Evolutionary relationships among pathogenic Candida species and relatives.

Small subunit rRNA sequences have been determined for 10 of the most clinically important pathogenic species of the yeast genus Candida (including Torulopsis [Candida] glabrata and Yarrowia [Candida] lipolytica) and for Hansenula polymorpha. Phylogenetic analyses of these sequences and those of Saccharomyces cerevisiae, Kluyveromyces marxianus var. lactis, and Aspergillus fumigatus indicate that Candida albicans, C. tropicalis, C. parapsilosis, and C. viswanathii form a subgroup within the genus. The remaining significant pathogen, T. glabrata, falls into a second, distinct subgroup and is specifically related to S. cerevisiae and more distantly related to C. kefyr (psuedotropicalis) and K. marxianus var. lactis. The 18S rRNA sequence of Y. lipolytica has evolved rapidly in relation to the other Candida sequences examined and appears to be only distantly related to them. As anticipated, species of several other genera appear to bear specific relationships to members of the genus Candida.     

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.     

Candida siamensis sp. nov., an anamorphic yeast species in the Saturnispora clade isolated in Thailand

Three strains of a novel anamorphic yeast species were isolated from natural samples collected in Thailand, including strain EF10 isolated from sediment in a mangrove forest, strain ST-473 from rotten wood, and strain ST-479 from a wild mushroom ( Hygrophorus sp.). Analysis of the D1/D2 domains of the large-subunit rRNA gene sequence revealed that the sequence of strain EF10 differed from the other two strains (ST-473 and ST-479), which had identical sequences, by only one nucleotide (nt) substitution in 535 nt. The closest species in terms of pairwise sequence similarity was Saturnispora mendoncae , with 32 nt substitutions and seven gaps in 535 nt. Phylogenetic analysis demonstrated that the three strains form a cluster with S. mendoncae and the other eight species in the Saturnispora clade. Phenotypic characteristics of the three strains were the same including proliferation by multilateral budding, absence of ascospores and negative diazonium blue B and urease reactions. The major ubiquinone was Q-7. On this basis, the three strains were assigned to a single novel species of the genus Candida , for which the name Candida siamensis sp. nov. is proposed. The type strain is EF10^T (=BCC 29901^T=NBRC 104878^T=CBS 11022^T).     

Analysis of fatty acid composition of Candida species by gas-liquid chromatography using a polar column

The fatty acid composition of representative Candida species was examined by gas-liquid chromatography (GLC) using a polar column. The major fatty acids were C14:0, C16:0, C18:0 saturated, C16:1 and C18:1 monoenoic series, with or without C18 polyunsaturated acids (C18:2 and C18:3). In Torulopsis glabrata and Saccharomyces cerevisiae the C18:2 and C18:3 acids were not found, but the C10:0 and C12:0 acids were detected in S. cerevisiae. These results indicated that the Candida genus could be distinguished from Torulopsis and Saccharomyces genera by GLC analysis of fatty acids. Quantitative differences in the fatty acid composition between cells grown at high temperature (37 degrees C) and low temperature (25 degrees C) were found generally in Candida species, and the amounts of C18 polyunsaturated acids (C18:2 and C18:3) increased in the cells grown at 25 degrees C. Each Candida species showed a characteristic profile in fatty acid composition. Determination of the cellular fatty acid composition in Candida species is likely to be useful for the grouping or chemotaxonomy of newer isolates of Candida species.     

Multigene phylogenetic analysis of the Trichomonascus, Wickerhamiella and Zygoascus yeast clades, and the proposal of Sugiyamaella gen. nov. and 14 new species combinations

Relationships among species assigned to the ascosporic yeast genera Sporopachydermia, Stephanoascus, Trichomonascus, Wickerhamiella and Zygoascus, and to the associated anamorphic genera Arxula, Blastobotrys, Sympodiomyces and Trigonopsis, were determined from phylogenetic analyses of gene sequences from the nearly complete large-subunit rRNA gene, the mitochondrial small-subunit rRNA gene, and cytochrome oxidase II. The genus Stephanoascus is polyphyletic, resulting in reassignment of two species to the older genus Trichomonascus and the third to Sugiyamaella gen. nov. (type species Sugiyamaella smithiae). The genera Sporopachydermia, Wickerhamiella and Zygoascus appear to be monophyletic. The species Pichia ofunaensis and P. tannicola are proposed for transfer to Zygoascus. Arxula, Blastobotrys and Sympodiomyces are members of the Trichomonascus clade, with the genus Blastobotrys having taxonomic priority for anamorphic states. Trigonopsis variabilis and three species of Candida represent a distinct clade. From the foregoing gene sequence analyses, the new ascosporic genus Sugiyamaella is proposed, as are 14 new species combinations and the new family Trichomonascaceae.     

用RAPD技术对特化等级裂腹鱼类亲缘关系的探讨

为确定特化等级裂腹鱼类的遗传分化关系 ,对 7种 2 2个裂腹鱼个体进行随机扩增多态DNA(RAPD)研究。从所使用的 40个随机引物中 ,选择了 37个扩增带谱清晰的引物进行分析。根据构建的分子系统树显示 ,特化等级裂腹鱼类划分为 3个属级分类单元较为合适 ,这与采用形态学特征进行系统分析所得出的结论一致。在 2 2个个体之间遗传距离矩阵中 ,最大的遗传距离指数达到了 90 38% ,此外 ,还有较多的遗传距离指数也在 6 0 %～ 90 %之间。通过分析 ,认为用RAPD标记技术来分析属级或属级以上分类单元的亲缘关系 ,具有一定的适用性。对于一些遗传差异较大的类群 (如裂腹鱼类 ) ,应用属级或属级以上分类单元的亲缘关系 ,很可能会出现个体之间遗传距离接近或达到 10 0 %的情况 ,从而无法探讨其相互之间的亲缘关系。     

A Consideration of the Species Relationships in Subtribe Brassicinae (Cruciferae) in View of Cluster Analysis of Morphological Characters

Abstract The taxonomic relationships of 53 species (122 strains) in subtribe Brassicinae were studied by using Euclidian distances calculated from 53 metric characters. Through cluster analysis applied to the species and subspecies in the genus Brassica , six large clusters could be defined. By the same method, Diplotaxis was grouped into four clusters, Erucastrum into two, and Sinapis into two. These clusters coincided in general with the taxonomic sections of Schulz (1936), but some exceptions were noted. Most of the exceptional species were those placed in critical positions by cytogenetical observations. It was found that cluster grouping reflected the cytogenetical relations of species fairly well.
Relationships among clusters and genera are represented by a Euclidian distance matrix, and the evolutionary trends of those taxa are discussed. Clusters B-3 (in Brassica) , D-1 ( in Diplotaxis ) and E-1 (in Erucastrum ) are closely related to each other, forming a complex. This complex is closely related to Sinapidendron. It is postulated that this complex and Sinapidendron might have retained some characters in common with their putative ancestor. Species in the other clusters are considered to be derived from that hypothetical ancestor in the course of evolutionary divergence.     

Physiological properties of some yeast strains

Twenty yeast strains have recently been isolated in pure cultures from natural and industrial sources and identified based mainly on physiological properties. The majority of the strains (15) are alcohologenic belonging to the genus Saccharomyces and comprise two brewer's (beer) yeast strains (S. carlsbergensis= S. uvarum A and B), two baker's yeast strains (S. cerevisiae CA and CP), one spirit yeast strain (S. cerevisiae CF) and ten wine yeast strains (S. cerevisiae var. ellipsoideus = S. ellipsoideus 1, 3, 4, 6, 8 and 9; S. oviformis 2, 5 and 7; and S. uvarum 10). The other 5 yeast strains belong to different species: Kloeckera apiculate, Candida mycoderma (Mycoderma vini), Pichia membranaefaciens, Rhodotorula glutinis and Torulopsis holmii, respectively.     

23种伞形科植物果实形态及其分类学意义

该实验采用徒手切片法对伞形科17属23种植物的果实进行了外部形态和解剖特征的观察,结果表明:伞形科果实有背腹压扁、两侧压扁和不压扁3种类型;侧棱有宽、有窄;油管的分布有棱槽单油管型和棱槽多油管型;花柱基多数为圆锥状,少数种的花柱基为扁平垫状;萼齿明显或不明显。通过进一步对属间和属内果实解剖特征的比较得出:(1)果实表面被钩刺或刚毛及果棱特征在属间差异明显,在属内表现出一致性,可作为伞形科属间分类的依据。(2)果实横切面的形状、胚乳腹面的凹凸以及萼齿的形态特征在属内种间的分类研究中有重要的意义。基于果实形态特征,编制了17属23种植物的分种检索表。     

Yeast biodiversity in hydromorphic soils with reference to grass-Sphagnum swamp in Western Siberia and the hammocky tundra region( Barrow, Alaska)]

The microbiological analysis of 78 samples taken from a boreal bog in Western Siberia and from a tundra wetland soil in Alaska showed the presence of 23 yeast species belonging to the genera Bullera, Candida, Cryptococcus, Debaryomyces, Hanseniaspora, Metschnikowia, Mrakia, Pichia, Rhodotorula, Saccharomyces, Sporobolomyces, Torulaspora, and Trichosporon. Peat samples from the boreal bog were dominated by eurytopic anamorphic basidiomycetous species, such as Rhodotorula mucilaginosa and Sporobolomyces roseus, and by the ascomycetous yeasts Candida spp. and Debaryomyces hansenii. These samples also contained two rare ascomycetous species (Candida paludigena and Schizoblastosporion starkeyi-henricii), which so far have been found only in taiga wetland soils. The wetland Alaskan soil was dominated by one yeast species (Cryptococcus gilvescens), which is a typical inhabitant of tundra soils. Therefore, geographic factors may serve for a more reliable prediction of yeast diversity in soils than the physicochemical or ecotopic parameters of these soils.     

云南杜鹃花上的酵母菌物种多样性

利用酵母菌常规分类学方法 ,对采自云南省东部、西部及中部地区杜鹃花上的 119株酵母菌进行了分类研究 ,以期弄清其属种分布特点 ,从而为发掘新种、开发酵母菌资源提供依据。这些酵母菌被归入3大类 10个属 ,显示了云南杜鹃花中酵母菌的种类多样性 ,其中优势属为假丝酵母属 (Candida)。     

Characteristics of Yeasts Isolated from Pacific Crab Meat

A total of 202 cultures of yeasts were isolated and characterized from king crab and Dungeness crab meat. A yeastlike organism, resembling Aureobasidium pullulans, and 15 different species distributed among the genera Rhodotorula, Cryptococcus, Torulopsis, Candida, and Trichosporon were represented. Nine of the species grew at 5 C or lower. Although two of the species grew at 37 C, none of the isolates had the characteristics of pathogenic species. Members of the Cryptococcus and Candida failed to grow at 37 C. Furthermore, species of the former genus were not pathogenic to mice. The pigmentation of the Rhodotorula cultures decreased in intensity as the incubation temperature was decreased. Biochemical activities of the different species were studied by use of triglycerides, lecithin, and proteins (casein, gelatin, and crab-meat protein) as substrates. Eight of the species could attack triglycerides; eight, lecithin; five, gelatin; one, casein; and one, crab protein. An organism, tentatively identified as Trichosporon sp., was very active in attacking each of the substrates tested and grew well at 0.5 C.     

Molecular phylogenetic study of the basidiomycetous anamorphic yeast genusTrichosporon and related taxa based on small subunit ribosomal DNA sequences

Small subunit ribosomal DNA sequences of all species of the basidiomycetous anamorphic yeast genusTrichosporon were determined, and phylogenetic trees were constructed by the neighbor-joining and maximum likelihood methods. The sequence data showed that, with the exception ofT. pullulans, the genus is monophyletic, although its members have two different major ubiquinones, Q9 and Q10. The genus can be divided phylogenetically into three major clusters. Species with Q10 as the major ubiquinone constitute a single cluster, while those with Q9 form two clusters.Trichosporon pullulans was phylogenetically distinct from other taxa of the genus. It is located in a cluster containingCystofilobasidium capitatum, Mrakía frigida, Xanthophyllomyces dendrorhous and three species ofUdeniomyces. This result sugests thatT. pullulans does not belong to the genusTrichosporon.     

禾本科广义拂子茅属的叶表皮形态研究

禾本科广义拂子茅属Calamagrostis Adans. s.l.是广布于全球温带和热带亚热带高山的一个大属, 常分为拂子茅属Calamagrostis Adans. s.s.和野青茅属Deyeuxia Beauv.。对国产5种拂子茅属和26种、1变种野青茅属植物在光镜下进行了叶表皮特征的观察。发现广义拂子茅属植物的叶表皮特征为典型的狐茅型, 很多结构在种间有丰富的变异式样, 如脉间长细胞形状、大小和细胞壁的厚度与弯曲程度, 短细胞形状和分布式样, 硅质体形状和分布式样, 气孔形状和分布式样, 以及刺毛形态和分布式样等。在国产种类中首次发现微乳突结构, 在很多种类中发现刺毛硅质化现象。用UPGMA对15个叶表皮性状进行分析, 结果分为两大支: 具加厚的长细胞、密集分布的短细胞和(或)刺毛以及刺毛硅质化的种类聚为一支; 具薄壁的长细胞、较稀疏的短细胞和(或)刺毛以及刺毛不发生硅质化的种类聚为另一支。这种分异与广义拂子茅属的属下系统相关性不大, 但与种的海拔分布有关。前一支的种类大多生长于高海拔(2600 m以上)地区, 而后一支的种类则大多生长在低海拔(2600 m以下)地区。     

Unveiling of novel radiations within Trichodesmium cluster by hetR gene sequence analysis

The filamentous nonheterocystous cyanobacterial genus Katagnymene is a common diazotrophic component of tropical and subtropical oceans. To assess the phylogenetic affiliation of this taxon, two partial 16S rRNA gene sequences and 25 partial hetR gene sequences originating from the genera Katagnymene and Trichodesmium collected from open, surface waters of the Atlantic, Indian, and Pacific oceans were compared. Single trichomes or colonies were identified morphologically by using light microscopy and then used directly as templates in hetR PCR analyses. In addition, three cultured strains, identified as Katagnymene pelagica, Katagnymene spiralis, and Trichodesmium sp., were examined. The data show that the genus Katagnymene is in the Trichodesmium cluster and that K. pelagica Lemmermann and K. spiralis Lemmermann are most likely one species, despite their different morphologies. Phylogenetic analyses also unveiled four distinct clusters in the Trichodesmium cluster, including one novel cluster. Our findings emphasize the conclusion that known morphological traits used to differentiate marine nonheterocystous cyanobacteria at the genus and species levels correlate poorly with genetic data, and a revision is therefore suggested.