- Volume 53, Issue 6, 2003
Volume 53, Issue 6, 2003
- Validation List No. 94
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Validation of publication of new names and new combinations previously effectively published outside the IJSEM
The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names and new combinations have appeared in volume 53, part 4, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles).
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- New Taxa
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- Archaea
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Methanocaldococcus indicus sp. nov., a novel hyperthermophilic methanogen isolated from the Central Indian Ridge
More LessAn autotrophic, hyperthermophilic methanogen, strain SL43T, was isolated from a deep-sea hydrothermal chimney sample collected on the Central Indian Ridge at a depth of 2420 m. The coccoid, surface-layer-carrying, Gram-negative-staining cells were heavily flagellated and exhibited a slight tumbling motility. The temperature range for growth at pH 6·5 was 50–86 °C, with optimum growth at 85 °C. The optimum pH for growth was 6·6 and the optimum NaCl concentration for growth was 30 g l−1. The novel isolate used H2 and CO2 as the only substrates for growth and produced methane. Selenium and yeast extract stimulated growth significantly. In the presence of CO2 and H2, the organism reduced elemental sulfur to hydrogen sulfide. Growth was inhibited by chloramphenicol and rifampicin, but not by ampicillin, kanamycin, penicillin or streptomycin. The G+C content of the genomic DNA was 30·7 mol%. On the basis of 16S rRNA gene sequence analysis, this organism was most closely related to Methanocaldococcus infernus MET (3·2 % distance). Its phylogenetic distinctiveness was confirmed by RFLP analysis of the 16S rDNA, a reliable tool for differentiating hyperthermophilic methanococci. On the basis of phylogenetic and physiological characteristics, it is proposed that strain SL43T (=DSM 15027T=JCM 11886T) be designated as the type strain of a novel species, Methanocaldococcus indicus sp. nov.
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- Other Bacteria
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Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level
More LessTwo thermophilic, Gram-negative, non-spore-forming, multicellular filamentous micro-organisms were isolated from thermophilic granular sludge in an upflow anaerobic sludge blanket reactor treating fried soybean-curd manufacturing waste water (strain UNI-1T) and from a hot spring sulfur-turf in Japan (strain STL-6-O1T). The filaments were longer than 100 μm and of 0·2–0·3 μm (strain UNI-1T) or 0·7–0·8 μm (strain STL-6-O1T) in width. Strain UNI-1T was a strictly anaerobic organism. The optimum temperature for growth was around 55 °C; growth occurred in the range 50–60 °C. The optimum pH for growth was around 7·0; growth occurred in the range pH 6·0–8·0. Strain STL-6-O1T was a facultatively aerobic bacterium. The optimum temperature for growth was around 55 °C; growth occurred in the range 37–65 °C. The optimum pH for growth was around 7·5–8·0; growth occurred in the range pH 7·0–9·0. The two organisms grew chemo-organotrophically on a number of carbohydrates and amino acids in the presence of yeast extract. The G+C content of the DNA of strains UNI-1T and STL-6-O1T was 54·5 and 59·0 mol%, respectively. Major cellular fatty acids for strain UNI-1T were C16 : 0, C15 : 0, C14 : 0 and C18 : 0, whereas those for strain STL-6-O1T were C18 : 0, C16 : 0, C17 : 0 and iso-C17 : 0. MK-10 was the major quinone from aerobically grown STL-6-O1T cells. Phylogenetic analyses based on 16S rDNA sequences revealed that both strains belong to an uncultured, previously recognized clone lineage of the phylum Chloroflexi (formerly known as green non-sulfur bacteria). These phenotypic and genetic properties suggested that each strain should be classified into a new independent genus; hence, the names Anaerolinea thermophila and Caldilinea aerophila are proposed for strains UNI-1T (=JCM 11387T=DSM 14523T) and STL-6-O1T(=JCM 11388T=DSM 14525T), respectively. These strains represent the type and sole species of the genera Anaerolinea and Caldilinea, respectively.
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‘Candidatus Phytoplasma oryzae’, a novel phytoplasma taxon associated with rice yellow dwarf disease
In addition to rice yellow dwarf (RYD) phytoplasma, several phytoplasmas infect gramineous plants, including rice orange leaf, bermuda grass white leaf, brachiaria grass white leaf and sugarcane white leaf phytoplasmas. To investigate whether the RYD phytoplasma is a discrete, species-level taxon, several isolates of the aforementioned phytoplasmas were analysed using PCR-amplified 16S rDNA sequences. Two RYD isolates, RYD-JT and RYD-Th, were almost identical (99·2 %), but were distinct (similarities of 96·3–97·9 %) from other phytoplasma isolates of the RYD 16S-group. The notion that the RYD phytoplasma constitutes a unique taxon is also supported by its unique insect vector (Nephotettix sp.), its unique host plant in nature (rice) and its limited geographical distribution (Asia). In Southern blot analysis, chromosomal and extrachromosomal DNA probes of the RYD phytoplasma reportedly did not hybridize with those of closely related phytoplasmas. These properties of the RYD phytoplasma clearly indicate that it represents a novel taxon, ‘Candidatus Phytoplasma oryzae’.
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Dialister invisus sp. nov., isolated from the human oral cavity
J. Downes, M. Munson and W. G. WadeSix strains of anaerobic, Gram-negative coccobacilli isolated from the root canals of patients with endodontic infections (five strains) and from a deep periodontal pocket (one strain) were subjected to a comprehensive range of phenotypic and genetic tests and were found to comprise a homogeneous group. Following 16S rRNA gene sequence analysis, they were found to be most closely related to Dialister pneumosintes, with 93 % sequence similarity between the two taxa. A novel species, Dialister invisus sp. nov., is proposed. Biochemically, the species is largely unreactive and is asaccharolytic, with only traces of acetate and propionate detected as metabolic end-products. The G+C content of the DNA of D. invisus strains is 45–46 mol%. The type strain is E7.25T (=CCUG 47026T=DSM 15470T).
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Balnearium lithotrophicum gen. nov., sp. nov., a novel thermophilic, strictly anaerobic, hydrogen-oxidizing chemolithoautotroph isolated from a black smoker chimney in the Suiyo Seamount hydrothermal system
More LessA novel, extremely thermophilic bacterium, designated strain 17ST, was isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc, Japan. The cells were rods with no apparent motility, most of which were narrow in the middle in the exponential-growth phase and had several polar flagella at both ends. Growth was observed between 45 and 80 °C (optimum temperature, 70–75 °C; doubling time, 80 min) and between pH 5·0 and 7·0 (optimum pH, 5·4). The isolate was a strictly anaerobic chemolithoautotroph that was capable of using molecular hydrogen as its sole energy source and carbon dioxide as its sole carbon source. Elemental sulfur (S0) was required for growth as an electron acceptor. The G+C content of the genomic DNA was 34·6 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that the isolate was related to Thermovibrio ruber ED11/3LLKT and Desulfurobacterium thermolithotrophum BSAT, whilst it appeared to be a novel lineage prior to the divergence of these genera. This isolate could also be differentiated from both T. ruber ED11/3LLKT and D. thermolithotrophum BSAT on the basis of physiological properties. The name Balnearium lithotrophicum gen. nov., sp. nov. is proposed for this isolate (type strain, 17ST=JCM 11970T=ATCC BAA-736T).
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Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm
The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909T (=KCTC 12089T=CCUG 47092T).
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- Proteobacteria
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Thialkalivibrio nitratireducens sp. nov., a nitrate-reducing member of an autotrophic denitrifying consortium from a soda lake
More LessStrain ALEN 2T was isolated from a mixed culture capable of complete autotrophic denitrification with thiosulfate as electron donor at pH 10; the mixed culture was enriched from sediment from Lake Fazda (Wadi Natrun, Egypt), a hypersaline alkaline lake. The isolate had large, non-motile, coccoid or barrel-shaped cells with intracellular sulfur globules. The bacterium was obligately chemolithoautotrophic. It grew with reduced sulfur compounds aerobically and anaerobically with nitrate as electron acceptor, nitrate being reduced to nitrite. It was moderately halophilic and obligately alkaliphilic. On the basis of genetic analysis and its unique phenotype, strain ALEN 2T (=DSM 14787T=UNIQEM 213T) is proposed as the type strain of a novel species of the genus Thialkalivibrio, Thialkalivibrio nitratireducens.
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Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing ε-proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough
More LessA novel mesophilic, sulfur- and thiosulfate-oxidizing bacterium, strain OK10T, was isolated from deep-sea sediments at the Hatoma Knoll in the Mid-Okinawa Trough hydrothermal field. Cells of strain OK10T were short rods, each being motile by means of a single polar flagellum. The isolate grew at 10–40 °C (optimum 25 °C) and pH 4·5–9·0 (optimum pH 6·5). It grew chemolithoautotrophically with elemental sulfur, sulfide and thiosulfate as sole electron donors and oxygen as electron acceptor. Molecular hydrogen did not support growth. The G+C content of the genomic DNA of strain OK10T was 35·2 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that the isolate belonged to the ε-Proteobacteria. On the basis of its physiological and molecular characteristics, strain OK10T (=ATCC BAA-671T=JCM 11897T) represents the sole species of a new genus, Sulfurimonas, for which the name Sulfurimonas autotrophica is proposed.
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Pseudoalteromonas sagamiensis sp. nov., a marine bacterium that produces protease inhibitors
A marine bacterium producing protease inhibitors was isolated from neritic sea water and was studied phenotypically, genotypically and phylogenetically. This bacterium (strain B-10-31T) produced three types of protease inhibitor, namely, marinostatin, monastatin and leupeptin, which were considerably different in terms of their chemical structure and properties. Strain B-10-31T was a rod-shaped, non-spore-forming, Gram-negative, strictly aerobic bacterium that was motile by means of one polar flagellum. The strain required Na+ for growth and exhibited optimal growth at 27 °C, pH 8·0 and 2 % (w/v) NaCl. It utilized various substrates, such as d-glucose, maltose, maltotriose, N-acetylglucosamine, l-threonine, l-serine, l-arginine, l-proline, l-α-alanine and l-glutamate, as the sole energy source. Ubiquinone-8 was the major respiratory quinone. The major fatty acids were C16 : 0, C16 : 1 ω7c, C16 : 1 ω9c and C18 : 1 ω7c. The G+C content of the DNA of strain B-10-31T was 42·0 mol%. Phylogenetic analysis, based on 16S rDNA sequences, showed that the strain clustered in the γ-Proteobacteria. The aerobic marine bacterium Pseudoalteromonas bacteriolytica was the species most closely related to the new isolate (90·4 % 16S rDNA sequence similarity); other described species in the γ-Proteobacteria cluster showed low levels of sequence similarity with strain B-10-31T (<90 %). Based on the above results, it is proposed that the novel marine bacterium should be classified as a new species, for which the name Pseudoalteromonas sagamiensis (type strain B-10-31T=JCM 11461T=DSM 14643T) is proposed.
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Vibrio superstes sp. nov., isolated from the gut of Australian abalones Haliotis laevigata and Haliotis rubra
Five alginolytic, facultatively anaerobic, non-motile bacteria were isolated from the gut of abalones Haliotis laevigata and Haliotis rubra. Phylogenetic analyses based on 16S rDNA data indicated that these strains are related closely to Vibrio halioticoli (98 % 16S rDNA sequence similarity). DNA–DNA hybridization and fluorescent amplified fragment length polymorphism fingerprinting demonstrated that the five strains constituted a single species that was different from all currently known vibrios. The name Vibrio superstes sp. nov. (type strain, LMG 21323T=IAM 15009T=G3-29T; DNA G+C content, 48·0–48·9 mol%) is proposed to encompass this novel taxon. Several phenotypic features were disclosed that discriminate V. superstes from other Vibrio species: V. superstes sp. nov. and V. halioticoli can be differentiated on the basis of 17 traits (indole production, β-galactosidase test and assimilation of 15 carbon compounds).
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Achromobacter insolitus sp. nov. and Achromobacter spanius sp. nov., from human clinical samples
More LessA polyphasic taxonomic study (employing whole-cell protein and fatty acid analyses, 16S rDNA sequencing, DNA–DNA hybridization, determination of DNA G+C content, antibiotic susceptibility testing and extensive phenotypic characterization) was performed on 10 isolates that appeared to be related to Alcaligenes faecalis. The isolates were recovered from diverse environments that included human clinical samples. 16S rDNA sequence analysis indicated that these isolates belonged to the genus Achromobacter. Whole-cell protein analysis distinguished two groups, which were confirmed by DNA–DNA hybridization. Based on the results of this study, the organisms were classified as two novel Achromobacter species, Achromobacter insolitus sp. nov. (type strain, LMG 6003T) and Achromobacter spanius sp. nov. (type strain, LMG 5911T). Achromobacter insolitus can be distinguished from Achromobacter spanius by its ability to grow on acetamide and to assimilate mesaconate and aconitate, and by its inability to assimilate diaminobutane. Various tests allow the differentiation of both novel species from other Achromobacter species, including growth on acetamide, denitrification and assimilation of d-glucose, d-xylose, mesaconate, aconitate and diaminobutane.
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Kerstersia gyiorum gen. nov., sp. nov., a novel Alcaligenes faecalis-like organism isolated from human clinical samples, and reclassification of Alcaligenes denitrificans Rüger and Tan 1983 as Achromobacter denitrificans comb. nov.
More LessA polyphasic taxonomic study was performed on nine isolates recovered from various human clinical samples. Phenotypically, these isolates resembled Alcaligenes faecalis. Whole-cell protein analysis distinguished two different species, and this was confirmed by DNA–DNA hybridizations. Cellular fatty acid analysis and 16S rDNA sequence analysis indicated that these isolates were related to the genera Alcaligenes, Bordetella, Achromobacter and Pigmentiphaga and belonged to the family Alcaligenaceae. On the basis of the results of this study, the organisms were classified in a novel genus, Kerstersia gen. nov. This genus comprises one species, Kerstersia gyiorum sp. nov. (type strain LMG 5906T=API 184-2-84T=CCUG 47000T), and several unnamed isolates. The DNA G+C content of members of the genus Kerstersia is between 61·5 and 62·9 mol%. On the basis of previously published DNA–DNA hybridization results and data from chemotaxonomic studies, it is proposed that Alcaligenes denitrificans Rüger and Tan 1983 be reclassified as Achromobacter denitrificans comb. nov.
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Fulvimarina pelagi gen. nov., sp. nov., a marine bacterium that forms a deep evolutionary lineage of descent in the order ‘Rhizobiales’
More LessThree brownish-yellow bacterial strains were isolated from the western Sargasso Sea by high-throughput culturing methods and characterized by polyphasic approaches. All isolates were Gram-negative, strictly aerobic, chemoheterotrophic, non-motile short rods that contained carotenoid pigments. Phylogenetic analyses based on 16S rRNA gene sequences, DNA–DNA hybridization and DNA G+C content, along with phenotypic characteristics, revealed that they belonged to the same species. The strains utilized a wide range of substrates, including pentoses, hexoses, oligosaccharides, sugar alcohols, organic acids and amino acids, as sole carbon sources. The DNA G+C content of the isolates ranged from 57·6 to 59·9 mol%. The predominant cellular fatty acid constituent was C18 : 1 ω7c, whilst C16 : 0, C18 : 0 and C19 : 0 ω8c cyclo were also abundant. The organism related most closely to these strains, as determined by 16S rDNA sequence comparison, was the recently described species Aurantimonas coralicida (93·3–93·8 % similarity). Phylogenetic analyses indicated that the strains formed a distinct and deep evolutionary lineage of descent, together with A. coralicida, within the order ‘Rhizobiales’ of the α-Proteobacteria. This lineage could not be associated with any of the ten known families in the order ‘Rhizobiales’. From polyphasic evidence, it is proposed that the strains be placed into a novel genus and species, Fulvimarina pelagi gen. nov., sp. nov. (type strain, HTCC2506T=ATCC BAA-666T=KCTC 12091T=DSM 15513T).
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Idiomarina loihiensis sp. nov., a halophilic γ-Proteobacterium from the Lō‘ihi submarine volcano, Hawai‘i
More LessDuring an investigation of bacterial diversity at hydrothermal vents on the Lō‘ihi Seamount, Hawai‘i, a novel bacterium (designated L2-TRT) was cultivated, which shares 99·9 % 16S rRNA gene sequence similarity over 1415 nt with an uncultured eubacterium from sediment at a depth of 11 000 m in the Mariana Trench. The nearest cultivated neighbour of L2-TRT, however, is Idiomarina abyssalis KMM 227T, with which it shares 98·9 % 16S rRNA sequence similarity. L2-TRT differed from I. abyssalis KMM 227T in several phenotypic respects, including growth at 46 °C and in medium that contained 20 % (w/v) NaCl. DNA–DNA hybridization data showed that L2-TRT did not belong to the species I. abyssalis (43·4 % DNA–DNA reassociation). Cells of L2-TRT were Gram-negative rods, 0·35 μm wide and 0·7–1·0 μm long, which were occasionally up to 1·8 μm in length. Cells were motile by a single polar or subpolar flagellum. The major fatty acid in L2-TRT was iso-C15 : 0 (32·6 %). The DNA G+C content was 47·4 mol%. Phenotypic and genotypic analyses indicated that L2-TRT could be assigned to the genus Idiomarina but, based on significant phenotypic and genotypic differences, constituted a novel species within this genus, Idiomarina loihiensis sp. nov., of which L2-TRT (=ATCC BAA-735T=DSM 15497T) is the type strain.
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Oceanisphaera litoralis gen. nov., sp. nov., a novel halophilic bacterium from marine bottom sediments
More LessA polyphasic taxonomic study was performed to characterize a new bacterial isolate, designated KMM 3654T, from a marine bottom sand sample. The strain was Gram-negative, encapsulated, aerobic, moderately halophilic and grew between 0·5 and 10 % NaCl and at 4–42 °C. Its DNA G+C content was 56·4 mol%. Isolate KMM 3654T was phylogenetically closely related to members of the genus Oceanimonas, showing 96·7 and 95·6 % 16S rRNA gene sequence similarity to Oceanimonas doudoroffii DSM 7028T and Oceanimonas baumannii ATCC 700832T, respectively. Strain KMM 3654T shared some physiological and chemotaxonomic properties with these two Oceanimonas species, but differed from them in morphology, growth at 4 °C, urease activity, weak phenol degradation and utilization of phenylacetate. On the basis of phenotypic and phylogenetic evidence, Oceanisphaera litoralis gen. nov., sp. nov. is proposed, with the type strain KMM 3654T (=DSM 15406T).
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Oceanicaulis alexandrii gen. nov., sp. nov., a novel stalked bacterium isolated from a culture of the dinoflagellate Alexandrium tamarense (Lebour) Balech
Five bacterial strains were isolated from a non-toxigenic strain of the marine dinoflagellate Alexandrium tamarense (Lebour) Balech CCMP 116 (NEPCC C116), during a survey of the diversity of bacteria associated with paralytic shellfish toxin-producing cultures of Alexandrium spp. (Dinophyta). All strains were strictly aerobic, Gram-negative, straight or curved rods. Cells were dimorphic, with stalks (or prosthecae) and non-motile or non-stalked and motile, by means of a single polar flagellum. The bacteria grew best at salt concentrations ranging from 2 to 10 % and growth occurred at 10 °C, but not at 50 °C. The G+C content of the chromosomal DNA of the strains was determined to be 61–62 mol%. Major cellular fatty acids of the bacteria presented a unique profile. 16S rRNA gene sequence analysis showed the five strains to be related to genera of budding bacteria of marine origin in the ‘Alphaproteobacteria’, namely, Hirschia, Maricaulis and Hyphomonas, although they exhibited substantial differences in morphology, substrate utilization and fatty acid profile to members of these genera. The five strains are proposed to comprise a new species of a new genus, Oceanicaulis alexandrii gen. nov., sp. nov., the type strain of which is C116-18T (=DSM 11625T=NCIMB 13905T).
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Thermomonas fusca sp. nov. and Thermomonas brevis sp. nov., two mesophilic species isolated from a denitrification reactor with poly(ε-caprolactone) plastic granules as fixed bed, and emended description of the genus Thermomonas
More LessPreviously, 22 aerobic Gram-negative bacteria were isolated from biofilms growing on granules of the synthetic polyester poly(ε-caprolactone); the granules were used as a fixed bed in a denitrification reactor. All the strains showed similar fatty acid profiles. The 16S rRNA gene sequences of five strains were phylogenetically related to Thermomonas spp. Repetitive extragenic palindromic DNA-PCR (REP-PCR) fingerprinting revealed four groups, and DNA hybridizations between representative strains showed that the strains belonged to two new species within the genus Thermomonas, for which the names Thermomonas fusca (type strain LMG 21737T=DSM 15424T) and Thermomonas brevis (type strain LMG 21746T=DSM 15422T) are proposed. Both species are able to grow at low temperatures, but not at 50 °C, and are non-haemolytic. Both species can be differentiated by several other phenotypic features from earlier described species of the genus Thermomonas. Cell extracts contain mainly branched fatty acids, with C15 : 0 iso, C17 : 1 iso ω9c, C11 : 0 iso 3OH and C11 : 0 iso as main constituents. The G+C content of the DNA of the novel species is between 67·6 and 68·7 mol%.
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Rheinheimera pacifica sp. nov., a novel halotolerant bacterium isolated from deep sea water of the Pacific
An aerobic, Gram-negative, non-fermentative, rod-shaped, motile, non-pigmented bacterium, KMM 1406T, was isolated from a sample of Pacific deep sea water and investigated for phenotypic characteristics, chemotaxonomic features and phylogenetic relationships. The deep-sea isolate exhibited growth in 0–8 % (w/v) NaCl and at 4–37 °C, hydrolytic activity on gelatin, Tween 80 and starch and lack of d-glucose utilization. The major fatty acids were C16 : 0, C16 : 1 ω9c, C17 : 1 ω8c and C18 : 1 ω7c. The DNA G+C content was 49·6 mol%. 16S rRNA gene sequence analysis revealed that strain KMM 1406T was related closely to Rheinheimera baltica DSM 14885T within the γ-Proteobacteria, with 96·8 % sequence similarity. On the basis of phenotypic and molecular data, a novel species, Rheinheimera pacifica sp. nov., is proposed. The type strain is KMM 1406T (=IAM 15043T=JCM 12090T=NRIC 0539T=CCUG 46544T).
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Herbaspirillum lusitanum sp. nov., a novel nitrogen-fixing bacterium associated with root nodules of Phaseolus vulgaris
Several bacterial strains were isolated from root nodules of Phaseolus vulgaris plants grown in a soil from Portugal. The strains were Gram-negative, aerobic, curved rod-shaped and motile. The isolates were catalase- and oxidase-positive. The TP-RAPD (two-primer randomly amplified polymorphic DNA) patterns of all strains were identical, suggesting that they belong to the same species. The complete 16S rDNA sequence of a representative strain was obtained and phylogenetic analysis based on the neighbour-joining method indicated that this bacterium belongs to the β-Proteobacteria and that the closest related genus is Herbaspirillum. The DNA G+C content ranged from 57·9 to 61·9 mol%. Growth was observed with many different carbohydrates and organic acids including caprate, malate, citrate and phenylacetate. No growth was observed with maltose, meso-inositol, meso-erythritol or adipate as sole carbon source. According to the phenotypic and genotypic data obtained in this work, the bacterium represents a novel species of the genus Herbaspirillum, and the name Herbaspirillum lusitanum sp. nov. is proposed. The type strain is P6-12T (=LMG 21710T=CECT 5661T).
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Psychrobacter okhotskensis sp. nov., a lipase-producing facultative psychrophile isolated from the coast of the Okhotsk Sea
More LessA facultatively psychrophilic bacterium, strain MD17T, which hydrolyses lipids at 5 °C, was isolated from the Monbetsu coast of the Okhotsk Sea in Hokkaido, Japan, when ice carried by the cold current came to the area. The isolate is an aerobic, non-motile coccobacillus that reduces nitrate to nitrite and hydrolyses Tweens 20, 40, 60 and 80, but not gelatin, DNA or alginic acid. The isolate grows at 0 °C, but not at temperatures higher than 36 °C; its optimum growth temperature is 25 °C. It grows in the presence of 0–10 % NaCl. Its major isoprenoid quinone is ubiquinone-8 (Q-8) and its DNA G+C content is 46·7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MD17T is closely related to Psychrobacter glacincola DSM 12194T (99·0 % similarity) and Psychrobacter immobilis DSM 7229T (98·7 % similarity). DNA–DNA hybridization revealed 45·9 % relatedness between strain MD17T and P. immobilis ATCC 43116T and 33·4 % between strain MD17T and P. glacincola ATCC 700754T. Based on physiological and biochemical characteristics, phylogenetic position (as determined by 16S rRNA gene sequence analysis) and DNA–DNA relatedness, it is concluded that the isolate should be designated as a novel species, for which the name Psychrobacter okhotskensis sp. nov. is proposed. The type strain is MD17T (=NCIMB 13931T=JCM 11840T).
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Sphingobium amiense sp. nov., a novel nonylphenol-degrading bacterium isolated from a river sediment
More LessA nonylphenol-degrading bacterial strain (YTT) was isolated previously from a river sediment sample obtained in Ami-machi, Ibaraki, Japan, and identified as a Sphingomonas species. In this study, the taxonomic relationship between strain YTT, a recently described nonylphenol-degrading strain, Sphingomonas cloacae, and Sphingobium yanoikuyae, which is phylogenetically related, was examined. Their phenotypic characteristics were compared and levels of DNA–DNA relatedness between these strains were determined. Based on the results of physiological and biochemical tests and DNA–DNA hybridization, it is proposed that strain YTT (=IAM 15006T=JCM 11777T=CIP 107839T) represents a novel species of the genus Sphingobium, Sphingobium amiense sp. nov.
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Pseudomonas rhizosphaerae sp. nov., a novel species that actively solubilizes phosphate in vitro
A bacterial strain (designated IH5T), isolated from rhizospheric soil of grasses growing spontaneously in Spanish soil, actively solubilized phosphates in vitro when bicalcium phosphate was used as a phosphorus source. This strain was Gram-negative, strictly aerobic, rod-shaped and motile. The strain produced catalase, but not oxidase. Cellulose, casein, starch, gelatin, aesculin and urea were not hydrolysed. Growth was observed with many carbohydrates as the carbon source. The main non-polar fatty acids detected were hexadecenoic acid (C16 : 1), hexadecanoic acid (C16 : 0) and octadecenoic acid (C18 : 1). The hydroxy fatty acids detected were 3-hydroxydecanoic acid (C10 : 0 3-OH), 3-hydroxydodecanoic acid (C12 : 0 3-OH) and 2-hydroxydodecanoic acid (C12 : 0 2-OH). Phylogenetic analysis of 16S rRNA indicated that this bacterium belongs to the genus Pseudomonas in the γ-subclass of the Proteobacteria and that the closest related species is Pseudomonas graminis. The DNA G+C content was 61 mol%. DNA–DNA hybridization showed 23 % relatedness between strain IH5T and P. graminis DSM 11363T. Therefore, strain IH5T belongs to a novel species from the genus Pseudomonas, for which the name Pseudomonas rhizosphaerae sp. nov. is proposed (type strain, IH5T=LMG 21640T=CECT 5726T).
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Marinobacter excellens sp. nov., isolated from sediments of the Sea of Japan
Five strains of halophilic, Gram-negative marine bacteria (KMM 3809T, KMM 3814, KMM 3815, KMM 3817 and KMM 3818) were isolated from sediments collected from Chazhma Bay, Sea of Japan. Phylogenetic 16S rRNA gene sequence-based analysis placed these bacteria in a clade within the genus Marinobacter in the γ-Proteobacteria. KMM 3809T showed highest 16S rRNA gene sequence similarity of 97·3 % to Marinobacter litoralis and 96·9 % to Marinobacter hydrocarbonoclasticus and Marinobacter aquaeolei. DNA–DNA hybridization between the five isolates was at the conspecific level (94–96 %) and that among the closest phylogenetic neighbours ranged from 45·0 to 62·5 %. The new organisms were susceptible to polymyxin. Predominant fatty acids were C16 : 0, C16 : 1 ω9c, C16 : 1 ω7c and C18 : 1 ω9c. Phylogenetic evidence, along with phenotypic and genotypic characteristics, showed that the bacteria constituted a novel species of the genus Marinobacter. The name Marinobacter excellens sp. nov. is proposed for this species, with the type strain KMM 3809T (=CIP 107686T).
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- Gram-Positive Bacteria
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Elevation of Mycobacterium tuberculosis subsp. caprae Aranaz et al. 1999 to species rank as Mycobacterium caprae comb. nov., sp. nov.
More LessMycobacterium tuberculosis complex isolates recovered from goats were originally classified as Mycobacterium tuberculosis subsp. caprae; however, this subspecies was recently reclassified as Mycobacterium bovis subsp. caprae. Besides biochemical (sensitivity to pyrazinamide) and epidemiological features, strains of this unusual member of the M. tuberculosis complex show a special combination of pncA, oxyR, katG and gyrA gene polymorphisms. Sequence analysis of the gyrB gene in these strains reveals special nucleotide substitutions not found in other members of the M. tuberculosis complex that can be used to differentiate caprine mycobacterial strains from M. bovis and other members of the M. tuberculosis complex. M. tuberculosis subsp. caprae now appears not to be restricted to Spanish goats, as strains of this organism have been isolated from cattle, wild boar and pigs. Its occurrence has also been reported in France, Austria and Germany. Two studies on the evolution of the M. tuberculosis complex based on the presence/absence of regions of difference have shown that the group of caprine isolates (or its ancestor) is older than M. bovis (or its ancestor). These findings reinforce the original suggestion that the caprine mycobacterial strains are a taxon of the M. tuberculosis complex, independent of M. bovis. Within the current context of the existing nomenclature of the M. tuberculosis complex, it is proposed that M. tuberculosis subsp. caprae be elevated to species status, as Mycobacterium caprae comb. nov., sp. nov.
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Soehngenia saccharolytica gen. nov., sp. nov. and Clostridium amygdalinum sp. nov., two novel anaerobic, benzaldehyde-converting bacteria
Two anaerobic, benzaldehyde-converting bacteria were isolated from an anaerobic upflow anaerobic sludge bed (UASB)-reactor treating potato starch waste water. Strain BOR-YT converted benzaldehyde to benzoate and benzylalcohol in approximately equimolar concentrations. Benzaldehyde conversion did not support growth. Strain BOR-YT was Gram-positive and rod-shaped, and its cells were slightly thickened in the middle. The strain was a mesophilic spore-former that grew between 15 and 40 °C, with optimum growth at 30–37 °C. The optimum pH for growth was pH 7·0. Strain BOR-YT grew on a wide range of carbohydrates and some other carbon sources including yeast extract, cysteine and serine. The G+C content of its DNA was 42 mol%. According to physiological characteristics and 16S rRNA gene sequence analysis, confirmed by DNA–DNA hybridization with its phylogenetic neighbours, strain BOR-YT belongs to a novel genus of cluster XII of the clostridia, namely Soehngenia; the name Soehngenia saccharolytica is proposed for the type species (type strain BOR-YT=DSM 12858T=ATCC BAA-502T). Strain BR-10T reduced benzaldehyde to benzylalcohol. This conversion was coupled to growth. In a medium containing yeast extract, the presence of benzaldehyde resulted in the accumulation of more than twofold more cells. Strain BR-10T was a Gram-positive organism that was characterized by oval- or rod-shaped cells with oval ends, which occurred singly, in pairs or sometimes in chains. The strain was moderately thermophilic and grew between 20 and 60 °C, with optimum growth at 45 °C. The optimum pH for growth was between pH 7·0 and 7·5. Strain BR-10T grew on a wide range of carbon sources including carbohydrates, yeast extract, casein and some amino acids. The G+C content of its DNA was 32 mol%. As determined by 16S rRNA gene sequence analysis, strain BR-10T represents a novel species of cluster XIVa of the clostridia; the name Clostridium amygdalinum is proposed for this novel species (type strain BR-10T=DSM 12857T=ATCC BAA-501T).
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Arthrobacter gandavensis sp. nov., for strains of veterinary origin
More LessThree strains of a previously undescribed, Gram-positive, coryneform bacterium, which were isolated from cattle, were subjected to polyphasic taxonomic analysis. Comparative 16S rRNA gene sequencing revealed that the unknown isolates were members of the genus Arthrobacter and were phylogenetically closely related to Arthrobacter luteolus. However, DNA–DNA hybridization indicated that the strains belonged to a new sub-lineage within the genus Arthrobacter. The unknown isolates can be distinguished from related species by biochemical tests. It is proposed that the Arthrobacter-like bacteria of veterinary origin should be classified in the genus Arthrobacter as Arthrobacter gandavensis sp. nov., with the type strain LMG 21285T (=DSM 15046T).
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Luteococcus sanguinis sp. nov., isolated from human blood
More LessAn unusual catalase-positive, Gram-positive, coccus-shaped bacterium that originated from a human blood specimen was subjected to a polyphasic taxonomic study. Cell-wall murein and lipid composition analyses indicated that the unknown isolate was a member of the genus Luteococcus. The results of comparative 16S rRNA gene sequence analysis were consistent with chemotaxonomic findings and showed that the unidentified bacterium represents a hitherto unknown sublineage within the genus Luteococcus that is closely related to, but distinct from, Luteococcus japonicus. On the basis of both phenotypic and phylogenetic evidence, it is proposed that the unknown bacterium from human blood should be classified as Luteococcus sanguinis sp. nov., with the type strain CCUG 33897T (=CIP 107216T).
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Aeromicrobium marinum sp. nov., an abundant pelagic bacterium isolated from the German Wadden Sea
More LessAn obligately salt-dependent Gram-positive bacterium, designated strain T2T, was isolated from surface waters of the German Wadden Sea. The organism exhibited optimum growth at salt concentrations similar to that of sea water. On the basis of phenotypic, chemotaxonomic and phylogenetic differences, it is concluded that strain T2T (=DSM 15272T=LMG 21768T) is the first marine species of the genus Aeromicrobium to be identified, for which the name Aeromicrobium marinum is proposed. It is also the first described marine bacterium within the family Nocardioidaceae. Strain T2T is a rod-shaped, aerobic, heterotrophic bacterium containing ll-diaminopimelic acid in the peptidoglycan and MK-9(H4) as the major menaquinone. The bacterium is characterized by high proportions of the fatty acids palmitic acid, oleic acid, tuberculostearic acid and hydroxypalmitic acid. DNA–DNA hybridization analysis showed the marine bacterium to display 29·1 % relatedness with Aeromicrobium fastidiosum DSM 10552T and 44·4 % relatedness with Aeromicrobium erythreum DSM 8599T. A. marinum was demonstrated to be an abundant member of the pelagic bacterial community in the German Wadden Sea since it represented about 1 % of the total bacterial population as revealed by dot-blot hybridization and most-probable-number counts.
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Brachybacterium muris sp. nov., isolated from the liver of a laboratory mouse strain
More LessA coccoid- to ovoid-shaped, Gram-positive bacterial strain, designated C3H-21T, was isolated from the liver of the laboratory mouse strain C3H/He and characterized by a polyphasic approach. The peptidoglycan type was variation A4γ with meso-diaminopimelic acid as the diagnostic cell-wall diamino acid and an interpeptide bridge of d-asp-d-Glu. The isolate contained menaquinone MK-7 (88 %) as the major component of the quinone system and minor amounts of menaquinone MK-8 (9 %) and menaquinone MK-6 (3 %). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, unidentified glycolipids and unidentified phospholipids. The fatty acid profile contained predominantly anteiso-C15 : 0 and significant amounts of iso-C16 : 0, iso-C14 : 0, anteiso-C17 : 0 and C19 : 0. The polyamine pattern consisted of spermine and spermidine as the major compounds. Genomic fingerprints clearly distinguished strain C3H-21T from other Brachybacterium species. The isolate shared the highest 16S rDNA sequence similarities with members of the genus Brachybacterium, in particular Brachybacterium sacelli LMG 20345T, Brachybacterium nesterenkovii DSM 9573T, Brachybacterium rhamnosum LMG 19848T, Brachybacterium alimentarium CNRZ 925T and Brachybacterium fresconis LMG 20336T (97·8–97·2 %). The results of biochemical/physiological characterization, chemotaxonomic characteristics and REP-PCR-generated fingerprints demonstrated that the isolate represents a novel species of the genus Brachybacterium, for which the name Brachybacterium muris (type strain C3H-21T=DSM 14560T=CCM 7047T) is proposed.
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Propionicimonas paludicola gen. nov., sp. nov., a novel facultatively anaerobic, Gram-positive, propionate-producing bacterium isolated from plant residue in irrigated rice-field soil
More LessTwo propionate-producing strains (WdT and Wf) that were isolated anaerobically from plant residue of irrigated rice-field soil in Japan were characterized phenotypically and phylogenetically. The growth rate of strain WdT was very slow in basal medium, but both growth and propionate production were stimulated significantly by the addition of cyanocobalamin. Strain Wf grew well in basal medium and produced substantial amounts of fermentation products, including propionate. Other phenotypic and phylogenetic characteristics of the two isolates were almost identical. Both were facultatively anaerobic, but much better growth was observed under anaerobic conditions. Cells were Gram-positive, non-motile, non-spore-forming and pleomorphic rods with irregular V- or crescent-shaped cell arrangements. Fermentation products from glucose in the presence of excess cyanocobalamin were acetate, lactate, a small amount of succinate and CO2, in addition to propionate. Both oxidase and catalase activities were negative. The strains possessed meso-diaminopimelic acid in their peptidoglycan and their major cellular fatty acids were C13 : 0, anteiso-C15 : 0 and C15 : 0. The isolates had high genomic DNA G+C contents (68·7 and 67·4 mol%, respectively). Menaquinones MK-9(H4) and MK-10(H4) were the predominant respiratory quinones. Phylogenetic analysis based on 16S rDNA sequences placed both strains in the Actinobacteria, with Micropruina glycogenica as their closest relative (sequence similarity values of 95·8 and 95·7 %, respectively). Microlunatus phosphovorus and Friedmanniella antarctica were also related closely to the isolates. As their morphological, physiological and chemotaxonomic characteristics were distinctly different from those of any related species, Propionicimonas paludicola gen. nov., sp. nov. is proposed to accommodate these strains. The type strain of the novel species is WdT (=JCM 11933T=DSM 15597T).
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Emended description of Janibacter terrae, including ten dibenzofuran-degrading strains and Janibacter brevis as its later heterotypic synonym
Ten Gram-positive strains that degraded dibenzofuran belonged to one homogeneous cluster with common biochemical and chemotaxonomic properties. The strains included the previously described strains [Terrabacter sp.] DPO 360 and DPO 1361 and were isolated from different locations in central Europe. They all shared menaquinone MK-8(H4) and meso-diaminopimelic acid in the cell wall and showed the same cellular fatty acid, polar lipid and RiboPrint patterns. Chemotaxonomic properties, as well as DNA G+C content (72·8 mol%), were consistent with those described for the genus Janibacter. Analysis of 16S rDNA sequences suggested a close relationship to Janibacter terrae and Janibacter brevis. DNA–DNA hybridization of two dibenzofuran-degrading strains (DPO 360 and DPO 1361) and the type strains of J. terrae and J. brevis revealed that these strains belong to the same species. An emended description of the species J. terrae is given. J. brevis is a later heterotypic synonym of J. terrae.
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Staphylococcus nepalensis sp. nov., isolated from goats of the Himalayan region
Four coagulase-negative, novobiocin-resistant cocci, designated CW1T, PM34, MM3 and RW78, were isolated from the respiratory tract of goats kept in the Himalayan region. The four isolates were assigned to a single species on the basis of almost identical biochemical and physiological traits, protein profiles obtained after SDS-PAGE and identical genomic fingerprints generated after enterobacterial repetitive intergenic consensus (ERIC)-PCR. Strain CW1T showed highest 16S rDNA sequence similarities to Staphylococcus cohnii subsp. urealyticus ATCC 49330T, Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305T, S. cohnii subsp. cohnii ATCC 29974T, Staphylococcus arlettae ATCC 43957T, Staphylococcus gallinarum ATCC 35539T, Staphylococcus succinus ATCC 700337T and Staphylococcus xylosus ATCC 29971T (99·0, 98·8, 98·8, 98·4, 98·2, 98·1 and 98·1 %, respectively), indicating its classification within the genus Staphylococcus. The polar lipid composition, fatty acid profiles, quinone systems and diagnostic cell-wall diamino acid were in agreement with the characteristics of the genus Staphylococcus. DNA–DNA hybridization with closely related Staphylococcus species suggested that strain CW1T represents an as-yet unrecognized species. Based on these results, a novel species of the genus Staphylococcus is described, Staphylococcus nepalensis sp. nov. The type strain is CW1T (=DSM 15150T=CCM 7045T) and the most dissimilar strain is PM34 (=DSM 15151=CCM 7046).
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Planococcus maritimus sp. nov., isolated from sea water of a tidal flat in Korea
More LessTwo Gram-positive, motile cocci, strains TF-9T and TF-16, were isolated from sea water of a tidal flat in Korea. Phylogenetic analysis based on 16S rDNA sequences showed that the strains fall within the radiation of the cluster comprising Planococcus citreus and Planococcus kocurii, and this cluster joined the clade comprising Planomicrobium species and Planococcus alkanoclasticus and Planococcus psychrophilus with a high bootstrap resampling value. Strains TF-9T and TF-16 contained MK-8, MK-7 and MK-6 as the predominant menaquinones. The major fatty acid was anteiso-C15 : 0. The DNA G+C contents of strains TF-9T and TF-16 were respectively 48 and 49 mol%. The level of 16S rDNA identity between strains TF-9T and TF-16 was 98·9 %. Strain TF-9T and TF-16 respectively exhibited levels of 16S rDNA identity of 97·2–98·4 and 96·9–99·5 % to the type strains of Planococcus kocurii, Planococcus citreus and Planococcus antarcticus. The mean level of DNA–DNA relatedness between strains TF-9T and TF-16 was 36·7 %. Strains TF-9T and TF-16 respectively exhibited levels of DNA–DNA relatedness of 7·1–43·4 and 3·5–80·9 % to Planococcus citreus DSM 20549T, Planococcus kocurii DSM 20747T and Planococcus antarcticus DSM 14505T. On the basis of the phenotypic, phylogenetic and genomic data, strain TF-9T (=KCCM 41587T=JCM 11543T) should be placed as a novel species of the genus Planococcus, for which the name Planococcus maritimus sp. nov. is proposed, and strain TF-16 should be classified as a member of Planococcus citreus.
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Corynebacterium suicordis sp. nov., from pigs
Nineteen strains of Gram-positive, non-motile, non-spore-forming, catalase-positive, rod-shaped bacteria isolated from pigs were characterized by using biochemical, molecular chemical and molecular genetic methods. Two distinct groups of organisms were discerned, based on their colonial morphology, CAMP (Christie–Atkins–Munch-Petersen) reaction and numerical profile by using the API Coryne system. The first group (13 strains) gave a doubtful discrimination between Corynebacterium striatum and Corynebacterium amycolatum, whilst the second group (six strains) were identified tentatively as Corynebacterium urealyticum. Comparative 16S rRNA gene sequencing studies demonstrated that all of the isolates belonged phylogenetically to the genus Corynebacterium. The first group of organisms was highly similar to Corynebacterium testudinoris with respect to 16S rRNA gene sequences and physiological characteristics, whereas the remaining six isolates formed a hitherto unknown subline within the genus, associated with a small subcluster of species that included Corynebacterium auriscanis and its close relatives. The unknown Corynebacterium sp. was distinguished readily from these and other species of the genus by biochemical tests. Based on both phenotypic and phylogenetic evidence, it is proposed that the new isolates from pigs should be classified as a novel species, Corynebacterium suicordis sp. nov. The type strain is P81/02T (=CECT 5724T=CCUG 46963T).
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Kitasatospora putterlickiae sp. nov., isolated from rhizosphere soil, transfer of Streptomyces kifunensis to the genus Kitasatospora as Kitasatospora kifunensis comb. nov., and emended description of Streptomyces aureofaciens Duggar 1948
A polyphasic study was undertaken to establish the taxonomic position of a rhizosphere isolate that had been assigned provisionally to the genus Kitasatospora. The organism, isolate F18-98T, was found to have chemical and morphological properties that were consistent with its classification as a Kitasatospora strain. Direct 16S rDNA sequence data confirmed the taxonomic position of the strain, following the generation of phylogenetic trees by using three treeing algorithms. The organism formed a 16S rDNA subclade with Kitasatospora azatica and Streptomyces kifunensis, but was distinguished readily from the latter by using a combination of biochemical and physiological properties. Genotypic and phenotypic data show that strain F18-98T should be classified in the genus Kitasatospora as a novel species, for which the name Kitasatospora putterlickiae sp. nov. is proposed; the type strain has been deposited in culture collections as strain F18-98T (=DSM 44665T=NCIMB 13932T). It is also proposed that Streptomyces kifunensis should be transferred to the genus Kitasatospora as Kitasatospora kifunensis comb. nov. An emended description of Streptomyces aureofaciens Duggar 1948 is also given.
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Reclassification of Subtercola pratensis Behrendt et al. 2002 as Agreia pratensis comb. nov.
More LessComparative analysis of 16S rDNA sequences revealed a close phylogenetic relationship (99·6 % similarity) between Subtercola pratensis Behrendt et al. 2002 and Agreia bicolorata Evtushenko et al. 2001 . The two species were found to share genus-specific chemotaxonomic characteristics such as the occurrence of d-ornithine and l-2,4-diaminobutyric acid in the peptidoglycan and the profile of cellular fatty acids and 1,1-dimethoxy-alkanes. DNA–DNA relatedness of only 47·8 % and differences in phenotypic features such as the menaquinone profile and oxidase and Voges–Proskauer reactions confirmed the distinct species status of S. pratensis and A. bicolorata. On the basis of the data from phylogenetic and phenotypic analyses, the reclassification of S. pratensis as Agreia pratensis comb. nov. is proposed. As a result of this reclassification, the two genera are coherent, in that the cell wall composition and 1,1-dimethoxy-alkane spectrum are significant genus-specific characteristics.
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Streptomyces luridiscabiei sp. nov., Streptomyces puniciscabiei sp. nov. and Streptomyces niveiscabiei sp. nov., which cause potato common scab disease in Korea
Three plant-pathogenic isolates of Streptomyces spp., isolated from potatoes with common scab disease lesions in Korea, are described as novel species. Morphological and physiological properties of these isolates were distinct from those of previously described Streptomyces species. Strain S63T has yellow-white, smooth, cylindrical spores that are borne in monoverticillus flexuous spore-chains. Strain S77T has purple-red, spiny spores that are borne in simple rectus flexuous spore-chains. Strain S78T has white, smooth, cylindrical spores that are borne in simple rectus flexuous spore-chains. These three isolates differed from known pathogenic strains by analysis of 16S rRNA gene sequences in a previous study. Furthermore, genetic uniqueness of our isolates was confirmed by sequencing of the 16S–23S internal transcribed spacer (ITS) region, which indicated that isolates S63T and S78T belong to the genus Streptomyces and have low homology to other Streptomyces species (less than 71·2 and 75·7 %, respectively). The 16S–23S ITS region of strain S77T was not amplified by these primer sets. DNA–DNA hybridization results for all three isolates show distant relationships to previously described Streptomyces species; therefore, on the basis of polyphasic evidence, the names Streptomyces luridiscabiei sp. nov. for strain S63T (=LMG 21390T=KACC 20252T), Streptomyces puniciscabiei sp. nov. for strain S77T (=LMG 21391T=KACC 20253T) and Streptomyces niveiscabiei sp. nov. for strain S78T (=LMG 21392T=KACC 20254T) are proposed.
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Lactobacillus kitasatonis sp. nov., from chicken intestine
More LessFour strains isolated from chicken small intestine and strains JCM 1038 and JCM 1039 (designated as Lactobacillus acidophilus) were characterized by phenotypic and molecular taxonomic methods. They were Gram-positive, catalase-negative, facultatively anaerobic rods that did not produce gas from glucose. These strains had similar phenotypic characteristics and exhibited intergroup DNA relatedness values of >77 %, indicating that they comprised a single species. The 16S rRNA gene sequence of a representative strain, JCM 1039T (designated as type strain in this study), was determined and aligned with those of other Lactobacillus species. JCM 1039T was placed in the Lactobacillus delbrueckii cluster of the genus Lactobacillus on the basis of phylogenetic analysis and formed an independent cluster that was distinct from its closest neighbours, Lactobacillus amylovorus, Lactobacillus crispatus, Lactobacillus gallinarum, L. acidophilus and Lactobacillus helveticus. Results of DNA–DNA hybridization experiments and whole-cell protein profiles clearly indicated that these strains represent a novel Lactobacillus species, for which the name Lactobacillus kitasatonis sp. nov. is proposed; the type strain of this species is JCM 1039T.
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Salinibacterium amurskyense gen. nov., sp. nov., a novel genus of the family Microbacteriaceae from the marine environment
More LessThree bacterial strains were isolated from sea-water samples taken from Amursky Bay of the Gulf of Peter the Great, East Sea. The isolates, designated KMM 3670, KMM 3673T and KMM 3928, were Gram-positive, non-motile, aerobic, non-spore-forming, irregular, rod-shaped actinobacteria. They grew well at mesophilic temperatures and neutral pH and tolerated up to 10 % NaCl, although salt was not essential for growth. The three strains shared all morphological properties and most physiological characteristics tested. Based on subsequent chemotaxonomic and phylogenetic analyses, it was evident that the strains represented a distinctive taxon in the family Microbacteriaceae. The strains contained a major amount of menaquinone with 11 isoprene units; lysine and ornithine were the major cell-wall diamino acids. In 16S rDNA analysis, the three strains formed an independent phylogenetic lineage within the tree encompassed by members of the family Microbacteriaceae. It is notable that the tested strains form the first described taxon of Microbacteriaceae that inhabits a marine aquatic environment. The three strains evidently merit recognition as a single species of a novel genus in the family Microbacteriaceae, for which the name Salinibacterium amurskyense gen. nov., sp. nov. (type strain, KMM 3673T=KCTC 9931T) is proposed.
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- Unicellular Eukaryotes
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Candida zemplinina sp. nov., an osmotolerant and psychrotolerant yeast that ferments sweet botrytized wines
More LessFour yeast strains isolated from fermenting botrytized grape musts in the Tokaj wine region of Hungary are shown to represent a new osmotolerant and psychrotolerant species. The new species, Candida zemplinina (type strain 10-372T=CBS 9494T=NCAIM Y016667T), is closely related to Candida stellata, a yeast common on overripe grapes and in sweet fermenting wines. The sequence of the D1/D2 domain of the C. zemplinina 10-372T 26S rDNA shows 8·1 % sequence difference when compared to its counterpart in C. stellata CBS 157T. In the conserved 5·8S gene of the ITS1–5·8S–ITS2 region the difference is 8 %. The D1/D2 domain differs only at two nucleotides from the homologous sequence of a yeast strain isolated from botrytized grapes in California, suggesting that C. zemplinina is a wine yeast that occurs in geographically distant localities.
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Bensingtonia changbaiensis sp. nov. and Bensingtonia sorbi sp. nov., novel ballistoconidium-forming yeast species from plant leaves
More LessSix ballistoconidium-forming yeast strains that were isolated from plant leaves collected on Changbai Mountain, north-east China, were assigned to the genus Bensingtonia Ingold emend. Nakase & Boekhout due to the formation of asymmetrical ballistoconidia, cream-coloured colonies and Q-9 as the major ubiquinone. Two separate groups, representing two novel Bensingtonia species, were recognized among these yeasts by 26S rDNA D1/D2 domain, internal transcribed spacer (ITS) region and 18S rDNA sequence analyses. The names Bensingtonia changbaiensis sp. nov. (type strain, CB 346T=AS 2.2310T=CBS 9497T) and Bensingtonia sorbi sp. nov. (type strain, CB 286T=AS 2.2303T=CBS 9498T) are proposed for these two species.
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Sporobolomyces bannaensis, a novel ballistoconidium-forming yeast species in the Sporidiobolus lineage
More LessAmong ballistoconidium-forming yeast strains isolated from various plant leaves collected in Banna, Yunnan Province, China, five strains that formed pink-coloured colonies and asymmetric ballistoconidia were classified in a single group and assigned to the genus Sporobolomyces by conventional and chemotaxonomic studies. Analyses of the internal transcribed spacer region and 26S rDNA D1/D2 domain sequences indicated that these strains represent a novel species with a close phylogenetic relationship to Sporobolomyces blumeae in the Sporidiobolus lineage, for which the name Sporobolomyces bannaensis sp. nov. is proposed (type strain Y41T=AS 2.2285T=CBS 9204T).
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Cryptococcus surugaensis sp. nov., a novel yeast species from sediment collected on the deep-sea floor of Suruga Bay
More LessA novel species of the genus Cryptococcus was isolated from sediment collected on the deep-sea floor of Suruga Bay, Japan. Nucleotide sequences of 18S rDNA, internal transcribed spacers, 5·8S rDNA and the D1/D2 region of 26S rDNA of strain SY-260T suggested affinities to a phylogenetic lineage that includes Cryptococcus luteolus. Comparisons of the rDNA sequences of each region clarified that strain SY-260T is related distantly to Bullera coprosmaensis and Bullera oryzae, but is distinct at the species level. As ballistoconidia and sexual reproduction were not observed in strain SY-260T, this strain is described as Cryptococcus surugaensis sp. nov. (type strain, SY-260T=JCM 11903T=CBS 9426T).
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- Evolution, Phylogeny And Biodiversity
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Molecular signatures in protein sequences that are characteristic of cyanobacteria and plastid homologues
More LessFourteen conserved indels (i.e. inserts or deletions) have been identified in 10 widely distributed proteins that appear to be characteristic of cyanobacterial species and are not found in any other group of bacteria. These signatures include three inserts of 6, 7 and 28 aa in the DNA helicase II (UvrD) protein, an 18–21 aa insert in DNA polymerase I, a 14 aa insert in the enzyme ADP-glucose pyrophosphorylase, a 3 aa insert in the FtsH protein, an 11–13 aa insert in phytoene synthase, a 5 aa insert in elongation factor-Tu, two deletions of 2 and 7 aa in ribosomal S1 protein, a 2 aa insert in the SecA protein, a 1 aa deletion and a 6 aa insert in the enzyme inosine-5′-monophosphate dehydrogenase and a 1 aa deletion in the major sigma factor. These signatures, which are flanked by conserved regions, provide molecular markers for distinguishing cyanobacterial taxa from all other bacteria and they should prove helpful in the identification of cyanobacterial species, simply on the basis of the presence or absence of these markers in the corresponding proteins. The signatures in six of these proteins (SecA, elongation factor-Tu, ADP-glucose pyrophosphorylase, phytoene synthase, FtsH and ribosomal S1 protein) are also commonly present in plastid homologues from plants and algae (chlorophytes, chromophytes and rhodophytes), indicating their specific relationship to cyanobacteria and supporting their endosymbiotic origin from these bacteria. In phylogenetic trees based on a number of these proteins (SecA, UvrD, DNA polymerase I, elongation factor-Tu) that were investigated, the available cyanobacterial homologues grouped together with high affinity (>95 % bootstrap value), supporting the view that the cyanobacterial phylum is monophyletic and that the identified signatures were introduced in a common ancestor of this group.
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Phylogenetic relationships and genotyping of the genus Streptococcus by sequence determination of the RNase P RNA gene, rnpB
More LessThe rnpB gene is universally present in bacterial species and encodes the RNA subunit of endoribonuclease P. In this study, rnpB was sequenced in 50 type strains and 29 additional strains of the genus Streptococcus. Putative secondary-structure models and possible interactions in RNase P RNA molecules are discussed. Phylogenetic relationships were studied and Bayesian, maximum-parsimony and minimum-evolution analyses supported six main clades that comprised 22 of the 50 species analysed. Phylogenetic inference was also studied for the 16S rRNA gene; it indicated a similar tree topology, but with weaker support values than for rnpB. Combined analysis of rnpB and 16S resulted in a phylogeny with significantly better support. Variability in the rnpB and 16S genes among all type strains, calculated as Shannon–Wiener information index values, was 0·45 for rnpB and 0·15 for 16S. Intraspecies proximity was assessed by principal coordinate analysis of rnpB for 32 strains of six closely related species (two clades) and showed species-specific clusters, but heterogeneity occurred in two species. It can be concluded that the rnpB gene is suitable for phylogenetic analysis of closely related taxa and has potential as a tool for species discrimination.
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Gene sequences useful for predicting relatedness of whole genomes in bacteria
More LessThirty-two protein-encoding genes that are distributed widely among bacterial genomes were tested for the potential usefulness of their DNA sequences in assigning bacterial strains to species. From publicly available data, it was possible to make 49 pairwise comparisons of whole bacterial genomes that were related at the genus or subgenus level. DNA sequence identity scores for eight of the genes correlated strongly with overall sequence identity scores for the genome pairs. Even single-gene alignments could predict overall genome relatedness with a high degree of precision and accuracy. Predictions could be refined further by including two or three genes in the analysis. The proposal that sequence analysis of a small set of protein-encoding genes could reliably assign novel strains or isolates to bacterial species is strongly supported.
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rDNA sequence analyses of Streptococcus dysgalactiae subsp. equisimilis isolates from pigs
The nucleotide sequences of 16S and 23S rRNA genes (rDNA) were determined for 11 isolates of Streptococcus dysgalactiae subsp. equisimilis from slaughtered pigs with endocarditis, arthritis or lymphadenitis and strain ATCC 35666, designated as a strain of subspecies equisimilis. The sequences of each of the genes were compared phylogenetically with the corresponding sequences of S. dysgalactiae subsp. dysgalactiae ATCC 43078T and ATCC 27957, which were also determined in this study. Based on the 16S rDNA analysis, the isolates of S. dysgalactiae subsp. equisimilis were divided into two distinct groups, designated groups 1 and 2. S. dysgalactiae subsp. equisimilis ATCC 35666 was closely related to the group 2 strains. The S. dysgalactiae subsp. dysgalactiae strains seemed to be associated with the group 1 strains, which was not consistent with the conventional subspecific classification of S. dysgalactiae. In contrast, the 23S rDNA analysis distinguished S. dysgalactiae subsp. dysgalactiae strains from subsp. equisimilis strains. This inconsistency between phylogenies based on 16S and 23S rDNA indicates that 23S rDNA is a more rigid marker for determining the phylogenetic relationships and taxonomic position of these organisms than is 16S rDNA.
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Evolution of symbiosis in the Vibrionaceae: a combined approach using molecules and physiology
More LessThe family Vibrionaceae is considered to be one of the most diverse and well-studied groups of bacteria. Here, evolution is assessed within the Vibrionaceae to determine whether multiple origins of eukaryotic associations have occurred within this diverse group of bacteria. Analyses were based on a large molecular dataset, along with a matrix that consisted of 100 biochemical and restriction digest characters. By using direct optimization methods to analyse both datasets individually and in combination, a total-evidence cladogram has been produced, which supports the hypothesis that several important symbionts (both mutualistic and pathogenic) within the Vibrionaceae are not monophyletic. This leads us to consider that symbiosis (and subsequently, associations with Eukarya) has evolved multiple times within the Vibrionaceae lineage.
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Phylogenetic affinities of the Trentepohliales inferred from small-subunit rDNA
More LessPhylogenetic analyses of the nuclear-encoded small-subunit rDNA sequences from taxa representing all of the major lineages of green algae, including new sequences for the Trentepohliales, consistently indicated that the subaerial Trentepohliales are closely related to ulvophycean marine green algae, particularly to the siphonous and hemisiphonous orders. The presence of phragmoplast-type cytokinesis in the order Trentepohliales remains enigmatic, and it is interesting that this type of cell division is associated with terrestrial (subaerial) habits.
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- Methods
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Rapid identification of filamentous actinomycetes to the genus level using genus-specific 16S rRNA gene restriction fragment patterns
More LessA rapid method for identifying filamentous actinomycete genera was developed based on 16S rRNA gene restriction fragment patterns. The patterns were generated by using specific restriction endonucleases to perform in silico digestions on the 16S rRNA gene sequences of all validly published filamentous actinomycete species. The method was applied to identifying actinomycete isolates from soil. Amplified 16S rDNA of soil actinomycetes was restricted with selected endonucleases and electrophoresed on agarose gels. The restriction fragment patterns of the unknown isolates were easily compared to the established patterns. Significantly, the genus Streptomyces could be differentiated from all other actinomycete genera by using only four restriction endonucleases, Sau3AI, AsnI, KpnI and SphI. This could be achieved in a time period of as little as a week, following PCR-template DNA isolation by a simple method. The identification method allowed unknown, non-Streptomyces soil isolates to be identified to a genus or small subgroup of genera. The genera in these subgroups could, in some cases, be distinguished by virtue of colony-morphology differences.
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- International Committee On Systematics Of Prokaryotes
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- Request For An Opinion
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The genus name Ensifer Casida 1982 takes priority over Sinorhizobium Chen et al. 1988, and Sinorhizobium morelense Wang et al. 2002 is a later synonym of Ensifer adhaerens Casida 1982. Is the combination ‘Sinorhizobium adhaerens’ (Casida 1982) Willems et al. 2003 legitimate? Request for an Opinion
More LessThe synonymy of the genera Ensifer and Sinorhizobium was recently reported, but it was proposed that the later-named genus, Sinorhizobium, take priority in nomenclature. There is no justification in the International Code of Nomenclature of Bacteria (Prokaryotes) for this step; Ensifer is the correct name of the genus, with Ensifer adhaerens as the type species. Species previously allocated to Sinorhizobium are here proposed as the new combinations Ensifer arboris, Ensifer fredii, Ensifer kostiensis, Ensifer kummerowiae, Ensifer medicae, Ensifer meliloti, Ensifer saheli, Ensifer terangae and Ensifer xinjiangensis. Sinorhizobium morelense was proposed in 2002 [ Wang, E. T., Tan, Z. Y., Willems, A., Fernández-López, M., Reinhold-Hurek, B. & Martínez-Romero, E., Int J Syst Evol Microbiol 52, 1687–1693, 2002 ], but a consideration of all published data indicate that it is a nitrogen-fixing genomovar and later heterotypic synonym of Ensifer adhaerens. A Request for an Opinion is made as to whether or not the combination ‘Sinorhizobium adhaerens’ ( Casida 1982 ) Willems et al. 2003 is legitimate.
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Proposal to conserve the adjectival form of the specific epithet in the reclassification of Bacteroides forsythus Tanner et al. 1986 to the genus Tannerella Sakamoto et al. 2002 as Tannerella forsythia corrig., gen. nov., comb. nov. Request for an Opinion
More LessWith reference to the first Principle of the International Code of Nomenclature of Bacteria, which emphasizes stability of names, it is proposed that the original adjectival form of the specific epithet be conserved in the reclassification of Bacteroides forsythus to the new genus Tannerella. Thus, Tannerella forsythensis Sakamoto et al. 2002 should be Tannerella forsythia Sakamoto et al. 2002 corrig., gen. nov., comb. nov., and we put forward a Request for an Opinion to the Judicial Commission regarding this correction.
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- Isep
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The collapse of the two-kingdom system, the rise of protistology and the founding of the International Society for Evolutionary Protistology (ISEP)
More LessThis paper provides a brief summary of the rise and acceptance of protistology as a modern, realistic approach to the evolutionary relationships and classification of unicellular eukaryotic organisms as well as the origins of the multicellular groups. The apparent reasons for the renaissance of this 19th-century concept in the 1970s are reviewed, with electron microscopy considered to be the key factor, strongly reinforced by molecular phylogenetic studies in the 1980s and 1990s. The foundation of the International Society for Evolutionary Protistology in 1975 accompanied this major alteration in the view of biological diversity. The current status of protistology relative to protozoology and phycology is discussed.
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Phragmoplastin, green algae and the evolution of cytokinesis
More LessPhragmoplast-mediated cell division characterizes the land plants in the streptophyte lineage and some species of the green algal orders Coleochaetales, Charales and Zygnematales that are basal to that lineage. This type of cell division is generally not found in the other green plant lineage, the chlorophyte algae. A well-developed phragmoplast-type cell division has been documented, however, in two subaerial green algae (Cephaleuros parasiticus and Trentepohlia odorata) belonging to the order Trentepohliales – an order that molecular sequence data place unequivocally within the chlorophytes rather than streptophytes. Is the phragmoplast-mediated cell division of the Trentepohliales a case of homology or non-homology? To gain more insight into this question, we are exploring the potential phylogenetic information inferred from gene sequences of phragmoplastin, a dynamin-like protein that has been associated with cell-plate formation during phragmoplast-mediated cytokinesis in land plants. Primers for green algae were designed based on an available phragmoplastin sequence from soybean and yielded PCR amplifications from the trentepohlialean green algae Trentepohlia and Cephaleuros and the leafy liverwort Bazzania. These are the first published data for phragmoplastins in algae and liverworts. Analysis of phragmoplastin gene sequences in chlorophyte and streptophyte green algae may help to chart the evolution of the development of the phragmoplast.
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Comparison of plastid 16S rRNA (rrn16) genes from Helicosporidium spp.: evidence supporting the reclassification of Helicosporidia as green algae (Chlorophyta)
More LessThe Helicosporidia are invertebrate pathogens that have recently been identified as non-photosynthetic green algae (Chlorophyta). In order to confirm the algal nature of the genus Helicosporidium, the presence of a retained chloroplast genome in Helicosporidia cells was investigated. Fragments homologous to plastid 16S rRNA (rrn16) genes were amplified successfully from cellular DNA extracted from two different Helicosporidium isolates. The fragment sequences are 1269 and 1266 bp long, are very AT-rich (60·7 %) and are similar to homologous genes sequenced from non-photosynthetic green algae. Maximum-parsimony, maximum-likelihood and neighbour-joining methods were used to infer phylogenetic trees from an rrn16 sequence alignment. All trees depicted the Helicosporidia as sister taxa to the non-photosynthetic, pathogenic alga Prototheca zopfii. Moreover, the trees identified Helicosporidium spp. as members of a clade that included the heterotrophic species Prototheca spp. and the mesotrophic species Chlorella protothecoides. The clade is always strongly supported by bootstrap values, suggesting that all these organisms share a most recent common ancestor. Phylogenetic analyses inferred from plastid 16S rRNA genes confirmed that the Helicosporidia are non-photosynthetic green algae, close relatives of the genus Prototheca (Chlorophyta, Trebouxiophyceae). Such phylogenetic affinities suggest that Helicosporidium spp. are likely to possess Prototheca-like organelles and organelle genomes.
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Highly organized structure in the non-coding region of the psbA minicircle from clade C Symbiodinium
More LessThe chloroplast genes of dinoflagellates are distributed among small, circular dsDNA molecules termed minicircles. In this paper, we describe the structure of the non-coding region of the psbA minicircle from Symbiodinium. DNA sequence was obtained from five Symbiodinium strains obtained from four different coral host species (Goniopora tenuidens, Heliofungia actiniformis, Leptastrea purpurea and Pocillopora damicornis), which had previously been determined to be closely related using LSU rDNA region D1/D2 sequence analysis. Eight distinct sequence blocks, consisting of four conserved cores interspersed with two metastable regions and flanked by two variable regions, occurred at similar positions in all strains. Inverted repeats (IRs) occurred in tandem or ‘twin’ formation within two of the four cores. The metastable regions also consisted of twin IRs and had modular behaviour, being either fully present or completely absent in the different strains. These twin IRs are similar in sequence to double-hairpin elements (DHEs) found in the mitochondrial genomes of some fungi, and may be mobile elements or may serve a functional role in recombination or replication. Within the central unit (consisting of the cores plus the metastable regions), all IRs contained perfect sequence inverses, implying they are highly evolved. IRs were also present outside the central unit but these were imperfect and possessed by individual strains only. A central adenine-rich sequence most closely resembled one in the centre of the non-coding part of Amphidinium operculatum minicircles, and is a potential origin of replication. Sequence polymorphism was extremely high in the variable regions, suggesting that these regions may be useful for distinguishing strains that cannot be differentiated using molecular markers currently available for Symbiodinium.
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Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies
More LessPhylogenetic analysis of small and large subunits of rDNA genes suggested that Foraminifera originated early in the evolution of eukaryotes, preceding the origin of other rhizopodial protists. This view was recently challenged by the analysis of actin and ubiquitin protein sequences, which revealed a close relationship between Foraminifera and Cercozoa, an assemblage of various filose amoebae and amoeboflagellates that branch in the so-called crown of the SSU rDNA tree of eukaryotes. To further test this hypothesis, we sequenced a fragment of the largest subunit of the RNA polymerase II (RPB1) from five foraminiferans, two cercozoans and the testate filosean Gromia oviformis. Analysis of our data confirms a close relationship between Foraminifera and Cercozoa and points to Gromia as the closest relative of Foraminifera.
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The excavate protozoan phyla Metamonada Grassé emend. (Anaeromonadea, Parabasalia, Carpediemonas, Eopharyngia) and Loukozoa emend. (Jakobea, Malawimonas): their evolutionary affinities and new higher taxa
More LessIt is argued here that the anaerobic protozoan zooflagellate Parabasalia, Carpediemonas and Eopharyngia (diplomonads, enteromonads, retortamonads) constitute a holophyletic group, for which the existing name Trichozoa is adopted as a new subphylum. Ancestrally, Trichozoa probably had hydrogenosomes, stacked Golgi dictyosomes, three anterior centrioles and one posterior centriole: the typical tetrakont pattern. It is also argued that the closest relatives of Trichozoa are Anaeromonada (Trimastix, oxymonads), and the two groups are classified as subphyla of a revised phylum Metamonada. Returning Parabasalia and Anaeromonadea to Metamonada, as in Grassé's original classification, simplifies classification of the kingdom Protozoa by reducing the number of phyla within infrakingdom Excavata from five to four. Percolozoa (Heterolobosea plus Percolatea classis nov.) and Metamonada are probably both ancestrally quadriciliate with a kinetid of four centrioles attached to the nucleus; the few biciliates among them are probably secondarily derived. Metamonada ancestrally probably had two divergent centriole pairs, whereas, in Percolozoa, all four centrioles are parallel. It is suggested that Discicristata (Percolozoa, Euglenozoa) are holophyletic, ancestrally with two parallel centrioles. In the phylum Loukozoa, Malawimonadea classis nov. is established for Malawimonas (with a new family and order also) and Diphyllatea classis nov., for Diphylleida (Diphylleia, Collodictyon), is transferred back to Apusozoa. A new class, order and family are established for the anaerobic, biciliate, tricentriolar Carpediemonas, transferring it from Loukozoa to Trichozoa because of its triply flanged cilia; like Retortamonas, it may be secondarily biciliate – its unique combination of putative hydrogenosomes and flanged cilia agree with molecular evidence that Carpediemonas is sister to Eopharyngia, diverging before their ancestor lost hydrogenosomes and acquired a cytopharynx. Removal of anaeromonads and Carpediemonas makes Loukozoa more homogeneous, being basically biciliate, aerobic and free-living, in contrast to Metamonada. A new taxon-rich rRNA tree supports holophyly of Discicristata and Trichozoa strongly, holophyly of Metamonada and Excavata and paraphyly of Loukozoa weakly. Mitochondria were probably transformed into hydrogenosomes independently in the ancestors of lyromonad Percolozoa and Metamonada and further reduced in the ancestral eopharyngian. Evidence is briefly discussed that Metamonada and all other excavates share a photosynthetic ancestry with Euglenozoa and are secondarily non-photosynthetic, as predicted by the cabozoan hypothesis for a single secondary symbiogenetic acquisition of green algal plastids by the last common ancestor of Euglenozoa and Cercozoa. Excavata plus core Rhizaria (Cercozoa, Retaria) probably form an ancestrally photophagotrophic clade. The origin from a benthic loukozoan ancestor of the characteristic cellular features of Percolozoa and Euglenozoa through divergent adaptations for feeding on or close to surfaces is also discussed.
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Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota)
More LessAn overview of the controversial proposal for the major eukaryote taxon ‘Excavata’ is presented. Excavata is predicted to include at least ten distinct groups: jakobids, Malawimonas, Trimastix, Carpediemonas, retortamonads, diplomonads, Heterolobosea, oxymonads, parabasalids and Euglenozoa. These ‘excavates' have broadly similar flagellar apparatus organizations, for which a ‘universal’ terminology is provided. Most, but not all, of these organisms share a distinctive suspension-feeding groove, as well as some or all of a set of seven other proposed cytoskeletal apomorphies. Cladistic analyses of morphological data do not resolve high-level relationships within Excavata. Excavate-rich molecular phylogenies recover some robust clades, but do not support or strongly refute the monophyly of Excavata. A partial classification for excavates is presented, with phylogenetic diagnoses for Excavata and for two novel taxon names, Fornicata (Carpediemonas, retortamonads, diplomonads) and Preaxostyla (Trimastix, oxymonads).
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 69 (2019)
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