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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.
... Ascospores are hyaline and vary in shape and ornamentation, in size, number of nuclei and lipid bodies; they can be globose to ellipsoid, sometimes fusoid, ovoid, also cylindrical, smooth or warted to spiny or reticulate, usually sheathless, but sheath occurring in some species such as Lotinia verna (Van Vooren et Vega 2018a), rarely with conical appendages, with very low to high lipid content. Anamorphs are known in many species and are hyphomycetous and blastic (Hansen et al. 2013, Jaklitsch et al. 2016, Ekanayaka et al. 2018, Döbbeler et al. 2021. ...
... Members of Pyronemataceae are mainly saprobic on all types of soil or dead plant material, but also develop on dung and burnt substrates. Some form ectomycorrhizal associations with vascular plants, some have been detected as symbionts of orchids (Hansen et al. 2013). Several Pyronemataceae are known to be bryoparasitic and are associated with mosses and liverworts (species in the genera Filicupula, Lamprospora, Neottiella, Octospora and Octosporopsis) (Egertová et al. 2015, Egertová et al. 2018. ...
... Several Pyronemataceae are known to be bryoparasitic and are associated with mosses and liverworts (species in the genera Filicupula, Lamprospora, Neottiella, Octospora and Octosporopsis) (Egertová et al. 2015, Egertová et al. 2018. Only Pyropyxis rubra has been recognised as a facultative pathogen of vascular plants (Hansen et al. 2013, Filippova et al. 2016). The family is mainly distributed from temperate to arctic-alpine regions, with a few taxa known from the tropics (Perry et al. 2007). ...
... 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.
... The remaining 11% were identified as Ascomycota, family Pezizaceae (Supporting Information, Table S10). Gomphonema are periphytic diatoms that attach to submerged surfaces, and Scutellinia are saprobic fungi that grow in soil and on wood (Guiry & Guiry, 2021;Hansen et al., 2013). There were no taxa with higher relative abundance in the communities exposed to MCA-treated wood compared with controls. ...
... There are 66 or more Scutellinia species that are widely distributed, especially in the Northern Hemisphere (Ainsworth, 2008). Scutellinia species are saprobic, growing in soil and mostly on wood (Hansen et al., 2013). Although Scutellinia are generally found in terrestrial subalpine regions, specimens have been documented on submerged wood in slowly moving freshwater streams in Oregon and elsewhere (Frank, 2014;Shearer, 1993). ...
Micronized copper azole (MCA) wood preservative formulations include Cu in nano form, and relatively little is known about longer‐term effects of Cu leached from MCA into wetland ecosystems. Here we tested the hypothesis that changes in soil microbiomes within reconstructed freshwater wetlands will be associated with exposure to elevated Cu concentrations originating from immersed MCA treated wood stakes. Eight replicate communities were assembled with Willamette Valley flood plain soil, and clonally propagated wetland plants within mesocosms. Inundated communities were equilibrated for 5 months before installation of MCA or control Southern Yellow Pine stakes (N=4 communities/experimental group). Soil samples were collected for 16S and ITS amplicon sequencing to quantify responses in prokaryotes and eukaryotes respectively at 15 timepoints, spanning 2 simulated seasonal dry downs, for up to 678 days. Physiochemical properties of water and soil were monitored at 20 and 12 timepoints respectively, over the same period. For both taxonomic groups of organisms, phylogenetic diversity increased and was positively correlated with elapsed days. Furthermore, there was significant divergence among eukaryotes during the second year based on experimental group. While the composition of taxa underwent succession over time, there was significantly reduced relative abundance of sequence variants from Gomphonema diatoms and Scutellinia fungi in communities where MCA wood stakes were present as compared to the controls. These focused microbiome shifts were positively correlated with surface water Cu and soil Cu concentrations, which were significantly elevated in treated communities. The reconstructed communities were effective systems for assessing potential impacts to wetland microbiomes after exposure to released copper. The results further inform post‐commercialization risk assessments on MCA treated wood. This article is protected by copyright. All rights reserved.
... Mykol., Prag: 149 (1842) Notes: This family produces hypogeous to epigeous ascomata with a variety of shapes, sessile to stalked, discoid to cupulate, turbinate to pulvinate, folded to solid. (Perry et al. 2007;Hansen et al. 2013;Pfister 2015a). In addition, members of this family are distinguished by inamyloid asci and smooth to ornamented ascospores (Pfister 2015a). ...
... More than 65 genera are included within this family, with around 50% of genera having available molecular data (Kajevska et al. 2013;Pfister 2015a;Ekanayaka et al. 2018). Recent phylogenies on the family were performed by Hansen et al. (2013) and Ekanayaka et al. (2018). ...
This is the twelfth contribution to the Fungal Diversity Notes series on fungal taxonomy, based on materials collected from many countries which were examined and described using the methods of morphology, anatomy, and strain culture, combined with DNA sequence analyses. 110 taxa are described and illustrated, including five new genera, 92 new species, eight new combinations and other taxonomic contributions (one new sequenced species, one new host and three new records) which are accommodated in 40 families and 1 incertae sedis in Dothideomycetes. The new genera are Amyloceraceomyces, Catenuliconidia, Hansenopezia, Ionopezia and Magnopulchromyces. The new species are Amyloceraceomyces angustisporus, Amylocorticium ellipsosporum, Arthrinium sorghi, Catenuliconidia uniseptata, Clavulina sphaeropedunculata, Colletotrichum parthenocissicola, Coniothyrium triseptatum, Cortinarius indorusseus, C. paurigarhwalensis, C. sinensis, C. subsanguineus, C. xiaojinensis, Diaporthe pimpinellae, Dictyosporella guizhouensis, Diplodia torilicola, Fuscoporia marquesiana, F. semiarida, Hansenopezia decora, Helicoarctatus thailandicus, Hirsutella hongheensis, Humidicutis brunneovinacea, Lentaria gossypina, L. variabilis, Lycoperdon lahorense, L. pseudocurtisii, Magnopulchromyces scorpiophorus, Moelleriella gracilispora, Neodevriesia manglicola, Neodidymelliopsis salvia, N. urticae, Neoroussoella magnoliae, Neottiella gigaspora, Ophiosphaerella chiangraiensis, Phaeotremella yunnanensis, Podosphaera yulii, Rigidoporus juniperinus, Rhodofomitopsis pseudofeei, Russula benghalensis, Scleroramularia vermispora, Scytinopogon minisporus, Sporormurispora paulsenii, Thaxteriellopsis obliqus, Tomentella asiae-orientalis, T. atrobadia, T. atrocastanea, T. aureomarginata, T. brevis, T. brunneoflava, T. brunneogrisea, T. capitatocystidiata, T. changbaiensis, T. citrinocystidiata, T. coffeae, T. conclusa, T. cystidiata, T. dimidiata, T. duplexa, T. efibulata, T. efibulis, T. farinosa, T. flavidobadia, T. fuscocrustosa, T. fuscofarinosa, T. fuscogranulosa, T. fuscopelliculosa, T. globospora, T. gloeocystidiata, T. griseocastanea, T. griseofusca, T. griseomarginata, T. inconspicua, T. incrustata, T. interrupta, T. liaoningensis, T. longiaculeifera, T. longiechinuli, T. megaspora, T. olivacea, T. olivaceobrunnea, T. pallidobrunnea, T. pallidomarginata, T. parvispora, T. pertenuis, T. qingyuanensis, T. segregata, T. separata, T. stipitata, T. storea, Trichoderma ceratophylletum, Tyromyces minutulus, Umbelopsis heterosporus and Xylolentia reniformis. The new combinations are Antrodiella descendena, Chloridium macrocladum, Hansenopezia retrocurvata, Rhodofomitopsis monomitica, Rh. oleracea, Fuscoporia licnoides, F. scruposa and Ionopezia gerardii. A new sequenced species (Graphis supracola), one new host (Aplosporella prunicola) and three new geographical records (Golovinomyces monardae, Paradictyoarthrinium diffractum and Prosthemium betulinum), are reported.
... 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.
... 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., NH 4 ⁺ ) 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 NH 4 ⁺ 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 its effect on fungal communities in arable soil.
Results:
p-CA showed the best antifungal activity. Coating seeds of common crop plants with p-CA-based preparation resulted in a significant reduction of growth of most of the tested pathogens. When applied to soil, both 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 any of the times examined. Shifts in the fungal community composition concerned less than 2 % of the total number of 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, as well as unidentified ASV from Diversisporales encompassing the arbuscular mycorrhizal fungi (AMF), were significantly depleted in soil samples treated with p-CA compared to Porter 250 EC.
Conclusion:
p-CA-based preparation has the potential to be used as an alternative to synthetic fungicides. It shows a similar effect on the organization of soil communities determining changes in the character of the communities of fungi in general as compared to PORTER 250 EC at a given time. Moreover, p-CA caused a reduction of ASVs belonging to Botrytis and Chromelosporium (plant pathogens) and ASVs of Diversisporales (containing arbuscular mycorrhizal fungi) compared to the analyzed commercial compound. This article is protected by copyright. All rights reserved.
... 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.
... What we do know is that this relationship is obligate (Döbbeler 1980) and that the hosts rarely seem to be weakened by the fungi. Today, there are well above one hundred known species of these so-called ‚bryophilous' or ‚bryoparasitic Pezizales' (Janošík 2020, Eckstein 2021, Kirk 2021, which are all closely related and probably form a monophyletic clade (Hansen et al. 2013, Janošík 2020. Bryophilous Pezizales received much attention in the late 19 th and early 20 th century when many species were described by Jean Louis Émile Boudier (1828 -1920), Fred Jay Seaver and Josef Velenovský (1858 -1949), but this was followed by a period during which new species were described at a much lower rate. ...
Eckstein, J., Sochorová, Z. & Janošík, L. 2021. Octospora oscarii spec. nov. (Pezizales), a bryophilous ascomycete on the pleurocarpous moss Pseudotaxiphyllum elegans (Hypnales). – Herzogia 34: 286 –298. The bryophilous ascomycete Octospora oscarii is described as a new species based on collections from Central Germany and the Czech Republic. It grows on the pleurocarpous moss Pseudotaxiphyllum elegans and is characterised by smooth ascospores and an infection on the rhizoids of its host. This is the first account of P. elegans as a host of bryophilous ascomycetes. Phylogenetic analyses of concatenated LSU, SSU and EF1-α gene sequences showed that the studied collections of this species form a well-supported monophyletic lineage differing from all previously studied species of bryophilous Pezizales. Macroscopic and microscopic features of the new species are illustrated by colour photographs and drawings, and are compared to those of the other species of bryophilous Pezizales similarly growing on pleurocarpous mosses.
... The most abundant OTUs in Table 5 is Pseudaleuria sp. (9.76%), belonging to the Pyronemataceae, whose members are often ectomycorrhizal symbionts [99]. Moreover, Pseudaleuria was found to be particularly abundant in healthy soils [100] and to have a negative correlation with the disease severity index of roots of Pisum sativum L. [101]. ...
In Colombia, the cultivation of deciduous fruit trees such as pear is expanding for socio-economic reasons and is becoming more and more important for the local population. Since organized cultivation is slowly replacing sustenance cultivation, scientific information on the present agro-environment is needed to proceed in this change in an organic and environmentally friendly way. In particular, this study is an accurate description of the mycobiota present in the bulk soil of two different high altitude pear orchards in the Colombian Andes. The metabarcoding of soil samples allowed an in-depth analysis of the whole fungal community. The fungal assemblage was generally dominated by Ascomycota and secondly by Mortierellomycota. As observed in other studies in Colombia, the genus Mortierella was found to be especially abundant. The soil of the different pear orchards appeared to host quite different fungal communities according to the soil physico-chemical properties. The common mycobiota contained 35 fungal species, including several species of Mortierella, Humicola, Solicoccozyma and Exophiala. Moreover, most of the identified fungal species (79%) were recorded for the first time in Colombian soils, thus adding important information on soil biodiversity regarding both Colombia and pear orchards.
... Perry et al. (2007) were the first to notice that Warcupia terrestris is phylogenetically nested within the family Pyronemataceae, despite its cleistothecioid habit. Later, HAnSen et al. (2013) reported that Warcupia is closely related to the highly reduced (gymnohymenial) genus Monascella Guarro & Arx, both forming a sister clade to the mainly apothecial genus Otidea (Pers.) Bonord. ...
The name Warcupia cupulata is here proposed for an apothecioid species described for the first time upon Greek, italian and Spanish collections probably associated with Cupressus, and the formerly cleis-tothecioid genus Warcupia is consequently amended. images of fresh samples and their main microscopical characters are provided, as well as phylogenetic analyses based on iTS rdnA sequences, and a combined dataset including 28S rdnA, tef1 and rpb2 data. Homologous sequences of the related genera Acervus and Arpinia were produced and published to support the phylogenetic study.
Riassunto: il binomio Warcupia cupulata viene qui proposto per una specie nuova apotecioide a seguito di raccolte effettuate in Grecia, italia e Spagna probabilmente associate a Cupressus; conseguentemente viene emendato il genere cleistotecioide Warcupia. Vengono proposte foto di esemplari freschi e di micro-scopia, nonché due analisi filogenetiche basate sull'iTS solamente e su un allineamento combinato dei mar-catori LSU, tef1 e rpb2. infine, al fine di supportare lo studio filogenetico, sono state prodotte e pubblicate sequenze omologhe di specie appartenenti ai generi Acervus e Arpinia.
Περίληψη: Η ονομασία Warcupia cupulata προτείνεται για ένα καινούργιο για την επιστήμη είδος με μορφή αποθήκιου, πιθανά συσχετιζόμενο με Κυπαρίσσια, που περιγράφεται από Ελληνικές, Ιταλικές και Ισπανικές συλλογές, και κατά συνέπεια το παλαιότερο γένος κλειστοθήκιων Warcupia τροποποιείται. Επισυνάπτεται εικονογραφία από φρέσκα δείγματα στο πεδίο μαζί με τα κύρια μικροσκοπικά χαρακτηριστικά τους, καθώς και φυλογενετικές αναλύσεις με βάση τόσο το iTS, όσο και συνδυασμένη ανάλυση των γονιδίων LSU, tef1 και rpb2. Ομόλογες ακολουθίες των σχετικών γενών Acervus και Arpinia δημοσιεύονται επιπρόσθετα για να υποστηρίξουν τη φυλογενετική μελέτη. λέξεις-κλειδιά: Acervus, Arpinia, Ascomycota, Pyronemataceae, φυλογενετική ανάλυση, ταξινόμιση.
... They produce hyphae that are attached to living rhizoids via appressoria with intracellular haustoria [39]. Previous research has suggested that these fungi are likely to obtain some nutrients from their host [20,40]. ...
Wildfires play a critical role in maintaining biodiversity and shaping ecosystem structure in fire-prone regions, and successional patterns involving numerous plant and fungal species in post-fire events have been elucidated. Evidence is growing to support the idea that some post-fire fungi can form endophytic/endolichenic relationships with plants and lichens. However, no direct observations of fire-associated fungal–moss interactions have been visualized to date. Therefore, physical interactions between a post-fire fungus, Pholiota carbonaria, and a moss, Polytrichum commune, were visually examined under laboratory conditions. Fungal appressoria were visualized on germinating spores and living protonemata within two weeks of inoculation in most growth chambers. Appressoria were pigmented, reddish gold to braun, and with a penetration peg. Pigmented, reddish gold to braun fungal hyphae were associated with living tissue, and numerous mature rhizoids contained fungal hyphae at six months. Inter-rhizoidal hyphae were pigmented and reddish gold to braun, but no structures were visualized on mature gametophyte leaf or stem tissues. Based on our visual evidence and previous work, we provide additional support for P. carbonaria having multiple strategies in how it obtains nutrients from the environment, and provide the first visual documentation of these structures in vitro.
... (Gryndler et al., 2014;Schneider-Maunoury et al., 2018. In addition, some suspicion exists, based on molecular detection only, for Thelephoraceae and Inocybaceae , Pyronemataceae (Hansen et al., 2013) and Helotiales (Wang et al., 2006). Such a dual, EM and endophytic interaction has been viewed as a persistence of the evolutionary past of EM fungi, if they evolved from endophytic species: in the so-called 'waiting room hypothesis', endophytism is considered as a niche from which the tighter and more elaborate mycorrhizal symbiosis can evolve Selosse et al., 2009;van der Heijden et al., 2015). ...
Stinging nettle (Urtica dioica L.) raises growing interest in phytomanagement because it commonly grows under poplar Short Rotation Coppices (SRC) set up at trace-metal (TM) contaminated sites and provides high-quality herbaceous fibres. The mycobiome of this non-mycorhizal plant and its capacity to adapt to TM-contaminated environments remains unknown. This study aimed at characterizing the mycobiome associated with nettle and poplar roots co-occurring at a TM-contaminated site. Plant root barcoding using the fungi-specific ITS1F-ITS2 primers and Illumina MiSeq technology revealed that nettle and poplar had distinct root fungal communities. The nettle mycobiome was dominated by Pezizomycetes from known endophytic taxa and from the supposedly saprotrophic genus Kotlabaea (which was the most abundant). Several ectomycorrhizal fungi such as Inocybe (Agaricomycetes) and Tuber (Pezizomycetes) species were associated with the poplar roots. Most of the Pezizomycetes taxa were present in the highly TM-contaminated area whereas Agaricomycetes tended to be reduced. Despite being a known non-mycorrhizal plant, nettle was associated with a significant proportion of ectomycorrhizal OTU (9.7%), suggesting some connexions between the poplar and the nettle root mycobiomes. Finally, our study raised the interest in reconsidering the fungal networking beyond known mycorrhizal interactions.
... accounting for almost a quarter of the total number of sequence reads. The Pyronemataceae family, shown to be one of the major dominants in the AEl horizon and the first-ranked in abundance in the lower horizons, are very diverse ecophysiologically [48]; in this study, the family was represented by three explicitly classified genera, namely Wilcoxina, Tarzetta, and Boubovia, all being common mycorrhizal fungi [49]. However, their dominance was not associated with subsoil environments before. ...
Vast areas of land in the forest-steppe of West Siberia are occupied by birch forests, the most common ecosystems there. However, currently, little is known about the microbiome composition in the underlying soil, especially along a sequence of soil genetic horizons. The study aimed at inventorying microbiome in genetic horizons of a typical Phaeozem under undisturbed birch forest in West Siberia. Bacteria and fungi were studied using 16S rRNA genes’ and ITS2 amplicon sequencing with Illumina MiSeq. Proteobacteria and Acidobacteria together accounted for two-thirds of the operational taxonomic units (OTUs) numbers and half of the sequences in each genetic horizon. Acidobacteria predominated in eluvial environments, whereas Proteobacteria, preferred topsoil. The fungal sequences were dominated by Ascomycota and Basidiomycota phyla. Basidiomycota was the most abundant in the topsoil, whereas Ascomycota increased down the soil profile. Thelephoraceae family was the most abundant in the A horizon, whereas the Pyronemataceae family dominants in the AEl horizon, ultimately prevailing in the subsoil. We conclude that soil genetic horizons shape distinct microbiomes, therefore soil horizontation should be accounted for while studying undisturbed soils. This study, representing the first description of bacterio- and mycobiomes in genetic horizons of the Phaeozem profile, provides a reference for future research.
... Species of the genus Trametes are well known for their ability to produce enzymes, which could assist in the defense of the plant against pathogens 36 . Similarly, species from Pezizomycetes have been reported to offer benefits to their host plants 37 . ...
Fungal endophytes have been increasingly recognized to promote host plant protection to pathogens, but knowledge of the multiple effects that they could have in crop diseases is still scarce. This work attempts to understand the role of fungal endophytes in crop diseases, specifically in reducing disease development and interfering on lifestyle transition of the pathogen. To accomplish this, the endophytic fungal community of reproductive organs of olive tree from two orchards showing different levels of anthracnose incidence, a major disease of olive fruits, was characterized and compared between them. The two orchards showed distinct endophytic communities, differing in species richness, abundance and composition, with highest isolation rates and richness of endophytes in the orchard with low anthracnose incidence. These differences among orchards were greater on fruits than on flowers, suggesting that these changes in endophytic fungal composition may influence the lifestyle shifts in pathogen (from latent to pathogen). A number of fungal taxa were found to be positively associated to one of the two orchards. The fungal endophytes best correlated with high incidence of anthracnose are pathogens, while endophytes-associated to low anthracnose incidence are described to protect plants. Altogether, the results suggest varying pathogen–endophyte interactions among the two orchards.
... The genus Otidea was suggested as monophyletic as a result of many multilocus phylogenetic analyses (Hansen et al., 2013;Olariaga et al., 2015). Recent extensive multilocus phylogenetic studies on this genus were conducted by Hansen and Olariaga (2015) and Olariaga et al. (2015). ...
... Using internal transcribed spacer (ITS) rDNA sequence data, they suggested that G. arenicola, G. tenuis and G. sepulta are monophyletic and G. foliacea and G. cervina could not be explicitly delimited. Hansen et al. (2013) investigated the phylogenetic relationships of Pyronemataceae by sequencing several genomic loci. These authors determined that Geopora is phylogenetically related to Tricharina in the Scutellinia-Trichophaea lineage. ...
A new Geopora species (Pyronemataceae), Geopora ramila was described and illustrated from the soil, under or in the vicinity of Helianthemum ledifolium var. ledifolium annual plant in Fars province, Iran. Morphologically, G. ramila is similar to G. pinyonensis and G. arenicola but distinguished from both by a combination of morphological characters including, color and size of ascocarps, size and shape of ascospores, habit and associated host. The ribosomal DNA internally transcribed spacer (rDNA ITS) sequence of the new species (Acc. No. MT108930 to MT108934) showed 87.82% identity with G. pinyonensis in the BLAST search in GenBank. ITS-based phylogenetic analysis clearly supports G. ramila is a new and distinctive species lacking close relatives among described species of Geopora.
... mix of AM and EM associated species in pine savannas, and predominantly AM associated species in prairies). Yet in both systems, indicator species represented known thermo-and drought tolerant fungal species including such as Geminibasidium in burned Longleaf pine savanna plots, as well as rapid post-fire colonizers like Talaromyces (Sharma 1981;McMullan-Fisher et al. 2011) and Pyronemetaceae (Hansen et al. 2013) in the post-fire tallgrass prairie plots. In both sites, fires remove most aboveground plant biomass and left sites exposed to the wind and sun, which likely favored drought-tolerant taxa. ...
Fire alters microbial community composition, and is expected to increase in frequency due to climate change. Testing whether microbes in different ecosystems will respond similarly to increased fire disturbance is difficult though, because fires are often unpredictable and hard to manage. Fire recurrent or pyrophilic ecosystems, however, may be useful models for testing the effects of frequent disturbance on microbes. We hypothesized that across pyrophilic ecosystems, fire would drive similar alterations to fungal communities including altering seasonal community dynamics. We tested fire's effects on fungal communities in two pyrophilic ecosystems, a Longleaf pine savanna and tallgrass prairie. Fire caused similar fungal community shifts including a) driving immediate changes that favored taxa able to survive fire and take advantage of post-fire environments, and b) altering seasonal trajectories due to fire-associated changes to soil nutrient availability. This suggests that fire has predictable effects on fungal community structure and intra-annual community dynamics in pyrophilic ecosystems, and that these changes could significantly alter fungal function. Parallel fire responses in these key microbes may also suggest that recurrent fires drive convergent changes across ecosystems, including less fire frequented systems that may start burning more often.
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 .
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 ) 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 ITS 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.
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).
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.
The revision of type material of Lasiobolidium spirale, type of the genus Lasiobolidium, is presented and illustrated with colour photographs for the first time. We also present the discovery of a new species, named Lasiobolidium mercantourense. Morphological and molecular data of this species are given, as well as a comparison with closest species. Finally, an updated key to Lasiobolidium is provided.
Sphaerosporella microspora is described as a new species based on morphological and molecular data. It is characterized by its sessile apothecia, surface smooth, ectal excipulum composed of cylindrical and angular cells, globose and smooth ascospores, and unmodified paraphyses. A detailed description, photographs of the fruit body and microstructure diagrams are provided.
Plastic film mulching (PF) can change soil properties and microbial community structure. However, the effect of PF on soil microbial interactions in different aggregate fractions is still unclear. We conducted a three-year field trial in black soil of northeastern China to evaluate the variation in soil microbial interactions and community structure in different aggregate fractions after PF. Compared with the control (CK), the PF treatment significantly decreased the humification index by 13.9% and chromophoric dissolved organic matter by 36.6% and significantly increased the fractal dimension by 4.8% and electrical conductivity by 22.8%. In addition, the PF treatment significantly decreased the relative abundances of Chloroflexi, Planctomycetes and Verrucomicrobia but significantly increased the relative abundance (RA) of Proteobacteria. Furthermore, the PF treatment significantly decreased the RA of Glomeromycota in megaaggregates (>2 mm, ME) and macroaggregates (0.25–2 mm) and the RA of Actinobacteria in microaggregates (<0.25 mm, MI), related to decreases in aggregate stability. Compared with the CK treatment, the PF treatment significantly decreased the bacterial Shannon index in ME but significantly increased the fungal Shannon index in MI. Moreover, β-1,4-glucosidase activity significantly influenced the community structure of soil bacteria and fungi. The PF treatment decreased soil microbial interactions, especially in ME. The keystone of the microbial network shifted from 0319-6A21 (Nitrospirae) to Gsoil-1167 (Actinobacteria) after PF. In short, PF decreased soil aggregate stability and microbial interactions in black soil in a subhumid area.
This paper describes five sarcosomataceous samples collected from southwestern China and provides an updated two locus phylogeny of Sarcosomataceae. Two new species, Donadinia echinacea and Plectania sichuanensis, are described based on morphological and phylogenetic analyses. Donadinia echinacea is a dematiaceous hyphomycete with pleurogenous, guttulate conidia. Plectania sichuanensis is a cup-fungus distinguished by its ochre hymenium and ellipsoid ascospores with small multiple oil droplets. Phylogenetic analysis based on ITS and LSU sequence data using broad taxon sampling supports establishment of the new species along with eight distinct clades within Sarcosomataceae.
Recent collections of unknown Trichophaea-like discomycetes made in Europe enabled the authors to explore the taxonomy of Trichophaea and allies, based on morphological, ecological and molecular data. Our 3-gene phylogeny confirms the paraphyly of the genus Trichophaea and designs a new systematics for this group of cup-fungi. Three new genera are published to accommodate several species previously assigned to Trichophaea or morphologically close genera: Perilachnea gen. nov. with Lachnea hemisphaerioides as type-species, Aurantiolachnea gen. nov. with Lachnea solsequia as type-species, and Parawilcoxina gen. nov. with P. inexpectata sp. nov. as type-species. some species of the genus Paratrichophaea belong to the cleistothecial genus Lasiobolidium, and furthermore two new species, L. trachysporum and L. coprophilum, are described. Paratrichophaea macrocystis is also combined in Lasiobolidium. Finally, three new species of Chaetothiersia, C. laricina, C. cupressicola and C. eguttulata are described. a new species of Perilachnea, P. ochraceoflava, is outlined from Italy, and a new species of Trichophaeopsis, T. asturiensis, is described from Spain. A total of 15 species are described and illustrated herein. Keys are provided.
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.