A phylogenetic study on galactose-containing Candida species based on 18S ribosomal DNA sequences

Phylogenetic relationships of 33 Candida species containing galactose in the cells were investigated by using 18S ribosomal DNA sequence analysis. Galactose-containing Candida species and galactose-containing species from nine ascomycetous genera were a heterogeneous assemblage. They were divided into three clusters (II, III, and IV) which were phylogenetically distant from cluster I, comprising 9 galactose-lacking Candida species, C. glabrata, C. holmii, C. krusei, C. tropicalis (the type species of Candida), C. albicans, C. viswanathii, C. maltosa, C. parapsilosis, C. guilliermondii, and C. lusitaniae, and 17 related ascomycetous yeasts. These three clusters were also phylogenetically distant from Schizosaccharomyces pombe, which contains galactomannan in its cell wall. Cluster II comprised C. magnoliae, C. vaccinii, C. apis, C. gropengiesseri, C. etchellsii, C. floricola, C. lactiscondensi, Wickerhamiella domercqiae, C. versatilis, C. azyma, C. vanderwaltii, C. pararugosa, C. sorbophila, C. spandovensis, C. galacta, C. ingens, C. incommunis, Yarrowia lipolytica, Galactomyces geotrichum, and Dipodascus albidus. Cluster III comprised C. tepae, C. antillancae and its synonym C. bondarzewiae, C. ancudensis, C. petrohuensis, C. santjacobensis, C. ciferrii (anamorph of Stephanoascus ciferrii), Arxula terrestris, C. castrensis, C. valdiviana, C. paludigena, C. blankii, C. salmanticensis, C. auringiensis, C. bertae, and its synonym C. bertae var. chiloensis, C. edax (anamorph of Stephanoascus smithiae), Arxula adeninivorans, and C. steatolytica (synonym of Zygoascus hellenicus). Cluster IV comprised C. cantarellii, C. vinaria, Dipodascopsis uninucleata, and Lipomyces lipofer. Two galactose-lacking and Q-8-forming species, C. stellata and Pichia pastoris, and 5 galactose-lacking and Q-9-forming species, C. apicola, C. bombi, C. bombicola, C. geochares, and C. insectalens, were included in Cluster II. Two galactose-lacking and Q-9-forming species, C. drimydis and C. chiropterorum, were included in Cluster III.     

A phylogenetic study of ubiquinone-7 species of the genus Candida based on 18S ribosomal DNA sequence divergence

To clarify phylogenetic relationships among ubiquinone 7 (Q7)-forming species of the genus Candida, we analyzed the nearly complete sequences of 18S ribosomal RNA genes (18S rDNAs) from fifty strains (including 46 type strains) of Candida species, and from 8 type strains of species/varieties of the genera Issatchenkia, Pichia and Saturnispora. Q7-forming Candida species were divided into three major groups (Group I, II, and III) and were phylogenetically distant from a group that includes the type species of the genus Candida. Group I included four clusters with basal branches that were weakly supported. The first cluster comprised C. vartiovaarae, C. maritima, C. utilis, C. freyschussii, C. odintsovae, C. melinii, C. quercuum, Williopsis saturnus var. saturnus, and W. mucosa. The second cluster comprised C. norvegica, C. montana, C. stellimalicola, C. solani, C. berthetii, and C. dendrica. Williopsis pratensis, W. californica, Pichia opuntiae and 2 related species, P. amethionina (two varieties), and P. caribaea were also included in this cluster. The third cluster comprised C. pelliculosa (anamorph of P. anomala), C. nitrativorans, and C. silvicultrix. The fourth cluster comprised C. wickerhamii and C. peltata, which were placed in the P. holstii - C. ernobii clade with Q8-containing species. Group II comprised C. pignaliae, C. nemodendra, C. methanolovescens, C. maris, C. sonorensis, C. pini, C. llanquihuensis, C. cariosilignicola, C. ovalis, C. succiphila (including its two synonyms), C. methanosorbosa, C. nitratophila, C. nanaspora, C. boidinii (including its two synonyms), W. salicorniae, and P. methanolica. Group III was composed of four clusters with strong bootstrap support. The first cluster comprised C. valida (anamorph of P. membranifaciens), C. ethanolica, C. pseudolambica, C. citrea, C. inconspicua, C. norvegensis, C. rugopelliculosa, and C. lambica. Three species and two varieties of the genus Issatchenkia were also included in this cluster. The second cluster comprised C. diversa, C. silvae, 4 Saturnispora species, and P. besseyi. The third comprised C. sorboxylosa, and the fourth comprised C. vini. Based on this 18S rDNA sequence analysis, it is evident that Q7-forming Candida species and the genera Pichia and Williopsis are polyphyletic. The genus Issatchenkia is suggested to be congeneric with the genus Pichia. The genus Saturnispora is phylogenetically definable.     

秦岭地区子囊菌酵母物种多样性研究

从陕西秦岭地区的果实和叶等不同基物上分离得到子囊菌酵母262株,利用26SrDNA的D1/D2区域序列分析并结合形态学特征对这些菌株进行了分类学研究,探讨了该地区子囊菌酵母的物种多样性及其分布。共鉴定出10属31种,其中优势属为假丝酵母属Candida,12种,(其中新种2个,另文发表)、酿酒酵母属Saccharomyces,5种、毕赤酵母属Pichia,5种和有孢汉逊酵母属Hanseniaspora,3种。对分离自陕西秦岭不同地区与海拔的同一个种的不同菌株进行了D1/D2序列分析比较,以探讨子囊菌酵母种内序列稳定性和变异幅度。     

Candida dajiaensis sp. nov., Candida yuanshanicus sp. nov., Candida jianshihensis sp. nov., and Candida sanyiensis sp. nov., four anamorphic, ascomycetous yeast species isolated from soil in Taiwan

Nine anamorphic, ascomycetous yeast strains belonging to the Pichia anomala clade were recovered from forest soil in 2006 in Taiwan. The nine yeast strains represent four novel yeast species based on the sequences of their D1/D2 domain of the large subunit (LSU) rRNA gene and their physiological characteristics. The scientific names of Candida dajiaensis sp. nov., Candida yuanshanicus sp. nov., Candida jianshihensis sp. nov., and Candida sanyiensis sp. nov. are proposed for these novel yeast species. The type strains are C. dajiaensis SM11S03(T) (=CBS 10590(T)=BCRC 23099(T)), C. yuanshanicus SY3S02(T) (=CBS 10589(T)=BCRC 23100(T)), C. jianshihensis SM8S04(T) (=CBS 10591(T)=BCRC 23096(T)), and C. sanyiensis SA1S06(T) (=CBS 10592(T)=BCRC 23094(T)). Sequence analysis of the D1/D2 of the LSU rRNA gene revealed that the three species, C. dajiaensis, C. yuanshanicus and Pichia onychis, shared a separate branch in the phylogenetic tree, C. jianshihensis is phylogenetically related to Candida ulmi and Pichia alni, and the phylogenetically closest relative of C. sanyiensis is Pichia populi.     

The phylogeny of the cactophilic yeasts based on the 18S ribosomal RNA gene sequences: the proposals of Phaffomyces antillensis and Starmera caribaea, new combinations.

The complete sequences of the 18S rRNA gene fragments of the type strains of the cactophilic yeast species, Pichia antillensis, Pichia caribaea, Phaffomyces opuntiae, Phaffomyces thermotolerans, Starmera amethionina var. amethionina, and Starmera amethionina var. pachycereana were determined and compared. The type strain of Phaffomyces opuntiae had two kinds of the 18S rRNA gene sequences of which base differences were counted to be 15 and of which the percent similarity was calculated to be 99.1. The type strains of P. antillensis, P. caribaea, and Starmera amethionina var. pachycereana had the Q-7 system. The phylogenetic analyses showed that the genera Phaffomyces and Starmera were monophyletic and distant from each other and from the other species examined of the ascogenous teleomorphic genera, and that P. antillensis and P. caribaea were included within the clusters of the genera Phaffomyces and Starmera, respectively. The two Pichia species were transferred to the genera Phaffomyces and Starmera as the new combinations, Phaffomyces antillensis and Starmera caribaea. The new family Phaffomycetaceae was proposed as the type genus Phaffomyces.     

Candida easanensis sp. nov., Candida pattaniensis sp. nov. and Candida nakhonratchasimensis sp. nov., three new species of yeasts isolated from insect frass in Thailand

Six strains of anamorphic yeasts isolated from insect frass collected in several regions of Thailand were assigned to the genus Candida based on the conventional taxonomic criteria used for yeast classification. These strains have Q-7 as the major ubiquinone and are suggested to have close relationships to the genus Pichia. Three strains, ST-225, ST-228 and ST-229, have identical nucleotide sequences in the D1/D2 domain of 26S rDNA and are closely related to Pichia japonica, but differ by six nucleotides (1.1% ) from this species. These three strains are considered to represent a single new species, which is described as Candida easanensis sp. nov. Two strains, ST-311 and ST-320, have identical sequences in the D1/D2 domain and resemble Pichia veronae and Pichia fabianii but differ from them by nine nucleotides (1.6%) in D1/D2 sequences. The two strains are described as Candida pattaniensis sp. nov. The remaining strain, ST-37, is related to Pichia americana and Pichia bimundalis but differs by six(1.1%) and seven (1.2%) nucleotides from these species, respectively. This strain is described as Candida nakhonratchasimensis sp. nov.     

Re-examining the phylogeny of clinically relevant Candida species and allied genera based on multigene analyses

Yeasts of the artificial genus Candida include plant endophytes, insect symbionts, and opportunistic human pathogens. Phylogenies based on rRNA gene and actin sequences confirmed that the genus is not monophyletic, and the relationships among Candida species and allied teleomorph genera are not clearly resolved. Protein-coding genes have been useful to resolve taxonomic positions among a broad range of fungi. Over 70 taxa of the genus Candida and its allied sexually reproducing genera were therefore selected, and their phylogenetic relationships were investigated using nuclear sequences of the largest subunit and second largest subunit of RNA polymerase II gene, actin, the second subunit of the mitochondrial cytochrome oxidase gene, and D1/D2 LSU rRNA gene. The DNA sequences were analysed by maximum parsimony and Bayesian inference, resulting in the recognition of six major phylogenetic groups (A-F). Group A contains six facultative pathogenic Candida species, which seem to have derived from nonpathogenic species, while Group B contains species of Clavispora, Metschnikowia, and Pichia guilliermondii. Species of Debaryomyces form an independent group C that is related to groups A and B. Pichia fermentans and other environmental species are concentrated in Group D. Group E, containing Pichia anomala, may be a sibling to group F, which is represented by the Saccharomyces species complex.     

Phylogenetic relationships among species of Pichia, Issatchenkia and Williopsis determined from multigene sequence analysis, and the proposal of Barnettozyma gen. nov., Lindnera gen. nov. and Wickerhamomyces gen. nov

Relationships among species assigned to the yeast genera Pichia, Issatchenkia and Williopsis , which are characterized by the ubiquinone CoQ-7 and inability to utilize methanol, were phylogenetically analyzed from nucleotide sequence divergence in the genes coding for large and small subunit rRNAs and for translation elongation factor-1α. From this analysis, the species separated into five clades. Species of Issatchenkia are members of the Pichia membranifaciens clade and are proposed for transfer to Pichia . Pichia dryadoides and Pichia quercuum are basal members of the genus Starmera . Williopsis species are dispersed among hat-spored taxa in each of the remaining three clades, which are proposed as the new genera Barnettozyma, Lindnera and Wickerhamomyces . Lineages previously classified as varieties of Pichia kluyveri , ' Issatchenkia ' scutulata, Starmera amethionina and ' Williopsis ' saturnus are elevated to species rank based on sequence comparisons.     

Three new thermotolerant methylotrophic yeasts, Candida krabiensis sp. nov., Candida sithepensis sp. nov., and Pichia siamensis sp. nov., isolated in Thailand

Five strains of thermotolerant methylotrophic yeasts isolated in Thailand were found to represent three new species in the genera Pichia and Candida, based on phylogenetic analysis of D1/D2 domain of 26S rDNA, in addition to the morphological, physiological, biochemical and chemotaxonomic characterization. Three strains, FS96 and FS101 from flowers and M02 from tree flux, were characterized by ubiquinone Q7, multilateral budding, and the formation of hat-shaped ascospores that are liberated at maturation. These strains showed identical nucleotide sequences in the D1/D2 domain and formed a cluster with Candida thermophila, "Pichia salicis" and Pichia angusta. They differed by 1.9% of nucleotide substitutions from Candida thermophila, the nearest species. They were considered to represent a single new species and are described as Pichia siamensis sp. nov. Two strains, N051 and S023, isolated from soil did not produce ascospores, proliferated by multilateral budding, did not demonstrate urease or DBB color reaction, and lacked sexual stages. These characteristics correspond to the genus Candida. Strains N051 and S023 differed by 2.8% and 1.9% of nucleotide substitutions in the D1/D2 domain from the nearest species, Candida nemodendra and Candida ovalis, respectively, and are considered to represent respective new species. N051 and S023 are described as Candida krabiensis sp. nov. and Candida sithepensis sp. nov., respectively.     

Yeast species associated with orange juice: evaluation of different identification methods

Five different methods were used to identify yeast isolates from a variety of citrus juice sources. A total of 99 strains, including reference strains, were identified using a partial sequence of the 26S rRNA gene, restriction pattern analysis of the internal transcribed spacer region (5.8S-ITS), classical methodology, the RapID Yeast Plus system, and API 20C AUX. Twenty-three different species were identified representing 11 different genera. Distribution of the species was considerably different depending on the type of sample. Fourteen different species were identified from pasteurized single-strength orange juice that had been contaminated after pasteurization (PSOJ), while only six species were isolated from fresh-squeezed, unpasteurized orange juice (FSOJ). Among PSOJ isolates, Candida intermedia and Candida parapsilosis were the predominant species. Hanseniaspora occidentalis and Hanseniaspora uvarum represented up to 73% of total FSOJ isolates. Partial sequence of the 26S rRNA gene yielded the best results in terms of correct identification, followed by classical techniques and 5.8S-ITS analysis. The commercial identification kits RapID Yeast Plus system and API 20C AUX were able to correctly identify only 35 and 13% of the isolates, respectively. Six new 5.8S-ITS profiles were described, corresponding to Clavispora lusitaniae, Geotrichum citri-aurantii, H. occidentalis, H. vineae, Pichia fermentans, and Saccharomycopsis crataegensis. With the addition of these new profiles to the existing database, the use of 5.8S-ITS sequence became the best tool for rapid and accurate identification of yeast isolates from orange juice.     

Evidence of recent interkingdom horizontal gene transfer between bacteria and <Emphasis Type="Italic">Candida parapsilosis</Emphasis>

Background  

To date very few incidences of interdomain gene transfer into fungi have been identified. Here, we used the emerging genome sequences of Candida albicans WO-1, Candida tropicalis, Candida parapsilosis, Clavispora lusitaniae, Pichia guilliermondii, and Lodderomyces elongisporus to identify recent interdomain HGT events. We refer to these as CTG species because they translate the CTG codon as serine rather than leucine, and share a recent common ancestor.     

Three new ascomycetous yeasts from insect-associated arboreal habitats

A new species of Pichia and two new species of Candida are described and were determined to be genetically isolated from all other currently recognized ascomycetous yeasts from their sequence divergence in the species-variable D1/D2 domain of large subunit (26S) ribosomal DNA. The three species were primarily isolated from the frass of wood-boring insects living in pine and spruce trees. The new species and their type strains are the following: Pichia ramenticola NRRL YB-1985 (CBS 8699), mating type alpha (NRRL YB-3835, CBS 8700, mating type a), Candida piceae NRRL YB-2107 (CBS 8701), and Candida wyomingensis NRRL YB-2152 (CBS 8703). Pichia ramenticola and C. piceae assimilate methanol as a carbon source; P. ramenticola is the first known heterothallic ascomycetous yeast to utilize this compound.     

Bullera taiwanensis sp nov and Bullera formosensis sp nov,two new ballistoconidium-forming yeast species isolated from plant leaves in Taiwan

Two strains of ballistoconidiogenous yeasts that contain xylose and form Q-10 ubiquinone were isolated from plant leaves collected in Taiwan and were found to represent two new species. The taxonomic properties of both coincide with the genus Bullera so they are described as Bullera taiwanensis sp. nov. and Bullera formosensis sp. nov. In a phylogenetic tree based on the nucleotide sequences of 18S ribosomal DNAs, these two species are distant from the clusters where the remaining members of the genus Bullera are located, i.e., Bullera taiwanensis is located in the Filobasidium lineage (Filobasidiales clade) and Bullera formosensis is located in the Cryptococcus humicola-Trichosporon lineage (Trichosporonales clade).     

Genomic fingerprints, ARDRA profiles and quinone systems for classification of Pasteurella sensu stricto

In order to investigate the relationships between species of the genus Pasteurella sensu stricto such as Pasteurella multocida, Pasteurella canis, Pasteurella stomatis, Pasteurella dagmatis, Pasteurella avium, Pasteurella volantium, Pasteurella gallinarum, Pasteurella species A, Pasteurella species B and "Pasteurella leonis" MCCM 00659 their genomic fingerprints and ARDRA profiles were compared and their quinone systems were analysed. Visual comparison of band patterns from rep-PCR (ERIC-, REP- and BOX-PCR) and the analyses of the combined band patterns by UPGMA (unweighted pair group method with averages) dendrogram derived from the combined fingerprint profiles demonstrated that each strain displays a distinct genomic fingerprint. In members of the same species several similarities in the band patterns were observed. Combined ARDRA profiles, obtained after digestion of amplified 23S rRNA coding genes with the enzymes DdeI, MseI and RsaI, revealed a dissection of the members of the genus Pasteurella sensu stricto into two groups which was in agreement with the two groups obtained from our analyses of the quinone systems. These two groups corresponded with the two phylogenetically determined subclusters 3A and 3B described previously. The species of subcluster 3A displayed a quinone system with ubiquinone Q-7 (32-56%) and ubiquinone Q-8 (44-63%) as major compounds. Members of subcluster 3B had a quinone system with ubiquinone Q-8 (86-97%) as the major compound. Based on these results it can be suggested that the genus Pasteurella sensu stricto should be restricted to the species of subcluster 3B including the species Pasteurella multocida, Pasteurella canis, Pasteurella stomatis, Pasteurella dagmatis and Pasteurella species B. In addition, evidence was found which would indicate that: 1) Pasteurella canis MCCM 00927 is misnamed and should be reclassified with Pasteurella multocida; 2) Pasteurella multocida subsp. septica may be classified as a separate species; and 3) "Pasteurella leonis" MCCM 00659 represents a separate species within subcluster 3B and thus could be described as a species of Pasteurella sensu stricto (also in a redefined genus) when more strains become available.     

内蒙古西部区酸粥中酵母菌的分离鉴定及优势菌分析

从内蒙古地区采集28份酸粥样品,从中分离出40株酵母菌,并对其进行了分子生物学鉴定和生物多样性分析。26S rDNA D1/D2区域 (600bp左右)碱基序列分析结果表明,酸粥中的酵母菌有Issatchenkia orientalis、Saccharomyces cerevisiae、Geotrichum sp.、Candida pararugosa、 Candida parapsilosis、Trichosporon asahii、Trichosporon coremiiforme、Clavispora lusitaniae和Candida tropicalis。经过分析,Issatchenkia orientalis(75%,Frequency percentage)为酸粥中的优势菌。     

The yeast community of sap fluxes of Costa Rican Maclura (Chlorophora) tinctoria and description of two new yeast species,Candida galis and Candida ortonii

We report on the yeast community associated with sap fluxes of Maclura tinctoria, family Moraceae, in the dry forest of the Area de Conservación Guanacaste, Costa Rica. Eleven samples yielded seven hitherto undescribed ascomycetous yeasts in the genera Candida and Myxozyma. We describe the two most abundant as new species. Candida galis utilizes very few carbon compounds limited to some alcohols and acids. Analysis of rDNA sequences suggests that it occupies a basal position with respect to the Pichia anomala clade, with no obvious sister species. Candida ortonii is also restricted in nutritional breadth, and growth is generally very slow. It is a sister species to Candida nemodendra. The type cultures are: C. galis, strain UWO(PS)00-159.2=CBS 8842; and C. ortonii, strain UWO(PS)00-159.3=CBS 8843.     

Yeast community survey in the Tagus estuary

The yeast community in the waters of the Tagus estuary, Portugal, was followed for over a year in order to assess its dynamics. Yeast occurrence and incidence were measured and this information was related to relevant environmental data. Yeast occurrence did not seem to depend upon tides, but river discharge had a dramatic impact both on the density and diversity of the community. The occurrence of some yeasts was partially correlated with faecal pollution indicators. Yeast isolates were characterized by microsatellite primed PCR (MSP-PCR) fingerprinting and rRNA gene sequencing. The principal species found were Candida catenulata, C. intermedia, C. parapsilosis, Clavispora lusitaniae, Debaryomyces hansenii, Pichia guilliermondii, Rhodotorula mucilaginosa and Rhodosporidium diobovatum. The incidence of these species was evaluated against the environmental context of the samples and the current knowledge about the substrates from which they are usually isolated.     

Mediated amperometry reveals two distinct modes of yeast responses to glucose

Mediated amperometry was exploited to monitor intracellular redox activity without cell disruption. Continuous measurements of menadione-mediated glucose currents at carbon paste electrodes with various immobilized intact wild type yeasts (Saccharomyces cerevisiae, Candida pulcherrima, Clavispora lusitaniae, Wickerhamomyces anomalus, Pichia guilliermondii, Kluyveromyces lactis var. lactis, Debaryomyces hansenii, Candida zeymolaydes and Candida tropicalis) revealed two distinct and previously unreported modes of development of the currents during the first 2 to 3 min. after subjection to glucose. A correlation among the values of the currents and the capacities of wild type yeasts to secrete various substances was observed.