- Volume 49, Issue 2, 1999
Volume 49, Issue 2, 1999
- Validation List
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- Notification List
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- New Taxa - Archaea
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Thermococcus barophilus sp. nov., a new barophilic and hyperthermophilic archaeon isolated under high hydrostatic pressure from a deep-sea hydrothermal vent
A novel barophilic, hyperthermophilic, anaerobic sulfur-metabolizing archaeon, strain MPT (T = type strain), was isolated from a hydrothermal vent site (Snakepit) on the Mid-Atlantic Ridge (depth, 3550 m). Enrichments and isolation were done under 40 MPa hydrostatic pressure at 95 °C. Strain MPT was barophilic at 75,80,85,90,95 and 98 °C, and was an obligate barophile between 95 and 100 °C (T max). For growth above 95 °C, a pressure of 15·0-17·5 MPa was required. The strain grew at 48·95 °C under atmospheric pressure. The optimal temperature for growth was 85 °C at both high (40 MPa) and low (0·3 MPa) pressures. The growth rate was twofold higher at 85 °C under in situ hydrostatic pressure compared to at low pressure. Strain MPT cells were motile, coccoid, 0·8-2·0 μm in diameter and covered by a hexagonal S-layer lattice. The optimum pH and NaCl concentration for growth at low pressure were 7·0 and 20·30 g I–1, respectively. The new isolate was an obligate heterotroph and utilized yeast extract, beef extract and peptone for growth. Growth was optimal in the presence of elemental sulfur. Rifampicin and chloramphenicol inhibited growth. The core lipids consisted of a major archaeol and a complex lipid pattern consisting of a major phospholipid. The DNA G+C content was 37·1 mol%. Sequencing of the 16S rRNA gene revealed that strain MPT belonged to the genus Thermococcus and it is proposed that this isolate should be designated as a new species, Thermococcus barophilus.
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Methanococcus vulcanius sp. nov., a novel hyperthermophilic methanogen isolated from East Pacific Rise, and identification of Methanococcus sp. DSM 4213Tas Methanococcus fervens sp. nov.
An autotrophic, hyperthermophilic methanogen (M7T) was isolated from a deep-sea hydrothermal chimney sample collected on the East Pacific Rise at depth of 2600 m. The coccoid-shaped cells are flagellated and exhibit a sligh tumbling motility. The temperature range for growth at pH 6·5 was 49–89 °C, with optimum growth at 80 °C. The optimum pH for growth was 6·5, and the optimum NaCI concentration for growth was around 25 g I–1. The new isolat used H2 and CO2 as the only substrates for growth and methane production. Tungsten, selenium and yeast extract stimulated growth significantly. In the presence of CO2 and H2 the organism reduced elemental sulphur to hydrogen sulphide. Growth was inhibited by chloramphenicol and rifampicin, but not by ampicillin, kanamycin, penicillin and streptomycin. The G+C content of the genomic DNA was 31 mol%. As determined by 16S rDNA gene sequence analysis, this organism was closely related to Methanococcus jannaschii strain JAL-1T. However, despite the high percentage of similarity between their 16S rDNA sequences (97·1 %), the DNA-DNA hybridization levels between these strains were less than 5%. On the basis of these observations and physiological traits, it is proposed that this organism should be placed in a new species, Methanococcus vulcanius. The type strain is M7T(= DSM 12094T) During the course of this study, the 16S rDNA sequence analysis placed Methanococcus sp. strain AG86T(= DSM 4213T) as a close relative of M. jannaschii strain JAL-1T. However, the weak level of DNA-DNA hybridization with this strain (< 10%) allowed the proposal that strain AG86Talso constitutes a new species, Methanococcus fervens.
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- New Taxa - Other Bacteria
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Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms
More LessThe current taxonomic classification of Chlamydia is based on limited phenotypic, morphologic and genetic criteria. This classification does not take into account recent analysis of the ribosomal operon or recently identified obligately intracellular organisms that have a chlamydia-like developmental cycle of replication. Neither does it provide a systematic rationale for identifying new strains. In this study, phylogenetic analyses of the 16S and 23S rRNA genes are presented with corroborating genetic and phenotypic information to show that the order Chlamydiales contains at least four distinct groups at the family level and that within the Chlamydiaceae are two distinct lineages which branch into nine separate clusters. In this report a reclassification of the order Chlamydiales and its current taxa is proposed. This proposal retains currently known strains with > 90% 16S rRNA identity in the family Chlamydiaceae and separates other chlamydia-like organisms that have 80–90% 16S rRNA relatedness to the Chlamydiaceae into new families. Chlamydiae that were previously described as ‘Candidatus Parachlamydia acanthamoebae ‘Amann, Springer, Schönhuber, Ludwig, Schmid, Müller and Michel 1997, become members of Parachlamydiaceae fam. nov., Parachlamydia acanthamoebae gen. nov., sp. nov. ‘Simkania’ strain Z becomes the founding member of Simkaniaceae fam. nov., Simkania negevensis gen. nov., sp. nov. The fourth group, which includes strain WSU 86-1044, was left unnamed. The Chlamydiaceae, which currently has only the genus Chlamydia, is divided into two genera, Chlamydia and Chlamydophila gen. nov. Two new species, Chlamydia muridarum sp. nov. and Chlamydia suis sp. nov., join Chlamydia trachomatis in the emended genus Chlamydia. Chlamydophila gen. nov. assimilates the current species, Chlamydia pecorum, Chlamydia pneumoniae and Chlamydia psittaci, to form Chlamydophila pecorum comb. nov., Chlamydophila pneumoniae comb. nov. and Chlamydophila psittaci comb. nov. Three new Chlamydophila species are derived from Chlamydia psittaci: Chlamydophila abortus gen. nov., sp. nov., Chlamydophila caviae gen. nov., sp. nov. and Chlamydophila felis gen. nov., sp. nov. Emended descriptions for the order Chlamydiales and for the family Chlamydiaceae are provided. These families, genera and species are readily distinguished by analysis of signature sequences in the 16S and 23S ribosomal genes.
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Analysis of the 16S rRNA gene of microorganism WSU 86-1044 from an aborted bovine foetus reveals that it is a member of the order Chlamydiales: proposal of Waddliaceae fam. nov., Waddlia chondrophila gen. nov., sp. nov.
More LessThe structural gene encoding the 16S rRNA of the new obligate intracellular organism presently designated WSU 86-1044T was sequenced and analysed to establish its phylogenetic relationships. The 16S rDNA sequence was most closely related to those of chlamydial species, having 84·7–85·3 % sequence similarity, while it had 72·4–73·2% similarity with rickettsia-like organisms. When the sequences of the four species of chlamydiae (Chlamydophila psittaci, Chlamydia trachomatis, Chlamydophila pneumoniae and Chlamydophila pecorum) were compared, they had > 93% sequence similarity indicating that WSU 86-1044T was not close enough to be in the same family as current Chlamydiaceae members. However, based on the 84·7–85·3% 16S rDNA sequence similarity of WSU 86-1044T and other previously described characteristics, WSU 86-1044T belongs to a novel family within the order Chlamydiales; hence, the proposal of Waddliaceae fam. nov., Waddlia chondrophila gen. nov., sp. nov.
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Spiroplasma poulsonii sp. nov., a new species associated with male-lethality in Drosophila willistoni, a neotropical species of fruit fly
Progenies from some wild-caught females of Drosophila willistoni and three other sibling species are entirely female. The proclivity for production of unisexual female progeny by these flies was named the sex ratio (SR) trait and was originally thought to be genetic. However, experiments in the laboratory of Donald F. Poulson in the early 1960s demonstrated that this ‘trait’ was vertically transmitted and infectious, in that it could be artificially transferrd by injection from infected females to non-infected females. Motile, helical micro-organisms were observed in females showing the trait. In 1979, the SR organisms were designated as group II in the informal spiroplasma classification system. The organisms proved to be extremely fastidious, but were eventually cultivated in a very complex cell-free medium (H-2) after initial co-cultivation with insect cells. Cultivation in the H-2 medium and the subsequent availability of a triply cloned strain (DW-1 T) permitted comparaltiv studies. Cells of strain DW-1 Twere helical, motile filaments 200–250 nm in diameter and were bound by a single trilaminar membrane. Cells plated on 1·8% Noble agar formed small satellite-free colonies 60–70 μm in diameter with dense centres and uneven edges. The temperature range for growth was 26–30 °C; optimum growth occurred at 30 °C, with a doubling time in H-2 medium of 15·8 h. The strain passed through filters with 220 nm, but not 100 nm, pores. Reciprocal serological comparisons of strain DW-1 Twith representatives of other spiroplasma groups showed an extensive pattern of one-way crossing when strain DW-1 Twas used as antigen. However, variable, usually low-level reciprocal cross-reactions were observed between strain DW-1 T and representatives of group I sub-groups. The genome size of strain DW-1 Twas 2040 kbp, as determined by PFGE. The G+C content was 26±1 mol%, as determined by buoyant density and melting point methods. The serological and molecular data indicate that strain DW-1 Tis separated from group I representative strains sufficiently to justify retention of its group status. Continued group designation is also indicated by the ability of SR spiroplasma to induce male lethality in Drosophila, their vertical transmissibility and their extremely fastidious growth requirements. Group II spiroplasmas, represented by strain DW-1 T(ATCC 43153 T), are designated Spiroplasma poulsonii.
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Simkania negevensis strain ZT: growth, antigenic and genome characteristics
More LessSimkania negevensis is the type species of Simkaniaceae, a recently proposed family in the order Chlamydiales. In the current study, growth, antigenic and genomic characteristics of this intracellular bacterium were investigated and compared to those of members of the family Chlamydiaceae. Growth of the organism, as assessed by infectivity assays, reached a plateau in 2–3 d although by light microscopy the cytopathic effect on the host cells increased for 12 or more days after infection. S. negevensis growth was unaffected by sulfadiazine. Cells infected by S. negevensis strain ZT were not recognized by either of two monoclonal antibodies specific for Chlamydiaceae LPS and several specific Chlamydiaceae ompA primers were unable to PCR amplify a S. negevensis gene. The S. negevensis genome contained one copy of the ribosomal operon. The genome size of S. negevensis strain ZT was determined by PFGE to be 1·7 Mbp, and the G+C content was 42·5 mol%. These data, taken together with other published data, are consistent with the proposal that S. negevensis belongs to a distinct family in the order Chlamydiales.
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Further determination of DNA relatedness between serogroups and serovars in the family Leptospiraceae with a proposal for Leptospira alexanderi sp. nov. and four new Leptospira genomospecies
DNA relatedness was determined among 303 strains of Leptospira and Leptonema. Included in the analysis were reference strains from 228 well-characterized and recognized serovars. The study included 268 serovars from 29 named and one or more unnamed serogroups. The strains clustered into 17 DNA hybridization groups, representing 12 previously described species (292 strains) and five new genomospecies (11 strains). The largest groups included Leptospira interrogans (91 strains from 82 serovars), Leptospira santarosai (61 strains from 59 serovars), Leptospira borgpetersenii (49 strains from 43 serovars), Leptospira kirschneri (29 strains from 26 serovars) and Leptospira noguchii (20 strains from 20 serovars). The new genomospecies include Leptospira genomospecies 1 (two strains, serovars pinagchang and sichuan), Leptospira genomospecies 2 (six strains, serovars lushui, manhao 3, manzhuang, nanding, mengla and yunnan), Leptospira genomospecies 3 (one strain, serovar holland), Leptospira genomospecies 4 (one strain, serovar hualin) and Leptospira genomospecies 5 (one strain, serovar saopaulo). With the exception of Ballum, all serogroups with greater than one serovar studied were genetically heterogeneous. Phenotypic tests, including optimal growth temperature, lipase activity and growth inhibition by copper sulfate or 2,6-diaminopurine, were of little use in differentiating DNA relatedness groups. The name Leptospira alexanderi sp. nov. is proposed for Leptospira genomospecies 2 (type strain L 60T= ATCC 700520T, serovar manhao 3).
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- New Taxa - Proteobacteria
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Desulfobacca acetoxidans gen. nov., sp. nov., a novel acetate-degrading sulfate reducer isolated from sulfidogenic granular sludge
More LessA mesophilic sulfate reducer, strain ASRB2T, was isolated with acetate as sole carbon and energy source from granular sludge of a laboratory-scale upflow anaerobic sludge bed reactor fed with acetate and sulfate. The bacterium was oval-shaped, 1·3 × 1·9-2·2 μm, non-motile and Gram-negative. Optimum growth with acetate occurred around 37 °C in freshwater medium (doubling time: 1·7-2·2 d). Enzyme studies indicated that acetate was oxidized via the carbon monoxide dehydrogenase pathway. Growth was not supported by other organic acids, such as propionate, butyrate or lactate, alcohols such as ethanol or propanol, and hydrogen or formate. Sulfite and thiosulfate were also used as electron acceptors, but sulfur and nitrate were not reduced. Phylogenetically, strain ASRB2T clustered with the delta subclass of the Proteobacteria. Its closest relatives were Desulfosarcina variabilis, Desulfacinum infernum and Syntrophus buswellii. Strain ASRB2T is described as the type strain of Desulfobacca acetoxidans gen. nov., sp. nov.
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Marinobacter aquaeolei sp. nov., a halophilic bacterium isolated from a Vietnamese oil-producing well
More LessSeveral strains of moderately halophilic and mesophilic bacteria were isolated at the head of an oil-producing well on an offshore platform in southern Vietnam. Cells were Gram-negative, non-spore-forming, rod-shaped and motile by means of a polar f lagellum. Growth occurred at NaCl concentrations between 0 and 20%; the optimum was 5% NaCl. One strain, which was designated VT8T, could degrade n-hexadecane, pristane and some crude oil components. It grew anaerobically in the presence of nitrate on succinate, citrate or acetate, but not on glucose. Several organic acids and amino acids were utilized as sole carbon and energy sources. The major components of its cellular fatty acids were C12:0 3-OH, C16:1 ω9c, C16:0 and C18:1 ω9c. The DNA G+C content was 55·7 mol%. 16S rDNA sequence analysis indicated that strain VT8T was closely related to Marinobacter sp. strain CAB (99·8% similarity) and Marinobacter hydrocarbonoclasticus (99·4% similarity). Its antibiotic resistance, isoprenoid quinones and fatty acids were similar to those of Marinobacter hydrocarbonoclasticus and Pseudomonas nautica. However, the whole-cell protein pattern of VT8T differed from that of other halophilic marine isolates, including P. nautica. DNA-DNA hybridization indicated that the level of relatedness to Marinobacter hydrocarbonoclasticus was 65% and that to P. nautica was 75 %. Further differences were apparent in Fourier-transformed IR spectra of cells and lipopolysaccharide composition. It is proposed that VT8T should be the type strain of a new species and should be named Marinobacter aquaeolei. P. nautica may have been misclassified, as suggested previously, and may also belong to the genus Marinobacter.
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Reclassification of non-pigmented Erwinia herbicola strains from trees as Erwinia billingiae sp. nov.
More LessTwenty-two Erwinia-like strains, isolated from trees since the late fifties and belonging to a distinct phenotypic group with resemblance to Pantoea agglomerans, were further characterized by conventional biochemical tests, the BIOLOG metabolic fingerprinting system and fatty acid analysis. Their phylogenetic positions were determined by comparing the 16S rRNA gene sequence of a representative strain to available sequences of Erwinia, Pantoea, Pectobacterium and Brenneria species. The strains were shown to belong to the genus Erwinia, with Erwinia rhapontici and Erwinia persicina as the closest phylogenetic relatives. The name Erwinia billingiae sp. nov. is proposed (type strain LMG 2613T) and a description of the species is given.
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Thiomicrospira kuenenii sp. nov. and Thiomicrospira frisia sp. nov., two mesophilic obligately chemolithoautotrophic sulfur-oxidizing bacteria isolated from an intertidal mud flat
More LessTwo new members of the genus Thiomicrospira were isolated from an intertidal mud flat sample with thiosulfate as the electron donor and CO2 as carbon source. On the basis of differences in genotypic and phenotypic characteristics, it is proposed that strain JB-A1T (= DSM 12350T) and strain JB-A2T (= DSM 12351T) are members of two new species, Thiomicrospira kuenenii and Thiomicrospira frisia, respectively. The cells were Gram-negative vibrios or slightly bent rods. Strain JB-A1T was highly motile, whereas strain JB-A2T showed a much lower degree of motility combined with a strong tendency to form aggregates. Both organisms were obligately autotrophic and strictly aerobic. Nitrate was not used as electron acceptor. Chemolithoautotrophic growth was observed with thiosulfate, tetrathionate, sulfur and sulfide. Neither isolate was able to grow heterotrophically. For strain JB-A1T, growth was observed between pH values of 4·0 and 7·5 with an optimum at pH 6·0, whereas for strain JB-A2T, growth was observed between pH 4·2 and 8·5 with an optimum at pH 6·5. The temperature limits for growth were between 3·5 and 42 °C and 3·5 and 39 °C, respectively. The optimum growth temperature for strain JB-A1T was between 29 and 33·5 °C, whereas strain JB-A2T showed optimal growth between 32 and 35 °C. The mean maximum growth rate on thiosulfate was 0·35 h–1 for strain JB-AT and 0·45 h–1 for strain JB-A2T.
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Legionella taurinensis sp. nov., a new species antigenically similar to Legionella spiritensis
A group of 42 Legionella-like organisms reacting specifically with Legionella spiritensis serogroup 1 antisera were collected throughout Europe by the Centre National de Référence (French National Reference Centre) for Legionella. This group of isolates differed somewhat from L. spiritensis in terms of biochemical reactions, ubiquinone content and protein profile. The latter two analyses revealed that one of these L. spiritensis-like isolates, Turin I no. 1T, was highly related, but not identical to any of the red autofluorescent species of Legionella. In fact, this strain was the first of these particular isolates recognized to emit a red autofluorescence when exposed to UV light. Profile analysis of randomly amplified polymorphic DNA established that the red autofluorescent L. spiritensis-like isolates constituted a homogeneous group distinct from Legionella rubrilucens and Legionella erythra. DNA-DNA hybridization studies involving the use of S1 nuclease confirmed that the indicated group of isolates are a new species of Legionella, for which the name Legionella taurinensis is proposed with strain Turin I no. 1T (deposited as ATCC 700508T) as the type strain.
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Classification of Alcaligenes faecalis-like isolates from the environment and human clinical samples as Ralstonia gilardii sp. nov.
A polyphasic taxonomic study that included DNA-DNA hybridizations, DNA base ratio determinations, 16S rDNA sequence analysis, whole-cell protein and fatty acid analyses, AFLP (amplified fragment length polymorphism) fingerprinting and an extensive biochemical characterization was performed on 10 strains provisionally identified as Alcaligenes faecalis-like bacteria. The six environmental and four human isolates belonged to the genus Ralstonia and were assigned to a new species for which the name Ralstonia gilardii sp. nov. is proposed. The type strain is LMG 5886T.
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Fundibacter jadensis gen. nov., sp. nov., a new slightly halophilic bacterium, isolated from intertidal sediment
More LessA moderately halophilic hydrocarbon-degrading bacterium was isolated from continuous cultures containing a suspension of intertidal sediment from the German North Sea coast with hexadecane as the sole carbon source. On the basis of phenotypic characteristics, fatty acid analysis and 16S rDNA sequence analysis, it was considered to be a new species belonging to a new genus. It is a Gram-negative, aerobic, rod-shaped bacterium, whose cell size varies. It grows at concentrations of 0·5–15% (w/v) NaCl and utilizes a restricted spectrum of carbon sources. The G+C content of the DNA is 63·6 mol %. Comparative 16S rDNA studies show a clear affiliation of this bacterium to the gamma subclass of the class Proteobacteria. Comparison of phylogenetic data indicate that it is most closely related to Marinobacter hydrocarbonoclasticus (88·9% similarity in 16S rRNA gene sequence). Since it is impossible to find a sufficiently closely related species, we propose the name Fundibacter jadensis gen. nov., sp. nov. for the bacteria. The type strain is T9T ( = DSM 12178T).
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Roseateles depolymerans gen. nov., sp. nov., a new bacteriochlorophyll a-containing obligate aerobe belonging to the β-subclass of the Proteobacteria
Strains 61AT(T = type strain) and 61B2, the first bacteriochlorophyll (BChl) a-containing obligate aerobes to be classified in the β-subclass of the Proteobacteria, were isolated from river water. The strains were originally isolated as degraders of poly(hexamethylene carbonate) (PHC). The organisms can utilize PHC and some other biodegradable plastics. The strains grow only under aerobic conditions. Good production of BChl a and carotenoid pigments is achieved on PHC agar plates and an equivalent production is observed under oligotrophic conditions on agar medium. Spectrometric results suggest that BChl a is present in light-harvesting complex I and the photochemical reaction centre. The main carotenoids are spirilloxanthin and its precursors. Analysis of the 16S rRNA gene sequence indicated that the phylogenetic positions of the two strains are similar to each other and that their closest relatives are the genera Rubrivivax, Ideonella and Leptothrix with similarities of 96·3, 96·2 and 96·1%, respectively. The cells are motile, straight rods and contain poly-β- hydroxybutyrate granules. Ubiquinone-8 is the predominant quinone. Vitamins are not required for growth. The G+C content of genomic DNA is 66·2–66·3 mol%. Genetic and phenotypic features suggest that the strains represent a new genus in the β-subclass which is evenly distant from known genera. Consequently, the name Roseateles depolymerans gen. nov., sp. nov. is proposed for the strains; the type strain of Roseateles depolymerans is strain 61AT(= DSM 11813T).
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DNA relatedness among the pathovars of Pseudomonas syringae and description of Pseudomonas tremae sp. nov. and Pseudomonas cannabina sp. nov. (ex Sutic and Dowson 1959)
More LessA total of 48 pathovars of Pseudomonas syringae and eight related species were studied by DNA-DNA hybridization (S1 nuclease method) and ribotyping. The existence of nine discrete genomospecies was indicated. Genomospecies 1 corresponded to P. syringae sensu stricto and included P. syringae pathovars syringae, aptata, lapsa, papulans, pisi, atrofaciens, aceris, panici, dysoxyli and japonica. Genomospecies 2 included P. syringae pathovars phaseolicola, ulmi, mori, lachrymans, sesami, tabaci, morsprunorum, glycinea, ciccaronei, eriobotryae, mellea, aesculi, hibisci, myricae, photiniae and dendropanacis and nomenspecies Pseudomonas savastanoi, Pseudomonas ficuserectae, Pseudomonas meliae and Pseudomonas amygdali, which are thus synonymous. P. amygdali is the earliest valid name for this genomospecies. Genomospecies 3 included P. syringae pathovars tomato, persicae, antirrhini, maculicola, viburni, berberidis, apii, delphinii, passiflorae, philadelphi, ribicola and primulae. We recommend strain CFBP 2212 of P. syringae pv. tomato to serve as the type strain. Genomospecies 4 included ‘Pseudomonas coronafaciens’ and P. syringae pathovars porri, garcae, striafaciens, atropurpurea, oryzae and zizaniae and corresponds to ‘P. coronafaciens’. Genomospecies 5 included P. syringae pv. tremae and corresponds to Pseudomonas tremae sp. nov. Genomospecies 6 included Pseudomonas viridiflava and the presently misidentified pathotype strains of P. syringae pv. ribicola and P. syringae pv. primulae and thus corresponds to P. viridiflava. Genomospecies 7 included P. syringae pv. tagetis and P. syringae pv. helianthi. We recommend strain CFBP 1694 of P. syringae pv. tagetis to serve as a reference strain. Genomospecies 8 included P. syringae pv. theae and Pseudomonas avellanae and thus corresponds to P. avellanae. Genomospecies 9 included P. syringae pv. cannabina and corresponds to Pseudomonas cannabina sp. nov. Ribotyping (Smal and Hincll endonucleases) could separate seven of the nine genomospecies. The unnamed genomospecies 3 and 7 will be named when phenotypic data are available for identification. Two species are described, P. tremae sp. nov. and P. cannabina sp. nov. Other species will be named when phenotypic data are available for identification.
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Sulfitobacter mediterraneus sp. nov., a new sulfite-oxidizing member of the α-Proteobacteria
Analysis of PCR products of 16S rDNA of 680 isolates from Mediterranean Sea mesocosm experiments with taxon-specific 16S rDNA oligonucleotides revealed that 262 isolates belonged to the α subclass of the class Proteobacteria. Partial 16S rDNA sequence analysis of selected isolates and oligonucleotide probing with a Sulfitobacter-specific 16S rDNA probe affiliated 33 strains to the genus Sulfitobacter. Analysis of the Haelll digest pattern of 16S rDNA revealed the presence of two groups; while 30 strains showed a pattern identical with that obtained for Sulfitobacter pontiacus DSM 10014T, a second group of three strains had a unique pattern that was different from that of the type strain. Five isolates of group 1 and one isolates of group 2, strain CH-B427T, were selected for detailed taxonomic analysis. All six isolates closely resembled the type strain Sulfitobacter pontiacus DSM 10014Tin physiological reactions. However, strain CH-B427Tdiffered quantitatively in the composition of fatty acids from Sulfitobacter pontiacus DSM 10014Tand showed only 98·2% 16S rDNA sequence similarity with strain DSM 10014T. DNA-DNA reassociation value obtained for strains DSM 10014Tand CH-B427Trevealed 46 % similarity. Based on the results of DNA-DNA reassociation and discrete differences in the nucleotide composition of 16S rDNA, a new species of the genus Sulfitobacter is proposed, designated Sulfitobacter mediterraneus sp. nov., the type strain being strain CH-B427T(= DSM 12244T).
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Description of Skermanella parooensis gen. nov., sp. nov. to accommodate Conglomeromonas largomobilis subsp. parooensis following the transfer of Conglomeromonas largomobilis subsp. largomobilis to the genus Azospirillum
More LessAs a consequence of the transfer of the type species Conglomeromonas largomobilis subsp. largomobilis to the genus Azospirillum, the name of the genus Conglomeromonas must be changed in accordance with Rule 37a(1) of the International Code of Nomenclature of Bacteria. Consequently, it is proposed that the subspecies Conglomeromonas largomobilis subsp. parooensis be transferred to the genus Skermanella gen. nov. as the type species Skermanella parooensis gen. nov., sp. nov. This taxon belongs to an isolated subline of descent in the Azospirillum branch of the α-Proteobacteria. The spelling of the specific epithet of Azospirillum largomobile is corrected to Azospirillum largimobile.
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Characterization of the anaerobic propionate-degrading syntrophs Smithella propionica gen. nov., sp. nov. and Syntrophobacter wolinii
More LessA strain of anaerobic, syntrophic, propionate-oxidizing bacteria, strain LYPT(= OCM 661T; T = type strain), was isolated and proposed as representative a new genus and new species, Smithella propionica gen. nov., sp. nov. The strain was enriched from an anaerobic digestor and isolated. Initial isolation was as a monoxenic propionate-degrading co-culture containing Methanospirillum hungateii JF-1Tas an H2- and formate-using partner. Later, an axenic culture was obtained by using crotonate as the catabolic substrate. The previously described propionate-degrading syntrophs of the genus Syntrophobacter also grow in co-culture with methanogens such as Methanospirillum hungateii, forming acetate, CO2 and methane from propionate. However, Smithella propionica differs by producing less methane and more acetate; in addition, it forms small amounts of butyrate. Smithella propionica and Syntrophobacter wolinii grew within similar ranges of pH, temperature and salinity, but they differed significantly in substrate ranges and catabolic products. Unlike Syntrophobacter wolinii, Smithella propionica grew axenically on crotonate, although very slowly. Co-cultures of Smithella propionica grew on propionat and grew slowly on crotonate or butyrate. Syntrophobacter wolinii and Syntrophobacter pfennigii grow on propionate plus sulfate, whereas Smithella propionica did not. Comparisons of 16S rDNA genes indicated that Smithella propionica is most closely related to Syntrophus, and is more distantly related to Syntrophobacter.
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Phylogenetic relationships among members of the Comamonadaceae, and description of Delftia acidovorans (den Dooren de Jong 1926 and Tamaoka et al. 1987 ) gen. nov., comb. nov.
More LessThe phylogenetic relationships among members of the family Comamonadaceae and several unclassified strains were studied by direct sequencing of their PCR-amplified 16S rRNA genes. Based on the 16S rRNA gene sequence analysis, members of the family formed a coherent group. The closest relatives are species of the Rubrivivax sub-group: Leptothrix discophora, Ideonella dechloratans and Rubrivivax gelatinosus. The genus Hydrogenophaga formed two subclusters, as did the species of Acidovorax, whereas the five species of the genus [Aquaspirillum] were polyphyletic. Comamonas acidovorans was phylogenetically distant from the type species of Comamonas, Comamonas terrigena. On the basis of this work and previous studies, Comamonas acidovorans is removed from the genus Comamonas and renamed as Delftia acidovorans gen. nov., comb. nov. Descriptions of the new genus Delftia and of the type species Delftia acidovorans, for which the type strain is ATCC 15668T, are presented.
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Roseivivax halodurans gen. nov., sp. nov. and Roseivivax halotolerans sp. nov., aerobic bacteriochlorophyll-containing bacteria isolated from a saline lake
More LessPhenotypic and phylogenetic studies were performed with two strains (OCh 239T and OCh 210T, T = type strain) of aerobic bacteriochlorophyll-containing bacteria isolated from the charophytes and the epiphytes on the stromatolites, respectively, of a saline lake located on the west coast of Australia. Both strains were chemoheterotrophic, Gram-negative and motile rods with subpolar flagella. Catalase and oxidase were produced. ONPG reaction was positive. Cells utilized d-glucose, acetate, butyrate, citrate, dl-lactate, dl-malate, pyruvate, succinate, l-aspartate and l-glutamate. Acids were produced from d-fructose and d-glucose. Bacteriochlorophyll a was synthesized under aerobic conditions. Strain OCh 239T had nitrate reductase and phosphatase. Acids were produced from l-arabinose, d-galactose, lactose, maltose, d-ribose and sucrose. The strain could grow in 0·20–0% (w/v) NaCI. Strain OCh 210T had urease. Hydrolysis of gelatin was positive. Acids were produced from d-xylose. The strain could grow in 0·5–20·0% (w/v) NaCI. The results of 16S rRNA sequence comparisons revealed that strains OCh 239T and OCh 210T formed a new cluster within the α-3 group of the α subclass of the class Proteobacteria. The similarity value of the 16S rRNA sequences between strains OCh 239T and OCh 210T was 95·8%. Therefore, it was concluded that these two strains should be placed in a new genus, Roseivivax gen. nov., as the new species Roseivivax halodurans sp. nov. and Roseivivax halotolerans sp. nov. The type species of the genus is Roseivivax halodurans. The type strains of Roseivivax halodurans and Roseivivax halotolerans are OCh 239T (= JCM 10272T) and OCh 210T (= JCM 10271T), respectively.
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More LessA sulfate-reducing bacterium, strain HDvT(T = type strain), was isolated from an anoxic ricefield soil. Cells were Gram-negative, non-sporulating curved rods motile by means of a single polar flagellum. Cytochrome c 3 and desulfoviridin were present. In the presence of sulfate, glycerol, 1,2- and 1,3-propanediol, dihydroxyacetone, pyruvate, lactate, fumarate, maleate, malate and succinate were incompletely oxidized mainly to acetate. Sulfite, thiosulfate, elemental sulfur, fumarate, maleate and malate were utilized as alternative electron acceptors. In the absence of added electron acceptors, pyruvate, fumarate, maleate, malate and dihydroxyacetone were fermented. The DNA base composition was 67 mol% G+C. The phylogenetic, phenotypic and physiological characteristics of strain HDvTindicate that it is a new species of the genus Desulfovibrio, for which the name Desulfovibrio burkinensis sp. nov is proposed; the type strain is HDvT(= DSM 6830T). Phylogenetic analysis confirmed that Desulfovibrio alcoholivorans was a distinct species supporting the previously published phenotypic data.
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A re-evaluation of the taxonomy of Paracoccus denitrificans and a proposal for the combination Paracoccus pantotrophus comb. nov.
Comparison of both 16S rRNA coding sequences and DNA-DNA hybridization of ten strains of α-subclass of Proteobacteria currently classified as strains of Paracoccus denitrificans has shown that they fall into two groups which are distinct from each other at the species level. Comparison with published data on the cytochrome c profiles and other 16S rRNA coding sequences in the literature has confirmed these observations and enabled several other strains also to be assigned to these two groups. Group A comprises strains ATCC 1774T (the type strain of P. denitrificans), LMD 22.2V, DSM 413T, ATCC 19367, ATCC 13543, DSM 1404, DSM 1405, Pd 1222 (a genetic modification of DSM 4131) and NCIMB 8944. Group B comprises ATCC 35512T (the original type strain of Thiosphaera pantotropha), LMD 82.5T, LMD 92.63, DSM 65, LMG 4218, IAM 12479, JCM 6892, DSM 11072, DSM 11073 and DSM 11104. In light of these findings, it is proposed that: (1) strains of group A are retained as P. denitrificans, with ATCC 17741T as the type strain of the type species; and (2) all strains of group B are assigned to the new species combination Paracoccus pantotrophus comb, nov., with strain ATCC 35512T as the type strain. Comparative 16S rRNA sequence analysis and DNA-DNA hybridization of strains of Paracoccus versutus confirm that this species is distinct from both P. denitrificans and P. pantotrophus, but that its nearest phylogenetic neighbour is P. pantotrophus.
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Assignment of Centers for Disease Control group IVc-2 to the genus Ralstonia as Ralstonia paucula sp. nov.
More LessAn integrated genotypic and phenotypic analysis of 12 Centers for Disease Control (CDC) group IVc-2 strains revealed that this taxon represents a novel species belonging to the genus Ralstonia. Comparative 16S rDNA sequence analysis allocated a representative CDC group IVc-2 strain to the Ralstonia branch of the ß subclass of the Proteobacteria. DNA–DNA hybridizations did not detect significant binding levels towards any presently known Ralstonia species, including Ralstonia pickettii. Its DNA base ratio is between 65 and 67 mol%. The name Ralstonia paucula sp. nov. is proposed, with strain LMG 3244 ( = CDC E6793), isolated from a human respiratory tract, as the type strain. R. paucula can be differentiated from other Ralstonia species by wholecell protein analysis, amplified rDNA restriction analysis and a variety of classical biochemical tests. Strains have been isolated from various human clinical and environmental sources.
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Thiorhodospira sibirica gen. nov., sp. nov., a new alkaliphilic purple sulfur bacterium from a Siberian soda lake
A new purple sulfur bacterium was isolated from microbial films on decaying plant mass in the near-shore area of the soda lake Malyi Kasytui (pH 9·5, 0·2% salinity) located in the steppe of the Chita region of south-east Siberia. Single cells were vibrioid- or spiral-shaped (3–4μm wide and 7–20 μm long) and motile by means of a polar tuft of flagella. Internal photosynthetic membranes were of the lamellar type. Lamellae almost filled the whole cell, forming strands and coils. Photosynthetic pigments were bacteriochlorophy II a and carotenoids of the spirilloxanthin group. The new bacterium was strictly anaerobic. Under anoxic conditions, hydrogen sulfide and elemental sulfur were used as photosynthetic electron donors. During growth on sulfide, sulfur globules were formed as intermediate oxidation products. They were deposited outside the cytoplasm of the cells, in the peripheral periplasmic space and extracellularly. Thiosulfate was not used. Carbon dioxide, acetate, pyruvate, propionate, succinate, fumarate and malate were utilized as carbon sources. Optimum growth rates were obtained at pH 9·0 and optimum temperature was 30 °C. Good growth was observed in a mineral salts medium containing 5 g sodium bicarbonate I–1 without sodium chloride. The new bacterium tolerated up to 60 g sodium chloride I–1 and up to 80 g sodium carbonates I–1. Growth factors were not required. The DNA G+C composition was 56·0–57·4 mol %. Based on physiological, biochemical and genetic characteristics, the newly isolated bacterium is recognized as a new species of a new genus with the proposed name Thiorhodospira sibirica.
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Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.
The genus Shewanella has been studied since 1931 with regard to a variety of topics of relevance to both applied and environmental microbiology. Recent years have seen the introduction of a large number of new Shewanella-like isolates, necessitating a coordinated review of the genus. In this work, the phylogenetic relationships among known shewanellae were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them into a consensus classification. Based on information generated from this study and obtained from the literature, a scheme for the identification of Shewanella species has been compiled. Key phenotypic characteristics were sulfur reduction and halophilicity. Fatty acid and quinone profiling were used to impart an additional layer of information. Molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in some cases. As a result, DNA-DNA hybridization and sequence analyses of a more rapidly evolving molecule (gyrB gene) were performed. Species-specific PCR probes were designed for the gyrB gene and used for the rapid screening of closely related strains. With this polyphasic approach, in addition to the ten described Shewanella species, two new species, Shewanella oneidensis and ‘Shewanella pealeana’, were recognized; Shewanella oneidensis sp. nov. is described here for the first time.
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Rhodovulum iodosum sp. nov. and Rhodovulum robiginosum sp. nov., two new marine phototrophic ferrous-iron-oxidizing purple bacteria
More LessTwo new strains of marine purple bacteria, N1T and N2T, were isolated from coastal sediment of the North Sea (Germany) with ferrous iron as the only electron donor for anoxygenic photosynthesis. The isolates are the first saltdependent, ferrous-iron-oxidizing purple bacteria characterized so far. Analysis of 16S rRNA gene sequences revealed an affiliation with the genus Rhodovulum, which until now comprises only marine species. The sequence similarity of both strains was 95·2 %, and their closest relative was Rhodovulum adriaticum. Like all known Rhodovulum species, the new strains had ovoid to rod-shaped cells, contained bacteriochlorophyll a and carotenoids of the spheroidene series, and were able to oxidize sulfide and thiosulfate. Like Rhodovulum adriaticum, both strains were unable to assimilate sulfate ; for growth they needed a reduced sulfur source, e.g. thiosulfate. In contrast to the new strains, none of the known Rhodovulum species tested was able to oxidize ferrous iron or iron sulfide. In growth experiments, strains N1T and N2T oxidized 65 and 95%, respectively, of the ferrous iron supplied. Electron diffraction analysis revealed ferrihydrite as the main product of ferrous iron oxidation. In addition, traces of magnetite were formed. Strains N1T (= DSM 12328T) and N2T (= DSM 12329T) are described as Rhodovulum iodosum sp. nov. and Rhodovulum robiginosum sp. nov., respectively.
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Aquabacterium gen. nov., with description of Aquabacterium citratiphilum sp. nov., Aquabacterium parvum sp. nov. and Aquabacterium commune sp. nov., three in situ dominant bacterial species from the Berlin drinking water system
More LessThree bacterial strains isolated from biofilms of the Berlin drinking water system were characterized with respect to their morphological and physiological properties and their taxonomic position. Phenotypically, the bacteria investigated were motile, Gram-negative rods, oxidase-positive and catalase-negative, and contained polyalkanoates and polyphosphate as storage polymers. They displayed a microaerophilic growth behaviour and used oxygen and nitrate as electron acceptors, but not nitrite, chlorate, sulfale or ferric iron. The substrates metabolized included a broad range of organic acids but no carbohydrates at all. The three species can be distinguished from each other by their substrate utilization, ability to hydrolyse urea and casein, cellular protein patterns and growth on nutrient-rich media as well as their temperature, pH and NaCI tolerances. Phylogenetic analysis, based on 16S rRNA gene sequence comparison, revealed that the isolates are affiliated to the β1-subclass of Proteobacteria. The isolates constitute three new species with internal levels of DNA relatedness ranging from 44·9 to 51·3%. It is proposed that a new genus, Aquabacterium gen. nov., should be created, including Aquabacterium citratiphilum sp. nov., Aquabacterium parvum sp. nov. and Aquabacterium commune sp. nov. The type species of the new genus is Aquabacterium commune. The type strain of A. citratiphilum is strain B4T(= DSM 11900T), the type strain of A. parvum is strain B6T(= DSM 11968Tand the type strain of A. commune is strain B8T(= DSM 11901T).
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More LessThe phylogenetic position of Gram-negative, strictly anaerobic, non-spore-forming bacteria, representing four different genera, was determined by analysis of their 16S rDNA sequences. Formivibrio citricus and Propionivibrio dicarboxylicus are members of the β-subclass of the class Proteobacteria. While Formivibrio citricus stands phylogenetically isolated, Propionivibrio dicarboxylicus is moderately related to members of the genus Rhodocyclus. Succinimonas amylolytica and Succinivibrio dextrinosolvens are members of the γ-subclass of the class Proteobacteria in which they, together with members of the genus Anaerobiospirillum and Ruminobacter amylophilus, form a separate line of descent. This phylogenetic group is described as Succinivibrionaceae fam. nov.
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Hydrogenophilus thermoluteolus gen. nov., sp. nov., a thermophilic, facultatively chemolithoautotrophic, hydrogen-oxidizing bacterium
More LessThe taxonomic positions of ‘Pseudomonas hydrogenothermophila’ strain TH-1 and ‘Flavobacterium autothermophilum’ strain TH-4 were studied by 16S rDNA sequencing. These organisms are Gram-negative, strictly aerobic, thermophilic facultatively chemolithoautotrophic hydrogen-oxidizing rods and have a DNA G+C content of 63–65 mol%. The major isoprenoid quinone is ubiquinone-8 an 3-hydroxy decanoic acid (3-OH C10:0) is the major 3-hydroxy cellular fatty acid, phylogenetic analysis based on 16S rDNA sequences placed strains TH-1Tand TH-4 in the β-subclass of the Proteobacteria. The taxonomic characteristics of these organisms are different from those of previously described aerobic, facultatively chemolithoautotrophic, hydrogen-oxidizing bacteria that belong to the β-subclass of Proteobacteria. On the basis of the information described above, a new genus and species, Hydrogenophilus thermoluteolus gen. nov., sp. nov., is described to include both strains. The type strain is strain TH-1T(= IFO 14978T).
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Burkholderia caribensis sp. nov., an exopolysaccharide-producing bacterium isolated from vertisol microaggregates in Martinique
More LessTwenty-one exopolysaccharide-producing strains were isolated from the 5–20 μm fraction of a vertisol in the south-east of the island of Martinique in the French West Indies. Although these strains were phenotypically identifie as Burkholderia cepacia or as Burkholderia glathei using BIOLOG microplates they did not cluster genotypically by amplified rDNA restriction analysis (ARDRA) with any described Burkholderia species. A phylogenetic analysis revealed that the rrs (16S rDNA) sequences of three representative strains clustered in a single branch within the genus Burkholderia and distantly from all of the previously described species of Burkholderia for which rrs sequences were available. DNA–DNA hybridization data as well as phenotypic analyses indicated that the 21 isolates represented a single and new species for which the name Burkholderia caribensis sp. nov. is proposed (type strain MWAP64TLMG 18531T).
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Desulfovibrio zosterae sp. nov., a new sulfate reducer isolated from surface-sterilized roots of the seagrass Zostera marina
More LessA sulfate-reducing bacterium, designated strain lacT, was isolated from surface-sterilized roots of the benthic macrophyte Zostera marina. Cells were motile by means of a single polar flagellum. Strain lacTutilized lactate, pyruvate, malate, ethanol, l-alanine, fumarate, choline and fructose with sulfate as electron acceptor. In addition, fumarate, pyruvate and fructose were also degraded without an external electron acceptor. Sulfate could be substituted with thiosulfate, sulfite and elemental sulfur. Optimal growth was observed between 32·5 and 34·5 °C, at an NaCl concentration of 0·2 M and in a pH range between 6·8 and 7·3. The G+C content of the DNA was 42·7±0·2 mol%. Desulfoviridin and catalase were present. Strain lacTcontained c-type cytochromes. Comparative 16S rRNA gene sequence analysis and the fatty acid pattern grouped this isolate into the genus Desulfovibrio. However, strain lacTdiffers from all other described Desulfovibrio species on the bases of its 16S rRNA gene sequence, the G+C content, its cellular lipid pattern and the utilization pattern of substrates. These characteristics establish strain lacT(= DSM 11974T) as a novel species of the genus Desulfovibrio, for which the name Desulfovibrio zosterae sp. nov. is proposed.
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Coenonia anatina gen. nov., sp. nov., a novel bacterium associated with respiratory disease in ducks and geese
More LessTaxon 1502 was originally described as a Riemerella anatipestifer-like bacterium causing exudative septicaemia in ducks and geese. In the present study, an integrated genotypic and phenotypic approach was used to elucidate the phylogenetic affiliation and taxonomic relationships of 12 strains of taxon 1502. Whole-cell protein and fatty acid analyses and an extensive biochemical examination by using conventional tests and several API microtest systems indicated that all isolates formed a homogeneous taxon, which was confirmed by DNA–DNA hybridizations. 16S rDNA sequence analysis of a representative strain (LMG 14382T) indicated that this taxon belongs to the Cytophaga–Flavobacterium–Bacteroides phylum and revealed a moderate but distinct relationship to species of the genus Capnocytophaga (overall 16S rDNA sequence identities were 88·8–90·2 %). Taxon 1502 is concluded to represent a single species that should be allocated to a novel genus, and the name Coenonia anatina gen. nov., sp. nov. is proposed. The DNA G+C content of representative strains was 35–36 mol% and the type strain is LMG 14382T.
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Thiomicrospira chilensis sp. nov., a mesophilic obligately chemolithoautotrophic sulfur-oxidizing bacterium isolated from a Thioploca mat
More LessA new member of the genus Thiomicrospira, which utilizes thiosulfate as the electron donor and CO2 as the carbon source, was isolated from a sediment sample dominated by the filamentous sulfur bacterium Thioploca. Although the physiological properties investigated are nearly identical to other described species of the genus, it is proposed that strain Ch-1Tis a member of new species, Thiomicrospira chilensis sp. nov., on the basis of differences in genotypic characteristics (16S rRNA sequence, DNA homology, G+C content). Strain Ch-1Twas highly motile with a slight tendency to form aggregates in the stationary growth phase. The organism was obligately autotrophic and strictly aerobic. Nitrate was not used as an electron acceptor. Chemolithoautotrophic growth was observed with thiosulfate, tetrathionate, sulfur and sulfide. The isolate was not able to grow heterotrophically. Growth of strain Ch-1Twas observed between pH 5·3 and 8·5 with an optimum at pH 7·0. The temperature range for growth was between 3·5 and 42 °C; the optimal growth temperature was between 32 and 37 °C. The mean maximum growth rate on thiosulfate was 0·4 h-1. This is the second Thiomicrospira species described that has a rodshaped morphology; therefore discrimination between vibrio-shaped Thiomicrospira and rod-shaped Thiobacilli is no longer valid.
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Description of Pseudaminobacter gen. nov. with two new species, Pseudaminobacter salicylatoxidans sp. nov. and Pseudaminobacter defluvii sp. nov.
More LessAn aerobic bacterium, strain BN12T, which degrades substituted naphthalenesulfonates and substituted salicylates was isolated from a 6-aminonaphthalene-2-sulfonate-degrading microbial consortium originating from the River Elbe, Germany. Chemotaxonomic investigations of quinones, polyamines and polar lipids allowed allocation of this strain to the α-subclass of the Proteobacteria and revealed similarity to species of the genera Aminobacter, Chelatobacter and Mesorhizobium. This was confirmed by typing with 16S rRNA-targeted oligonucleotide probes and 16S rDNA sequencing and phylogenetic analysis, indicating that BN12T clusters most closely with a strain ‘ Thiobacillus’ THI 051T and with the above genera but comprising a separate branch. DNA–DNA hybridizations demonstrated that strain BN12T is different from all species of Aminobacter currently described and recognized. The fatty acid patterns, substrate utilization profile and biochemical characteristics displayed no obvious similarity to the characteristics of Aminobacter and Chelatobacter species. ‘Thiobacillus’ THI 051T, however, revealed phenotypic similarities to BN12T. Furthermore, 16S rRNA sequences of Chelatobacter heintzii showed a high similarity to the 16S rRNA sequences of all currently recognized Aminobacter species. On the basis of these and previously published results, the new genus Pseudaminobacter is proposed, harbouring the two new species Pseudaminobacter salicylatoxidans sp. nov. and Pseudaminobacter defluvii sp. nov. The type strains are BN12T ( = DSM 6986T) and THI 051T (= IFO 1457T), respectively.
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Erwinia pyrifoliae sp. nov., a novel pathogen that affects Asian pear trees (Pyrus pyrifolia Nakai)
More LessA novel pathogen from Asian pears (Pyrus pyrifolia Nakai) was analysed by sequencing the 16S rDNA and the adjacent intergenic region, and the data were compared to related Enterobacteriaceae. The 16S rDNA of the Asian pear pathogen was almost identical with the sequence of Erwinia amylovora, in contrast to the 16S–23S rRNA intergenic transcribed spacer region of both species. A dendrogram was deduced from determined sequences of the spacer regions including those of several related species such as Erwinia amylovora, Enterobacter pyrinus, Pantoea stewartii subsp. stewartii and Escherichia coli. Dendrograms derived from 121 biochemical characteristics including Biotype 100 data placed the Asian pear pathogen close to Erwinia amylovora and more distantly to other members of the species Erwinia and to the species Pantoea and Enterobacter. Another DNA relatedness study was performed by DNA hybridizations and estimation of ΔT m values. The Asian pear strains constituted a tight DNA hybridization group (89–100%) and were barely related to strains of Erwinia amylovora (40–50%) with a ΔT m in the range of 5·2–6·8. The G+C content of DNA from the novel pathogen is 52 mol %. Therefore, it is proposed that strains isolated from Asian pears constitute a new species and the name Erwinia pyrifoliae is suggested; the type strain is strain Ep16/96T (= CFBP 4172T = DSM 12163T).
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- New Taxa - Gram-Positive Bacteria
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Corynebacterium sundsvallense sp. nov., from human clinical specimens
Three strains of a previously undescribed catalase-positive non-lipophilic coryneform bacterium isolated from human clinical specimens were characterized by phenotypic and molecular taxonomic methods. Morphologically the unknown bacterium consisted of pleomorphic rods, some of which displayed bulges/knobs at their ends. All three strains were similar in that they produced acid from fructose, glucose, maltose and sucrose and were urease-positive. Chemotaxonomic investigations revealed the presence of meso-diaminopimelic acid and short-chain mycolic acids consistent with the genus Corynebacterium sensu stricto. Comparative 16S rRNA gene sequencing showed that the three strains are genealogically highly related and constitute a new subline within the genus Corynebacterium, displaying >3% sequence divergence with recognized species. The unknown bacterium was distinguished from currently validly published Corynebacterium species by phenotypic tests, including electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from clinical specimens be classified as Corynebacterium sundsvallense sp. nov. The type strain is CCUG 36622T.
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Reclassification of the species Kocuria erythromyxa ( Brooks and Murray 1981 ) as Kocuria rosea ( Flügge 1886 )
More LessComparison of phenotypic, chemotaxonomic and genomic properties of the type strains of Kocuria rosea and Kocuria erythromyxa indicates that these taxa are members of the same species. The conclusion is based upon 16S rDNA similarity of 99·9% [Rainey, F. A., et al. (1997). Int J Syst Barteriol 47, 510-514], DNA-DNA reassociation of 95%, identical fatty acid patterns and almost identical physiological reactions against substrates provided by the BIOLOG plate. According to Rule 42 of the International Code of Nomenclature of Bacteria, which requires that the oldest legitimate epithet be retained when taxa of equal rank are united, Kocuria (Micrococcus) rosea (Flügge 1886) has priority over Kocuria (Deinococcus) erythromyxa (Brooks and Murray 1981).
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Tessaracoccus bendigoensis gen. nov., sp. nov., a Gram-positive coccus occurring in regular packages or tetrads, isolated from activated sludge biomass
More LessAn isolate of a Gram-positive bacterium, designated strain Ben 106T, was obtained in pure culture by micromanipulation of a biomass sample obtained from a laboratory-scale sequencing batch reactor. This isolate grew axenically as cocci or clusters of cocci arranged in regular tetrads and was morphologically similar to the dominant organism observed in the biomass. This morphology resembled that of some Gram-positive and -negative bacteria and the so-called 'G-bacteria' commonly seen in activated sludge samples. Strain Ben 106T is a non-motile, facultative anaerobe. It is oxidase-negative, catalase-positive and is capable of reducing nitrate. This organism can grow between 20 and 37 °C, with an optimum temperature of 25 °C. The pH range for growth is between 6·0 and 9·0, with an optimum pH of 7·5. The isolate stained positively for intracellular polyphosphate granules. The diagnostic diamino acid of the peptidoglycan is ll-diaminopimelic acid (ll-A2pm) with a glycine moiety at position 1 of the peptide subunit, which characterizes the presence of a rare peptidoglycan (type A3-γ′). Two menaquinones, MK-9(H4) and MK-7(H4), are present and the main cellular fatty acid is 12-methyltetradecanoic acid. The G+C content is 74 mol%. From phenotypic characteristics and 16S rDNA sequence analysis, the isolate differed sufficiently from its closest phylogenetic relatives, namely Propionibacterium propionicum, Propioniferax innocua, Friedmanniella antarctica, Luteococcus japonicus and Microlunatus phosphovorus in the A1 subdivision of the Gram-positive bacteria (i.e. Firmicutes with a high G+C content), suborder Propionibacterineae, to be placed in a new genus, Tessaracoccus, as Tessaracoccus bendigoensis gen. nov., sp. nov. The type strain is Ben 106T (= ACM 5119T).
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Abiotrophia balaenopterae sp. nov., isolated from the minke whale (Balaenoptera acutorostrata)
More LessPhenotypic and phylogenetic studies were performed on a hitherto undescribed micro-organism isolated from a minke whale (Balaenoptera acutorostrata). Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strain constituted a new subline close to, but distinct from, Abiotrophia adiacens and Abiotrophia elegans. The unknown bacterium was readily distinguished from these two Abiotrophia species by biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Abiotrophia balaenopterae sp. nov., the type strain of which is M1975/96/1T (= CCUG 37380T).
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Reclassification of Amycolatopsis rugosa Lechevalier et al. 1986 as Prauserella rugosa gen. nov., comb. nov.
More LessAn almost complete sequence of the 16S rDNA of the type strain of Amycolatopsis rugosa was determined following direct sequencing of the amplified gene. The sequence was aligned with those of representatives of the family Pseudonocardiaceae and related actinomycetes and phylogenetic trees were inferred by using three tree-making algorithms. The organism formed a distinct clade within the evolutionary radiation occupied by the family Pseudonocardiaceae. It was also readily distinguished from all of the validly described genera classified in this taxon by using a combination of chemical and morphological markers. On the basis of these genotypic and phenotypic differences, the name Prauserella gen. nov. is proposed for a new genus containing the previously misclassified Amycolatopsis rugosa. The type strain of Prauserella rugosa is DSM 43194T (= ATCC 43014T = NCIMB 8926T).
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Bacillus marismortui sp. nov., a new moderately halophilic species from the Dead Sea
More LessA group of 91 moderately halophilic, Gram-positive, rod-shaped strains were isolated from enrichments prepared from Dead Sea water samples collected 57 years ago. These strains were examined for 117 morphological, physiological, biochemical, nutritional and antibiotic susceptibility characteristics. All strains formed endospores and were motile, strictly aerobic and positive for catalase and oxidase. They grew in media containing 5–25% (w/v) total salts, showing optimal growth at 10% (w/v). Eighteen strains were chosen as representative isolates and were studied in more detail. All these strains had meso-diaminopimelic acid in the cell wall and a DNA G+C content of 39·0–42·8 mol%; they constitute a group with levels of DNA-DNA similarity of 70-100%. The sequences of the 16S rRNA genes of three representative strains (strains 123T, 557 and 832) were almost identical (99·9%), and placed the strains in the low G+C content Gram-positive bacteria. On the basis of their features, these isolates should be regarded as members of a new species of the genus Bacillus, for which the name Bacillus marismortui sp. nov. is proposed. The type strain is strain 123T (= DSM 12325T = ATCC 700626T = CIP 105609T = CECT 5066T).
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Transfer of Bacillus lentimorbus and Bacillus popilliae to the genus Paenibacillus with emended descriptions of Paenibacillus lentimorbus comb. nov. and Paenibacillus popilliae comb. nov.
More LessAlmost complete 16S rRNA gene sequences were generated for the type strains of the obligate insect pathogens Bacillus lentimorbus and Bacillus popilliae and a second strain of Bacillus popilliae (NRRL B-4081) received as ‘Bacillus popilliae var. melolonthae’. A phylogenetic tree was constructed which grouped these strains into a well defined subcluster within the genus Paenibacillus. Bacillus popilliae NRRL B-4081 occupied an intermediate position between the type strains of Bacillus lentimorbus and Bacillus popilliae but with a marked clustering to the latter. The phylogenetic assignment of these strains to Paenibacillus is in contrast to earlier studies which placed these bacteria in the genus Bacillus, close to Bacillus subtilis. Indeed, the rRNA sequences generated in this study share less than 88% similarity to the deposited sequences for Bacillus popilliae ATCC 14706T and Bacillus lentimorbus ATCC 14707T. The results obtained by using different tree algorithms, bootstrap analysis, branch lengths and verification by signature nucleotide analysis supported the reclassif ication of these species in the genus Paenibacillus as Paenibacillus lentimorbus comb. nov. and Paenibacillus popilliae comb. nov.
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Phylogenetic and phenotypic evidence for the transfer of Eubacterium aerofaciens to the genus Collinsella as Collinsella aerofaciens gen. nov., comb. nov.
More LessThree strains of Eubacterium aerofaciens, JCM 10188T, JCM 7790 and JCM 7791, and 178 freshly isolated strains of the Eubacterium aerofaciens group from human faeces were characterized by biochemical tests, cell wall peptidoglycan type and 16S rRNA analysis. The Eubacterium aerofaciens group was divided into four groups by fermentation patterns of sucrose and cellobiose, and were further divided into 16 sub-groups by fermentation patterns of aesculin, salicin and amygdalin. All of the strains of the Eubacterium aerofaciens group were shown to be phylogenetically distantly related to Eubacterium limosum, which is the type species of genus Eubacterium. Eubacterium aerofaciens was shown to have a specific phylogenetic association with Coriobacterium glomerans. All the strains belonging to Eubacterium aerofaciens resembled Coriobacterium glomerans in possessing a high G+C content (60 mol%). Cell wall analysis, however, revealed the presence of different A4β (l-Ala)-d-Glu-l-Orn-l-Asp peptidoglycan types. Based on a 16S rRNA sequence divergence of greater than 9% with Coriobacterium glomerans and the presence of a unique peptidoglycan type, a new genus, Collinsella, is proposed for Eubacterium aerofaciens, with one species, Collinsella aerofaciens. The type strain of Collinsella aerofaciens is JCM 10188T.
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The family Coriobacteriaceae: reclassification of Eubacterium exiguum ( Poco etal. 1996 ) and Peptostreptococcus heliotrinreducens ( Lanigan 1976 ) as Slackia exigua gen. nov., comb. nov. and Slackia heliotrinireducens gen. nov., comb. nov., and Eubacterium lentum (Prevot 1938) as Eggerthella lenta gen. nov., comb. nov.
16S rRNA gene sequences were determined for Eubacterium exiguum and Peptostreptococcus heliotrinreducens. These species were found to be closely related and, together with Eubacterium lentum, to constitute a branch of the Coriobacteriaceae. Two new genera are proposed on the basis of phenotypic characteristics and 16S rRNA gene sequence comparisons: Slackia to include the bile-sensitive species Eubacterium exiguum and P. heliotrinreducens, and Eggerthella to include the bile-resistant Eubacterium lentum. It is proposed that Eubacterium exiguum and Peptostreptococcus heliotrinreducens are transferred to the genus Slackia gen. nov. as Slackia exigua gen. nov., comb. nov. (type strain ATCC 700122T) and Slackia heliotrinireducens gen. nov., comb. nov. (type strain NTCC 11029T). respectively, and Eubacterium lentum is transferred to the genus Eggerthella gen. nov. as Eggerthella lenta gen. nov., comb. nov. with Eggerthella lenta as the type species.
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Thermaerobacter marianensis gen. nov., sp. nov., an aerobic extremely thermophilic marine bacterium from the 11000 m deep Mariana Trench
More LessA novel extremely thermophilic bacterium was isolated from the world's deepest sea-floor, the Mariana Trench Challenger Deep at a depth of 10897 m. Cells were Gram-reaction variable, non-spore-forming and non-motile rods without flagella. Growth was observed between 50 and 80 °C (optimum: 74–76 C; 90 min doubling time), pH 5·4 and 9·5 (optimum: pH 7·0–7·5) and 0·5 and 5% sea salts (optimum: 2 % sea salts). The isolate was a strictly aerobic heterotroph capable of utilizing as sole energy and carbon source: yeast extract, peptone, cellulose, starch, chitin, casein, Casamino acids, a variety of sugars, carboxylic acids and amino acids. The G+C content of the genomic DNA was 72·5 mol%. Phylogenetic analysis based on 16S rRNA sequences placed this aerobic, high-G+C-content bacterium among the members of the Gram-positive, low-G+C-content anaerobic thermophilic bacteria within the Bacillus-Clostridium subphylum. On the basis of the physiological and molecular properties of the new isolate, the name Thermaerobacter marianensis gen. nov., sp. nov. (type strain 7p75aT = JCM 10246T) is proposed.
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NOTE
More LessTwo strains of a Gram-positive catalase-negative, facultatively anaerobic coccus originating from human sources were characterized by phenotypic and molecular taxonomic methods. The strains were found to be identical to each other based on 16S rRNA gene sequencing and constitute a new subline within the genus Facklamia. The unknown bacterium was readily distinguished from Facklamis hominis and Facklamia ignava by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence it is proposed that the unknown bacterium be classified as Facklamia sourekii sp. nov., the type strain of which is CCUG 28783AT.
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NOTE
More LessSaccharomonospora species were subjected to DNA-DNA relatedness determination to investigate their genetic relationships based on genomic DNA. The levels of DNA-DNA relatedness among the type strains of the four validly described Saccharomonospora species ranged from 18 to 46%. Saccharomonospora viridis KCTC 9156. which was described as ′Saccharomonospora internatus′ but later reclassified as a member of S. viridis, showed a similarity level of 90% to S. viridis KCTC 9115T. Saccharomonospora sp. strain K180 exhibited levels of DNA-DNA relatedness that are indicative of a new species. Saccharomonospora azurea exhibited levels of DNA-DNA homology of 84–95% to ′Saccharomonospora caesia′ strains including the type strain. Therefore, on the basis of DNA-DNA relatedness data and taxonomic data described previously, it is proposed that ′S. caesia′ should be considered as a synonym of S. azurea.
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