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A phylogenetic overview of the family Pyronemataceae (Ascomycota, Pezizales)
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 Pyronemataceae, and several pyronemataceous 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 pyronemataceous 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.
... Pyronemataceae Corda is the largest and most heterogeneous family of Pezizales J. Schröt., encompassing 78 genera and approximately 660 currently recognized species (Kirk et al. 2008). However, the taxonomy of Pyronemataceae has been extremely controversial on several issues and while the positioning of many genera within the family has recently been resolved (Laessøe and Hansen 2007;Perry et al. 2007), the species recognition problem has attracted much less attention (Tamm et al. 2010;Guevara-Guerrero et al. 2012). ...
... (Liu and Zhuang 2006), Chaetothiersia Perry and Pfister (Perry and Pfister 2008) and Geopora Harkn. (Tamm et al. 2010), but only a few Scutellinia species have been included in large level studies (Perry et al. 2007;Hansen et al. 2013). In this study, a large set of Scutellinia samples were analyzed based on the comparison of the sequences of the internal-transcribed spacer region (ITS) and the large subunit (LSU) ribosomal gene. ...
... This result was in agreement with the morphology of this species that is different from Scutellinia. These results also confirmed those of Perry et al. (2007) that, on the basis of LSU sequence, placed S. erinaceus near the genus Kotlabaea and at the root of other Scutellinia sp. pl. ...
The genus Scutellinia consists of cup fungi belonging to the Pyronemataceae (Ascomycota). It comprises more than 100 species with a worldwide distribution. Species delimitation is based on morphological characteristics of the ascocarps, such as spore size, form and ornamentation as well as size and morphology of hairs that typically cover the external surface of the ascoma. These characters are, however, highly variable and species recognition challenging. In this paper, ribosomal DNA traits such as the internal transcribed spacer and the large subunit ribosomal gene were sequenced in several Scutellinia samples and, along with all available sequences on public database, used to improve the knowledge about taxonomy and phylogeny of this genus. Based on sequence similarity and trees topology, about 50 phylogenetic species were recognized and their phylogenetic relationships disclosed.
... This was illustrated when an examination of the same material resulted in different classification schemes due to alternative points of view [6,9,12]. Initial phylogenetic analysis placed Acervus within Pyronemataceae [13] and Acervus species formed a highly-supported monophyletic group. Zhuang et al. [1] [3]. ...
... Relevant sequences from GenBank are listed in Table 3 [1][2][3]13]. Sequences were assembled using BioEdit v.7.0.5.3 [23] and aligned using MAFFT v.7.110 online program (http://mafft.cbrc.jp/alignment/server/) ...
... Acervus is a small group in the family Pyronemataceae [16]. Phylogenetic methods have resolved some classification problems in this genus [1][2][3]13,14]. Nonetheless, some features of Acervus remain problematic. ...
Acervus (Pyronemataceae, Pezizales) is a saprobic genus in Pezizomycetes, characterized by colored apothecia, subcylindrical to cylindrical asci and guttulate ascospores. We collected four Acervus samples from China and Thailand. Descriptions and illustrations are introduced for all fresh samples. One new record of A. globulosus from Thailand, one new species, A. rufus, two known species, A. epispartius and A. stipitatus from China are reported. Phylogenetic analysis based on five genes, the large subunit rRNA (LSU), the translation elongation factor-1 alpha (tef1-α), the second largest subunit of RNA polymerase II (rpb2), the largest subunit of RNA polymerase II (rpb1), and the small subunit rRNA (SSU), revealed the distinct position of the new species. The new species is set apart by its red apothecia. A key to Acervus species is also given.
... Based on Alkhesraji ( 2012) Pyronemataceae family is the largest belonging to Pezizales that including 78 genera representing approximately half of the known species within the order (Hansen & Pfister 2006). According to (Kirk et al. 2008;Perry et al. 2007) that Pyronemataceae includes approximately 80 genera and around 660 species. In terms of this fungi ecology it includes epigeous, semi -hypogeous to hypogeous species that cover and quite broad vary of niches, fruiting on all types of soil and in wood lands or burnt ground (Liu & Zhuang, 2006a). ...
... In terms of this fungi ecology it includes epigeous, semi -hypogeous to hypogeous species that cover and quite broad vary of niches, fruiting on all types of soil and in wood lands or burnt ground (Liu & Zhuang, 2006a). The ascoma morphology is highly diverse, including discoid, pulvinate and cupulate the apothecia as well as hypogeous ptychothecial and stereotypical ascomata (Burdsall, 1968;Perry et al. 2007).The most species are saprotrophic an increasing proportion is identified as ectomycorrhizal symbionts (Laessoe & Hansen 2007). In addition, the Pyronemataceae family have been taxonomically argumentative as they are not conjunct by common morphological traits neither macro-nor microscopically (Perry et al. 2007). ...
... The ascoma morphology is highly diverse, including discoid, pulvinate and cupulate the apothecia as well as hypogeous ptychothecial and stereotypical ascomata (Burdsall, 1968;Perry et al. 2007).The most species are saprotrophic an increasing proportion is identified as ectomycorrhizal symbionts (Laessoe & Hansen 2007). In addition, the Pyronemataceae family have been taxonomically argumentative as they are not conjunct by common morphological traits neither macro-nor microscopically (Perry et al. 2007). While the positioning of many genera has recently been resolved with confidence within Pyronemataceae (Hansen & Pfister 2006;Laessoe & Hansen 2007;Perry et al. 2007), the problem of species recognition and diversity of species estimates particularly for the sequestrate genera which has attracted much less attention In Iraq there are only a few surveys conducted for these species in this subject have been published. ...
The survey was carried out From January to April of 2018 on macrofungi samples collected from different places in Halabja province located in north eastern parts of Iraq-Kurdistan region. This region is rich in forest trees and pasture lands with diversity of shrubs and herbs and is expected to support the growth of several macro fungal species. However, this part of Kurdistan in Iraq is still unexplored from macrofungal point of view. In this paper three species from Pezizaceae and Pyronemataceae families that belonging to (Pezizales, Ascomycota), were reported from Iraqi Kurdistan. These macrofungal species are recorded for the first time from Iraq. Also the species were identified and showing their locations distributed on a map prepared for this purpose, and the photographs were taken of the specimens in which environment they grows.
... Based on Alkhesraji ( 2012) Pyronemataceae family is the largest belonging to Pezizales that including 78 genera representing approximately half of the known species within the order (Hansen & Pfister 2006). According to (Kirk et al. 2008;Perry et al. 2007) that Pyronemataceae includes approximately 80 genera and around 660 species. In terms of this fungi ecology it includes epigeous, semi -hypogeous to hypogeous species that cover and quite broad vary of niches, fruiting on all types of soil and in wood lands or burnt ground (Liu & Zhuang, 2006a). ...
... In terms of this fungi ecology it includes epigeous, semi -hypogeous to hypogeous species that cover and quite broad vary of niches, fruiting on all types of soil and in wood lands or burnt ground (Liu & Zhuang, 2006a). The ascoma morphology is highly diverse, including discoid, pulvinate and cupulate the apothecia as well as hypogeous ptychothecial and stereotypical ascomata (Burdsall, 1968;Perry et al. 2007).The most species are saprotrophic an increasing proportion is identified as ectomycorrhizal symbionts (Laessoe & Hansen 2007). In addition, the Pyronemataceae family have been taxonomically argumentative as they are not conjunct by common morphological traits neither macro-nor microscopically (Perry et al. 2007). ...
... The ascoma morphology is highly diverse, including discoid, pulvinate and cupulate the apothecia as well as hypogeous ptychothecial and stereotypical ascomata (Burdsall, 1968;Perry et al. 2007).The most species are saprotrophic an increasing proportion is identified as ectomycorrhizal symbionts (Laessoe & Hansen 2007). In addition, the Pyronemataceae family have been taxonomically argumentative as they are not conjunct by common morphological traits neither macro-nor microscopically (Perry et al. 2007). While the positioning of many genera has recently been resolved with confidence within Pyronemataceae (Hansen & Pfister 2006;Laessoe & Hansen 2007;Perry et al. 2007), the problem of species recognition and diversity of species estimates particularly for the sequestrate genera which has attracted much less attention In Iraq there are only a few surveys conducted for these species in this subject have been published. ...
Abstract
The survey was carried out From January to April of 2018 on macrofungi samples collected from different places in Halabja
province located in north eastern parts of Iraq-Kurdistan region. This region is rich in forest trees and pasture lands with
diversity of shrubs and herbs and is expected to support the growth of several macro fungal species. However, this part of
Kurdistan in Iraq is still unexplored from macrofungal point of view. In this paper three species from Pezizaceae and
Pyronemataceae families that belonging to (Pezizales, Ascomycota), were reported from Iraqi Kurdistan. These macrofungal
species are recorded for the first time from Iraq. Also the species were identified and showing their locations distributed on
a map prepared for this purpose, and the photographs were taken of the specimens in which environment they grows.
Key words: Pezizaceae, Pyronemataceae, Ascomycota, Kurdistan region, Halabja province.
... Phylogram was constructed using closely related sequences retrieved from GenBank and published data (Perry et al., 2007). As Pfister (1984) already pointed out that H. hemispaerica is highly supported epigeous sister group to hypogeous Genea, Genabea and Gilkeya. ...
... As Pfister (1984) already pointed out that H. hemispaerica is highly supported epigeous sister group to hypogeous Genea, Genabea and Gilkeya. The epigeous habit of this taxon may be a secondarily derived condition (Perry et al., 2007). Kimbrough (1994) found that ascospore ontogeny of G. gardnerii was very similar to that observed in H. hemisphaerica. ...
In order to explore the biodiversity of mushrooms from Pakistan, authors come across a new Humaria sp. associated with Pinus wallichiana from Pakistan’s part of Himalayan moist temperate forests. Morpho-anatomical and phylogenetic characterization were used to elucidate their taxonomic affinities. Morphological and phylogenetic analysis confirms that it is a new species of Humaria. Humaria laevispora is subsequently described in detail and compared to closely related taxa Humaria hemisphaerica. The analysis also reveals that epigeous Humaria sp. is sister to hypogeous Genea spp. reflecting epigeous habit in Humaria a derived condition. Bangladesh J. Plant Taxon. 28(2): 379-384, 2021 (December)
... Only Pyropyxis rubra has been recognised as a facultative pathogen of vascular plants (Hansen et al. 2013, Filippova et al. 2016). The family is mainly distributed from temperate to arctic-alpine regions, with a few taxa known from the tropics (Perry et al. 2007). ...
... Molecular phylogenetic studies (Perry et al. 2007, Hansen et al. 2013, Ekanayaka et al. 2018) have shown that the Pyronemataceae is a highly polyphyletic group of the Pezizales and have led to some genera being included into or excluded from the family. The group is being studied intensively, and many new taxa have also been described in recent years , Stielow et al. 2013, Van Vooren et al. 2015, Lindemann et Bohning 2016, Van Vooren et Vega 2018b, Van Vooren et al. 2021. ...
... Nowadays the taxonomical criteria to identify Geopora species are size and shape of the ascospores and asci, composition of the excipular tissues, position of the ascoma in the ground, reaction to various stains, guttulation and the length of excipular hairs (Burdsall 1965, 1968, Tamm et al. 2010, Flores-Rentería et al. 2014. These criteria are nevertheless not sufficient for species with very similar morphological features and are difficult to identify at the species level (Perry et al. 2007, Tamm et al. 2010. Due to limited morphological characters and overlappings in morphological characters especially in ascoma and ascospores size among Geopora species, some misidentifications have been made when using these characteristics (Guevara-Guerrero et al. 2012). ...
... Tamm et al. (2010) and Southworth & Frank (2011), showed that using of molecular data is needed in order to identify and separate Geopora species correctly. In recent years, several studies have focused on Geopora phylogeny using several loci, and these have allowed the main species to be clearly defined (Perry et al. 2007, Tamm et al. 2010, Gordon & Gehring 2011, Guevara-Guerrero et al. 2012. As an example, Tamm et al. (2010) studied the phylogenetic relationships in genus Geopora. ...
A new Geopora species (Pyronemataceae), Geopora ramila was described and illustrated from the soil, under or in the vicinity of Helianthemum ledifolium var. ledifolium annual plant in Fars province, Iran. Morphologically, G. ramila is similar to G. pinyonensis and G. arenicola but distinguished from both by a combination of morphological characters including, color and size of ascocarps, size and shape of ascospores, habit and associated host. The ribosomal DNA internally transcribed spacer (rDNA ITS) sequence of the new species (Acc. No. MT108930 to MT108934) showed 87.82% identity with G. pinyonensis in the BLAST search in GenBank. ITS-based phylogenetic analysis clearly supports G. ramila is a new and distinctive species lacking close relatives among described species of Geopora.
... The Pyronemataceae (Pezizales, Ascomycota) is a morphologically and ecologically diverse group of fungi that has proven taxonomically challenging (HAnsen et al., 2013;Perry et al., 2007). The family includes taxa with a wide variety of nutritional modes, including ectomycorrhizae e.g. ...
... exclusively sequestrate hypogeous forms that have lost forcible ascospore discharge can be found in the genera Densocarpa, Gelinipes nom. prov., Genea, Genabea, Hydnocystis, Myrmecocystis, and Picoa (KumAr et al., 2017;Perry et al., 2007;AlVArAdo et al., 2018). Both cupulate and trufflelike forms are known to occur in the same genus, such as in Geopora, Otidea, and Humaria (GueVArA et al., 2012;smiTH & HeAly, 2009;Al-VArAdo et al., 2018). ...
Molecular investigations into two truffle-like fungi within the Pyronemataceae (Pezizales, Ascomycota) revealed hidden diversity that required further clarification of generic and species boundaries of the hypogeous, ptychothecial members of this family. Here we describe Terracavicola echinospora gen. et. sp. nov. from mexico and we transfer Pachyphlodes lateritia from the western united states into the genus Geopora
as Geopora lateritia comb. nov. We provide molecular phylogenetic evidence based on iTs and 28s ribosomal dnA for the placement of both taxa and provide detailed morphological analyses. We also discuss the taxonomy of other morphologically similar taxa in Pyronemataceae with an emphasis on the lineage that includes Geopora, Hoffmannoscypha, Picoa, and Tricharina.
... Ya o & S p o o n e r a n d Octosporopsis U. Lindemann & M. Vega, which are also associated with bryophytes, in having ornamented and more or less globose ascospores. Phylogenetic analyses based on the molecular data showed that Lamprospora forms a distinct clade within bryophilous Pezizales (Perry et al. 2007;Hansen et al. 2013) and that the inclusion of Lamprospora in Octospora considered by some authors in the past should not be adhered to any longer. However, further studies are needed to fully resolve relationships with species from the other genera mentioned above, some of which seem to be closely related to Lamprospora (Perry et al. 2007;Stenroos et al. 2010). ...
... Phylogenetic analyses based on the molecular data showed that Lamprospora forms a distinct clade within bryophilous Pezizales (Perry et al. 2007;Hansen et al. 2013) and that the inclusion of Lamprospora in Octospora considered by some authors in the past should not be adhered to any longer. However, further studies are needed to fully resolve relationships with species from the other genera mentioned above, some of which seem to be closely related to Lamprospora (Perry et al. 2007;Stenroos et al. 2010). ...
Lamprospora densireticulata sp. nov. is described and illustrated based on fresh collections from Austria, Croatia, Cyprus, France, Germany, Hungary and Spain. Its most important distinguishing characters are subglobose ascospores ornamented with a fine, irregular dense net and the infection on rhizoids of its host moss Aloina ambigua. Two other similar species differing mainly in their host mosses and ecology are also described in detail: these are L. carbonicola infecting Funaria hygrometrica occuring on soil and L. dictydiola growing on Tortula muralis on walls, stones or rocks. Phylogenetic analyses of ITS and LSU rDNA show that the studied collections of all three species form well-supported monophyletic clades exhibiting only very little polymorphism within the individual species. Comparative tables listing other morphologically similar species of Lamprospora and Octospora are provided.
... En la tabla 1 están enlistadas las secuencias que se usaron en este estudio. Svrcek que corresponden a los géneros más emparentados con Jafnea (Perry et al., 2007). Para la obtención de la filogenia se usaron los criterios de máxima parsimonia, máxima verosimilitud e inferencia bayesiana. ...
... El género Jafnea se caracteriza por poseer apotecios en forma de copa, provistos de vellosidades en toda la superficie externa de apotecio, excípulo dividido en medular de textura intrincada y ectal de textura angular a globosa, ascosporas ligeramente cilíndricas a subfusoides y verrugosas (Korf, 1960;Eckblad, 1968). Actualmente se le clasifica dentro de la familia Pyronemataceae, en donde los géneros más cercanos son Acervus, Otidea, Pyropyxis y Smardaea (Perry et al., 2007). Jafnea se distingue de Acervus que presenta apotecios sésiles y densamente cespitosos, con ascosporas lisas (Kanouse, 1938); de Otidea porque éste presenta apotecios asimétricos, ascosporas lisas o en pocas especies ornamentadas y la superficie externa del ascoma glabra a furfurácea (Eckblad, 1968); Pyropyxis presenta ascosporas lisas y vellosidades moniliformes hialinas en la superficie externa del apotecio (Egger, 1984); y finalmente Smardaea tiene ascoporas verrugosas de tonos violáceos a fuscovioláceos (Svrček, 1969). ...
... vermutete Zugehörigkeit von P. ovalispora zur Gattung Boubovia wird durch die Untersuchungsergebnisse vonPerry et al. (2007) unterstützt: Die Sequenzierungen ergaben, dass P. ovalispora nahe bei B. luteola lokalisiert ist und damit in einen anderen Clade fällt als die rundsporigen Pulvinula-Arten.* Eine der beiden beiPerry et al. 2007 verwendeten Sequenzen von P. ovalispora ist mittlerweile unter dem Namen B. nicholsonii in der GenBank zu finden; auf Nachfrage teilte Karen Hansen, eine der Autorinnen des Artikels mit, dass sie entschieden habe, den Namen B. nicholsonii zu verwenden. ...
... vermutete Zugehörigkeit von P. ovalispora zur Gattung Boubovia wird durch die Untersuchungsergebnisse vonPerry et al. (2007) unterstützt: Die Sequenzierungen ergaben, dass P. ovalispora nahe bei B. luteola lokalisiert ist und damit in einen anderen Clade fällt als die rundsporigen Pulvinula-Arten.* Eine der beiden beiPerry et al. 2007 verwendeten Sequenzen von P. ovalispora ist mittlerweile unter dem Namen B. nicholsonii in der GenBank zu finden; auf Nachfrage teilte Karen Hansen, eine der Autorinnen des Artikels mit, dass sie entschieden habe, den Namen B. nicholsonii zu verwenden. Die zweite, unter dem Namen P. ovalispora in der GenBank geführte Sequenz werde auch noch umbenannt. ...
Key words: Baltic Sea, Mecklenburg-Western Pomerania, Fischland-Darß-Zingst, coastal dunes, gray dunes, cliff funga, Ascobolus behnitziensis, Pulvinula ovalispora, Peziza merdae, P. fimeti, P. perdicina, Phlebia ochraceofulva, Oligoporus floriformis, Maireina monaca, Clitocybe barbularum, Clitocybe boletispora spec. nov., Mycena chlorantha, Psathyrella almerensis, Cortinarius fusisporus, Phragmidium potentillae
Summary: We report a number of ascomycetes and basidiomycetes from the 3rd Dune Mycological Workshop held at the Fischland-Darß-Zingst peninsula. Typical fungi of the cliff-flora are presented as well as collections from the gray-dunes and the forest of Darß. The first collection of Peziza merdae from Mecklenburg-Western Pomerania is discussed and compared with two similar species P. fimeti and P. perdicina (=moravecii). Furthermore P. merdae is reported from Corsica for the first time. The cyphelloide basidiomycete Maireina monaca was rediscovered after 100 years, this is discussed in detail within the context of the genus Maireina. Ascobolus behnitziensis and Pulvinula ovalispora typical coastal species found on steep slopes also described in detail. Cortinarius fusisporus, Phragmidium potentillae on Potentilla recta, Psathyrella almerensis and Clitocybe barbularum were detected in Mecklenburg-Western Pomerania for the first time. A Clitocybe from the gray dunes with boletoid spores is described new as Clitocybe boletispora. Oligoporus floriformis, Phlebia ochraceofulva, and Mycena chlorantha are presented as well in the gray dunes.
... Following the new classification of Pezizomycetes and its unique order Pezizales proposed by Jaklitsch et al. (2016) and Wijayawardene et al. (2017), a new system is proposed by Ekanayaka et al. (2018) based on a five-genes phylogeny, introducing five new families although these results had been previously suggested by the works of Perry et al. (2007), Hansen et al. (2013) and Bonito et al. (2013). This is a difficult exercise that requires not only phylogenetic competence but also a sound taxonomic knowledge of the group, particularly as the authors choose to illustrate their system with descriptions and illustrations of species which they refer to as being representative which in our opinion are not always suitable for this purpose. ...
... Pseudombrophilaceae 1) Lasiobolidium is placed in this family based on sequences of L. orbicularis which is not the type species. L. spirale, the type-species, appears in a different clade, in Pyronemataceae (Perry et al., 2007). 3) The monograph of Pseudombrophila by Brummelen (1995) is cited in final references, but not in this part of the text. ...
Following the new classification of Pezizomycetes and its unique order Pezizales proposed by Jaklitsch et al. (2016) and Wijayawardene et al. (2017), a new system is proposed by Ekanayaka et al. (2018) based on a five-genes phylogeny, introducing five new families although these results had been previously suggested by the works of Perry et al. (2007), Hansen et al. (2013) and Bonito et al. (2013). This is a difficult exercise that requires not only phylogenetic competence but also a sound taxonomic knowledge of the group, particularly as the authors choose to illustrate their system with descriptions and illustrations of species which they refer to as being representative which in our opinion are not always suitable for this purpose. After carefully reading the article, we noted many mistakes, imprecise data and superfluous remarks that should be brought to the attention of readers. This note can be considered as a post-publication review.
... It is important to emphasize that many of the confirmed ECM plants from Oceania are endemic and therefore are likely to host unique ECM fungi. Known lineages of ECM fungi specific to Oceania also deserve further study, including endemic Mesophelliaceae and other unique members of the Hysterangiales as well as the /aleurina and /austropaxillus lineages (Davoodian et al. 2021;Hosaka et al. 2008;Perry et al. 2007;Skrede et al. 2011). ...
The tropics were long considered to have few ectomycorrhizal fungi, presumably due to a paucity of ectomycorrhizal host plants relative to higher-latitude ecosystems. However, an increase in research in tropical regions over the past 30 years has greatly expanded knowledge about the occurrence of tropical ectomycorrhizal fungi. To assess their broad biogeographic and diversity patterns, we conducted a comprehensive review and quantitative data analysis of 49 studies with 80 individual data sets along with additional data from GlobalFungi to elucidate tropical diversity patterns and biogeography of ectomycorrhizal fungi across the four main tropical regions: the Afrotropics, the Neotropics, Southeast Asia, and Oceania. Generalized linear models were used to explore biotic and abiotic influences on the relative abundance of the 10 most frequently occurring lineages. We also reviewed the available literature and synthesized current knowledge about responses of fungi to anthropogenic disturbances, and their conservation status and threats. We found that /russula-lactarius and /tomentella-thelephora were the most abundant lineages in the Afrotropics, the Neotropics, and Southeast Asia, whereas /cortinarius was the most abundant lineage in Oceania, and that /russula-lactarius, /inocybe, and /tomentella-thelephora were the most species-rich lineages across all of the tropical regions. Based on these analyses, we highlight knowledge gaps for each tropical region. Increased sampling of tropical regions, collaborative efforts, and use of molecular methodologies are needed for a more comprehensive view of the ecology and diversity of tropical ectomycorrhizal fungi. ARTICLE HISTORY
... This species belongs to the Pyronemataceae family, which is the largest and most heterogeneous family of Pezizales. This family has traditionally been considered saprotrophic, but the trophic strategies of most species are not well studied and remain undocumented (Perry et al., 2007). An increasing number of species are being identified as EM associates (Tedersoo et al., 2010). ...
Les contaminations entrainent des dégradations générant des dysfonctionnements des sols et des atteintes à leurs fonctions écologiques. Le phytomanagement, qui utilise des espèces végétales pour extraire, contenir ou dégrader des polluants, apparaît comme une solution adaptée pour produire de la biomasse végétale tout en favorisant la réhabilitation de ces sols délaissés. Les approches récentes s’accordent sur l'importance des associations végétales dans l’optimisation de ces dispositifs. Ce projet de thèse s’articule autour d’un dispositif agroforestier novateur, associant la grande ortie (Urtica dioica L.) à une plante modèle dans le domaine, le peuplier. Dans des plantations de peuplier, l’ortie offre de nouvelles perspectives liées à son aptitude à se développer spontanément sur des sites contaminés et à la qualité de sa fibre végétale, utilisables pour la fabrication de biomatériaux.A partir de deux sites ateliers contaminés par les éléments trace métalliques (ETM) et différentes approches disciplinaires, ces travaux ont permis i) de mieux comprendre le fonctionnement de cedispositif peuplier-ortie à l’interface rhizosphérique et sa réponse aux ETM via des approches de barcoding environnemental et de métabolomique ciblée ii) d’appréhender le rôle des plantes modèles dans la restauration écologique de ces sites au travers d’études phytosociologique et entomologique et évaluer l’implication des communautés associées dans les flux d’ETM par uneapproche écotoxicologique, et finalement iii) de caractériser et optimiser le potentiel économique de ce dispositif selon une approche agroécologique. Enfin, cette thèse ambitionne d’être un travail de référence pour les futurs projets de phytomanagement basés sur des associations arbres – orties.
... BLaSTn (aLTSCHUL et al., 1990) was used to select the most closely related sequences from the International nucleotide Sequence database Collaboration public database (InSdC, CoCHRane et al., 2011). The sequences retrieved were mainly from studies conducted by HanSen et al. (2013), peRRy et al. (2007 and Van VooRen et al. (2017). Sequences first were aligned in MeGa 5.0 software (TaMURa et al., 2011) with its Clustal W application and then realigned manually as needed to establish positional homology. ...
Two new tricharinoid species, Paratricharina confusa and Hellenicoscyphus hyalotrichus, are described and illustrated based on collections from Spain and Greece. The morphological features are compared with the most closely related species, especially Paratricharina poiraultii. A multigene analysis showing their taxonomic position is presented and discussed.
... We identified the families Nitrosomonadaceae and Chromatiaceae as containing ammonium oxidizing bacteria (AOB), and the families Nitrosophaeraceae and Nirtosotaleaceae as containing ammonium oxidizing archaea (AOA; Alves et al., 2018;Guo et al., 2020;Laanbroek et al., 2012;Purkhold et al., 2000). Additionally, since fire appeared to be important in shaping soil chemistry and microbial community composition, we selected the following fungal families with known responses to fire to examine more closely: Venturiaceae, Trichocomaceae, Pyronemataceae, Morchellaceae, Thelephoraceae, Gomphaceae, Cantharellaceae, and Russulaceae (Perry et al., 2007;Stendell et al., 1999;Whitman et al., 2019). ...
Healthy forests are vital components of terrestrial ecosystems for their raw materials, high biodiversity, cycling of nutrients, and potential to sequester carbon. However, these ecosystems are sensitive to disturbances, and anthropogenic activities pose a serious threat to forest ecosystems globally. For example, human activities have dramatically altered multiple historical disturbance regimes in forests, including suppressing fire, increasing the density of large herbivores, and reducing the size of canopy gaps, among other disturbances. Such disturbances can have dramatic impacts on microbially-mediated forest soil functions, but more research is needed to determine the collective impacts of these disturbances. In this study, we investigated the interactive effects of disturbances, namely the legacies of fire, large herbivore densities, and canopy gap creation, in a deciduous forest soil. We determined that forest floor and mineral soil carbon and nitrogen pools were shaped by multiple disturbances, but fire was more influential than the other disturbances. The abundance of several functionally-relevant microbial taxa were significantly impacted by fire, and the effect was more pronounced in the mineral soil than in the forest floor. Together, these findings demonstrate that multiple disturbances, especially a legacy of fire, exerts long-term control over soil carbon, nitrogen and microbial dynamics in a deciduous forest system.
... Rhodoscypha sp. habits the boreal and temperate forests of the Northern Hemisphere associated with non-bryophilous plants (Perry et al., 2007). This genus is reported with low frequency in Dryas octopetala and Bistorta vivipara (Mundra et al. 2015). ...
Abies religiosa's forests are severely endangered as a result of climate change; to save this species and its biological interactions, population assisted migration is discussed in forest management, but not in the microbial ecology field. Our objectives were to analyze its mycorrhizal networks; and, with this data, to identify potential facilitator plants and it's most important mycorrhizal fungal links. This information could be used together in assisted migration programs to connect Abies religiosa saplings to their mycorrhizal network and improve their field establishment. We collected 47 rhizosphere samples from 19 plant species and sequenced their fungal ITS2 region by Illumina. In the whole fungal community, 464 species were mycorrhizal fungi with assigned guild (32%). In this subset, 85 fungi are arbuscular, 365 ectomycorrhizal and 14 from orchid-mycorriza. The Abies religiosa bipartite network is low nested and highly modular, and has a scale-free architecture. Besides Abies religiosa, the plants with the largest degree and the lowest average shortest path were Salix paradoxa, Muhlenbergia spp., and Baccharis conferta. The most important fungal nodes are species of Cortinarius, Genea, Rhodoscypha, Russula, and Tomentella. We suggest to evaluate the Abies' future establishment in the following scheme: in the first year reintroduce Muhlenbergia spp., and Baccharis conferta, in the second year Salix paradoxa, and in the third year–once the mycorrhizal network is reestablished– Abies religiosa' saplings in close proximity of these plants. This scheme is proposed using the data and network analyses of the present study.
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... Along with sequences newly generated in this study, relevant data from the GenBank database were used (https://blast.ncbi.nlm.nih.gov; sequences originate from Perry & al. 2007, Hansen & al. 2013, Vega & al. 2017, and Egertová & al. 2018. Sequences were assembled, edited, and aligned using Geneious (ver. ...
Lamprospora benkertii is described as a new species based on collections from Georgia, Germany, Norway, Slovakia, and Switzerland. It is characterized by orange apothecia without a fimbriate margin, globose ascospores with a seaveri -type ornamentation comprising strong ridges forming a reticulum and a secondary reticulum formed by fine ridges within the meshes of the primary reticulum. The fungus infects rhizoids of Trichostomum crispulum . Delineation of the new species is supported by LSU and EF1α sequence analyses. Lamprospora benkertii is compared with other Lamprospora species with a seaveri -type or similar ascospore ornamentation: L. ascoboloides , L. cailletii , L. dicranellae , L. funigera , L. hispanica , L. irregulariata , L. leptodictya , L. norvegica , L. paechnatzii , L. seaveri. We also present an updated key for this group of species as well as a more complete description of L. hispanica based on our observations from several collections. New host specificity data are provided for L. hispanica , L. leptodictya , L. norvegica , and L. paechnatzii .
... However, we did find evidence of initial changes in the abundance of specific fungal ASVs, particularly in Pyronemataceae sp. and Russula (adjusted p-value < 0.01; log2Fold > 2). Although the specific nature of most Pyronemataceae is unknown, different members of the family have been characterized as saprobes or ectomycorrhizal [85,86], while Russula is a large ECM genus with both nitrophobic and nitrophilic species, and is typically dominant in older stands [71,78,87]. Within the other ASVs recruited by the roots, the nitrophobic Suillus was negatively affected by both arginine phosphate and ammonium nitrate ( Figure 5) while Piloderma, which has the ability to take up, use and deliver amino acids to Scots pine [88], responded positively to the addition of arginine phosphate but not ammonium nitrate ( Figure 5). ...
Scots pine (Pinus sylvestris L.) is one of the most economically important species to the Swedish forest industry, and cost-efficient planting methods are needed to ensure successful reestablishment after harvesting forest stands. While the majority of clear-cuts are replanted with pre-grown seedlings, direct seeding can be a viable option on poorer sites. Organic fertilizer has been shown to improve planted seedling establishment, but the effect on direct seeding is less well known. Therefore, at a scarified (disc trencher harrowed) clear-cut site in northern Sweden, we evaluated the effect of early, small-scale nitrogen addition on establishment and early recruitment of fungi from the disturbed soil community by site-planted Scots pine seeds. Individual seeds were planted using a moisture retaining germination matrix containing 10 mg nitrogen in the form of either arginine phosphate or ammonium nitrate. After one growing season, we collected seedlings and assessed the fungal community of seedling roots and the surrounding soil. Our results demonstrate that early, small-scale N addition increases seedling survival and needle carbon content, that there is rapid recruitment of ectomycorrhizal fungi to the roots and rhizosphere of the young seedlings and that this rapid recruitment was modified but not prevented by N addition.
... The Pezizales order was identifiable with a 1.5% relative abundance in rhizosphere soil of ectomycorrhizal treatment. In the soil of ectomycorrhizal treatment of poplar plantation on the family level, Pyronemataceae, known as paraphyletic and ectomycorrhizal [73] former, was detected with lower relative abundances, while on the genus level Ocroconis belonging to the Pyronemataceae family and ectomycorrhizal symbionts containing the Pezizaceae family was represented with significantly higher abundance (Figure 6c,d). Thus, the relatively higher abundance of fungi belonging to Pezizaceae and Pyronemataceae in our study may be promoted by ectomycorrhizal inoculation [74][75][76]. ...
The impact of chemical fertilization on rhizosphere soil communities is a growing concern due to the changes they cause on microbes in soil ecosystems. The present study aims to compare mycorrhizal inoculation and fertilizer applications on bacterial and fungal communities in rhizosphere soil of intensively cultivated Robinia pseudoacacia and Populus × euramericana plantations using the Illumina Miseq sequencing platform. Our results revealed that the different host plants and applied treatments did not significantly affect soil bacterial diversity, but interfered with native rhizosphere bacterial communities in plantation sites. In contrast, host plants and inorganic fertilizer had a strong effect at the family and genus level on the composition of soil fungal communities. In conclusion, our findings suggest that the structure and composition of the fungal community are more sensitive to the nutrient sources in soil than bacteria.
... Our query sequence Blast produced the highest hits for Geopora sumneriana from Italy (JF908024, 99.82 identity) and G. sumneriana from India (MN200944, 100 identity). Tarzetta catinus and Trichophaea hybrida were chosen for rooting purpose due to their close phylogenetic relationship with Geopora species (Perry & al. 2007, Saba & al. 2019. The best tree recovered from ML analysis (-lnL = 1925.2196) is shown in Fig. 1. ...
A new record of Geopora sumneriana is presented from Pakistan. Specimens were collected under Cedrus deodara trees in Chitral district of Khyber Pakhtunkhwa province during 2018. The newly reported specimens are illustrated and described using morphological characters and phylogenetic analysis of the internal transcribed spacer region (ITS).
... The new variety differs in its smaller spores and ascomata, the latter also maturing more slowly (ForT & GUArro, 1986). Perry et al. (2007) were the first to notice that Warcupia terrestris is phylogenetically nested within the family Pyronemataceae, despite its cleistothecioid habit. Later, HAnSen et al. (2013) reported that Warcupia is closely related to the highly reduced (gymnohymenial) genus Monascella Guarro & Arx, both forming a sister clade to the mainly apothecial genus Otidea (Pers.) ...
The name Warcupia cupulata is here proposed for an apothecioid species described for the first time upon Greek, italian and Spanish collections probably associated with Cupressus, and the formerly cleis-tothecioid genus Warcupia is consequently amended. images of fresh samples and their main microscopical characters are provided, as well as phylogenetic analyses based on iTS rdnA sequences, and a combined dataset including 28S rdnA, tef1 and rpb2 data. Homologous sequences of the related genera Acervus and Arpinia were produced and published to support the phylogenetic study.
Riassunto: il binomio Warcupia cupulata viene qui proposto per una specie nuova apotecioide a seguito di raccolte effettuate in Grecia, italia e Spagna probabilmente associate a Cupressus; conseguentemente viene emendato il genere cleistotecioide Warcupia. Vengono proposte foto di esemplari freschi e di micro-scopia, nonché due analisi filogenetiche basate sull'iTS solamente e su un allineamento combinato dei mar-catori LSU, tef1 e rpb2. infine, al fine di supportare lo studio filogenetico, sono state prodotte e pubblicate sequenze omologhe di specie appartenenti ai generi Acervus e Arpinia.
Περίληψη: Η ονομασία Warcupia cupulata προτείνεται για ένα καινούργιο για την επιστήμη είδος με μορφή αποθήκιου, πιθανά συσχετιζόμενο με Κυπαρίσσια, που περιγράφεται από Ελληνικές, Ιταλικές και Ισπανικές συλλογές, και κατά συνέπεια το παλαιότερο γένος κλειστοθήκιων Warcupia τροποποιείται. Επισυνάπτεται εικονογραφία από φρέσκα δείγματα στο πεδίο μαζί με τα κύρια μικροσκοπικά χαρακτηριστικά τους, καθώς και φυλογενετικές αναλύσεις με βάση τόσο το iTS, όσο και συνδυασμένη ανάλυση των γονιδίων LSU, tef1 και rpb2. Ομόλογες ακολουθίες των σχετικών γενών Acervus και Arpinia δημοσιεύονται επιπρόσθετα για να υποστηρίξουν τη φυλογενετική μελέτη. λέξεις-κλειδιά: Acervus, Arpinia, Ascomycota, Pyronemataceae, φυλογενετική ανάλυση, ταξινόμιση.
... However, these Smardaea species have semiglobular apiculi at the ends, which are not present in Aleurina species (Zhuang & Korf 1986), supporting the Mexican material in Smardaea. Perry & al. (2007) supported Aleurina and Smardaea as independent genera because they are in different clades. Smardaea isoldae is characterized by the green to olivaceous hymenium and external surface, shape, size, and ornamentation of the ascospores and its growth on dead wood in a tropical cloud forest. ...
Smardaea isoldae is described from Sierra Madre Oriental, Hidalgo State, Mexico. The new species is distinguished by its olivaceous coloration, habit on dead wood, and tropical cloud forest habitat. The holotype is deposited in ENCB Herbarium. A key to Smardaea species is presented.
... The most abundant OTU was assigned to the Kotlabaea genus, accounting for more than 26% of all sequences. This species belongs to the Pyronemataceae, one of the largest family of Pezizales traditionally considered saprotrophic, although the trophic strategies of most species remain undocumented (Perry et al., 2007). Indeed, an increasing number of them are being identified as EM (Tedersoo et al., 2010). ...
Stinging nettle (Urtica dioica L.) raises growing interest in phytomanagement because it commonly grows under poplar Short Rotation Coppices (SRC) set up at trace-metal (TM) contaminated sites and provides high-quality herbaceous fibres. The mycobiome of this non-mycorhizal plant and its capacity to adapt to TM-contaminated environments remains unknown. This study aimed at characterizing the mycobiome associated with nettle and poplar roots co-occurring at a TM-contaminated site. Plant root barcoding using the fungi-specific ITS1F-ITS2 primers and Illumina MiSeq technology revealed that nettle and poplar had distinct root fungal communities. The nettle mycobiome was dominated by Pezizomycetes from known endophytic taxa and from the supposedly saprotrophic genus Kotlabaea (which was the most abundant). Several ectomycorrhizal fungi such as Inocybe (Agaricomycetes) and Tuber (Pezizomycetes) species were associated with the poplar roots. Most of the Pezizomycetes taxa were present in the highly TM-contaminated area whereas Agaricomycetes tended to be reduced. Despite being a known non-mycorrhizal plant, nettle was associated with a significant proportion of ectomycorrhizal OTU (9.7%), suggesting some connexions between the poplar and the nettle root mycobiomes. Finally, our study raised the interest in reconsidering the fungal networking beyond known mycorrhizal interactions.
... Further noteworthy characteristics are the binucleate ascospores within 8-spored asci. According to Perry et al. (2007), species of the family Pyronemataceae form uninucleate ascospores. Jaklitsch et al. (2016) similarly characterise the Octospora lineage, comprising all the bryophilous genera of Pezizales and a few others, as having uninucleate ascospores in 8-spored asci (see also e.g. ...
Octospora doebbeleri, a new bryophilous species infecting rhizoids of the acrocarpous moss Dicranoweisia cirrata, is described and illustrated based on collections from the Czech Republic. The delineation of the new species, based on the unique set of morphological characters, is also supported by phylogenetic analysis of LSU and SSU nrDNA and EF1α. Morphologically, O. doebbeleri is characterised by apothecia with a thin margin and ellipsoid, mostly binucleate ascospores ornamented with small isolated warts. Differences from other morphologically similar species of Octospora are discussed.
... The genus is not popular to study in this era, compared with the Bulgaria and Galiella as the same Pyronemataceae. Perry et al. (2007) had been studied the phylogenetics of the family Pyronemataceae, but they did not mention Trichaleurina in their phylogenetic tree. The knowledge of Trichaleurina is not often mentioned compared with other genera that have similar characters of morphology, i.e., Bulgaria, Galiella, and Sarcosoma. ...
Trichaleurina is a fleshy mushroom with goblet-shaped within Pezizales. Many genera have a morphology similar to Trichaleurina, such as Bulgaria and Galiella. Some previous reports had been described fungi like Trichaleurina as Sarcosoma. Indonesia has been reported that has Trichaleurina specimen (the new name of Sarcosoma) by Boedijn. This research aimed to obtain, characterize, and determine the Trichaleurina around IPB University. Field exploration for fungal samples was used in the Landscape Arboretum of IPB University. Ascomata of Trichaleurina were collected, observed, and preserved using FAA. The specimen was deposited into Herbarium Bogoriense with collection code BO 24420. The molecular phylogenetic tree using RAxML was used to identify the species of the specimen. Morphological data were used to support the species name of the specimen. Specimen BO 24420 was identified as Tricahleurina javanica with 81% bootstrap value. Molecular identification was supported by the morphological data, such as the two oil globules and the size of mature ascospores.
... Mykol., Prag: 149 (1842) Notes: This family produces hypogeous to epigeous ascomata with a variety of shapes, sessile to stalked, discoid to cupulate, turbinate to pulvinate, folded to solid. (Perry et al. 2007;Hansen et al. 2013;Pfister 2015a). In addition, members of this family are distinguished by inamyloid asci and smooth to ornamented ascospores (Pfister 2015a). ...
This is the twelfth contribution to the Fungal Diversity Notes series on fungal taxonomy, based on materials collected from many countries which were examined and described using the methods of morphology, anatomy, and strain culture, combined with DNA sequence analyses. 110 taxa are described and illustrated, including five new genera, 92 new species, eight new combinations and other taxonomic contributions (one new sequenced species, one new host and three new records) which are accommodated in 40 families and 1 incertae sedis in Dothideomycetes. The new genera are Amyloceraceomyces, Catenuliconidia, Hansenopezia, Ionopezia and Magnopulchromyces. The new species are Amyloceraceomyces angustisporus, Amylocorticium ellipsosporum, Arthrinium sorghi, Catenuliconidia uniseptata, Clavulina sphaeropedunculata, Colletotrichum parthenocissicola, Coniothyrium triseptatum, Cortinarius indorusseus, C. paurigarhwalensis, C. sinensis, C. subsanguineus, C. xiaojinensis, Diaporthe pimpinellae, Dictyosporella guizhouensis, Diplodia torilicola, Fuscoporia marquesiana, F. semiarida, Hansenopezia decora, Helicoarctatus thailandicus, Hirsutella hongheensis, Humidicutis brunneovinacea, Lentaria gossypina, L. variabilis, Lycoperdon lahorense, L. pseudocurtisii, Magnopulchromyces scorpiophorus, Moelleriella gracilispora, Neodevriesia manglicola, Neodidymelliopsis salvia, N. urticae, Neoroussoella magnoliae, Neottiella gigaspora, Ophiosphaerella chiangraiensis, Phaeotremella yunnanensis, Podosphaera yulii, Rigidoporus juniperinus, Rhodofomitopsis pseudofeei, Russula benghalensis, Scleroramularia vermispora, Scytinopogon minisporus, Sporormurispora paulsenii, Thaxteriellopsis obliqus, Tomentella asiae-orientalis, T. atrobadia, T. atrocastanea, T. aureomarginata, T. brevis, T. brunneoflava, T. brunneogrisea, T. capitatocystidiata, T. changbaiensis, T. citrinocystidiata, T. coffeae, T. conclusa, T. cystidiata, T. dimidiata, T. duplexa, T. efibulata, T. efibulis, T. farinosa, T. flavidobadia, T. fuscocrustosa, T. fuscofarinosa, T. fuscogranulosa, T. fuscopelliculosa, T. globospora, T. gloeocystidiata, T. griseocastanea, T. griseofusca, T. griseomarginata, T. inconspicua, T. incrustata, T. interrupta, T. liaoningensis, T. longiaculeifera, T. longiechinuli, T. megaspora, T. olivacea, T. olivaceobrunnea, T. pallidobrunnea, T. pallidomarginata, T. parvispora, T. pertenuis, T. qingyuanensis, T. segregata, T. separata, T. stipitata, T. storea, Trichoderma ceratophylletum, Tyromyces minutulus, Umbelopsis heterosporus and Xylolentia reniformis. The new combinations are Antrodiella descendena, Chloridium macrocladum, Hansenopezia retrocurvata, Rhodofomitopsis monomitica, Rh. oleracea, Fuscoporia licnoides, F. scruposa and Ionopezia gerardii. A new sequenced species (Graphis supracola), one new host (Aplosporella prunicola) and three new geographical records (Golovinomyces monardae, Paradictyoarthrinium diffractum and Prosthemium betulinum), are reported.
... Pyronemataceae is the largest, most heterogenous, and least studied family in Pezizales. In their LSUbased phylogenetic study of the family, Perry et al. (2007) found that morphological characters traditionally used for subfamilial classification were not phylogenetically informative above the genus level. Given that Pyronemataceae is characterized by a lack of unifying morphological characteristics, it is fitting that S. lignatile with its enigmatic morphology would belong to this group. ...
Thirteen new species are formally described: Cortinarius brunneocarpus from Pakistan, C. lilacinoarmillatus from India, Curvularia khuzestanica on Atriplex lentiformis from Iran, Gloeocantharellus neoechinosporus from China, Laboulbenia bernaliana on species of Apenes, Apristus, and Philophuga (Coleoptera, Carabidae) from Nicaragua and Panama, L. oioveliicola on Oiovelia machadoi (Hemiptera, Veliidae) from Brazil, L. termiticola on Macrotermes subhyalinus (Blattodea, Termitidae) from the DR Congo, Pluteus cutefractus from Slovenia, Rhizoglomus variabile from Peru, Russula phloginea from China, Stagonosporopsis flacciduvarum on Vitis vinifera from Italy, Strobilomyces huangshanensis from China, Uromyces klotzschianus on Rumex dentatus subsp. klotzschianus from Pakistan. The following new records are reported: Alternaria calendulae on Calendula officinalis from India; A. tenuissima on apple and quince fruits from Iran; Candelariella oleaginescens from Turkey; Didymella americana and D. calidophila on Vitis vinifera from Italy; Lasiodiplodia theobromae causing tip blight of Dianella tasmanica ‘variegata’ from India; Marasmiellus subpruinosus from Madeira, Portugal, new for Macaronesia and Africa; Mycena albidolilacea, M. tenuispinosa, and M. xantholeuca from Russia; Neonectria neomacrospora on Madhuca longifolia from India; Nothophoma quercina on Vitis vinifera from Italy; Plagiosphaera immersa on Urtica dioica from Austria; Rinodina sicula from Turkey; Sphaerosporium lignatile from Wisconsin, USA; and Verrucaria murina from Turkey. Multi-locus analysis of ITS, LSU, rpb1, tef1 sequences revealed that P. immersa, commonly classified within Gnomoniaceae (Diaporthales) or as Sordariomycetes incertae sedis, belongs to Magnaporthaceae (Magnaporthales). Analysis of a six-locus Ascomycota-wide dataset including SSU and LSU sequences of S. lignatile revealed that this species, currently in Ascomycota incertae sedis, belongs to Pyronemataceae (Pezizomycetes, Pezizales).
... The fast-growers (eg., Oxalobacteraceae and Xanthomonadaceae) (Green et al., 2007) and potential pathogenic fungi Xenopolyscytalum (Tyub et al., 2018), Nectriaceae (Lombard et al., 2015), Chaetomiaceae (Violi et al., 2007), and Herpotrichiellaceae (Crous et al., 2007) were also highly enriched in the Module #1. Meanwhile, Module #2 and Module #3 were dominated by opportunistic pathogens such as Flavobacteriaceae (Bernardet et al., 2002), Pyronemataceae (Perry et al., 2007) and Xylariales (Yee et al., 2009). Module #4 consisted of plant-growth-promoting and fast-growing phylotypes from Chitinophagaceae (Madhaiyan et al., 2015) and potential pathogens from Comamonadaceae (Willems, 2014) and ...
There is a current lack of mechanistic understanding on the relationships between a soil microbial community, crop production, and nutrient fertilization. Here, we combined ecological network theory with ecological resistance index to evaluate the responses of microbial community to additions of multiple inorganic and organic fertilizers, and their associations with wheat production in a 35-year field experiment. We found that microbial phylotypes were grouped into four major ecological clusters, which contained a certain proportions of fast-growers, copiotrophic groups, and potential plant pathogens. The application of combined inorganic fertilizers and cow manure led to the most resistant (less responsive) microbial community, which was associated with the highest levels of plant production, nutrient availability, and the lowest relative abundance of potential fungal plant pathogens after 35 years of nutrient fertilization. In contrast, microbial community was highly responsive (low resistance) to inorganic fertilization alone or plus wheat straw, which was associated with lower crop production, nutrient availability, and higher abundance of potential fungal plant pathogens. Our work demonstrates that the response of microbial community to long-term nutrient fertilizations largely regulates plant production in agricultural ecosystems, and suggests that manipulating these microbial phylotypes may offer a sustainable solution to the maintenance of field productivity under long-term nutrient fertilization scenarios.
... The combination of molecular and morphological data is considered the most reliable approach to define species in this genus (Southworth & Frank 2011, Guevara-Guerrero & al. 2012, Flores-Rentería & al. 2014. Perry & al. (2007) studied the phylogenetic relationships of Pyronemataceae. Using LSU ribosomal DNA (rDNA) sequence data, they suggested that Geopora is monophyletic. ...
A new species, Geopora ahmadii, is described and illustrated based on material from Punjab, Pakistan. This species is characterized by sessile, cup- to saucer-shaped, partly immersed apothecia with whitish to grayish hymenial surfaces; broad ellipsoid, mostly uniguttulate ascospores; and brown excipular hairs. Phylogenetic analyses of the nrDNA ITS region with maximum parsimony, maximum likelihood, and Bayesian inference methods reveal that G. ahmadii is distinct from other described Geopora species. A collection previously identified as Geopora arenosa from Rawalakot, Pakistan, likely represents a second locality of G. ahmadii.
... Phylogram generated from maximum likelihood analysis based on combined ITS, LSU, SSU and TEF1-a sequence data for Boubovia species and several closely related genera in Ascodesmidaceae. Related sequences are taken fromPerry et al. (2007),Hansen et al. (2013),Lindemann et al. (2015) andKušan et al. (2018). Sixteen strains are included in the combined analyses which comprise 3584 characters (669 characters for ITS, 890 characters for LSU, 1043 characters for SSU, 982 characters for TEF1-a) after alignment.Pseudoboubovia benkertii (V.K. 3202) is used as the outgroup taxon. ...
This article is the tenth series of the Fungal Diversity Notes, where 114 taxa distributed in three phyla, ten classes, 30 orders and 53 families are described and illustrated. Taxa described in the present study include one new family (viz. Pseudoberkleasmiaceae in Dothideomycetes), five new genera (Caatingomyces, Cryptoschizotrema, Neoacladium, Paramassaria and Trochilispora) and 71 new species, (viz. Acrogenospora thailandica, Amniculicola aquatica, A. guttulata, Angustimassarina sylvatica, Blackwellomyces lateris, Boubovia gelatinosa, Buellia viridula, Caatingomyces brasiliensis, Calophoma humuli, Camarosporidiella mori, Canalisporium dehongense, Cantharellus brunneopallidus, C. griseotinctus, Castanediella meliponae, Coprinopsis psammophila, Cordyceps succavus, Cortinarius minusculus, C. subscotoides, Diaporthe italiana, D. rumicicola, Diatrypella delonicis, Dictyocheirospora aquadulcis, D. taiwanense, Digitodesmium chiangmaiense, Distoseptispora dehongensis, D. palmarum, Dothiorella styphnolobii, Ellisembia aurea, Falciformispora aquatic, Fomitiporia carpinea, F. lagerstroemiae, Grammothele aurantiaca, G. micropora, Hermatomyces bauhiniae, Jahnula queenslandica, Kamalomyces mangrovei, Lecidella yunnanensis, Micarea squamulosa, Muriphaeosphaeria angustifoliae, Neoacladium indicum, Neodidymelliopsis sambuci, Neosetophoma miscanthi, N. salicis, Nodulosphaeria aquilegiae, N. thalictri, Paramassaria samaneae, Penicillium circulare, P. geumsanense, P. mali-pumilae, P. psychrotrophicum, P. wandoense, Phaeoisaria siamensis, Phaeopoacea asparagicola, Phaeosphaeria penniseti, Plectocarpon galapagoense, Porina sorediata, Pseudoberkleasmium chiangmaiense, Pyrenochaetopsis sinensis, Rhizophydium koreanum, Russula prasina, Sporoschisma chiangraiense, Stigmatomyces chamaemyiae, S. cocksii, S. papei, S. tschirnhausii, S. vikhrevii, Thysanorea uniseptata, Torula breviconidiophora, T. polyseptata, Trochilispora schefflerae and Vaginatispora palmae). Further, twelve new combinations (viz. Cryptoschizotrema cryptotrema, Prolixandromyces australi, P. elongatus, P. falcatus, P. longispinae, P. microveliae, P. neoalardi, P. polhemorum, P. protuberans, P. pseudoveliae, P. tenuistipitis and P. umbonatus), an epitype is chosen for Cantharellus goossensiae, a reference specimen for Acrogenospora sphaerocephala and new synonym Prolixandromyces are designated. Twenty-four new records on new hosts and new geographical distributions are also reported (i.e. Acrostalagmus annulatus, Cantharellus goossensiae, Coprinopsis villosa, Dothiorella plurivora, Dothiorella rhamni, Dothiorella symphoricarposicola, Dictyocheirospora rotunda, Fasciatispora arengae, Grammothele brasiliensis, Lasiodiplodia iraniensis, Lembosia xyliae, Morenoina palmicola, Murispora cicognanii, Neodidymelliopsis farokhinejadii, Neolinocarpon rachidis, Nothophoma quercina, Peroneutypa scoparia, Pestalotiopsis aggestorum, Pilidium concavum, Plagiostoma salicellum, Protofenestella ulmi, Sarocladium kiliense, Tetraploa nagasakiensis and Vaginatispora armatispora).
... The family Pyronemataceae is not only highly diverse in terms of morphology but also ecologically (Perry et al. 2007. It includes six related genera that obligately grow on bryophytes -Octospora Hedw., Lamprospora De Not., Neottiella (Cooke) Sacc., Octosporopsis U.Lindem. ...
Octospora conidiophora is described as a new species, based on collections from South Africa. It is characterised by apothecia with a distinct margin, smooth or finely warted ellipsoid ascospores, stiff, thick-walled hyaline hairs, warted mycelial hyphae and growth on pleurocarpous mosses Trichosteleum perchlorosum and Sematophyllum brachycarpum (Hypnales) on decaying wood in afromontane forests. It is the first species of bryophilous Pezizales in which an anamorph has been observed; it produces long, claviform, curved, hyaline and transversely septate conidia. Three other cryptic species of Octospora were detected using three molecular markers (LSU and SSU nrDNA and EF1α), but these could not be distinguished phenotypically. These are not described formally here and an informal species aggregate O. conidiophora agg. is established for them. The new species and finds of Lamprospora campylopodis growing on Campylopus pyriformis and Neottiella albocincta on Atrichum androgynum represent the first records of bryophilous Pezizales in South Africa. https://mycokeys.pensoft.net/article/34571/
... However due to a lack of other morphological differences some authors have suggested combining Lamprospora and Octospora. The concept of three separable genera has been sustained lately based on the results of sequencing studies by Perry et al. (2007) and Hansen et al. (2013). We here follow this conclusion and apply the name Lamprospora arvensis (Velen.) ...
Abstract: Lamprospora arvensis (Velen.) Svrček is reported from Germany and Portugal for the first time. A description and illustrations of both macroscopic and microscopic characters are provided. The German report on the bryophyte host Ceratodon purpureus (Hedw.) Brid. is compared to the Portuguese one on Pleuridium acuminatum Lindb., a moss which so far has not previously been identified as a host. Several morphological differences suggest the existence of two taxa in Europe. These differences are discussed and the distribution of Lamprospora arvensis in Europe is given.
... & M. Vega (Pyronemataceae, Pezizales). The genus Octospora includes more than 80 species, mostly obligate bryoparasites (Arnolds 1992;Benkert 1993;Döbbeler 1997;Khare 2003;Perry & al. 2007;Kirk & al. 2008;Egertová & al. 2015). Octospora leucoloma Hedw. ...
Eight taxa from the pezizalean genus Octospora have been so far reported from Bulgaria. Data on the known distribution in the country are presented. Octospora gyalectoides and O. musci-muralis var. musci-muralis are recorded for the first time in Bulgaria. Concise descriptions and illustrations of the studied specimens are provided. New localities of O. leucoloma are also reported. These three Octospora taxa are bryoparasitic fungi growing on or among mosses. The associated bryophytes have been identified.
... Sequences obtained from the Peziza specimens were further investigated by a phylogenetic analysis in order to complement and confirm or revise the previous taxonomic assignment. The sequences used to infer the phylogenetic analysis were chosen on the bases of BLASTN results isolating a sub-dataset of taxonomically close well annotated sequences, and according to the outcomes of recent phylogenetic studies (Harrington and Potter, 1997;Hansen et al., 2002;Weinstein et al., 2002;Hansen and Pfister, 2006;Perry et al., 2007;Ekanayaka et al., 2016). ...
Despite their essential role in the environment, the number of known fungal species is still low compared to the recent estimates of the fungal biodiversity (from 2.2 to 3.8 million species), principally because of their often cryptic or ambiguous morphological traits. Recent studies have reported that only about approx. 35,000 correctly identified fungal species are represented by DNA sequences in public databases. This corresponds to a mere 1% of the estimated total number of species. Thus, the linkage of curated DNA sequence data to properly identified voucher specimens is of fundamental importance to fill the present gap between the different sizes of described and sequenced fungal diversity. For this purpose, mycological herbarium collections are considered an important source for fungal DNA-barcoding, and collection-based sequencing is a relevant priority for the coming decades. Unfortunately, ancient herbarium samples have both time and conservation related DNA damages, besides exogenous DNA contamination, that make nucleic acid extraction and amplification challenging. Here, we present the results of DNA extraction, ITS2 amplification and Illumina MiSeq sequencing of 36 specimens from the Saccardo Mycological Herbarium that were collected in the late XIX century and assigned to the genus Peziza. High-throughput sequencing was chosen as an alternative to the conventional Sanger- and cloning-based methods to overcome the high fragmentation of the ancient DNA and the massive occurrence of non-target DNA from fungal contaminants. Our approach has permitted the assignment of ITS2 sequences to 23 out of the 36 specimens studied in this work, thus providing a univocal DNA sequence for those one century old samples. Furthermore, the ITS2 sequence analysis has permitted a taxonomic study of the samples that has resulted in a re-evaluation of five samples at the species level and 18 samples at genus or higher level. Our results highlight the possibility to apply the technique presented in this work also to the old and more precious type specimens in order to relate a DNA sequence to these important samples, coupling the traditional morphological description of the species with a DNA sequence.
Sarcoscyphaceae (Pezizales) is distinguished by small to large, vividly-coloured sessile to stipitate apothecia, plurinucleate and pigmented paraphyses, operculate asci with thick walls, and plurinucleate, uniguttulate to multiguttulate ascospores with smooth walls or ornamentations. We collected more than 40 Sarcoscyphaceae specimens from dead twigs or wood. Based on morphology and phylogeny, these species belong to Cookeina, Nanoscypha, Phillipsia, Pithya, and Sarcoscypha. Among these, we introduce three new species–Nanoscypha aequispora, Pithya villosa, and Sarcoscypha longitudinalis. Phylogenetic analyses based on ITS, LSU, SSU, rpb2, and tef-1α gene regions indicate the relationships of these species within Sarcoscyphaceae. Meanwhile, we propose Ph. gelatinosa as a synonym of Ph. domingensis. One new record of C. sinensis is reported from Thailand.
The first known collection of Smardaea verrucispora in Italy, from a wood around
Rome, is here described. The morphological description is accompanied by a brief
historical-nomenclatural discussion, a comparison with similar species and
illustrated with photography in habitat, microscopic photographs and drawings.
Are also provided an updated key and a phylogenetic tree is that compares some
of our collections belonging to the Smardaea genus with sequences of other species
already present in GenBank.
Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.
The revision of type material of Lasiobolidium spirale, type of the genus Lasiobolidium, is presented and illustrated with colour photographs for the first time. We also present the discovery of a new species, named Lasiobolidium mercantourense. Morphological and molecular data of this species are given, as well as a comparison with closest species. Finally, an updated key to Lasiobolidium is provided.
Sphaerosporella microspora is described as a new species based on morphological and molecular data. It is characterized by its sessile apothecia, surface smooth, ectal excipulum composed of cylindrical and angular cells, globose and smooth ascospores, and unmodified paraphyses. A detailed description, photographs of the fruit body and microstructure diagrams are provided.
Five species of hygrophoroid fungi belonging to the genera Cuphophyllus and Hygrocybe are reported from the African island nation, Republic of São Tomé and Príncipe. These taxa represent two new species (C. laranja, H. macambrarensis), one undetermined taxon, and two new distributional reports. Comprehensive descriptions, line drawings, color photographs, and comparisons with allied taxa based on morphology and molecular sequence data (ITS) are provided.
Recent collections of unknown Trichophaea-like discomycetes made in Europe enabled the authors to explore the taxonomy of Trichophaea and allies, based on morphological, ecological and molecular data. Our 3-gene phylogeny confirms the paraphyly of the genus Trichophaea and designs a new systematics for this group of cup-fungi. Three new genera are published to accommodate several species previously assigned to Trichophaea or morphologically close genera: Perilachnea gen. nov. with Lachnea hemisphaerioides as type-species, Aurantiolachnea gen. nov. with Lachnea solsequia as type-species, and Parawilcoxina gen. nov. with P. inexpectata sp. nov. as type-species. some species of the genus Paratrichophaea belong to the cleistothecial genus Lasiobolidium, and furthermore two new species, L. trachysporum and L. coprophilum, are described. Paratrichophaea macrocystis is also combined in Lasiobolidium. Finally, three new species of Chaetothiersia, C. laricina, C. cupressicola and C. eguttulata are described. a new species of Perilachnea, P. ochraceoflava, is outlined from Italy, and a new species of Trichophaeopsis, T. asturiensis, is described from Spain. A total of 15 species are described and illustrated herein. Keys are provided.
Riassunto: Donadinia helvelloides viene segnalata per la prima volta in italia a seguito di raccolte effettuate in Sicilia. il ritrovamento avvenuto nel "Bosco Tassita" sui Monti nebrodi conferma la sua associazione con Taxus baccata. viene proposto un albero filogenetico aggiornato del genere Donadinia e pubblicate foto a colori di materiale fresco e di microscopia.
Parole chiave: Ascomycota, filogenesi, Tassita di Caronia, tassonomia, Urnula. First report of Donadinia helvelloides (Pezizales, Sarcosomataceae) in Italy
Abstract: Donadinia helvelloides is recorded for the first time in italy based on collections made in Sicily. The finding in the "Bosco Tassita" within the nebrodi Mountains Park confirms its link to wood debris of Taxus baccata. An updated phylogenetic studies on the genus Donadinia is proposed along with color pictures of fresh samples and microscopic details.
This article provides an outline of the classification of the kingdom Fungi (including fossil fungi. i.e. dispersed spores, mycelia, sporophores, mycorrhizas). We treat 19 phyla of fungi. These are Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. The placement of all fungal genera is provided at the class-, order- and family-level. The described number of species per genus is also given. Notes are provided of taxa for which recent changes or disagreements have been presented. Fungus-like taxa that were traditionally treated as fungi are also incorporated in this outline (i.e. Eumycetozoa, Dictyosteliomycetes, Ceratiomyxomycetes and Myxomycetes). Four new taxa are introduced: Amblyosporida ord. nov. Neopereziida ord. nov. and Ovavesiculida ord. nov. in Rozellomycota, and Protosporangiaceae fam. nov. in Dictyosteliomycetes. Two different classifications (in outline section and in discussion) are provided for Glomeromycota and Leotiomycetes based on recent studies. The phylogenetic reconstruction of a four-gene dataset (18S and 28S rRNA, RPB1, RPB2) of 433 taxa is presented, including all currently described orders of fungi.
The occurrence of Pseudaleuria fibrillosa in Sicily (Italy) is reported for the first time. This species is rather uncommon and localised, with few records, scattered in Europe. A detailed description with macro- and microscopical features of the collection is provided with the results of a phylogenetic analysis, all together with colour pictures of fresh specimens and microscopical elements.
Chaetothiersia vernalis, a new genus and species of Pyronemataceae (Ascomycota, Pezizales) from California. Fungal Diversity 28: 65-72. 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.
There are 234 fungal species listed in the record of decision (ROD) for amendments to Forest Service and Bureau of Land Management planning documents within the range of the northern spotted owl. There are four strategies to established guidelines for the survey and management of various organisms, including amphibians, mammals, bryophytes, mollusks, vascular plants, lichens, arthropods, and fungi. Strategy 1 (S1) entailed compiling all known distribution and ecological information on 147 fungus species. Other strategies convey protection or encourage the collecting of additional geographic and habitat information. Upon further taxonomic examination of the S1 fungal species, it was determined that only 135 separate species existed, with the others reduced to synomomy. Most of these S1 fungal species are poorly known and uncommon to rare. A few S1 fungal species were revealed to be much more common than previously thought. This handbook was designed to facilitate understanding of the life history of all S1 and protection buffer species and to aid in their discovery and identification. Each species is represented by a condensed description, a set of distinguishing features, and information on substrate, habitat, and seasonality. We also present a list of known sites within the range of the northern spotted owl, a distribution map and additional references to introduce the available literature on a particular species. A set of artificial taxonomic keys is presented to aid the worker in identification. A partially illustrated glossary helps introduce the novice to mycological terms.
The Parsimony Ratchet1 is presented as a new method for analysis of large data sets. The method can be easily implemented with existing phylogenetic software by generating batch command files. Such an approach has been implemented in the programs DADA (Nixon, 1998) and Winclada (Nixon, 1999). The Parsimony Ratchet has also been implemented in the most recent versions of NONA (Goloboff, 1998). These implementations of the ratchet use the following steps: (1) Generate a starting tree (e.g., a "Wagner" tree followed by some level of branch swapping or not). (2) Randomly select a subset of characters, each of which is given additional weight (e.g., add 1 to the weight of each selected character). (3) Perform branch swapping (e.g., "branch-breaking" or TBR) on the current tree using the reweighted matrix, keeping only one (or few) tree. (4) Set all weights for the characters to the "original" weights (typically, equal weights). (5) Perform branch swapping (e.g., branch-breaking or TBR) on the current tree (from step 3) holding one (or few) tree. (6) Return to step 2. Steps 2-6 are considered to be one iteration, and typically, 50-200 or more iterations are performed. The number of characters to be sampled for reweighting in step 2 is determined by the user; I have found that between 5 and 25% of the characters provide good results in most cases. The performance of the ratchet for large data sets is outstanding, and the results of analyses of the 500 taxon seed plant rbcL data set (Chase et al., 1993) are presented here. A separate analysis of a three-gene data set for 567 taxa will be presented elsewhere (Soltis et al., in preparation) demonstrating the same extraordinary power. With the 500-taxon data set, shortest trees are typically found within 22 h (four runs of 200 iterations) on a 200-MHz Pentium Pro. These analyses indicate efficiency increases of 20×-80× over "traditional methods" such as varying taxon order randomly and holding few trees, followed by more complete analyses of the best trees found, and thousands of times faster than nonstrategic searches with PAUP. Because the ratchet samples many tree islands with fewer trees from each island, it provides much more accurate estimates of the "true" consensus than collecting many trees from few islands. With the ratchet, Goloboff's NONA, and existing computer hardware, data sets that were previously intractable or required months or years of analysis with PAUP* can now be adequately analyzed in a few hours or days.
Were the first ascomycetes yeast-like (unicellular) or filamentous with complex multicellular growth? Molecular studies have indicated that the earliest lineages of ascomycetes were mostly yeast-like and without complex, multicellular fruit bodies. The genus Neolecta stands out as an exception. Neolecta spp. have filamentous growth and discomycete-type of fruit bodies, but constitute one of the basal lineages both in rRNA and RPB2 gene trees. In this paper, we have used 10 previously unpublished and 30 GenBank β-tubulin genes to test the phylogenetic position of Neolecta spp. We compared the phylogenetic information from the amino acid sequences (485 characters) with the phylogenetic information content of 33 characters from intron gains and losses. Due to gene duplications, two paralogous versions of β-tubulin genes occurred in four species included in our analysis. Although phylogenetic interpretation of β-tubulin gene trees was complicated by a history of gene duplications, intron gains and losses, and by unequal rates of amino acid substitution, Neolecta species never formed a monophyletic group with any of the sequences from the filamentous ascomycetes in the Pezizomycotina (euascomycetes) in parsimony or distance analyses. Like the RPB2 and rRNA genes, the β-tubulin genes support the hypotheses of an early divergence of Neolecta from superficially similar filamentous ascomycetes. Neolecta could become a key taxon particularly in comparative studies between the fungal model organisms in the mainly unicellular (=yeast-like) taxa Saccharomyces and Schizosaccharomyces and the filamentous fruit-body forming taxa Neurospora and Aspergillus.
The internal transcribed spacers (ITS) of the nuclear ribosomal DNA have been sequenced from 29 collections of Phillipsia, mainly from the New World. The P. domingensis complex, collections with a range of colors but otherwise referable to P. domingensis s.l. based on spore ornamentation, were studied. Three distinctive species of Phillipsia also were included. The sequences were analysed to infer phylogenetic relationships within Phillipsia, using parsimony. Morphological features were studied separately, and then evaluated in the context of the ITS phylogeny. Four distinct rDNA lineages, supported by ascospore ornamentation, were identified: the P. crispata, the P. domingensis, the P. olivacea and the P. carnicolor lineages. SEM photographs of the ascospores are presented. Phillipsia lutea and another yellow form were nested within the P. domingensis complex, of those with reddish hymenial colors. Color has been emphasized in taxonomy of Phillipsia, but these results suggest that individuals with strikingly different coloration may be closely related. Levels of ITS sequence divergence in the P. domingensis lineage were low. Based on these data, and morphology as studied thus far, there is no justification for recognizing segregate species within the P. domingensis complex. The Old World collections of the P. domingensis complex were nested within the New World collections, which implies that the P. domingensis lineage is geographically widespread. Phillipsia rugospora is placed in synonymy with P. olivacea and a detailed description of this taxon is given. A lectotype is designated for P. olivacea.
The order Pezizales has been divided into two suborders. One suborder, the Sarcoscyphineae, was originally described to include members whose asci were characterized by an unusual apical structure, the suboperculum. Disagreements as to how this structure should be defined, and indeed, whether or not it exists at all, have rendered the status of the suborder controversial. The two families within this suborder are the Sarcoscyphaceae and the Sarcosomataceae. Recent ultrastructural work demonstrates that there is an apical thickening which is restricted to the Sarcoscyphaceae. In order to test the monophyly of the suborders of the Pezizales and examine the relationships within the Sarcoscyphineae, phylogenetic analyses were carried out using DNA sequence data from the 18S rRNA gene. The strict consensus tree based upon these data shows both the Sarcoscyphineae and the Pezizineae as paraphyletic. These data suggest that the subordinal taxa currently recognized within the Pezizales should be abandoned and the taxonomy revised to reflect phylogenetic relationships. Strongly supported clades (i.e., greater than 95% bootstrap value, 1500 replicates) include: the Pezizaceae, the Morchellaceae, the Sarcoscyphaceae, the Helvellaceae, and a clade that includes the Sarcosomataceae (which is paraphyletic), and the Otidiaceae (represented only by 2 taxa). The genus Pindara, formerly placed in the Sarcoscyphaceae, is nested within the Helvellaceae, and Wynnea, assigned to the Sarcosomataceae by some authors, is positioned in the Sarcoscyphaceae.
Septal pore structures are described in asci, ascogenous hyphae, paraphyses, and excipular cells of species of Cheilymenia and Scutellinia (tribe Scutellinieae), and Acervus and Caloscypha (tribe Sowerbyelleae) of the Pyronemataceae. The ascus pore plugs of Cheilymenia and Scutellinia begin as a single electron-opaque band across the pore but develop into banded hemispherical structures within the ascus. Ascus pores of Acervus and Caloscypha are filled with an electron-opaque matrix in young asci, but by maturity they are plugged by a hemispherical, electron opaque structure with membranelike, translucent borders. Pores of the ascogenous hyphae of Cheilymenia and Scutellinia are occluded by Woronin bodies covered by deeply staining amorphous material. Plugging of ascogenous hyphal pores in Acervus and Caloscypha is similar to that of their asci. Lamellate structures are found in the pores of excipular cells in all species studied.
Structure and development of septal pore organelles in Acervus and Caloscypha are very similar to those found in members of the tribe Aleurieae but differ significantly from those of the Scutellinieae. Comparisons of pore structures of these two tribes are made with those of the Pezizaceae and Asco-bolaceae. The taxonomic and phylogenetic significance of these data is discussed.
Ascocarps of an operculate discomycete were produced in soils of a red pine pot culture inoculated with E-strain chlamydospores extracted from soils of a Douglas-fir nursery in Oregon. A new taxon, Tricharina mikolae, is proposed in honor of Dr. Peitsa Mikola. Monoand polyspore isolates show different growth characters and sizes of chlamydospores on both MMN and PDA plates. They form typical ectendomycorrhizae with red pine in flask cultures. Polyspore isolates produce ascocarps in the mycorrhizal synthesis cultures identical to those found initially in soil, whereas monospore isolates do not. This indicates that the fungus is heterothallic. The relationship between E-strain fungi and Complexipes moniliformis is also discussed.
Hydnocystis Tul. & Tul. is shown to be a monotypic genus containing only H. piligera Tul. & Tul. in the family Geneaceae of the Tuberales. Sepultaria (Cooke) Boud. (Pezizales) is shown to be congeneric with the older genus Geopora Harkness. Two new forms and a new subspecies, all hypogeous, are proposed for Geopora. Two species of Sepultaria and several in Hydnocystis are transferred to Geopora. Hydnocystis convolute McAlpine is transferred and renamed Peziza jactata Burdsall & Korf.
The fine structure of septa in asci, ascogenous hyphae, paraphyses, and excipular cells of apothecia is described in species of Aleuria, Anthracobia, Leucoscypha, and Octospora of the tribe Aleurieae, subfamily Scutellinioideae of the Pyronemataceae. An electron-opaque, hemispherical structure similar to that present in the Ascobolaceae was found in the ascal septa of all taxa. The hemispherical structure in the Aleurieae differs, however, in zonation and in the presence of an electron-translucent band bordering the pore in most species. Similar pore structures were found in the ascogenous hyphae of all species studied. Septal pores of paraphyses and excipular cells possess an electron-opaque, lamellate structure characteristic of taxa in the Pezizales. Evidence suggests that septa of genera in this tribe are more similar to those of the Ascobolaceae than to those of the Pezizaceae. Phylogenetic aspects of the data are discussed.
Two species of the genus Pustulina, P. cupularis and P. gaillardiana comb, nov., have been described and illustrated. The description of P. cupularis is based on the study of Fung. rhen. No. 1878, Peziza cupularis L., in FH which has been designated the neotype specimen of this species. Three Indian collections of P. cupularis, made by the authors, have also been compared with the type. Pustularia patavina, on the basis of the study of type specimen No. 1777 Peziza patavina from PAD, has been shown to belong to the genus Leucoscypha.
A list of the psilopezioid genera is given with nomenclatural and taxonomic comments. The genera Pachyella and Psilopezia are accepted and an emended circumscription is provided. Psilopezia is treated as a member of the tribe Otideeae in the Pyronemataceae and Pachyella as a member of the Pezizaceae. A key to the genera of psilopezioid fungi, Psilopezia, Pachyella, Iodophanus, Thecotheus, Peiziza, and “Peziza” lechithina, is included.
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
Parsimony, maximum-likelihood and Bayesian analyses of SSU rDNA sequences of representative taxa 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 Otideaceae). 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.
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.
Genea and Genabea are considered ectomycorrhizal (EM) symbionts of higher plants, but because of their hypogeous habit, dark coloration and the small size of their ascomata, relatively little is known about these genera. Ascomata of six morphological species of Genea and one of Genabea were frequently collected at a single site in xeric Quercus woodlands of California’s Sierra Nevada foothills. While most collections were easily referred to known species, those putatively identified as Genea harknessii and Genea arenaria were problematic. Genea harknessii collections appeared relatively homogenous based on morphology, but significant ITS variation revealed by rDNA sequencing suggested cryptic species diversity. Specimens of G. arenaria approximated the brief, original species description except for abundant clumps of septate setae formed at the apex of peridial warts. To verify the identity of this species we reexamined the holotype and analyzed morphology and ITS sequences of G. arenaria ascomata from a wide geographic range. To authenticate the EM status of Genea and Genabea with Quercus we collected healthy EM of Quercus douglasii and Quercus wislizenii and compared their ITS sequences to those from ascomata. We detected nine distinct ITS types of Genea and Genabea on roots. Two new species described here as Genea bihymeniata sp. nov. and Genea cazaresii sp. nov., were discovered during study of herbarium specimens. A phylogenetic analysis of 28 s rDNA from Genea and Genabea indicated three distinct lineages: Genea, Genabea and a third represented by Genea intermedia. For the latter we propose Gilkeya gen. nov. to accommodate the single known species, Gilkeya compacta comb. nov. A dichotomous key to all known Genea, Genabea and Gilkeya spp. from western North America is presented.
The most important recent views concerning the relationships between families and genera within the Pezizales are summarized. Attention is also paid to the delimitation of this order from the Tuberales and the Plectomycetes. Many ideas of the great pioneers of the systematics of discomycetes at the turn of the last century are still of importance in present classifications. Many macroscopic and microscopic morphological characters they used proved to be very practical for identification, though some of them appear to be of value only at a low taxonomic level. In recent years characters obtained from cytology, histochemistry, ultrastructure, possible anamorph connections, and molecular structure of proteins and DNA became available for classification. The correct evaluation of these new characters is one of the main problems of the present systematics of the Pezizales.
This article presents an overview of remarkable findings of bryoparasitic Pezizales in the Netherlands collected in the period 1995-2002. These collections provide further insight into the distribution, ecology, morphology and host relationships of the species described, some of which represent unknown taxa. Three new species are described, primarily or exclusively based on collections from the Netherlands: Octospora neerlandica, O. fissidentis and O. nemoralis. The following connections with host-mosses were observed: Tortula ruralis s. str., T ruraliformis, T virescens with O. neerlandica, and Fissidens bryoides with O. fissidentis as well as O. nemoralis. As a result of the intensive field survey, the number of species known from the Netherlands has increased from 14 to 40. This indicates that current knowledge on the distribution of bryoparasitic Pezizales is very incomplete in many countries.
Ultrastructure of septa, asci, ascogenous hyphae, and excipular cells of apothecia of selected species of Helvella is described. Electron-opaque, hemispherical structures appear in the basal pores of young asci and with age become more pronounced within the ascus cytoplasm, eventually assuming a dumbbell-shaped appearance. Characteristic electron-opaque and -translucent, "V"-shaped bands develop within the plug on the ascus side of the pore. An electron-translucent torus separates the pore plug from the septal pore border. Similar pore structures are also found in ascogenous hyphae. Septal pores of paraphyses and excipular cells possess an electron-opaque, lamellate structure characteristic of other taxa of Pezizales. Unlike pores of asci and ascogenous hyphae, those of paraphyses and excipulum also have typical spherical Woronin bodies. Septal pore structures of asci and ascogenous hyphae are unlike those of the Pezizaceae and Ascobolaceae and, although distinct, are more like those ofthe Aleurieae and Otidieae ofthe humariaceous fungi, especially those of Geopyxis. Phylogenetic aspects of these data are discussed.
Several minute dung-inhabiting discomycetes have been classified in the family Thelebolaceae, which has traditionally been included in the order Pezizales. The non-operculate type-genus Thelebolus has recently been excluded from the Pezizales. The phylogenetic distribution of other genera associated with Thelebolaceae is still obscure. We have analysed ca. 580 bp from a variable part of the nuclear SSU rRNA gene from Ascozonus, Ceccobius, Lasiobolus and Thecotheus, and compared these with ca. 1700 bp sequences from Thelebolus, Pleospora, Pezizales, Leotiales and Leotiales-related taxa. In the resulting trees, Ascozonus and Caccobius group with Thelebolus and the inoperculate discomycetes; Lesiobolus groups with Ascodesmis, and Thecotheus with Ascobolus within Pezizales. SEM pictures of fruit-bodies and ascus apices of Ascozonus, and ascospores from Thecotheus are presented to illustrate characteristic features of these taxa.
Carotenoids are colored terpenoids. The majority of the more than 600 carotenoid derivatives known to date consist of a 40 carbon skeleton. Only a few bacteria are able to synthesize C30 carotenoids or those with 45 or 50 carbon atoms (Goodwin 1980). The color of the carotenoids is determined by the polyene chain. A minimum of seven conjugated double bonds is necessary for light absorption in the visible spectral region. The increase of the conjugated system in an acyclic carotenoid shifts the color from yellow via orange and bright red to dark red in a maximally desaturated C40 molecule with 15 conjugated double bonds. In prokaryotes the carotenoids carry cyclic end groups. In most cases it is a β-ionone or ε-ring. Keto groups at position 2 of the acyclic chain or at position 4 of the ionone ring contribute to a conjugated double-bond system.