates were most closely related to Pichia anomala, with which each strain had from zero to two differences in the 26S rDNA D1/D2 domain nucleotide sequence; for this reason, they were thought to be the same as, or sister species of, P. anomala. Of the four yeast isolates, only one strain, M21T, had an 18S rDNA sequence that differed from those of P. anomala IFO 10213T and the other three isolates, having 20 substitutions and two gaps. Strain M21T showed lower cation (Li+) tolerance (⩽0·3 M LiCl) than P. anomala IFO 10213T or the other three strains (⩽0·5 M LiCl). Furthermore, the DNA–DNA hybridization data indicated that M21T was clearly distinct from P. anomala IFO 10213T and the other three isolates. The ability of strain M21T to assimilate d-arabinose distinguished it from P. anomala IFO 10213T and the other three isolates; it also differed in that it was able to grow at 37 and 40 °C. Strain M21T grew by multilateral budding, produced persistent asci, in which between one and four hat-shaped ascospores were formed, and contained ubiquinone Q-7. On the basis of this polyphasic characterization, strain M21T represents a novel species within the Q-7-containing group of the genus Pichia, for which the name Pichia myanmarensis is proposed. The type strain is M21T (=NBRC 11090T=JCM 12922T=CBS 9786T).
Metschnikowia hamakuensis sp. nov., Metschnikowia kamakouana sp. nov. and Metschnikowia mauinuiana sp. nov., three endemic yeasts from Hawaiian nitidulid beetles
Authors: Lachance Marc-André , Ewing Curtis P. , Bowles Jane M. , Starmer William T.
Published: May 2005

Three heterothallic, haplontic yeast species,Metschnikowia hamakuensis,Metschnikowia kamakouanaandMetschnikowia mauinuiana, are described from isolates associated with endemic nitidulid beetles living on various endemic plants on three Hawaiian islands. As morphospecies, they are similar toMetschnikowia hawaiiensis, but based on mating compatibility and ascospore formation, they can be assigned clearly to distinct biological species. Analysis of ITS/5·8S and D1/D2 large subunit rDNA sequences shows that, withM. hawaiiensisand two other isolates, these species form a distinct subclade within the large-sporedMetschnikowiaspecies, indicating that they are Hawaiian endemics. Type cultures are:M. hamakuensis, UWOPS 04-207.1T=CBS 10056T=NRRL Y-27834T(type, h+) and UWOPS 04-204.1=CBS 10055=NRRL Y-27833 (allotype, h−);M. kamakouana, UWOPS 04-112.5T=CBS 10058T=NRRL Y-27836T(type, h+) and UWOPS 04-109.1=CBS 10057=NRRL Y-27835 (allotype, h−); andM. mauinuiana, UWOPS 04-190.1T=CBS 10060T=NRRL Y-27838T(type, h+) and UWOPS 04-110.4=CBS 10059=NRRL Y-27837 (allotype, h−).
Natrinema altunense sp. nov., an extremely halophilic archaeon isolated from a salt lake in Altun Mountain in Xinjiang, China
Authors: Xu Xue-Wei , Ren Pei-Gen , Liu Shuang-Jiang , Wu Min , Zhou Pei-Jin
Published: May 2005

A novel extremely halophilic strain, AJ2T, was isolated from Ayakekum salt lake located in the Altun Mountain National Nature Reserve in Xinjiang, China. This isolate was neutrophilic, motile and grew in a wide range of MgCl2 concentrations (0·005–1·0 M). The major polar lipids of the isolate were C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate. A comprehensive 16S rRNA gene sequence analysis revealed that the isolate shared 96·6–97·7 % sequence identity with Natrinema species. The isolate, however, could be genetically differentiated from these species by DNA–DNA hybridization analysis and on the basis of its physiological properties. On the basis of the polyphasic evidence, strain AJ2T (=AS 1.3731T=JCM 12890T) represents the type strain of a novel species, for which the name Natrinema altunense sp. nov. is proposed.
Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum
Authors: Vanparys Bram , Heylen Kim , Lebbe Liesbeth , De Vos Paul
Published: May 2005

A Gram-negative, rod-shaped, non-spore-forming bacterium was isolated from a nitrifying inoculum. On the basis of 16S rRNA gene sequence similarity, LMG 22862T was shown to belong to the family Sphingobacteriaceae, related to Pedobacter africanus (98·0 %) and Pedobacter heparinus (97·6 %). The results of 16S rRNA gene sequence analysis, DNA–DNA hybridization, SDS-PAGE, analysis of the fatty acid composition and physiological and biochemical tests allowed genotypic and phenotypic differentiation of LMG 22862T from Pedobacter species with validly published names. LMG 22862T therefore represents a novel species within this genus, for which the name Pedobacter caeni sp. nov. is proposed, with the type strain LMG 22862T (=DSM 16990T).
Effects of regulated discharge on burbot migration
Authors: Paragamian V. L. , Hardy R. , Gunderman B.
Published: May 2005

Burbot Lota lota movement and river discharge were studied in the Kootenai River, Idaho, U.S.A. and British Columbia, Canada, downstream of Libby Dam, Montana, U.S.A. A total of 24 adult burbot with transmitters were tracked from 1994 to 2000, for analysis of a travel distance of ≥5 km in ≤10 days termed ‘stepwise movement’. Of 44 ‘stepwise movements’, significantly greater movements during pre‐spawning and spawning were observed when average daily discharges from Libby Dam were <300 m3 s−1, with a mean of 176 m3 s−1, similar to pre‐dam conditions. Burbot travelled at a greater rate during all seasons (3·36 km day−1) at discharges >300 m3 s−1(mean = 1·84 km day−1) than at discharges >300 m3 s−1 but no difference was found for the pre‐spawning and spawning period. Burbot that started ‘stepwise movements’ in low discharge conditions frequently stopped during low discharges.
Lacustrine spawning: is this a new reproductive strategy among ‘large’ African cyprinid fishes?
Authors: De Graaf M. , Nentwich E. D. , Osse J. W. M. , Sibbing F. A.
Published: May 2005

Changes in the gonado‐somatic index and abundance of the different Labeobarbus species in the mouths of four major afferent rivers of Lake Tana, Ethiopia, were monitored monthly during 1999 and 2000. Riverine spawning was characteristic for seven of Lake Tana's 15 contemporary Labeobarbus species. These seven did not show spatial segregation among afferent rivers but significant temporal segregation occurred in aggregating in the river mouths and migrating towards the upstream spawning areas during the breeding season (June–October). Among the eight other species, peak gonad development occurred generally in the same period as in the riverine spawners. These species, however, did not aggregate in the river mouths during the breeding period and were absent from the upstream spawning areas. A derived, novel strategy, lacustrine spawning was hypothesized for these eight Labeobarbus species. This hypothesis was further supported by observations of running female fishes in the littoral zones distant from any of the afferent rivers. This derived strategy is only common among the littoral‐dwelling Labeobarbus species with restricted distribution patterns. At present it is thought that sequential waves of speciation and habitat divergence followed by trophic specialization, shaped the diversity of Lake Tana labeobarbs.
Temporal variability of pelagic fish assemblages around fish aggregation devices: biological and physical influences
Authors: Dempster T.
Published: May 2005

Pelagic fishes were counted around four fish aggregation devices (FADs) moored between 3 and 10 km offshore on the continental shelf off Sydney, Australia. Visual counts were made at FADs on 81 days periodically from April 1999 to April 2002. Surface water temperature and current speed were also measured at the FADs. Assemblages of fishes at FADs followed a seasonal pattern, however, biological and physical variables influenced seasonal structure greatly. Abundances at FADs were greatest in spring due to the appearance of large schools (100s to 1000s) of juvenile Trachurus sp. In contrast, diversity was far greater in summer and autumn, principally due to the appearance of schools (10s to 100s) of juvenile Coryphaena hippurus(Coryphaenidae), and other warm water species from January to May when water temperatures were >20° C. Short‐term variability differed among species; C. hippurus fluctuated greatly among counts separated by 2–3 days, while Seriola lalandi(Carangidae) and Alutera monoceros(Monacanthidae) abundances were more stable, indicating greater residence times at FADs for these two species. Marked differences in fish assemblages occurred between times when predators were present and absent, with few small fishes being observed when piscivorous predators occurred at FADs, regardless of season. Furthermore, abundances of C. hippurus and A. monoceros were correlated with current speed, with greatest abundances observed when currents were strong and weak, respectively. The results indicated that much of the temporal variability in fish assemblages at moored FADs could be explained by biological and physical factors.