The use of karyotyping in the systematics of yeasts

The use of electrophoretic karyotyping in systematics of yeasts is discussed. New data are provided on the karyotypes of the medically important fungiHortaea werneckii, Filobasidiella (=Cryptococcus)neoformans, andMalassezia species.Hortaea werneckii has twelve to eighteen bands of chromosomal DNA, ranging in size between 500 and 2300 kb. The karyotypes ofFilobasidiella neoformans consist of seven to fourteen bands of chromosomal DNA. The varietiesneoformans andbacillispora cannot be separated by their karyotypes, and no obvious correlation was found with serotypes, geography or habitat. All strains ofMalassezia pachydermatis studied have similar karyotypes consisting of five bands, whereas inM. furfur, four different karyotypes are prevalent. However, each of these karyotypes is stable.     

A reevaluation of the genus Malassezia by means of genome comparison

Results of a study of the genus Malassezia on the basis of genome characters confirm that two species should be maintained, M. furfur and M. pachydermatis. The two forms associated with skin disease, frequently referred to as Pityrosporum orbiculare and P. ovale, were found to be synonymous, the name M. furfur having priority. Malassezia pachydermatis, hitherto regarded as a strictly zoophilic species, may also be found on humans.     

Atypical non-lipid-dependent strains of <Emphasis Type="Italic">Malassezia furfur</Emphasis>

Members of the yeast genus Malassezia, including atypical strains, are lipophilic except for Malassezia pachydermatis. New physiological features that characterize atypical Malassezia strains are mainly associated with alteration in Tween assimilation pattern — such isolates still require lipids for growth. We isolated three non-lipid-dependent strains of Malassezia from patients with diagnosed atopic dermatitis (AD). These isolates could not be identified to the species level via their physiological properties. Phylogenetic trees, based on the D1/D2 regions of the 26S rDNA gene sequences and nucleotide sequences of the ITS1-5.8S-ITS2 rRNA region, showed the isolates to belong to Malassezia furfur. Three non-lipid dependent isolates from AD skin were conspecific, and sequences analysis proved them to be M. furfur.     

Confirmation of the nomenclatural status ofMalassezia pachydermatis

Malassezia strains from dogs and rhinoceros all proved identical using mole % G + C and nDNA/DNA reassociation experiments. The use of the nameMalassezia pachydermatis, originally described for a strain isolated from a rhinoceros, is thus justified for non lipid-dependent strains of other sources.     

Suitability of lipid materials for culture ofMalassezia as evaluated from its cellular fatty acid composition

Malassezia is a facultative or obligatory lipophilic yeast. We devised new lipid-supplemented media suitable for the culture ofMalassezia. Malassezia furfur andM. pachydermatis grew well on both solid and liquid media supplemented with creaming powder preparations which are commercially available at moderate prices. Striking differences were found between the cellular fatty acid compositions ofM. furfur grown on media supplemented with creaming powder and that grown on media with conventional olive oil.Malassezia furfur grown on media with olive oil had nearly the same fatty acid composition as olive oil, with C18:1 amounting to 80%, while that grown on media supplemented with creaming powder had C16, C18:1 and C18:2 as the principal components. The use of these supplementary lipids appeared not to inhibit the normal synthesis of fatty acid inM. furfur. For the culture ofM. pachydermatis, media supplemented with creaming powder were also found more suitable than lipid-free media. The media devised are considered excellent, because they appear to provide a more natural growth environment forMalassezia.     

Extracellular enzymatic activity of Malassezia spp. isolates

Extracellular enzymatic activity of different species of Malassezia spp was evaluated. Thirty-three isolates of animal origin (dogs and cats) and stock culture samples were studied. Twenty isolates of M. pachydermatis, 8 of M. furfur, 2 of M. sympodialis and M. globosa and one of M. restricta, M. obtusa and M. slooffiae were examined. The enzymatic activity was investigatedusing Api Zym system. The enzymatic patterns showed light differences. Esterase lipase, Phosphatase acid and Naphtol-AS-BI-phosphohydrolase were produced in significant amounts from most isolates excepted for M. restricta, confirming the limited enzymatic activity of this species. Data obtained from the other new species described after the revision of the genus, appear to be quite homogeneous. Dixon’s broth appeared to be a valid medium for the growth of all Malassezia spp. This revised version was published online in June 2006 with corrections to the Cover Date.     

Saccharomyces barnetti andSaccharomyces spencerorum: two new species ofSaccharomyces sensu lato (van der Walt)

In the course of a study of DNA base sequence homology, 19 strains labelled asSaccharomyces exiguus, its imperfect state,Candida holmii, orC. milleri were examined. Results confirmed the separation ofC. milleri as a separate species. The remaining strains can be divided into three distinct groups of genomic relatedness. The type cultures ofS. exiguus andC. holmii form a cluster with 10 other strains showing variable reassociation values ranging from 100 to 40%. The remaining four strains comprise two separate species showing no nucleotide relatedness between themselves nor to either theS. exiguus complex or toC. milleri. Physiological analyses demonstrate that it is possible to separate these four taxa on the basis of a few simple tests. The two new species are described respectively asSaccharomyces barnetti honoring James Barnett in recognition of his invaluable work in the field of yeast taxonomy andSaccharomyces spencerorum in honor of J.F.T. and Dorothy M. Spencer who have made innumerable contributions to the genetics and biotechnological application of yeasts.     

Molecular Analysis of Malassezia Microflora from Patients with Pityriasis Versicolor

Background: Pityriasis versicolor (PV) is a superficial infection of the stratum corneum caused by Malassezia species. Eleven species have been identified within this genus, namely M. globosa, M. restricta, M. sympodialis, M. furfur, M. obtusa, M. slooffiae, M. pachydermatis, M. dermatis, M. japonica, M. yamatoensis, M. nana. M. furfur has long been identified as the causative fungus of PV. However, recent studies using the culture and isolation identified by morphological and physiological characteristics suggest that M. globosa is the causative agent of PV. Objectives: The aim of this study was to examine the distribution of PV microorganisms with a molecular-based non-culture method. Patients: The subjects were 49 patients with PV (32 males, 17 females; 16–83 years old) who visited our outpatient clinic. Methods: Samples were taken from lesions for direct microscopy with methylene blue and detected Malassezia species without M. pachydermatis and M. nana using a non-culture-based method consisting of nested PCR with specific primers. Results: The most frequently isolated species were M. globosa and M. restricta (both 93.9%). Only M. globosa was detected from the lesion in which the mycelial form alone was observed microscopically, but M. restricta was not. Conclusions: Our results suggest that M. globosa is the causative agent of PV.     

Studies on the diversity of the distinct phylogenetic lineage encompassing Glomus claroideum and Glomus etunicatum

Morphological and molecular characters were analysed to investigate diversity within isolates of the Glomus claroideum/Glomus etunicatum species group in the genus Glomus. The inter- and intra-isolate sequence diversity of the large subunit (LSU) rRNA gene D2 region of eight isolates of G. claroideum and G. etunicatum was studied using PCR-single strand conformational polymorphism (SSCP)-sequencing. In addition, two isolates recently obtained from Southern China were included in the analysis to allow for a wider geographic screening. Single spore DNA isolation confirmed the magnitude of gene diversity found in multispore DNA extractions. An apparent overlap of spore morphological characters was found between G. claroideum and G. etunicatum in some isolates. Analysis of the sequence frequencies in all G. etunicatum and G. claroideum isolates (ten) showed that four LSU D2 sequences, representing 32.1% of the clones analysed for multispore extraction (564) were found to be common to both species, and those sequences were the most abundant in four of the ten isolates analysed. The frequency of these sequences ranged between 23.2% and 87.5% of the clones analysed in each isolate. The implications for the use of phenotypic characters to define species in arbuscular mycorrhizal fungi are discussed. The current position of G. claroideum/G.etunicatum in the taxonomy of the Glomeromycota is also discussed.     

Single copy DNA homology in sea stars

Summary The sequence homology in the single copy DNA of sea stars has been measured. Labeled single copy DNA fromPisaster ochraceus was reannealed with excess genomic DNA fromP. brevispinus, Evasterias troschelii, Pycnopodia helianthoides, Solaster stimpsoni, andDermasterias imbricata. Reassociation reactions were performed under two criteria of salt and temperature. The extent of reassociation and thermal denaturation characteristics of hybrid single copy DNA molecules follow classical taxonomic lines.P. brevispinus DNA contains essentially all of the sequences present inP. ochraceus single copy tracer whileEvasterias andPycnopodia DNAs contain 52% and 46% of such sequences respectively. Reciprocal reassociation reactions with labeledEvasterias single copy DNA confirm the amount and fidelity of the sequence homology. There is a small definite reaction of uncertain homology betweenP. ochraceus single copy DNA andSolaster orDermasterias DNA. SimilarlySolaster DNA contains sequences homologous to approximately 18% ofDermasterias unique DNA. The thermal denaturation temperatures of heteroduplexes indicate that the generaPisaster andEvasterias diverged shortly after the divergence of the subfamilies Pycnopodiinae and Asteriinae. The twoPisaster species diverged more recently, probably in the most recent quarter of the interval since the separation of the generaPisaster andEvasterias.     

Chloroplast DNA reassociation and grass phylogeny

Sequence variation in chloroplast DNA (cpDNA) as measured by DNA reassociation was examined in 12 grass species to address systematic problems in thePoaceae at the subfamilial and tribal levels. Two species,Petunia (Solanaceae) andGlycine (Leguminosae), were included to determine degrees of sequence divergence in cpDNA between monocots and dicots. The data were analyzed phenetically and phylogenetically. Species were segregated into four major groups that corresponded to the subfamiliesPooideae, Oryzoideae, Chloridoideae, andPanicoideae. Representatives of thePooideae andOryzoideae grouped together as did members of theChloridoideae andPanicoideae. ThePooideae split into two major groups corresponding to the recently recognized supertribesTriticanae andPoanae. Internodes between subfamily branches were short which might indicate a burst of divergence in the family early in its evolution. Sequence similarity values between the monocot grass species and the two dicot taxa ranged from 0.15 to 0.27, representing the highly conserved sequences of the chloroplast genome.     

Occurrence and Population Size of <Emphasis Type="Italic">Malassezia</Emphasis> spp. in the External Ear Canal of Dogs and Cats Both Healthy and with Otitis

Malassezia yeasts are commensal organisms of human and animal skin that occasionally act as pathogens; lipid-dependent species are associated with human skin disorders. The aim of this work was to evaluate the occurrence, risk factors and population size of different species of Malassezia in the external ear canal of dogs and cats with and without otitis externa. Between 2001 and 2003, 107 healthy animals (25 cats and 82 dogs) and 123 animals with chronic otitis exteirna (48 cats and 75 dogs) were clinically examined. Sterile cotton swabs were used to collect specimens from the external ear canal and culture tests and cytological examinations were performed to detect the presence and population size of Malassezia yeasts. Malassezia yeasts were isolated from 72.9% and 40% of the cats and from 57.3% and 28.0% of the dogs, with and without otitis externa, respectively. Malassezia was frequently isolated from animals under 5 years of age. The highest prevalence of positive samples was reported in winter for cats and in autumn for dogs. Dogs with pendulous ears showed a higher incidence of infection than dogs with erect ears. More Malassezia yeasts were recovered from animals with otitis (i.e. 59.6 colony forming units – CFUs – for cats and 66.0 CFUs for dogs) than healthy animals. Out of the 413 isolates obtained from animals with and without otitis, 403 (97.6%) were identified as M. pachydermatis and 10 (2.4%) as M. globosa. A statistical evaluation of the occurrence of Malassezia yeasts in dogs and cats revealed that predisposing factors for Malassezia infections are sampling period for cats, and type of ear for dogs. The largest population of Malassezia yeasts was detected in animals with otitis, suggesting a role in the occurrence of lesions.     

Phylogenetic relationship withinFusarium sambucinum Fuckel sensu lato,determined from ribosomal RNA sequences

Partial ribosomal RNA nucleotide sequences were determined for 11 strains ofFusarium sambucinum Fuckelsensu lato to assess by molecular genetic means, Nirenberg's recent morphotaxonomic interpretation which split the species into three distinct taxa:F. sambucinum sensu stricto, F. torulosum, and one other species, as yet unnamed (Fusarium species nova). Four sequence patterns were identified among the 11 strains. Two sequences that varied at one site were found among strains ofF. sambucinum, strains ofF. torulosum andFusarium sp. nov. showed no intraspecific variation. Interspecific comparisons revealed nucleotide sequence differences of 3–9 substitutions in the ca. 240 nucleotide rRNA segment examined. Although interspecific differences are not large in terms of percent nucleotide substitution, they are much larger than the observed intraspecific variation and support the morphological interpretation distinguishing three taxa. When the data were analysed using parsimony and bootstrapping, the three taxon tree was well supported. The phylogenetic arrangement of these strains is congruent with secondary metabolite profile similarities.     

The 5S DNA units ofAcacia species (Mimosaceae)

The DNA sequence structure of 5S DNA units inAcacia species, including representatives from the three subgenera ofAcacia, have been determined. The data was interpreted to suggest that at least three lineages of 5S DNA sequences exist inAcacia and the proposal was made that the lineages be named5S Dna-1, 5S Dna-2, and5S Dna-3. The5S Dna-1 lineage was represented by units fromA. boliviana andA. bidwilli, the5S Dna-2 lineage by units fromA. melanoxylon, A. pycnantha, A. ulicifolia, A. boliviana, A. bidwillii, andA. albida, and the5S Dna-3 lineage by units fromA. bidwillii, A. boliviana, andA. senegal. Based on this interpretation of the sequence data, the Australian species of subg.Phyllodineae grouped together as a cluster, quite separate from the subgeneraAculeiferum andAcacia. As expected from the analyses of morphological characters, the 5S DNA units fromAcacia albida (syn.Faidherbia albida) were quite separate from the otherAcacia spp.     

Three new species ofBullera isolated from leaves in the Ogasawara Islands

Thirteen strains of ballistoconidium-forming yeasts were isolated from leaves collected in the Ogasawara Islands, Japan. They represent three different species in the genusBullera on the basis of morphological, physiological, and biochemical characteristics, analyses of the sequences of internal transcribed spacer regions and small subunit ribosomal DNA, and a nuclear DNA-DNA hybridization study. Three new species,Bullera boninensis (five strains),B. waltii (seven strains), andB. schimicola (one strain), are proposed for these 13 strains.     

Isolation of Malassezia globosa and M. sympodialis from patients with pityriasis versicolor in Spain

Pityriasis versicolor is a superficial infection of the stratum corneum by several yeast species formerly collectively named Malassezia furfur. The genus Malassezia has been recently enlarged with new species. With the exception of M. pachydermatis, the remaining six species have an absolute requirement in vitro for supplementation of long-chain fatty acids in media. These lipophilic yeasts comprise six species: M. furfur, M. globosa, M. obtusa, M. restricta, M. slooffiae and M. sympodialis. The aim of this study was to establish whether there was any association between the various species of Malassezia and pityriasis versicolor lesions. Thus, we studied the isolates from 79 patients with pityriasis versicolor, both from lesions and from apparently healthy skin close to the visible lesions. In pityriasis versicolor lesions, the species most frequently isolated was M. globosa (90%), followed by M. sympodialis (41%). Almost all isolates (99%) belonged to one of these two species. The most frequent pattern was M. globosa as the sole species (58% of cases), although the association with M. sympodialis was also frequent (30%). These results confirmed M. globosa as the main agent of pityriasis versicolor and M. sympodialis as the second agent in importance. Malassezia globosa was found to be a species with high levels of esterase and lipase enzymes of probable importance in their pathogenicity. This revised version was published online in June 2006 with corrections to the Cover Date.     

<Emphasis Type="Italic">Malassezia</Emphasis> spp. in Acoustic Meatus of Bats (<Emphasis Type="Italic">Molossus molossus</Emphasis>) of the Amazon Region,Brazil

The yeasts of the Malassezia genus are opportunistic microorganisms and can cause human and animal infections. They are commonly isolated from the skin and auricular canal of mammalians, mainly dogs and cats. The present study was aimed to isolate Malassezia spp. from the acoustic meatus of bats (Molossus molossus) in the Montenegro region, “Rondônia”, Brazil. From a total of 30 bats studied Malassezia spp. were isolated in 24 (80%) animals, the breakdown by species being as follows (one Malassezia sp. per bat, N = 24): 15 (62.5%) M. pachydermatis, 5 (20.8%) M. furfur, 3 (12.5%) M. globosa and 1 (4.2%) M. sympodialis. This study establishes a new host and anatomic place for Malassezia spp., as it presents the first report ever of the isolation of this genus of yeasts in the acoustic meatus of bats.     

Non-equivalency of genera inAngiospermae: Evidence from DNA hybridization studies

The problem of taxa equivalency in phylogenetically distant groups can hardly be solved by comparing morphological differences alone. An attempt is made to approach the problem by means of DNA comparisons, e.g., DNA hybridization. Data obtained forCompositae, Umbelliferae andIridaceae indicate that both unique and repetitive DNA sequence comparisons lead to the conclusions that genera within these families are not equivalent, e.g., the differences in the DNA among the species ofIris are much more pronounced than among those ofAchillea; some genera ofUmbelliferae occupy an intermediate position.     

莪术基原植物DNA条形码序列的筛选与鉴定

为寻找适用于中药材莪术基原植物鉴定的DNA条形码序列,探索快速高效的莪术基原植物鉴定的新方法,该文首先利用扩增成功率和测序成功率对中药材莪术三种基原植物,9个样本的7种DNA条形码序列(ITS、ITS2、matK、psbA-trnH、trnL-trnF、rpoB和atpB-rbcL)进行评估,然后利用MEGA6.0软件对获得的高质量的序列通过变异位点分析、遗传距离计算和系统树分析等进一步进行评估,最后将筛选到的DNA条形码序列对未知基原的待测样品进行基原鉴定。结果表明:(1) ITS、ITS2和matK等条形码序列在莪术基原植物中的扩增或测序成功率较低,难以应用于实际鉴定;而psbA-trnH、trnL-trnF和rpoB条形码序列变异位点信息过少,不足于区分莪术的三种不同基原植物;只有atpB-rbcL条形码序列的扩增和测序成功率较高,容易获得高质量的序列,同时序列长度(642～645 bp)理想,变异位点多(11个),可实现莪术的三种不同基原的区分鉴别。(2)待测样品经基于atpB-rbcL序列构建的系统发育树鉴别为温郁金。综上所述,叶绿体atpB-rbcL序列能够准确鉴定莪术不同基原植物,可以作为中药材莪术基原植物鉴定的条形码序列。