Showing papers in "International Journal of Systematic and Evolutionary Microbiology in 1994"
TL;DR: Amorphous metal alloys are employed in acoustic devices dependent upon the properties of low acoustic velocity and low attenuation, such as wire, strip and bulk delay lines.
Abstract: Because a natural entity “species” cannot be recognized as a group of strains that is genetically well separated from its phylogenetic neighbors, a pragmatic approach was taken to define a species by a polyphasic approach (L. G. Wayne, D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Truper, Int. J. Syst. Bacteriol. 37:463-464, 1987), in which a DNA reassociation value of about 70% plays a dominant role. With the establishment of rapid sequence analysis of 16S rRNA and the recognition of its potential to determine the phylogenetic position of any prokaryotic organism, the role of 16S rRNA similarities in the present species definition in bacteriology needs to be clarified. Comparative studies clearly reveal the limitations of the sequence analysis of this conserved gene and gene product in the determination of relationships at the strain level for which DNA-DNA reassociation experiments still constitute the superior method. Since today the primary structure of 16S rRNA is easier to determine than hybridization between DNA strands, the strength of the sequence analysis is to recognize the level at which DNA pairing studies need to be performed, which certainly applies to similarities of 97% and higher.
6,188 citations
TL;DR: The 16S rRNA gene sequences were determined by PCR direct sequencing and were compared with more than 80 previously determined clostridial sequences and the previously published sequences of representative species of other low- G + C-content gram-positive genera, thereby providing an almost complete picture of the genealogical interrelationships of theClostridia.
Abstract: The 16S rRNA gene sequences of 34 named and unnamed clostridial strains were determined by PCR direct sequencing and were compared with more than 80 previously determined clostridial sequences and the previously published sequences of representative species of other low- G+C-content gram-positive genera, thereby providing an almost complete picture of the genealogical interrelationships of the clostridia. The results of our phylogenetic analysis corroborate and extend previous findings in showing that the genus Clostridium is extremely heterogeneous, with many species phylogenetically intermixed with other sporeforming and non-sporeforming genera. The genus Clostridium is clearly in need of major revision, and the rRNA structures defined in this and previous studies may provide a sound basis for future taxonomic restructuring. The problems and different possibilities for restructuring are discussed in light of the phenotypic and phylogenetic data, and a possible hierarchical structure for the clostridia and their close relatives is presented. On the basis of phenotypic criteria and the results of phylogenetic analyses the following five new genera and 11 new combinations are proposed: Caloramator gen. nov., with Caloramator fervidus comb. nov.; Filifactor gen. nov., with Filifactor villosus comb. nov.; Moorella gen. nov., with Moorella thermoacetica comb. nov. and Moorella thermoautotrophica comb. nov.; Oxobacter gen. nov., with Oxobacter pfennigii comb. nov.; Oxalophagus gen. nov., with Oxalophagus oxalicus comb. nov.; Eubacterium barkeri comb. nov.; Paenibacillus durum comb. nov.; Thermoanaerobacter kivui comb. nov.; Thermoanaerobacter thermocopriae comb. nov.; and Thermoanerobacterium thermosaccharolyticum comb. nov.
1,567 citations
TL;DR: Comparisons with sequences of 16S rDNAs obtained from the GenBank data base revealed that the two citrus greening disease BLOs belong to the alpha subdivision of the class Proteobacteria, and it is proposed that this new group of bacteria is called "liberobacter".
Abstract: Using the PCR, we amplified the 16S ribosomal DNAs (rDNAs) of an Asian strain and an African strain of the uncultured, gram-negative, walled, phloem-limited bacterium-like organism (BLO) associated with citrus greening disease. We evaded coamplification of chloroplast 16S rDNA by using restriction enzymes; the chloroplast 16S rDNA was sensitive to Bcl I digestion and resistant to Eco RI digestion, while the 16S rDNA of the BLO was resistant to Bcl I digestion and sensitive to Eco RI digestion. The 16S rDNA of the African BLO strain was amplified from Bcl I-digested DNA extracted from infected periwinkle leaf midribs. The Asian strain was isolated from plant extract by using a specific monoclonal antibody coated onto the surface of a PCR tube. The 16S rDNAs of the two BLO strains were cloned and sequenced. Comparisons with sequences of 16S rDNAs obtained from the GenBank data base revealed that the two citrus greening disease BLOs belong to the alpha subdivision of the class Proteobacteria. Even though their closest relatives are members of the alpha-2 subgroup, these BLOs are distinct from this subgroup as we observed only 87.5% homology between the 16S rDNAs examined. Therefore, the two BLOs which we studied probably are members of a new lineage in the α subdivision of the Proteobacteria. We propose the trivial name “liberobacter” for this new group of bacteria and will wait until additional characteristics have been determined before we propose a formal name.
592 citations
TL;DR: The nuclease MseI restriction polymorphism of the amplicons provided a useful tool for identifying B. burgdorferi sensu stricto, which previously was the only Lyme disease Borrelia species known to occur in the United States.
Abstract: The organization of the ribosomal genes is unique in Borrelia burgdorferi in that the rrl (23S) and rrf (5S) genes are tandemly duplicated. We took advantage of this uniqueness to assess the restriction polymorphism of PCR products obtained with primers at the 3' end of the first rrf gene and at the 5' end of the second rrl gene. An amplicon that was 226 to 266 bp long was generated from 99 to 100 B. burgdorferi sensu lato strains. The nuclease MseI restriction polymorphism of the amplicons provided a useful tool for identifying B. burgdorferi sensu stricto, Borrelia garinii, Borrelia afzelii (formerly group VS461), and Borrelia japonica (formerly group F63B). Furthermore, it allowed us to recognize four new genomic groups, which were confirmed by DNA-DNA hybridization data. Two of these genomic groups comprised European strains, and the other two groups contained American strains. The American genomic groups involved vectors with enzootic cycles quite different from those of B. burgdorferi sensu stricto, which previously was the only Lyme disease Borrelia species known to occur in the United States. Our method could be used for rapid screening of strain collections and for epidemiological and medical purposes.
490 citations
TL;DR: The generically misclassified organism Flavobacterium breve is included in the revived genus Empedobacter as Em Pedobacter brevis, whereas the genericallyMisclassified organism Weeksella zoohelcum is includedIn the new genus Bergeyella as Bergeyellas zoohel Cum.
Abstract: Our present knowledge concerning the genotypic, chemotaxonomic, and phenotypic characteristics of members of the genus Flavobacterium and some related genera, including the genus Weeksella, was used to revise the classification of these organisms. The generically misclassified organisms Flavobacterium balustinum, Flavobacterium gleum, Flavobacterium indologenes, Flavobacterium indoltheticum, Flavobacterium meningosepticum, and Flavobacterium scophthalmum are included in a new genus, Chryseobacterium, with Chryseobacterium gleum as the type species. The generically misclassified organism Flavobacterium breve is included in the revived genus Empedobacter as Empedobacter brevis, whereas the generically misclassified organism Weeksella zoohelcum is included in the new genus Bergeyella as Bergeyella zoohelcum.
416 citations
TL;DR: Two of the clusters identified on the basis of SDS-PAGE data are genotypically and phenotypically distinct groups that belong on the Rhizobium meliloti-RhZobium fredii rRNA branch and contains strains isolated in Africa, in Brazil, and in New Zealand from different leguminous species.
Abstract: A total of 80 bacterial strains isolated from different Sesbania and Acacia species growing in various sites in Senegal (West Africa) were compared with 35 reference strains of Rhizobium, Bradyrhizobium, Azorhizobium, and Agrobacterium species and with 33 representative strains of the different groups of Brazilian isolates described on the basis of the results of a numerical analysis of the whole-cell protein patterns obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Fifty-two strains could be placed in three protein electrophoretic clusters, two of which were different from the clusters containing various reference or representative strains, while 30 other strains could not be placed in any group. The strains belonging to the three clusters were studied by determining their nodulation host ranges and their morphological, physiological, and auxanographic characteristics. Representative strains of the three clusters were also genotypically characterized by determining their DNA base compositions, by performing DNA-DNA and DNA-rRNA hybridization experiments, and by determining their 16S rRNA gene sequences. Our results showed that two of the clusters identified on the basis of SDS-PAGE data are genotypically and phenotypically distinct groups that belong on the Rhizobium meliloti-Rhizobium fredii rRNA branch. The third cluster is localized on the Rhizobium loti rRNA branch in the vicinity of Rhizobium huakuii and contains strains isolated in Africa, in Brazil, and in New Zealand from different leguminous species. On the basis of the results of the present study, we propose to emend the genus Sinorhizobium and to reclassify R. meliloti as Sinorhizobium meliloti comb. nov. In addition, two new species, Sinorhizobium saheli and Sinorhizobium teranga, are proposed for isolates from Senegal.
396 citations
TL;DR: This note is presented in advance of discussions by the International Committee on Systematic Bacteriology at the forthcoming congress (July 1994) so that there may be discussions and reaction by colleagues.
Abstract: The problem that the proposal for recording the properties of putative taxa of procaryotes attempts to redress arises because the International Code of Nomenclature of Bacteria is not able to provide sensible regulation of nomenclature for new taxa defined by very limited data, such as a nucleotide sequence for a small portion of the genome. The constructors of the original code (1957) and the Judicial Commission considering the 1976 and 1990 revisions did not foresee or act upon the possibilities for molecular description and typification of procaryotes that were not yet cultivable. As a result, formal names are being proposed for uncultivated procaryotes whose uniqueness is defined only by very limited characteristics, such as differences in a molecular sequence. As the editors of two journals concerned with the systematics of procaryotes, we recognize that the problem will increase as the available technology gains wider use and becomes easier to apply. Accordingly, this note is presented in advance of discussions by the International Committee on Systematic Bacteriology at the forthcoming congress (July 1994) so that there may be discussions and reaction by colleagues.
298 citations
TL;DR: A phylogenetic analysis confirmed that the family Vibrionaceae should include only Photobacterium and Vibrio species; that Aeromonas species deserve family rank; and that Plesiomonas shigelloides is linked to the family Enterobacteriaceae.
Abstract: We sequenced nearly complete small-subunit rRNAs of 54 reference strains belonging to the genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas. We then performed a phylogenetic analysis by comparing the sequences which we obtained with all other known sequences for bacteria belonging to the gamma subgroup of the Proteobacteria (thus providing a data base consisting of 70 sequences for the genera investigated), using methods such as neighbor joining, maximum likelihood, and maximum parsimony, as well as bootstrap, to assess the robustness of each topology. Our results confirmed that the family Vibrionaceae should include only Photobacterium and Vibrio species (but not Vibrio marinus); that Aeromonas species deserve family rank; and that Plesiomonas shigelloides is linked to the family Enterobacteriaceae. The genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas, together with the family Enterobacteriaceae, the family Pasteurellaceae, and probably the genus Alteromonas, form a robust monophyletic unit within the gamma 3 subgroup of the Proteobacteria.
280 citations
TL;DR: The sequence of Francisella novicida was virtually identical to the sequences of the F. tularensis strains, thereby supporting the hypothesis that these organisms are members of the same species.
Abstract: The 16S ribosomal DNAs (rDNAs) of two strains of Francisella tularensis and one strain of Francisella philomiragia were sequenced. On the basis of phylogenetic analysis data, the genus Francisella was placed in the γ subclass of the Proteobacteria. The most closely related organism was the intracellular bacterium Wolbachia persica. The sequenced 16S rDNA molecules of the Francisella species exhibited very high levels of similarity (98.5 to 99.9%). Two variable regions, comprising 390 to 450 nucleotides of the 16S rDNA molecules of 17 additional Francisella strains, including members of the species F. tularensis and F. philomiragia, were also sequenced. At most, six nucleotide differences were observed among the sequences of the F. tularensis strains. The sequence of Francisella novicida was virtually identical to the sequences of the F. tularensis strains, thereby supporting the hypothesis that these organisms are members of the same species. On the basis of the observed differences, primer pairs were designed to distinguish strains by using the PCR at the genus, species, and subspecies levels. This permitted sensitive identification of strains belonging to the genus Francisella and discrimination of the species F. tularensis and F. philomiragia.
268 citations
TL;DR: The phylogenetic relationships of 17 phytopathogenic mycoplasmalike organisms (MLOs) representing seven major taxonomic groups established on the basis of MLO 16S ribosomal DNA (rDNA) restriction patterns were examined by performing a sequence analysis of the 16S rDNA gene.
Abstract: The phylogenetic relationships of 17 phytopathogenic mycoplasmalike organisms (MLOs) representing seven major taxonomic groups established on the basis of MLO 16S ribosomal DNA (rDNA) restriction patterns were examined by performing a sequence analysis of the 16S rDNA gene. The sequence data showed that the MLOs which we examined are members of a relatively homogeneous group that evolved monophyl-etically from a common ancestor. In agreement with results obtained previously with other MLOs, our results also revealed that the organisms are more closely related to Acholeplasma laidlawii and other members of the anaeroplasma clade than to any other mollicutes. A phylogenetic tree based on 16S rDNAs showed that the MLOs which we examined can be divided into the following five primary clusters: (i) the aster yellows strain cluster; (ii) the apple proliferation strain cluster; (iii) the western-X disease strain cluster; (iv) the sugarcane white leaf strain cluster; and (v) the elm yellows strain cluster. The aster yellows, western-X disease, and elm yellows strain clusters were divided into two subgroups each. MLOs whose 16S rDNA sequences have been determined previously by other workers can be placed in one of the five groups. In addition to the overall division based on 16S rDNA sequence homology data, the primary clusters and subgroups could be further defined by a number of positions in the 16S rDNAs that exhibited characteristic compositions, especially in the variable regions of the gene.
262 citations
TL;DR: On the basis of the results of a 16S rRNA analysis and the inability of the organism to use sulfate as an electron acceptor, strain JW/IU-DC1 is described as the type strain of the new taxon Desulfitobacterium dehalogenans gen. nov.
Abstract: An organism that is able to reductively ortho-dechlorinate 2,4-dichlorophenol and 3-chloro-4-hydroxyphenylacetate (3-Cl-4-OHPA) was isolated from a methanogenic lake sediment. This organism, an anaerobic, motile, Gram-type-positive, rod-shaped bacterium, grew in the presence of 0.1% yeast extract when pyruvate, lactate, formate, or hydrogen was used as the electron donor for reductive dehalogenation of 3-Cl-4-OHPA. Sulfite, thiosulfate, and sulfur were reduced to sulfide, nitrate was reduced to nitrite, and fumarate was reduced to succinate. Dissimilatory reduction of sulfate could not be demonstrated, and no adenylylsulfate reductase was detected with an immunoassay. The organism fermented two pyruvate molecules to one lactate molecule, one acetate molecule, and one carbon dioxide molecule. The pH and temperature optima for both growth and dechlorination of 3-Cl-4-OHPA were 7.5 and 38°C, respectively. The doubling time under these conditions was approximately 3.5 h. On the basis of the results of a 16S rRNA analysis and the inability of the organism to use sulfate as an electron acceptor, strain JW/IU-DC1 is described as the type strain of the new taxon Desulfitobacterium dehalogenans gen. nov., sp. nov.
TL;DR: In this article, the 16S ribosomal DNAs of three obligately aerobic, bacteriochlorophyll a-containing bacteria, “Roseococcus thiosulfatophilus,” “Erythromicrobium ramosum, and new isolate T4T (T = type strain), were analyzed.
Abstract: We analyzed the 16S ribosomal DNAs of three obligately aerobic, bacteriochlorophyll a-containing bacteria, “Roseococcus thiosulfatophilus,” “Erythromicrobium ramosum,” and new isolate T4T (T = type strain), which was obtained from a marine cyanobacterial mat. “Roseococcus thiosulfatophilus” is a member of the α-1 subclass of the Proteobacteria and is moderately related to Rhodopila globiformis, Thiobacillus acidophilus, and Acidiphilium cryptum (level of sequence similarity, 90%). “Erythromicrobium ramosum” and isolate T4T are closely related to Erythrobacter longus and Porphyrobacter neustonensis (level of sequence similarity, 95%). These organisms are members of the α-4 subclass of the Proteobacteria. Strain T4T is a motile, red or orange bacterium. The major carotenoids are bacteriorubixanthinal and erythroxanthin sulfate. In vivo measurements revealed bacteriochlorophyll absorption maxima at 377, 590, 800, and 868 nm. Strain T4T grows in the presence of 5 to 96%‰ salinity and uses glucose, fructose, acetate, pyruvate, glutamate, succinate, and lactate as substrates. On the basis of its distinct phylogenetic position and phenotypic characteristics which are different from those of Erythrobacter longus, we propose that strain T4T should be placed in a new species of the genus Erythrobacter, Erythrobacter litoralis. The descriptions of “Roseococcus thiosulfatophilus” and “Erythromicrobium ramosum” are emended.
TL;DR: The results of DNA-rRNA hybridization studies indicated that these two species belong to a separate genus in the alpha subclass (rRNA superfamily IV) of the Proteobacteria, for which the name Brevundimonas is proposed.
Abstract: The taxonomic positions of strains previously assigned to Pseudomonas diminuta and Pseudomonas vesicularis were investigated by a polyphasic approach. The results of DNA-rRNA hybridization studies indicated that these two species belong to a separate genus in the α subclass (rRNA superfamily IV) of the Proteobacteria, for which the name Brevundimonas is proposed. Genus delineation and species delineation were determined by comparing the results of numerical analyses of whole-cell protein patterns, fatty acid compositions, and phenotypic characteristics and by measuring DNA base ratios and degrees of DNA relatedness. Taxonomic characteristics of Brevundimonas diminuta and Brevundimonas vesicularis strains were compared with characteristics of reference strains belonging to the following phylogenetically related taxa: a group of organisms gathered in Enevold Falsen group 21, the genera Sphingomonas and Rhizomonas, and the generically misclassified organisms [Pseudomonas] echinoides and “[Pseudomonas] riboflavina.”
TL;DR: The taxonomic status of 16 collection strains of chickpea (Cicer arietinum L.) rhizobia were compared with reference strains belonging to different genera and species of the family Rhizobiaceae and it was confirmed that therhizobia that nodulate chickpeas cannot be assigned to a previously described species.
Abstract: The taxonomic status of 16 collection strains of chickpea (Cicer arietinum L.) rhizobia which were previously determined to belong to two groups (groups A and B) were compared with reference strains belonging to different genera and species of the family Rhizobiaceae. We used the following taxonomic, phylogenetic, and phenotypic characteristics and approaches to study these organisms: DNA homology, guanine-plus-cytosine content, restriction fragment length polymorphism of the amplified 16S-intergenic spacer rRNA gene, partial 16S rRNA sequencing, and auxanographic tests performed with 147 carbon sources. Similar groups of chickpea strains were identified by the different approaches. The chickpea strains were found to belong to the genus Rhizobium regardless of the phylogenetic group to which they belonged (group A or B). All strains fell into a tight cluster which included Rhizobium loti and Rhizobium galegae, and the group B strains were closely related to R. loti. An analysis of partial 16S ribosomal DNA sequences revealed identical nucleotide sequences for the slowly growing strains and fast-growing strains that were used as representatives of groups A and B, respectively, and these organisms fell into the Rhizobium-Agrobacterium lineage. When the sequences of these organisms were compared with the partial sequences of Rhizobium huakuii and R. loti, one- and two-nucleotide mismatches were observed, respectively, indicating that the chickpea rhizobia are closely related to these two species. The DNA-DNA hybridization data revealed that the chickpea rhizobia exhibited low levels of homology (less than 17%) to previously described Rhizobium and Bradyrhizobium species. Moreover, when we compared chickpea strains to R. loti and R. huakuii, the most closely related species as determined by the partial 16S rRNA sequence analysis, the homology values ranged from 21 to 52% and the delta Tm values were greater than 5 degrees C (delta Tm is the difference between the denaturation temperatures of the heterologous and homologous duplexes). These results confirmed that the rhizobia that nodulate chickpeas cannot be assigned to a previously described species. Within the chickpea rhizobia, the DNA homology values obtained when members of groups A and B were compared were less than 38%, indicating that the group A and group B organisms belong to different species. Furthermore, these organisms can be distinguished from each other by the results of phenotypic tests. We propose that the group B chickpea rhizobia should be assigned to a new species, Rhizobium ciceri; UPM-Ca7 is the type strain of R. ciceri.
TL;DR: A number of Bacillus strains isolated from desert soil samples were shown to belong to a previously unidentified species, for which the name Bacillus mojavensis is proposed.
Abstract: A number of Bacillus strains isolated from desert soil samples were shown to belong to a previously unidentified species, for which we propose the name Bacillus mojavensis. The type strain is RO-H-1 (= NRRL B-14698). On the basis of restriction digest data, B. mojavensis is most closely related to Bacillus amyloliquefaciens, Bacillus atrophaeus, and Bacillus subtilis. So far, B. mojavensis can be distinguished from B. subtilis only by differences in whole-cell fatty acid composition, divergence in DNA sequence, and resistance to genetic transformation between taxa (in addition to reduced genome relatedness values). Sequence divergence and sexual isolation may prove to be more useful than metabolic characteristics for delimiting cryptic Bacillus species.
TL;DR: A general strategy in which a polyphasic approach was used to characterize a new species of Lactobacillus pontis is described, and a phylogenetic tree which reflected the relationships of this species to other lactobacilli is constructed.
Abstract: The microflora of sourdough preparations was investigated by examining the physiological characteristics, whole-cell protein patterns, and 16S rRNA sequences of Lactobacillus isolates. Strains isolated from sourdough were placed in the species Lactobacillus brevis, Lactobacillus sanfrancisco, and Lactobacillus reuteri. 16S rRNA sequences were determined for L. brevis, Lactobacillus fructivorans, Lactobacillus fermentum, L. sanfrancisco, and L. reuteri, and oligonucleotide probes for fast specific identification of these sourdough lactobacilli were deduced. The physiological characteristics, protein patterns, and 16S rRNA sequences of these organisms were compared with data for other sourdough lactobacilli and additional reference strains. Strains of a Lactobacillus species were isolated from rye sourdough; these strains may account for most of the flora in sourdough made from wheat or rye. These organisms were differentiated from other sourdough lactobacilli by their protein pattern, 16S rRNA sequence, G+C content, and physiological properties. The 16S rRNA sequence of this species was determined, and we constructed a phylogenetic tree which reflected the relationships of this species to other lactobacilli. This organism is closely related to L. reuteri. A new Lactobacillus species, Lactobacillus pontis, is proposed. The type strain is L. pontis LTH 2587 (= DSM 8475 = LMG 14187). We describe a general strategy in which a polyphasic approach was used to characterize a new species.
TL;DR: The phylogenetic position and various genotypic, chemotaxonomic, and classical phenotypic characteristics of 21 gram-negative avian isolates were studied and a new taxon is proposed, for which the name Ornithobacterium rhinotracheale is proposed.
Abstract: The phylogenetic position and various genotypic, chemotaxonomic, and classical phenotypic characteristics of 21 gram-negative avian isolates were studied. These strains constitute a genotypically homogeneous taxon in rRNA superfamily V, as shown by DNA-rRNA hybridization data. Determination of the 16S rRNA sequence of this taxon revealed its detailed position within the “flavobacter” subgroup of the “flavobacter-bacteroides” phylum as described by Gherna and Woese (R. Gherna and C. R. Woese, Syst. Appl. Microbiol. 15:513-521, 1992). This new taxon is only distantly related to other members of the “flavobacter-bacteroides” phylum and is therefore given separate generic status. The DNA-DNA binding values for members of this taxon, for which we propose the name Ornithobacterium rhinotracheale, confirmed that all of the strains are highly interrelated (DNA-DNA binding values greater than 90% were measured). The G+C contents of members of this taxon are between 37 and 39 mol%. An analysis of the cellular proteins and fatty acids and classical phenotypic characteristics allowed us to distinguish O. rhinotracheale from phenotypically similar taxa, such as Riemerella anatipestifer and Capnocytophaga species. The respiratory quinone content (menaquinone 7) and carbohydrate pattern of O. rhinotracheale conform with the respiratory quinone contents and carbohydrate patterns of other members of rRNA superfamily V.
TL;DR: The results indicated that the strains isolated from Hainan Province fell into two distinct phena, the slowly growing rhizobia and the fast-growing rhZB, which might be further divided into three specific groups.
Abstract: A total of 63 strains of rhizobia isolated from Hainan Province, a tropical region of the People's Republic of China, and 27 representative strains belonging to the genera Rhizobium, Bradyrhizobium, and Agrobacterium were compared by performing numerical taxonomy, DNA hybridization, and DNA base composition analysis to determine the relationships among these rhizobia. The results indicated that the strains isolated from Hainan Province fell into two distinct phena, the slowly growing rhizobia and the fast-growing rhizobia. The slowly growing rhizobia, which formed three subphena that seemed to be three subspecies, are Bradyrhizobium japonicum strains. The fast-growing strains belong to the genus Rhizobium and might be further divided into three specific groups. Sometimes both slowly growing rhizobia and fast-growing rhizobia were isolated from host plants belonging to the same genus or species or even from the same nodule. There was no correlation between hosts and the distribution of rhizobia in the subphena. Isolates obtained from members of the same host genus or species fell into different groups or subgroups.
TL;DR: The 16S rRNAs of 15 species of actinomycetes belonging to the genera Actinokineospora and Saccharothrix and the family Pseudonocardiaceae were sequenced and it was suggested that these organisms should be classified in an emended genus Pseud onocardia.
Abstract: The 16S rRNAs of 15 species of actinomycetes belonging to the genera Actinokineospora and Saccharothrix and the family Pseudonocardiaceae, including Amycolatopsis, Amycolata, Pseudonocardia, Saccharomonospora, and Saccharopolyspora species, were sequenced by using reverse transcriptase. The sequences were analyzed along with the sequences of reference actinomycetes by using distance matrix and parsimony methods. The wall chemotype IV genus Actinokineospora was found to be closely related to species of the genus Saccharothrix which have chemotype III walls. Together, these two genera formed a clade which was closely related to members of the family Pseudonocardiaceae which have chemotype IV walls. However, the phylogenetic branching pattern did not unambiguously resolve whether the members of all three taxa should be placed in a single family. We suggest, therefore, that the genera Actinokineospora and Saccharothrix should remain outside the family Pseudonocardiaceae until additional sequence or phenotypic data are available to decide the issue. The sequences of species belonging to the genera Amycolata and Pseudonocardia were always recovered as a mixed group in phylogenetic trees, and we propose that these organisms should be classified in an emended genus Pseudonocardia. This proposal is strongly supported by previously published lipid, ribosomal protein, and ultrastructure data.
TL;DR: Two new species, Porphyromonas gingivicanis and P. crevioricanis, are proposed for black-pigmented, asaccharolytic, anaerobic, nonmotile, non-spore-forming, gram-negative, rod-shaped organisms.
Abstract: Two new species, Porphyromonas gingivicanis and Porphyromonas crevioricanis, are proposed for blackpigmented, asaccharolytic, anaerobic, nonmotile, non-spore-forming, gram-negative, rod-shaped organisms. These organisms were isolated from the gingival crevicular fluids of beagles. P. gingivicanis and P. crevioricanis do not grow in the presence of 20% bile. They exhibit less than 5% DNA-DNA homology with the type strains of Porphyromonas gingivalis (strain ATCC 33277), Porphyromonas endodontalis (strain ATCC 35406), and Porphyromonas asaccharolytica (strain ATCC 25260), which were isolated from humans, or with the type strains of Porphyromonas salivosa (strain NCTC 11632) and Porphyromonas circumdentaria (strain NCTC 12469), which were isolated from cats. The major cellular fatty acid of P. gingivicanis and P. crevioricanis is 13-methyltetradecanoic acid (iso-C15:0 acid). Glutamate and malate dehydrogenases are present in both species, and 6-phosphogluconate and glucose-6-phosphate dehydrogenases are absent; neither organism exhibits trypsin activity. P. gingivicanis and P. crevioricanis produce large amounts of acetic and isovaleric acids and minor amounts of isobutyric and succinic acids as end products of metabolism in GAM medium. P. gingivicanis also produces large amounts of butyric acid and small amounts of propionic acid, while P. crevioricanis produces large amounts of propionic acid and minor amounts of butyric and phenylacetic acids. The G+C contents of the DNA of P. gingivicanis is 41 to 42 mol%; the G+C content of the DNA of P. crevioricanis is 44 to 45 mol%. Catalase is produced by P. gingivicanis but not by P. crevioricanis; strains of P. crevioricanis agglutinate sheep erythrocytes, but strains of P. gingivicanis do not. The type strain of P. gingivicanis is NUM 301 (= ATCC 55562), and the type strain of P. crevioricanis is NUM 402 (= ATCC 55563).
TL;DR: Cellular fatty acid profiles were determined for species in 33 genera of anaerobic gram-negative bacilli and were confirmed to be a useful taxonomic tool and the three genus pairs that were most difficult to distinguish visually were identified.
Abstract: Cellular fatty acid profiles were determined for species in 33 genera of anaerobic gram-negative bacilli and were confirmed to be a useful taxonomic tool. Most of the genera could be differentiated by visual inspection of their profiles. The three genus pairs that were most difficult to distinguish visually (Bacteroides and Prevotella, Pectinatus and Megamonas, and Serpulina and Bilophila) and the species of these genera were differentiated by the MIDI (Microbial ID, Inc.) identification system. Similarities in cellular fatty acid profiles may be correlated with similarities in other phenotypic characteristics, but more often there is no other obvious phenotypic relationship. Although medium components may not change the constituents detected or the ratios among the constituents detected for some species, identical medium changes may result in vast differences in the profiles obtained with other species. Thus, if a worker wishes to compare profiles of various taxa, it is essential that the same cultural and analytical conditions be used.
TL;DR: Plant-associated bacteria were characterized and are discussed in relation to authentic members of the genus Pseudomonas sensu stricto and it is proposed that Pseudomanas plantarii and Pseudoms glumae should be transferred to the genus Burkholderia.
Abstract: Plant-associated bacteria were characterized and are discussed in relation to authentic members of the genus Pseudomonas sensu stricto. Bacteria belonging to Pseudomonas rRNA group II are separated clearly from members of the genus Pseudomonas sensu stricto (Pseudomonas fluorescens rRNA group) on the basis of plant association characteristics, chemotaxonomic characteristics, DNA-DNA hybridization data, rRNA-DNA hybridization data, and the sequences of 5S and 16S rRNAs. The transfer of Pseudomonas cepacia, Pseudomonas mallei, Pseudomonas pseudomallei, Pseudomonas caryophylli, Pseudomonas gladioli, Pseudomonas pickettii, and Pseudomonas solanacearum to the new genus Burkholderia is supported; we also propose that Pseudomonas plantarii and Pseudomonas glumae should be transferred to the genus Burkholderia. Isolate VA-1316T (T = type strain) was distinguished from Burkholderia species on the basis of physiological characteristics and DNA-DNA hybridization data. A new species, Burkholderia vandii sp. nov. is proposed for this organism; the type strain of B. vandii is VA-1316 (= JCM 7957).
TL;DR: A new genus, Couchioplanes, is proposed for motile actinomycetes based on morphological, physiological, and chemotaxonomic data and the results of DNA-DNA hybridization and comparative 16S rRNA studies, for these organisms.
Abstract: During our taxonomic study of motile actinomycetes, soil isolate RA 335 was found to form a blue substrate mycelium and aerial mycelia with motile arthrospores and to have lysine as the cell wall diamino acid. Actinoplanes caeruleus IFO 13939T (T = type strain) and “Actinoplanes azureus” IFO 13993T are known to have the same characteristics. Therefore, the taxonomic position of these three strains was studied. Aerial mycelia of these strains fragmented during the growth cycle and produced motile spores arranged in chains within the mycelia. Sporangia were not observed. The strains contained menaquinone 9(H4), had guanine-plus-cytosine contents of 69.9 to 72.1 mol%, and had D-glutamic acid, D- and L-serine, glycine, L-alanine, and L-lysine as cell wall amino acids (type A3α). The taxonomic characteristics of these strains differ from those of the previously described motile actinomycetes. On the basis of morphological, physiological, and chemotaxonomic data and the results of DNA-DNA hybridization and comparative 16S rRNA studies, we propose a new genus, Couchioplanes, for these organisms. The type species is Couchioplanes caeruleus comb. nov. (type strain, IFO 13939), which is divided into two subspecies, Couchioplanes caeruleus subsp. caeruleus subsp. nov. (type strain, IFO 13939) for A. caeruleus IFO 13939T and strain RA 335 and Couchioplanes caeruleus subsp. azureus (type strain, IFO 13993) for “A. azureus” IFO 13993T.
TL;DR: A novel extremely halophilic archaeon (archaebacterium) was isolated from rock salt obtained from an Austrian salt mine and it is proposed that this isolate should be recognized as a new species and should be named Halococcus salifodinae.
Abstract: A novel extremely halophilic archaeon (archaebacterium) was isolated from rock salt obtained from an Austrian salt mine. The deposition of the salt is thought to have occurred during the Permian period (225 × 106 to 280 × 106 years ago). This organism grew over a pH range of 6.8 to 9.5. Electron microscopy revealed cocci in tetrads or larger clusters. The partial 16S rRNA sequences, polar lipid composition, and menaquinone content suggested that this organism was related to members of the genus Halococcus, while the whole-cell protein patterns, the presence of several unknown lipids, and the presence of pink pigmentation indicated that it was different from previously described coccoid halophiles. We propose that this isolate should be recognized as a new species and should be named Halococcus salifodinae. The type strain is Blp (= ATCC 51437 = DSM 8989). A chemotaxonomically similar microorganism was isolated from a British salt mine.
TL;DR: The general observations suggest that GroEL proteins provide valuable evolutionary tools for defining evolutionary relationships among the eubacterial lineage of life.
Abstract: The essential GroEL proteins represent a subset of molecular chaperones ubiquitously distributed among species of the eubacterial lineage, as well as in eukaryote organelles. We employed these highly conserved proteins to infer eubacterial phylogenies. GroEL from the species analyzed clustered in distinct groups in evolutionary trees drawn by either the distance or the parsimony method, which were in general agreement with those found by 16S rRNA comparisons (i.e., proteobacteria, chlamydiae, bacteroids, spirochetes, firmicutes [gram-positive bacteria], and cyanobacteria-chloroplasts). Moreover, the analysis indicated specific relationships between some of the aforementioned groups which appeared not to be clearly defined or controversial in rRNA-based phylogenetic studies. For instance, a monophyletic origin for the low-G+C and high-G+C subgroups among the firmicutes, as well as their specific relationship to the cyanobacteria-chloroplasts, was inferred. The general observations suggest that GroEL proteins provide valuable evolutionary tools for defining evolutionary relationships among the eubacterial lineage of life.
TL;DR: With few exceptions, the marine Rhodobacter species can be differentiated phenotypically from the freshwater species on the basis of salt requirement for optimal growth, sulfide tolerance, final oxidation product of sulfide, and polar lipid composition and it is proposed that all marine RhodOBacter species should be transferred to the genus Rhodovulum gen. nov.
Abstract: Phylogenetic relationships among species of the genus Rhodobacter and related taxa were elucidated by studying 16S rRNA sequence information and genomic DNA homology data. The 16S rRNA gene was amplified by the PCR and was sequenced directly by a combined method consisting of cycle sequencing and automated fluorescence detection. Pairwise sequence comparisons and a distance matrix analysis showed that the Rhodobacter species could be divided into two major clusters; one cluster included the freshwater and terrestrial species, and the other cluster contained the marine species. The cluster containing the freshwater Rhodobacter species also included Rhodopseudomonas blastica and was linked more closely to the chemotroph Paracoccus denitrificans and the aerobic phototroph Roseobacter denitrificans than to the cluster containing the marine Rhodobacter species. Genomic DNA-DNA hybridization data supported the results of 16S ribosomal DNA sequence comparisons. With few exceptions, the marine Rhodobacter species can be differentiated phenotypically from the freshwater species on the basis of salt requirement for optimal growth, sulfide tolerance, final oxidation product of sulfide, and polar lipid composition. Thus, we propose that all marine Rhodobacter species should be transferred to the genus Rhodovulum gen. nov.; Rhodovulum sulfidophilum comb. nov. is the type species of this genus.
TL;DR: The phylogeny, physiology, morphology, lipid content, and high G+C content of strain H168 are sufficiently different from those of genera belonging to the family Haloanaerobiaceae to justify the definition of a new genus.
Abstract: The occurrence of thermophilic, halophilic anaerobic bacteria in the sediment of a Tunisian salted lake was tested in samples collected at 20-cm intervals down to a depth of 1.20 m. A long rod, present only in the 40-to 60-cm layer, was isolated at 60°C in a medium containing 100 g of NaCl per liter and designated strain H168. This strain produced acetate, ethanol, H2, and CO2 from glucose metabolism. Fructose, xylose, ribose, cellobiose, and starch were also oxidized. The optimum temperature for growth was 60°C. No growth was obtained at 42 or 70°C. Strain H168 grew optimally in NaCl concentrations ranging from 50 to 100 g per liter, with the upper and lower limits of growth around 200 and 40 g per liter, respectively. The G+C ratio of the DNA was 39.6 mol %. Although halophilic, moderately thermophilic bacteria have been characterized among anaerobes, particularly within methanogens, strain H168 is the first true thermophilic (growing above 60°C) halophilic anaerobic bacterium described so far. The phylogeny, physiology, morphology, lipid content, and high G+C content of strain H168 are sufficiently different from those of genera belonging to the family Haloanaerobiaceae to justify the definition of a new genus.
DSM1
TL;DR: The occurrence of MK-9(H2) as the predominant menaquinone, the presence of relatively long-chain mycolic acids, and the phylogenetic position as determined by a 16S ribosomal DNA sequence analysis provide strong evidence that both R. aichiensis and N. amarae should be transferred to the genus Gordona.
Abstract: We investigated the taxonomic status of Rhodococcus aichiensis DSM 43978T (T = type strain) and Nocardia amarae DSM 43392T by using both chemotaxonomic and genetic methods. The occurrence of MK-9(H2) as the predominant menaquinone, the presence of relatively long-chain mycolic acids (48 to 62 carbon atoms), and the phylogenetic position as determined by a 16S ribosomal DNA sequence analysis provide strong evidence that both R. aichiensis and N. amarae should be transferred to the genus Gordona as Gordona aichiensis and Gordona amarae, respectively.
TL;DR: Rhizobial isolates that were obtained from both surface and deep soil samples in the Sahelian and Sudano-Guinean areas of Senegal (West Africa) under Acacia albida trees were compared with representative strains of known rhizobials species and genera to determine the taxonomic positions of these organisms and the relationships between isolates obtained from the surface and isolate obtained from deep soil.
Abstract: Rhizobial isolates that were obtained from both surface and deep soil samples in the Sahelian and Sudano-Guinean areas of Senegal (West Africa) under Acacia albida trees were compared with representative strains of known rhizobial species and genera. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of proteins was used to determine the taxonomic positions of these organisms and the relationships between isolates obtained from the surface and isolates obtained from deep soil. Most of the isolates belonged to eight electrophoretic clusters containing representative strains of Bradyrhizobium japonicum, Bradyrhizobium elkanii, and Bradyrhizobium sp. Isolates were also characterized by the Biolog system, and the results were compared with the results obtained by SDS-PAGE of total proteins; the level of correlation was very low. DNA-rRNA hybridizations with 16S or 23S rRNA from Bradyrhizobium japonicum LMG 6138T (T = type strain) confirmed that most of the protein electrophoretic clusters belong in the Bradyrhizobium-Rhodopseudomonas rRNA complex. Sequencing of 16S rRNA genes showed that some of the A. albida-nodulating isolates belong to a separate lineage together with representatives of other protein electrophoretic clusters. Other isolates that belong to the same electrophoretic cluster as the type strain of Bradyrhizobium japonicum are considered members of the lineage represented by this type strain. The first lineage is as far removed from Bradyrhizobium japonicum as it is from the genus Afipia, Blastobacter denitrificans, and the genus Rhodopseudomonas. The possible relationship among electrophoretic group, geographic origin, and depth of isolation at a particular site is discussed.
TL;DR: A small, anaerobic, gram-positive coccobacillus that reduces cholesterol to coprostanol was isolated from a hog sewage lagoon and it is proposed that it should be the type strain of a new species in the genus Eubacteria, Eubacterium coproStanoligenes.
Abstract: A small, anaerobic, gram-positive coccobacillus that reduces cholesterol to coprostanol was isolated from a hog sewage lagoon. This isolate, strain HLT (T = type strain) does not require cholesterol for growth, but it requires lecithin and has phospholipase activity. Much acid is produced by the fermentation of amygdalin, lactose, and salicin. Arabinose, cellobiose, fructose, glucose, mannose, and melibiose are fermented weakly. Acetic, formic, and succinic acids are produced, as is hydrogen. The isolate does not reduce nitrate, produce indole, or hydrolyze starch and gelatin. Esculin is hydrolyzed. The properties of strain HLT are most similar to those of members of the genus Eubacterium. Because strain HL (= ATCC 51222) has unique morphological and physiological properties, we propose that it should be the type strain of a new species in the genus Eubacterium, Eubacterium coprostanoligenes.