bluuebunny/crossref_metadata_2025 huggingface dataset:
Nocardioides aquiterrae sp. nov., isolated from groundwater in Korea
Authors: Yoon Jung-Hoon , Kim In-Gi , Kang Kook Hee , Oh Tae-Kwang , Park Yong-Ha
Published: January 2004

A bacterial strain, GW-9T, which was isolated from groundwater in Korea, was subjected to a polyphasic taxonomic study using phenotypic characterization and phylogenetic and genetic methods. Phylogenetic analysis based on 16S rDNA sequences showed that strain GW-9T forms an evolutionary lineage within the radiation enclosing Nocardioides species and, in particular, a coherent cluster with Nocardioides pyridinolyticus. The cell-wall peptidoglycan type of strain GW-9T was based on ll-diaminopimelic acid as the diamino acid, indicating wall chemotype I. The predominant menaquinone was MK-8(H4). Strain GW-9T had a cellular fatty acid profile containing straight-chain, branched, unsaturated and 10-methyl fatty acids. The major fatty acid was iso-C16 : 0. The DNA G+C content of strain GW-9T was 73 mol%. The 16S rDNA of strain GW-9T was 99·2 % similar to that of the type strain of Nocardioides pyridinolyticus and 94·9–96·0 % similar to sequences of the type strains of other Nocardioides species. Differences in phenotypic characteristics and genetic distinctiveness indicate that strain GW-9T is separate from previously described Nocardioides species. Therefore, on the basis of the data presented, a novel species of the genus Nocardioides, Nocardioides aquiterrae sp. nov., is proposed. The type strain is strain GW-9T (=KCCM 41647T=JCM 11813T).
Amycolatopsis decaplanina sp. nov., a novel member of the genus with unusual morphology
Authors: Wink Joachim , Gandhi Julia , Kroppenstedt Reiner M. , Seibert Gerhard , Sträubler Bettina , Schumann Peter , Stackebrandt Erko
Published: January 2004

Strain DSM 44594T, which produces the glycopeptide antibiotic decaplanin, is a member of the genusAmycolatopsisbased on 16S rRNA gene sequence analysis and chemotaxonomic properties. It is the first member of this genus that is reported to form pseudosporangia, which resemble those of members of the genusKibdelosporangium. Phylogenetically, the novel taxon is related toAmycolatopsis orientalis,Amycolatopsis lurida,Amycolatopsis azurea,Amycolatopsis japonicaandAmycolatopsis keratiniphila. Morphological, cultural and physiological properties, the production of a unique glycolipid and DNA–DNA similarity of <55 % with phylogenetically related strains reveal that strain DSM 44594Trepresents a novel species of the genus, for which the nameAmycolatopsis decaplaninasp. nov. (type strain, FH 1845T=DSM 44594T=NRRL B-24209T) is proposed.
Phylogenetic analysis of Streptomyces spp. isolated from potato scab lesions in Korea on the basis of 16S rRNA gene and 16S–23S rDNA internally transcribed spacer sequences
Authors: Song Jaekyeong , Lee Seong-Chan , Kang Jun-Won , Baek Hyung-Jin , Suh Joo-Won
Published: January 2004

The 16S rRNA gene sequences for 34 strains, including 11 isolates, were determined to classify scab-causingStreptomycesspp. and relatives isolated from potato scab lesions collected in Jeju, Korea. The 16S–23S rDNA internally transcribed spacer (ITS) sequences were determined to investigate whether the 16S–23S ITS region is useful for analysing intra- and interspecific relationships in these bacteria. On the basis of phylogenetic analysis of 16S rRNA gene sequences, most of the isolates were classified asStreptomyces scabieiandStreptomyces acidiscabies. Isolate KJO61 was placed in an ambiguous taxonomic position betweenStreptomyces reticuliscabieiandStreptomyces turgidiscabies. 16S–23S ITS region sequence analysis showed that tRNA genes were not found in this region ofStreptomycesspp. The 16S–23S ITS regions ofStreptomycesspp. exhibited various lengths and highly variable sequence similarities (35–100 %) within strains as well as intra- and interspecies. It was revealed thatStreptomyces europaeiscabieicould be clearly differentiated fromStreptomyces scabiei. However, it was clarified that ITS regions are not useful in phylogenetic analysis ofStreptomycesspp.
Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment
Authors: Jeon Che Ok , Park Woojun , Ghiorse William C. , Madsen Eugene L.
Published: January 2004

Strain CJ2T, capable of growth on naphthalene as a sole carbon and energy source, was isolated from coal-tar-contaminated freshwater sediment. The Gram reaction of strain CJ2Twas negative. The cells were non-spore-forming, non-motile cocci (without flagella). The isolate was found to be an aerobic heterotroph capable of utilizing glucose and other simple sugars. Growth was observed between 4 and 25 °C (optimum, 20 °C) and between pH 6·0 and 9·0 (optimum, pH 7·0–7·5). The G+C content of the genomic DNA was 61·5 mol% and the major quinone was ubiquinone-8. The peptidoglycan of strain CJ2Twas determined as belonging to type A1-γ,meso-diaminopimelic acid. The major fatty acids of strain CJ2Twere 16 : 1ω7c(67·0 %), 16 : 0 (19·6 %), 18 : 1ω7c(∼7·9 %) and 10 : 0 3-OH (∼2·5 %). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Mycolic acid and glycolipids could not be detected. Comparative 16S rDNA analysis indicated that strain CJ2Tis related to the familyComamonadaceaeand that the nearest phylogenetic relative wasPolaromonas vacuolata34-PT(97·1 % similarity). On the basis of the physiological and molecular properties, the naphthalene-degrading isolate was designatedPolaromonas naphthalenivoranssp. nov. The type strain is CJ2T(=ATCC BAA-779T=DSM 15660T).
Thermodesulfatator indicus gen. nov., sp. nov., a novel thermophilic chemolithoautotrophic sulfate-reducing bacterium isolated from the Central Indian Ridge
Authors: Moussard H. , L'Haridon S. , Tindall B. J. , Banta A. , Schumann P. , Stackebrandt E. , Reysenbach A.-L. , Jeanthon C.
Published: January 2004

A thermophilic, marine, anaerobic, chemolithoautotrophic, sulfate-reducing bacterium, strain CIR29812T, was isolated from a deep-sea hydrothermal vent site at the Kairei vent field on the Central Indian Ridge. Cells were Gram-negative motile rods that did not form spores. The temperature range for growth was 55–80 °C, with an optimum at 70 °C. The NaCl concentration range for growth was 10–35 g l−1, with an optimum at 25 g l−1. The pH range for growth was 6–6·7, with an optimum at approximately pH 6·25. H2and CO2were the only electron donor and carbon source found to support growth of the strain. However, several organic compounds were stimulatory for growth. Sulfate was used as electron acceptor, whereas elemental sulfur, thiosulfate, sulfite, cystine, nitrate and fumarate were not. No fermentative growth was observed with malate, pyruvate or lactate. The phenotypic characteristics of strain CIR29812Twere similar to those ofThermodesulfobacterium hydrogeniphilum, a recently described thermophilic, chemolithoautotrophic sulfate-reducer. However, phylogenetic analyses of the 16S rRNA gene sequences showed that the new isolate was distantly related to members of the familyThermodesulfobacteriaceae(similarity values of less than 90 %). The chemotaxonomic data (fatty acids and polar lipids composition) also indicated that strain CIR29812Tcould be distinguished fromThermodesulfobacterium commune, the type species of the type genus of the familyThermodesulfobacteriaceae. Finally, the G+C content of the genomic DNA of strain CIR29812T(46·0 mol%) was not in the range of values obtained for members of this family. On the basis of phenotypic, chemotaxonomic and genomic features, it is proposed that strain CIR29812Trepresents a novel species of a new genus,Thermodesulfatator, of whichThermodesulfatator indicusis the type species. The type strain is CIR29812T(=DSM 15286T=JCM 11887T).
Nocardia asiatica sp. nov., isolated from patients with nocardiosis in Japan and clinical specimens from Thailand
Authors: Kageyama Akiko , Poonwan Natteewan , Yazawa Katsukiyo , Mikami Yuzuru , Nishimura Kazuko
Published: January 2004

Five strains isolated from two patients with nocardiosis in Japan and three clinical samples from Thailand were found to have morphological, biochemical and chemotaxonomic properties consistent with their classification in the genus Nocardia. DNA–DNA hybridization, coupled with sequence analysis of 16S rDNA, indicated that these strains belong to a novel species of the genus Nocardia, named Nocardia asiatica sp. nov. because the isolation sites were in Asian countries; the type strain is IFM 0245T (=NBRC 100129T=JCM 11892T=DSM 44668T).
Petrotoga mexicana sp. nov., a novel thermophilic, anaerobic and xylanolytic bacterium isolated from an oil-producing well in the Gulf of Mexico
Authors: Miranda-Tello Elizabeth , Fardeau Marie-Laure , Thomas Pierre , Ramirez Florina , Casalot Laurence , Cayol Jean-Luc , Garcia Jean-Louis , Ollivier Bernard
Published: January 2004

A novel anaerobic, thermophilic, xylanolytic, motile rod-shaped bacterium with a sheath-like outer structure (toga) was isolated from a Mexican oil well in the Gulf of Mexico. Strain MET12Twas a Gram-negative bacterium, reducing elemental sulfur, thiosulfate and sulfite to hydrogen sulfide. Its optimum growth conditions were 55 °C, pH 6·6, 3 % NaCl and 0·15 % MgCl2.6H2O. The DNA G+C content was 36·1 mol%. Phylogenetically, strain MET12Twas related to members of genusPetrotoga, with similarities toPetrotoga mobilis,Petrotoga sibirica,Petrotoga miothermaandPetrotoga oleariavarying from 97·6 to 98·8 %. However DNA–DNA relatedness values between these species and strain MET12Twere lower than 70 %. As strain MET12T(=DSM 14811T=CIP 107371T) was genomically and phenotypically different from existingPetrotogaspecies, it is proposed as the type strain of a novel species,Petrotoga mexicanasp. nov.
Paenibacillus favisporus sp. nov., a xylanolytic bacterium isolated from cow faeces
Authors: Velázquez Encarna , de Miguel Trinidad , Poza Margarita , Rivas Raúl , Rosselló-Mora Ramón , Villa Tomás G.
Published: January 2004

During a search for xylan-degrading micro-organisms, a sporulated bacterium was recovered from recent and old cow dung and rectal samples. The isolates were identified as members of a novel species of the genusPaenibacillus, based on 16S rRNA gene sequences. According to the results of phylogenetic analysis, the most closely related species wasPaenibacillus azoreducens. Phenotypic and chemotaxonomic analyses and DNA–DNA hybridization experiments also showed that the isolates belonged to a novel species of the genusPaenibacillus. The novel species is a facultatively anaerobic, motile, Gram-variable, sporulated rod. The spores of this rod-shaped micro-organism occur in slightly swollen sporangia and are honeycomb-shaped. The main fatty acid is anteiso-branched C15 : 0. Growth was observed with many carbohydrates, including xylan, as the only carbon source and gas production was not observed from glucose. The novel species produces a wide variety of hydrolytic enzymes, such as xylanases, cellulases, amylases, gelatinase, urease andβ-galactosidase. On the contrary, it does not produce caseinase, phenylalanine deaminase or lysine decarboxylase. According to the data obtained in this work, the strains belong to a novel species, for which the namePaenibacillus favisporussp. nov. is proposed (type strain, GMP01T=LMG 20987T=CECT 5760T).
Polyphasic characterization of xanthomonads isolated from onion, garlic and Welsh onion (Allium spp.) and their relatedness to different Xanthomonas species
Authors: Roumagnac P. , Gagnevin L. , Gardan L. , Sutra L. , Manceau C. , Dickstein E. R. , Jones J. B. , Rott P. , Pruvost O.
Published: January 2004

Bacterial blight is an emerging disease that affects primarily onion, but also garlic and Welsh onion. The present study was undertaken to characterize the causative xanthomonad(s) by a polyphasic approach using a worldwide collection of 33 bacterial strains. Analysis of 16S rRNA gene sequence similarities indicated that the causal agent belongs to the campestris core in the genus Xanthomonas, which is in agreement with results of phenotypic characterization (analyses of carbon source utilization and fatty acid methyl esters). However, DNA–DNA hybridization, thermal stability of DNA reassociation and fluorescent amplified fragment length polymorphism analysis allowed the causal agent to be identified as a pathovar of Xanthomonas axonopodis.
Desulfatibacillum aliphaticivorans gen. nov., sp. nov., an n-alkane- and n-alkene-degrading, sulfate-reducing bacterium
Authors: Cravo-Laureau Cristiana , Matheron Robert , Cayol Jean-Luc , Joulian Catherine , Hirschler-Réa Agnès
Published: January 2004

A novel marine sulfate-reducing bacterium, strain CV2803T, which is able to oxidize aliphatic hydrocarbons, was isolated from a hydrocarbon-polluted marine sediment (Gulf of Fos, France). The cells were rod-shaped and slightly curved, measuring 0·6×2·2–5·5 μm. Strain CV2803Tstained Gram-negative and was non-motile and non-spore-forming. Optimum growth occurred in the presence of 24 g NaCl l−1, at pH 7·5 and at a temperature between 28 and 35 °C. Strain CV2803Toxidized alkanes (from C13to C18) and alkenes (from C7to C23). The DNA G+C content was 41·4 mol%. Comparative sequence analyses of the 16S rRNA gene and dissimilatory sulfite reductase (dsrAB) gene and those of other sulfate-reducing bacteria, together with its phenotypic properties, indicated that strain CV2803Twas a member of a distinct cluster that contained unnamed species. Therefore, strain CV2803T(=DSM 15576T=ATCC BAA-743T) is proposed as the type strain of a novel species in a new genus,Desulfatibacillum aliphaticivoransgen. nov., sp. nov.
Erwinia papayae sp. nov., a pathogen of papaya (Carica papaya)
Authors: Gardan Louis , Christen Richard , Achouak Wafa , Prior Philippe
Published: January 2004

Bacterial canker of papaya (Carica papaya) emerged during the 1980s in different islands of the Caribbean. Nineteen strains of Gram-negative, rod-shaped, non-spore-forming bacteria isolated from papaya were compared to 38 reference and type strains of phytopathogenic Enterobacteriaceae and related bacteria. Phylogenetic analysis of 16S rRNA gene sequences showed that the papaya strains belonged to the genus Erwinia. The DNA G+C content of strain CFBP 5189T, 52·5 mol%, is in the range of the genus Erwinia. The 19 papaya strains were all pathogenic to papaya and were differentiated clearly from type or reference strains of phytopathogenic enterobacteria and related bacteria by phenotypic tests. The papaya strains constituted a discrete DNA hybridization group, indicating that they belonged to a unique genomic species. Thus, strains pathogenic to papaya belong to a novel species for which the name Erwinia papayae sp. nov. is proposed, with the type strain CFBP 5189T (=NCPPB 4294T).
Hespellia stercorisuis gen. nov., sp. nov. and Hespellia porcina sp. nov., isolated from swine manure storage pits
Authors: Whitehead Terence R. , Cotta Michael A. , Collins Matthew D. , Lawson Paul A.
Published: January 2004

Four Gram-positive-staining, strictly anaerobic, non-spore-forming, rod-shaped organisms were isolated from a pig manure storage pit. Comparative 16S rRNA gene sequence analysis revealed that the isolates belonged to two related but distinct groups. Sequence analysis showed that the two groups of isolates were highly related to each other (approx. 97 % 16S rRNA gene sequence similarity), forming a distinct cluster within theClostridium coccoidessuprageneric rDNA grouping. Biochemical and physiological studies confirmed the division of the isolates into two related, albeit distinct, groups. Based on both phenotypic and phylogenetic evidence, it is proposed that the unidentified rod-shaped isolates from pig manure should be classified in a novel genus,Hespelliagen. nov., asHespellia stercorisuissp. nov. andHespellia porcinasp. nov. The type species of the novel genus isH. stercorisuis(type strain, PC18T=NRRL B-23456T=CCUG 46279T=ATCC BAA-677T) and the type strain ofH. porcinais PC80T(=NRRL B-23458T=ATCC BAA-674T).
Lactobacillus paracollinoides sp. nov., isolated from brewery environments
Authors: Suzuki Koji , Funahashi Wataru , Koyanagi Masahiro , Yamashita Hiroshi
Published: January 2004

Three novel strains isolated from brewery environments are described. These strains were Gram-positive, facultatively anaerobic, heterofermentative rods that did not exhibit catalase activity. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that these strains belong to the genusLactobacillusand are most closely related toLactobacillus collinoides(approximately 99 % similarity). The novel strains could be differentiated fromL. collinoideson the basis of DNA–DNA relatedness, differences in beer-spoilage ability and the inability to utilized-fructose. These isolates represent a novel species, for which the nameLactobacillus paracollinoidessp. nov. is proposed. The type strain is LA2T(=DSM 15502T=JCM 11969T).
Bacillus novalis sp. nov., Bacillus vireti sp. nov., Bacillus soli sp. nov., Bacillus bataviensis sp. nov. and Bacillus drentensis sp. nov., from the Drentse A grasslands
Authors: Heyrman Jeroen , Vanparys Bram , Logan Niall A. , Balcaen An , Rodríguez-Díaz Marina , Felske Andreas , De Vos Paul
Published: January 2004

A group of 42 isolates were isolated from the soil of several disused hay fields, in the Drentse A agricultural research area (The Netherlands), that were taken out of production at different times. The group represents hitherto-uncultured Bacillus lineages that have previously been found, by a non-cultural method, to be predominant in soil. The strains were subjected to a polyphasic taxonomic study, including (GTG)5-PCR, 16S rDNA sequence analysis, DNA–DNA hybridizations, DNA base-ratio determination, fatty acid analysis and morphological and biochemical characterization. By comparing the groupings obtained by (GTG)5-PCR and 16S rDNA sequence analysis, six clusters of similar strains could be recognized. A DNA–DNA relatedness study showed that these clusters represented five novel genospecies. Further analysis supported the proposal of five novel species in the genus Bacillus, namely Bacillus novalis sp. nov. (type strain IDA3307T=R-15439T=LMG 21837T=DSM 15603T), Bacillus vireti sp. nov. (type strain IDA3632T=R-15447T=LMG 21834T=DSM 15602T), Bacillus soli sp. nov. (type strain IDA0086T=R-16300T=LMG 21838T=DSM 15604T), Bacillus bataviensis sp. nov. (type strain IDA1115T=R-16315T=LMG 21833T=DSM 15601T) and Bacillus drentensis sp. nov. (type strain IDA1967T=R-16337T=LMG 21831T=DSM 15600T).
Ottowia thiooxydans gen. nov., sp. nov., a novel facultatively anaerobic, N2O-producing bacterium isolated from activated sludge, and transfer of Aquaspirillum gracile to Hylemonella gracilis gen. nov., comb. nov.
Authors: Spring Stefan , Jäckel Udo , Wagner Michael , Kämpfer Peter
Published: January 2004

Strain K11Twas isolated from activated sludge of a municipal wastewater-treatment plant. Phylogenetic analysis of the 16S rRNA gene sequence revealed that it represents a distinct line of descent within theComamonadaceae. The novel strain was a Gram-negative, catalase- and oxidase-positive, non-motile, straight to slightly curved rod. Polyhydroxyalkanoate granules were stored intracellularly as reserve material. Colonies on agar plates were small, regular and characterized by a water-insoluble yellow pigment. Unbranched fatty acids 16 : 1ω7c, 16 : 0 and 18 : 1ω7cdominated the cellular fatty acid pattern and ubiquinone-8 (Q-8) was the major component of the respiratory lipoquinones, both traits typical of members of theComamonadaceae. A distinguishing characteristic was the presence of the two hydroxy fatty acids 10 : 0 3-OH and 12 : 0 2-OH, each in significant amounts. The G+C content of the DNA was 59 mol%. Strain K11Twas capable of aerobic chemolithoheterotrophic growth using thiosulfate as an additional substrate, but could not grow autotrophically with thiosulfate or hydrogen. Facultative anaerobic growth was possible with nitrate and nitrite as electron acceptors, but not with ferric iron, sulfate or by fermentation. The sole end product of denitrification was N2O; nitrite accumulated only transiently in small amounts. Based upon phylogenetic and phenotypic evidence, it is proposed to establish the novel taxonOttowia thiooxydansgen. nov., sp. nov., represented by the type strain K11T(=DSM 14619T=JCM 11629T).Aquaspirillum gracilewas among the phylogenetically most closely related species to strain K11T. This species has been wrongly classified, and it is proposed to reclassify it asHylemonella gracilisgen. nov., comb. nov. The type strain is ATCC 19624T(=DSM 9158T).
Blastococcus saxobsidens sp. nov., and emended descriptions of the genus Blastococcus Ahrens and Moll 1970 and Blastococcus aggregatus Ahrens and Moll 1970
Authors: Urzì Clara , Salamone Paola , Schumann Peter , Rohde Manfred , Stackebrandt Erko
Published: January 2004

Ten Gram-positive, aerobic bacterial strains with coccoid cells occurring singly, in pairs, tetrads and small aggregates were isolated from the surface of marble and calcareous stones. The peptidoglycan containedmeso-diaminopimelic acid as the diagnostic diamino acid. The major menaquinone was MK-9(H4). The cellular fatty acid pattern consisted mainly of iso-branched chain components. According to their phylogenetic position, the organisms are members of the familyGeodermatophilaceae, clustering close toBlastococcus aggregatusDSM 4725T. Based on a combination of phenotypic, chemotaxonomic and genotypic characteristics, strain BC444Tand seven relatives group apart from strains BC412 (=DSM 44517) and BC521 (=DSM 44518), which themselves form two individual lineages. DNA–DNA reassociation studies revealed that members of the three lineages were only remotely related toB. aggregatus DSM 4725T; as the strain-rich cluster containing BC444Tshared low DNA similarity values with strains BC412 and BC521, it will be described as a novel species ofBlastococcus, for which the nameBlastococcus saxobsidenssp. nov. is proposed. The type strain is BC444T(=DSM 44509T=NRRL 24246T).
Bacillus odysseyi sp. nov., a round-spore-forming bacillus isolated from the Mars Odyssey spacecraft
Authors: Duc Myron T. La , Satomi Masataka , Venkateswaran Kasthuri
Published: January 2004

A round-spore-formingBacillusspecies that produces an exosporium was isolated from the surface of the Mars Odyssey spacecraft. This novel species has been characterized on the basis of phenotypic traits, 16S rDNA sequence analysis and DNA–DNA hybridization. According to the results of these analyses, this strain belongs to the genusBacillusand is a Gram-positive, aerobic, rod-shaped, endospore-forming eubacterium. Ultrathin sections of the spores showed the presence of an exosporium, spore coat, cortex and core. 16S rDNA sequence similarities between this strain,Bacillus fusiformisandBacillus silvestriswere ∼96 % and DNA–DNA reassociation values with these two bacilli were 23 and 17 %, respectively. Spores of the novel species were resistant to desiccation, H2O2and UV and gamma radiation. Of all strains tested, the spores of this strain were the most consistently resistant and survived all of the challenges posed, i.e. exposure to conditions of desiccation (100 % survival), H2O2(26 % survival), UV radiation (10 % survival at 660 J m−2) and gamma radiation (0·4 % survival). The name proposed for this novel bacterium isBacillus odysseyisp. nov.; the type strain is 34hs-1T(=ATCC PTA-4993T=NRRL B-30641T=NBRC 100172T).
Exploring prokaryotic taxonomy
Authors: Lilburn Timothy G. , Garrity George M.
Published: January 2004

Techniques drawn from exploratory data analysis, using tools found in the S-Plus statistical software package, have been used to inspect and maintain theBergey's Taxonomic Outlineand to move towards an automated and community-based means of working on the outline. These techniques can be used to classify sequences from unnamed and uncultured organisms, to visualize errors in the taxonomy or in the curation of the sequences, to suggest emendations to the taxonomy or to the classification of extant species and to complement the visualization of phylogenies based on treeing methods. A dataset of more than 9200 aligned small-subunit rRNA sequences was analysed in the context of the current taxonomic outline. The use of the algorithm in exploring and modifying the taxonomy is illustrated with an example drawn from the familyComamonadaceae.
Belliella baltica gen. nov., sp. nov., a novel marine bacterium of the Cytophaga–Flavobacterium–Bacteroides group isolated from surface water of the central Baltic Sea
Authors: Brettar Ingrid , Christen Richard , Höfle Manfred G.
Published: January 2004

Two bacterial isolates from the Baltic Sea, BA1 and BA134T, were characterized for their physiological and biochemical features, fatty acid profiles and phylogenetic position based on 16S rRNA gene sequences. The strains were isolated from surface water of the central Baltic Sea during the decay of a plankton bloom. Phylogenetic analysis of their 16S rRNA gene sequences revealed a clear affiliation to the family ‘Flexibacteriaceae’ and showed highest sequence similarity (91 %) toCyclobacterium marinum. The G+C content of the DNA was 35·4 mol%. The strains were pink-coloured due to carotinoids, Gram-negative, rod-shaped and catalase- and oxidase-positive. Growth was observed at 0–6 % salinity, with good growth at 0–3 %. Temperature for growth was 4–37 °C, with an optimum around 25 °C. The fatty acid profiles were dominated by branched-chain fatty acids (70 %), with a high abundance of iso-C15 : 0(29–33 %), iso-C17 : 1ω9c(7–10 %) and C17 : 1ω6c(5–10 %). According to their morphology, physiology, fatty acid composition, 16S rRNA gene sequences and DNA–DNA similarity, on one hand, the described bacteria are considered to be members of the same novel species; on the other hand, they are suggested as a novel genus of the family ‘Flexibacteriaceae’. To honour the late aquatic microbiologist Russell T. Bell, the nameBelliella balticagen. nov, sp. nov. is suggested for the Baltic Sea isolates, for which the type strain is BA134T(=DSM 15883T=LMG 21964T=CIP 108006T).
Caminibacter profundus sp. nov., a novel thermophile of Nautiliales ord. nov. within the class ‘Epsilonproteobacteria’, isolated from a deep-sea hydrothermal vent
Authors: Miroshnichenko M. L. , L'Haridon S. , Schumann P. , Spring S. , Bonch-Osmolovskaya E. A. , Jeanthon C. , Stackebrandt E.
Published: January 2004

A novel moderately thermophilic, microaerobic to anaerobic, chemolithoautotrophic bacterium, designated strain CRT, was isolated from a deep-sea hydrothermal vent site at 36°N on the Mid-Atlantic Ridge. Cells were Gram-negative, non-motile rods. The organism grew at 45–65 °C and pH 6·5–7·4, with optimum growth at 55 °C and pH 6·9–7·1. The NaCl range for growth was 5–50 g l−1(optimum 30 g l−1). Strain CRTwas an obligate chemolithoautotroph, growing with H2as energy source, sulfur, nitrate or oxygen as electron acceptors and CO2as carbon source. Hydrogen sulfide and ammonium were the respective products of sulfur and nitrate reduction. The G+C content of the genomic DNA was 32·1 mol%. Based on 16S rRNA gene sequence analysis, this organism was most closely related toCaminibacter hydrogeniphilus(94·9 % similarity). On the basis of phenotypic and phylogenetic data, it is proposed that the isolate represents a novel species,Caminibacter profundussp. nov. The type strain is CRT(=DSM 15016T=JCM 11957T). The phylogenetic data also correlate well with the significant phenotypic differences between the lineage encompassing the generaNautiliaandCaminibacterand other members of the class ‘Epsilonproteobacteria’. The lineage encompassing the generaNautiliaandCaminibacteris therefore proposed as a new order,Nautilialesord. nov., represented by a single family,Nautiliaceaefam. nov.
Ulvibacter litoralis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the green alga Ulva fenestrata
Authors: Nedashkovskaya Olga I. , Kim Seung Bum , Han Suk Kyun , Rhee Moon Soo , Lysenko Anatoly M. , Falsen Enevold , Frolova Galina M. , Mikhailov Valery V. , Bae Kyung Sook
Published: January 2004

Two heterotrophic, aerobic, Gram-negative, pigmented and non-motile marine bacteria that were isolated from the green algaUlva fenestratawere studied by polyphasic taxonomic methods. 16S rDNA sequence analysis indicated that strain KMM 3912Tformed a distinct lineage within the familyFlavobacteriaceae. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses, the novel bacteria were classified asUlvibacter litoralisgen. nov., sp. nov. The type strain is KMM 3912T(=KCTC 12104T=CCUG 47093T).
Methanocalculus chunghsingensis sp. nov., isolated from an estuary and a marine fishpond in Taiwan
Authors: Lai Mei-Chin , Lin Chih-Chien , Yu Ping-Hung , Huang Yi-Feng , Chen Sheng-Chung
Published: January 2004

Three novel halotolerant, hydrogenotrophic methanogens, designated strains K1F9705bT, K1F9705c and O1F9704a, were isolated from an estuary in Eriln Shi, Taiwan, and from a nearby marine water aquaculture fishpond. These isolates were irregular cocci that stained Gram-negative. Strains K1F9705bTand K1F9705c were non-motile, but strain O1F9704a was weakly motile with flagella. They were able to use formate and H2/CO2to form methane, but they could not catabolize acetate, methanol, trimethylamine or secondary alcohols. Acetate was required for cell growth. Tungsten greatly stimulated the growth of strains K1F9705bTand K1F9705c, but did not affect the growth of strain O1F9704a. Optimal pH and temperature for growth of these three isolates were respectively 7·2 and 37 °C. Optimal NaCl concentration for growth was 0·5 % for strain O1F9704a and 1·0 % for strains K1F9705c and K1F9705bT. Moreover, all strains grew well at up to 8–12 % NaCl. Analysis of the 16S rRNA gene revealed that these isolates are members of the genusMethanocalculus, but are distinct fromMethanocalculus taiwanensis,Methanocalculus pumilusandMethanocalculus halotolerans, with sequence similarities of 98·4, 98·3 and 98·2 %, respectively. In addition, strain K1F9705bTpossessed 85, 80, 37, 29 and 10 % DNA–DNA relatedness to strain K1F9705c, strain O1F9704a,M. pumilus,M. halotoleransandM. taiwanensis, respectively. Analysis of protein profiles and theMrof surface (S)-layer glycoprotein subunits showed that these three new isolates are closely related to, but distinct from, knownMethanocalculusspecies. A novel species,Methanocalculuschunghsingensissp. nov., is proposed for strains K1F9705bT, K1F9705c and O1F9704a. The type strain is K1F9705bT(=OCM 772T=DSM 14646T).
Williamsia maris sp. nov., a novel actinomycete isolated from the Sea of Japan
Authors: Stach James E. M. , Maldonado Luis A. , Ward Alan C. , Bull Alan T. , Goodfellow Michael
Published: January 2004

The taxonomic position of a marine actinomycete, strain SJS0289/JS1T, was determined using a polyphasic taxonomic approach. The organism, which had phenotypic properties consistent with its classification in the genusWilliamsia, formed a distinct clade in the 16S rRNA gene tree together with the type strain ofWilliamsia muralis, but was readily distinguished from this species using DNA–DNA relatedness and phenotypic data. The genotypic and phenotypic data show that the organism merits recognition as a new species ofWilliamsia. The name proposed for the new species isWilliamsia maris; the type strain is SJS0289/JS1T(=DSM 44693T=JCM 12070T=KCTC 9945T=NCIMB 13945T).
Marinospirillum insulare sp. nov., a novel halophilic helical bacterium isolated from kusaya gravy
Authors: Satomi M. , Kimura B. , Hayashi M. , Okuzumi M. , Fujii T.
Published: January 2004

A novel species that belongs to the genusMarinospirillumis described on the basis of phenotypic characteristics, phylogenetic analysis of 16S rRNA andgyrBgene sequences and DNA–DNA hybridization. Four strains of helical, halophilic, Gram-negative, heterotrophic bacteria were isolated from kusaya gravy, which is fermented brine that is used for the production of traditional dried fish in the Izu Islands of Japan. All of the new isolates were motile by means of bipolar tuft flagella, of small cell size, coccoid-body-forming and aerophilic; it was concluded that they belong to the same bacterial species, based on DNA–DNA hybridization values (>70 % DNA relatedness). DNA G+C contents of the new strains were 42–43 mol% and they had isoprenoid quinone Q-8 as the major component. Phylogenetic analysis of 16S rRNA gene sequences indicated that the new isolates were members of the genusMarinospirillum; sequence similarity of the new isolates toMarinospirillum minutulum,Marinospirillum megateriumandMarinospirillum alkaliphilumwas 98·5, 98·2 and 95·2 %, respectively. Phylogenetic analysis based on thegyrBgene indicated that the new isolates had enough phylogenetic distance fromM. minutulumandM. megateriumto be regarded as different species, with 84·7 and 78·7 % sequence similarity, respectively. DNA–DNA hybridization showed that the new isolates had <36 % DNA relatedness toM. minutulumandM. megaterium, supporting the phylogenetic conclusion. Thus, a novel species is proposed:Marinospirillum insularesp. nov. (type strain, KT=LMG 21802T=NBRC 100033T).
Bartonella chomelii sp. nov., isolated from French domestic cattle (Bos taurus)
Authors: Maillard Renaud , Riegel Philippe , Barrat Francine , Bouillin Corinne , Thibault Danielle , Gandoin Christelle , Halos Lénaig , Demanche Christine , Alliot Annie , Guillot Jacques , Piémont Yves , Boulouis Henri-Jean , Vayssier-Taussat Muriel
Published: January 2004

Two strains of bacteria isolated from the blood of French domestic cows were found to be similar to Bartonella species on the basis of phenotypic characteristics. Genotypic analysis based on sequence comparison of the 16S rRNA and citrate synthase (gltA) genes and on DNA–DNA hybridization showed that the two isolates represent a distinct and new species of Bartonella. Moreover, the phylogenetic analysis inferred from comparison of 16S rRNA and gltA sequences demonstrated that the new Bartonella species is related to other ruminant-derived Bartonella species. The name Bartonella chomelii is proposed for the new species. The type strain of Bartonella chomelii sp. nov. is A828T (=CIP 107869T=CCUG47497T).
Vibrio hispanicus sp. nov., isolated from Artemia sp. and sea water in Spain
Authors: Gomez-Gil B. , Thompson F. L. , Thompson C. C. , Garcia-Gasca A. , Roque A. , Swings J.
Published: January 2004

Three Gram-negative, small, motile, rod-shaped bacteria were isolated from Artemia sp. and sea water in Barcelona, Spain, during 1990 and 1991. They were fermentative, oxidase-positive, sensitive to vibriostatic agent O/129, arginine dihydrolase-positive, lysine and ornithine decarboxylase-negative and grew in the absence of NaCl. They differed from phenotypically related species by their ability to grow at 4 °C and utilize l-rhamnose. Cloning of the 16S rRNA gene of the type strain produced two different 16S rRNA gene sequences, which differed by 15 bases (0·99 %); comparison of these sequences with those deposited in GenBank showed close relationships with Vibrio proteolyticus (97·6 % similarity), Vibrio diazotrophicus (97·9 %), Vibrio campbellii (96·8 %) and Vibrio alginolyticus (96·8 %), among others. DNA–DNA hybridization levels with the closest phylogenetically related Vibrio species were <26·4 %. Sufficient evidence is provided to support the identity of the three strains analysed as members of a novel species of the genus Vibrio, for which the name Vibrio hispanicus sp. nov. is proposed, with the type strain LMG 13240T (=CAIM 525T=VIB 213T).
Thermovibrio ammonificans sp. nov., a thermophilic, chemolithotrophic, nitrate-ammonifying bacterium from deep-sea hydrothermal vents
Authors: Vetriani Costantino , Speck Mark D. , Ellor Susan V. , Lutz Richard A. , Starovoytov Valentin
Published: January 2004

A thermophilic, anaerobic, chemolithoautotrophic bacterium was isolated from the walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise at 9° 50′ N. Cells of the organism were Gram-negative, motile rods that were about 1·0 μm in length and 0·6 μm in width. Growth occurred between 60 and 80 °C (optimum at 75 °C), 0·5 and 4·5 % (w/v) NaCl (optimum at 2 %) and pH 5 and 7 (optimum at 5·5). Generation time under optimal conditions was 1·57 h. Growth occurred under chemolithoautotrophic conditions in the presence of H2and CO2, with nitrate or sulfur as the electron acceptor and with concomitant formation of ammonium or hydrogen sulfide, respectively. Thiosulfate, sulfite and oxygen were not used as electron acceptors. Acetate, formate, lactate and yeast extract inhibited growth. No chemoorganoheterotrophic growth was observed on peptone, tryptone or Casamino acids. The genomic DNA G+C content was 54·6 mol%. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the organism was a member of the domainBacteriaand formed a deep branch within the phylumAquificae, withThermovibrio ruberas its closest relative (94·4 % sequence similarity). On the basis of phylogenetic, physiological and genetic considerations, it is proposed that the organism represents a novel species within the newly described genusThermovibrio. The type strain isThermovibrio ammonificansHB-1T(=DSM 15698T=JCM 12110T).
Should names reflect the evolution of bacterial species?
Authors: Dellaglio Franco , Felis Giovanna E. , Germond Jacques-Edouard
Published: January 2004

Systematics is the process of characterizing and arranging bacterial diversity in an orderly manner, recognizing groups of similar organisms in a hierarchical scheme whose basic entity is the species. To allow the exchange of scientific knowledge, taxa have to be named. Taxa are not static entities since they are subject to evolution, the direction of which can be inferred by using a wide range of techniques targeting specific traits. However, it is not clear how this dynamism should be reflected in taxonomic nomenclature. In the present report, several considerations are presented that deal with the relationship between the evolution of taxa and their nomenclature; an example is given which concerns the nomenclature of the species Lactobacillus delbrueckii.
Hydrogenimonas thermophila gen. nov., sp. nov., a novel thermophilic, hydrogen-oxidizing chemolithoautotroph within the ε-Proteobacteria, isolated from a black smoker in a Central Indian Ridge hydrothermal field
Authors: Takai Ken , Nealson Kenneth H. , Horikoshi Koki
Published: January 2004

A novel thermophilic bacterium, strain EP1-55-1%T, was isolated from anin-situcolonization system deployed in a superheated, deep-sea, hydrothermal vent emission at the Kairei Field on the Central Indian Ridge in the Indian Ocean. The cells were highly motile rods, each possessing a single polar flagellum. Growth was observed between 35 and 65 °C (optimum temperature, 55 °C; 70 min doubling time) and between pH 4·9 and 7·2 (optimum, pH 5·9). The isolate was a microaerobic-to-anaerobic chemolithoautotroph capable of using molecular hydrogen as the sole energy source and carbon dioxide as the sole carbon source. Molecular oxygen, nitrate or elemental sulfur (S0) could serve as electron acceptors to support growth. The G+C content of the genomic DNA was 34·6 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that strain EP1-55-1%Trepresents the first strain for which taxonomic properties have been characterized within the previously uncultivated phylogroup classified as belonging to the uncultivatedε-Proteobacteriagroup A; the nameHydrogenimonas thermophilagen. nov., sp. nov. is proposed, with strain EP1-55-1%T(=JCM 11971T=ATCC BAA-737T) as the type strain.
Sulfurihydrogenibium azorense, sp. nov., a thermophilic hydrogen-oxidizing microaerophile from terrestrial hot springs in the Azores
Authors: Aguiar P. , Beveridge T. J. , Reysenbach A.-L.
Published: January 2004

Five hydrogen-oxidizing, thermophilic, strictly chemolithoautotrophic, microaerophilic strains, with similar (99–100 %) 16S rRNA gene sequences were isolated from terrestrial hot springs at Furnas, São Miguel Island, Azores, Portugal. The strain, designated Az-Fu1T, was characterized. The motile, 0·9–2·0 μm rods were Gram-negative and non-sporulating. The temperature growth range was from 50 to 73 °C (optimum at 68 °C). The strains grew fastest in 0·1 % (w/v) NaCl and at pH 6, although growth was observed from pH 5·5 to 7·0. Az-Fu1Tcan use elemental sulfur, sulfite, thiosulfate, ferrous iron or hydrogen as electron donors, and oxygen (0·2–9·0 %, v/v) as electron acceptor. Az-Fu1Tis also able to grow anaerobically, with elemental sulfur, arsenate and ferric iron as electron acceptors. The Az-Fu1TG+C content was 33·6 mol%. Maximum-likelihood analysis of the 16S rRNA phylogeny placed the isolate in a distinct lineage within theAquificales, closely related toSulfurihydrogenibium subterraneum(2·0 % distant). The 16S rRNA gene of Az-Fu1Tis 7·7 % different from that ofPersephonella marinaand 6·8 % different fromHydrogenothermus marinus. Based on the phenotypic and phylogenetic characteristics presented here, it is proposed that Az-Fu1Tbelongs to the recently described genusSulfurihydrogenibium. It is further proposed that Az-Fu1Trepresents a new species,Sulfurihydrogenibium azorense.
Nitratireductor aquibiodomus gen. nov., sp. nov., a novel α-proteobacterium from the marine denitrification system of the Montreal Biodome (Canada)
Authors: Labbé Normand , Parent Serge , Villemur Richard
Published: January 2004

The Montreal Biodome operates a methanol-fed denitrification system that treats the water in its three million litre marine mesocosm. An unknown bacterium, named strain NL21T, was isolated from this system on TSA and R2A agar. The organism is a Gram-negative, rod-shaped (1×3 μm) facultative aerobe. Optimal growth conditions on R2A agar are 30–35 °C, pH 7–7·5 and 1 % (w/w) NaCl. Phylogenetic analysis of the 16S rDNA sequence reveals that strain NL21Tforms a novel lineage in the family ‘Phyllobacteriaceae’ within theα2 subgroup of theProteobacteria. The closest related genera areAminobacter,Pseudaminobacter,MesorhizobiumandDefluvibacter. Major cellular fatty acids are C18 : 1ω7c(75 %), C19 : 0ω8ccyclopropane (9·4 %) and C18 : 0(4·2 %). The DNA G+C content of strain NL21T(57 mol%) differs from those of all other described members of the ‘Phyllobacteriaceae’ (60–64 mol%). Strain NL21Treduces nitrate to nitrite, but does not reduce nitrite to nitrogen gas. Only a few sugars and amino acids can serve as carbon sources. Strain NL21Tis able to grow without salt and tolerates up to 5 % NaCl. Phylogenetic analysis, as well as physiological and biochemical tests, showed that strain NL21Twas different from all other members of the ‘Phyllobacteriaceae’ with validly published names. Strain NL21Ttherefore represents a novel genus, for which the nameNitratireductor aquibiodomusgen. nov., sp. nov. is proposed, with the type strain NL21T(=DSM 15645T=ATCC BAA-762T).
Methylocella tundrae sp. nov., a novel methanotrophic bacterium from acidic tundra peatlands
Authors: Dedysh Svetlana N. , Berestovskaya Yulia Y. , Vasylieva Lina V. , Belova Svetlana E. , Khmelenina Valentina N. , Suzina Natalia E. , Trotsenko Yuri A. , Liesack Werner , Zavarzin George A.
Published: January 2004

A novel species, Methylocella tundrae, is proposed for three methanotrophic strains (T4T, TCh1 and TY1) isolated from acidic Sphagnum tundra peatlands. These strains are aerobic, Gram-negative, non-motile, dinitrogen-fixing rods that possess a soluble methane monooxygenase and utilize the serine pathway for carbon assimilation. Strains T4T, TCh1 and TY1 are moderately acidophilic organisms capable of growth between pH 4·2 and 7·5 (optimum 5·5–6·0) and between 5 and 30 °C (optimum 15 °C). The major phospholipid fatty acid is 18 : 1ω7c. The DNA G+C content of strain T4T is 63·3 mol%. The three strains possess almost identical 16S rRNA gene sequences and are most closely related to two previously identified species of Methylocella, Methylocella palustris (97 % similarity) and Methylocella silvestris (97·5 % similarity). DNA–DNA hybridization values of strain T4T with Methylocella palustris KT and Methylocella silvestris BL2T were respectively 27 and 36 %. Thus, the tundra strains represent a novel species, for which the name Methylocella tundrae sp. nov. is proposed. Strain T4T (=DSM 15673T=NCIMB 13949T) is the type strain.
Nocardiopsis alkaliphila sp. nov., a novel alkaliphilic actinomycete isolated from desert soil in Egypt
Authors: Hozzein Wael N. , Li Wen-Jun , Ali Mohammed Ibrahim A. , Hammouda Ola , Mousa Ahmed S. , Xu Li-Hua , Jiang Cheng-Lin
Published: January 2004

An alkaliphilic actinomycete strain, designated YIM 80379T, was isolated from a soil sample collected from the eastern desert of Egypt and subjected to polyphasic taxonomy. The strain produced substrate and aerial mycelia on different media, with an optimum pH for growth of 9·5–10 and scarce or no growth at pH 7. Strain YIM 80379Tcontainedmeso-diaminopimelic acid, no diagnostic sugars, type PIII phospholipids and MK-10(H6) and MK-10(H8) as the predominant menaquinones. All of these characters assign isolate YIM 80379Tconsistently to the genusNocardiopsis. This was confirmed by 16S rDNA analysis. It can be differentiated from allNocardiopsisspecies with validly published names by phenotypic characteristics, phylogenetic analysis and DNA–DNA hybridization results. On the basis of polyphasic evidence, a novel species,Nocardiopsis alkaliphilasp. nov., is proposed. The type strain of the species is YIM 80379T(=CCTCC AA001031T=DSM 44657T).
Flavobacterium degerlachei sp. nov., Flavobacterium frigoris sp. nov. and Flavobacterium micromati sp. nov., novel psychrophilic bacteria isolated from microbial mats in Antarctic lakes
Authors: Van Trappen Stefanie , Vandecandelaere Ilse , Mergaert Joris , Swings Jean
Published: January 2004

Taxonomic studies were performed on 36 strains that were isolated from microbial mats in Antarctic lakes of the Vestfold Hills, the Larsemann Hills and the McMurdo Dry Valleys. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains are related to members of the genusFlavobacterium; sequence similarity values with their nearest phylogenetic neighbours ranged from 96·8 to 98·5 %. Results of DNA–DNA hybridization and comparison of repetitive extragenic palindromic DNA-PCR fingerprinting patterns revealed that these strains are members of three distinct species. Genotypic results, together with phenotypic characteristics, allowed the differentiation of these species from relatedFlavobacteriumspecies with validly published names. The isolates are Gram-negative, chemoheterotrophic, rod-shaped cells that are psychrophilic and moderately halotolerant; their DNA G+C contents range from 33·1 to 34·5 mol%. Their whole-cell fatty acid profiles are similar and include C15 : 0, anteiso-C15 : 0, iso-C15 : 0, C15 : 1ω6c, iso-C16 : 0, iso-C16 : 03-OH and summed feature 3 (which comprises iso-C15 : 02-OH, C16 : 1ω7cor both) as major fatty acid components. On the basis of these results, three novel species are proposed, namelyFlavobacterium degerlacheisp. nov. (consisting of 14 strains, with LMG 21915T=DSM 15718Tas the type strain),Flavobacterium micromatisp. nov. (consisting of three strains, with LMG 21919T=CIP 108161Tas the type strain) andFlavobacterium frigorissp. nov. (consisting of 19 strains, with LMG 21922T=DSM 15719Tas the type strain).