Species identification in the genus Saprolegnia (Oomycetes): Defining DNA-based molecular operational taxonomic units

The lack of a robust taxonomy in the genus Saprolegnia is leading to the presence of incorrectly named isolates in culture collections and of an increasing number of misassigned sequences in DNA databases. Accurate species delimitation is critical for most biological disciplines. A recently proposed approach to solve species delimitation (taxonomic diagnosis system) of difficult organisms is the definition of molecular operational taxonomic units (MOTUs). We have used 961 sequences of nrDNA ITS from culture collections (461 sequences) and GenBank (500 sequences), to perform phylogenetic and clustering optimization analyses. As result, we have identified 29 DNA-based MOTUs in agreement with phylogenetic studies. The resulting molecular clusters support the validity of 18 species of Saprolegnia and identify 11 potential new ones. We have also listed a number of incorrectly named isolates in culture collections, misassigned species names to GenBank sequences, and reference sequences for the species. We conclude that GenBank represents the main source of errors for identifying Saprolegnia species since it possesses sequences with misassigned names and also sequencing errors. The presented taxonomic diagnosis system might help setting the basis for a suitable identification of species in this economically important genus.     

<Emphasis Type="Italic">Cleistocybe</Emphasis>, a new genus of Agaricales

A new clitocyboid genus of Agaricales, Cleistocybe, is described to accommodate the isolated evolutionary position of the new species Cleistocybe vernalis inferred by a previously published multigene phylogenetic study. Cleistocybe is distinguished from other clitocyboid lineages by a combination of morphological characters, including lamellae that become gray in age, an interwoven hymenophoral trama with divergent elements when young, strongly interwoven pileipellis with pigmented and encrusted hyphae, white spore deposit, a distinct or ephemeral fibrillose to submembranous partial veil, and smooth, inamyloid basidiospores that are inequilateral in profile view. Cleistocybe encompasses two species, C. vernalis and Clitocybe gomphidioides, based on morphological comparisons with C. vernalis. Clitocybe subvelosa is confirmed as conspecific with C. gomphidioides based on morphological and ITS sequence comparisons of type collections. Cleistocybe is known only from western North America in coniferous forests and appears most closely related to the ectomycorrhizal genus Catathelasma and the saprotrophic genera Callistosporium, Macrocybe, and Pleurocollybia based on nLSU-rDNA phylogenetic analysis. Together these lineages constitute the Catathelasma clade.     

Two new species of the Heterobasidion insulare complex based on morphology and molecular data

Two new species of Heterobasidion, H. amyloideum and H. tibeticum, are described and illustrated from eastern Himalayas. Both species are closely related to the Heterobasidion insulare complex in morphology, but they differ in presence of cystidia and amyloid skeletal hyphae in the context. Phylogenetically, the combined RPB1 and RPB2 sequence data supports H. amyloideum and H. tibeticum as two distinct species within the H. insulare complex.     

Coltriciella minuscula sp. nov., a new species of poroid fungus on Pinus merkusii from an Indonesian tropical forest

Coltriciella minuscula sp. nov. is described and illustrated from a specimen collected on Pinus merkusii from Bogor, Indonesia. This species is characterized by the size of its basidiocarp up to 4 mm in diam, with long hair on the stipe and with ornamented spores. Both morphological distinctiveness and phylogenetic separation based upon analyses of nrDNA ITS sequences support the establishment of this new species. Morphological dissimilarities between C. minuscula and closely related species are discussed.     

Phylogenetic basis for a taxonomic dissection of the genus Clostridium

The 16S rDNA-based phylogenetic analysis of the genus Clostridium has been completed by determination of the phylogenetic position of the type strains of 15 species and two non-validated species. These strains are members of phylogenetic clusters I, III, IV, V, IX, XIVa and XVIII as defined previously by Collins et al. [Int. J. Syst. Bacteriol. 44 (1994) 812-826]. Members of the genus Clostridium span a large evolutionary distance and the genus is not a phylogenetically coherent taxon but is intermixed with members of different genera, exhibiting a combination of Clostridium- and non-Clostridium-type properties. Anaerobacter polyendosporus, Syntrophococcus sucromutans and Acetivibrio multivorans also cluster within the radiation of Clostridium species. Although several taxa have been described for former Clostridium species with distinct phenotypic properties, the majority of Clostridium species, which are not members of the core cluster I, can at present not be reclassified as long as taxon-specific, phenotypic properties are not available.     

Legume growth-promoting rhizobia: An overview on the Mesorhizobium genus

The need for sustainable agricultural practices is revitalizing the interest in biological nitrogen fixation and rhizobia-legumes symbioses, particularly those involving economically important legume crops in terms of food and forage. The genus Mesorhizobium includes species with high geographical dispersion and able to nodulate a wide variety of legumes, including important crop species, like chickpea or biserrula. Some cases of legume-mesorhizobia inoculant introduction represent exceptional opportunities to study the rhizobia genomes evolution and the evolutionary relationships among species. Complete genome sequences revealed that mesorhizobia typically harbour chromosomal symbiosis islands. The phylogenies of symbiosis genes, such as nodC, are not congruent with the phylogenies based on core genes, reflecting rhizobial host range, rather than species affiliation. This agrees with studies showing that Mesorhizobium species are able to exchange symbiosis genes through lateral transfer of chromosomal symbiosis islands, thus acquiring the ability to nodulate new hosts. Phylogenetic analyses of the Mesorhizobium genus based on core and accessory genes reveal complex evolutionary relationships and a high genomic plasticity, rendering the Mesorhizobium genus as a good model to investigate rhizobia genome evolution and adaptation to different host plants. Further investigation of symbiosis genes as well as stress response genes will certainly contribute to understand mesorhizobia-legume symbiosis and to develop more effective mesorhizobia inoculants.     

Renoprotective chemical constituents from an edible mushroom,Pleurotus cornucopiae in cisplatin-induced nephrotoxicity

Pleurotus cornucopiae (Pleurotaceae) is an edible and medicinal mushroom widely distributed in Korea, China, and Japan. The MeOH extract of the fruiting bodies of P. cornucopiae showed renoprotective effects against cisplatin-induced kidney cell damage. Chemical investigation of the MeOH extract led to the isolation and identification of 12 compounds including noransine (1), uridine (2), uracil (3), (3β, 5α, 6β, 22E, 24S) -ergosta-7, 22-diene-3, 5, 6, 9-tetrol (4), (22E,24S)-ergosta-7,22-diene-3β,5α,6β-triol (5), (22E,24R)-ergosta-8(14),22-diene-3β,5α,6β,7α-tetrol (6), cerebroside B (7), (2R) -N- [(1S, 2R, 3E, 7E) -1- [(β-d-glucopyranosyloxy) methyl] -2-hydroxy-8-methyl-3, 7-heptadecadien-1-yl] -2-hydroxy-heptadecanamide (8), cerebroside D (9), nicotinamide (10), 1,2-bis(hydroxymethyl)-4,5-dimethoxybenzene (11), and benzoic acid (12). Among them, compounds 1 and 11 were isolated as naturally occurring products for the first time, though they were reported as synthetic products in previous papers. All of the compounds (except 8 and 11) abrogated cisplatin-induced LLC-PK1 cell damage in a dose-dependent manner. Of special note, compounds 2, 5, 6, and 12 ameliorated cisplatin-induced nephrotoxicity to 80% of the control value at 10 μM. The protective effects of compounds 2, 5, 6, and 12 were mediated via the deactivation of JNK-caspase 3 apoptotic cascade. This study is the first to demonstrate that the chemical constituents of P. cornucopiae display renoprotective effects against anticancer drug-induced damage in kidney cells.     

报春花属藏报春组、毛茛叶报春组的界定和系统发育关系:核糖体DNA ITS序列证据

报春花属(Primula L.)藏报春组(sect. Auganthus Pax ex Balf. f.)和毛茛叶报春组(sect. Ranunculoides Chen et C. M. Hu)的界定一直是没有解决的问题.应用核糖体DNA ITS序列数据探讨其系统发育关系.取样包括藏报春组和毛茛叶报春组的全部5个种以及其他一些相关组的代表种.ITS系统树表明,陕西羽叶报春(P.filchnerae Knuth)应与藏报春(P. sinensis Sabine ex Lindl.)和野藏报春(P. rupestris Balf. f. et Farrer)一起置于藏报春组;毛茛叶报春组只含两种:毛茛叶报春(P. cicutariifolia Pax)和安徽羽叶报春(P. merrilliana Schltr.).这两组并不具密切亲缘关系,它们在报春花属中与其他组的关系还需进一步研究.研究也表明ITS序列可以为报春花属的系统发育重建提供大量可靠资料.     

The genus Pleurotus in Argentina

Macro- and micromorphological characters of specimens of the genus Pleurotus (Fr.) P. Kumm. in Argentina obtained in the field and from different national herbaria were analyzed. Cultivation techniques were used to obtain basidiomata, allowing for a macro- and micromorphological study of fresh developing fruit bodies. We concluded that in Argentina there are, so far, six species, namely P. albidus, P. cystidiosus, P. ostreatus, P. pulmonarius, P. rickii and P. djamor, the latter with three varieties: var. djamor, var. cyathiformis and var. roseus.     

Phylogenetic relationship of four new species related to southwestern Sichuan Fagopyrum based on morphological and molecular characterization

Background and aimsRecently, four wild Fagopyrum species, Fagopyrum crispatifolium J. L. Liu, Fagopyrum pugense T. Yu, Fagopyrum qiangcai D. Q. Bai and Fagopyrum wenchuanense J. R. Shao, have been identified and described based on their morphological characters. This study investigates the phylogenetic relationship, nucleotide sequence polymorphisms of internal transcribed spacers (ITSs) and the maturase K (matK) gene within four wild species related to western Sichuan buckwheat. F. wenchuanense is closely related to Fagopyrum gracilipes while F. qiangcai is closely related to Fagopyrum esculentum based on their morphological differences. However, F. wenchuanense is more closely related to Fagopyrum cymosum and F. qiangcai is closer to Fagopyrum lineare and Fagopyrum leptopodum from the viewpoint of the ITS, and matK analysis. In addition, F. gracilipes is closer to F. pugense and Fagopyrum crispatofolium than to F. qiangcai. F. wenchuanense belongs to the cymosum group, while F. qiangcai, F. pugense and F. crispatifolium are classified into the urophyllum group based on their morphological and molecular analysis. Conducting morphological and molecular studies provide a better understanding of evolutionary mechanisms and genetic relationships of cultivated and wild buckwheat in western Sichuan, China.     

Distribution and molecular phylogeny of the dinoflagellate genus Ostreopsis in Thailand

The toxic benthic dinoflagellate genus Ostreopsis has been connected to the production of palytoxin and its analogs in many tropical and temperate areas. Although the type species, O. siamensis, was originally described from the Gulf of Thailand in 1901, little is known about the species composition and distribution of the genus Ostreopsis in Thailand. In this study, a total of 64 Ostreopsis strains isolated from the Andaman Sea as well as the Gulf of Thailand were investigated by analyzing the nucleotide sequences of the LSU rDNA D1/D2, D8/D10 and ITS-5.8S rDNA regions. Phylogenetic analyses (BI and ML) resulted in some of the strains being assigned to previously described clades, O. cf. ovata and Ostreopsis sp. 6, and revealed the existence of a novel clade named Ostreopsis sp. 7, which exhibited large genetic distances from the other clades. Among O. cf. ovata, several strains from Thailand were formed into a new subclade, the Thailand subclade, whereas a few strains belonged to the South China Sea subclade. Morphometric characteristics such as the cell sizes of the two O. cf. ovata subclades and those of Ostreopsis sp. 7 were not significantly different from each other (p > 0.05). Their characteristics were similar but slightly different from those of O. ovata and were significantly different from those of Ostreopsis sp. 6 (p < 0.05). Toxicities of Ostreopsis from Thailand were evaluated using mouse bioassay. Strains of Ostreopsis sp. 6 and Ostreopsis sp. 7 tested were highly toxic, while the two subclades of O. cf. ovata strains seemed to be nontoxic. This study suggests that toxic Ostreopsis sp. 7 is distributed in the Andaman Sea, whereas the two subclades of O. cf. ovata and toxic Ostreopsis sp. 6 are distributed in the Gulf of Thailand.     

The anamorphic genus Calcarisporiella is a new member of the Mucoromycotina

The phylogenetic position of the anamorphic genus Calcarisporiella was investigated. Three isolates of Calcarisporiella, including an authentic strain and a newly obtained isolate, were analyzed phylogenetically using rDNA sequences. The result indicated that Calcarisporiella, which was classified as an ascomycetous anamorph, is a member of Mucoromycotina. It formed an independent clade separated from the other known orders of this subphylum.     

Mycoparasitism between Squamanita paradoxa and Cystoderma amianthinum (Cystodermateae, Agaricales)

Circumstantial evidence, mostly morphological and ecological, points to ten different mushroom host species for up to fifteen species of the mycoparasitic genus Squamanita. Here, molecular evidence confirms Cystoderma amianthinum as the host for S. paradoxa, a sporadically occurring and rarely collected mycoparasite with extreme host specificity. This is only the second study to use molecular techniques to reveal or confirm the identity of a cecidiocarp of Squamanita species. Phylogenetic analysis of combined nuclear ribosomal RNA genes suggests the monophyly of Squamanita, Cystoderma, and Phaeolepiota, a clade referred to as the tribe Cystodermateae. If true, S. paradoxa and C. amianthinum would represent a relatively closely related species pair involved in a mycoparasitic symbiosis.     

The genus Ramalina in Brazil

Abstract: Twenty-two species of Ramalina are reported from Brazil. Their taxonomy is discussed and a key is provided. Ramalina denticulata var. stephanophora is reduced to synonymy with R. aspera, R. flagellifera with R. camptospora, R. denticulata var. subolivacea and R. complanata f. reagens with R. complanata, R. dendriscoidella and R. tenella with R. dendroides, and R. bicolor with R. gracilis. Ramalina asahinae, R. calcarata, R. pusiola, R. sorediosa, and R. sprengelii are new to Brazil.     

A review of the genus Hebeloma in Svalbard

Between 1960 and 2009, regular visits to Svalbard were made and a number of Hebeloma spp. were collected by several mycologists. We have studied 249 such collections, many from the Herbarium in Oslo (O) and from the private herbarium of the first author. The collections represent 17 different species. Of the 17 species, five (H. louiseae, H. pallidolabiatum, H. perexiguum, H. pubescens and H. spetsbergense) are only known from Svalbard. In this paper we discuss the habitat and apparent associates of the 17 species recorded, as well as their frequency of occurrence within our sample, and compare this with our data from other regions of the northern hemisphere. A further analysis compares the records we have from the collection of basidiomes with data published from root analysis of mycorrhizal associates on Svalbard. Root associate data strongly suggest the occurrence of an unknown Hebeloma species, not close to any of the infrageneric groups known to occur in arctic habitats.     

The genus Anisotes (Acanthaceae), a taxonomic revision

The genus Anisotes Nees is revised. A total of 24 taxa had previously been described. In the present revision 19 species, 3 subspecies and 1 variety are recognized. A new infrageneric classification of Anisotes is proposed.
In the general part the morphology, with special emphasis on pollen morphology, and the diagnostic characters of the genus are outlined. Phytogeographical and ecological aspects are discussed in relation to the phytogeographical division of Africa.     

The genus Macrorungia (Acanthaceae), a taxonomic revision

The genus Macrorungia C. B. Clarke is revised. 5 taxa have previously been proposed in the genus; the present revision recognises 3, viz. Macrorungia galpinii C. Baden sp. nov., M. longistrobus C. B. Clarke and M. pubinervia (T. Anders.) C. B. Clarke. The delimitation between Anisotes and Macrorungia is discussed. Phytogeographical and ecological aspects are discussed in relation to the phytogeog–raphical division of Africa.     

The genus Cremastra (Orchidaceae), a taxonomic revision

The genus Cremastra is revised. A total of 8 taxa have earlier been proposed, but in the present revision 2 species are recognized: C. appendiculata and C. unguiculata. Hyacinthorchis variabilis is here considered a variety: C. appendiculata var. variabilis comb. et stat. nov.