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A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected life history traits
Abstract
Pyronemataceae is the largest and most heterogeneous family of Pezizomycetes. It is morphologically and ecologically highly divers, comprising saprobic, ectomycorrhizal, bryosymbiotic and parasitic species, occurring in a broad range of habitats (on soil, burnt ground, debris, wood, dung and inside living bryophytes, plants and lichens). To assess the monophyly of Pyronemataceae and provide a phylogenetic hypothesis of the group, we compiled a four-gene dataset including one nuclear ribosomal and three protein-coding genes for 132 distinct Pezizomycetes species (4437 nucleotides with all markers available for 80% of the total 142 included taxa). This is the most comprehensive molecular phylogeny of Pyronemataceae, and Pezizomycetes, to date. Three hundred ninety-four new sequences were generated during this project, with the following numbers for each gene: RPB1 (124), RPB2 (99), EF-1α (120) and LSU rDNA (51). The dataset includes 93 unique species from 40 genera of Pyronemataceae, and 34 species from 25 genera representing an additional 12 families of the class. Parsimony, maximum likelihood and Bayesian analyses suggest that Pyronemataceae is paraphyletic due to the nesting of both Ascodesmidaceae and Glaziellaceae within the family. Four lineages with taxa currently classified in the family, the Boubovia, Geopyxis, Pseudombrophila and Pulvinula lineages, form a monophyletic group with Ascodemidaceae and Glaziellaceae. We advocate the exclusion of these four lineages in order to recognize a monophyletic Pyronemataceae. The genus Coprotus (Thelebolales, Leotiomycetes) is shown to belong to Pezizomycetes, forming a strongly supported monophyletic group with Boubovia. Ten strongly supported lineages are identified within Pyronemataceae s. str. Of these, the Pyropyxis and Otidea lineages are identified as successive sister lineages to the rest of Pyronemataceae s. str. The highly reduced (gymnohymenial) Monascella is shown to belong to Pezizomycetes and is for the first time suggested to be closely related to the cleistothecial Warcupia, as a sister group to the primarily apothecial Otidea. None of the lineages of pyronemataceous taxa identified here correspond to previous families or subfamily classifications. Ancestral character state reconstructions (ASR) using a Bayesian approach support that the ancestors of Pezizomycetes and Pyronemataceae were soil inhabiting and saprobic. Ectomycorrhizae have arisen within both lineages A, B and C of Pezizomycetes and are suggested to have evolved independently seven to eight times within Pyronemataceae s.l., whereas an obligate bryosymbiotic lifestyle has arisen only twice. No reversals to a free-living, saprobic lifestyle have happened from symbiotic or parasitic Pyronemataceae. Specializations to various substrates (e.g. burnt ground and dung) are suggested to have occurred several times in mainly saprobic lineages. Although carotenoids in the apothecia are shown to have arisen at least four times in Pezizomycetes, the ancestor of Pyronemataceae s. str., excluding the Pyropyxis and Otidea lineages, most likely produced carotenoids, which were then subsequently lost in some clades (- and possibly gained again). Excipular hairs were found with a high probability to be absent from apothecia in the deepest nodes of Pezizomycetes and in the ancestor of Pyronemataceae s. str. True hairs are restricted to the core group of Pyronemataceae s. str., but are also found in Lasiobolus (Ascodesmidaceae), the Pseudombrophila lineage and the clade of Chorioactidaceae, Sarcoscyphaceae and Sarcosomataceae. The number of gains and losses of true hairs within Pyronemataceae s.str., however, remains uncertain. The ASR of ascospore guttulation under binary coding (present or absent) indicates that this character is fast evolving and prone to shifts.
... Sphaerosporella (Svrček) Svrček & Kubička is a genus based on Sphaerospora subgen. Sphaerosporella Svrček to encompass hairy cup-fungi with rounded and smooth ascospores (SVRČEK, 1948 PERRY et al. (2007) and the fourgene phylogeny proposed by HANSEN et al. (2013) suggest these two taxa are congeneric. From a nomenclatural point of view, Trichophaea Boud. ...
... Here Sphaerosporella forms an independent clade, different from Trichophaea spp., but this phylogeny based on a combination of ITS and LSU regions does not give any statistical support for this clade (both with Maximum Likelihood and Bayesian inference methods). The strongest support is shown higher in their tree, in a lineage comprising Trichophaea spp., in agreement with several previous phylogenies (PERRY et al., 2007;HANSEN et al., 2013;VAN VOOREN et al., 2017;VAN VOOREN et al., 2021). ...
... sinceSCHUMACHER (1988: 166) revised an authentic collection of Peziza hybrida Sowerby, designated as lectotype, and considered it as a prior synonym of T. gregaria. I do not open here the question of this choice, although the latter partly contradicts SOWERBY's (1803) protologue of P. hybrida.Phylogenetic studies byPERRY et al. (2007),HANSEN et al. (2013) andVAN VOOREN et al. (2021) have shown that T. gregaria does not belong to the genus Trichophaea s. str., but to Wilcoxina Chin S. Yang & Korf. This genus was originally published for a group of tricharinoid species, with Tricharina mikolae Chin S. Yang & H.E. Wilcox as type. ...
Some taxonomic issues concerning some genera of Pezizales, as well as their nomenclatural implications , are discussed. The first issue concerns the status of Sphaerosporella, the second clarifies the taxo-nomic position of Trichophaea gregaria, and the third addresses the nomenclature of the Geopora lineage.
... [1] based on multigene phylogenetic analysis (ITS, LSU, SSU, and tef1-α, rpb2) and was segregated from the family Pyronemataceae according to Perry et al. [2]. Previously, the family Pyronemataceae was considered polyphyletic by Hansen et al. [3] with the Geopyxis lineage and by Kumar et al. [4] with the Tarzetta-Geopyxis lineage. Currently, this family is represented by Tarzetta (Cooke) Lambotte as the type genus Geopyxis (Pers.) ...
... accessed on 15 January 2024) still considers it a monogeneric family. The genus Tarzetta has a restricted distribution mostly in temperate forests, which forms ectomycorrhizal associations, generally with trees and shrubs of the genera Abies Mill., Alnus Mill., Quercus L., Pinus L., and Pseudotsuga Carrière [3,[5][6][7]. Tarzetta species are characterized as small to medium apothecia (2-30 mm), sessile to stipitate, deeply cupulate, and grey to beige but sometimes ochraceous or yellowish and rarely orange. Most of the species present a hymenium whitish or concolorous to the external zone of the apothecia, with a margin that ...
The genus Tarzetta is distributed mainly in temperate forests and establishes ectomycorrhizal associations with angiosperms and gymnosperms. Studies on this genus are scarce in México. A visual, morphological, and molecular (ITS-LSU) description of T. americupularis, T. cupressicola, T. davidii, T. durangensis, T. mesophila, T. mexicana, T. miquihuanensis, T. poblana, T. pseudobronca, T. texcocana, and T. victoriana was carried out in this work, associated with Abies, Quercus, and Pinus. The results of SEM showed an ornamented ascospores formation by Mexican Taxa; furthermore, the results showed that T. catinus and T. cupularis are only distributed in Europe and are not associated with any American host.
... Thus, carotenoids have recently been studied as one of the classes of lipids considered in chemotaxonomy, since 60% of the studied fungi contain them (Verscheure et al., 2002). In particular, the production of carotenoids is a synapomorphic trait characterizing a monophyletic gro-up Pyronemataceae (Hansen et al., 2013) and can be an additional and useful criterion for species identification, since classical morphological studies of Pyronemataceae fungi have not always been satisfactory for this group, as many genera are heterogeneous. The accumulation of carotenoids in the lipid globules of sclerotia of P. domesticum was found, which corresponds to the data for other fungi of the Pyronemataceae family (Hansen et al., 2013). ...
... In particular, the production of carotenoids is a synapomorphic trait characterizing a monophyletic gro-up Pyronemataceae (Hansen et al., 2013) and can be an additional and useful criterion for species identification, since classical morphological studies of Pyronemataceae fungi have not always been satisfactory for this group, as many genera are heterogeneous. The accumulation of carotenoids in the lipid globules of sclerotia of P. domesticum was found, which corresponds to the data for other fungi of the Pyronemataceae family (Hansen et al., 2013). In addition, the content of γ-carotene and its derivatives -neurosporaxanthin and its methyl ester is considered as an important taxonomic parameter in the taxonomy of the coprophilous fungus Iodophanus carneus (Pers.) ...
Three pyrophilous discomycetes species (Anthracobia maurilabra (Cooke) Boud., Pyronema domesticum (Sowerby) Sacc. and Tricharina praecox (P. Karst.) Dennis) have been cultivated and studied in vitro. Cultures were obtained from fresh apothecia сollected in the Holosiivskyi National Nature Park (Kyiv, Ukraine). The culture growth and morphological characteristics of the studied fungi on different media (beer wort agar, Czapek Dox agar, potato-dextrose agar) were analyzed. All investigated species can quite easily grow under laboratory conditions on different tested nutrient media. Potato-dextrose agar was the most suitable medium for the enhancement of radial growth and the best expresses all the phenotypes of the colony of studied fungi. Macro- and micromorphological descriptions of all fungal colonies and illustrations are provided. The micromorphological analysis showed that common to the mycelium of all studied species of fungi was the presence of numerous drops of oil in the hyphae, anastomoses like T. praecox, а net- like structure of A. maurilabra similar to nematode capture hook. Beside this, A. maurilabra and P. domesticum formed the sexual stage under experimental conditions. Forming fruiting bodies of A. maurilabra in culture has not been reported before. Moreover, P. domesticum was found to form abundant dark brown sclerotia on potato-dextrose agar and Czapek Dox agar. Possible pigment composition in the P. domesticum sclerotia is discussed based on the Raman spectroscopy study, performed on this genus for the first time. The established cultural characteristics can be useful for taxonomic identification of fungal species and for pure quality control of mycelial cultures during their introduction, preservation and future potential applications in biotechnological areas.
... 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. ...
... The 3-gene phylogeny ( fig.1) based on a combination of LSU, tef1 (exons) and rpb2 (exons) was mainly focused on the /Scutellinia-Trichophaea lineages as delineated by HanSen et al. (2013). The new Paratricharina species forms a non-significant clade together with Paratricharina poiraultii (pp 0.64, ML 38). ...
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.
... 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. ...
... In LSU, five collections are fully identical (MN394601 -holotype, MN400066, MN394592, MN394614, and MN394602), with three others differing only in a single nucleotide (MG949136, MN394603 and KC012684 -published as L. norvegica by Hansen & al. 2013) and one other in another single nucleotide (MN394594). Lamprospora paechnatzii was identified as the closest relative of L. benkertii; L. hispanica, which is morphologically very similar to L. benkertii, differs strongly both in LSU and EF1α (data not shown). ...
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 .
... Phylogenetic relationships assessed based on LSU, SSU rDNA, and RPB2 amino acid sequences strongly supported the monophyly of the Rhizinaceae, including Rhizina undulata, P. omnivora, and Psilopezia deligata (bootstrap proportions 86%, Bayesian posterior probabilities 100%; Marek et al. 2009). Furthermore, recent studies suggests that Caloscyphaceae and Rhizinaceae form a monophyletic group as sister to the rest of the "B-lineage" of Pezizomycetes, that is, Discinaceae, Morchellaceae, Helvellaceae, and Tuberaceae (Hansen et al. 2013, using LSU rDNA, RPB1, RPB2, EF-1a sequences; Mattupalli et al. 2021, using 100 BUSCO genes from a smaller taxon sampling). Despite the use of a touchdown PCR protocol that would compensate for potential differences between the primer and the priming site in the target species (Rossetto 2001), none of the 24 SSR primers in this study showed amplification with any of the closely related species (Table 2). ...
... It produces large apothecia, 4 to 15 cm broad, and survives through thick-walled ascospores; it is not known to produce sclerotia. Caloscyphaceae and Rhizinaceae include some of the very few pathogens known in the Pezizomycetes (Hansen et al. 2013). ...
Phymatotrichopsis omnivora, is a member of Pezizomycetes, and causes root rot disease on a broad range of dicotyledonous plants. Utilizing recently generated draft genome sequence data from four P. omnivora isolates, we developed simple sequence repeat (SSR) markers and identified both mating type genes (MAT1-1-1 and MAT1-2-1) in this fungus. To understand the genetic diversity of P. omnivora isolates (n=43) and spore mats (n=29) collected from four locations (Oklahoma, Texas, Arizona in US, and Mexico) and four host crops (cotton, alfalfa, peach, and soybean), we applied 24 SSR markers and showed that out of the 72 P. omnivora isolates and spore mats tested, 41 were distinct genotypes. Further, the developed SSR markers did not show cross transferability to other close relatives of P. omnivora in the class Pezizomycetes. A multiplex PCR detecting both mating type idiomorphs and a reference gene (TUB2) was developed to screen P. omnivora isolates. Based on the dataset we tested, P. omnivora is a heterothallic fungus with both mating types present in the US in a ratio close to 1:1. We tested P. omnivora spore mats obtained from spatially distinct disease rings that developed in a center-pivot alfalfa field and showed that both mating types can be present not only in the same field but also within a single spore mat. This study shows that P. omnivora has the genetic toolkit for generating sexually diverse progeny providing impetus for future studies that focus on identifying sexual morphs in nature.
... Ascomycota, which accounted over 65% of total fungal communities, had significant saprotrophic capacity (Xiong et al., 2014;Maharachchikumbura et al., 2015). An in-depth analysis showed that species of Pseudaleuria (Ascomycota, Pezizomycetes), which were identified as ectomycorrhizal-undefined saprotrophs, were abundant in slightly acidic soils (Supplementary Figure S3) and facilitated plant uptake of nutrients (Hansen et al., 2013;Ma et al., 2023). This indicates that slightly acidic degrees are beneficial for Pseudaleuria growth in Jiaodong Peninsula, which in turn enhances soil productivity (Xiang et al., 2020). ...
Introduction
Soil acidification imperils soil health and hinders the agricultural sustainability. As being more tolerant than bacteria to soil acidification, so it would be more meaningful for agricultural management and crop yield to characterize fungal community in acidic soils and manifest its key drivers.
Method
This study investigated the composition and diversity of fungal communities and its key driving factors by collecting 90 soil samples from the acidic region of Jiaodong Peninsula China, spanning 3 × 10 ⁴ km ² .
Results
The results indicated that most soil pH values ranged from 5.01 to 6.42, and the exchangeable acidity (E A ) content raised significantly ( p < 0.01) along with soil acidic degree increasing. However, no significant differences were found in fungal community diversity and composition among various soil samples, which were all predominantly habited with the phyla of Ascomycota and Basidiomycota. Results of the linear discriminant analysis effect size (LEfSe) analysis revealed that saprophytic fungi were biomarkers of the slightly acidic soil (pH 6.0–6.5), including Nectriaceae, Thielavia, Nectria, Haematonectria , and unclassified Microascaceae , while plant pathogenic fungi, such as Didymellaceae, were biomarkers of the soils pH < 5.5. Similarly, the FUNGuild results also indicated that saprophytic fungi and pathogenic fungi were the dominant functional guilds in the investigated acidic soils, accounting for 66% of the total fungal communities. Redundancy analysis (RDA) revealed that soil pH as well as nitrate nitrogen ( NO 3 − -N) and total nitrogen (TN) significantly associated with fungal community at the phylum level, whilst soil pH was the only factor significantly linked to individual fungal classes ( p < 0.01 or 0.05). The further Mantel test analysis and structural equation modeling (SEM) suggested that, in contrast to the negative and directive driving of soil pH on fungal communities' variation, the specific plant pathogenic fungi, Gibberella and Didymellaceae, were significantly and positively associated with soil acidic characteristics ( p < 0.05).
Discussion
These findings highlighted that, in addition to modulating the variation of soil fungal community, soil acidification might prime some plant pathogens development. So that, more attentions should be focused on impact of soil acidification on fungal ecology, as well as plant pathogenic fungi.
... These results are in line with the findings of Davide et al. (2016) in which the addition of manure could increase the relative abundance of Proteobacteria and Firmicutes. Pyronemataceae produces carotenoids, which are beneficial for plant photosynthesis (Hansen et al. 2013). Trichocomaceae can promote the formation of soil aggregates and the decomposition of organic matter (Daynes et al. 2012). ...
Purpose
High pH; high concentrations of Na⁺, and ; and nutrient deficiency are the main limiting factors in soda saline‒alkali soil. This study proposes a novel and effective method for ameliorating soda saline‒alkali soil in Northeast China, and further explores the underlying mechanism of this method.
Methods
In this study, a pot experiment was conducted. Vermicompost (V), traditional compost (T), and maize straw (S) were used individually or in combination (V + S and T + S) to improve saline alkali-soil. The control group (CK) was set without any external addition. Physical and chemical indicators and microbial community structures were analyzed at different stages to reveal remediation mechanisms.
Results
Compared with those in the CK treatment, the greatest decreases in pH, exchangeable sodium percentage, and (+ were observed in the V treatment, with values of 0.61 units, 59.41%, and 42.70%, respectively. The highest contents of humic acid and fulvic acid appeared in the V treatment, which, compared with those in the CK treatment, increased by 106 and 649%, respectively. The V + S treatment resulted in the highest urease activity, 0.84 mg ‒N g⁻¹ (24 h)⁻¹. Compared with those in the CK treatment, the relative abundance of Bacillaceae, Rhizobiaceae, Clostridiaceae, and Sphingomonadaceae in the V + S treatment increased by 10.41, 137, 285 and 241%, respectively. Linear discriminant analysis effect size revealed that Pseudomonas, Bacillaceae, and Sphingomonadaceae were the dominant bacteria in the V + S treatment. The V + S treatment resulted in the highest alfalfa aboveground biomass, which was 2.73 times greater than that in the CK treatment.
Conclusions
The results indicate that vermicompost best eliminates salt‒alkali barriers. The combined application of vermicompost and maize straw promoted the recruitment of beneficial microorganisms. Both vermicompost alone and vermicompost in combination with maize straw significantly improved the soda saline–alkali soil.
... Bryosymbiotics taxa such as Lamprospora, Leucoloma, Neottiella, Octospora, Octosporella, and Octosporopsis are clustered in a clade characterized by forming small discoid, cupuliform, or peritecioid apothecia, and have an obligate association with bryophytes. This association has been interpreted as parasitic in nature or bryosymbiotic species (Perry et al. 2007;Hansen et al. 2013;Quintero et al. 2020). If we consider that Mexico could harbor about 1591 species of mosses, the diversity of bryosymbiotic fungi could increase considerably among ascomycetes and basidiomycetes (Delgadillo-Moya 2014; Hernández-Rodríguez and Delgadillo-Moya 2021). ...
Neottiella albocincta (Berk. & M.A. Curtis) Sacc., N. rutilans (Fr.) Dennis, Octospora maireana (Seaver) Yei Z. Wang, and O. texensis Benkert are reported for the first time from Mexico. These species, all belonging to the family Pyronemataceae, have close relationships with several species of mosses such as those in the genera Archidium Brid., Atrichum P. Beauv., and Polytrichum Hedw. The specimens were collected in montane cloud forest, riparian and Quercus forest in the states of Puebla and Tamaulipas. With the addition of these species, the number of bryosymbiotic fungi in Mexico increases to five.
... However, Perry et al. (2007) showed in their phylogenetic study of Pyronemataceae that Boubovia luteola and Pulvinula ovalispora are strongly supported sister taxa. Then Hansen et al. (2013) further confirmed by phylogenetic analyses that Boubovia nicholsonii (as Pulvinula ovalispora) belongs within Boubovia, which formed a strongly supported group with the type species Boubovia luteola. It also showed for the first time that Boubovia is closely related to Coprotus and Ascodesmidaceae. ...
The author describes three species in the genus Boubovia (Velen.) Svrček from Norway with emphasis on their appearance and ecology. This is observations and collecting of data over a period of 30 years. Other potential Boubovia species are indicated.
... Eight-spored asci and hyaline ellipsoid ascospores are inamyloid and smooth to finely verrucous. This genus includes ectomycorrhizal fungi that grow and fructify in burned or disturbed soils (burnt ground) in coniferous or montane forests (Saccardo 1889, Kimbrough and Gibson 1990, Vralstad et al. 1998, Hansen et al. 2013, Wang et al. 2016. ...
Geopyxis is an ectomycorrhizal genus found in temperate forests. The members form yellow and orange to brown apothecia that range from 3-25 mm in diameter. Its ascospores are smooth to finely verrucous. The specimen collected from Mount Tlaloc, Texcoco, State of Mexico, was identified as Geopyxis carolinae sp. nov. This species typically forms sessile apothecia, cupuliform to discoid, and its ascospores are the largest [17-23(25) × 10-12 µm] within the genus. The species was found growing on a burnt ground associated with Abies religiosa. Multi-gene phylogenetic analyses inferred from ITS and LSU sequence data confirmed that Geopyxis carolinae is distinct from other Geopyxis spp. The new species is described, illustrated, and compared with similar taxa based on molecular and morphological data.
... The amplification programme for the ITS and LSU regions was as follows: initial denaturation at 95 °C for 5 min; then, 35-45 cycles of 95 °C for 45-60 s, 50-58 °C for 50 s and 72 °C for 1 min; followed by a final extension at 72 °C for 10 min. PCR amplifications of the RPB1 and RPB2 regions followed O'Donnell et al. [33] and Hansen et al. [34], respectively. PCR products were visualised in a 1% agarose gel and stained with SYBR Safe DNA Gel Stain (Invitrogen-Thermo Fisher Scientific, Inc., Waltham, MA, USA), using a UV trans-illuminator. ...
The aim of this study is to carry out a taxonomic revision of the groups Calamistratum
and Geraniodorum of the genus Inosperma sect. Inosperma in Europe. For this purpose, a multigenic
phylogenetic analysis was carried out using the ITS, LSU, RPB1 and RPB2 markers, covering a total
of 111 sequences, including those generated from the existing type-material collections. This analysis
led to the recognition of nine clades or terminal groups for the European continent, correlating
with nine morphological species. Three of them, I. calamistratum, I. neohirsutum sp. nov. and I. turietoense
sp. nov., are distributed in humid and temperate forests, whereas I. geminum sp. nov., I. geraniodorum,
I. gracilentum sp. nov., I. praetermissum comb. nov., I. subhirsutum and I. veliferum seem to
be restricted to the colder altimontane, boreal and alpine climates. It is concluded that the study of
morphological and ecological characteristics allows the recognition of species without the need for
an often-subjective interpretation of organoleptic characteristics. Inocybe hirsuta is considered a synonym
of Inosperma calamistratum, Inosperma praetermissum as a different species from I. calamistratum,
and Inocybe geraniodora var. gracilenta f. salicis-herbaceae as a synonym of I. praetermissum. Four new
species and one new combination are proposed. A key for the recognition of the European species
is provided. Illustrations and photographs of macro- and micromorphological characters and SEM
spores of all species are presented.
... Geopyxis species have been found to be saprophytic, facultative biotrophic, weakly parasitic, mutualistic, and endophytic or endolichenic under certain conditions (Laessøe and Hansen, 2007;Perry et al., 2007;Hansen et al., 2013;Hua Wang et al., 2016). In Europe, Geopyxis species have mostly been reported under the names G. carbonaria, G. alpina Höhn., G. foetida Velen., and G. majalis (Fr.) ...
Geopyxis (Pers.) Sacc. (Pyronemataceae, Pezizales) is a genus of fungi known for its
characteristic post-fire species such as Geopyxis carbonaria (Alb. & Schwein.) Sacc. These species produce abundant apothecia in burnt soils of boreal or mountainous coniferous forests. Geopyxis is a small group of species that currently has a cosmopolitan distribution, with 27 Geopyxis names listed in Index Fungorum. This species produces cup-shaped or flattened apothecia that are small to medium in size, ranging from 0.3-2.5 cm in diameter, and are stalked or stalkless. Geopyxis can be distinguished from other Pyronemataceae members by its smooth receptacle surface, yellow, orange to brown apothecial colors, smooth or very finely wrinkled
... Saprobic Pezizomycetes was the second-most dominant fungal taxon, accounting for 10.4 % of fungal module 1 of the chemical fertilization and 17.3 % of fungal module 5 of the organic fertilization (Fig. 4). Saprobic Pezizomycetes are ectomycorrhizal symbionts that have roots and consume plant sugars, which help plants absorb nutrients (Hansen et al., 2013). According to Ning et al. (2020), organic fertilization produced more Pezizomycetes than inorganic fertilization. ...
Partial substitution of chemical nitrogen (N) fertilizers with organic amendments is important for improving soil fertility and crop yield. Microorganisms play an important role in soil fertility by driving energy and nutrient cycles in the soil. However, there is limited information on the link between soil fertility and the microbial community under organic substitutions. Here, we investigated the soil fertility index and fertilization-sensitive operational taxonomic units (OTUs) of bacterial and fungal communities under different organic N substitution rates from 0 % to 100 % during four years of constant fertilization in an intensively-farmed vegetable field. Our results demonstrated that the 20 % and 50 % substitution rates could improve the soil fertility by 35.0 % and 27.5 %, respectively, compared with the 0 % substitution rate while ensuring crop yield. The 20 % to 100 % substitution rates significantly increased bacterial richness and diversity, as well as fungal diversity, compared with the 0 % substitution rate. Bacterial communities showed many more differences between the 0 % and other organic substitutions than in the fungal communities. Of the bacterial networks, the dominant sensitive OTUs are Phycisphaerae and Acidobacteria Subgroup_6 for the 0 % substitution rate and Gammaproteobacteria and Alphap-roteobacteria for other organic substitutions. Of the fungal networks, Sordariomycetes and Pezizomycetes were the dominant sensitive OTUs in all fertilization treatments. The assembly patterns of bacterial and fungal communities were induced toward deterministic processes under chemical N fertilization, which were restrained from this process under organic N fertilization. Furthermore, soil fertility produced a significant influence on the bacterial community (dominated by deterministic processes) but not on the fungal community (dominated by stochastic processes). In conclusion, understanding the survival patterns of fertilization-sensitive microorganisms is fundamental to manage soil fertility, which will help to address the needs of targeted smart agriculture through the cultivation of specific microbial taxa in the future.
... This has been followed by Korf (1972) and subsequent authors. The modern classification based on molecular phylogeny confirmed the position of Humaria inside the family Pyronemataceae inside its own linage (Perry et al., 2007;Hansen et al., 2013;Van Vooren et al., 2021). Fuckel (1870) characterized this genus as having terrestrial ascomata, cupuliform apothecia when young, discoid when mature, gregarious, sessile, with tomentose hairs; asci cylindrical, elongated, containing 8 spores; ascospores oval to oblong-oval, containing 1-3 guttules, hyaline; filiform paraphyses. ...
Humaria (Pyronemataceae, Ascomycota) is an ectomycorrhizal genus of fungi, mainly distributed in temperate forest. It is characterized by cupuliform to discoid apothecia that are covered with abundant hairs throughout the exterior of the brown ascomata, and by ellipsoid, hyaline, warty ascospores. There are 66 accepted species of which only one has been recorded in Mexico. The present study aims to describe a new species of Humaria with morphological, ecological and molecular data, found in Quercus forests from Tamaulipas, Mexico.
... (Strobiloscyphaceae, Pezizales; Ekanayaka et al. 2018) for RPB2. Referring to the taxon sampling by Hansen et al. (2013), whose dataset is wellbalanced and showed strong phylogenetic support for each family of Pezizales, we selected and downloaded individual sequences from GenBank. Other sequences from recent phylogenetic studies of Pezizales (e.g., Pfister et al. 2008Pfister et al. , 2019Carbone et al. 2013;Perić et al. 2013;Angelini et al. 2018;Ekanayaka et al. 2018) were also included. ...
Harmoniella junipericola, a new hyphomycete inhabiting on leaf litter of Juniperus chinensis (Cupressaceae) in Japan is described based on morphological characters on natural substrates and in culture and phylogenetic analyses using the sequences of internal transcribed spacer (ITS), large subunit nrRNA gene (LSU; 28S), DNA-directed RNA polymerase I largest subunit gene (RPB1), and DNA-directed RNA polymerase II second largest subunit gene (RPB2). The fungus belongs to the monotypic/monogeneric family Strobiloscyphaceae (one genus with two species; Pezizales) typified by Strobiloscypha. Brief notes are added on morphological and ecological comparisons among H. chrysocephala (type species, in Ukraine), H. campanaensis (in Chile), and H. junipericola. Using the ITS sequences deposited in the DNA Data Bank, additional operational taxonomic units (OTUs) of Harmoniella and phylogenetically related sequences are briefly discussed based on the data from East Asia (Japan, China), Middle East (Israel), Europe (France, Italy, Portugal), and North America (USA).
... The wild RP and GPXXL, which live in the same region, have a similar abundance pattern: a relatively high proportion of fungi from the Mrakiaceae family. Pyronemataceae comprises saprobic, ectomycorrhizal, bryosymbiotic, and parasitic species that occur in a broad range of habitats (in soil, burnt ground, debris, wood, and dung and inside living bryophytes, plants, and lichens; Hansen et al., 2013). (Whetzel, 1945). ...
Numerous gut microbial studies have focused on bacteria. However, archaea, viruses, fungi, protists, and nematodes are also regular residents of the gut ecosystem. Little is known about the composition and potential interactions among these six kingdoms in the same samples. Here, we unraveled the complex connection among them using approximately 123 gut metagenomes from 42 mammalian species (including carnivores, omnivores, and herbivores). We observed high variation in bacterial and fungal families and relatively low variation in archaea, viruses, protists, and nematodes. We found that some fungi in the mammalian intestine might come from environmental sources (e.g., soil and dietary plants), and some might be native to the intestine (e.g., the occurrence of Neocallimastigomycetes). The Methanobacteriaceae and Plasmodiidae families (archaea and protozoa, respectively) were predominant in these metagenomes, whereas Onchocercidae and Trichuridae were the two most common nematodes, and Siphoviridae and Myoviridae the two most common virus families in these mammalian gut metagenomes. Interestingly, most of the pairwise co-occurrence patterns were significantly positive among these six kingdoms, and significantly negative networks mainly occurred between fungi and prokaryotes (both bacteria and archaea). Our study revealed some inconvenient characteristics in the mammalian gut microorganism ecosystem: (1) the community formed by members of the analyzed kingdoms reflects the life history of the host and the potential threat posed by pathogenic protists and nematodes in mammals; and (2) the networks suggest the existence of predicted mutualism among members of these six kingdoms and of the predicted competition, mainly among fungi and other kingdoms.
... At the genus level, Trichophaea, Wilcoxina, and Geopora (Pyronemataceae, Pezizales, Ascomycota) were the most abundant on root tips. Taxa in the family Pyronemataceae have strong adaptability to stress (Mikryukov et al. 2021), and host plants can profit from mineral adsorption mediated by this fungal family (Hansen et al. 2013). Specifically, the abundance proportion of Wilcoxina was significantly higher in seedlings grown with the soil microbial legacy of trees than in seedlings inoculated with the soil microbial legacies of herbs and shrubs (Fig. 4a, b). ...
AimSoil microbial legacy is a potentially important regulator of the associations of plants and mycorrhizal fungi. However, our understanding of how plant performance and root-associated fungi react to distinct soil microbial legacies during subalpine forest succession remains unclear.MethodsA pot experiment of two coniferous (Picea asperata Mast. and Abies fargesii var. faxoniana (Rehder & E. H. Wilson) Tang S. Liu) tree seedlings, using sterilized soil inoculated with the soil microbial legacy of herbs, shrubs, and trees, was conducted in a greenhouse. Plant biomass, root morphological traits (total root length, root surface area, and the number of root tips), the percentage of ectomycorrhizal (EcM) root colonization, root-associated fungal communities, and soil inorganic nitrogen content were measured.ResultsBoth coniferous seedling performance and EcM colonization were facilitated when grown in the soil microbial legacies of shrubs and trees rather than herbs. Correspondingly, soil microbial legacy favored root-associated EcM Ascomycetes and EcM fungi with ‘short-distance’ exploration type. The soil microbial legacies of trees induced a greater relative abundance of Wilcoxina, while those of herbs and shrubs resulted in greater abundances of Trichophaea, Geopora, and Hebeloma (belonging to ‘short-distance’ exploration type). Notably, the relative abundances of ‘short-distance’ explorers were positively correlated with root biomass.Conclusions
Soil microbial legacy may affect tree seedling establishment and modify plant performance across successional stages by regulating the colonization, composition, and exploration type of root-associated fungi.
... Plants can improve their health or enhance their resistance against biotic and abiotic stresses by affecting the assembly of rhizosphere microorganisms, especially by enriching plant growth-promoting bacteria and fungi (Pieterse et al., 2014). Three PGPF genera (Hansen et al., 2013;Ozimek & Hanaka, 2020;Wang, Zhang, et al., 2017), Mortierella, Chaetomium and Pseudombrophila were found to be increased gradually from the inside to the outside of the roots ( Figure S10), implying that soybean prefer to accumulate such fungi far from their roots. Mortierella elongata has the potential to symbiotically interact with PGPRs like Burkholderia in the rhizosphere soil (Uehling et al., 2019). ...
Plant roots significantly influence soil microbial diversity, and soil microorganisms play significant roles in both natural and agricultural ecosystems. Although the genetically modified (GM) crops with enhanced insect and herbicide resistance are thought to have unmatched yield and stress resistance advantages, thorough and in‐depth case studies still need to be carried out in a real‐world setting due to the potential effects of GM plants on soil microbial communities. In this study, three treatments were used: a recipient soybean variety Jack, a triple transgenic soybean line JD321, and the glyphosate‐treated JD321 (JD321G). Three sampling stages (flowering, seed filling and maturing), as well as three host niches of soybean rhizosphere [intact roots (RT), rhizospheric soil (RS) and surrounding soil (SS)] were established. In comparison to Jack, the rhizospheric soil of JD321G had higher urease activity and lower nitrite reductase at the flowering stage. Different treatments and different sampling stages existed no significant effects on the compositions of microbial communities at different taxonomic levels. However, at the genus level, the relative abundance of three plant growth‐promoting fungal genera (i.e. Mortierella, Chaetomium and Pseudombrophila) increased while endophytic bacteria Chryseobacterium and pathogenic bacteria Streptomyces decreased from the inside to the outside of the roots (i.e. RT → RS → SS). Moreover, two bacterial genera, Bradyrhizobium and Ensifer were more abundant in RT than in RS and SS, as well as three species, Agrobacterium radiobacter, Ensifer fredii and Ensifer meliloti, which are closely related to nitrogen‐fixation. Furthermore, five clusters of orthologous groups (COGs) associated to nitrogen‐fixation genes were higher in RT than in RS, whereas only one COG annotated as dinitrogenase iron‐molybdenum cofactor biosynthesis protein was lower. Overall, the results imply that the rhizosphere host niches throughout the soil–plant continuum largely control the composition and function of the root‐associated microbiome of triple transgenic soybean.
... Pezizomycetes, mainly represented by Phymatotrichopsis, were found to have frequently occurred in the canal sediments obtained before floods, with an average high relative abundance of 2.0%, but could not be detected after floods. Pezizomycetes are commonly found around the world, but their representative constituent taxonomic groups are unevenly distributed [37]. Pezizaceae (belonging to Pezizomycetes) has been reported to show a particularly high diversity in temperate regions [38]. ...
Floods are frequent natural disasters and could have serious impacts on aquatic environments. Eukaryotic communities in artificial canals influenced by floods remain largely unexplored. This study investigated the spatiotemporal variabilities among eukaryotes in response to floods in the Grand Canal, China. Generally, 781,078 sequence reads were obtained from 18S rRNA gene sequencing, with 304,721 and 476,357 sequence reads detected before and after flooding, respectively. Sediment samples collected after the floods exhibited a higher degree of richness and biodiversity but lower evenness than those before the floods. The eukaryotic communities changed from Fungi-dominated before floods to Stramenopile-dominated after floods. The spatial turnover of various species was the main contributor to the longitudinal construction of eukaryotes both before the floods (βSIM = 0.7054) and after the floods (βSIM = 0.6858). Some eukaryotic groups responded strongly to floods and might pose unpredictable risks to human health and environmental health. For example, Pezizomycetes, Catenulida, Glomeromycetes, Ellipura, etc. disappeared after the floods. Conversely, Lepocinclis, Synurale, Hibberdiales, Acineta, Diptera, and Rhinosporidium were all frequently detected after the floods, but not prior to the floods. Functional analyses revealed amino acid metabolism, carbohydrate metabolism, translation, and energy metabolism as the main metabolic pathways, predicting great potential for these processes in the Grand Canal.
... Winter et al., 2019), which may be more conducive to the parasitism of P. graminis on wheat roots (K. Hansen et al., 2013;Mestre and Fontenla, 2021). In conclusion, the occurrence of Wheat yellow mosaic virus disease affects the composition of soil fungal community, but there are many reasons for this change, such as soil physicochemical interaction and soil nutrient imbalance (C.H. Kong et al., 2008;C. ...
Rhizosphere-associated microbes have important implications for plant health, but knowledge of the association between the pathological conditions of soil-borne virus-infected wheat and soil microbial communities, especially changes in fungal communities, remains limited. We investigated the succession of fungal communities from bulk soil to wheat rhizosphere soil in both infected and healthy plants using amplicon sequencing methods, and assessed their potential role in plant health. The results showed that the diversity of fungi in wheat rhizosphere and bulk soils significantly differed post wheat yellow mosaic virus disease onset. The structure differences in fungal community at the two wheat health states or two compartment niches were evident, soil physicochemical properties (i.e., NH4 ⁺) contribute to differences in fungal community structure and alpha diversity. Comparison analysis showed Mortierellomycetes and Dothideomycetes as dominant communities in healthy wheat soils at class level. The genus Pyronemataceae and Solicoccozyma were significantly are significantly enriched in rhizosphere soil of diseased plant, the genus Cystofilobasidium, Cladosporium, Mortierella, and Stephanonectria are significantly enriched in bulk soil of healthy plant. Co-occurrence network analysis showed that the fungi in healthy wheat soil has higher mutual benefit and connectivity compared with diseased wheat. The results of this study demonstrated that the occurrence of wheat yellow mosaic virus diseases altered both fungal community diversity and composition, and that NH4 ⁺ is the most important soil physicochemical factor influencing fungal diversity and community composition.
... Many phenomena associated with fungal dispersal are particularly noticeable in bryophilous Pezizales. This monophyletic group of operculate ascomycetes consists of almost 200 described and numerous undescribed species from the genera Lamprospora, Neottiella, Octospora, Octosporella, Octosporopsis and most likely also Filicupula (Stenroos et al., 2010;Hansen et al., 2013;Döbbeler and Davison, 2021;Eckstein, 2022;Index Fungorum, 2022). All these species are closely associated with bryophytes and are usually treated as their biotrophic parasites (e.g., Benkert, 1995;Davey and Currah, 2006). ...
Fungal spores are morphologically highly diverse and are therefore frequently used as diagnostic characters in taxonomy. However, the connection between spore morphology and fungal ecology remains poorly understood. Using phylogenetic comparative analyses, we investigated the putative relationships between four ascospore traits and the dominant place of infection, host ecology, and host taxonomic placement in 123 species of biotrophic parasites of bryophytes. Ascospore shape, ornamentation height and relative lipid content are significantly correlated in bryophilous Pezizales. Species attached by their hyphae to bryophyte rhizoids have more globose ascospores with higher ornamentation and relative lipid content than species attached to aboveground organs. Furthermore, some ascospore traits are significantly associated with host lifespan, habitat preferences, and taxonomic placement of their host bryophytes. Our results suggest that the ascospore morphology in this fungal group is closely linked to its ecology and several of the detected relationships point to the existence of distinct dispersal strategies.
... As the largest phylum of fungi, Ascomycota degrades persistent organic matter, such as lignin and keratin. In addition, many ascomycetes could form symbiotic mycorrhiza and lichen, thus playing an important role in soil nutrient cycling [18]. On the 7th and 15th days of L1 treatment, Polyporales and Microascus were found enriched. ...
Pesticides can affect non-target microorganisms in the soil and are directly related to soil microecological health and environmental safety. Oxathiapiprolin is a piperidinyl thiazole isoxazoline fungicide that shows excellent control effect against oomycete fungal diseases, including late blight, downy mildew, root rot, stem rot, and blight. Though it can exist stably in the soil for a long time, its effects on soil microbial structure and diversity are not well investigated. In the present study, the effects of oxathiapiprolin on the abundance and diversity of soil fungal communities in typical farmland were studied. The results show that the abundance and diversity of soil fungi were increased by oxathiapiprolin treatment with differences not significant on the 30th day. Oxathiapiprolin was found to change the structure of soil fungal communities, among which Ascomycota and Mortierellomycota were the most affected. Undefined saprophytic fungi increased in the treatment groups, and the colonization of saprophytic fungi can act as a major contributor to the function of soil microbial communities. This study lays a solid foundation regarding environmental behavior with the use of oxathiapiprolin in soil and details its scientific and rational use.
... and related genera represent an exceptional group of ascomycetes. They share many of the key characteristics with the majority of Pezizales including vividly coloured apothecia, ascus type, and colourless, one-celled ascospores but deviate by their lifestyle as highly adapted obligate parasites (Hansen et al. 2013). Many Pezizales are saprotrophic or mycorrhizal, but species of Octospora and related genera grow on various lineages of mosses and liverworts and exhibit narrow host ranges, often restricted to a single species (Egertová et al. 2018b, Sochorová et al. 2020, Vega et al. 2021, Németh et al. 2022. ...
Two species of the hepaticolous genus Octosporella (Pyronemataceae, Pezizales) have
been recorded from southern Australia on host species that are hitherto unknown as substrates for
ascomycetes. Octosporella australis sp. nov. is characterized by large setose ascomata, 3- or
4-spored asci, large ellipsoidal ascospores, 36–65 × 10–15 μm, with unthickened spore walls at cell
poles and occurring on the terrestrial liverwort Lethocolea pansa (Jungermanniales). Three collections were gathered on Kangaroo Island, South Australia, on seasonally flooded riverbanks. Phylogenetic analyses of the LSU, SSU and EF1-α sequences showed that the collections of this new
species form a well-supported monophyletic group and clearly differ from all other species of
Octosporella. The second species was assigned to O. jungermanniarum agg. which is widely distributed in Europe on several unrelated liverworts. The Australian collection deviates in its somewhat narrower ascospores, but molecular analyses placed the studied specimen among European
collections of O. jungermanniarum from various host species. This species infects the liverwort
Lophocolea semiteres (Jungermanniales) and was recorded on the Fleurieu Peninsula on mossy
rocks. Apart from a single collection of O. nematospora from New Zealand, these Australian collections are the only records of Octosporella species for the whole Southern Hemisphere. Both
species have multinucleate ascospores and O. australis, with predominantly 8-nucleate ascospores,
has the highest known number of nuclei in ascospores among all studied species of octosporaceous
fungi and the whole family Pyronemataceae.
... (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. ...
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.
... It comprises saprobic, ectomycorrhizal, bryosymbiotic and parasitic species occurring in a broad range of habitats. 52 After 4 weeks, soil treated with p-CA (A) was depleted in Chromelosporium and Myrmecridium and enriched in sequences assigned to Lasiosphaeris, Arthrobotrys, unidentified reads within Capnodiales, Humicola, and Lophiotrema. Soil treated with Porter 250 EC (B) was depleted in sequences assigned to Podospora as well as unidentified reads within Pleosporales and enriched with sequences assigned to Botrytis and unidentified reads within Diversisporales (Fig. 2). ...
BACKGROUND
The study aimed to develop a new formulation based on active substances of natural origin to protect plant seedlings against fungal pathogens, and to evaluate the effect of this formulation on fungal communities in arable soil.
RESULTS
Coating seeds of common crop plants with a p‐coumaric acid (p‐CA)‐based preparation resulted in a significant reduction in the growth of most of the tested pathogens. When applied to soil, both the p‐CA‐based formulation and Porter 250 EC had a similar overall effect on soil fungal communities and significantly altered the structure of fungal communities at all of the times examined. Shifts in the fungal community composition concerned less than 2% of the total number of amplicon sequence variants (ASVs). The strongest impact of the formulations on soil microbiota was recorded at the fourth week of treatment. Two ASVs assigned to Botrytis and Chromelosporium, known as plant pathogens, and an unidentified ASV from Diversisporales encompassing the arbuscular mycorrhizal fungi (AMF), were significantly depleted in soil samples treated with p‐CA in comparison with Porter 250 EC.
CONCLUSION
The p‐CA‐based preparation has the potential to be used as an alternative to synthetic fungicides. It shows a similar effect to Porter 250 EC on the organization of soil communities, determining changes in the character of the communities of fungi in general, at any given time. Moreover, p‐CA caused a reduction in ASVs belonging to Botrytis and Chromelosporium (plant pathogens) and ASVs of Diversisporales (containing arbuscular mycorrhizal fungi) in comparison with the commercial compound that was analyzed. © 2022 Society of Chemical Industry.
... Members of the genus exhibit a wide range of ascomatal forms, with split to entire, sessile to stipitate, cupulate to ear-shaped epigeous apothecia, as well as closed, solid ascomata in hypogeous taxa, and are mainly distributed in temperate zones of Europe, North America, and Asia in the northern hemisphere, with a few from the arctic-alpine regions. Species of Otidea are considered to be ectomycorrhizal and thus play important roles in forest ecosystems [4][5][6][7][8][9]. ...
The emergence of molecular systematics has greatly helped researchers to identify fungal species. China has abundant Otidea species resources, and a number of new species of Otidea have been recently proposed. However, many old specimens in herbaria are mainly identified by morphology rather than molecular methods. In this study, 11 specimens deposited in Chinese herbaria and one newly collected Otidea species from northern China were identified based on morphological and phylogenetic analyses. Four gene fragments (ITS, LSU, rpb2, and tef1-α) were used to elucidate the phylogenetic relationships of species within Otidea. A total of nine phylogenetic species are recognized, of which four are described as new species, namely O. bomiensis, O. gongnaisiensis, O. hanzhongensis, and O. shennongjiana. Among the known species were O. aspera and O. sinensis.
... Forward and reverse sequences were utilised to create consensus sequences by BioEdit v. 7.0.9.0 (Hall 1999) and BLASTn searched in NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi) to identify the genus-level taxonomic status. Phylogenetic analyses were performed, based on the sequences generated in this study and recently published data (Hansen et al. 2013, Vu et al. 2019, Schoch et al. 2009, Hansen et al. 2005, Lindemann et al. 2019, Manoch et al. 2013, Sun et al. 2020, Visagie et al. 2015, Wang et al. 2016, Wang et al. 2017, Yilmaz et al. 2012, Yilmaz et al. 2014, which were downloaded from GenBank (https://www.ncbi.nlm.nih.gov/genbank/) ( Table 3). The multiple alignments were automatically generated using MAFFT v. 7 webserver (https://mafft. ...
Rosa roxburghii Tratt., a deciduous shrub of the family Rosaceae, is usually used as food and medicinal materials and also cultivated as an ornamental. Plant endophytic fungi are a large class of microbial resources not fully researched, with great potential applications. Two strains of Ascodesmis and Talaromyces were isolated during a survey of biodiversity on endophytic fungi of R. roxburghii in China. Multigene phylogenetic analyses showed that each of the two fungi formed a distinct lineage and separated from known congeneric species and they are proposed as two novel taxa.
Ascodesmis rosicola sp. nov. usually has one or two conspicuous simple or branched ridges extending to the majority of the ascospore surface and remarkably small asci, distinguishing it from the previously-described species in the genus Ascodesmis . Talaromyces rosarhiza sp. nov., of the section Talaromyces, is closely related to T. francoae . It differs from the latter by having both monoverticillate and biverticillate conidiophores, while those of T. francoae are biverticillate. Both novel endophytes are illustrated and described.
Fungi are one of the most diverse groups of organisms with an estimated number of species in the range of 2–3 million. The higher-level ranking of fungi has been discussed in the framework of molecular phylogenetics since Hibbett et al., and the definition and the higher ranks (e.g., phyla) of the ‘true fungi’ have been revised in several subsequent publications. Rapid accumulation of novel genomic data and the advancements in phylogenetics now facilitate a robust and precise foundation for the higher-level classification within the kingdom. This study provides an updated classification of the kingdom Fungi , drawing upon a comprehensive phylogenomic analysis of Holomycota , with which we outline well-supported nodes of the fungal tree and explore more contentious groupings. We accept 19 phyla of Fungi, viz . Aphelidiomycota , Ascomycota , Basidiobolomycota , Basidiomycota , Blastocladiomycota , Calcarisporiellomycota , Chytridiomycota , Entomophthoromycota , Entorrhizomycota , Glomeromycota , Kickxellomycota , Monoblepharomycota , Mortierellomycota , Mucoromycota , Neocallimastigomycota , Olpidiomycota , Rozellomycota , Sanchytriomycota, and Zoopagomycota . In the phylogenies, Caulochytriomycota resides in Chytridiomycota ; thus, the former is regarded as a synonym of the latter, while Caulochytriomycetes is viewed as a class in Chytridiomycota . We provide a description of each phylum followed by its classes. A new subphylum, Sanchytriomycotina Karpov is introduced as the only subphylum in Sanchytriomycota . The subclass Pneumocystomycetidae Kirk et al. in Pneumocystomycetes , Ascomycota is invalid and thus validated. Placements of fossil fungi in phyla and classes are also discussed, providing examples.
Sepultariella semi-immersa (Pyronemataceae, Ascomycota) was identified in a new locality for macrofungal diversity in Türkiye from Çanakkale Onsekiz Mart University Terzioğlu Campus. S. semi-immersa, which constitutes a species comlex, is included in the Sepultariella clade. This study gives a detailed description of the species, geographical coordinates, photographs taken in its natural habitat, and its phylogenetic position in the genus Sepultariella based on molecular data. The Internal transcribed spacer (ITS) region sequence determined the evolutionary and phylogenetic relationship within the genus but S. semi-immersa, which might constitute a species complex.
Scutellinia blumenaviensis is recorded for the first time on Guadeloupe Island (France). A description of the macro-and microscopic characters and the ecology is provided, as well as photographic documentation. The morphological identification has been supported genetically by comparing the 28S rDNA with the only available sequence that exists in public databases, and the first ITS2 rDNA has been produced. A combined ITS-28S phylogenetic study to show its position in the genus Scutellinia is also provided.
Résumé : Scutellinia blumenaviensis est enregistrée pour la première fois en Guadeloupe (France). Une description des caractères macro-et microscopiques et l'écologie sont fournis, ainsi qu'une documentation photographique. L'identification morphologique est supportée génétiquement par comparaison du mar-queur 28S de l'ADN ribosomal avec la seule séquence disponible dans les bases de données publiques, et la première séquence ITS2 a été générée. Une étude phylogénétique d'une combinaison ITS-28S est éga-lement fournie pour montrer sa position dans le genre Scutellinia.
In the present study, specimens kept in Fungarium of Van Yüzüncü Yıl University-Türkiye (VANF) were evaluated based on morphological and molecular characters, and identified as Dissingia confusa as a new record from Eastern Türkiye. Ascocarp, hymenium, stipe, ascospores, ascus and paraphyses were considered as diagnostic morphological characters and the nucleotide sequences of the large subunit (LSU) ribosomal DNA and the translation elongation factor 1-alpha (TEF1-α) were referred as molecular data. A phylogenetic analysis was performed with Maximum parsimony and Bayesian inference methods. The DNA sequences of 15 (7 for TEF1-α) Dissingia and 27 (14 for TEF1-α) Helvella specimens downloaded from the GenBank database were included in the analysis to estimate phylogeny between the two close genera. Morphological evaluations and genetic evidences confirmed that Dissingia is phylogenetically separated from Helvella at genus level and helped to identify the studied specimens as D. confusa as a new record in Türkiye. Detailed description, colour images of fresh and dried ascomata, along with photographs of microscopic characters and the obtained phylogenetic trees are given.
Soil microorganisms play a crucial role in nutrient cycling, maintaining soil fertility, and carbon sequestration in soil. However, our understanding of the adaptive mechanisms and driving factors of microbial community structure in non-calcareous fluvo-aquic soil under different fertilization treatments remains limited. A field experiment was designed with winter wheat-summer maize rotation system started in 1978. Five treatments were selected: CK (no fertilizers); N (nitrogen); NPK (nitrogen, phosphorus and potassium); M (60,000 kg pig manure ha−1); MN (60,000 kg pig manure + 276 kg N ha−1). The results showed that N, NPK, M and MN treatment significantly increased soil organic carbon (SOC) and total nitrogen (TN) by 22.7% and 38.8%, 23.1% and 30.5%, 113.4% and 141.6%, 167.1% and 304.1% compared to CK, respectively. Long-term fertilization (NPK, M, and MN) alters the structure of soil microbial communities through improvements in soil carbon and nitrogen cycles and soil enzyme activities. Additionally, pig manure application significantly enhanced the relative abundance of Pezizomycetes (35.9%) and Firmicutes (23.4%). Redundancy analysis (RDA) indicated that TN and SOC are the primary factors driving the changes in soil bacterial communities. TN and catalase activity are the main factors driving the changes in the soil fungal community. Overall, long-term fertilization, especially the addition of organic resources, can strengthen the biological regulation processes in soil ecosystems to maintain or enhance soil fertility.
Dissingia confusa (Harmaja) K. Hansen & X.H. Wang , housed in the Fungarium of Van Yüzüncü Yıl University (VANF) is identified as a new record from Eastern Türkiye based on morphological and molecular characters. Pileus, hymenium, stipe, spore, ascus and paraphyse structures are used as morphological features and the nucleotide sequences of the large subunıt (LSU) and translation elangation factor 1-alpha (TEF1-α) regions are utulized as molecular data. The analyses are supplemented with an additional sample of 15 (7 for TEF1-α) Dissigia and 27 (14 for TEF1-α) Helvella specimens downloaded from GenBank database to figure phylogeny between two close genera. Morphological studies and genetic evidences confirm that Dissingia is phylogenetically separated from Helvella at genus level and Dissingia confusa is firstly identified in Türkiye. A detailed description, colour pictures of fresh and dried specimens, as well as images of microscopical characters and phylogenetic trees are provided.
This article is the 15th contribution in the Fungal Diversity Notes series, wherein 115 taxa from three phyla, nine classes, 28 orders, 48 families, and 64 genera are treated. Fungal taxa described and illustrated in the present study include a new family, five new genera, 61 new species, five new combinations, one synonym, one new variety and 31 records on new hosts or new geographical distributions. Ageratinicolaceae fam. nov. is introduced and accommodated in Pleosporales. The new genera introduced in this study are Ageratinicola, Kevinia, Pseudomultiseptospora (Parabambusicolaceae), Marasmiellomycena, and Vizzinia (Porotheleaceae). Newly described species are Abrothallus altoandinus, Ageratinicola kunmingensis, Allocryptovalsa aceris, Allophoma yuccae, Apiospora cannae, A. elliptica, A. pallidesporae, Boeremia wisteriae, Calycina papaeana, Clypeococcum lichenostigmoides, Coniochaeta riskali-shoyakubovii, Cryphonectria kunmingensis, Diaporthe angustiapiculata, D. campylandrae, D. longipapillata, Diatrypella guangdongense, Dothiorella franceschinii, Endocalyx phoenicis, Epicoccum terminosporum, Fulvifomes karaiensis, F. pannaensis, Ganoderma ghatensis, Hysterobrevium baoshanense, Inocybe avellaneorosea, I. lucida, Jahnula oblonga, Kevinia lignicola, Kirschsteiniothelia guangdongensis, Laboulbenia caprina, L. clavulata, L. cobiae, L. cosmodisci, L. nilotica, L. omalii, L. robusta, L. similis, L. stigmatophora, Laccaria rubriporus, Lasiodiplodia morindae, Lyophyllum agnijum, Marasmiellomycena pseudoomphaliiformis, Melomastia beihaiensis, Nemania guangdongensis, Nigrograna thailandica, Nigrospora ficuum, Oxydothis chinensis, O. yunnanensis, Petriella thailandica, Phaeoacremonium chinensis, Phialocephala chinensis, Phytophthora debattistii, Polyplosphaeria nigrospora, Pronectria loweniae, Seriascoma acutispora, Setoseptoria bambusae, Stictis anomianthi, Tarzetta tibetensis, Tarzetta urceolata, Tetraploa obpyriformis, Trichoglossum beninense, and Tricoderma pyrrosiae. We provide an emendation for Urnula ailaoshanensis Agaricus duplocingulatoides var. brevisporus introduced as a new variety based on morphology and phylogeny.
Amylascus is a genus of ectomycorrhizal truffles within Pezizaceae that is known from Australia and contains only two described species, A. herbertianus and A. tasmanicus . Species of Amylascus are closely related to truffles ( Pachyphlodes , Luteoamylascus ) and cup fungi ( Plicariella ) from the Northern Hemisphere. Here we reevaluate the species diversity of Amylascus and related taxa from southern South America and Australia based on new morphological and molecular data. We identify previously undocumented diversity and morphological variability in ascospore color, ascospore ornamentation, hymenial construction, epithecium structure and the amyloid reaction of the ascus in Melzer’s reagent. We redescribe two Amylascus species from Australia and describe seven new Amylascus species, five from South America and two from Australia. This is the first report of Amylascus species from South America. We also describe the new South American genus Nothoamylascus as sister lineage to the Pachyphlodes - Amylascus - Luteoamylascus clade (including Amylascus , Luteoamylascus , Pachyphlodes , and Plicariella ). We obtained ITS sequences of mitotic spore mats from Nothoamylascus erubescens gen. & sp. nov. and four of the seven newly described Amylascus species, providing the first evidence of mitotic spore mats in Amylascus . Additional ITS sequences from mitotic spore mats reveal the presence of nine additional undescribed Amylascus and one Nothoamylascus species that do not correspond to any sampled ascomata. We also identify three additional undescribed Amylascus species based on environmental sequences from the feces of two ground-dwelling bird species from Chile, Scelorchilus rubecula and Pteroptochos tarnii . Our results indicate that ascomata from Amylascus and Nothoamylascus species are rarely collected, but molecular data from ectomycorrhizal roots and mitotic spore mats indicate that these species are probably common and widespread in southern South America. Finally, we present a time-calibrated phylogeny that is consistent with a late Gondwanan distribution. The time since the most recent common ancestor of: 1) the family Pezizaceae had a mean of 276 Ma (217–337 HPD); 2) the Amylascus - Pachyphlodes - Nothoamylascus - Luteoamylascus clade had a mean of 79 Ma (60–100 HPD); and 3) the Amylascus - Pachyphlodes clade had a mean of 50 Ma (38–62 HPD). The crown age of Pachyphlodes had a mean of 39 Ma (25–42 HPD) and Amylascus had a mean age of 28 Ma (20–37 HPD), falling near the Eocene-Oligocene boundary and the onset of the Antarctic glaciation (c. 35 Ma).
The brown cupulate saddle fungi with villus surface in China, have long been named as Helvella macropus, a well-known European and North American species. In this study, Helvella fruiting bodies from Austria, China (the Tibetan Plateau), and Germany were examined. Phylogenetic analyses of combined LSU, TEF and HSP90 sequence data showed that the Chinese H. macropus-like samples represent two phylogenetic species, one of which is H. macropus s.s., and the other is H. guttata, which is introduced as new species here. Helvella guttata and H. macropus are described and illustrated in detail and compared with their similar species. In addition, a key to the morphologically recognizable taxa of the H. macropus complex is provided.
Helvella lacunosa and its allies are widely distributed in the Northern Hemisphere and perform important functions in ecosystems. A comprehensive study on 101 collections of Helvella lacunosa, including those deposited in four Chinese fungaria or collected recently from 10 provinces, was conducted based on morphological and molecular characteristics. Phylogenies of "Helvella la-cunosa clade" inferred from Hsp90, ITS, LSU, and TEF were reconstructed with 49 lineages recognized, of which 25 lineages occurred in China, and each represented an individual species. Sixteen new species were determined with detailed descriptions and illustrations. Two new Chinese records were reported. Species concepts and their distinctions in macro-and micro-features were discussed.
Three new genera, six new species, three combinations, six epitypes, and 25 interesting new host and / or geographical records are introduced in this study. New genera: Neoleptodontidium (based on Neoleptodontidium aquaticum), and Nothoramularia (based on Nothoramularia ragnhildianicola). New species: Acremonium aquaticum (from cooling pad water, USA, Cladophialophora laricicola (on dead wood of Larix sp., Netherlands), Cyphellophora neerlandica (on lichen on brick wall, Netherlands), Geonectria muralis (on moss growing on a wall, Netherlands), Harposporium illinoisense (from rockwool, USA), and Neoleptodontidium aquaticum (from hydroponic water, USA). New combinations: Cyphellophora deltoidea (based on Anthopsis deltoidea), Neoleptodontidium aciculare (based on Leptodontidium aciculare), and Nothoramularia ragnhildianicola (based on Ramularia ragnhildianicola). Epitypes: Cephaliophora tropica (from water, USA), Miricatena prunicola (on leaves of Prunus serotina, Netherlands), Nothoramularia ragnhildianicola (on Ragnhildiana ferruginea, parasitic on Artemisia vulgaris, Germany), Phyllosticta multicorniculata (on needles of Abietis balsamea, Canada), Thyronectria caraganae (on twigs of Caragana arborescens, Ukraine), and Trichosphaeria pilosa (on decayed Salix branch, Netherlands). Furthermore, the higher order phylogeny of three genera regarded as incertae sedis is resolved, namely Cephaliophora (Ascodesmidaceae, Pezizales), Miricatena (Helotiales, Leotiomycetes), and Trichosphaeria (Trichosphaeriaceae, Trichosphaeriales), with Trichosphaeriaceae being an older name for Plectosphaerellaceae.
Citation: Crous PW, Akulov A, Balashov S, Boers J, Braun U, Castillo J, Delgado MA, Denman S, Erhard A, Gusella G, Jurjević Ž, Kruse J, Malloch DW, Osieck ER, Polizzi G, Schumacher RK, Slootweg E, Starink-Willemse M, van Iperen AL, Verkley GJM, Groenewald JZ (2023). New and Interesting Fungi. 6. Fungal Systematics and Evolution 11: 109–156. doi: 10.3114/fuse.2023.11.09
Species of Discinaceae are common macrofungi with a worldwide distribution. Some of them are commercially consumed, while a few others are reported as poisonous. Two genera were accepted in the family: the epigeous Gyromitra with discoid, cerebriform to saddle-shaped ascomata and the hypogeous Hydnotrya with globose or tuberous ascomata. However, due to discrepancies in their ecological behaviors, a comprehensive investigation of their relationship was not thoroughly explored. In this study, phylogenies of Discinaceae were reconstructed using sequence analyses of combined and separate three gene partitions (internal transcribed spacer [ITS], large subunit ribosomal DNA [LSU], and translation elongation factor [TEF]) with a matrix containing 116 samples. As a result, the taxonomy of the family was renewed. Eight genera were recognized: two of them (Gyromitra and Hydnotrya) were retained, three (Discina, Paradiscina, and Pseudorhizina) were revived, and three (Paragyromitra, Pseudodiscina, and Pseudoverpa) were newly established. Nine new combinations were made in four genera. Two new species in Paragyromitra and Pseudodiscina and an un-named taxon of Discina were described and illustrated in detail based on the materials collected from China. Furthermore, a key to the genera of the family was also provided.
IMPORTANCE Taxonomy of the fungal family Discinaceae (Pezizales, Ascomycota) was significantly renewed on the basis of sequence analyses of internal transcribed spacer (ITS), large subunit ribosomal DNA (LSU), and translation elongation factor (TEF). Eight genera were accepted, including three new genera; two new species were described; and nine new combinations were made. A key to the accepted genera of the family is provided. The aim of this study is to deepen the understanding of the phylogenetic relationships among genera of the group, as well as the associated generic concepts.
Garry oak (Quercus garryana Douglas ex Hook.) is the only oak native to British Columbia (BC), where it occupies the northernmost extent of its range. The ecosystem it occupies in BC has been greatly reduced in size and fragmented by European settlement. Garry oak forms ectomycorrhizas that are essential to its existence and will likely play an important role in the response of this tree to climate change. Yet, relatively little is known about the ectomycorrhizal fungi associated with Garry oak in BC. In this study, we have documented the occurrence of fungi forming ectomycorrhizas with Garry oak at six locations on Vancouver Island by sequencing the internal transcribed spacer region of ectomycorrhizal root tips collected from Garry oak stands. Of the 47 species we detected, only about 20% can be confidently assigned to known species because not all species have been sequenced and many sequences in public databases are incorrectly or incompletely identified, but the majority of them belong to a community of fungi associated primarily with oaks or other members of Fagaceae. The uniqueness of this community of ectomycorrhizal fungi indicates that the possible expansion of the range of Garry oak in BC in response to climate change may be limited by the co-migration of its ectomycorrhizal fungi.
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 replacement of chemical fertilizer with organic fertilizer has been shown to boost soil fertility and crop yield. However, there is limited information on fertilization schemes suitable for sustainable production in rice-broad bean-rice-garlic rotation system. The goal of this research was to explore the transformations in microbial community compositions and networks under different types of fertilization in the garlic season with a reasonable fertilization, leading to determine the best fertilization scheme suitable for long-term deployment of garlic season. A long-term field test (2015–2021) was performed in a rice-broad bean-rice-garlic rotation system using four treatments: CK, without fertilizer; CF, chemical fertilizer only; T40, 40 % of chemical nitrogen replaced by organic fertilizer; T100, 100 % of chemical nitrogen replaced by organic fertilizer. The results showed that long-term use of T40 not only increased the levels of soil nutrients (carbon and nitrogen) and stabilized the pH but also had a positive effect on garlic yield compared with CF. Appling organic fertilizers increased the diversity of bacteria but reduced fungal diversity, which may be related to the rotation pattern. Organic fertilizers (T40, T100) also increased the relative abundance of beneficial microbes, which promoted nutrient cycling and plant growth. However, the application of chemical fertilizers alone (CF) or large amounts of organic fertilizer (T100) for extended times promoted the growth of methanogens, which might lead to increased CH4 emissions. The potentially favorable microbes (Pseudaleuria, Mortierella, and Lophotrichus) were positively associated with garlic yield, shown by Spearman's correlation analysis. Organic fertilizer enhanced the complexity of the soil bacterial and archaeal co-occurrences/interactions and stimulated competitive relationships between bacteria, as shown by network analysis. However, the fungal network showed the opposite trend, which may be related to the fact that organic fertilizers could provide more favorable growth conditions for saprophytic fungi. In summary, organic fertilizer used as a partial replacement for chemical fertilizer increased soil nutrient content and altered both the diversity and functions of soil microbial communities, thereby improving garlic productivity. It could be concluded that 40 % of the total nitrogen from organic fertilizers and the remaining 60 % from chemical fertilizers was a reasonable fertilization scheme for garlic in rice-broad bean-rice-garlic rotation system.
Rhizosphere-associated microbes have important implications for plant health, but knowledge of the association between the pathological conditions of soil-borne virus-infected wheat and soil microbial communities, especially changes in fungal communities, remains limited. We investigated the succession of fungal communities from bulk soil to wheat rhizosphere soil in both infected and healthy plants using amplicon sequencing methods, and attempted to assess their potential role in plant health. Fungal diversity and richness decreased significantly from the bulk soil to the wheat rhizosphere soil, and had fewer fungi in the bulk soil of infected plant than healthy plants. The structure differences in fungal community at the two wheat health statuses or two compartment niches were obvious, soil physicochemical properties (i.e., NH 4 ⁺ and soil organic carbon) contribute to differences in fungal community structure and alpha diversity. Comparison analysis showed Mortierellomycetes and Dothideomycetes are found as dominant communities in healthy wheat soils at class level. The genus Cystofilobasidium , Cladosporium , Mortierella and Stephanonectria are significantly enriched in bulk soil of healthy plant. Furthermore, co-occurrence network analysis showed that the fungi in healthy wheat soil has higher mutual benefit and connectivity compared with diseased wheat. In conclusion, we demonstrate that the occurrence of soil-borne viral diseases causes changes in the fungal community that depend on soil abiotic factors.
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.
Forty-one isolates of post-fire Ascomycetes, representing 1 species of Sphaeriales and 25 species of Pezizales, were tested for ability to hydrolyze amylose, amylopectin, gelatin, xylan, lipid, pectin, chitin, cellulose, and lignin. Isolates were also assayed for the presence of phenol oxidase enzymes: laccase, tyrosinase and peroxidase. The majority of isolates were able to degrade amylose, amylopectin, gelatin, and xylan, and were unable to utilize chitin. Cellulose, lignin, and pectin utilization showed the least variation between isolates of the same species. Pectin hydrolysis and phenol oxidase production were strongly influenced by the pH of the medium. Phenol oxidase production was identified in both saprotrophs and biotrophs. However, lignin degradation was primarily observed in the saprotrophs. It is hypothesized that phenol oxidases in post-fire Pezizales function in lignin degradation in saprotrophs, but function primarily in detoxification of host-produced phenols in biotrophs. Tests were able to identify guilds of fungi associated with non-lignified substrates (e.g. litter, fine roots) and lignified substrates (e.g. wood, woody roots). Tests also helped distinguish between saprotrophic and biotrophic modes of nutrition. The majority of post-fire Pezizales appear to be opportunistic decomposers or facultative biotrophs adapted to the transient post-fire environment.
Serpentine soils, rich in iron, magnesium, and heavy metals, select for unique plant communities and for endemic species.
Because mycorrhizal fungi mediate the interaction between plants and soil, we hypothesized that distinct ectomycorrhizal fungi
would colonize Quercus garryana roots on serpentine and nonserpentine soils. We sampled roots of Q. garryana on serpentine soils at two locations in the Klamath-Siskiyou Mountains of southwestern Oregon and identified ectomycorrhizas
by morphological and molecular methods. The same six most abundant and most frequent mycorrhizal species, Cenococcum geophilum, Tuber candidum, Genea harknessii, Tomentella sp., Sebacina sp., and Inocybe sp., were found on serpentine and nonserpentine soils. Based on similarities calculated using the Sørensen index in Non-metric
Multidimensional Scaling, mycorrhizal communities on serpentine and nonserpentine soils were not significantly different.
This study showed that ectomycorrhizal species associated with Q. garryana exhibit edaphic tolerance and were neither reduced nor excluded by serpentinite or peridotite parent materials.
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.
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.
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.
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.
The occurrence of 93 species of soil inhabiting Pezizales was studied on the basis of 699 site descriptions and soil samples, the latter analyzed for 15 edaphic variables. For species represented by 10 samples or more, the median value of each of the edaphic variables is given, and the range of pH, water soluble Al, CaCO3, and 0.2 N H2SO4–soluble P. For species represented by from 5 to 9 samples the range of pH and organic matter is given. 13 habitat types are described. The verges of forest roads proved to be the most important habitat type (247 sites, 57 species). The distribution in Denmark of 20 common species is compared with the geographical variation in quaternary and prequaternary geology, and with the distribution of soil types. It is concluded that the importance in the investigation area of disturbed ground as a habitat for soil inhabiting Pezizales is due to unleached mineral soil being brought to the surface, creating edaphic conditions favourable to a large number of species. – Although it is impossible, on the basis of the present investigation, to state definitively whether one or more edaphic variables are of particular importance in determining the occurrence of the species, there are certain indications that pH – and in some cases organic matter – are of special significance. A grouping of the species into five ecological groups on the basis of the median value of pH and organic matter is proposed. The habitats of soil inhabiting Pezizales in the investigation area and in other parts of the world are compared.
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.
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.
Coming back to Paris was an emotional experience for me, because it was 45 years ago as a graduate student I came on a pilgrimage to meet one of the most influential of people who have ever worked with discomycetes, Mme Marcelle LeGal. She greeted me and treated me with the kind of courtesy and interest that I hope all of us can express towards those who come green and wanting to learn. It was an experience I will never forget, and one which led me in future years to propose a genus Galiella in her honour, and to copropose Marcellina also in her honour, and on whose back many of us stand today. The other great figure of that period on whose contributions much of our classification lies is Jan A. Nannfeldt, another mycologist I met that same year in Uppsala where I went to meet and learn from him.
Genera that have been included in the family Thelebolaceae Eckblad are considered for the structure of the apical apparatuses of their asci. In the absence of such information, other characters could sometimes be used to clarify their most likely taxonomic position. The affinities of Cleistothelebolus, Coprobolus, Coprotiella, Dennisiopsis, Lasiobolidium, Lasiothelebolus, Leptokalpion, Mycoarctium, Ochotrichobolus, and Zukalina are discussed. The ultrastructure of ascus tops has been studied in Thelebolus microsporus, T. coemansii, T. caninus, T. crustaceus, T. polysporus, T. nanus, T. stercoreus, Caccobius minusculus, Lasiobolus pilosus, L. cuniculi, L. monascus, Ascozonus woolhopensis, A. solmslaubachii, Ramgea annulispora, Coprotus lacteus, and Trichobolus zukalii. At least six different types of asci can be distinguished within the fungi studied by electron microscopy. (1) The first (typical) Thelebolus type, in Thelebolus microsporus, T. crustaceus, T. stercoreus, Caccobius, Ramgea, and Pseudascozonus, opening after splitting within the inner wall layer in the apex, mostly accompanied by a central apical thickening. (2) The second Thelebolus type, in T. caninus and T. polysporus, with a breakdown of the inner layer in the apex above the subapical ring, followed by an irregular tear in the outer layer. (3) The third Thelebolus type, in T. microsporus and T. coemansii, with an irregular operculum just above the subapical ring. (4) The Ascozonus type, restricted to Ascozonus, with a very prominent subapical ring and a very small operculum. (5) The Trichobolus type, restricted to the uni-ascal multi-spored genera Trichobolus and Leptokalpion, without any trace of a subapical ring or weakened zone, showing a very large operculum or an irregular tear, caused by a regular retraction of the outer layer from a circular apical region. (6) The asci of Lasiobolus and Coprotus agree with the earlier defined Octospora type. New combinations were necessary for Thelebolus coemansii and Ascozonus solms-laubachii.
Boubovia vermiphila spec. nov. (Pezizales) is described from the mycologically interesting Hvaler archipelago in southern Norway, occurring on casts of earthworms. The relationship with Pulvinula and Boubovia luteola is discussed. Some distinctive characters between Pulvinula and Boubovia are considered.
Parasitism is extremely rare within the order Pezizales, but some genera include obligate parasites of moss. Parasitism on mosses is a generic character of Lamprospora, Neottiella, Octospora and Octosporella, and is correlated with morphological and anatomical characters. The paper considers host mosses, and their taxonomic and ecological position, as well as the moss communities that include host mosses. -from Author
Some of the most revolutionary changes in the systematics of various divisions of algae and certain classes of fungi were the results of unique differences found in the ultrastructure of septa. Among the fungi, septal ultrastructure has played a significant role in helping to delineate classes and subclasses of basidiomycetes. The application of septal ultrastructure to ascomycete systematics has been limited. Yet, there are strikingly different types of septal pore organelles in various groups of ascomycetes. This presentation demonstrates that septal structures may be useful in delimiting various groups of ascomycetes. The major focus is on septal structures associated with asci, ascogenous hyphae, and excipular cells of families of Pezizales. The use of these characters to show phylogenetic linkages between the epigeous and hypogeous tuberalean Pezizales is demonstrated. Septa as taxonomic criteria in other groups of ascomycetes are also discussed.
A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing
methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform
(FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid
residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy
of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length.
Two different heuristics, the progressive method (FFT‐NS‐2) and the iterative refinement method (FFT‐NS‐i), are implemented
in MAFFT. The performances of FFT‐NS‐2 and FFT‐NS‐i were compared with other methods by computer simulations and benchmark
tests; the CPU time of FFT‐NS‐2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT‐NS‐i is over
100 times faster than T‐COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
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.
The rotifer-capturing fungus Cephaliophora muscicola has many systematic and nomenclatural problems. It was described originally as Lecophagus fasciculatus and classified as a Zygomycete. To address the systematic position of this fungus and to infer the phylogenetic relationsips within other hyphomycetes, we determined and analyzed 18S rDNA sequences of C. muscicola and several of its predacious and nonpredacious relatives. Our phylogenetic analyses indicate that C. muscicola forms a monophyletic clade with nematophagous hyphomycetes, such as Arthrobotrys spp. This result indicates that the predacious nature of these fungi might be plesiomorphic for this lineage. The nonpredacious species of Cephaliophora, including the type species C. tropica, are distantly related to this lineage. Therefore the rotifer-capturing species of Cephaliophora, C. muscicola and C. longispora, are transfered to the anamorphic genus Lecophagus, and we have emended the genus accordingly.
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. Mono- and 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.
The carbonicolous discomycete, Sphaerosporella brunnea, formed ectomycorrhizae with jack pine (Pinus banksiana) in monoxenic cultures and in open containers. In addition, mycorrhizae were formed with species of Picea, Larix, and Populus. The mycorrhizae were characterized by thin mantles and large diameter hyphal cells with Woronin bodies at the septa. Sphaerosporella brunnea is unusual as a mycorrhizal symbiont due to its taxonomic position, carbonicolous nature, very rapid growth rate, and ease of ascospore germination.
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.
British species of Octosporella are considered and a new genus Filicupula is proposed to accommodate Pseudonectria suboperculata (syn. Octosporella suboperculata) based on a revision of the type collection.
Sporocarpic tissues of Glaziella aurantiaca were examined with light and electron microscopy in order to gain information on the possible teleomorphic nature of the fungus. The results from light microscopic studies indicate that the spores, which were presumed to be chlamydospores by earlier investigators, are actually ascospores that develop in unispored asci. The asci arise in locules from pockets of pseudoparenchyma within the thin walls of the sporocarps. Plasmogamy is presumably by hyphal conjugation. The sporocarpic hyphae are regularly septate and the septa are quite typical of ascomycetes, with electron-opaque material plugging a central pore and one or more associated Woronin bodies. The spore wall has a thick inner and thin outer wall, separated by a relatively complex zone of transition. Both walls are of a uniform granular consistency at the EM level. The outer wall is, in part, fused to the surrounding hyphae of the sporocarp. The spore cytoplasm has abundant glycogen deposits interspersed with lipid globules. Silver proteinate and barium permanganate post-staining observations were made on hyphae, septa, spore walls and cytoplasm. A new order, the Glaziellales, and a new family, the Glaziellaceae, are proposed for Glaziella aurantiaca, since it cannot be comfortably accommodated in any existing order of fungi. Its possible relationships to other fungi and possible mycorrhizal status are discussed.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
The qualitative and quantitative composition of the carotenoids of Plectania coccinea (Scop. ex Fr.) Fuck., is reported. Beside β-carotene (I) four new carotenoids, plectaniaxanthin (V), plectaniaxanthin-2′-ester (IV), plectaniaxanthin-1′,2′-diester (II) and 2′-dehydro-plectaniaxanthin-1′-ester (III), were isolated. The chemical structures of these carotenoids were established by chemical and physical methods, including direct comparison with synthetic V and VIII. The smooth hydrolysis of the tertiary esters is discussed.