Size and sequence heterogeneity in the ITS1 of Xylaria hypoxylon isolates

Armillaria mexicana, a newly described species from Mexico

Armillaria mexicana (Agaricales, Physalacriaceae) is described as a new species based on morphology, DNA sequence data, and phylogenetic analyses. It clearly differs from previously reported Armillaria species in North, Central, and South America. It is characterized by the absence of fibulae in the basidioma, abundant cheilocystidia, and ellipsoidal, hyaline basidiospores that are apparently smooth under light microscope, but slightly to moderately rugulose under scanning electron microscope. It is differentiated from other Armillaria species by macromorphological characters, including annulus structure, pileus and stipe coloration, and other structures. DNA sequence data (nuc rDNA internal transcribed spacers [ITS1-5.8S-ITS2 = ITS], 28S D-domain, 3' end of 28S intergenic spacer 1, and translation elongation factor 1-α [TEF1]) show that A. mexicana sequences are quite distinct from sequences of analogous Armillaria species in GenBank. In addition, sequences of ITS of the A. mexicana ex-type culture reveal an ITS1 of 1299 bp and an ITS2 of 582 bp, the longest ITS regions reported thus far in fungi. Phylogenetic analysis based on TEF1 sequences place A. mexicana in a well-separated, monophyletic clade basal to the polyphyletic A. mellea complex.

Phylogenetic relationships of Chlamydomyces, Harzia, Olpitrichum, and their sexual allies, Melanospora and Sphaerodes

Phylogenetic analyses using internal transcribed spacer (ITS), large subunit rRNA (LSU), and small subunit (SSU) sequence data showed that Harzia, Chlamydomyces, and Olpitrichum are con-generic. Thus, Chlamydomyces, and Olpitrichum were reduced to synonymy of Harzia. The generic concept was amended and expanded accordingly. Eight new combinations were proposed. Melanospora and Sphaerodes are phylogenetically related to Harzia. However, several members of Melanospora and Sphaerodes are polyphyletic and belong to Hypocreales or Microascales in Sordariomycetes. The Proteophiala morph is not only a crucial morphological character, but also has a phylogenetical significance in defining Melanosporales. It is hypothesized that the taxa with synanamorphic or asexual Proteophiala all belong to Ceratostomataceae, Melanosporales.

Hypoxylon pulicicidum sp. nov. (Ascomycota, Xylariales), a pantropical insecticide-producing endophyte

BACKGROUND

Nodulisporic acids (NAs) are indole diterpene fungal metabolites exhibiting potent systemic efficacy against blood-feeding arthropods, e.g., bedbugs, fleas and ticks, via binding to arthropod specific glutamate-gated chloride channels. Intensive medicinal chemistry efforts employing a nodulisporic acid A template have led to the development of N-tert-butyl nodulisporamide as a product candidate for a once monthly treatment of fleas and ticks on companion animals. The source of the NAs is a monophyletic lineage of asexual endophytic fungal strains that is widely distributed in the tropics, tentatively identified as a Nodulisporium species and hypothesized to be the asexual state of a Hypoxylon species.

METHODS AND RESULTS

Inferences from GenBank sequences indicated that multiple researchers have encountered similar Nodulisporium endophytes in tropical plants and in air samples. Ascomata-derived cultures from a wood-inhabiting fungus, from Martinique and closely resembling Hypoxylon investiens, belonged to the same monophyletic clade as the NAs-producing endophytes. The hypothesis that the Martinique Hypoxylon collections were the sexual state of the NAs-producing endophytes was tested by mass spectrometric analysis of NAs, multi-gene phylogenetic analysis, and phenotypic comparisons of the conidial states. We established that the Martinique Hypoxylon strains produced an ample spectrum of NAs and were conspecific with the pantropical Nodulisporium endophytes, yet were distinct from H. investiens. A new species, H. pulicicidum, is proposed to accommodate this widespread organism.

CONCLUSIONS AND SIGNIFICANCE

Knowledge of the life cycle of H. pulicicidum will facilitate an understanding of the role of insecticidal compounds produced by the fungus, the significance of its infections in living plants and how it colonizes dead wood. The case of H. pulicicidum exemplifies how life cycle studies can consolidate disparate observations of a fungal organism, whether from environmental sequences, vegetative mycelia or field specimens, resulting in holistic species concepts critical to the assessment of the dimensions of fungal diversity.

Molecular and morphological evidence for the delimitation of Xylaria hypoxylon

Xylaria hypoxylon, the type species of Xylaria (Xylariaceae, Sordariomycetes), was first described by Linnaeus as Clavaria hypoxylon from Sweden. Saccardo and other mycologists assumed a cosmopolitan distribution for this species. However, contradictory reports in the literature on its morphoanatomical characters and strongly inconsistent rDNA sequence data attributed to this species in GenBank suggested the existence of an unresolved species complex. To address this lack of clarity, molecular and morphological characters of numerous specimens and corresponding cultures of X. hypoxylon and related taxa from Europe were studied. Newly obtained 5.8S/ITS nrDNA sequence data were compared with published data and sequences of reference strains. European populations of X. hypoxylon from various hosts exhibited consistent rDNA sequence data and a relatively uniform holomorphic morphology, except for one specimen from Sweden that deviated in its ascospore morphology. Some samples from western United States showed DNA sequence data being identical to those of specimens from Europe, confirming a North American occurrence of X. hypoxylon. DNA sequences and morphology of other extra-European material however showed substantial deviations. Definitely not conspecific with the European material examined in this study is a strain, assigned to X. hypoxylon, the DNA sequence data of which have been used in various phylogenetic studies as a representative of Xylariaceae and Xylariales respectively. This material probably represents X longiana.

High diversity and morphological convergence among melanised fungi from rock formations in the Central Mountain System of Spain

Melanised fungi were isolated from rock surfaces in the Central Mountain System of Spain. Two hundred sixty six isolates were recovered from four geologically and topographically distinct sites. Microsatellite-primed PCR techniques were used to group isolates into genotypes assumed to represent species. One hundred and sixty three genotypes were characterised from the four sites. Only five genotypes were common to two or more sites. Morphological and molecular data were used to characterise and identify representative strains, but morphology rarely provided a definitive identification due to the scarce differentiation of the fungal structures or the apparent novelty of the isolates. Vegetative states of fungi prevailed in culture and in many cases could not be reliably distinguished without sequence data. Morphological characters that were widespread among the isolates included scarce micronematous conidial states, endoconidia, mycelia with dark olive-green or black hyphae, and mycelia with torulose, isodiametric or moniliform hyphae whose cells develop one or more transverse and/or oblique septa. In many of the strains, mature hyphae disarticulated, suggesting asexual reproduction by a thallic micronematous conidiogenesis or by simple fragmentation. Sequencing of the internal transcribed spacers (ITS1, ITS2) and 5.8S rDNA gene were employed to investigate the phylogenetic affinities of the isolates. According to ITS sequence alignments, the majority of the isolates could be grouped among four main orders of Pezizomycotina: Pleosporales, Dothideales, Capnodiales, and Chaetothyriales. Ubiquitous known soil and epiphytic fungi species were generally absent from the rock surfaces. In part, the mycota of the rock surfaces shared similar elements with melanised fungi from plant surfaces and fungi described from rock formations in Europe and Antarctica. The possibility that some of the fungi were lichen mycobionts or lichen parasites could not be ruled out.

Pigment chemistry, taxonomy and phylogeny of the Hypoxyloideae (Xylariaceae)

The Hypoxyloideae (Xylariaceae with Nodulisporium-like anamorphs) were evaluated by a morphological and HPLC-based chemotaxonomic survey of more than 2000 specimens and cultures. Conspecificity of recent records with ancient type specimens were established in many cases by HPLC, since their characteristic metabolites may remain stable for over 200 years. Most constitute novel natural products that were identified in the course of concurrent "mycochemical" studies. A comparison of HPLC profiles considering relationships within the Hypoxyloideae as inferred from the biogenesis of these pigments agreed fairly with concurrent molecular phylogenetic studies, based on sequences of actin, beta-tubulin, and 5.8S/ITS nrDNA genes. Anamorphic morphology and secondary metabolism of cultures agreed well at generic level and above. A combination of chemical and morphological traits is favored over PCR-based approaches for species discrimination, if only relatively few taxa of these diverse genera have been sequenced. An overview on the chemical structures and biological activities of the characteristic metabolites is provided, their ecological importance is discussed, and the utility of chemotaxonomy to support and predict phylogenetic relationships in the Hypoxyloidae is demonstrated. A polythetic approach is most useful to elucidate the phylogeny of the Xylariaceae. Chemotaxonomy to assess fungal biodiversity has considerable utility.

Cryptic long internal repeat sequences in the ribosomal DNA ITS1 gene of the dinoflagellate Cochlodinium polykrikoides (dinophyceae): a 101 nucleotide six-repeat track with a palindrome-like structure

Extremely long PCR fragments were generated by PCR amplification of ITS and 5.8S rDNA from Cochlodinium polykrikoides against other dinoflagellates. These patterns were consistent among geographically different isolates of C. polykrikoies. DNA sequencing reactions revealed that the PCR products were 1,166 bp in length and consisted of 813 bp of ITS1, 160 bp of 5.8S rDNA and 193 bp of ITS2. Thus, the long length was caused mainly by the long ITS1 sequence. Cryptically, the ITS1 contained a tract of 101 bp that occurs six times in tandem. The six repeated elements had identical nucleotide sequences. ITS1, therefore, separated three distinct regions: the 5' end (122 bp), the six parallel repeats (606 bp), and the 3' region (85 bp). Interestingly, both the single and six-repeat sequences should be palindrome-like sequences. In inferred secondary structures, both repeat sequences formed a long helical structure. This is the first reported discovery of comparatively long internal repeats in the ITS1 of dinoflagellates.