Pseudozyma pruni sp. nov., a novel ustilaginomycetous anamorphic fungus from flowers in Taiwan

Two ustilaginomycetous anamorphic strains were isolated from flowers in Taiwan. Phylogenetic analysis based on the combined rRNA gene sequence of internal transcribed spacer 1 (ITS1)-5.8S-ITS2 and large-subunit D1/D2 domains indicated that the closest recognized species was Pseudozyma fusiformata. The results of DNA-DNA hybridization and physiological characteristics showed that the two strains represent a novel species within the genus Pseudozyma. The name Pseudozyma pruni sp. nov. is proposed, with FIRDI 005(T) (=BCRC 34227(T) =CBS 10937(T)) as the type strain.

Phylogenetic study of two truffles, Tuber formosanum and Tuber furfuraceum, identified from Taiwan

Truffles are one of the most valuable edible fungi and have drawn extensive research interests worldwide. In Taiwan, two species of truffle, Tuber formosanum and Tuber furfuraceum, have been identified and reported. Although the morphological features of these two truffles have been described, lack of molecular identification has led to difficulties with firmly establishing their relatedness to other truffles. In this study, we utilized the internal transcribed spacer (ITS) and beta-tubulin gene sequences to generate the phylogenetic relationship of T. formosanum and T. furfuraceum with other taxonomic relatives. Our analysis revealed five/three major phylogenetic clades according to the 5.8S-ITS2/beta-tubulin gene sequences and corroborated with their morphological characterization. Tuber formosanum highly resembles the Tuber indicum B complex, while T. furfuraceum is most similar to Tuber huidongense. Based on a molecular clock, we estimated that T. furfuraceum and T. formosanum would have diverged from their close relatives in mainland China between 10.2 and 4.1 Ma, respectively. Based on the results, we propose that these two Tuber species found in Taiwan might originate from the common ancestors with some truffle species in China. However, due to a long divergence time and geographical separation, they have evolved into indigenous species of Taiwan.

5.8S-28S rRNA interaction and HMM-based ITS2 annotation

The internal transcribed spacer 2 (ITS2) of the nuclear ribosomal repeat unit is one of the most commonly applied phylogenetic markers. It is a fast evolving locus, which makes it appropriate for studies at low taxonomic levels, whereas its secondary structure is well conserved, and tree reconstructions are possible at higher taxonomic levels. However, annotation of start and end positions of the ITS2 differs markedly between studies. This is a severe shortcoming, as prediction of a correct secondary structure by standard ab initio folding programs requires accurate identification of the marker in question. Furthermore, the correct structure is essential for multiple sequence alignments based on individual structural features. The present study describes a new tool for the delimitation and identification of the ITS2. It is based on hidden Markov models (HMMs) and verifies annotations by comparison to a conserved structural motif in the 5.8S/28S rRNA regions. Our method was able to identify and delimit the ITS2 in more than 30000 entries lacking start and end annotations in GenBank. Furthermore, 45000 ITS2 sequences with a questionable annotation were re-annotated. Approximately 30000 entries from the ITS2-DB, that uses a homology-based method for structure prediction, were re-annotated. We show that the method is able to correctly annotate an ITS2 as small as 58 nt from Giardia lamblia and an ITS2 as large as 1160 nt from humans. Thus, our method should be a valuable guide during the first and crucial step in any ITS2-based phylogenetic analysis: the delineation of the correct sequence. Sequences can be submitted to the following website for HMM-based ITS2 delineation: http://its2.bioapps.biozentrum.uni-wuerzburg.de.

Molecular community analysis of arbuscular mycorrhizal fungi in roots of geothermal soils in Yellowstone National Park (USA)

To better understand adaptation of plants and their mycorrhizae to extreme environmental conditions, we analyzed the composition of communities of arbuscular mycorrhizal fungi (AMF) in roots from geothermal sites in Yellowstone National Park (YNP), USA. Arbuscular mycorrhizal fungi were identified using molecular methods including seven specific primer pairs for regions of the ribosomal DNA that amplify different subgroups of AMF. Roots of Dichanthelium lanuginosum, a grass only occurring in geothermal areas, were sampled along with thermal and nonthermal Agrostis scabra and control plants growing outside the thermally influenced sites. In addition, root samples of Agrostis stolonifera from geothermal areas of Iceland were analyzed to identify possible common mycosymbionts between these geographically isolated locations. In YNP, 16 ribosomal DNA phylotypes belonging to the genera Archaeospora, Glomus, Paraglomus, Scutellospora, and Acaulospora were detected. Eight of these phylotypes could be assigned to known morphospecies, two others have been reported previously in molecular studies from different environments, and six were new to science. The most diverse and abundant lineage was Glomus group A, with the most frequent phylotype corresponding to Glomus intraradices. Five of the seven phylotypes detected in a preliminary sampling in a geothermal area in Iceland were also found in YNP. Nonthermal vegetation was dominated by a high diversity of Glomus group A phylotypes while nonthermal plants were not. Using multivariate analyses, a subset of three phylotypes were determined to be associated with geothermal conditions in the field sites analyzed. In conclusion, AMF communities in geothermal soils are distinct in their composition, including both unique phylotypes and generalist fungi that occur across a broad range of environmental conditions.

Q-RT-PCR for assessing archaea, bacteria, and fungi during leaf decomposition in a stream

Leaf disks of Tilia cordata were exposed for up to 5 weeks in a first-order stream in Nova Scotia, Canada. The exponential decay rate k was 0.008 day(-1). Ergosterol levels increased linearly to a maximum of 134 microg g(-1) dry leaf mass. Release of conidia peaked at 700 day(-1) mg(-1) on leaves that had been exposed for 3 weeks; after 5 weeks, it declined to 15 mg(-1). In total, 23 taxa of aquatic hyphomycetes were distinguished. Anguillospora filiformis contributed over 76% of the conidia during weeks 1, 2, and 3, and 16.5% in week 5. Three sets of primers specific for Bacteria, Archaea, and Fungi were applied in quantitative real-time polymerase chain reaction (Q-RT-PCR) to estimate relative DNA amounts. Archaeal DNA was consistently present at low levels. Bacterial and fungal DNA peaked between weeks 2 and 3, and declined in week 5. With the exception of week 1, fungal DNA exceeded bacterial DNA by between 12 and 110%.

Genetic differences in internal transcribed spacer 1 between Dermanyssus gallinae from wild birds and domestic chickens

We investigated the presence of the poultry red mite or the chicken mite, Dermanyssus gallinae De Geer, Acari: Dermanyssidae, in wild bird populations in four different geographical regions of Sweden. The mites identified as D. gallinae were compared genetically with D. gallinae from egg-producing poultry farms in the same regions. The small subunit (SSU) gene, the 5.8S ribosomal RNA (rRNA) gene and the two internal transcribed spacers (ITS) of the rRNA genes were used in the genetic analysis. All D. gallinae mites had identical SSU rRNA, 5.8S rRNA and ITS2 sequences independent of their origin. By contrast, we identified significant differences in the ITS1 sequences. Based on the differences in the ITS1 sequences, the mites could be divided into two genotypes, of wild and domesticated origin, with no variation within the groups. These results imply that wild bird populations are of low importance, if any, as natural reservoirs of D. gallinae in these four geographical regions of Sweden.

Optimization for the production of exopolysaccharide from Fomes fomentarius in submerged culture and its antitumor effect in vitro

A medicinal mushroom Fomes fomentarius, was isolated from the fruiting body of a wild F. fomentarius and identified by ITS-5.8S rDNA sequencing analysis. Then, the optimization of submerged culture conditions and nutritional requirements of mycelial biomass and exopolysaccharide (EPS) production from F. fomentarius was studied using orthogonal matrix method. Under the optimal culture condition, the maximum EPS concentration reached 3.64 g l(-1), which is about four times higher than that at the basal medium. Furthermore, the EPS from F. fomentarius has a direct antiproliferative effect in vitro on SGC-7901 huaman gastric cancer cells in a dose- and time-dependent manner. Moreover, it was about three times that EPS at noncytocxity concentration of 0.25 mg ml(-1) could sensitize doxorubicin(Dox)-induced growth inhibition of SGC-7901 cells after 24h treatment.

Different mechanisms for pseudouridine formation in yeast 5S and 5.8S rRNAs

The selection of sites for pseudouridylation in eukaryotic cytoplasmic rRNA occurs by the base pairing of the rRNA with specific guide sequences within the RNA components of box H/ACA small nucleolar ribonucleoproteins (snoRNPs). Forty-four of the 46 pseudouridines (Psis) in the cytoplasmic rRNA of Saccharomyces cerevisiae have been assigned to guide snoRNAs. Here, we examine the mechanism of Psi formation in 5S and 5.8S rRNA in which the unassigned Psis occur. We show that while the formation of the Psi in 5.8S rRNA is associated with snoRNP activity, the pseudouridylation of 5S rRNA is not. The position of the Psi in 5.8S rRNA is guided by snoRNA snR43 by using conserved sequence elements that also function to guide pseudouridylation elsewhere in the large-subunit rRNA; an internal stem-loop that is not part of typical yeast snoRNAs also is conserved in snR43. The multisubstrate synthase Pus7 catalyzes the formation of the Psi in 5S rRNA at a site that conforms to the 7-nucleotide consensus sequence present in other substrates of Pus7. The different mechanisms involved in 5S and 5.8S rRNA pseudouridylation, as well as the multiple specificities of the individual trans factors concerned, suggest possible roles in linking ribosome production to other processes, such as splicing and tRNA synthesis.

Morphological and genetic characteristics of the entomopathogenic fungus Ophiocordyceps nutans and its host insects

We examined the morphology, genetic variation, and insect host species of the fungus Ophiocordyceps nutans. Fifty-two fruit bodies collected in Hokkaido, Japan, were grouped by host species, and 19 samples were analysed. The ranges of the lengths and breadths of all fruit body parts were similar among host groups. In the genetic analysis, the 5.8S rDNA region showed completely identical sequences, although differences of up to six nucleotides were recognized in the ITS regions. The distance values between our samples using the Kimura two-parameter model were lower than 0.007. Thus, the O. nutans examined here were concluded to form a closely related group with little detectable variability that parasitized nine hemipteran species.

Cytogenetic and molecular characterization of the Abies alba genome and its relationship with other members of the Pinaceae

Genome size, karyotype structure, heterochromatin distribution, position and number of ribosomal genes, as well as the ITS2 sequence of the internal transcribed spacer (ITS) were analysed in silver fir (Abies alba Mill.). The analysis also included characterization of the Arabidopsis-type of telomeric repeats in silver fir and in related species. The results were compared with results from other species of the Pinaceae, to evaluate phylogeny and chromosomal and molecular evolution in the Pinaceae. Integrated chromosomal data provided insights into chromosome and karyotype evolution in the Pinaceae. The evolutionary trend for GC-rich heterochromatic blocks seems to involve loss of blocks that are not associated with rDNA. Similarly, numerous large blocks of interstitial plant telomeric repeats that are typical for all analysed species of the genus Pinus were not observed in the evolutionarily younger genera, such as Abies, Picea and Larix. On the contrary, the majority of telomeric sequences in these three genera appeared confined to the chromosome ends. We confirmed the current position of Abies and Tsuga in subfamily Abietoideae and the position of Pinus in the subfamily Pinoideae based on ITS2 sequences. Pseudotsuga is placed together with Larix into the subfamily Laricoideae. We conclude that the current position of the genus Picea in the subfamily Abietoideae should be reconsidered and, possibly, the genus Picea should be reclassified as a separate subfamily, Piceoideae, as recently proposed.

Alternaria jesenskae sp. nov., a new species from Slovakia on Fumana procumbens (Cistaceae)

Alternaria jesenskae sp. nov. recovered from seeds of a shrubby perennial plant Fumana procumbens (Cistaceae) in Slovakia is described and illustrated. The new taxon can be clearly separated from the other related large-spored and filament-beaked Alternaria species based on sequences of the ITS1, 5.8S and ITS2 region as well as by its distinctive morphology. Even though the molecular data have shown close relatedness with A. multirostrata, the new species is morphologically most similar to A. tomatophila distinguished primarily by the pronounced colony pigmentation, conidial septation and beak branching.

[Ribosomal DNA ITS sequence of analysis of Psammosilene tunicoides from different populations]

OBJECTIVE

To analyze the ribosomal ITS sequence variation of Psammosilene tuncolides W. C. Wu et C. Y. Wu from different populations, for identifying different local populations.

METHODS

A pair of primers of 18SP1 and 26SP2 with PCR technique had been applied to study the ITS sequences.

RESULTS

The sequences of ITS1, ITS2 and 5.8S are 225-229 bp, 166-170 bp and 261-264 bp. Among 12 local populations, the sequence of Kunming, Lijiang, Gejiu, Heqing of Yunnan and Yanyuan of Sichuan showed no variation, there were 1-4 variable sites (including 5.8S coding region) in pairwise comparison of the other 7 local populations, including Xuanwei, Huize, Zhongdian, Baoshan of Yunnan, Muli of Sichuan and Linzhi of Tibet.

CONCLUSION

Comparative analysis shows that the ITS sequences of different local populations in the middle of Yunnan, southwest of Sichuan and west, northwest of Yunnan, southeast of Tibet, southwest of Sichuan have different fingerprint character, so the ITS sequences can be used to identify different local populations. The variation of ITS sequence of Psammosilene tunicoides is related to its geographical distribution.

Interaction between an isolate of dark-septate fungi and its host plant Saussurea involucrata

A dark-septate endophytic (DSE) fungus EF-M was isolated from the roots of an alpine plant Saussurea involucrata Kar. et Kir. ex Maxim. The fungus was identified by sequencing the PCR-amplified rDNA 5.8S gene and ITS regions. The sequence was compared with similar sequences in the GenBank, and results showed that EF-M was congeneric to Leptodontidium. Resynthesis study was conducted to clarify the relationship between the root endophyte EF-M and the host plant S. involucrata using the material grown in sterile culture bottle. In roots recovered 6 weeks after inoculation, epidermal cells were colonized by intercellular and intracellular hyphae and "microsclerotia" formed within individual cells in the epidermis layers. However, hyphae did not invade the cortex and the stele. There were no profound effects of endophyte EF-M on plant root development, but significant differences were detected in plant height and shoot dry weight between the treatments. The present study is the first report hitherto on DSE fungi in S. involucrata.

Detection and identification of wild yeast contaminants of the industrial fuel ethanol fermentation process

Monitoring for wild yeast contaminants is an essential component of the management of the industrial fuel ethanol manufacturing process. Here we describe the isolation and molecular identification of 24 yeast species present in bioethanol distilleries in northeast Brazil that use sugar cane juice or cane molasses as feeding substrate. Most of the yeast species could be identified readily from their unique amplification-specific polymerase chain reaction (PCR) fingerprint. Yeast of the species Dekkera bruxellensis, Candida tropicalis, Pichia galeiformis, as well as a species of Candida that belongs to the C. intermedia clade, were found to be involved in acute contamination episodes; the remaining 20 species were classified as adventitious. Additional physiologic data confirmed that the presence of these major contaminants cause decreased bioethanol yield. We conclude that PCR fingerprinting can be used in an industrial setting to monitor yeast population dynamics to early identify the presence of the most important contaminant yeasts.

Geosmithia fungi are highly diverse and consistent bark beetle associates: evidence from their community structure in temperate Europe

Geosmithia spp. (Ascomycota: Hypocreales) are little-studied, dry-spored fungi that occur in galleries built by many phloeophagous bark beetles. This study mapped the distribution and environmental preferences of Geosmithia species occurring in galleries of temperate European bark beetles. One hundred seven host tree samples of 16 tree species infested with 23 subcortical insect species were collected from across Europe during the years 1997-2005. Over 600 Geosmithia isolates from the beetles were sorted into 17 operational taxonomic units (OTUs) based on their phenotype similarity and phylogeny of internal transcribed spacer (ITS) region of rDNA (ITS1-5.8S-ITS2). The OTUs represent six known species and eight undescribed taxa. Ninety-two samples infested with subcortical insects were characterized by the presence/absence of OTUs and the similarity among the samples was evaluated. Geographically distant populations of the same beetle species host relatively uniform Geosmithia communities across large geographic areas (ranging from southern Bulgaria to the Czech Republic). This suggests effective dispersal of Geosmithia spp. by bark beetles. Clustering of similar samples in ordination analysis is correlated predominantly with the isolation source (bark beetles and their respective feeding plant), but not with their geographical origin. The composition of the Geosmithia OTU community of each bark beetle species depends on the degree of isolation of the species' niches. Thus, Geosmithia communities associated with regularly co-occurring bark beetle species are highly similar. The similarity decreases with decreasing frequency of beetle species' co-occurrence, a pattern resembling that of entomochoric ophiostomatoid fungi. These findings suggest that: 1) communities of Geosmithia spp. are vector-specific; 2) at least in some cases, the association between Geosmithia OTUs and bark beetles may have been very stable and symbioses are likely to be a fundamental factor in the speciation of Geosmithia fungi; and 3) that even nonsticky spores of Geosmithia are suitable for maintaining an insect-fungus association, contrary to previous hypotheses.

Ophiostoma species (Ascomycetes: Ophiostomatales) associated with bark beetles (Coleoptera: Scolytinae) colonizing Pinus radiata in northern Spain

Bark beetles (Coleoptera: Scolytinae) are known to be associated with fungi, especially species of Ophiostoma sensu lato and Ceratocystis. However, very little is known about these fungi in Spain. In this study, we examined the fungi associated with 13 bark beetle species and one weevil (Coleoptera: Entiminae) infesting Pinus radiata in the Basque Country of northern Spain. This study included an examination of 1323 bark beetles or their galleries in P. radiata. Isolations yielded a total of 920 cultures, which included 16 species of Ophiostoma sensu lato or their asexual states. These 16 species included 69 associations between fungi and bark beetles and weevils that have not previously been recorded. The most commonly encountered fungal associates of the bark beetles were Ophiostoma ips, Leptographium guttulatum, Ophiostoma stenoceras, and Ophiostoma piceae. In most cases, the niche of colonization had a significant effect on the abundance and composition of colonizing fungi. This confirms that resource overlap between species is reduced by partial spatial segregation. Interaction between niche and time seldom had a significant effect, which suggests that spatial colonization patterns are rarely flexible throughout timber degradation. The differences in common associates among the bark beetle species could be linked to the different niches that these beetles occupy.

[Analysis of ITS sequences of some medicinal plants and their related species in Salvia]

Molecular systematic techniques were applied to reveal the genetic diversity of medicinal plants and their related species in Salvia. The internal transcribed spacer (ITS) as well as 5.8S rDNA sequences of 27 samples of Salvia were amplified using PCR method and sequenced. Mega 3.1 was used to analyze the genetic diversity within genus. The complete sequences of ITS plus 5.8S rDNA are about 612-617 bp. A phylogenetic tree generated by Neighbor-Joining method partly supported the morphological classification within Salvia, but incompatible results were also obtained in the treatment of phylogenetic positions of some species such as Salvia trijuga, Salvia flava var. flava and Salvia flava var. megalentha. The ITS regions of present Salria species showed considerable variation between subgenera in contrast with the conservative 5.8S rDNA sequences. The native Salvia species might have a different origin from the foreign species. The phylogenetic positions of subgenera and sections inferred by ITS analysis were comparable with that of traditional classification, while the phylogeny within sections is still doubtful due to limited information in ITS sequence and need to be further proved by other evidence. ITS analysis in this study supports the rationality of using species from Drymosphace section as substitute drug resources of Dan shen, but also reveals significant genetic differences between high mountain Dan shen species such as Salvia przewalskii with traditional Dan shen origins.

Cylindrocarpon pauciseptatum sp. nov., with notes on Cylindrocarpon species with wide, predominantly 3-septate macroconidia

A Cylindrocarpon species with up to 10 microm wide, straight and predominantly 3-septate macroconidia, subglobose to ovoidal microconidia and chlamydospores, is described as Cyl. pauciseptatum. It is most similar to Cyl. austrodestructans but no chlamydospores and microconidia are formed in the latter. Similar macroconidia also occur in Cyl. theobromicola, which forms oval to ellipsoidal microconidia at least sparsely and has slightly curved macroconidia, and Cyl. destructans var. crassum, which forms abundant 1-celled microconidia. DNA sequence data of the internal transcribed spacer regions 1 and 2 plus the 5.8S rDNA and the partial beta-tubulin gene were used for phylogenetic inferences. Cylindrocarpon pauciseptatum and Cyl. macrodidymum are monophyletic and are closely related to other species of Cylindrocarpon sensu stricto including members of the Cyl. destructans (teleomorph, Neonectria radicicola) species complex, which accommodates Cyl. liriodendri (teleomorph, Neon. liriodendri), Cyl. destructans var. crassum and Cyl. austrodestructans (teleomorph, Neonectria austroradicicola comb. nov.). Cylindrocarpon theobromicola is distantly related to species of Cylindrocarpon sensu stricto or Neonectria sensu stricto. It clustered among cylindrocarpon-like species with curved macroconidia, of which some belong to the Neon. mammoidea group. Relatively voluminous cells in sporodochial conidiophores of Cyl. theobromicola resembled those described for Campylocarpon, which is closely related to members of the Neon. mammoidea group including Cyl. theobromicola. Cylindrocarpon pauciseptatum has been isolated from roots of Vitis spp. in South-eastern Europe (Slovenia) as well as New Zealand, where it also occurs on roots of Erica melanthera.

A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota)

Chytridiomycota (chytrids) is the only phylum of true Fungi that reproduces with motile spores (zoospores). Chytrids currently are classified into five orders based on habitat, zoospore characters and life cycles. In this paper we estimate the phylogeny of the chytrids with DNA sequences from the ribosomal RNA operon (18S+5.8S+28S subunits). To our surprise the morphologically reduced parasites Olpidium and Rozella comprise two entirely new, and separate, lineages on the fungal tree. Olpidium brassicae groups among the Zygomycota, and Rozella spp. are the earliest branch to diverge in the fungal kingdom. The phylogeny also suggests that Chytridiomycota is not monophyletic and there are four major lineages of chytrids: Rozella spp., Olpidium brassicae, the Blastocladiales and a "core chytrid clade" containing the remaining orders and families and the majority of flagellated fungi. Within the core chytrid group 11 subclades can be identified, each of which correlates well with zoospore ultrastructure or morphology. We provide a synopsis of each clade and its morphological circumscription. The Blastocladiales appears to be the sister taxon of most nonflagellated fungi. Based on molecular phylogenetic and ultrastructural characters this order is elevated to a phylum, the Blastocladiomycota.

Evidence for local ciliate endemism in an alpine anoxic lake

Despite its long history, biogeography has received relatively little attention within the field of microbial ecology. Consequently, a fierce debate rages whether protists inhabit restricted geographic areas (endemism hypothesis) or are globally dispersed (ubiquitous dispersal hypothesis). The data presented in this article support the endemism hypothesis. We succeeded in isolating an oligohymenophorean ciliate from a microbial mat in a meromictic anoxic alpine lake (Alatsee) in Germany. The ciliary pattern and the morphometry of this isolate are remarkably similar to Urocentrum turbo (Mueller, 1786) Nitzsch, 1827. However, the organism does not possess trichocysts, a conspicuous and characteristic feature of U. turbo. Instead, the U. turbo-like isolate from lake Alatsee displays merely trichocyst anlagen ("ghosts") in the cytoplasm that are only visible after protargol impregnation and which become never attached to the cell's cortex. Despite the distinctness of this difference, such a morphospecies has not been described from any other environment. Thus, we suggest that the U. turbo-like isolate from lake Alatsee is a local endemic ecotype, although the sequences of the 18S rRNA, ITS1, 5.8S rRNA, and ITS2 genes are nearly identical to those of U. turbo (Mueller, 1786) Nitzsch, 1827. This indicates that neither 18S rDNA nor ITS1, ITS2, and 5.8S rDNA sequences are reliable means to conclusively resolve different morphospecies or ecotypes of ciliates. As a consequence, we argue that protist species richness can only be reliably accounted for by considering both molecular and morphological data.

Differences in the species composition of arbuscular mycorrhizal fungi in spore, root and soil communities in a grassland ecosystem

Most studies on the species composition of arbuscular mycorrhizal fungi (AMF) have solely analysed mycorrhizal roots or AM spores collected from soil samples. However, the spore production rate and proportions of AMF mycelium in roots and soils have all been shown to vary substantially in a taxon-specific manner. Therefore, in the study presented here we used a molecular approach to analyse the species composition of AMF in spores, intra-radical and extra-radical mycelium in an intensively farmed meadow in central Germany. By polymerase chain reaction and sequencing of the ITS region members of seven different families and species groups within Glomeromycota were identified. The data revealed remarkable differences in the composition of AMF taxa both between the spores and the mycelia, and between the two types of mycelia. Glomus group Ab was dominant in roots and spores, in accordance with previous research. However, members of this group were rarely detected as extra-radical mycelium, in which Paraglomeraceae were dominant, although we found no evidence for the presence of Paraglomeraceae in roots or spores, even when a specific primer set was used. These results may be interpreted as a further indication that AMF are not necessarily obligate symbionts of plants.

Molecular phylogenetics of strains morphologically identified as Fonsecaea pedrosoi from clinical specimens

A phylogenetic study based on sequence analysis of the ribosomal internal transcribed spacer (ITS) 1, 5.8S and ITS2 region was performed in 33 strains morphologically identified as Fonsecaea pedrosoi from clinical specimens and living environments, preserved at the Research Center for Pathogenic Fungi and Microbial Toxicoses, Chiba University. The strains of Fonsecaea were divided into two major clades: Group A, representing F. pedrosoi sensu de Hoog et al.; and Group B, representing F. monophora. We identified new lineages: Group B was further clustered into three subgroups, B-1, B-2 and B-3, which were phylogenetically distinct from each other. The subgroups B-1, B-2 and B-3 are thought to be mainly predominant in Africa and Central and South America, Japan and China, and Europe and North America, respectively. Thus, polymorphism in Group B is rather considered to be caused by its geographic parameter. We demonstrate for the first time that all clinical isolates from Japan are monophyletic, belonging to a new lineage of F. monophora.

Evaluation of polymerase chain reaction-based ribosomal DNA sequencing technique for the diagnosis of mycotic keratitis

PURPOSE

To evaluate the polymerase chain reaction (PCR) and sequencing-based ribosomal deoxyribonucleic acid (rDNA) typing technique for rapid and sensitive diagnosis of fungal keratitis.

DESIGN

Laboratory investigation.

METHODS

The present study included culture-based methods along with PCR and ITS2/5.8S rDNA sequencing to evaluate fungal infections in 32 corneal scrapings from patients with suspected mycotic keratitis.

RESULTS

Good correlation was found between the culture and PCR rDNA sequencing-based methods. We also identified fungal strains that were noncultivable in routine culture medium and fungal strains, which have been reported scarcely in previous reports from eastern Indian studies.

CONCLUSIONS

The PCR and rDNA sequencing-based approaches may be useful alternatives to culture-based techniques for the rapid and sensitive diagnosis of fungal keratitis. We found that clinically significant pathogenic fungal strains can be detected and differentiated by this method in a short period. This method therefore is useful for the early treatment of fungal infection.

Diphyllobothrium nihonkaiense (Yamane et al., 1986) in Switzerland: First molecular evidence and case reports

We report the first cases of locally-acquired Diphyllobothrium nihonkaiense (Yamane, Kamo, Bylund and Wikgren, 1986) in Switzerland, confirmed by genetic analysis (18S rRNA, COI and ITS1-5.8S rRNA-ITS2 genes). Diphyllobothriasis in this country is attributed to the tapeworm D. latum (Linnaeus, 1758) but the increasing popularity of raw fish culinary specialities (sushi, carpaccio, tartare) brings out a new diagnostic problem, so that people can get infected by exotic species of tapeworms.

[Nucleotide composition and contents of CpG and CpNpG in the ITS1, ITS2 and 5.8S rRNA of the representatives of phylogenetic branches of melanthiales-liliales and melanthiales and melanthiales-asparagales (angiospermae, monocotyledones) reflects a characteristic feature of evolution]

Variations of nucleotide composition and frequency of CpG and CpNpG sequences in the clusters of nuclear ribosomal genes of taxa, belonging to two phylogenetic branches of Angiospermae have been statistically analyzed. This region of eucaryotic genomes is nucleolus organizer and functions in a separate compartment of cell nucleus that can do running here processes it is enough specific. It is shown that level of evolution advance of a taxon, defined on morphological data, is in positive correlation with quantitative value of dC, CpG and CpNpG. This is found in contradiction with beliefs about the general rules of the transformation of nucleotide composition in evolution, that suggest a CpG suppression. Cryptaffinous taxa being connecting link between a well morphological outlined taxonomic group, differ to be raised in