- Volume 56, Issue 6, 2006
Volume 56, Issue 6, 2006
- New Taxa
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- Proteobacteria
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Thalassomonas agarivorans sp. nov., a marine agarolytic bacterium isolated from shallow coastal water of An-Ping Harbour, Taiwan, and emended description of the genus Thalassomonas
More LessA marine agarolytic bacterium, designated strain TMA1T, was isolated from a seawater sample collected in a shallow-water region of An-Ping Harbour, Taiwan. It was non-fermentative and Gram-negative. Cells grown in broth cultures were straight or curved rods, non-motile and non-flagellated. The isolate required NaCl for growth and exhibited optimal growth at 25 °C and 3 % NaCl. It grew aerobically and was incapable of anaerobic growth by fermenting glucose or other carbohydrates. Predominant cellular fatty acids were C16 : 0 (17.5 %), C17 : 1 ω8c (12.8 %), C17 : 0 (11.1 %), C15 : 0 iso 2-OH/C16 : 1 ω7c (8.6 %) and C13 : 0 (7.3 %). The DNA G+C content was 41.0 mol%. Phylogenetic, phenotypic and chemotaxonomic data accumulated in this study revealed that the isolate could be classified in a novel species of the genus Thalassomonas in the family Colwelliaceae. The name Thalassomonas agarivorans sp. nov. is proposed for the novel species, with TMA1T (=BCRC 17492T=JCM 13379T) as the type strain.
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Azospirillum melinis sp. nov., a group of diazotrophs isolated from tropical molasses grass
More LessFifteen bacterial strains isolated from molasses grass (Melinis minutiflora Beauv.) were identified as nitrogen-fixers by using the acetylene-reduction assay and PCR amplification of nifH gene fragments. These strains were classified as a unique group by insertion sequence-PCR fingerprinting, SDS-PAGE protein patterns, DNA–DNA hybridization, 16S rRNA gene sequencing and morphological characterization. Phylogenetic analysis of the 16S rRNA gene indicated that these diazotrophic strains belonged to the genus Azospirillum and were closely related to Azospirillum lipoferum (with 97.5 % similarity). In all the analyses, including in addition phenotypic characterization using Biolog MicroPlates and comparison of cellular fatty acids, this novel group was found to be different from the most closely related species, Azospirillum lipoferum. Based on these data, a novel species, Azospirillum melinis sp. nov., is proposed for these endophytic diazotrophs of M. minutiflora, with TMCY 0552T (=CCBAU 5106001T=LMG 23364T=CGMCC 1.5340T) as the type strain.
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Psychrobacter cryohalolentis sp. nov. and Psychrobacter arcticus sp. nov., isolated from Siberian permafrost
Three Gram-negative, non-motile, non-pigmented, oxidase-positive coccobacilli capable of growth at temperatures from −10 to 30 °C and salinities of 0 to 1.7 M NaCl were isolated from Siberian permafrost and characterized. Both 16S rRNA and gyrB gene sequencing studies placed the isolates in the Gammaproteobacteria within the genus Psychrobacter. However, with higher bootstrap values and reproducible tree topologies, gyrB represented a more reliable phylogenetic marker for the taxonomy of Psychrobacter species. DNA–DNA hybridization data supported gyrB tree topologies and established two relatedness groups within the three isolates; neither of these groups was related at the species level to any previously described Psychrobacter species. The two groups of isolates could be differentiated phenotypically from 13 previously described Psychrobacter species using API strips. These results support the existence of two novel species of Psychrobacter, for which we propose the names Psychrobacter cryohalolentis sp. nov. (type strain K5T=DSM 17306T=VKM B-2378T) and Psychrobacter arcticus sp. nov. (type strain 273-4T=DSM 17307T=VKM B-2377T).
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Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera
A heterotrophic, antibiotic-producing bacterium, strain T5T, was isolated from the German Wadden Sea, located in the southern region of the North Sea. Sequence analysis of the 16S rRNA gene of this strain demonstrated close affiliation with Roseobacter gallaeciensis BS107T (99 % similarity), but the results of genotypic (DNA–DNA hybridization and DNA G+C content) and phenotypic characterization revealed that strain T5T represents a novel species. The novel organism is strictly aerobic, Gram-negative, rod-shaped, motile and forms brown-pigmented colonies. Strain T5T produces the antibiotic tropodithietic acid throughout the exponential phase which inhibits the growth of bacteria from different taxa, as well as marine algae. Strain T5T requires sodium ions and utilizes a wide range of substrates, including oligosaccharides, sugar alcohols, organic acids and amino acids. The DNA G+C content is 55.7 mol%. Comparative 16S rRNA gene sequence analysis revealed that strains T5T and Roseobacter gallaeciensis BS107T group with Leisingera methylohalidivorans as their closest described relative within the Roseobacter clade (97.9 and 97.6 % sequence similarity, respectively) and with Ruegeria algicola (96.6 and 96.5 % similarity, respectively) of the Alphaproteobacteria. Comparison of strains T5T and Roseobacter gallaeciensis BS107T with Roseobacter denitrificans and Roseobacter litoralis showed striking differences in 16S rRNA gene sequence similarities, chemical composition, pigmentation, presence of bacteriochlorophyll a and antibiotic production. On the basis of these results, it is proposed that Roseobacter gallaeciensis is reclassified as the type species of a new genus, Phaeobacter, as Phaeobacter gallaeciensis comb. nov. (type strain BS107T=CIP 105210T=ATCC 700781T=NBRC 16654T=DSM 17395T). Strain T5T (=LMG 22475T=DSM 16374T) is proposed as the type strain of a novel species of this genus, Phaeobacter inhibens sp. nov. At the same time, emended descriptions are provided of the genera Roseobacter, Ruegeria and Leisingera, as well as reclassifying Ruegeria algicola as the type species of a new genus, Marinovum, with the name Marinovum algicola comb. nov.
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Tetrathiobacter mimigardefordensis sp. nov., isolated from compost, a betaproteobacterium capable of utilizing the organic disulfide 3,3′-dithiodipropionic acid
In this study, a novel betaproteobacterium, strain DPN7T, was isolated under mesophilic conditions from compost because of its capacity to utilize the organic disulfide 3,3′-dithiodipropionic acid. Analysis of the 16S rRNA gene sequence of strain DPN7T revealed 98.5 % similarity to that of Tetrathiobacter kashmirensis LMG 22695T. Values for sequence similarity to members of the genera Alcaligenes, Castellaniella and Taylorella, the nearest neighbours of the genus Tetrathiobacter, were about 95 % or less. The DNA G+C content of strain DPN7T was 55.1 mol%. The level of DNA–DNA hybridization between strain DPN7T and T. kashmirensis LMG 22695T was 41 %, whereas it was much lower between strain DPN7T and Alcaligenes faecalis LMG 1229T (7 %) or Castellaniella defragrans LMG 18538T (5 %). This genotypic divergence was supported by differences in biochemical and chemotaxonomic characteristics. For this reason, and because of the differences in the protein and fatty acid profiles, strain DPN7T should be classified within a novel species of Tetrathiobacter, for which the name Tetrathiobacter mimigardefordensis sp. nov. is proposed. The type strain is strain DPN7T (=DSM 17166T=LMG 22922T).
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Herbaspirillum hiltneri sp. nov., isolated from surface-sterilized wheat roots
The genus Herbaspirillum of the Betaproteobacteria mainly comprises diazotrophic bacteria with a potential for endophytic and systemic colonization of a variety of plants. The plant-associated bacterial isolates N3T, N5 and N9 were derived from surface-sterilized wheat roots. After phylogenetic analysis of 16S rRNA gene sequence data the isolates could be allocated to the genus Herbaspirillum, and 99.9 % similarity to the sequence of Herbaspirillum lusitanum P6-12T was found. A set of 16S rRNA gene-targeted oligonucleotide probes was developed for the identification of the three novel isolates and H. lusitanum (Hhilu446), and for the specific detection of several other Herbaspirillum species described recently. For higher phylogenetic resolution, the 23S rRNA gene sequences of all members of the genus was sequenced and used to construct a phylogenetic tree. Isolates N3T, N5 and N9 formed a group that was distinct from all other Herbaspirillum species. In addition, isolate N3T and H. lusitanum P6-12T exhibited a DNA–DNA hybridization value of only 25 %. The value for DNA–DNA hybridization between N3T and other members of the genus Herbaspirillum was between 14 and 32 %; DNA–DNA hybridization between strain N3T and isolates N5 and N9 produced values above 95 %. This places the three isolates as representatives of a novel species within the genus Herbaspirillum. A Biolog GN2 assay supported this conclusion. The major fatty acids were C16 : 1 ω7c, C16 : 0 and C18 : 1 ω7c, and the DNA G+C content ranged from 60.9 to 61.5 mol%. Therefore these three isolates should be classified within a novel species, for which the name Herbaspirillum hiltneri sp. nov. is proposed. The type strain is N3T (=DSM 17495T=LMG 23131T).
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Rubellimicrobium thermophilum gen. nov., sp. nov., a red-pigmented, moderately thermophilic bacterium isolated from coloured slime deposits in paper machines
Six red-pigmented strains of the Alphaproteobacteria with optimal growth between 45 and 54 °C were previously isolated from coloured biofilms in two fine-paper machines and one pulp dryer. The strains were found to be resistant to 15 p.p.m. 2,2-dibromo-3-nitrilopropionamide, a common industrial biocide. 16S RNA gene sequence similarity of the isolates was 99.7–100 %. Ribotyping using the restriction enzymes PvuII and EcoRI showed that four of the isolates (C-lvk-R2A-1, C-lvk-R2A-2T, C-R2A-52d and C-R2A-5d) belong to a single species. 16S rRNA gene-based phylogenetic analysis revealed that, together with Rhodobacter blasticus ATCC 33485T, the isolates form a deep line of descent (94.7–94.9 % sequence similarity) within the family Rhodobacteraceae loosely affiliated with the Rhodobacter/Paracoccus clade. The isolates were strictly aerobic and oxidase-positive (catalase was weakly positive) and utilized a wide range of substrates including pentoses, hexoses, oligosaccharides and sugar alcohols. The predominant constituents in their cellular fatty acid profiles were C19 : 0 cyclo ω8c (39–44 %), C18 : 0 (21–24 %) and C16 : 0 (21–23 %). Fatty acids present in smaller amounts included C18 : 1 ω7c, C10 : 0 3-OH, C18 : 1 ω7c 11-methyl, C20 : 2 ω6,9c and C17 : 0 cyclo, amongst others. Polar lipids included diphosphatidylglycerol, phosphatidylcholine and an unidentified aminolipid, but not phosphatidylethanolamine. Carotenoid pigments were synthesized but bacteriochlorophyll a was not. The polyamine patterns consisted of the major compounds putrescine, spermidine and sym-homospermidine. The major respiratory lipoquinone was ubiquinone Q-10. The DNA G+C content was 69.4–70.2 mol%. On the basis of the phylogenetic and phenotypic evidence, the biofilm isolates were classified in a new genus, Rubellimicrobium gen. nov.; four of the isolates are assigned to the type species, Rubellimicrobium thermophilum gen. nov., sp. nov. Strain C-lvk-R2A-2T (=CCUG 51817T=DSM 16684T=HAMBI 2421T) is the type strain of Rubellimicrobium thermophilum.
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Stenotrophomonas dokdonensis sp. nov., isolated from soil
More LessA Gram-negative, rod-shaped, Stenotrophomonas-like bacterial strain, DS-16T, was isolated from soil from Dokdo, Korea, and subjected to a polyphasic taxonomic study. Strain DS-16T grew optimally at pH 6.0–7.0 and 30 °C in the presence of 0.5 % (w/v) NaCl. It contained Q-8 as the predominant ubiquinone and iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1 ω9c as the major fatty acids. The DNA G+C content was 65.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-16T joined the cluster comprising Stenotrophomonas species. The levels of 16S rRNA gene sequence similarity between strain DS-16T and the type strains of Stenotrophomonas species ranged from 95.5 to 97.5 %. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness of strain DS-16T, demonstrated that this novel strain differs from Stenotrophomonas species with validly published names. On the basis of phenotypic, phylogenetic and genetic data, strain DS-16T (=KCTC 12543T=CIP 108839T) should be classified in the genus Stenotrophomonas as a member of a novel species, for which the name Stenotrophomonas dokdonensis sp. nov. is proposed.
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Rhodoblastus sphagnicola sp. nov., a novel acidophilic purple non-sulfur bacterium from Sphagnum peat bog
An isolate of purple non-sulfur bacteria was obtained from an acidic Sphagnum peat bog and designated strain RST. The colour of cell suspensions of this bacterium growing in the light under anaerobic conditions is purplish red. Cells of strain RST are rod-shaped, 0.8–1.0 μm wide and 2.0–6.0 μm long, motile by means of polar flagella, reproduce by budding and have a tendency to form rosette-like clusters in older cultures. The cells contain lamellar intracytoplasmic membranes underlying, and parallel to, the cytoplasmic membrane. The photosynthetic pigments are bacteriochlorophyll a and carotenoids; the absorption spectrum of living cells shows maxima at 377, 463, 492, 527, 592, 806 and 867 nm. The cells grow photoheterotrophically under anaerobic or microaerobic conditions with various organic carbon sources or grow photolithoautotrophically with H2 and CO2. Strain RST is a moderately acidophilic organism exhibiting growth at pH values between 4.8 and 7.0 (with an optimum at pH 5.2–5.5). The major fatty acids are 16 : 1ω7c and 18 : 1ω7c; the major quinones are Q-10 and Q-9. The DNA G+C content of strain RST is 62.6 mol%. Analysis of the 16S rRNA gene sequence revealed that the novel isolate is most closely related (97.3 % sequence similarity) to the type strain ATCC 25092T of the moderately acidophilic purple non-sulfur bacterium Rhodoblastus acidophilus, formerly named Rhodopseudomonas acidophila. However, in contrast to Rbl. acidophilus, strain RST is not capable of aerobic growth in the dark, has no spirilloxanthin among the carotenoids and differs in the pattern of substrate utilization. The value for DNA–DNA hybridization between strain RST and Rbl. acidophilus ATCC 25092T is only 22 %. Thus, strain RST represents a novel species of the genus Rhodoblastus, for which the name Rhodoblastus sphagnicola sp. nov. is proposed. Strain RST (=DSM 16996T=VKM B-2361T) is the type strain.
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- Eukaryotic Micro-Organisms
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Diversity within the current algal species Prototheca zopfii: a proposal for two Prototheca zopfii genotypes and description of a novel species, Prototheca blaschkeae sp. nov.
More LessIn order to clarify the intraspecies taxonomic position of the non-photosynthetic algal species Prototheca zopfii, as well as the aetiology of bovine mammary protothecosis, a selection of P. zopfii strains isolated from clinical cases of protothecal mastitis and from various environmental habitats was characterized using a polyphasic molecular approach. Based on sequence analysis of the 18S rRNA gene, which showed distinct differences between the three currently known biotypes or ‘variants’, specific oligonucleotides were designed and used in biotype-specific PCRs. Furthermore, the pattern of cellular fatty acids was evaluated. Typing by means of these techniques revealed that the previously defined biotypes of P. zopfii were clearly different. Based on sequence analysis, the pattern of fatty acids and physiological characteristics, it is proposed that biotype 3 should be reclassified as representing a novel species, Prototheca blaschkeae sp. nov. (type strain, RZIII-3T=SAG 2064T). Furthermore, it is proposed that P. zopfii merits reclassification as a species comprising at least two genotypes that in future could probably be considered to represent two subspecies.
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Four psychrotolerant species with high chemical diversity consistently producing cycloaspeptide A, Penicillium jamesonlandense sp. nov., Penicillium ribium sp. nov., Penicillium soppii and Penicillium lanosum
Penicillium jamesonlandense is a novel species from Greenland that grows exceptionally slowly at 25 °C and has an optimum temperature for growth of 17–18 °C. The novel species is more psychrotolerant than any other Penicillium species described to date. Isolates of this novel species produce a range of secondary metabolites with a high chemical diversity, represented by kojic acid, penicillic acid, griseofulvin, pseurotin, chrysogine, tryptoquivalins and cycloaspeptide. Penicillium ribium, another novel psychrotolerant species from the Rocky Mountains, Wyoming, USA, produces asperfuran, kojic acid and cycloaspeptide. Originally reported from an unidentified Aspergillus species isolated from Nepal, cycloaspeptide A is reported here for the first time from the two novel Penicillium species and two known psychrotolerant species with high chemical diversity, Penicillium soppii and Penicillium lanosum. All species, except P. ribium, produce a combination of cycloaspeptide and griseofulvin. However, P. ribium (3/5 strains) produced the precursor to griseofulvin, norlichexanthone. The type strain of Penicillium jamesonlandense sp. nov. is DAOM 234087T (=IBT 21984T=IBT 24411T=CBS 102888T) and the type strain of Penicillium ribium sp. nov. is DAOM 234091T (=IBT 16537T=IBT 24431T).
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- Other Gram-Positive Bacteria
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Sinococcus qinghaiensis gen. nov., sp. nov., a novel member of the order Bacillales from a saline soil in China
A Gram-positive, non-spore-forming isolate, designated YIM 70212T, was isolated from a hypersaline soil sample collected from Qinghai, north-west China. Cells of the isolate were orange-pigmented, motile cocci with multiple flagella. A polyphasic taxonomic investigation was carried out on the isolate. The organism grew at 10–45 °C and pH 7.5–11.0, with optimum growth at 28 °C and pH 8.0–9.5. Strain YIM 70212T grew optimally in the presence of 10 % NaCl, KCl or MgCl2.6H2O and growth was observed in 1–25 % NaCl, KCl or MgCl2.6H2O. The peptidoglycan type was A1γ. Ribose and minor amounts of galactose were detected as the whole-cell sugars. MK-5 was the only menaquinone. The major cellular fatty acids were ai-C15 : 0 (52.4 %) and ai-C17 : 0 (26.5 %). The DNA G+C content was 47.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 70212T formed a distinct lineage within the order Bacillales and was most closely related to members of the genus Marinococcus, showing 16S rRNA gene sequence similarity levels of 91.0–91.4 %. Based on the high 16S rRNA gene sequence divergence and differences in phenotypic characteristics, it is proposed that the unknown strain be classified in a novel genus and species with the name Sinococcus qinghaiensis gen. nov., sp. nov.; the type strain of Sinococcus qinghaiensis is YIM 70212T (=KCTC 3943T=DSM 17008T).
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Caldalkalibacillus thermarum gen. nov., sp. nov., a novel alkalithermophilic bacterium from a hot spring in China
A thermophilic, alkaliphilic and catalase-positive bacterium, designated strain HA6T, was isolated from a hot spring in China. The strain was aerobic and chemo-organotrophic and grew optimally at 60 °C, pH 8.5 and 1.5 % (w/v) NaCl. The cells were Gram-positive rods, forming single terminal endospores. The predominant cellular fatty acids were iso-C15 : 0 and iso-C17 : 0. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The genomic DNA G+C content was 45.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain HA6T formed a distinct lineage within the family Bacillaceae and was most closely related to Bacillus horti K13T and Bacillus smithii DSM 4216T, with sequence similarities of 91.8 and 93.1 %, respectively. On the basis of its physiological and molecular properties, strain HA6T should be placed in a novel genus and species, for which the name Caldalkalibacillus thermarum gen. nov., sp. nov. is proposed. The type strain of Caldalkalibacillus thermarum is strain HA6T (=CGMCC 1.4242T=JCM 13486T).
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Leuconostoc pseudoficulneum sp. nov., isolated from a ripe fig
More LessSix strains of lactic acid bacteria (LAB) were isolated from a ripe fig. These strains constituted a highly homogeneous, but distinct, cluster that was separate from other LAB species in a polyphasic approach including dot-blot DNA–DNA hybridization, SDS-PAGE whole-cell protein profiling, carbohydrate fermentation ability, growth characteristics, enzymic profiling, pulsed-field gel electrophoresis macrorestriction analysis and RFLPs. Phylogenetic analysis based on 16S rRNA gene sequencing positioned a representative strain, LC51T, in a distinct line of descent within the recently described clade comprising Leuconostoc ficulneum, Leuconostoc fructosum and Leuconostoc durionis; L. ficulneum was its closest neighbour (98 % sequence similarity). DNA–DNA hybridization values and chemotaxonomic and biochemical characteristics, including enzymic profiles detected with API ZYM microtubes, confirmed that this group of strains is distinct from L. ficulneum and represents a novel species within the genus Leuconostoc. Taking into account the common origin and phylogenetic proximity, the name Leuconostoc pseudoficulneum sp. nov. is proposed. Strain LC51T (=DSM 15468T=CECT 5759T) is the type strain; the DNA G+C content of this strain is 44.5 mol%.
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Ornithinibacillus gen. nov., with the species Ornithinibacillus bavariensis sp. nov. and Ornithinibacillus californiensis sp. nov.
More LessA Gram-positive, aerobic, rod-shaped, motile, endospore-forming bacterium was isolated from pasteurized milk from Bavaria, Germany. 16S rRNA gene sequence similarities indicated that strain WSBC 24001T was most closely related to Virgibacillus species (95.3–96.1 %), Oceanobacillus species (95.6–95.7 %), Bacillus firmus IAM 12464T (95.5 %) and Bacillus niacini IFO 15566T (95.2 %). However, strain WSBC 24001T showed the highest level of sequence similarity to an unnamed strain, MB-9T (97.6 %), which was isolated from coastal surface sediments in California. Hence, this strain was included in our study. The genomic DNA G+C contents of strains WSBC 24001T and MB-9T were 36.4 mol and 40.8 mol%, respectively. The major respiratory quinone of both strains was menaquinone MK-7 and the peptidoglycan type was A4β (l-orn←d-Asp). The polar lipid profiles of these strains contained a predominance of diphosphatidylglycerol and moderate to minor amounts of phosphatidylglycerol, an unknown phospholipid and an unknown aminophospholipid. However, strain WSBC 24001T could be distinguished from strain MB-9T by the presence of an unknown lipid. The fatty acid profiles of the two strains comprised mainly iso- and anteiso-branched acids, but showed some significant quantitative differences in the amounts of certain acids. The DNA–DNA relatedness value (15.5 %) clearly demonstrated that strains WSBC 24001T and MB-9T are representatives of two different species. On the basis of their phylogenetic position and morphological, physiological and chemotaxonomic properties, a novel genus is proposed, Ornithinibacillus gen. nov., with two novel species, the type species Ornithinibacillus bavariensis sp. nov. (type strain WSBC 24001T=DSM 15681T=CCM 7096T) and Ornithinibacillus californiensis sp. nov. (type strain MB-9T=DSM 16628T=CCM 7237T).
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Reclassification of Thermoanaerobium acetigenum as Caldicellulosiruptor acetigenus comb. nov. and emendation of the genus description
More LessAlthough the type species of the genus Thermoanaerobium, Thermoanaerobium brockii, was transferred to Thermoanaerobacter, Thermoanaerobium acetigenum was not transferred. Therefore, Thermoanaerobium acetigenum should be reclassified. Based on 16S rRNA gene sequence analysis and re-examination of physiological properties of the type strain, X6BT (=DSM 7040T=ATCC BAA-1149T), we propose that Thermoanaerobium acetigenum should be reclassified as Caldicellulosiruptor acetigenus comb. nov. Strain X6BT contains two separate 16S rRNA genes bracketing another species in the phylogenetic 16S rRNA gene-based tree.
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Mycobacterium arupense sp. nov., a non-chromogenic bacterium isolated from clinical specimens
Several Mycobacterium-like organisms related to the Mycobacterium terrae complex have been isolated from clinical samples. In the clinical microbiology laboratory, partial 16S rRNA gene sequencing (approximately the first 500 bp) rather than full 16S rRNA gene sequencing is often used to identify Mycobacterium species. Partial 16S rRNA gene sequence analysis revealed 100 % similarity between 65 clinical isolates and Mycobacterium sp. MCRO 6 (GenBank accession no. X93032). Even after sequencing the nearly full-length 16S rRNA gene, closest similarity was only 99.6 % to Mycobacterium nonchromogenicum ATCC 19530T. Sequencing of the nearly full-length 16S rRNA gene, the 16S–23S internal transcribed spacer region and the hsp65 gene did not reveal genotypic identity with the type strains of M. nonchromogenicum, M. terrae or Mycobacterium triviale. Although sequence analysis suggested that these clinical isolates represented a novel species, mycolic acid analysis by HPLC failed to distinguish them from M. nonchromogenicum. Therefore, phenotypic analysis including growth characterization, antibiotic susceptibility testing and biochemical testing was performed. These strains from clinical samples should be recognized as representing a novel species of the genus Mycobacterium, for which the name Mycobacterium arupense sp. nov. is proposed. The type strain is AR30097T (=ATCC BAA-1242T=DSM 44942T).
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- Evolution, Phylogeny And Biodiversity
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Phylogenetic relationships within the order Halobacteriales inferred from 16S rRNA gene sequences
More LessPhylogenetic relationships within the halophilic archaea were inferred from comparisons of the 16S rRNA gene sequences from 61 strains, representing 18 genera with validly published names within the order Halobacteriales. Trees produced using distance-matrix (least-squares and neighbour-joining) methods affirm with strong bootstrap support that the members of the order Halobacteriales are a monophyletic group. Ten genera were supported as monophyletic groups [Haloarcula, Halobiforma, Halococcus, Haloferax, Halorubrum, Halosimplex (multiple sequences from a single strain), Natrialba, Natrinema, Natronococcus and Natronorubrum] and eight genera were represented by a single strain (Halobacterium, Halobaculum, Halogeometricum, Halomicrobium, Halorhabdus, Halosimplex, Natronobacterium and Natronomonas). The genus Haloterrigena was always paraphyletic, and the phylogenetic placement of and sister groups to Halobacterium and Natronomonas could not be resolved. Both treeing methods failed to resolve the deep branching patterns within the order Halobacteriales and the relationships between the major clades. Additional representation from the currently monospecific genera and/or the use of other macromolecules may be required to resolve the relationships within the order Halobacteriales.
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Phylogenetic history of plastid-targeted proteins in the peridinin-containing dinoflagellate Heterocapsa triquetra
More LessThe evolutionary history and relationship between plastids of dinoflagellate algae and apicomplexan parasites have been controversial both because the organelles are unusual and because their genomes contain few comparable genes. However, most plastid proteins are encoded in the host nucleus and targeted to the organelle, and several of these genes have proved to have interesting and informative evolutionary histories. We have used expressed sequence tag (EST) sequencing to generate gene sequence data from the nuclear genome of the dinoflagellate Heterocapsa triquetra and inferred phylogenies for the complete set of identified plastid-targeted proteins. Overall, dinoflagellate plastid proteins are most consistently related to homologues from the red algal plastid lineage (not green) and, in many of the most robust cases, they branch with other chromalveolate algae. In resolved phylogenies where apicomplexan data are available, dinoflagellates and apicomplexans are related. We also identified two cases of apparent lateral, or horizontal, gene transfer, one from the green plastid lineage and one from a bacterial lineage unrelated to plastids or cyanobacteria.
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Phylogenetic position of Multicilia marina and the evolution of Amoebozoa
Recent molecular phylogenetic studies have led to the erection of the phylum Amoebozoa, uniting naked and testate lobose amoebae, the mycetozoan slime moulds and amitochondriate amoeboid protists (Archamoebae). Molecular data together with ultrastructural evidence have suggested a close relationship between Mycetozoa and Archamoebae, classified together in the Conosea, which was named after the cone of microtubules that, when present, is characteristic of their kinetids. However, the relationships of conoseans to other amoebozoans remain unclear. Here, we obtained the complete small-subunit (SSU) rRNA gene sequence (2746 bp) of the enigmatic, multiflagellated protist Multicilia marina, which has formerly been classified either in a distinct phylum, Multiflagellata, or among lobose amoebae. Our study clearly shows that Multicilia marina belongs to the Amoebozoa. Phylogenetic analyses including 60 amoebozoan SSU rRNA gene sequences revealed that Multicilia marina branches at the base of the Conosea, together with another flagellated amoebozoan, Phalansterium solitarium, as well as with Gephyramoeba sp., Filamoeba nolandi and two unidentified amoebae. This is the first report showing strong support for a clade containing all flagellated amoebozoans and we discuss the position of the root of the phylum Amoebozoa in the light of this result.
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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 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)