New genes for phylogenetic studies of lichenized fungi: glyceraldehyde-3-phosphate dehydrogenase and beta-tubulin genes

Abstract:Primers for amplification and sequencing of partial glyceraldehyde-3-phosphate dehydrogenase (gpd) gene were designed for lichenized fungi. The 5′ gpd primer is most probably fungal specific, since a BLAST search in GenBank found identical sequences only from ascomycetous taxa, whereas the 3′ gpd primer was more universal. Utility of the gpd primers and previously designed beta-tubulin primers was tested in nine lichen taxa. Both the gpd and beta-tubulin primer pairs amplified in most of the taxa examined: the gpd primers generated a c. 1100 nucleotide fragment, whereas the PCR product obtained from the beta-tubulin primers was c. 900 nucleotides long. The gpd amplification products of Cladonia arbuscula and C. rangiferina were sequenced and both were found to contain three introns, the length of which varied between 49 to 83 nucleotides. To examine the applicability of gpd sequences in resolving relationships within Ascomycota, trees were calculated from 22 fungal gpd sequences obtained from GenBank together with the twoCladonia sequences using parsimony jackknifing. The gpd tree was compared with the SSU rDNA tree of the respective species (or genera). A similar analysis of the beta-tubulin gene was not performed, because only a few beta-tublin sequences from the same taxa were available in GenBank. The gpd tree was well resolved but in conflict with the SSU rDNA tree. In contrast to the SSU rDNA tree, the gpd tree did not support the monophyly of the Ascomycota. Analysis of the combined data set produced a tree very similar to that of the SSU rDNA data. However, the relationship of Lecanorales to the other orders remained unresolved. Even though gpd and beta-tubulin are highly conserved proteins, the third codon positions and introns are variable and both genes have the potential for inferring phylogenetic relationships at the lower taxonomic levels in the lichenized fungi. The two genes may be useful even below species level, depending on the species investigated.     

Ophiostomatoid fungi associated with hardwood-infesting bark and ambrosia beetles in Poland: Taxonomic diversity and vector specificity

Fungi in the orders Ophiostomatales and Microascales (Ascomycota), often designated as ophiostomatoid fungi, are frequent associates of scolytine bark and ambrosia beetles that colonize hardwood and coniferous trees. Several species, e.g., Ophiostoma novo-ulmi, are economically damaging pathogens of trees. Because little is known regarding the ophiostomatoid fungi in Europe, we have explored the diversity of these fungi associated with hardwood-infesting beetles in Poland. This study aims to clarify the associations between fungi in the genera Ambrosiella, Graphium (Microascales), Graphilbum, Leptographium, Ophiostoma and Sporothrix (Ophiostomatales) and their beetle vectors in hardwood ecosystems. Samples associated with 18 bark and ambrosia beetle species were collected from 11 stands in Poland. Fungi were isolated from adult beetles and galleries. Isolates were identified based on morphology, DNA sequence comparisons for five gene regions (ITS, LSU, ßT, TEF 1-α, and CAL) and phylogenetic analyses. In total, 36 distinct taxa were identified, including 24 known and 12 currently unknown species. Several associations between fungi and bark and ambrosia beetles were recorded for the first time. In addition, associations between Dryocoetes alni, D. villosus, Hylesinus crenatus, Ernoporus tiliae, Pteleobius vittatus and ophiostomatoid fungi were reported for the first time, and Sporothrix eucastanea was reported for the first time outside of the USA. Among the species of Ophiostomatales, 14 species were in Ophiostoma s. l., two species were in Graphilbum, nine species were in Sporothrix, and seven species were in Leptographium s. l. Among the species of Microascales, three species were in Graphium, and one was in Ambrosiella. Twenty taxa were present on the beetles and in the galleries, twelve only on beetles, and four only in galleries. Bark and ambrosia beetles from hardwoods appear to be regular vectors, with ophiostomatoid fungi present in all the beetle species. Most ophiostomatoid species had a distinct level of vector/host specificity, although Ophiostoma quercus, the most frequently encountered species, also had the greatest range of beetle vectors and tree hosts. Plant pathogenic O. novo-ulmi was found mainly in association with elm-infesting bark beetles (Scolytus multistriatus, S. scolytus, and P. vittatus) and occasionally with H. crenatus on Fraxinus excelsior and with Scolytus intricatus on Quercus robur.     

Unseen fungal biodiversity and complex inter-organismal interactions in Protea flower heads

A unique microbiome occurs within the flower heads of various Protea species endemic to Africa. These include two lineages of ophiostomatoid fungi, Knoxdaviesia (Microascales) and Sporothrix (Ophiostomatales), that have members occurring exclusively in this environment and that rely on mites as their primary mode of spore dissemination. The mites, in turn, attach to the bodies of Protea-pollinating beetles and the beaks and bodies of birds for long-distance movement, establishing a hierarchical dispersal network for the ophiostomatoid fungi. This inter-organismal network is highly successful, achieving fungal dispersal over vast distances. Multiple species of fungi, mites and bacteria have been described from this unique niche over the past four decades. The intricacies of their symbiotic interactions continue to be unravelled. This review covers all current knowledge of the “distinctly African” Protea-ophiostomatoid fungus environment and illustrates the depth of a fascinating unseen fungal biodiversity niche.     

Ophiostomatoid fungi can emit the bark beetle pheromone verbenone and other semiochemicals in media amended with various pine chemicals and beetle-released compounds

Fungal volatile compounds can mediate fungal-insect interactions. Whether fungi can emit insect pheromones and how volatile chemicals change in response to chemicals the fungi naturally encounter is poorly understood. We analyzed volatiles emitted by Grosmannia clavigera (symbiont of the mountain pine beetle) and Ophiostoma ips (symbiont of the pine engraver beetle) growing in liquid media amended with compounds that the fungi naturally encounter: (−)-α-pinene, (+)-α-pinene, (−)-trans-verbenol, verbenone, or ipsdienol. Nine volatile compounds were identified among the fungal and amendment treatments. Volatiles qualitatively and quantitatively differed between fungal species and among amendment treatments. The bark beetle anti-aggregation pheromone (−)-verbenone was detected from both fungi growing in (−)-trans-verbenol-amended media. G. clavigera and O. ips can emit beetle pheromones and other beetle semiochemicals, suggesting that ophiostomatoid fungi could contribute to the chemical ecology of bark beetles. However, such contributions could be modulated by the presence of other environmental chemicals.     

Are the mitochondrial cox1 and cob genes suitable markers for species of Dinophysis Ehrenberg?

The identification of Dinophysis species with similar morphology but different toxic (Diarrhetic Shellfish Poisoning, DSP) potential is a crucial task in harmful algae monitoring programmes. The taxonomic assignment of Dinophysis species using molecular markers is a difficult task due to extremely low interspecific variability within their nuclear ribosomal genes and intergenic regions. Mitochondrial cox1 gene has been proposed as a better specific marker for Dinophysis species based on its higher resolution for two morphologically related species (Dinophysis acuminata and Dinophysis ovum) of the “Dinophysis acuminata complex”. In this study, the potential of two mitochondrial genes (mt cox1 and cob) to discriminate among six Dinophysis species (field isolates and cultures) associated with DSP events was explored. Neither mt cox1 nor cob genes provided enough resolution for all species of Dinophysis. The cob gene showed very poor resolution and grouped all Dinophysis spp. in a common clade. In contrast, the cox1 phylogeny distinguished 5 clades in the Dinophysiales – the “acuminata complex”, the “caudata group”, “acuta + norvegica” and Phalacromaspp. However, within the “D. acuminata complex” mtcox1 is so far the unique marker that differentiates D. acuminata from other species: isolates of D. ovum and Dinophysis sacculus had almost identical sequences (only four mismatches), but they were well separated from D. acuminata. D. acuminata and Dinophysis skagii (considered a life cycle stage of the former) showed identical cox1 sequences. Probes towards this gene can be useful in Mediterranean and Western Iberia sites where the co-occurrence of close morphotypes of D. acuminata and D. sacculus pose a problem for monitoring analyses. This is the first report on cultures of D. sacculus and its phylogenetic relation with other species of the D. acuminata complex.     

Multilocus phylogeny and species delimitation within the genus Glauconycteris (Chiroptera,Vespertilionidae), with the description of a new bat species from the Tshopo Province of the Democratic Republic of the Congo

The genus Glauconycteris Dobson, 1875 currently contains 12 species of butterfly bats, all endemic to sub‐Saharan Africa. Most species are rarely recorded, with half of the species known from less than six geographic localities. The taxonomic status of several species remains problematic. Here, we studied the systematics of butterfly bats using both morphological and molecular approaches. We examined 45 adult specimens for external anatomy and skull morphology, and investigated the phylogeny of Glauconycteris using DNA sequences from three mitochondrial genes and 116 individuals, which in addition to outgroup taxa, included nine of the twelve butterfly bat species currently recognized. Four additional nuclear genes were sequenced on a reduced sample of 69 individuals, covering the outgroup and Glauconycteris species. Our molecular results show that the genus Glauconycteris is monophyletic, and that it is the sister‐group of the Asian genus Hesperoptenus. Molecular dating estimates based on either Cytb or RAG2 data sets suggest that the ancestor of Glauconycteris migrated into Africa from Asia during the Tortonian age of the Late Miocene (11.6–7.2 Mya), while the basal diversification of the crown group occurred in Africa at around 6 ± 2 Mya. The species G. superba is found to be the sister‐group of G. variegata, questioning its placement in the recently described genus Niumbaha. The small species living in tropical rainforests constitute a robust clade, which contains three divergent lineages: (i) the “poensis” group, which is composed of G. poensis, G. alboguttata, G. argentata, and G. egeria; (ii) the “beatrix” group, which contains G. beatrix and G. curryae; and (iii) the “humeralis” group, which includes G. humeralis and a new species described herein. In the “poensis” group, G. egeria is found to be monophyletic in the nuclear tree, but polyphyletic in the mitochondrial tree. The reasons for this mito‐nuclear discordance are discussed.     

Two new Microascus species with spinous conidia isolated from pig farm soils in China

Two scopulariopsis-like fungi were isolated when surveying fungi in pig farm soils in China. Sexual structures of these fungi were not observed and their conidia had spinous walls. Phylogenetic analysis based on nucleotide sequences of the internal transcribed spacer 1 and 2 and intervening 5.8S ribosomal RNA gene (ITS), large subunit ribosomal RNA gene (LSU), beta-tubulin (tub2) and translation elongation factor 1-alpha (tef1) gene showed that they were new members of the genus Microascus, and the name M. aculeatus and M. spinosporus were introduced. Genetically the two new species clustered in a well-supported clade close to M. longicollis, but differed in producing relatively long branches. Morphologically M. aculeatus could be distinguished by its conidia with sparse but long spines; M. spinosporus resembled three species of the genus Scopulariopsis, S. asperula, S. brevicaulis and S. flava, but was different in the color of colony and conidia, and the form of conidiophores.     

Actividad antifúngica in vitro de la micafungina

BackgroundMicafungin is a new and very useful pharmacological tool for the treatment of invasive mycoses with a wide antifungal spectrum for the most common pathogenic fungi. Micafungin is especially active against the genera Candida and Aspergillus. Its antifungal mechanism is based on the inhibition of the β-1,3- D-glucan synthesis, an essential molecule for the cell wall architecture, with different con sequences for Candida and Aspergillus, being micafungin fungicide for the former and fungistatic for the latter.AimTo describe the in vitro antifungal spectrum of micafungin based in the scientific and medical lite rature of recent years.MethodsWe have done a bibliographic retrieval using the scientific terms, “micafungin”, “activity”, “Candida”, “Aspergillus”, “fungi”, “mycos*”, “susceptibility”, in PubMed/Medline from the National Library of Medicine de EE.UU. from 2005 to 2009.ResultsWe can underline that most than 99% of Candida isolates are susceptible to ≤ 2 μg/ml of micafungin. MIC are very low (≤ 0.125 μg/ml) for most clinical isolates of the species Candida albicans, Candida glabrata, Candida tropicalis and Candida krusei while Candida parapsilosis and Candida guilliermondii isolates are susceptible to anidulafungin concentrations ≤ 2 μg/ml. The activity of micafungin is excellent against those medical important species of Aspergillus. However, its activity is very low against Cryptococcus and the Zygomycetes.ConclusionsThe excellent activity of micafungin has made this antifungal a first line therapeutic indication for candidemia and invasive candidiasis in non-neutropenic patients.     

Effects of water potential and solute on the growth and interactions of two fungal symbionts of the mountain pine beetle

We investigated the effect of water potential (WP) on the growth of, and interaction between, two ophiostomatoid fungi, Grosmannia clavigera and Ophiostoma montium, associated with the mountain pine beetle (Dendroctonus ponderosae). The WP of malt extract agar was amended by adding potassium chloride (KCl) or sucrose. Growth of both fungi decreased with WP on KCl-amended media. Growth of G. clavigera also decreased with WP on sucrose-amended media, although growth was stimulated on these media compared to unamended treatments. Growth of O. montium remained relatively constant on sucrose-amended media, confounding the effect of WP on this species. Both fungi were able to colonize media occupied by the other species, but at a slower rate than on unoccupied media, indicating competition. In most treatments, G. clavigera grew faster than O. montium and colonized a greater area when the two fungi were inoculated concurrently but distant to one another on a Petri dish. However, when each fungus was inoculated adjacent to a 10-d-old well-established colony of the other species, O. montium colonized occupied media more effectively than G. clavigera considering the growth rate of each species alone. Thus, G. clavigera dominated primary (uncolonized) resources on most media, whereas O. montium was more effective in colonizing secondary (occupied) resources. The differential response of the two fungi to sucrose indicates that they may use different carbon sources, or use different carbon sources at different rates, in the tree. Fine-scale resource partitioning, differences in primary and secondary resource capture abilities, and the non-equilibrium dynamics in an attacked tree over time, could all act to promote the co-existence of two unit-restricted dispersers on a discontinuous resource.     

Spirometra species from Asia: Genetic diversity and taxonomic challenges

Despite considerable controversy concerning the taxonomy of species within the genus Spirometra, human sparganosis and spirometrosis mainly in Asia and Europe has long been confidently ascribed to Spirometra erinaceieuropaei. Recently, the mitochondrial genomes of purported “S. erinaceieuropaei”, “Spirometra decipiens” and “Spirometra ranarum” from Asia have been determined. However, it has been pointed out that the morphological criteria used for identifying these species are unsuitable and thus these identifications are questionable. In the present study, therefore, Spirometra samples from Asia were re-examined based on mitochondrial cytochrome c oxidase subunit 1 gene sequences and the identification of these species was discussed. Haplotype network and phylogenetic analyses revealed that: i) two distinct Spirometra species, Type I and Type II, are present in Asia and neither of which is close to likely European “S. erinaceieuropaei”; ii) Type I is genetically diverse and widely distributed, however Type II is known so far from Japan and Korea; iii) “S. decipiens” and “S. ranarum” reported from Asia are conspecific with Type I; iv) Type I is probably conspecific with Spirometra mansoni, and Type II may represent an undescribed species.     

Isolation and sequence analysis of a β-tubulin gene from arbuscular mycorrhizal fungi

A full-length β-tubulin gene has been cloned and sequenced from Gigaspora gigantea and Glomus clarum, two arbuscular mycorrhizal fungi (AMF) species in the phylum Glomeromyota. The gene in both species is organized into five exons and four introns. Both genes are 94.9% similar and encode a 447 amino acid protein. In comparison with other fungal groups, the amino acid sequence is most similar to that of fungi in the Chytridiomycota. The codon usage of the gene in both AMF species is broad and biased in favor of an A or a T in the third position. The four introns varied in length from 87 to 168 bp for G. gigantea and from 90 to 136 bp for G. clarum. Of all fungi in which full-length sequences have been published, only AMF do not have an intron before codon 174. The introns positioned at codons 174 and 257 in AMF match the position of different introns in β-tubulin genes of some Zygomycete, Basidiomycete, and Ascomycete fungi. The 5′ and 3′ splice site consensus sequences are similar to those found in introns of most fungi. Sequence analysis from single-strand conformation polymorphism analysis confirmed the presence of two β-tubulin gene copies in G. clarum, but only one copy was evident in G. gigantea based on Southern hybridization analysis.     

Differential RNA accumulation of two β-tubulin genes in arbuscular mycorrhizal fungi

RNA was isolated from spores of different arbuscular mycorrhizal (AM) fungi and used for RT-PCR with degenerate primers for beta-tubulin genes. PCR products were cloned and the sequence of several clones was analysed for each fragment. Comparison of sequences identified two loci for beta-tubulin genes with different GC content and codon usage. Btub1 sequences were most similar to beta-tubulin genes from the Oomycota, while Btub2 sequences showed highest similarity to sequences from the Zygomycota. RT-PCR experiments were carried out to monitor RNA accumulation patterns of Btub1 and Btub2 in asymbiotic germinating spores and in symbiotic extraradical hyphae of three different AM fungi. This indicated that Btub1 is constitutively expressed in Gigaspora rosea, but down-regulated during symbiosis in Glomus mosseae and Glomus intraradices. In contrast, Btub2 showed constitutive expression in the two Glomus species, but down-regulation in G. rosea. Further analysis of different fungi indicated that Btub2 primers could be used to specifically monitor RNA accumulation of AM fungi in environmental samples.     

Knoxdaviesia capensis: dispersal ecology and population genetics of a flower-associated fungus

Protea-associated fungi are dispersed between flower heads by mites, beetles and possibly birds. For the ophiostomatoid fungus, Knoxdaviesia proteae, these vectors offer regular dispersal between distant floral hosts. Unlike K. proteae, Knoxdaviesia capensis occupies multiple Protea host species. In this study, we aimed to determine whether the generalist K. capensis shares the long-distance dispersal pattern with specialist K. proteae and whether it moves freely between different host species. We evaluated the genetic structure of K. capensis from five populations of a wide-spread host and between sympatric hosts. Twelve K. capensis-specific microsatellite markers were developed and applied to 90 individuals. K. capensis showed high genetic diversity and almost maximal genotypic diversity. All populations were poorly differentiated, indicating the presence of long-distance dispersal. No differentiation could be detected between sympatric host populations, suggesting free dispersal between different hosts. This implies that the beetle and bird vectors that pollinate Protea species show the same non-specific movement.     

Rhizobium indicum sp. nov., isolated from root nodules of pea (Pisum sativum) cultivated in the Indian trans-Himalayas

Three strains of rhizobia isolated from effective root nodules of pea (Pisum sativum L.) collected from the Indian trans-Himalayas were characterized using 16S rRNA, atpD and recA genes. Phylogeny of the 16S rRNA genes revealed that the newly isolated strains were members of the genus Rhizobium with ≥99.9% sequence similarity to the members within the “Rhizobium leguminosarum” group. Phylogenetic analyses based on the concatenated sequences of atpD and recA gene, and 92 core genes extracted from the genome sequences indicated that strains JKLM 12A2^T and JKLM 13E are grouped as a separate clade closely related to R. laguerreae FB206^T. In contrast, the strain JKLM 19E was placed with “R. hidalgonense” FH14^T. Whole-genome average nucleotide identity (ANI) values were 97.6% within strains JKLM 12A2^T and JKLM 13E, and less than 94% with closely related species. The digital DNA-DNA hybridization (dDDH) values were 81.45 within the two strains and less than 54.8% to closely related species. The major cellular fatty acids were C_18:1w7c in summed feature 8, C_{14:0 3OH}/C_{16:1 iso I} in summed feature 2, and C_18:0. The DNA G + C content of JKLM 12A2^T and JKLM 13E was 60.8 mol%. The data on genomic, chemotaxonomic, and phenotypic characteristics indicates that the strains JKLM 12A2^T and JKLM 13E represent a novel species, Rhizobium indicum sp. nov. The type strain is JKLM 12A2^T (= MCC 3961^T = KACC 21380^T = JCM 33658^T). However, the strain JKLM 19E represents a member of “R. hidalgonense” and the symbiovar viciae.     

Carotenoid biosynthesis and the evolution of carotenogenesis genes in rust fungi

Diseases caused by rust fungi pose a significant threat to global plant production. Although carotenoid pigments are produced in spores of nearly all rust species, the corresponding biosynthesis pathway(s) have not been investigated. Here, candidate genes for carotenoid biosynthesis in Puccinia graminis f. sp. tritici (Pgt) were identified, cloned and functionally complemented using specifically engineered strains of Escherichia coli. A part of the carotenoid biosynthesis pathway in rust fungi was elucidated, with only two genes, CrtYB and CrtI, catalysing the reactions from geranyl–geranyl diphosphate (GGPP) to γ-carotene. The CrtYB gene encodes a bi-functional lycopene cyclase/phytoene synthase, which catalyses the condensation of two GGPP into phytoene, as well as the cyclisation of the ψ-end of lycopene to form γ-carotene. The CrtI gene encodes a phytoene desaturase that carries out four successive desaturations of phytoene, through the intermediates phytofluene and neurosporene to lycopene. The evolution of carotenoid pigmentation in rust fungi, including Pgt, P. graminis avenae, P. graminis secalis (Pgs), P. graminis lolli, P. striiformis f. sp. tritici, P. striiformis f. sp. pseudohordei, P. striiformis f. sp. hordei, the “scabrum” rust (putative hybrids between Pgt and Pgs), P. triticina, and P. hordei, was investigated by phylogenetic analysis. Both CrtYB and CrtI were found to be closely related among rust fungi, other pathogenic fungi, and some aphids. Our results provide a springboard to increase the understanding of the physiological role(s) of carotenoid pigments in rust fungi, to better understand evolution within the Pucciniales, and to develop robust molecular diagnostics for rust fungi.     

Fungal associates of the tree-killing bark beetle,Ips typographus,vary in virulence,ability to degrade conifer phenolics and influence bark beetle tunneling behavior

The bark beetle Ips typographus carries numerous fungi that could be assisting the beetle in colonizing live Norway spruce (Picea abies) trees. Phenolic defenses in spruce phloem are degraded by the beetle's major tree-killing fungus Endoconidiophora polonica, but it is unknown if other beetle associates can also catabolize these compounds. We compared the ability of five fungi commonly associated with I. typographus to degrade phenolic compounds in Norway spruce phloem. Grosmannia penicillata and Grosmannia europhioides were able to degrade stilbenes and flavonoids faster than E. polonica and grow on minimal growth medium with spruce bark constituents as the only nutrients. Furthermore, beetles avoided medium amended with phenolics but marginally preferred medium colonized by fungi. Taken together our results show that different bark beetle-associated fungi have complementary roles in degrading host metabolites and thus might improve this insect's persistence in well defended host tissues.     

Ophiostomatoid fungi isolated from Japanese red pine and their relationships with bark beetles

We isolated ophiostomatoid fungi from bark beetles infesting Pinus densiflora and their galleries at 24 sites in Japan. Twenty-one ophiostomatoid fungi, including species of Ophiostoma, Grosmannia, Ceratocystiopsis, Leptographium, and Pesotum, were identified. Among these, 11 species were either newly recorded in Japan or were previously undescribed species. Some of these fungal species were isolated from several bark beetles, but other species were isolated from only a particular beetle species. Thus, it is suggested that some ophiostomatoid fungi have specific relationships with particular beetle species. In addition, fungus-beetle biplots from redundancy analysis (RDA) summarizing the effects of beetle ecological characteristics suggested that the association patterns between bark beetles and the associated fungi seemed to be related to the niches occupied by the beetles.