Deoxyribonucleic Acid Reassociation Research Articles

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

Taxonomic Relationship of Black-Pigmented Bacillus subtilis Strains and a Proposal for Bacillus atrophaeus sp. nov.

The taxonomic position of Bacillus subtilis strains that produce soluble black pigment is unclear. To assess the genetic relatedness between the pigmented and nonpigmented strains, deoxyribonucleic acid (DNA) reassociation was measured spectrophotometrically. Among the 40 pigmented strains examined, two distinct DNA relatedness groups were found. A total of 25 strains (group 1) showed 24 to 34% DNA relatedness and 15 strains (group 2) showed 70 to 100% relatedness to Bacillus subtilis type strain NRRL NRS-744. The intragroup DNA relatedness values for each group ranged from 85 to 100%; the intergroup relatedness values ranged from 20 to 35%. A multilocus enzyme electrophoresis analysis revealed a low level of similarity between group 1 and group 2 or the nonpigmented group. The group 2 strains and the nonpigmented strains clustered in a common group, indicating the close genetic relationship of these organisms. My results strongly suggest that group 2 is a pigmented variant of B. subtilis, but group 1 is a new species, for which the name Bacillus atrophaeus is proposed. The type strain of the new species is strain NRRL NRS-213.

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

Deoxyribonucleic Acid Relatedness Among Species of Saccharomyces Sensu Lato

The generic name Saccharomyces was introduced by Meyen (1838) and defined by Reess (1870). Over the years, the genus included a variable number of phylogenetically heterogeneous species. From about 21 species (Guilliermond, 1912), the genus grew to 30 species and 3 varieties (Lodder and Kreger-van Rij, 1952), and then to 41 species and 6 varieties (van der Walt, 1970). Recently, an extensive reevaluation of the genus left only 7 accepted species (Yarrow, 1984a). During this time, the genus was alternately reorganized and divided. Van der Walt (1965) placed many species in the newly established taxon Kluyveromyces on the basis of spore shape and ascus fragility. Later, Saccharomyces was subdivided into four variously related groups (van der Walt, 1970; Yarrow and Nakase, 1975). Group I represented Saccharomyces sensu stricto and included those species closely related to S. cerevisiae Meyen ex Hansen. These species were subsequently reduced to synonymy with S. cerevisiae on the basis of physiological, morphological and mol % guanine plus cytosine (G+ C) similarities, as well as an absence of reproductive isolation (Naumov, 1969; Yarrow and Nakase, 1975; Yarrow, 1984a). This was partially confirmed by several nuclear deoxyribonucleic acid (nDNA) reassociation studies (Rosini et al., 1982; Vaughan Martini and Kurtzman, 1985; Vaughan Martini and Martini, 1987), although the number of species within the group was found to be actually three: S. cerevisiae, S. bayanus Sacc. and S. pastorianus Hansen. Group II included species closely related to S. bailii Linden, and which are presently assigned to the newly reestablished genus, Zygosaccharomyces (van der Walt and Johannsen, 1975; Yarrow, 1984a). Group III, on the other hand, comprised strains related to S. rosei (Guill.) Lodder et Kreger-van Rij and these species are presently part of the genus Torulaspora (Yarrow, 1984b). Group IV comprised a number of phylogenetically heterogeneous species, and of the 10 listed in the 1970 edition of The Yeasts: A Taxo-

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

Four species of the unicellular green alga Chlorella, C. vulgaris, C. luteoviridis, C. minutissima, and C. zofingiensis, were characterized with respect to DNA similarities as determined by quantitative DNA hybridization procedures. In contrast to previous DNA hybridization procedures. In contrast to previous results, C. vulgaris turned out to be a homogeneous species with the exception of strain 211-11c of the Gottingen collection, which was shown to belong to C. kessleri. Similary, C. luteoviridis and C. minutissima represent well defined species in terms of phenotypic and genotypic features. Whitin C. zofingiensis on strain is clearly different with respect to DNA base composition and DNA hybridization data even though it shares phenotypic characteristics with the other strains of C. zofingiensis.

Taxonomic Revision of the Yeast Genus Kluyveromyces by Nuclear Deoxyribonucleic Acid Reassociation

Deoxyribonucleic acid relatedness among the type strains of all taxa and known anamorphs assigned to the yeast genus Kluyveromyces was assessed by the optical reassociation technique. Three groups of species related at the 95% level or higher were found: (i) K. lactis including K. drosophilarum, K. phaseolosporus, K. vanudeni, and the anamorph Candida sphaerica; (ii) K. marxianus with K. bulgaricus, K. cicerisporus, K. fragilis, K. wikenii, and the anamorphs Candida kefyr, Candida macedoniensis, and Candida pseudotropicalis; (iii) K. thermotolerans with K. veronae and the anamorph Candida dattila. The remaining species, including the recently described K. blattae and K. waltii, are not related to each other or to the members of the above three groups. The nomen nudum K. cellobiovorus is not conspecific with any of the species of the genus. The species assignment obtained by nuclear deoxyribonucleic acid reassociation does not entirely conform with the previously proposed reorganization of the genus Kluyveromyces (J.-P. van der Walt and E. Johannsen, p. 224–251, in N. J. W. Kreger-van Rij, ed., The Yeasts. A Taxonomic Study, 1984).

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

Three newly delimited species of Saccharomyces sensu stricto.

Deoxyribonucleic acid reassociation studies of 24 different wine and beer-associated strains of Saccharomyces confirmed the presence of three separate species. S. cerevisiae and S. bayanus strains had only 22% of their genomes in common. S. pastorianus, with intermediate hybridization values between S. cerevisiae and S. bayanus (52 and 72%, respectively) could possibly be a natural hybrid of the two species. S. pastorianus replaces S. carlsbergensis with which it is homologous for 93% of its genome, since the former species was described first by Hansen in 1904. These data do not agree with the results of traditional physiological tests.

Interspecific Discontinuity in the Genus Clavispora Rodrigues de Miranda by Phenetic Analysis, Genomic Deoxyribonucleic Acid Reassociation, and Restriction Mapping of Ribosomal Deoxyribonucleic Acid

Heterothallic strains belonging to the biologically distinct yeast species Clavispora opuntiae and Clavispora lusitaniae were studied by three different methods. The type cultures of the two yeast species exhibited 8% relatedness as measured by reassociation of unique deoxyribonucleic acid. Ten strains of C. opuntiae and nine strains of C. lusitaniae were compared on the basis of their physiological phenotypes and the restriction maps of their ribosomal deoxyribonucleic acid (rDNAs). Although the two species possessed many similarities as well as certain amounts of intraspecific variation by both approaches, they appeared to constitute well-defined entities. Unlike C. opuntiae, C. lusitaniae always utilized l-rhamnose as the sole carbon source and was resistant to 10 mg of cycloheximide per liter. Strains of C. opuntiae did not utilize l-lysine as the sole nitrogen source or utilized it very weakly, whereas all strains of C. lusitaniae grew rapidly on this compound. By contrast, the hydrolysis of Tween 80 and the utilization of lactic acid, citric acid, and hexadecane tended to be more pronounced in C. opuntiae. The rDNA repeating unit was 9.0 kilobases long in C. lusitaniae, as compared with 7.6 kilobases in C. opuntiae. The conserved region identified previously in the rDNA of C. opuntiae was found almost intact in the rDNA of C. lusitaniae, but the variable regions differed substantially between the two species.

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

Deoxyribonucleic Acid Reassociation between Strains of Lactobacillus animalis, Lactobacillus odontolyticus, and Strains Resembling Lactobacillus acidophilus Isolated from Animals

Lactobacillus animalis comprises homofermentative strains from animals which are recognized by their polypeptide patterns. Physiologically these strains resemble Lactobacillus murinus and Lactobacillus ruminis, but are distinguished from the former by guanine-plus-cytosine content and from the latter by peptidoglycan type. Deoxyribonucleic acid-deoxyribonucleic acid homology confirmed that L. animalis is a homogeneous taxon distinct from L. acidophilus.

Electrophoretic Isoenzyme Variation in Kluyveromyces Populations and Revision of Kluyveromyces marxianus (Hansen) van der Walt

Natural isolates of Kluyveromyces from a variety of habitats were compared on the basis of seven isoenzyme patterns. Some strains of Candida considered to be Kluyveromyces anamorphs, as well as one strain each of Candida sake, Saccharomyces cerevisiae, and Pichia fluxuum, were also examined. The isoenzyme patterns readily substantiated the relationships between the anamorphs and their putative teleomorphs and the nonmember status of strains not belonging to the genus. A multivariate analysis of the electrophoretic patterns indicated that isolates belonging to the Kluyveromyces lactis and Kluyveromyces marxianus deoxyribonucleic acid reassociation groups are not phenotypically continuous with one another or with the former species Kluyveromyces dobzhanskii, and thus we propose to reinstate these taxa as separate species. Taxa previously described as Kluyveromyces thermotolerans and Kluyveromyces waltii also appeared to constitute reproductively isolated natural populations. When the results of isoenzyme electrophoresis were compared with deoxyribonucleic acid reassociation data and with mating compatibility patterns determined by other workers, we found that deoxyribonucleic acid relatedness gives a more accurate view of relationships among Kluyveromyces species.

Resolution of the Varietal Relationship within the Species Pichia opuntiae and Establishment of a New Species, Pichia thermotolerans comb. nov.

The varietal relationship within the species Pichia opuntiae was determined by a study of deoxyribonucleic acid relatedness and by a comparison of the electrophoretic mobilities of 12 metabolic enzymes. The nuclear genomes of P . opuntiae var. opuntiae and P . opuntiae var. thermotolerans showed about 28% relative binding to hydroxylapatite in intervarietal deoxyribonucleic acid reassociation experiments, and the allozymes encoded by eight loci were different in the two taxa. Based on these molecular criteria, as well as allopatry, different host plants, and weak sexual interaction, P . opuntiae var. thermotolerans is raised to the rank of species as Pichia thermotolerans (Starmer et al.) Holzschu et al. comb. nov.

Deoxyribonucleic Acid Reassociation Between Actinomyces denticolens and Other Actinomyces Species from Dental Plaque

The status of the new species Actinomyces denticolens was established by deoxyribonucleic acid-deoxyribonucleic acid homology. The level of homology with Actinomyces naeslundii, Actinomyces viscosus, and Actinomyces howellii was low in each case.

Lactobacillus piscicola, a New Species from Salmonid Fish

The name Lactobacillus piscicola sp. nov. is proposed for a group of 17 bacterial strains that were isolated from diseased rainbow trout (Salmo gairdneri), cutthroat trout (Salmo clarki), and chinook salmon (Oncorhynchus tshawytscha). This bacterium was found most frequently in infected fish which had suffered some form of stress, such as that which occurs at spawning. Occasionally, pathological signs in the internal organs or skin were observed. Phenotypically, L. piscicola belongs to the family Lactobacillaceae and can be distinguished from other species of Lactobacillus by its morphology and physiological characteristics. dl-Lactic acid was produced homofermentatively from glucose. Diaminopimelic acid was present in the cell wall peptidoglycan. The 17 isolates were closely related genetically, as demonstrated by similar percent guanine-plus-cytosine contents (35 mol%) and high deoxyribonucleic acid reassociation values, both characteristics of a single species. The isolates exhibited less than 10% deoxyribonucleic acid reassociation with other reference Lactobacillus strains with similar guanine-plus-cytosine contents. Strain B270 (= ATCC 35586), which was isolated in 1970 from diseased cutthroat brood trout at Bandon Hatchery in Oregon, is designated the type strain of this new species of Lactobacillus.

Nucleic Acid Hybridization Studies and Deoxyribonucleic Acid Base Compositions of Anaerobic, Gram-Positive Cocci

Deoxyribonucleic acid-deoxyribonucleic acid reassociation and deoxyribonucleic acid-ribosomal ribonucleic acid cistron similarity studies showed that the anaerobic, gram-positive cocci comprise a rather heterogeneous group of bacteria. The deoxyribonucleic acid-ribosomal ribonucleic acid hybridization studies distinguished seven groups. Groups 1 and 2 consisted of Peptostreptococcus magnus and Peptostreptococcus prevotii, respectively. Peptostreptococcus asaccharolyticus ATCC 14963T (T = type strain) and Peptostreptococcus indolicus ATCC 29427T formed a third group, and Peptostreptococcus asaccharolyticus DSM 20364 together with Hare group VIII strain NCTC 9820 formed group 4. Peptostreptococcus anaerobius DSM 20357 was more closely related to Eubacterium tenue ATCC 25553T and Clostridium lituseburense ATCC 25759T than to any of the other species studied. Peptostreptococcus micros strains DSM 20468T and DSM 20367 together with strains belonging to Hare group IX formed group 6, and group 7 consisted of Peptostreptococcus parvulus DSM 20469T. Strains of different Hare groups were all assigned to one of the seven groups or to the genus Staphylococcus (Hare group VIIb strain NCTC 9819) or the genus Streptococcus (Hare group VIa strain NCTC 9806). The anaerobic cocci also have a diversity of murein structures. This is the first report showing that strains belonging to the same species have different murein types.

Deoxyribonucleic Acid Relatedness of Bacillus circulans Jordan 1890 Strains

Deoxyribonucleic acid reassociation measurements revealed that 50 of 111 Bacillus circulans Jordan 1890 strains examined could be separated into 10 groups of genetically related organisms. The results of deoxyribonucleic acid relatedness studies and phenotypic comparisons suggested that five of these groups were hitherto undescribed species and that four others probably represented previous ly, but inadequately, described species. The tenth group, which included the type strain, represented the species B. circulans sensu stricto. Our data show that B. circulans and Bacillus macerans Schardinger 1905 are genetically and phenotypically distinct species. Thus, the phenotypic heterogeneity of the species B. circulans sensu lato is not due to inherent variability of genetically related strains but rather is due to inclusion of genetically unrelated organisms in this taxon.

Deoxyribonucleic Acid Reassociation Between Strains of Bacillus firmus, Bacillus lentus, and Intermediate Strains

Deoxyribonucleic acid homologies were examined in 23 strains labeled Bacillus firmus, Bacillus lentus, or intermediate between these two species. With one exception (strain NRS 1560), the 11 strains assigned to B. firmus showed high homologies with the deoxyribonucleic acid of the type strain of B. firmus (ATCC 14575). However, the strains labeled B. lentus (five strains) or intermediate (seven strains) showed low homologies (approximately 5%) with the standard strains of B. firmus and with each other, except for one intermediate strain (NRS 1369), which showed high homology (98%) with one of the standard strains of B. firmus, and strains NRS 883 and NRS 1262 (both labeled B. lentus), which showed high homology (50%) with each other.

Taxonomy of Bacillus circulans Jordan 1890: Base Composition and Reassociation of Deoxyribonucleic Acid

The guanine-plus-cytosine (G+C) contents of 123 strains previously identified as Bacillus circulans Jordan 1890 were determined. Of the strains examined, only 18 had G+C contents of 37 to 41 mol%, a range that included the G+C content (38.1 mol%) of the type strain. A major portion of the strain (93 strains) had G+C contents in the range from 46 to 55 mol%. For seven strains the G+C contents ranged from 42 to 45 mol%, and for another small group of five strains the G+C contents ranged from 56 to 61 mol%. Deoxyribonucleic acid reassociation studies revealed that 10 of the 18 strains with G+C contents of 37 to 41 mol% were closedly related genetically to each other and to the type strain. This genetically related group was phenotypically quite homogeneous. Our results strongly suggested that most of the strains were misclassified as B. circulans. Consequently, the phenotypic heterogeneity of the species B. circulans Jordan 1890 was not due to inherent variability of genetically related strains, but to variability introduced by inclusion of genetically unrelated organisms.

Analysis of Antigens of Rhodococcus Species by Rocket Immunoelectrophoresis

Seventeen representative strains of Rhodococcus and related taxa were analyzed for antigenic relationships by rocket immunoelectrophoresis. A good correlation was found between data from this form of analysis and previously reported numerical phenetic and deoxyribonucleic acid reassociation data. Rhodococcus ruber and Rhodococcus erythropolis strains formed distinct clusters in a dendrogram produced by average linkage analyses for dissimilarity matrices. Rhodococcus equi, Nocardia asteroides, and an unidentified Rhodococcus strain formed single-member clusters, whereas Rhodococcus coprophilus was found to be heterogeneous. In contrast, R. erythropolis and R. ruber were found to be distinct species. The discrepancies between deoxyribonucleic acid pairing and rocket immunoelectrophoresis results can be explained on the basis of suboptimal antigen or antiserum preparations.