Santelli, C.M., et al., 2010. Promotion of Mn(II) Oxidation and Remediation of Coal Mine Drainage in Passive Treatment Systems by Diverse Fungal and Bacterial Communities. Applied and Environmental Microbiology , 76 , pp. 4871-4875.Abstract

Biologically active, passive treatment systems are commonly employed for removing high concentrations of dissolved Mn(II) from coal mine drainage (CMD). Studies of microbial communities contributing to Mn attenuation through the oxidation of Mn(II) to sparingly soluble Mn(III/IV) oxide minerals, however, have been sparse to date. This study reveals a diverse community of Mn(II)-oxidizing fungi and bacteria existing in several CMD treatment systems.

Han, J.G., et al., 2010. Scutellinia jejuensis (Pezizales), a new species from Korea. Mycotaxon , 112 , pp. 47-53.Abstract

A new species of Scutellinia discovered in Jeju, Korea, Scutellinia jejuensis, is formally introduced. A combination of morphological characteristics and sequence analysis of the partial LSU rDNA demonstrates that the fungus represents a species distinct from all other subglobose to globose-spored Scutellinia species.

Schoch, C.L., et al., 2009. The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits. Systematic Biology , 58 , pp. 224-239.Abstract

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.

Lucking, R., et al., 2009. Fungi evolved right on track. Mycologia , 101 , pp. 810-822.Abstract

Dating of fungal divergences with molecular clocks thus far has yielded highly inconsistent results. The origin of fungi was estimated at between 660 million and up to 2.15 billion y ago, and the divergence of the two major lineages of higher Fungi, Ascomycota and Basidiomycota, at between 390 million y and LIP to 1.5 billion y ago. Assuming that these inconsistencies stein from various causes, we reassessed the systematic placement of the most important fungal fossil, Paleopyrenomycites, and recalibrated internally unconstrained, published molecular clock trees by applying uniform calibration points. As a result the origin of fungi was re-estimated at between 760 million and 1.06 billion y ago and the origin of the Ascomycota at 500-650 million y ago. These dates are much more consistent than previous estimates, even if based on the same phylogenies and molecular clock trees, and they are also much better in line with the fossil record of fungi and plants and the ecological interdependence between filamentous fungi and land plants. Our results do not provide evidence to suggest the existence of ancient protolichens as an alternative to explain the ecology of early terrestrial fungi in the absence of land plants.

Santelli, C.M., et al., 2009. Mn(II)-oxidizing fungi in metal contaminated environments. Geochimica Et Cosmochimica Acta , 73 , pp. A1156-A1156. PDF
Smith, M.E. & Pfister, D.H., 2009. Tuberculate Ectomycorrhizae of Angiosperms: The Interaction between Boletus Rubropunctus (Boletaceae) and Quercus Species (Fagaceae) in the United States and Mexico. American Journal of Botany , 96 , pp. 1665-1675.Abstract

Tuberculate ectomycorrhizae (TECM) are unique structures in which aggregates of ectomycorrhizal roots are encased in a covering of fungal hyphae. The function of TECM is unknown, but they probably enhance the nitrogen nutrition and disease resistance of host plants. Trees in the Pinaceae form TECM with species of Rhizopogon and Suillus (Suillineae, Boletales). Similar tubercules are found with diverse angiosperms, but their mycobionts have not been phylogenetically characterized. We collected TECM in Mexico and the USA that were similar to TECM in previous reports. We describe these TECM and identify both the plant and fungal symbionts. Plant DNA confirms that TECM hosts are Quercus species. ITS sequences from tubercules and sclerotia (hyphal aggregations that serve as survival structures) matched sporocarps of Boletus rubropunctus. Phylogenetic analyses confirm that this fungus belongs to the suborder Boletineae (Boletales). This is the first published report of TECM formation in the Boletineae and of sclerotia formation by a Boletus species. Our data suggest that the TECM morphology is all adaptive feature that has evolved separately in two suborders of Boletales (Suillineae and Boletineae) and that TECM formation is controlled by the mycobiont because TECM are found on distantly related angiosperm and gymnosperm host plants.

Pfister, D.H., 2008. Early illustrations of Xylaria species. North American Fungi , 3 , pp. 161-166.Abstract

Four 17th and early 18th Century examples of illustrations of Xylaria species are presented. One of the earliest illustrations of a Xylaria species is that in Mentzel’s Pugillus rariorum plantarumpublished in 1682 and which Fries referred to Sphaeria polymorpha. An 1711 illustration by Marchant is noteworthy in the detail of the observations; perithecia and ascospores are noted and illustrated. Marchant considered this fungus to be related to marine corals. The plate was subsequently redone and incorporated by Micheli in his 1729 publication, Nova plantarum genera; this Micheli plate was listed by Fries under a different species, Sphaeria digitata. Although Fries mentions several illustrations ofSphaeria hypoxylon not all the sources he cited contain illustrations. The earliest illustration associated with this species that was located is Micheli’s in 1729. These illustrations are included along with discussion of the authors and books in which the illustrations appear.

Pfister, D.H., Matocec, N. & Kusan, I., 2008. Integrated studies in the classification of the Pezizaceae, re-evaluation of the genus Pachyella with a new segregate genus Adelphella. Mycologia Montengrina , 11 , pp. 7-17. PDF
Perry, B.A. & Pfister, D.H., 2008. Chaetothiersia vernalis, a new genus and species of Pyronemataceae (Ascomycota, Pezizales) from California. Fungal Diversity , 28 , pp. 65-72.Abstract

Chaetothiersia vernalis, collected from the northern High Sierra Nevada of California, is described as a new genus and species. This fungus is characterized by stiff, superficial, brown excipular hairs, smooth, eguttulate ascospores, and a thin ectal excipulum composed of globose to angular-globose cells. Phylogenetic analyses of nLSU rDNA sequence data support the recognition of Chaetothiersia as a distinct genus, and suggest a close relationship to the genus Paratrichophaea.

Pfister, D.H., Slater, C. & Hansen, K., 2008. Chorioactidaceae: a new family in the Pezizales (Ascomycota) with four genera. Mycological Research , 112 , pp. 513-527.Abstract

Molecular phylogenetic and comparative morphological studies provide evidence for the recognition of a new family, Chorioactidaceae, in the Pezizales. Four genera are placed in the family: Chorioactis, Desmazierella, Neournula, and Wolfina. Based on parsimony, likelihood, and Bayesian analyses of LSU, SSU, and RPB2 sequence data, Chorioactidaceae represents a sister clade to the Sarcosomataceae, to which some of these taxa were previously referred. Morphologically these genera are similar in pigmentation, excipular construction, and asci, which mostly have terminal opercula and rounded, sometimes forked, bases without croziers. Ascospores have cyanophilic walls or cyanophilic surface ornamentation in the form of ridges or warts. So far as is known the ascospores and the cells of the paraphyses of all species are multinucleate. The six species recognized in these four genera all have limited geographical distributions in the northern hemisphere. (c) 2007 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

LoBuglio, K.F. & Pfister, D.H., 2008. A Glomerella species phylogenetically related to Colletotrichum acutatum on Norway maple in Massachusetts. Mycologia , 100 , pp. 710-715.Abstract

A fungus isolated from Norway maple (Acer platanoides) in the Boston, Massachusetts, area was determined to be it species of Glomerella, the teleomorph of Colletotrichum, acutatum. Pure. cultures of the fungus were obtained from discharged ascospores from perithecia in leaf tissue. This fungus was determined to be homothallic based oil the observation of perithecial development in cultures of single-spore isolates grown oil minimal salts media and with Sterile toothpicks. A morphological and molecular analysis was conducted to determine the taxonomic position of this fungus. Parsimony analyses of a combined nucleotide dataset of the ITS and LSU rDNA re-ion, and of the D1-D2 LSU rDNA re-ion, indicated diat. this species has phylogenetic affinifies with Colletotrichum acutatum, C. acutatum f. Sp. pineum, C. lupini, C. phormii and G. miyabeana. These results are significant because C. acutatum has not been reported oil Acer platanoides. Ill addition the consistent presence of perithecia on leaf tissue and in culture is unusual for Colletotrichum in. suggesting that the teleomorphic state is' important ill file life cycle of this fungus.

Bidartondo, M.I., et al., 2008. Preserving accuracy in GenBank. Science , 319 , pp. 1616-1616. PDF
Pfister, D.H. & Eyjolfsdottir, G.G., 2007. New records of cup-fungi from Iceland with comments an some previously reported species. Nordic Journal of Botany , 25 , pp. 104-112.Abstract

Twelve species of cup-fungi in the orders Pezizales and Helotiales are reported for the first time from Iceland and comments are made on eight species previously reported. Distributions and habitats are noted. Newly reported records of species occurrences are as follows: Ascocoryne cylichnium, Gloeotinia granigena, Melastiza flavorubens, Octospora melina, O. leucoloma, Ombrophila violacea, Peziza apiculata sensu lato, P. phyllogena, P. succosa, Pseudombrophila theioleuca, Ramsbottomia macracantha and Tarzetta cupularis. Recent work allows the re-identification of Peziza granulosa as P. fimeti.

Perry, B.A., Hansen, K. & Pfister, D.H., 2007. A phylogenetic overview of the family Pyronemataceae (Ascomycota, Pezizales). Mycological Research , 111 , pp. 549-571.Abstract

Partial sequences of nuLSU rDNA were obtained to investigate the phylogenetic relationships of Pyronemataceae, the largest and least studied family of Pezizales. The dataset includes sequences for 162 species from 51 genera of Pyronemataceae, and 39 species from an additional 13 families of Pezizales. Parsimony, ML, and Bayesian analyses suggest that Pyronemataceae is not monophyletic as it is currently circumscribed. Ascodesmidaceae is nested within Pyronemataceue, and several pyronernataceous taxa are resolved outside the family. Glaziellaceae forms the sister group to Pyronemataceae in ML analyses, but this relationship, as well as those of Pyronemataceae to the other members of the lineage, are not resolved with support. Fourteen clades of pyronernataceous taxa are well supported and/or present in all recovered trees. Several pyronemataceous genera are suggested to be non-monophyletic, including Anthracobia, Cheilymenia, Geopyxis, Humaria, Lasiobolidium, Neottiella, Octospora, Pulvinula, Stephensia, Tricharina, and Trichophaea. Cleistothecial and truffle or truffle-like ascomata forms appear to have evolved independently multiple times within Pyronemataceae. Results of these analyses do not support previous classifications of Pyronemataceae, and suggest that morphological characters traditionally used to segregate the family into subfamilial groups are not phylogenetically informative above the genus level. (c) 2007 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Iturriaga, T. & Pfister, D.H., 2006. A monograph of the genus Cookeina (Ascomycota, Pezizales, Sarcoscyphoceae). Mycotaxon , 95 , pp. 137-180.Abstract

Eight species of the wood inhabiting pantropical genus Cookeina are described and illustrated. The genus Cookeina is characterized by large, stipitate or sessile brightly colored apothecial ascoma, with or without hairs, and by distinctive, thick-walled asci that have eccentricly placed opercula. An overview of the morphology, development and life histories of the species are given along with discussion of their relationships. A new species, C. colensoiopsis, is described from Venezuela, C. speciosa is recognized as a species complex, and a lectotype is designated for C. sinensis.

Yang, S. & Pfister, D.H., 2006. Monotropa uniflora plants of eastern Massachusetts form mycorrhizae with a diversity of russulacean fungi. Mycologia , 98 , pp. 535-540.Abstract

Plant species in the subfamily Monotropoideae are mycoheterotrophs; they obtain fixed carbon from photosynthetic plants via a shared mycorrhizal network. Previous findings show mycoheterotrophic plants exhibit a high level of specificity to their mycorrhizal fungi. In this study we explore the association of mycorrhizal fungi and Monotropa uniflora (Mono tropoideae: Ericaceae) in eastern North America. We collected M. uniflora roots and nearby basidiomycete sporocarps from four sites within a 100 km(2) area in eastern Massachusetts. We analyzed DNA sequences of the internal transcribed spacer region (ITS) from the fungal nuclear ribosomal gene to assess the genetic diversity of fungi associating with M. uniflora roots. In this analysis we included 20 ITS sequences from Russula sporocarps collected nearby, 44 sequences of Russula or Lactarius species from GenBank and 12 GenBank sequences of fungi isolated from M. uniflora roots in previous studies. We found that all 56 sampled M. uniflora mycorrhizal fungi were members of the Russulaceae, confirming previous research. The analysis showed that most of the diversity of mycorrhizal fungi spreads across the genus Russula. ITS sequences of the mycorrhizal fungi consisted of 20 different phylotypes: 18 of the genus Russula and two of Lactafius, based on GenBank searches. Of the sampled plants, 57% associated with only three of the 20 mycorrhizal fungi detected in roots, and of the 25 sporocarp phylotypes collected three, were associated with M. uniflara. Furthermore the results indicate that the number of different fungal phylotypes associating with M. uniflora of eastern North America is higher than that of western North America but patterns of fungal species abundance might be similar between mycorrhizae from the two locations.

James, T.Y., et al., 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature , 443 , pp. 818-822.Abstract

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.

Hansen, K. & Pfister, D.H., 2006. Systematics of the Pezizomycetes - the operculate discomycetes. Mycologia , 98 , pp. 1029-1040.Abstract

The Pezizomycetes (order Pezizales) is an early diverging lineage within the Pezizomycotina. A shared derived character, the operculate ascus, supports the Pezizales as monophyletic, although functional opercula have been lost in certain taxa. Phylogenetic relationships within Pezizales were studied using parsimony and Bayesian analyses of partial SSU and LSU rDNA sequences from 100 taxa representing 82 genera and 13 of the 15 families currently recognized. Three primary lineages are identified that more or less correspond to the A, B and C lineages resolved in previous analyses using SSU rDNA: (A) Ascobolaceae and Pezizaceae; (B) Discinaceae-Morchellaceae and Helvellaceae-Tuberaceae; (C) Ascodesmidaceae, Glaziellaceae, Pyronemataceae, Sarcoscyphaceae and Sarcosomataceae. In contrast the monotypic Rhizinaceae and Caloscyphaceae are resolved as two independent lineages. Bayesian analyses support a relationship among Rhizina and two species of Psilopezia (Pyronemataceae). Only lineage C is highly supported. The B and C lineages form a strongly supported monophyletic group. None of these lineages corresponds to earlier proposed suborders. The A and B lineages are supported by certain morphological features (e.g. ascus bluing reaction in iodine, cytology of spores and paraphyses, septal pore structures and excipulum structure); these characters have been Subject to homoplasy. Lineage C is the largest and most heterogeneous, and no unifying morphological features support its recognition. The Pyronemataceae, in which almost half of the species in the order are found, is not monophyletic because the Ascodesmidaceae and Glaziellaceae are nested within it. The relationships among all families in the C lineage remain uncertain. The origin of various forms of ascomata, including hypogeous forms (truffles and truffle-like), epigeous cleistothecia, simple reduced apothecia and highly elaborate, stipitate forms (helvelloid and morchelloid), are discussed.

Hansen, K., LoBuglio, K.F. & Pfister, D.H., 2005. Evolutionary relationships of the cup-fungus genus Peziza and Pezizaceae inferred from multiple nuclear genes: RPB2, beta-tubulin, and LSU rDNA. Molecular Phylogenetics and Evolution , 36 , pp. 1-23.Abstract

To provide a robust phylogeny of Pezizaceae, partial sequences from two nuclear protein-coding genes, RPB2 (encoding the second largest subunit of RNA polymerase II) and β-tubulin, were obtained from 69 and 72 specimens, respectively, to analyze with nuclear ribosomal large subunit RNA gene sequences (LSU). The three-gene data set includes 32 species of Peziza, and 27 species from nine additional epigeous and six hypogeous (truffle) pezizaceous genera. Analyses of the combined LSU, RPB2, and β-tubulin data set using parsimony, maximum likelihood, and Bayesian approaches identify 14 fine-scale lineages within Pezizaceae. Species of Peziza occur in eight of the lineages, spread among other genera of the family, confirming the non-monophyly of the genus. Although parsimony analyses of the three-gene data set produced a nearly completely resolved strict consensus tree, with increased confidence, relationships between the lineages are still resolved with mostly weak bootstrap support. Bayesian analyses of the three-gene data, however, show support for several more inclusive clades, mostly congruent with Bayesian analyses of RPB2. No strongly supported incongruence was found among phylogenies derived from the separate LSU, RPB2, and β-tubulin data sets. The RPB2 region appeared to be the most informative single gene region based on resolution and clade support, and accounts for the greatest number of potentially parsimony informative characters within the combined data set, followed by the LSU and the β-tubulin region. The results indicate that third codon positions in β-tubulin are saturated, especially for sites that provide information about the deeper relationships. Nevertheless, almost all phylogenetic signal in β-tubulin is due to third positions changes, with almost no signal in first and second codons, and contribute phylogenetic information at the "fine-scale" level within the Pezizaceae. The Pezizaceae is supported as monophyletic in analyses of the three-gene data set, but its sister-group relationships is not resolved with support. The results advocate the use of RPB2 as a marker for ascomycete phylogenetics at the inter-generic level, whereas the β-tubulin gene appears less useful. © 2005 Elsevier Inc. All rights reserved.

Hansen, K., Perry, B.A. & Pfister, D.H., 2005. Phylogenetic origins of two cleistothecial fungi, Orbicula parietina and Lasiobolidium orbiculoides, within the operculate discomycetes. Mycologia , 97 , pp. 1023-1033.Abstract

Parsimony, maximum-likelihood and Bayesian analyses of SSU rDNA sequences of representative Laxa of Pezizomycetes, Eurotiomycetes, Dothideomycetes. Leotiomycetes and Sordariomycetes, all strongly support the cleistothecial fungi Orbicula parietina and Lasiobolidium. orbiculoides to be of pezizalean origin. Previous hypotheses of close affinities with cleistothecial Or highly reduced fungi now placed in the Thelebolales, Eurotiales or Onygenales are rejected. Orbicula parietina and L. orbiculoides are deeply nested within Pyronemataceae (which subsumes the families Ascodesmidaceae, Glaziellaceae and Otideaceac). LSU rDNA sequences suggest that Orbicula is nested within the apothecia-forming genus Pseudombrophila (including Nannfeldtiella and Fimaria) and that L. orbiculoides is closely related. Ascodesmis and Lasiobolus, which have been suggested as closely related to Orbicula and Lasiobolidium, are identified as a sister lineage to the Pseudombrophila lineage. Cleistothecial forms that have lost the ascus operculum and ability to discharge spores actively have evolved at least once in the Pseudombrophila lineage. Some species of Pseudombrophila produce subglobular ascomata initials that are closed early in development and open only in the mid-mesohymenial phase. We hypothesize that, in the Pseudombrophila, lineage, ascomata forms that never open are derived from ascomata that open late in development. The placement of O. parietina and L. orbiculoides within Pseudombrophila is supported by morphological characters, ecology and temperature optima for fruiting.