Diatrypasimilis australiensis, a novel xylarialean fungus from mangrove.

A marine xylarialean fungus, isolated from roots of Rhizophora (mangrove) in Australia, displays morphology of eight ellipsoidal dark brown ascospores in a cylindrical ascus having a refractive apical apparatus. Each ascospore has a longitudinal germ slit. The fungus grew very slowly and produced dark brown water-soluble pigment(s) on various media. It developed unique, column-shaped, indeterminate synnemata on which needle-shaped conidia were produced. The sexual stage of this fungus was not observed under the laboratory conditions tested. Molecular phylogenetic analyses of the combined sequences of nuclear ribosomal RNA genes and their internal transcribed spacers placed it at a basal position in the clade of Diatrypaceae of the Xylariales with comparatively high statistical support. However the morphological features and phylogenetic position of this organism do not closely resemble any known fungal taxa. Therefore this fungus is proposed to be a representative of a novel taxon and described as Diatrypasimilis australiensis gen. et sp. nov.

Koralionastetales, a new order of marine Ascomycota in the Sordariomycetes.

Based on molecular studies using 1760 bp of the nuSSU and 604 bp of the nuLSU rRNA genes and using morphological characters, the genera Koralionastes and Pontogeneia are assigned to the new order Koralionastetales, family Koralionastetaceae, class Sordariomycetes. Koralionastetales is a sister group to Lulworthiales; differences in morphological characters are expressed in the ascospores and the presence/absence of periphyses and paraphyses. A new species of Pontogeneia, P. microdictyi from Microdictyon sp. in the Bahamas, is described.

The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

Detection and identification of fungi intimately associated with the brown seaweed Fucus serratus.

The filamentous fungi associated with healthy and decaying Fucus serratus thalli were studied over a 1-year period using isolation methods and molecular techniques such as 28S rRNA gene PCR-denaturing gradient gel electrophoresis (DGGE) and phylogenetic and real-time PCR analyses. The predominant DGGE bands obtained from healthy algal thalli belonged to the Lindra, Lulworthia, Engyodontium, Sigmoidea/Corollospora complex, and Emericellopsis/Acremonium-like ribotypes. In the culture-based analysis the incidence of recovery was highest for Sigmoidea marina isolates. In general, the environmental sequences retrieved could be matched unambiguously to isolates recovered from the seaweed except for the Emericellopsis/Acremonium-like ribotype, which showed 99% homology with the sequences of four different isolates, including that of Acremonium fuci. To estimate the extent of colonization of A. fuci, we used a TaqMan real-time quantitative PCR assay for intron 3 of the beta-tubulin gene, the probe for which proved to be species specific even when it was used in amplifications with high background concentrations of other eukaryotic DNAs. The A. fuci sequence was detected with both healthy and decaying thalli, but the signal was stronger for the latter. Additional sequence types, representing members from the Dothideomycetes, were recovered from the decaying thallus DNA, which suggested that a change in fungal community structure had occurred. Phylogenetic analysis of these environmental sequences and the sequences of isolates and type species indicated that the environmental sequences were novel in the Dothideomycetes.

Exploring the diversity of marine-derived fungal polyketide synthases.

Using an approach based on polymerase chain reaction (PCR), we examined the diversity of polyketide synthase (PKS) genes present in 160 marine fungal isolates, representing 142 species. We obtained ketosynthase (KS) domain PCR products from 99 fungal isolates, representing Dothideomycetes, Sordariomycetes, Eurotiomycetes, and incertae sedis. Sequence similarity searches and phylogenetic analysis of 29 marine partial-KS-encoding sequences revealed domains predicted to encode reducing, nonreducing, and 6-methylsalicylic acid PKSs. Bioinformatic analysis of an alignment of the KS sequences from marine-derived fungi revealed no unique motifs in this region. However, several specificity-determining positions were apparent between fungal 6-methylsalicylic acid PKSs as compared with either reducing or nonreducing PKSs. Evaluation of these positions in the context of a modelled three-dimensional protein structure highlighted their potential use as PKS classification markers. Evaluating primer-binding sites was necessary to obtain KS domain fragments from putative PKSs while maintaining a level of sequence information adequate to properly classify and characterize them.

Marine fungal lineages in the Hypocreomycetidae.

Phylogenetic analyses of DNA sequences from protein coding and ribosomal nuclear loci support the placement of a number of marine fungal species associated with a well-supported clade containing fungicolous species of Melanospora and wood inhabiting Coronophorales. Three subclades containing marine species were recovered including Torpedospora radiata plus T. ambispinosa, Swampomyces species plus Juncigena adarca, and two Etheirophora species plus additional Swampomyces species. The monophyly of these three subclades, as well as a subclade containing representatives of Coronophorales and Melanospora, is well supported statistically. However, relationships among the different subclades remain largely unresolved. A sister relationship for this group with Hypocreales is significantly supported by Bayesian and ML methods. In addition to the Halospheariales and Lulworthiales, this clade, which is characterized by considerable morphological and ecological diversity, represents a third major clade of marine Sordariomycetes.

Reconstructing the early evolution of Fungi using a six-gene phylogeny.

The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.

The halotolerant fungus Glomerobolus gelineus is a member of the Ostropales.

Glomerobolus gelineus is a halotolerant species with a unique method of ballistic propagation. The absence of both sexual and asexual spores made reliable placement of this species, based on morphology alone, within the current fungal classification problematical. A phylogenetic analysis of the large and small nuclear ribosomal subunit and the second largest subunit of RNA polymerase II placed this fungus within the Ostropales, an order comprising lichenized and saprobic species, with good statistical support. Subsequently, a more detailed analysis that combined the nuc LSU rDNA and the mt SSU rDNA confirmed a close relationship to the Stictidaceae. The phylogenetic placement of G. gelineus is also supported by morphological characters. We postulate that the hyphoma lobes of Glomerobolus correspond to the periphysoidal layer in the apothecium of Stictis, and the propagule to the hymenium. Moreover, the presence of crystals in the outer lobes of G. gelineus is another indication of its relationship with Ostropales, which have characteristic crystalliferous hyphae. The placement of Glomerobolus within the Ostropales further expands the ecological diversity exhibited by this order. It also provides a phylogenetic hypothesis for assessing the homology of the enigmatic hyphomal morphology with apothecia-forming Ascomycota.

An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny.

The Sordariomycetes is one of the largest classes in the Ascomycota, and the majority of its species are characterized by perithecial ascomata and inoperculate unitunicate asci. It includes more than 600 genera with over 3000 species and represents a wide range of ecologies including pathogens and endophytes of plants, animal pathogens and mycoparasites. To test and refine the classification of the Sordariomycetes sensu Eriksson (2006), the phylogenetic relationship among 106 taxa from 12 orders out of 16 in the Sordariomycetes was investigated based on four nuclear loci (nSSU and nLSU rDNA, TEF and RPB2), using three species of the Leotiomycetes as outgroups. Three subclasses (i.e. Hypocreomycetidae, Sordariomycetidae and Xylariomycetidae) currently recognized in the classification are well supported with the placement of the Lulworthiales in either a basal group of the Sordariomycetes or a sister group of the Hypocreomycetidae. Except for the Microascales, our results recognize most of the orders as monophyletic groups. Melanospora species form a clade outside of the Hypocreales and are recognized as a distinct order in the Hypocreomycetidae. Glomerellaceae is excluded from the Phyllachorales and placed in Hypocreomycetidae incertae sedis. In the Sordariomycetidae, the Sordariales is a strongly supported clade and occurs within a well supported clade containing the Boliniales and Chaetosphaeriales. Aspects of morphology, ecology and evolution are discussed.

A re-evaluation of Lulworthiales: relationships based on 18S and 28S rDNA.

The Lulworthiales consists of four genera: three that were removed from the Halosphaeriales, namely Lulworthia, Lindra, and Kohlmeyeriella; and Spathulospora, reassigned from the Spathulosporales. However, studies have shown that neither Lulworthia nor Lindra are monophyletic genera. This study was therefore undertaken to re-evaluate the genera of the Lulworthiales based on the SSU and LSU rDNA genes. Taxonomic revisions are proposed here for Lulworthia crassa, L. lignoarenaria, L. uniseptata and Lindra marinera: Lulworthia crassa is transferred into the genus Kohlmeyeriella; Lulwoidea gen. nov. is established for L. lignoarenaria; Lulwoana gen. nov. is established for L. uniseptata; and Lindra marinera is reduced to synonymy with L. thalassiae. Taxonomic descriptions are emended for the genus Lulworthia s. str., and for L. grandispora and Lindra thalassiae. A neotype is designated for Lulworthia grandispora.

The phylogenetic position of Spathulospora based on DNA sequences from dried herbarium material.

The phylogenetic position of the marine ascomycete genus Spathulospora was investigated using partial SSU and LSU DNA sequences obtained from dried herbarium specimens. Spathulospora was represented by the two species S. adelpha and S. antarctica. Phylogenetic analyses using Bayesian, parsimony, and neighbour-joining algorithms on SSU and LSU data sets agreed with the placement of Spathulospora. Both Spathulospora species are each others closest relatives, and group within the Lulworthiales (Sordariomycetes, Ascomycota) with support in all analyses. Members of the morphologically similar insect parasites in the Laboulbeniomycetes are not closely related to Spathulospora. Despite several striking morphological differences between Spathulospora and Lulworthiales, an important shared morphological character was found that until now had not been recognized. Ascospores of Spathulospora and some members of the Lulworthiales have apical chambers containing mucus believed to be involved in ascospore attachment. A closest relative to Spathulospora could not be determined.

Octopodotus stupendus gen. & sp. nov. and Phyllachora paludicola sp. nov., two marine fungi from Spartina alterniflora.

The coelomycete Octopodotus stupendus and the ascomycete Phyllachora paludicola are described as obligate marine fungi from the decomposing salt-marsh plant, Spartina alterniflora. Both species fruit only on the leaf blades, not on the leaf sheaths. Whereas O. stupendus is known so far only from North Carolina, P. paludicola has been collected from Florida to Delaware. The total number of marine fungi reported from Spartina spp. is 41.

Decorospora, a new genus for the marine ascomycete Pleospora gaudefroyi.

In this paper, we investigate the phylogenetic placement of Pleospora gaudefroyi using partial SSU as well as ITS ribosomal DNA sequences. Both SSU and ITS data sets agreed in the placement of P. gaudefroyi. Parsimony and neighbor-joining analyses of each data set placed P. gaudefroyi within the Pleosporaceae with 100% bootstrap support. Pleospora gaudefroyi was sister taxon in the Pleosporaceae represented by Alternaria alternata, Cochliobolus sativus, Pleospora herbarum, Pyrenophora tritici-repentis and Setosphaeria rostrata. Pleospora gaudefroyi was separated from other genera in the Pleosporaceae in 94% of the bootstrap replicates in parsimony and neighbor-joining analyses. When P. gaudefroyi was constrained to monophyly with P. herbarum, all resulting trees were significantly worse than the optimal tree in both Kishino-Hasegawa and Shimodaira-Hasegawa tests. Pleospora gaudefroyi was therefore excluded from Pleospora, and transferred to the new genus Decorospora placed in the Pleosporaceae. Decorospora (Dothideomycetes) has characteristic ascospores enclosed in a sheath with 4-5 apical extensions. The distribution and substrate types for D. gaudefroyi are summarized and updated based on additional collections.