A genome sequence-based approach to taxonomy of the genus Nocardia

The genus Nocardia includes both pathogens and producers of useful secondary metabolites. Although 16S rRNA analysis is required to accurately discriminate among phylogenetic relationships of the Nocardia species, most branches of 16S rRNA-based phylogenetic trees are not reliable. In this study, we performed in silico analyses of the genome sequences of Nocardia species in order to understand their diversity and classification for their identification and applications. Draft genome sequences of 26 Nocardia strains were determined. Phylogenetic trees were prepared on the basis of multilocus sequence analysis of the concatenated sequences of 12 genes (atpD-dnaJ-groL1-groL2-gyrB-recA-rpoA-secA-secY-sodA-trpB-ychF) and a bidirectional best hit. To elucidate the evolutionary relationships of these genes, the genome-to-genome distance was investigated on the basis of the average nucleotide identity, DNA maximal unique matches index, and genome-to-genome distance calculator. The topologies of all phylogenetic trees were found to be essentially similar to each other. Furthermore, whole genome-derived and multiple gene-derived relationships were found to be suitable for extensive intra-genus assessment of the genus Nocardia.     

Numerical taxonomy of some taxa of the genus Fucus in the Iberian Peninsula

A study of morphological variation patterns in three Iberian Fucus species has been carried out. Data on 36 features from 113 specimens have been studied by numerical methods (PCA, discriminant analysis and ANOVA).The PCA ordination displayed a continuous trend of variation in the following Fucus species: F. ceranoides, F. vesiculosus and F. spiralis. However, no obvious morphological discontinuities have been observed. In addition, three varieties of F. spiralis and five of F. vesiculosus have been identified.At the varietal level discriminant functions could be used for identifying 93–100% of the individuals within F. vesiculosus and 72–91% of F. spiralis.The most discriminating diagnostic character appeared to be the midrib size, as detected by ANOVA procedures.Some qualitative characters, such as presence of vesicles, dioecious-monoecious character and receptacle edge shape, frond and receptacle shape, have been also important for discriminating specific and infraspecific taxa.A nomenclatural discussion of varietal taxa is also included.     

Phylogeny and taxonomy of the genus Cylindrocladiella

The genus Cylindrocladiella was established to accommodate Cylindrocladium-like fungi that have small, cylindrical conidia and aseptate stipe extensions. Contemporary taxonomic studies of these fungi have relied on morphology and to a lesser extent on DNA sequence comparisons of the internal transcribed spacer regions (ITS 1, 2 and 5.8S gene) of the ribosomal RNA and the ??-tubulin gene regions. In the present study, the identity of several Cylindrocladiella isolates collected over two decades was determined using morphology and phylogenetic inference. A phylogeny constructed for these isolates employing the ??-tubulin, histone H3, ITS, 28S large subunit and translation elongation factor 1-alpha gene regions resulted in the identification of several cryptic species in the genus. In spite of the 18 new Cylindrocladiella species described in this study based on morphological and sequence data, several species complexes remain unresolved.     

Biochemical markers in taxonomy of the genus Cunninghamella

The chemical composition of fatty acids and ubiquinones was studied in 18 strains of Cunninghamella, to establish quantitative and qualitative differences within the genus. Fatty acids analysis has shown the presence of four groups. Ubiquinone analysis, through high performance liquid chromatography (HPLC), demonstrated the existence of three different groups based on the ubiquinone type. The average percentage of fatty acids of the species Cunninghamella elegans and Cunninghamella bertholletiae, show variations in linolenic and stearic acids, suggesting the possibility of differentiation between the two species.     

Numerical taxonomy of Streptococcus

A numerical taxonomic study of strains of Streptococcus, together with representatives of allied genera, showed 28 reasonably distinct phenons. The major areas, with their phenons, were: (a) enterococcal species group (S. faecalis, S. faecium, 'S. avium' and a proposed new species 'S. gallinarum'); (b) paraviridans species group (S. bovis, S. equinus, S. salivarius, 'S. casseliflavus', S. mutans, S. raffinolactis and an unidentified Oral Group I); (c) lactic species group (S. lactis including S. cremoris); (d) thermophilic species group (S. thermophilus); (e) viridans species group (S. mitis, S. sanguis, a proposed new species 'S. oralis' and 'S. milleri'); (f) pyogenic species group (S. agalactiae, S. pyogenes, S. equi, 'S. equisimilis' including 'S. zooepidemicus, and a cluster of Lancefield Group B strains of human origin); (g) parapyogenic species group (S. uberis, 'S. dysgalactiae', and a cluster of strains of Lancefield Groups R, S and T). Species of Aerococcus, Gemella, Leuconostoc and Pediococcus are very closely related to the streptococci.     

Integrative taxonomy of the cave-dwelling mysids of the genus Hemimysis

The genus Hemimysis (Malacostraca: Mysida: Mysidae) encompasses near-bottom, demersal and cave-dwelling mysids living in the marine, brackish and freshwater habitats around the European coast, from the Caspian Sea to the Scandinavian Peninsula. We conducted cladistic analysis of 52 morphological characters of all nine species and three subspecies of the genus Hemimysis. We also completed a molecular analysis based on three molecular markers of Hemimysis lamornae (Couch, 1856) found in the English Channel, the Mediterranean Sea, and the Black Sea. Both analyses did not support monophyly of Hemimysis lamornae. We thus consider the former subspecies H. lamornae pontica (Czerniavsky, 1882 Chevaldonné, P., &; Lejeusne, C. (2003). Regional warming‐induced species shift in north‐west Mediterranean marine caves. Ecology Letters, 6, 371–379. doi:10.1046/j.1461-0248.2003.00439.x.[Crossref], [Web of Science ®] , [Google Scholar]) and H. lamornae mediterranea Bacescu, 1936 Bacescu, M. (1936). Hemimysis lamornae sbsp. reducta, nov. sbsp. et Hemimysis anomala dans les eaux roumaines de la Mer Noire (avec une etude comparative des forms de Hem. lamornae des autres mers: H. l. typica et H.l. mediterranea, nov. sbsp.). Annales Scientifiques de L’Universite de Jassy, 23, 331–338. [Google Scholar] as valid species. Analysis of mitochondrial cytochrome oxidase subunit I (COI) sequences of H. pontica shows no significant divergence between mysids living in the marine caves of Crimea and Bulgaria. Morphological trends in Hemimysis are discussed, H. pontica Czerniavsky, 1882 Chevaldonné, P., &; Lejeusne, C. (2003). Regional warming‐induced species shift in north‐west Mediterranean marine caves. Ecology Letters, 6, 371–379. doi:10.1046/j.1461-0248.2003.00439.x.[Crossref], [Web of Science ®] , [Google Scholar] is redescribed, and a new key to all 11 species of the genus is given.     

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 Göttingen 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.     

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

DNA hybridization techniques showed Chlorella fusca var. vacuolata and C. kessleri to be homogeneous species with DNA homologies of 90–100% C. fusca var. fusca and var. rubescens, however, have only about 15% DNA homology with C. fusca var. vacuolata and should no longer be regarded as varieties. A good correlation was found so far between biochemical and physiological characters used in the taxonomy of Chlorella and DNA relatedness. Mutant strains of Chlorella were tested for DNA homologies to prove the reliability of the taxonomical interpretation.     

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

The genetic relationships of nine strains of Chlorella saccharophila were determined by DNA hybridization techniques. Four strains are closely related to the type strain 211-9a and one strain seems to be moderately related, whereas the taxonomic position of the remaining three strains is not clear. C. saccharophila, like C. sorokiniana, is another species of Chlorella containing strains which are heterogeneous in their overall DNA base sequence and partly also in morphological, biochemical and physiological characters.     

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

DNA homologies of 14 strains of Chlorella protothecoides were determined. All strains are related by a high degree of DNA similarity (96–102% D) with the exception of strain 211-11 a which proved to belong to C. kessleri. There is, however, no detectable DNA homology with strains of the genus Prototheca which is supposed to have evolved from C. protothecoides by loss of photosynthetic pigments. Even within Prototheca the low degree of DNA similarity indicates a heterogeneity similar to that observed in the genus Chlorella.