- Volume 52, Issue 2, 2002
Volume 52, Issue 2, 2002
- Articles
-
-
-
The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.
More LessEukaryotes and archaebacteria form the clade neomura and are sisters, as shown decisively by genes fragmented only in archaebacteria and by many sequence trees. This sisterhood refutes all theories that eukaryotes originated by merging an archaebacterium and an alpha-proteobacterium, which also fail to account for numerous features shared specifically by eukaryotes and actinobacteria. I revise the phagotrophy theory of eukaryote origins by arguing that the essentially autogenous origins of most eukaryotic cell properties (phagotrophy, endomembrane system including peroxisomes, cytoskeleton, nucleus, mitosis and sex) partially overlapped and were synergistic with the symbiogenetic origin of mitochondria from an alpha-proteobacterium. These radical innovations occurred in a derivative of the neomuran common ancestor, which itself had evolved immediately prior to the divergence of eukaryotes and archaebacteria by drastic alterations to its eubacterial ancestor, an actinobacterial posibacterium able to make sterols, by replacing murein peptidoglycan by N-linked glycoproteins and a multitude of other shared neomuran novelties. The conversion of the rigid neomuran wall into a flexible surface coat and the associated origin of phagotrophy were instrumental in the evolution of the endomembrane system, cytoskeleton, nuclear organization and division and sexual life-cycles. Cilia evolved not by symbiogenesis but by autogenous specialization of the cytoskeleton. I argue that the ancestral eukaryote was uniciliate with a single centriole (unikont) and a simple centrosomal cone of microtubules, as in the aerobic amoebozoan zooflagellate Phalansterium. I infer the root of the eukaryote tree at the divergence between opisthokonts (animals, Choanozoa, fungi) with a single posterior cilium and all other eukaryotes, designated 'anterokonts' because of the ancestral presence of an anterior cilium. Anterokonts comprise the Amoebozoa, which may be ancestrally unikont, and a vast ancestrally biciliate clade, named 'bikonts'. The apparently conflicting rRNA and protein trees can be reconciled with each other and this ultrastructural interpretation if long-branch distortions, some mechanistically explicable, are allowed for. Bikonts comprise two groups: corticoflagellates, with a younger anterior cilium, no centrosomal cone and ancestrally a semi-rigid cell cortex with a microtubular band on either side of the posterior mature centriole; and Rhizaria [a new infrakingdom comprising Cercozoa (now including Ascetosporea classis nov.), Retaria phylum nov., Heliozoa and Apusozoa phylum nov.], having a centrosomal cone or radiating microtubules and two microtubular roots and a soft surface, frequently with reticulopodia. Corticoflagellates comprise photokaryotes (Plantae and chromalveolates, both ancestrally with cortical alveoli) and Excavata (a new protozoan infrakingdom comprising Loukozoa, Discicristata and Archezoa, ancestrally with three microtubular roots). All basal eukaryotic radiations were of mitochondrial aerobes; hydrogenosomes evolved polyphyletically from mitochondria long afterwards, the persistence of their double envelope long after their genomes disappeared being a striking instance of membrane heredity. I discuss the relationship between the 13 protozoan phyla recognized here and revise higher protozoan classification by updating as subkingdoms Lankester's 1878 division of Protozoa into Corticata (Excavata, Alveolata; with prominent cortical microtubules and ancestrally localized cytostome--the Parabasalia probably secondarily internalized the cytoskeleton) and Gymnomyxa [infrakingdoms Sarcomastigota (Choanozoa, Amoebozoa) and Rhizaria; both ancestrally with a non-cortical cytoskeleton of radiating singlet microtubules and a relatively soft cell surface with diffused feeding]. As the eukaryote root almost certainly lies within Gymnomyxa, probably among the Sarcomastigota, Corticata are derived. Following the single symbiogenetic origin of chloroplasts in a corticoflagellate host with cortical alveoli, this ancestral plant radiated rapidly into glaucophytes, green plants and red algae. Secondary symbiogeneses subsequently transferred plastids laterally into different hosts, making yet more complex cell chimaeras--probably only thrice: from a red alga to the corticoflagellate ancestor of chromalveolates (Chromista plus Alveolata), from green algae to a secondarily uniciliate cercozoan to form chlorarachneans and independently to a biciliate excavate to yield photosynthetic euglenoids. Tertiary symbiogenesis involving eukaryotic algal symbionts replaced peridinin-containing plastids in two or three dinoflagellate lineages, but yielded no major novel groups. The origin and well-resolved primary bifurcation of eukaryotes probably occurred in the Cryogenian Period, about 850 million years ago, much more recently than suggested by unwarranted backward extrapolations of molecular 'clocks' or dubious interpretations as 'eukaryotic' of earlier large microbial fossils or still more ancient steranes. The origin of chloroplasts and the symbiogenetic incorporation of a red alga into a corticoflagellate to create chromalveolates may both have occurred in a big bang after the Varangerian snowball Earth melted about 580 million years ago, thereby stimulating the ensuing Cambrian explosion of animals and protists in the form of simultaneous, poorly resolved opisthokont and anterokont radiations.
-
-
-
Phylogenetic analysis of Xanthomonas species based upon 16S-23S rDNA intergenic spacer sequences.
More LessPhylogenetic relationships of 17 species of Xanthomonas were assessed based on analysis of 16S-23S rDNA intergenic spacer (ITS) sequences; a higher level of resolution was obtained than that revealed by 16S rDNA analysis. ITS sequences varied in size from 492 to 578 nt within the genus and the similarity among sequences ranged from 63 to 99%. Major differences were found for the hyacinthi group, which included Xanthomonas albilineans, Xanthomonas hyacinthi, Xanthomonas sacchari, Xanthomonas theicola and Xanthomonas translucens. A common ITS structure with tRNA(Ala) and tRNA(Ile) embedded within the sequence was found for all ITS sequences of Xanthomonas species and for Stenotrophomonas maltophilia. These tRNAs were highly conserved and divided the ITS sequence into three regions (ITS1, ITS2 and ITS3). ITS1 and ITS2 sequences of Xanthomonas species showed mean similarities of 87.1 and 86.8%, respectively, and differences consisted of substitution and addition/deletion of 1-5 nt. ITS2 showed remarkable variation in sequence length: most species had an ITS2 of 19-20 nt, whereas a long insertion of 51-56 nt was found in Xanthomonas codiaei, X. hyacinthi, Xanthomonas melonis, X. theicola and X. translucens. For ITS3 the most striking alteration was seen in X. hyacinthi, which showed a large deletion of 44 nt. The ITS phylogenetic tree grouped Xanthomonas species into six major clusters. Cluster I included Xanthomonas arboricola, Xanthomonas axonopodis, Xanthomonas bromi, Xanthomonas campestris, X. campestris pv. gardneri, Xanthomonas cassavae, X. codiaei, Xanthomonas cucurbitae, Xanthomonas fragariae, Xanthomonas hortorum, X. melonis, Xanthomonas oryzae, Xanthomonas pisi, Xanthomonas vasicola and Xanthomonas vesicatoria. The species X. albilineans, X. sacchari, X. hyacinthi, X. theicola and X. translucens represented distinct clusters (II-VI). Topology of the 16S-23S rDNA ITS phylogenetic tree was very similar to that of the 16S rDNA tree reported previously, but more clusters were discriminated because of the higher level of diversity among the ITS sequences (16.2%) compared with the 16S rDNA sequences (1.8%).
-
-
-
Pseudomonas mosselii sp. nov., a novel species isolated from clinical specimens.
Twenty-two fluorescent pseudomonad strains of clinical origin received as Pseudomonas fluorescens (10 strains), Pseudomonasputida (10 strains) and Pseudomonas sp. (2 strains), and 33 type strains of the genus Pseudomonas were studied by numerical analysis based on 280 phenotypic characters. Twelve of the 22 clinical isolates clustered within a specific group, cluster IV. The other strains clustered within groups containing well-characterized fluorescent Pseudomonas species or did not cluster. Strains belonging to cluster IV were phenotypically different from all other clusters and subclusters of fluorescent pseudomonads. DNA-DNA hybridization showed that cluster IV corresponded to a genomic group sharing 72-100% DNA relatedness. DNA-DNA hybridization values with 67 strains representing 30 species of the genus Pseudomonas sensu stricto, including six recently described species (Pseudomonas veronii, Pseudomonas rhodesiae, Pseudomonas libanensis, 'Pseudomonas orientalis', 'Pseudomonas cedrella' and Pseudomonas monteilii), were below 49%, the value found for P. monteilii. The DNA G+C content of the type strain was 63 mol%. Comparison of the 16S rRNA gene sequence of a representative strain of cluster IV (CFML 90-83T) with sequences of other strains of the genus Pseudomonas revealed that strain CFML 90-83T was part of the P. fluorescens intrageneric cluster. On the basis of phenotypic, DNA-DNA hybridization and phylogenetic analyses, a novel species, Pseudomonas mosselii sp. nov., is proposed for the 12 strains of cluster IV. The type strain is P. mosselii CFML 90-83T (= ATCC BAA-99T = CIP 105259T). The P. mosselii strains are phenotypically homogeneous and can be differentiated from other fluorescent species by several phenotypic features, including pyoverdine typing.
-
-
-
Comamonas koreensis sp. nov., a non-motile species from wetland in Woopo, Korea.
A bacterial strain, designated YH12T, was isolated from a wetland sample collected from Woopo, Republic of Korea, and characterized using a polyphasic approach. Analysis of 16S rDNA indicated that the isolate formed a monophyletic clade with the members of the genus Comamonas. The closest phylogenetic relative among the valid species was Comamonas testosteroni, with 96.6% 16S rDNA similarity. The chemotaxonomic properties of the wetland isolate supported its membership of the genus Comamonas, as it contained ubiquinone Q-8 as a major respiratory quinone and hexadecanoic, methylene-hexadecanoic and octadecenoic acids as major cellular fatty acids. The G+C content of the DNA was 66 mol%. The isolate is a gram-negative, non-pigmented, rod-shaped, oxidase- and catalase-positive, non-motile, non-endospore-forming and non-fermentative bacterium. The phenotypic properties of the isolate were compared with those of the type strains of Comamonas terrigena, C. testosteroni and Delftia acidovorans. A number of tests, including motility, can differentiate our isolate from related taxa. On the basis of the 16S rDNA phylogenetic, chemotaxonomic and phenotypic evidence given in this study, it is proposed that strain YH12T (= KCTC 12005T = IMSNU 11158T) be assigned as the type strain of a novel species of the genus Comamonas, Comamonas koreensis sp. nov.
-
-
-
Bartonella bovis Bermond et al. sp. nov. and Bartonella capreoli sp. nov., isolated from European ruminants.
Two novel species of Bartonella isolated from European ruminants are described. Bartonella capreoli sp. nov. was isolated from the blood of roe-deer (Capreolus capreolus) captured in Chizé, France. The type strain is IBS 193T (= CIP 106691T = CCUG 43827T). It is distinct from another European ruminant isolate that originated from a cow from a French herd of 430 dairy cattle. The latter isolate belongs to a novel species named Bartonella bovis Bermond et al. sp. nov. The type strain is strain 91-4T (= CIP 106692T = CCUG 43828T). The two bacteria appeared as small, fastidious, aerobic, oxidase-negative, gram-negative rods. Their biochemical properties were similar to those of members of the genus Bartonella. The sequences of the 16S rRNA and citrate synthase genes obtained from the two type strains were highly related to sequences of the different Bartonella species. Hybridization values when testing type strains of recognized Bartonella species, obtained with the nuclease/trichloroacetic acid method, support the creation of two novel species.
-
-
-
Desulfotomaculum thermobenzoicum subsp. thermosyntrophicum subsp. nov., a thermophilic, syntrophic, propionate-oxidizing, spore-forming bacterium.
More LessFrom granular sludge from a laboratory-scale upflow anaerobic sludge bed reactor operated at 55 degrees C with a mixture of volatile fatty acids as feed, a novel anaerobic, moderately thermophilic, syntrophic, spore-forming bacterium, strain TPO, was enriched on propionate in co-culture with Methanobacterium thermoautotrophicum Z245. The axenic culture was obtained by using pyruvate as the sole source of carbon and energy. The cells were straight rods with pointed ends and became lens-shaped when sporulation started. The cells were slightly motile. The optimum growth temperature was 55 degrees C and growth was possible between 45 and 62 degrees C. The pH range for growth of strain TPO was 6-8, with an optimum at pH 7-7.5. Propionate was converted to acetate, CO2 and CH4 by a co-culture of strain TPO with Methanobacterium thermoautotrophicum Z245. In pure culture, strain TPO could grow fermentatively on benzoate, fumarate, H2/CO2, pyruvate and lactate. Sulphate could serve as inorganic electron acceptor when strain TPO was grown on propionate, lactate, pyruvate and H2/CO2. The G+C content was 53.7 mol%. Comparison of 16S rDNA sequences revealed that strain TPO is related to Desulfotomaculum thermobenzoicum (98%) and Desulfotomaculum thermoacetoxidans (98%). DNA-DNA hybridization revealed 88.2% reassociation between strain TPO and D. thermobenzoicum and 83.8% between strain TPO and D. thermoacetoxidans. However, both organisms differ physiologically from strain TPO and are not capable of syntrophic propionate oxidation. It is proposed that strain TPO should be classified as new subspecies of D. thermobenzoicum as D. thermobenzoicum subsp. thermosyntrophicum.
-
-
-
Gelria glutamica gen. nov., sp. nov., a thermophilic, obligately syntrophic, glutamate-degrading anaerobe.
More LessA novel anaerobic, gram-positive, thermophilic, spore-forming, obligately syntrophic, glutamate-degrading bacterium, strain TGO(T), was isolated from a propionate-oxidizing methanogenic enrichment culture. The axenic culture was obtained by growing the bacterium on pyruvate. Cells were rod-shaped and non-motile. The optimal temperature for growth was 50-55 degrees C and growth occurred between 37 and 60 degrees C. The pH range for growth was 5.5-8 with optimum growth at pH 7. In pure culture, strain TGO(T) could grow on pyruvate, lactate, glycerol and several sugars. In co-culture with the hydrogenotrophic methanogen Methanobacterium thermautotrophicum strain Z-245, strain TGO(T) could grow on glutamate, proline and Casamino acids. Glutamate was converted to H2, CO2, propionate and traces of succinate. Strain TGO(T) was not able to utilize sulphate, sulphite, thiosulphate, nitrate or fumarate as electron acceptors. The G+C content was 33.8 mol%. Sequence analysis of the 16S rDNA revealed that strain TGO(T) belongs to the thermophilic, endospore-forming anaerobes, though no close relations were found. Its closest relations were Moorella glycerini (92%) and Moorella thermoacetica (90%). Strain TGOT had an unusually long 16S rDNA of more than 1700 bp. The additional base pairs were found as long loops in the V1, V7 and V9 regions of the 16S rDNA. However, the loops were not found in the 16S rRNA. The name Gelria glutamica gen. nov., sp. nov. is proposed for strain TGO(T).
-
-
-
Rhodococcus jostii sp. nov., isolated from a medieval grave.
More LessThe taxonomic position of a bacterial strain isolated from the femur of the remains of Jost Lucemburský, margrave in Moravia, Brno (Czech Republic), was investigated by phenotypic, chemotaxonomic and molecular taxonomic methods. The chemotaxonomic characteristics, including the cell-wall amino acid and sugar compositions, the quinone system and the fatty acid profile, were in good agreement with those of the genus Rhodococcus. The G+C content of the DNA was 67.4 mol%. Comparative 16S rRNA gene sequencing demonstrated that the unknown strain represents a distinct line of descent within the genus Rhodococcus. The nearest relatives of the bacterium were Rhodococcus opacus and Rhodococcus percolatus. The unknown bacterium was readily distinguished from these species by using phenotypic methods. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Rhodococcus jostii sp. nov. The type strain is strain IFO 16295T (= CCM 4760T).
-
-
-
Paenibacillus chinjuensis sp. nov., a novel exopolysaccharide-producing bacterium.
More LessA novel exopolysaccharide-producing bacterium (WN9T) was isolated from Chinju, Korea, and was identified as a member of the genus Paenibacillus on the basis of phenotypic characteristics and phylogenetic inference based on 16S rDNA sequence. This organism is a facultatively anaerobic, endospore-forming rod. The diamino acid found in the peptidoglycan is meso-diaminopimelic acid. The predominant menaquinone is MK-7. The major cellular fatty acid is anteiso-C15:0. The G+C content is 53 mol%. The phylogenetic tree shows that strain WN9T falls within the radiation of a cluster comprising the Paenibacillus species. The levels of 16S rDNA similarity between strain WN9T and the type strains of validly described Paenibacillus species are 92.1-95.8%. Strain WN9T is clearly distinguishable from some phylogenetically related Paenibacillus species on the basis of DNA-DNA relatedness data and phenotypic characters. Therefore, on the basis of these data, a novel species of the genus Paenibacillus, Paenibacillus chinjuensis sp. nov., is proposed. The type strain is strain WN9T (= KCTC 8951PT = JCM 10939T).
-
-
-
Reclassification of Eubacterium formicigenerans Holdeman and Moore 1974 as Dorea formicigenerans gen. nov., comb. nov., and description of Dorea longicatena sp. nov., isolated from human faeces.
More LessTwo strains of a gram-positively staining, obligately anaerobic, non-spore-forming, rod-shaped bacterium, designated strains 111-13A and 111-35T, were isolated from human faeces. Analysis of the 16S rRNA gene sequences indicated that these strains were members of the Clostridium coccoides rRNA group of organisms. The nearest relatives of the unknown bacterium were Eubacterium formicigenerans (having a sequence similarity of 94%) and an uncultured bacterium (similarity > 99%). Characterization studies indicated that the unidentified faecal bacterium was biochemically distinct from Eubacterium formicigenerans, members of the Clostridium coccoides group and all other described Eubacterium species. On the basis of the data from these studies, it is proposed that the hitherto unknown rod-shaped bacterium be designated a species of a novel genus, namely Dorea longicatena gen. nov., sp. nov., and that Eubacterium formicigenerans be transferred to this genus as Dorea formicigenerans gen. nov., comb. nov.
-
-
-
Ilyobacter insuetus sp. nov., a fermentative bacterium specialized in the degradation of hydroaromatic compounds.
More LessThe mesophilic, anaerobic bacterium strain VenChi2T was isolated with quinic acid (1,3,4,5-tetrahydroxy-cyclohexane-1-carboxylic acid) as the sole source of carbon and energy. Of more than 30 substrates tested, only quinic acid and shikimic acid (3,4,5-trihydroxy-1-cyclohexene-1-carboxylic acid) were utilized, yielding acetate, propionate, butyrate, H2 and CO2 as fermentation products. Sugars, alcohols, (di-)carboxylic acids, amino acids and aromatic compounds were not fermented and no external electron acceptors were used. Strain VenChi2T is a gram-negative, strictly anaerobic, coccoid rod; it does not employ the classical hydroaromatic pathway of aerobic bacteria for the degradation of hydroaromatic compounds (no aromatic intermediates involved). Comparative 16S and 23S rDNA sequence analyses placed strain VenChi2T in the fusobacteria phylum, with the closest relatives among species of the genera Ilyobacter and Propionigenium. The results indicate that, disregarding the taxonomically misplaced Ilyobacter delafieldii, which is a member of the clostridia, the validly described Ilyobacter and Propionigenium species are phylogenetically intermixed. Based on its phenotypic properties, strain VenChi2T (= DSM 6831T = ATCC BAA-291T) is assigned to the genus Ilyobacter as the type strain of a novel species, Ilyobacter insuetus sp. nov.
-
-
-
Biochemical and genetic evidence for the transfer of Mycobacterium tuberculosis subsp. caprae Aranaz et al. 1999 to the species Mycobacterium bovis Karlson and Lessel 1970 (approved lists 1980) as Mycobacterium bovis subsp. caprae comb. nov.
More LessWe propose to replace the species designation Mycobacterium tuberculosis subsp. caprae (Aranaz et al. 1999) by Mycobacterium bovis subsp. caprae comb. nov., since isolates of this subspecies share their main growth, biochemical and genetic characteristics with M. bovis and not with M. tuberculosis. These include negative biochemical test results for niacin accumulation and nitrate reduction as well as genetic features like the presence of an M. bovis-specific mutation in the oxyR locus, absence of the mtp40 sequence and a specific mutation in the gyrB gene, all of which have been described as characteristics for the differentiation of M. bovis. The only obvious biochemical character that differentiates the caprae subtype from other M. bovis isolates is susceptibility to pyrazinamide (PZA), which is due to the lack of a single point mutation in the pncA gene. However, susceptibility to PZA among clinical isolates of M. bovis isolates has been reported previously and, thus, may now been explained by a PZA-susceptible subspecies of M. bovis. We conclude that the species designation M. tuberculosis subsp. caprae is misleading and not correct in light of the biochemical and genetic characteristics and propose that the accurate designation of isolates of this subtype is M. bovis subsp. caprae.
-
-
-
Helicobacter nemestrinae ATCC 49396T is a strain of Helicobacter pylori (Marshall et al. 1985) Goodwin et al. 1989, and Helicobacter nemestrinae Bronsdon et al. 1991 is therefore a junior heterotypic synonym of Helicobacter pylori.
More LessHelicobacter nemestrinae Bronsdon et al. 1991, a gastric helicobacter species isolated from a pigtailed macaque, is thought to be the species most closely related to the important human pathogen Helicobacter pylori. The only available strain of this taxon is the type strain, ATCC 49396T. We sequenced seven housekeeping genes and two flagellin genes for H. nemestrinae ATCC 49396T. If ATCC 49396T were a separate species, these sequences should have been distinct from those of H. pylori. Instead, all sequences clustered together with sequences obtained previously for 20 or more H. pylori isolates from diverse geographical locations. The 16S rDNA sequence differed from that reported previously for this strain by 38 nucleotides and was most similar to that of H. pylori 85D08 (accession no. U00769), which was isolated from a rhesus macaque. It differed by less than 1% from 16S rDNA sequences of numerous other H. pylori strains, including the type strain, NCTC 11637T (= ATCC 43504T). These data indicate that the strain currently distributed as H. nemestrinae ATCC 49396T is really a strain of H. pylori and that H. nemestrinae Bronsdon et al. 1991 is a junior heterotypic synonym of Helicobacter pylori (Marshall et al. 1985) Goodwin et al. 1989.
-
-
-
Propionivibrio limicola sp. nov., a fermentative bacterium specialized in the degradation of hydroaromatic compounds, reclassification of Propionibacter pelophilus as Propionivibrio pelophilus comb. nov. and amended description of the genus Propionivibrio.
More LessStrain GolChi1T, a mesophilic, anaerobic bacterium, was isolated with quinic acid (1,3,4,5-tetrahydroxy-cyclohexane-1-carboxylic acid) as the sole source of carbon and energy. Of more than 30 substrates tested, only the hydroaromatic compounds quinic acid and shikimic acid (3,4,5-trihydroxy-1-cyclohexene-1-carboxylic acid) were utilized, yielding acetate and propionate as the only fermentation products. Sugars, alcohols, (di-)carboxylic acids, amino acids and aromatic compounds were not fermented and no external electron acceptors were used. Strain GolChi1T is a gram-negative, rod-shaped, aerotolerant anaerobe that possesses superoxide dismutase; it does not employ the classical hydroaromatic pathway of aerobic bacteria for the degradation of hydroaromatic compounds (no aromatic intermediates involved). 16S-rRNA-based phylogenetic analyses revealed a common origin of this isolate and Rhodocyclus, Propionibacter and Propionivibrio species. High sequence similarity (> 96%) and phenotypic traits indicated a closer relationship between strain GolChi1T and the type species of the monospecific genera Propionivibrio and Propionibacter but, due to its phenotypic properties, strain GolChi1T could not be assigned conclusively to either of these taxa. We propose (i) the amended description of the genus Propionivibrio, (ii) the reclassification of Propionibacter pelophilus Meijer et al. 1999 as Propionivibrio pelophilus comb. nov. and (iii) designation of Propionivibrio limicola sp. nov., with the type strain GolChi1T (= DSM 6832T = ATCC BAA-290T).
-
-
-
Classification of three airborne bacteria and proposal of Hymenobacter aerophilus sp. nov.
Three aerobic, gram-negative, rod-shaped, non-spore-forming, red-pigmented, airborne bacteria (I/26-Cor1T, I/32A-Cor1 and I/74-Cor2) collected in the Museo Correr (Venice, Italy) were investigated to determine their taxonomic status by analysing their biochemical, physiological and chemotaxonomic features and the G+C content of genomic DNA and by comparing their genomic fingerprints. Additionally, the almost complete 16S rRNA gene sequence of strain I/26-Cor1T was analysed. The three strains were nearly identical in their morphological, physiological, biochemical and chemotaxonomic properties. The strains contained a menaquinone system with the predominant menaquinone MK-7 and a fatty acid profile with C15:0 anteiso, C15:0 iso and C16:1 predominant. Phosphatidylethanolamine and several unidentified lipids were detected in the polar lipid profiles. The polyamine pattern consisted of sym-homospermidine as the major compound. meso-Diaminopimelic acid was found as the characteristic cell-wall diamino acid. The DNA base composition of the three strains ranged from 60 to 63 mol% G+C. Phylogenetically, strain I/26-Cor1T was most closely related to Hymenobacter actinosclerus (95.8% 16S rRNA gene sequence similarity). Physiological and genomic characteristics indicated that the two strains I/26-Cor1T and I/32A-Cor1 are representatives of the same species. The phylogenetic distance to any validly described taxon as indicated by 16S rRNA gene sequence similarities demonstrates that I/26-Cor1T and I/32A-Cor1 represent a novel species, for which the name Hymenobacter aerophilus sp. nov. is proposed, with the type strain I/26-Cor1T (= DSM 13606T = LMG 19657T). I/32A-Cor1 (= DSM 13607 = LMG 19658) is another strain of the species Hymenobacter aerophilus. Since the taxonomic status of strain I/74-Cor2 within the genus Hymenobacter was not determined unambiguously, it is designated Hymenobacter sp. I/74-Cor2 (= DSM 13611 = LMG 19659).
-
-
-
Identification of isolates from soybean nodules in Xinjiang Region as Sinorhizobium xinjiangense and genetic differentiation of S. xinjiangense from Sinorhizobium fredii.
More LessEight fast-growing rhizobial isolates from Xinjiang soils were identified as Sinorhizobium xinjiangense by analyses of 16S rRNA gene sequences, SDS-PAGE of proteins, intergenic spacer sequences and DNA-DNA hybridization. Based on all of the results, these isolates and the reference strains for S. xinjiangense were a distinct genomic species, although the 16S rRNA genes were closely related to that of Sinorhizobium fredii.
-
-
-
Species distinction of the ascomycetous heterothallic yeast-like fungus Stephanoascus ciferrii complex: description of Candida allociferrii sp. nov. and reinstatement of Candida mucifera Kocková-Kratochvílová et Sláviková.
More LessThe nucleotide sequences of the 18S rRNA gene (rDNA) from nine strains of the heterothallic ascomycetous Stephanoascus ciferrii complex were determined and the strains were separated into three groups according to their sequences. 18S rDNA sequences were identical within the same group. In group A the 18S rDNA sequences had no introns; in group B there was one group I intron, Sc1506-1 at position 1506; and in group C there were two group I introns, Sc943 at position 943 and Sc1506-2 at position 1506. Sc1506-1 and Sc1506-2 at position 1506 exhibited 19 base differences but were very similar. Therefore, it is suggested that these introns existed in the common ancestor of groups B and C, and that they were vertically inherited. DNA similarity values showed that the strains within the same group were of identical species. Group B included the isotype strains of Stephanoascus ciferrii and the type strains of Candida ciferrii and Sporothrix catenata; this confirmed that group B strains correspond to Stephanoascus ciferrii and that Candida ciferrii and Sporothrix catenata are synonyms of Stephanoascus ciferrii. The single member of group C, strain IFO 10918T, corresponds to the type strain of Candida mucifera and was independent of the other tested strains. Thus, Candida mucifera should be regarded as an independent species from Stephanoascus ciferrii. It is suggested that group A strains might comprise a new Stephanoascus species, but since group A strains could not form asci by themselves in this study they are described as a new species for which the name Candida allociferrii sp. nov. (type strain IFO 10194T) is proposed.
-
-
-
Thermomonas haemolytica gen. nov., sp. nov., a gamma-proteobacterium from kaolin slurry.
Four aerobic, gram-negative bacterial strains isolated from kaolin slurry used in the production of paper were subjected to a polyphasic analysis and characterization to determine their taxonomic position. Analysis of the 16S rDNA sequences of the four strains revealed that they represent a new lineage within the gamma-Proteobacteria, related to the genera Xanthomonas, Pseudoxanthomonas, Stenotrophomonas, Luteimonas, Xylella and Rhodanobacter. Analysis of the quinone system, the polyamines, the fatty acids and the polar lipids revealed a combination of characteristics that is unique and not described for the phylogenetic relatives. The four strains contain a ubiquinone Q-8, spermidine as the major polyamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the predominant polar lipids, and a fatty acid profile with predominantly iso-branched fatty acids. The G+C content of the genomic DNA was determined to be within the narrow range 67.1-68.7 mol%. Determination of DNA relatedness, as well as riboprint band patterns and amplified fragment length polymorphism profiles, clearly demonstrated that the four strains are members of a single species. Antibiotic-susceptibility patterns were identical for the four strains. Although showing a high degree of similarites in physiological and biochemical patterns, each of the four strains could be distinguished from the others on the basis of a few biochemical characteristics. On the basis of the estimates of phylogenetic relationships derived from the 16S rDNA sequence analyses, the observed chemotaxonomic characteristics and other phenotypic traits, a new genus, Thermomonas gen. nov., and species, Thermomonas haemolytica sp. nov., are proposed for the strains A50-7-3T (= DSM 13605T = LMG 19653T), B 50-7-1 (= DSM 13598 = LMG 19655), D50-7-1 (= DSM 13610 = LMG 19656) and B50-8-1 (= DSM 13599 = LMG 19654), with strain A50-7-3T as the type strain.
-
-
-
Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the Bacteria from saltern crystallizer ponds.
Five brightly red-pigmented, motile, rod-shaped, extremely halophilic bacteria were isolated from saltern crystallizer ponds in Alicante (two strains) and Mallorca (three strains), Spain. They grew optimally at salt concentrations between 20 and 30% and did not grow below 15% salts. Thus, these isolates are among the most halophilic organisms known within the domain Bacteria. The temperature optimum was 37-47 degrees C. A single, yet to be identified pigment was present, with an absorption maximum at 482 nm and a shoulder at 506-510 nm. The G+C content of the DNA was 66.3-67.7 mol% and, together, they formed a homogeneous genomic group with DNA-DNA similarities above 70%. The 16S rRNA gene sequences were almost identical to sequences recovered earlier from the saltern biomass by amplification of bacterial small-subunit rRNA genes from DNA extracted from the environment. This phylotype, earlier described as 'Candidatus Salinibacter', was shown by fluorescence in situ hybridization to contribute between 5 and 25% of the prokaryote community of the saltern crystallizers. We have therefore succeeded in isolating a bacterium from the natural environment that, although being a major component of the community, was previously known by its phylotype only. Isolation of the organism now allows formal description of a novel genus and species, for which we propose the name Salinibacter ruber gen. nov., sp. nov. The type strain is strain M31T (= DSM 13855T = CECT 5946T).
-
-
-
16S-23S rDNA internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Fusobacterium.
The 16S-23S rDNA internal transcribed spacer (ITS) regions of all currently defined Fusobacterium species and related taxa such as Leptotrichia buccalis, Sebaldella termitidis and Streptobacillus moniliformans, were analysed to examine inter- and intraspecies as well as subspecies relationships. For the ITS-amplification, a new eubacterial universal primer pair was designed and used. The majority of the Fusobacterium strains, along with L. buccalis showed one major, and two to three weaker, distinct bands (short and long versions) with lengths of 800-830 bp and 1000-1100 bp. Nevertheless, six other patterns were also found within the genus Fusobacterium, demonstrating its heterogeneity. The ITS region was sequenced and found to consist both of conserved motifs, which functioned as a framework for alignment, and of variable sites, which provided high phylogenetic resolution. Analyses of the ITS-DNA sequences and ITS relative length (short version) allowed species and subspecies differentiation in most cases. The results confirmed the strikingly distant relationship between Fusobacterium prausnitzii and the genus Fusobacterium. Fusobacterium nucleatum subspecies, along with Fusobacterium naviforme, Fusobacterium simiae and Fusobacterium periodonticum, formed a cluster with an inherently high potential for diversification. Other clusters were formed by Fusobacterium necrophorum subspecies with Fusobacterium gonidaformans and by Fusobacterium varium with Fusobacterium mortiferum and Fusobacterium ulcerans. Fusobacterium russii as well as Fusobacterium perfoetens formed separate branches. Fusobacterium necrophorum subspp. necrophorum and funduliforme on the one hand, and Fusobacterium varium and Fusobacterium mortiferum on the other, were found to be very similar, even at the high-resolution ITS level.
-
-
-
Bacillus pycnus sp. nov. and Bacillus neidei sp. nov., round-spored bacteria from soil.
More LessBacillus sphaericus sensu lato currently consists of seven or more groups of unrelated taxa, one of which is B. sphaericus sensu stricto and another of which is Bacillus fusiformis. Members of two groups (groups 6 and 7), in common with all other B. sphaericus-like organisms, are unable to grow anaerobically or to use common hexoses, pentoses and hexitols as sources of carbon, have G+C contents of 34-36 mol % and form round spores. Groups 6 and 7 can be differentiated from other B. sphaericus-like organisms by low DNA relatedness and by variations in whole-cell fatty acid composition. Unique characteristics of group 6 include the ability to oxidize beta-hydroxybutyrate, the non-requirement for biotin and thiamin and failure to grow in 5% NaCl. Distinctive traits of group 7 include the inability to oxidize pyruvate and a requirement for biotin, thiamin and cystine for growth. These data show that groups 6 and 7 represent two novel species, for which the names Bacillus pycnus sp. nov. and Bacillus neidei sp. nov., respectively, are proposed; the corresponding type strains are NRRL NRS-1691T (= JCM 11075T) and NRRL BD-87T (= JCM 11077T).
-
-
-
Weissella kimchii sp. nov., a novel lactic acid bacterium from kimchi.
A gram-positive, catalase-negative, non-sporulating, facultatively anaerobic, short rod-shaped bacterium, with cells measuring 0.3-0.5 x 1-2 microm and designated strain CHJ3T, was isolated from partially fermented kimchi, a traditional Korean fermented vegetable food. The strain produced CO2 gas, D-lactate from glucose and dextran from sucrose and hydrolysed aesculin and arginine. It also fermented N-acetylglucosamine, amygdalin, arbutin, cellobiose, D-fructose, galactose, beta-gentiobiose, gluconate, D-glucose, maltose, D-mannose, salicin, sucrose and D-xylose. The G+C content of the DNA was 48.2 mol%. Phylogenetic analysis of 16S rRNA showed that strain CHJ3T is a member of the genus Weissella. The nearest phylogenetic relative of strain CHJ3T was Weissella confusa, with 16S rRNA similarity of 98.3%. However, strain CHJ3T could be differentiated from W. confusa on the basis of some phenotypic characteristics, analysis of whole-cell protein patterns and DNA-DNA hybridization data. These data suggest that strain CHJ3T be classified in the genus Weissella as a novel species, Weissella kimchii sp. nov. The type strain is CHJ3T (= KCCM 41287T = DSM 14295T = KCTC 3746T).
-
-
-
Pseudomonas lini sp. nov., a novel species from bulk and rhizospheric soils.
The taxonomic position of eight fluorescent Pseudomonas strains isolated from bulk and rhizospheric soils, and from water was examined. These eight strains clustered in one phenon together with Pseudomomas mandelii (CFBP 4844T), but could still be differentiated from this type strain by four phenotypic features. The eight stains exhibited internal DNA-DNA hybridization values ranging from 60 to 100%, with deltaTm below 5 degrees C (3.9 and 4.3 degrees C) for the lowest values (60 and 66%). The percentages of hybridization with type or reference strains of other Pseudomonas species tested ranged from 12 to 60% (deltaTm = 5.5 degrees C), indicating that the eight isolates studied constituted a discrete DNA homology group. Comparison of the 16S rDNA sequence of the strain representing this group (CFBP 5737T) with the sequences of other strains belonging to the genus Pseudomonas revealed that strain CFBP 5737T was a member of this genus and that these bacteria did not cluster with any previously described species of the genus Pseudomonas. The eight isolates belonged to two siderovars different from those described so far. On the basis of the results of phenotypic, DNA-DNA and phylogenetic analyses, and of siderotyping, a new species, Pseudomonas lini sp. nov. (type strain CFBP 5737T) is proposed.
-
-
-
Nocardiopsis halotolerans sp. nov., isolated from salt marsh soil in Kuwait.
A polyphasic taxonomic study of a halotolerant micro-organism, isolated from Kuwait salt marsh soil, revealed that this strain represents a novel Nocardiopsis species. The strain produced substrate and aerial mycelium, grew at 28-35 degrees C in salt concentrations of 0-15% and was slightly keratinolytic. Results of the 165 rDNA sequence comparison revealed that strain F100T clustered with strains of the genus Nocardiopsis. This is consistent with other data such as: (i) growth characteristics, i.e. the formation of a white to yellow aerial mycelium and the typical zig-zag form of hyphae, which fragment when ageing; (ii) the presence of DL-diaminopimelic acid and glucose plus ribose in whole-cell hydrolysates; (iii) the presence of phosphatidyl choline, phosphatidyl inositol, phosphatidyl glycerol, phosphatidyl methylethanolamine and diphosphatidyl glycerol in polar lipid extracts; (iv) the presence of menaquinones MK-10(H(0-6)) and MK-11(H(0-6)) in the non-polar fraction; (v) the presence of iso/anteiso-branched plus 10-methyl-branched fatty acids, showing the diagnostic combination for Nocardiopsis spp. of 14-methyl-hexadecanoic acid (18%), oleic acid (9%) and tuberculostearic acid (2%); and (v) the absence of mycolic acids. Analysis of 16S rDNA revealed that strain F100T represents a distinct taxon within Nocardiopsis. Based upon phenotypic differences to other members of the genus, a novel species, Nocardiopsis halotolerans sp. nov., is proposed. The type strain of the species is F100T (= DSM 44410T = NRRL B-24124T).
-
-
-
Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies.
More LessPhylogenetic trees showing the evolutionary relatedness of Enterobacteriaceae based upon gyrB and 16S rRNA genes were compared. Congruence among trees of these molecules indicates that the genomes of these species are not completely mosaic and that molecular systematic studies can be carried out. Phylogenetic trees based on gyrB sequences appeared to be more reliable at determining relationships among Serratia species than trees based on 16S rRNA gene sequences. gyrB sequences from Serratia species formed a monophyletic group validated by significant bootstrap values. Serratia fonticola had the most deeply branching gyrB sequence in the Serratia monophyletic group, which was consistent with its atypical phenotypic characteristics. Klebsiella and Enterobacter genera seemed to be polyphyletic, but the branching patterns of gyrB and 16S rRNA gene trees were not congruent. Enterobacter aerogenes was grouped with Klebsiella pneumoniae on the gyrB phylogenetic tree, which supports that this species could be transferred to the Klebsiella genus. Unfortunately, 16S rRNA and gyrB phylogenetic trees gave conflicting evolutionary relationships for Citrobacter freundii because of its unusual gyrB evolutionary process. gyrB lateral gene transfer was suspected for Hafnia alvei. Saturation of gyrB genes was observed by the pairwise comparison of Proteus spp., Providencia alcalifaciens and Morganella morganii sequences. Depending on their level of variability, 16S rRNA gene sequences were useful for describing phylogenetic relationships between distantly related Enterobacteriaceae, whereas gyrB sequence comparison was useful for inferring intra- and some intergeneric relationships.
-
-
-
Vibrio calviensis sp. nov., a halophilic, facultatively oligotrophic 0.2 microm-fiIterabIe marine bacterium.
More LessA gram-negative, facultatively anaerobic, straight to slightly curved rod-shaped bacterium (RE35F/12T) sensitive to vibriostatic agent O/129 was previously isolated from sea water (Western Mediterranean Sea, Bay of Calvi, Corsica, France) by 0.2 microm-membrane filtration. Strain RE35/F12T (= CIP 107077T = DSM 14347T) was facultatively oligotrophic, halophilic, required Na+ for growth and produced acid but no gas from D-glucose under anaerobic conditions. Comparative 165 rRNA gene-sequence analyses demonstrated that the bacterium is most closely related (94.3%) to Vibrio scophthalmi. Similarities to the sequences of all other established Vibrio species ranged from 93.6% (with Vibrio aestuarianus) to 90.7% (with Vibrio rumoiensis). Strain RE35/F12T occupies a distinct phylogenetic position; this is similar to the case of Vibrio hollisae, because RE35F/12T represents a relatively long subline of descent sharing a branching point with the outskirts species V. hollisae. The G+C content of the DNA was 49.5 mol%. Ubiquinone Q-8 was the main respiratory lipoquinone, and 16:1omega9cis, 16:0 and 18:1trans9, cis11 were the major cellular fatty acids, 16:1omega9cis being predominant. The polyamine pattern was characterized by the presence of the triamine sym-norspermidine. On the basis of the polyphasic information summarized above, a new Vibrio species is described for which the name Vibrio calviensis sp. nov. is proposed.
-
-
-
Saccharomonospora halophila sp. nov., a novel halophilic actinomycete isolated from marsh soil in Kuwait.
More LessAn actinomycete, strain 8T, was isolated from marsh soil in Kuwait. The strain was aerobic, gram-positive, halophilic and produced light blue to greyish aerial mycelium. The warty spores were sessile, occurring singly or in pairs on aerial mycelium. The mycelium was stable and did not fragment during ageing. Chemotaxonomic markers of the isolate were consistent with its classification as Saccharomonospora. The strain possessed meso-diaminopimelic acid as the diagnostic amino acid in the peptidoglycan. The diagnostic sugars were arabinose and galactose; polar lipids were phosphatidyl inositol, phosphatidyl ethanolamine, hydroxy-phosphatidyl ethanolamine, lyso-phosphatidyl ethanolamine and diphosphatidyl glycerol; the principal menaquinone was MK-9(H4); and the iso/anteiso-branched fatty acid pattern was combined with 10-methyl-branched and 2-hydroxy-branched fatty acids. Saccharomonospora cyanea DSM 44106T was the closest phylogenetic neighbour of strain 8T, showing 96.8% 16S rDNA sequence similarity. These data, together with distinct physiological traits, led to the conclusion that the novel isolate represents a new species within the genus Saccharomonospora for which the name Saccharomonospora halophila sp. nov. is proposed. The type strain is strain 8T (= DSM 44411T =NRRL B-24125T).
-
-
-
Stenotrophomonas acidaminiphila sp. nov., a strictly aerobic bacterium isolated from an upflow anaerobic sludge blanket (UASB) reactor.
Two of several strictly aerobic, mesophilic bacteria isolated from a lab-scale upflow anaerobic sludge blanket (UASB) reactor treating a petrochemical wastewater, strains AMX 17 and AMX 19T, were subjected to detailed taxonomic study. Cells were gram-negative, motile, non-sporulating, straight to curved rods with a polar flagellum. The isolates exhibited phenotypic traits of members of the genus Stenotrophomonas, including cellular fatty acid composition and the limited range of substrates that could be used. Sugars and many amino acids were utilized. Antibiotic susceptibility and physiological characteristics were determined. The DNA base composition was 66.9 mol% G+C. Phylogenetic analysis revealed that the nearest relatives were Stenotrophomonas maltophilia LMG 11114, Stenotrophomonas nitritireducens DSM 12575T and Pseudomonas pictorum ATCC 23328T (similarity of 98.1-98.8%). Xanthomonas species, S. maltophilia LMG 958T and Stenotrophomonas africana CIP 104854T showed high 16S rRNA sequence similarities (96.4-97.3%). The high similarity found in cellular fatty acid profiles and identical partial 16S rRNA sequences (500 bp) for strains AMX 17 and AMX 19T indicate that they belong to the same species. DNA-DNA hybridizations revealed respectively 26.7, 31, 65.8 and 43.6% homology between isolate AMX 19T and S. africana CIP 104854T, S. maltophilia CIP 60.77T, S. nitritireducens DSM 12575T and P. pictorum ATCC 23328T. These results allow the proposal of strain AMX 19T (= DSM 13117T = ATCC 700916T = CIP 106456T) as representative of a novel species of the genus Stenotrophomonas, with the name Stenotrophomonas acidaminiphila sp. nov.
-
-
-
Arthrobacter nasiphocae sp. nov., from the common seal (Phoca vitulina).
More LessAn unknown gram-positive, catalase-positive, strictly aerobic, rod-shaped bacterium was isolated from the nasal cavities of two common seals. Chemical analysis revealed the presence in the bacterium of a hitherto unknown cell-wall murein [type: L-Lys-L-Ala2-Gly(2-3)-L-Ala (Gly)]. Comparative 16S rRNA gene sequencing showed that the unidentified rod was related to the Arthrobacter group of organisms, although sequence divergence values of >3% from established members of this genus indicated that it represents a novel species. On the basis of phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium from seals (Phoca vitulina) be classified as a novel species, Arthrobacter nasiphocae sp. nov. The type strain of Arthrobacter nasiphocae is CCUG 42953T.
-
-
-
A mathematical method for determining genome divergence and species delineation using AFLP.
More LessThe delineation of bacterial species is presently achieved using direct DNA-DNA relatedness studies of whole genomes. It would be helpful to obtain the same genomically based delineation by indirect methods, provided that descriptions of individual genome composition of bacterial genomes are obtained and included in species descriptions. The amplified fragment length polymorphism (AFLP) technique could provide the necessary data if the nucleotides involved in restriction and amplification are fundamental to the description of genomic divergences. Firstly, in order to verify that AFLP analysis permits a realistic exploration of bacterial genome composition, the strong correspondence between predicted and experimental AFLP data was demonstrated using Agrobacterium strain C58 as a model system. Secondly, a method is proposed for determining current genome mispairing and evolutionary genome divergences between pairs of bacteria, based on arbitrary sampling of genomes by using AFLP. The measure of current genome mispairing was validated by comparison with DNA-DNA relatedness data, which itself correlates with base mispairing. The evolutionary genome divergence is the estimated rate of nucleotide substitution that has occurred since the strains diverged from a common ancestor. Current genome mispairing and evolutionary genome divergence were used to compare members of Agrobacterium, used as a model of closely related genomic species. A strong and highly significant correlation was found between calculated genome mispairing and DNA-DNA relatedness values within genomic species. The canonical 70% DNA-DNA hybridization value used to delineate genomic species was found to correspond to a range of current genome mispairing of 13-13.6%. These limits correspond to 0.097 and 0.104 nucleotide substitutions per site, respectively. In addition, experimental data showed that the large Ti and cryptic plasmids of Agrobacterium had little effect on the estimation of genome divergence. Evolutionary genome divergence was used for phylogenetic inferences. Data showed that members of the same genomic species clustered consistently, as supported by bootstrap resampling. On the basis of these results, it is proposed that the genomic delineation of bacterial species could be based, in future, on phylogenetic groups supported by bootstraps and genome descriptions of individual strains, obtained by AFLP analysis, recorded in accessible databases; this approach might eventually replace DNA-DNA hybridization studies.
-
-
-
Proposal of Ureaplasma parvum sp. nov. and emended description of Ureaplasma urealyticum (Shepard et al. 1974) Robertson et al. 2001.
The phenotypic and genotypic properties of Ureaplasma urealyticum (family Mycoplasmataceae, order Mycoplasmatales, class Mollicutes) are reviewed here. The 14 recognized serovar standard strains found in humans exhibit no serological cross-reactivity with ureaplasmas from other hosts and uniquely express human immuoglobulin A1 protease activity. However, they exhibit many characteristics which place them in two distinct clusters known as the parvo biovar (or biovar 1 or B) and the T960T biovar (or biovar 2 or A). Established phenotypic markers of the biovars include clustering of antigenic types, polypeptide patterns of whole-cell preparations, differential inhibition by manganese, and polymorphism among their ureases, pyrophosphatases and diaphorases. Established genotypic markers of the biovars are DNA-DNA hybridization of 60% between biovars, and distinctive RFLP patterns and genome sizes. Divergent nucleotide sequences of several highly conserved genes attest to the phylogenetic distinctiveness of the two biovars. PCRs founded upon the sequences for 16S rRNA, the 16S-23S rRNA intergenic regions, the genus-defining urease, the serovar-defining, multiple-banded antigen genes or randomly amplified polymorphic DNA tests differentiate the biovars unambiguously. With the availability of rapid, reliable and economical tests for biovar determination, it is now appropriate to propose that the taxonomic status of U. urealyticum be emended. Serovar standard strains exhibiting traits of biovar parvo (serovars 1, 3, 6 and 14) will be designated as a separate species, Ureaplasma parvum sp. nov., as befits its smaller genome size. The serovar 3 standard (strain 27T) will be the type strain of U. parvum and is represented by ATCC 27815T and NCTC 11736T. Serovar standard strains exhibiting traits of biovar T960T (2, 4, 5, 7, 8T, 9, 10, 11, 12 and 13) will retain the U. urealyticum designation and type strain, the serovar 8 standard (strain T960T), represented by ATCC 27618T and NCTC 10177T.
-
-
-
Obligate bacterial endosymbionts of Acanthamoeba spp. related to the beta-Proteobacteria: proposal of 'Candidatus Procabacter acanthamoebae' gen. nov., sp. nov.
All obligate bacterial endosymbionts of free-living amoebae currently described are affiliated with the alpha-Proteobacteria, the Chlamydiales or the phylum Cytophaga-Flavobacterium-Bacteroides. Here, six rod-shaped gram-negative obligate bacterial endosymbionts of clinical and environmental isolates of Acanthamoeba spp. from the USA and Malaysia are reported. Comparative 16S rDNA sequence analysis demonstrated that these endosymbionts form a novel, monophyletic lineage within the beta-Proteobacteria, showing less than 90% sequence similarity to all other recognized members of this subclass. 23S rDNA sequence analysis of two symbionts confirmed this affiliation and revealed the presence of uncommon putative intervening sequences of 146 bp within helix-25 that shared no sequence homology to any other bacterial rDNA. In addition, the 23S rRNA of these endosymbionts displayed one polymorphism at the target site of oligonucleotide probe BET42a that is conserved in all other sequenced beta-Proteobacteria. Intra-cytoplasmatic localization of the endosymbionts within the amoebal host cells was confirmed by electron microscopy and fluorescence in situ hybridization with a specific 16S rRNA-targeted oligonucleotide probe. Based on these findings, the provisional name 'Candidatus Procabacter acanthamoebae' is proposed for classification of a representative of the six endosymbionts of Acanthamoeba spp. studied in this report. Comparative 18S rDNA sequence analysis of the Acanthamoeba host cells revealed their membership with either Acanthamoeba 18S rDNA sequence type T5 (Acanthamoeba lenticulata) or sequence type T4, which comprises the majority of all Acanthamoeba isolates.
-
-
-
Paenibacillus graminis sp. nov. and Paenibacillus odorifer sp. nov., isolated from plant roots, soil and food.
More LessSixteen gram-positive endospore-forming bacteria previously isolated from soil, plant rhizospheres, plant roots and pasteurized pureed vegetables were studied to determine their taxonomic positions. The isolates were formerly identified as Bacillus circulans based on their biochemical characters using API galleries. Two of these strains, RSA19T and TOD45T, were recently assigned to the genus Paenibacillus based on phylogenetic analysis of their 16S rRNA (rrs) gene sequence. In the present work, the sixteen isolates were assigned to two genomospecies using DNA-DNA hybridization, in agreement with rrs gene sequence analysis. These genomospecies can also be differentiated on the basis of their cultural and biochemical characters into two novel species, for which the names Paenibacillus graminis sp. nov. (type strain RSA19T = ATCC BAA-95T = LMG 19080T) and Paenibacillus odorifer sp. nov. (type strain TOD45T = ATCC BAA-93T = LMG 19079T) are proposed.
-
-
-
Arcanobacterium hippocoleae sp. nov., from the vagina of a horse.
More LessA polyphasic taxonomic study was performed on a previously unidentified gram-positive, facultatively anaerobic, diphtheroid-shaped organism isolated from a vaginal discharge of a horse. Comparative 16S rRNA gene sequencing demonstrated that the strain was a member of the genus Arcanobacterium, but sequence divergence values of >4% with described species of this genus (viz: Arcanobacterium haemolyticum, Arcanobacterium bernardiae, Arcanobacterium phocae, Arcanobacterium pluranimalium and Arcanobacterium pyogenes) demonstrated that the isolate represented a novel species. The unknown bacterium was readily distinguished from other Arcanobacterium species by biochemical tests. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Arcanobacterium hippocoleae sp. nov. The type strain of A. hippocoleae is CCUG 44697T (= CIP 106850T).
-
-
-
Nocardiopsis compostus sp. nov., from the atmosphere of a composting facility.
More LessThree strains (KS8, KS9T and KS21), isolated from air samples near a composting facility, were subjected to taxonomic analyses (characterized using a polyphasic approach). Morphological and chemotaxonomic characteristics of the isolates were in agreement with those described for members of the genus Nocardiopsis. On the basis of 16S rRNA sequence comparison and phenotypic tests, KS21 clearly belonged to Nocardiopsis alba. KS8 and KS9T showed less than 98% 16S rRNA gene sequence similarity to any of the previously described Nocardiopsis species. The polar lipid profiles of both isolates consisted of four major compounds, phosphatidylmonomethylethanolamine, phosphatidylcholine, diphosphatidylglycerol and phosphatidylglycerol, in addition to two unknown phospholipids. The major menaquinones in KS8 and KS9T were MK-10(H8), MK-11(H8), MK-10(H6) and MK-12. Furthermore, MK-13, MK-11(H6), MK-9(H8) and MK-10(H4) could be detected in significant amounts. The fatty acid composition included iso- and anteiso-branched acids combined with tuberculostearic acid (Me18:0), straight-chain saturated (16:0, 18:0) and unsaturated (16:1, 17:1, 18:1) fatty acids. On the basis of these results, KS8 and KS9T clearly represent a novel species of the genus Nocardiopsis, for which the name Nocardiopsis compostus sp. nov. is proposed (type strain KS9T = DSM 44551T= NRRL B-24145T).
-
-
-
Emended descriptions of the genus Micrococcus, Micrococcus luteus (Cohn 1872) and Micrococcus lylae (Kloos et al. 1974).
Nine yellow-pigmented, spherical bacterial strains isolated from a medieval wall painting (strain D7), from indoor air (strains 3, 6, 7, 13C2, 38, 83 and 118) and from an activated-sludge plant (strain Ballarat) were classified by a polyphasic approach. Analyses of the 16S rRNA gene sequences of three representatives (strains D7, 118 and Ballarat) indicated that they all belong to the genus Micrococcus. The three isolates shared the highest sequence similarities with Micrococcus luteus DSM 20030T (97.9-98%), Micrococcus antarcticus AS 1.2372T (97.9-98.3%) and Micrococcus lylae DSM 20315T (97.5-97.9%). DNA-DNA reassociation studies clearly demonstrated that all nine isolates belong to the species M. luteus. However, neither their chemotaxonomic features nor their physiological and biochemical properties were consistent with those of M. luteus DSM 20030T. In contrast to M. luteus DSM 20030T, all isolates investigated possessed MK-8(H2) as the major respiratory quinone, and strain Ballarat had an A4alpha peptidoglycan type. On the basis of analyses of their Fourier transform-infrared spectroscopy spectra, isolates D7, 3, 6, 7, 13C2, 38, 83 and 118 could be grouped into a single cluster separate from M. luteus DSM 20030T, strain Ballarat and M. lylae DSM 20315T. In addition, all these isolates could be distinguished from M. luteus DSM 20030T by their ability to assimilate D-maltose, D-trehalose, DL-3-hydroxybutyrate, DL-lactate, pyruvate and L-histidine and to hydrolyse casein. Strains D7, 3, 6, 7, 13C2, 38, 83 and 118 differed from both M. luteus DSM 20030T and strain Ballarat by their ability to assimilate acetate, L-phenylalanine, L-serine and phenylacetate. Furthermore, REP-PCR fingerprinting yielded one common band for these strains, whereas this band was not observed for M. luteus DSM 20030T, strain Ballarat or M. lylae DSM 20315T. On the basis of these data, the species M. luteus can be divided into three biovars that are distinguished by several chemotaxonomic and biochemical traits: biovar I, represented by M. luteus DSM 20030T; biovar II, represented by strains D7 (= DSM 14234 = CCM 4959), 3, 6, 7, 13C2, 38, 83 and 118; and biovar III, represented by strain Ballarat (= DSM 14235 = CCM 4960). On the basis of the results generated in this study, emended descriptions of the genus Micrococcus and the species M. luteus and M. lylae are given.
-
-
-
Lactobacillus diolivorans sp. nov., a 1,2-propanediol-degrading bacterium isolated from aerobically stable maize silage.
Inoculation of maize silage with Lactobacillus buchneri (5 x 10(5) c.f.u. g(-1) of maize silage) prior to ensiling results in the formation of aerobically stable silage. After 9 months, lactic acid bacterium counts are approximately 10(10) c.f.u. g(-1) in these treated silages. An important subpopulation (5.9 x 10(7) c.f.u. g(-1)) is able to degrade 1,2-propanediol, a fermentation product of L. buchneri, under anoxic conditions to 1-propanol and propionic acid. From this group of 1,2-propanediol-fermenting, facultatively anaerobic, heterofermentative lactobacilli, two rod-shaped isolates were purified and characterized. Comparative 16S rDNA sequence analysis revealed that the newly isolated bacteria have identical 16S rDNA sequences and belong phylogenetically to the L. buchneri group. DNA-DNA hybridizations, whole-cell protein fingerprinting and examination of phenotypic properties indicated that these two isolates represent a novel species, for which the name Lactobacillus diolivorans sp. nov. is proposed. The type strain is LMG 19667T (= DSM 14421T).
-
-
-
Leuconostoc ficulneum sp. nov., a novel lactic acid bacterium isolated from a ripe fig, and reclassification of Lactobacillus fructosus as Leuconostoc fructosum comb. nov.
An isolate, designated strain FS-1T, was recovered from a ripe fig. Phylogenetic analysis of the 16S rRNA genes and DNA-DNA reassociation values showed that the organism represented a novel species of the genus Leuconostoc closely related to Lactobacillus fructosus. The novel isolate could be distinguished from the type strain of Lactobacillus fructosus by the fatty acid composition and several phenotypic and growth characteristics. In strain FS-1T, 18:1 delta9 (18:1omega9c) was present in relatively large amounts whilst, in Lactobacillus fructosus, this fatty acid was a minor component. Strain FS-1T and Lactobacillus fructosus produced acid in API 50CHL microtubes from glucose, fructose and mannitol within 48 h, whereas only strain FS-1T also fermented trehalose, gluconate, turanose and sucrose after 48 h. Other differences in acid production from carbohydrates also distinguished strain FS-1T from Lactobacillus fructosus. Both organisms were heterofermentative with fructose as a substrate and fermented glucose only in the presence of fructose, as determined by nuclear magnetic resonance studies. Strain FS-1T was catalase-positive. On the basis of the phylogenetic analysis, DNA-DNA reassociation values, physiological and biochemical characteristics and fatty acid composition, the name Leuconostoc ficulneum is proposed for the novel species represented by strain FS-1T, and it is proposed that Lactobacillus fructosus be reclassified in the genus Leuconostoc as Leuconostoc fructosum comb. nov.
-
-
-
Thioalkalivibrio thiocyanoxidans sp. nov. and Thioalkalivibrio paradoxus sp. nov., novel alkaliphilic, obligately autotrophic, sulfur-oxidizing bacteria capable of growth on thiocyanate, from soda lakes.
More LessNine strains of haloalkaliphilic, obligately autotrophic, sulfur-oxidizing bacteria able to grow with thiocyanate (SCN-) as the sole energy and nitrogen source were isolated from soda lakes in South-East Siberia, Kenya and Egypt after enrichment on sodium carbonate minerals buffered at pH 10 with thiocyanate as the substrate. The isolates fell into two groups that were substantially different in terms of cell morphology, growth parameters and the ability to oxidize carbon disulfide. The bacteria were able to oxidize sulfide, polysulfide, sulfur and tetrathionate, as well as thiocyanate. Two isolates belonged to an extremely halotolerant type growing in the presence of up to 4 M Na+. Cyanate (CNO-) was the main nitrogen-containing intermediate during thiocyanate degradation in both groups. According to DNA-DNA hybridization data and phylogenetic analysis, both groups of isolates belong to a recently described genus of haloalkaliphilic sulfur-oxidizing bacteria, i.e. Thioalkalivibrio, belonging to the gamma-Proteobacteria, in which where they represent two new species. The species name Thioalkalivibrio paradoxus (type strain ARh 1T = DSM 13531T = JCM 11367T) is proposed for the group with barrel-shaped cells, and the species name Thioalkalivibrio thiocyanoxidans (type strain ARh 2T, DSM 13532T = JCM 11368T) is proposed for the group with vibrio-shaped cells. The diagnosis of the genus Thioalkalivibrio is amended according to the new data.
-
-
-
Streptococcus entericus sp. nov., isolated from cattle intestine.
Biochemical, molecular chemical and molecular genetic studies were performed on an unknown gram-positive, catalase-negative, coccus-shaped organism isolated from the intestine of a cow affected with catarrhal enteritis. The organism was tentatively identified as a streptococcal species based on results of cellular morphological and biochemical tests. 16S rRNA gene sequencing studies confirmed its provisional identification as a member of the genus Streptococcus, but the organism did not correspond to any recognized species of this genus. The nearest phylogenetic relatives of the unknown coccus from a calf were Streptococcus acidominimus and Streptococcus suis. The unknown bacterium, however, was distinguished from these species and other animal streptococci by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on both phenotypic and phylogenetic findings, it is proposed that the unknown bacterium be classified as a novel species of the genus Streptococcus, Streptococcus entericus sp. nov. The type strain is CECT 5353T (= CCUG 44616T).
-
-
-
Thiobaca trueperi gen. nov., sp. nov., a phototrophic purple sulfur bacterium isolated from freshwater lake sediment.
Two strains of a novel species of phototrophic micro-organism were isolated from the sediments of a shallow, freshwater, eutrophic lake. Both strains grew photolithoheterotrophically with sulfide as an electron donor, transiently accumulating intracellular sulfur globules. Photolithoautotrophic growth was not observed. One strain was designated BCH(T) (the type strain) and was studied in most detail. Cells contained bacteriochlorophyll a, and the dominant carotenoid was lycopene. Cell suspensions were brown. The photosynthetic membranes had a vesicular arrangement. Acetate, propionate, pyruvate, succinate and fumarate were each used as electron donors and carbon sources in the presence of sulfide and bicarbonate. In the presence of light, growth did not occur with hydrogen, thiosulfate or iron(II). The optimum temperature for growth was between 25 and 30 degrees C, the maximum being 36 degrees C. The G+C content of the genomic DNA of strain BCH(T) was 63 mol%. Analysis of the 16S RNA genes showed that both strains belonged to the gamma-subclass of the Proteobacteria but were phylogenetically distinct from any described phototrophic organisms within the Chromatiaceae. On the basis of phylogenetic and physiological differences from other phototrophic microorganisms, strain BCH(T) is described as a novel species of a new genus, Thiobaca trueperi gen. nov., sp. nov.
-
-
-
Emended description of Paracoccus kondratievae.
More LessAn aerobic, facultatively chemolithotrophic and methylotrophic strain, GB, was isolated from a maize rhizosphere. On the basis of comparative analysis of its phenotypic and genotypic properties, it is proposed that strain GB(T) (= VKM B-2222T = NCIMB 13773T) be assigned to the genus Paracoccus as Paracoccus kondratievae sp. nov.
-
-
-
Revision of haemotrophic Mycoplasma species names.
More LessThe recently proposed transfer of four rickettsias from the genera Haemobartonella and Eperythrozoon to the genus Mycoplasma with the Candidatus status is herein revised. This is because the Candidatus designation is for new, incompletely described taxa, in order to give them a provisional status. Thus, 'Candidatus Mycoplasma haemofelis' is revised to Mycoplasma haemofelis comb. nov., nom. nov., 'Candidatus Mycoplasma haemomuris' is revised to Mycoplasma haemomuris comb. nov., nom. nov., 'Candidatus Mycoplasma haemosuis' is revised to Mycoplasma haemosuis comb. nov., nom. nov. and 'Candidatus Mycoplasma wenyonii' is revised to Mycoplasma wenyonii comb. nov.
-
Volumes and issues
-
Volume 74 (2024)
-
Volume 73 (2023)
-
Volume 72 (2022 - 2023)
-
Volume 71 (2020 - 2021)
-
Volume 70 (2020)
-
Volume 69 (2019)
-
Volume 68 (2018)
-
Volume 67 (2017)
-
Volume 66 (2016)
-
Volume 65 (2015)
-
Volume 64 (2014)
-
Volume 63 (2013)
-
Volume 62 (2012)
-
Volume 61 (2011)
-
Volume 60 (2010)
-
Volume 59 (2009)
-
Volume 58 (2008)
-
Volume 57 (2007)
-
Volume 56 (2006)
-
Volume 55 (2005)
-
Volume 54 (2004)
-
Volume 53 (2003)
-
Volume 52 (2002)
-
Volume 51 (2001)
-
Volume 50 (2000)
-
Volume 49 (1999)
-
Volume 48 (1998)
-
Volume 47 (1997)
-
Volume 46 (1996)
-
Volume 45 (1995)
-
Volume 44 (1994)
-
Volume 43 (1993)
-
Volume 42 (1992)
-
Volume 41 (1991)
-
Volume 40 (1990)
-
Volume 39 (1989)
-
Volume 38 (1988)
-
Volume 37 (1987)
-
Volume 36 (1986)
-
Volume 35 (1985)
-
Volume 34 (1984)
-
Volume 33 (1983)
-
Volume 32 (1982)
-
Volume 31 (1981)
-
Volume 30 (1980)
-
Volume 29 (1979)
-
Volume 28 (1978)
-
Volume 27 (1977)
-
Volume 26 (1976)
-
Volume 25 (1975)
-
Volume 24 (1974)
-
Volume 23 (1973)
-
Volume 22 (1972)
-
Volume 21 (1971)
-
Volume 20 (1970)
-
Volume 19 (1969)
-
Volume 18 (1968)
-
Volume 17 (1967)
-
Volume 16 (1966)
-
Volume 15 (1965)
-
Volume 14 (1964)
-
Volume 13 (1963)
-
Volume 12 (1962)
-
Volume 11 (1961)
-
Volume 10 (1960)
-
Volume 9 (1959)
-
Volume 8 (1958)
-
Volume 7 (1957)
-
Volume 6 (1956)
-
Volume 5 (1955)
-
Volume 4 (1954)
-
Volume 3 (1953)
-
Volume 2 (1952)
-
Volume 1 (1951)