Distinction of species in Aureobasidium and related genera by PCR-ribotyping

Taxonomic markers for differentiation of the anamorph genera Aureobasidium, Hormonema and Kabatiella were developed using PCR-ribotyping with the primers 5.8S-R and LR7 for amplification and the restriction enzymes Alul, DdeI, Hhal, MspI and RsaI for digestion. Aureobasidium and Hormonema are optimally differentiated with MspI; DdeI is particularly useful to distinguish aureobasidium, Kabatiella and Selenophoma. Relationships of the anamorph genera Aureobasidium, Hormoneng and Kabatiella with the teleomorph genera Pringsheimia and Dothiora are discussed.     

Intraspecific variability and exopolysaccharide production inAureobasidium pullulans

Forty seven strains of the black yeasts,Aureobasidium pullulans andHormonema dematioides, and the type strain ofHormonema macrosporum were examined using PCR-ribotyping and universally primed PCR with subsequent hybridization. Four groups (populations) were distinguished withinA. pullulans with PCR-ribotyping, which largely coincided with UP-PCR/hybridization groups. The UP-PCR technique revealed a greater degree of heterogeneity between the groups studied. Five strains identified asHormonema dematioides on the basis of physiological and morphological data formed a group recognizable with PCR-ribotyping and UP-PCR/hybridization, which also includedH. macrosporum. Aureobasidium pullulans is characterized by the absence of RsaI restriction sites in rDNA amplified with primers 5.8S-R and LR7, whileHormonema species possessed several bands after RsaI digestion. For analysis of distance between populations, PCR-ribotyping with AluI and MspI is sufficient. Strains ofA. pullulans produce exopolysaccharides in liquid media with different nitrogen sources, while the strains ofHormonema synthesize minor amounts of polysaccharides in media with peptone. Populations ofA. pullulans differ slightly from each other in their optimal, medium-dependent production of polysaccharides.     

Nutritional physiology and selective isolation ofExophiala dermatitidis

The nutritional physiology of ten strains ofExophiala dermatitidis was investigated. The growth reactions to lactose, citrate, nitrate, nitrite, lysine, creatine and creatinine differ from those found in closely related black yeasts. In addition, it is the onlyExophiala species which is able to grow at 40° C. A selective medium containingmeso-erythritol as sole carbon source was evaluated. This medium is particularly useful for the isolaton of black yeasts from lungs of patients with cystic fibrosis as well as from the environment.     

A new variety of Aureobasidium pullulans characterized by exopolysaccharide structure, nutritional physiology and molecular features

The black yeast Aureobasidium pullulans (de Bary) Arnaud is known to synthesize the exopolysaccharide pullulan, a poly--1,6-maltotriose. Nine strains were found to produce additional aubasidan-like EPS, i.e. glucans with -1,4-D-, -1,6-D- and -1,3-D-glycosidic bonds. These strains had previously been found to deviate in genotypic characters. Additional physiological differences were found: the optimal nitrogen source for exopolysaccharide production in liquid medium was NaNO₃ for aubasidan-producing strains, and (NH₄)₂SO₄ for the remaining strains. A new variety, A. pullulans var. aubasidani Yurlova, is described for the strains producing aubasidan-like components. The new variety can be distinguished from A. pullulans var. pullulans by the absence of assimilation of methyl--D-glucoside and lactose.     

Karyology and hyphal characters as taxonomic criteria in Ascomycetous black yeasts and related fungi

Mycelial development of seventy-three strains of black yeasts and related fungi were studied, and numbers of nuclei per hyphal cell were counted. Two main patterns were apparent in expanding hyphae, viz. (1) uninucleate expanding hyphal cells, septum formation strictly following mitosis, and (2) multinucleate, branched, aseptate hyphal tips, septa being formed in a later stage, leading to oligo- or uninucleate mature cells. Characteristic genera in the two groups areExophiala andAureobasidium, respectively. InZasmidium and in someRamichloridium species all mycelial cells are oligonucleate. The character is indicative for relationships at the family level in black yeasts.     

Coenzyme Q systems in ascomycetous black yeasts

72 Strains belonging to 44 species of ascomycetous black yeasts were analyzed for their coenzyme Q systems. Prevalent were Q-10 and dihydrogenated Q-10 systems. Members of the Dothidealean suborder Dothideineae have Q-10 (H₂), while those belonging to the suborder Pseudosphaeriineae mostly have Q-10. The anamorph genus Exophiala Carmichael and the teleomorph genus Capronia Sacc. seem to be heterogenous.     

Nutritional physiology of type isolates of currently accepted species ofExophiala andPhaeococcomyces

Nutritional physiological and tolerance tests were performed for all type strains of species currently classified in the black yeast generaExophiala andPhaeococcomyces, including some additional type strains of taxa recently reidentified asExophiala species. Most describedExophiala species can be distinguished by physiological characters.Exophiala jeanselmei with its varieties, andE. castellanii should all be retained as separate taxa. The pairs of strainsMycotorula schawii/Exophiala dermatitidis, Hormodendrum negronii/Exophiala jeanselmei var.lecaniicorni andSporotrichum gougerotii/Torula bergeri were found to be conspecific. Phenetic analyses of physiological data support the identity ofPhaeococcomyces exophialae as a yeast-like synanamorph ofExophiala spinifera. The taxonomic positions of the generaNadsoniella, Phaeoannellomyces andWangiella are discussed. The generaExophiala andPhaeococcomyces are unrelated.     

Comparative physiology,biochemistry, and the taxonomy ofChlorella (Chlorophyceae)

According to biochemical and physiological characters, 77 strains ofChlorella were assigned to 12 taxa. The characters used are presence or absence of hydrogenase, formation of secondary carotenoids under nitrogen-deficient conditions, liquefaction of gelatin, products of glucose fermentation, ability to reduce nitrate, thiamine requirement, acid tolerance, salt tolerance, thermophily, and base composition of DNA (GC content). On the other hand, certain nutritional characters, i. e., utilization of organic carbon and nitrogen compounds, were found to be more or less strain-specific, highly variable, and therefore unsuitable for taxonomy.Presented at the symposium Speciation and the Species Concept during the XIIth International Botanical Congress, Leningrad, July 8, 1975.     

The taxonomy of the genusFrankia

Summary A discussion covering the problems ofFrankia taxonomy was held at the Frankia Workshop in Wageningen, September 4–6, 1983. It was agreed that the genusFrankia can be satisfactorily defined, but that solid criteria for species determination are not now available and that use of specific names should be avoided for the present.     

Comparative studies on physiology and taxonomy of obligately purinolytic clostridia

Eleven strains of obligately purinolytic clostridia have been studied with respect to their assignment to the three type strains of Clostridium acidiurici, C. cylindrosporum, and C. purinolyticum. DNA/DNA-hybridization proved to be the method of choice for differentiation whereas phenotypic characteristics such as spore morphology, substrate spectra, nutritional requirements, product formation, and sensitivity against various antibiotics did not allow unequivocal identification. All strains depended on selenite for growth.     

Phylogeny and taxonomy of rhizobia

Rhizobia are bacteria that form nitrogen-fixing nodules on the roots, or occasionally the shoots, of legumes. There are currently more than a dozen validly named species, but the true number of species is probably orders of magnitude higher. The named species are listed and briefly discussed. Sequences of the small subunit ribosomal RNA (SSU or 16S rRNA) support the well-established subdivision of rhizobia into three genera: Rhizobium, Bradyrhizobium, and Azorhizobium. These all lie within the alpha subdivision of the Proteobacteria, but on quite distinct branches, each of which also includes many bacterial species that are not rhizobia. It has been clear for several years that Rhizobium, on this definition, is still too broad and is polyphyletic: there are many non-rhizobia within this radiation. Recently, therefore, it has been suggested that this genus should be split into four genera, namely Rhizobium (R. leguminosarum, R. tropici, R. etli), Sinorhizobium (S. fredii, S. meliloti, S. teranga, S. saheli), Mesorhizobium (M. loti, M. huakuii, M ciceri, M. tianshanense, M. mediterraneum), and a fourth, unnamed, genus for the current R. galegae. The evidence and pros and cons are reviewed.     

Phaeotheca triangularis, a new meristematic black yeast from a humidifier

Two strains of a new species of meristematic fungi, described as Phaeotheca triangularis, were isolated from moisteners of air-conditioning systems. The species is believed to be related to dothideaceous black yeasts. Its morphology, ultrastructure and nutritional physiology are reported.     

Recent developments inRhizobium taxonomy

Recent developments inRhizobium taxonomy are presented from a molecular and evolutionary point of view. Analyses of ribosomal RNA gene sequences provide a solid basis to infer phylogenies in the Rhizobiaceae family. These studies confirmed thatRhizobium andBradyrhizobium are only distantly related and showed thatRhizobium andBradyrhizobium are related to other groups of bacteria that are not plant symbionts.Rhizobium andAgrobacterium species are intermixed. Differences in plasmid content may explain to a good extent the different behavior ofRhizobium andAgrobacterium as symbionts or pathogens. Other approaches to identify and classify bacteria such as DNA-DNA hybridization, fatty acid analysis, RFLP and RPD-PCR techniques and phylogenies derived from other genes are in general agreement to the groupings derived by ribosomal sequences. Only a small proportion of nodulated legumes have been sampled for their symbionts and more knowledge is required on the systematics and taxonomy ofRhizobium andBradyrhizobium species.     

Debaryomyces udenii,sp. nov. (Saccharomycetaceae), a new species from soil

A new, soil-associated species of the genus Debaryomyces, D. udenii, is described. The species is characterized by pusticulate rather than verrucate ascospores, and slowly lytic asci.     

Physiology, biochemistry and taxonomy of deep-sea nitrile metabolising Rhodococcus strains

A collection of nitrile-hydrolysing rhodococci was isolated from sediments sampled from a range of deep coastal, and abyssal and hadal trench sites in the NW Pacific Ocean, as part of our programme on the diversity of marine actinomycetes. Nitrile-hydrolysing strains were obtained by batch enrichments on nitrile substrates with or without dispersion and differential centrifugation pre-treatment of sediments, and were recovered from all of the depths sampled (approximately 1100–6500 m). Two isolates obtained from the Ryukyu (5425 m) and Japan (6475 m) Trenches, and identified as strains of Rhodococcus erythropolis,were chosen for detailed study. Both of the deep-sea isolates grew at in situ temperature (4°C), salinities (0–4% NaCl) and pressures (40–60 MPa), results that suggest, but do not prove, that they may be indigenous marine bacteria. However, the absence of culturable Thermoactinomycespoints to little or no run off of terrestrial microbiota into these particular trench sediments. Nitrile-hydrolysis by these rhodococci was catalysed by a nitrile hydratase–amidase system. The hydratase accommodated aliphatic, aromatic and dinitrile substrates, and enabled growth to occur on a much wider range of nitriles than the only other reported marine nitrile-hydrolysing R. erythropolis which was isolated from coastal sediments. Also unlike the latter strain, the nitrile hydratases of the deep-sea rhodococci were constitutive. The possession of novel growth and enzyme activities on nitriles by these deep-sea R. erythropolisstrains recommends their further development as industrial biocatalysts.     

Assessment of phenotypic and genetic diversity in the yeast genusMetschnikowia

The taxonomy of the yeast genusMetschnikowia has undergone profound changes over the past century. Major developments, from the capacity to obtain pure cultures of parasitic species to progress associated with the extensive use of molecular biology tools in yeast systematics, are briefly reviewed. Results from past work and new data are combined to evaluate evolutionary relationships and clarify the classification of both terrestrial and aquatic species. Recent physiological studies, including the utilization of non-conventional carbon and nitrogen sources, and characteristics like lipolytic activity and maximum temperatures for growth, are presented. The assessment of the genetic diversity within the genus by restriction analysis of the mitochondrial DNA and by the production of specific DNA probes has been explored. The results indicate the potential application of the latter in rapid identification procedures.     

Epicuticular wax morphology and the taxonomy ofRosa (sectionCaninae, subsectionRubiginosae)

Classification within the genusRosa is problematic due to ± continuous variation of morphological characters. The dogroses, (Rosa, sectionCaninae) are classified only by their unique meiotic system not by directly visible characters. The intrasectional structure remains insufficient, as the characters (glands, hairs and prickles) are known to exhibit great morphological divergence affected by both genetic plasticity and environmental influences. Taxonomy of dogroses follows a highly artificial system which allows us to identify morphospecies, which are not necessarily evolutionary species. However, SEM-studies in theCaninae revealed that all taxa of the subsectionRubiginosae are characterised by a granule type of epicuticular waxes, whereas members from the other subsections (with three exceptions) form triangular rodlets. Comparison with specimens grown under the same conditions confirmed these findings on natural populations and additionally revealed that following artificial hybridism, offspring develop the maternal type of wax structure due to the matroclinal inheritance in this section.     

Molecular phylogeny,taxonomy, and evolution of Geosiphon pyriformis and arbuscular mycorrhizal fungi

Geosiphon pyriformis(Kütz.) v. Wettstein is the only known example of a fungus living in endocytobiotic association with a cyanobacterium. The close phylogenetic relationship of Geosiphonwith some arbuscular mycorrhizal fungi (AMF) and the phylogenetic position of Geosiphonare shown in detail. Comprehensive small subunit (SSU) rRNA sequence analyses allow the erection of a new, molecular phylogeny-based taxonomic system for the AMF, including Geosiphon (Geosiphonaceae). Within the recently described phylum Glomeromycota (with one class, Glomeromycetes), a system including four orders was proposed. The erection of several new families will also be necessary. Evolutionary implications are discussed, referring to different possibilities of the influence of AMF on the colonization of the terrestrial habitat by plants.