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Comprehensive analysis of the volatilome of Scytinostroma portentosum
Abstract
Fruiting bodies of the corticoid fungus Scytinostroma portentosum, known as mothball crust, have been sampled from a dead branch of sallow. Volatile organic compounds of the samples were extracted by means of liquid/liquid extraction and purified by solvent assisted flavour evaporation. In addition, solid-phase microextraction was applied on one fruiting body sample. The odour active compounds were identified by gas chromatography-mass spectrometry and olfactometry on two columns of different polarity and described by sensory detection. Furthermore, an aroma extract dilution analysis was performed to identify the main flavour compounds. The main odour compounds of S. portentosum with an FD factors ≥16 were 3-chloroindole responsible for the typical mothball odour, the mushroom odours oct-1-en-3-ol and oct-1-en-3-one, methyl p-anisate having an anise-like smell, the bloomy and sweet smelling terpenes linalool and nerolidol, as well as benzylacetone and methyl hexadecanoate. Herewith, a comprehensive aroma active volatilome of S. portentosum is presented.
... The VOC profile of individual fungal species or strain varies depending on the cultivation medium, type of nutrients, incubation time temperature as well as other environmental parameters (Morath et al., 2012). The source of knowledge about VOCs comes from a variety of disciplines, see Fig. 2. Ruhl et al. (2018) presented comprehensive aroma active volatilome of the corticoid fungus Scytinostroma portentosum; as main odor compounds 3-chloroindole, oct-1-en-3-ol, oct-1-en-3-one, methyl 4-methoxybenzoate, linalool, nerolidol, benzylacetone and methyl hexadecanoate were estimated. Eight fungal VOCs including acetoin, ethyl acetate, cisgrandisol, 3-methylbutan-1-ol, 2-methyl-propan-1-ol, 2-methylbutan-1-ol, 2-phenylethyl acetate, and 2-phenylethanol produced by two ophiostomatoid fungi, Grosmannia clavigera and Ophiostoma ips, were identified. ...
Fungi are undoubtedly one of the most widespread groups of organisms on Earth. In addition to their multiple uses in various areas of human activities, fungi produce numerous volatile organic compounds (VOCs) based on hydrocarbons, alcohols, phenols, amines, carbonyl and carboxyl derivatives and heterocycles. These VOCs are able to affect both the surrounding organisms and the quality of the environment. This chapter provides an up-to date overview of the most important VOCs emitted by various not only microscopic fungi (including yeasts and molds, with increased attention being paid to Trichoderma spp.), but also macroscopic fungi (mushrooms). Negative effects of mixtures of VOCs emitted by fungi as well as individual active volatile compounds on plant pathogens and insect pests are discussed, including the corresponding mechanism of action together with the beneficial effects of VOCs on plant growth and postharvest storage of crops. Attention is focused on the most important VOCs of fungi, which give them a special taste and aroma, and their use in the food industry with an emphasis on providing quality food and beverages, characterized by excellent sensory properties and extended shelf life.
... More than 300 distinct fungal volatile organic compounds (VOCs) have been identified so far, being in many cases aroma active (Dickschat 2017) that determine, e.g. the quality of edible fungal fruiting bodies. VOC profiles of several fungi have been analysed so far (Chen and Ho 1986;Costa et al. 2015;Dickschat 2017;Fraatz and Zorn 2011;Kleofas et al. 2015;Rühl et al. 2018;Venkateshwarlu et al. 1999). However, studies investigating volatilomes (the composition of all VOCs produced by a fungus during one time point) are often focusing on one developmental stage ignoring potential dynamics in VOC release. ...
In fungi, little is known about connections between volatile organic compound (VOC) formation and developmental stages that are amongst others triggered by fruiting-related genes (FRGs). We analysed the volatilomes of Schizophyllum commune during different developmental stages in a variety of FRG-deletion strains and wild-type strains. The deletion strains Δ tea1 Δ tea1 , Δ wc-2 Δ wc-2 and Δ hom2 Δ hom2 were unable to develop fruiting bodies, and Δ fst4 Δ fst4 formed only rudimentary fruiting body structures. Early developmental stages of these strains were dominated by esters, including methyl 2-methylbutanoate, ethyl 2-methylbutanoate, isobutyl 2-methylpropionate, and 2-methylbutyl acetate, of which the last three were not found in the headspace (HS) of the wild-type samples. Compared to the wild type, in the HS of hom2 con samples, that are able to form fruiting bodies, methyl 2-methylbutanoate was the most abundant substance at early stages (68–81% of the total peak area). In contrast to fruiting body forming strains, Δ tea1 Δ tea1 , Δ wc-2 Δ wc-2 , Δ hom2 Δ hom2 and Δ fst4 Δ fst4 showed less sesquiterpenes in the HS. However, the sesquiterpenes found in the HS of FRG-deletion strains, namely, ( E )-nerolidol, δ-cadinene, L-calamenene, α-bisabolol and β-bisabolene, were not present in hom2 con or wild-type strains that mainly formed fruiting bodies and barely mycelium. Several sesquiterpenes, including α-guaiene, chamigrene and γ-gurjunene, were only found in presence of fruiting bodies. Our results show remarkable connections between FRGs, fruiting body development and VOC production in S. commune , especially counting for sesquiterpenes. Future studies are needed to reveal whether FRGs directly regulates VOC formation or indirectly by changing the phenotype.
... In der heutigen Forschung geht dies bis hin zum "Volatilome", also der Gesamtheit der VOCs einer Art, die deren spezifischen Geruch ausmachen (z. B. Rühl et al. 2018). ...
Like almost all living beings, fungi produce many diverse odours, often rather conspicuous ones. Consequently, fungal odours serve as an identifying character. However, relevant information in the literature is often ambiguous. Moreover, not all mycologists or mushroomers are able to correctly classify fungal odours because odour perception is strongly affected by the social context.
The ecological functions of the scents are exceedingly diverse. They serve in the intra- and interspecific communication, which can take a cooperative or an antagonistic role. Especially the function of fragrance combinations (“bouquets”) is often unclear. This question and, in addition, the issue of guild-specific odour characteristics deserve further clarification, above all with molecular methods.
Filamentous fungi harbor the genetic potential for the biosynthesis of several secondary metabolites including various volatile organic compounds (VOCs). Nonetheless, under standard laboratory conditions, many of these VOCs are not formed. Furthermore, little is known about enzymes involved in the production of fungal VOCs. To tap these interesting topics, we developed an approach to identify enzymes putatively involved in the fungal VOC biosynthesis. In this chapter, we highlight different fungal cultivation methods and techniques for the extraction of VOCs, including a method that allows the noninvasive analysis of VOCs. In addition using terpene synthases as an example, it is depicted how enzymes putatively involved in VOC synthesis can be identified by means of bioinformatic approaches. Transcriptomic data of chosen genes combined with volatilome data obtained during different developmental stages is demonstrated as a powerful tool to identify enzymes putatively involved in fungal VOC biosynthesis. Especially with regard to subsequent enzyme characterization, this procedure is a target-oriented way to save time and efforts by considering only the most important enzymes.
Covering: up to September 2020
Mushroom-forming fungi of the division Basidiomycota have traditionally been recognised as prolific producers of structurally diverse and often bioactive secondary metabolites, using the methods of chemistry for research. Over the past decade, -omics technologies were applied on these fungi, and sophisticated heterologous gene expression platforms emerged, which have boosted research into the genetic and biochemical basis of the biosyntheses. This review provides an overview on experimentally confirmed natural product biosyntheses of basidiomycete polyketides, amino acid-derived products, terpenoids, and volatiles. We also present challenges and solutions particular to natural product research with these fungi. 222 references are cited.
This review presents, from a critical perspective, the most remarkable and recent applications of solid-phase microextraction (SPME) as a sample preparation tool for mass-spectrometry-based targeted and untargeted metabolomics and lipidomics. In this review, the advantages and disadvantages of SPME as an approach for extracting/enriching metabolites of interest, either in targeted or untargeted studies, are discussed. In addition, special attention is given to SPME’s suitability for use with in vivo and non-destructive sampling in order to capture a representative snapshot of the metabolome. Finally, future directions for further validating SPME’s applicability in the metabolomics field are highlighted.
A taxonomic monograph of the ascomycete genus Taeniolella (asexual dematiaceous hyphomycetes, sexual
morphs unknown) is provided. Recent phylogenetic analyses demonstrated the polyphyly of this genus. The type species
of Taeniolella pertains to the Kirschsteiniotheliaceae within Dothideomycetes, while other saprobic species clustered
far away within Sordariomycetes, Savoryellaceae s. lat., and Lindgomycetaceae, whereas lichenicolous species belong
to a monophyletic clade that represents the order Asterotexiales, but for most species assigned to Taeniolella sequence
data and phylogenetic analyses are not yet available. The main focus of the present taxonomic study was on a revision
of the lichenicolous Taeniolella species. Since the currently available phylogenetic analyses do not allow final taxonomic
conclusions at generic rank, the exclusion of lichenicolous species from Taeniolella s. lat. has been postponed pending a
broader sampling and more phylogenetic data of allied ascomycete genera within the order Asterotexiales. For the interim,
Taeniolella s. lat., including lichenicolous and saprobic species, is maintained. The taxonomic background, history, generic
description and discrimination from morphologically confusable genera, phylogeny, biology, host range and distribution,
and species concept of Taeniolella species are briefly outlined and discussed. Keys to the species of Taeniolella divided by
ecological groups (lichenicolous taxa, saprobic taxa) are provided, supplemented by a tabular key to lichenicolous species
based on host (lichen) families and genera. Twenty-nine lichenicolous species and a Taeniolella sp. (putative asexual
morph of Sphaerellothecium thamnoliae) as well as 16 saprobic species are described in detail and illustrated by drawings,
macroscopic photographs, light microscopic and SEM micrographs, including six new lichenicolous species (T. arctoparmeliae
on Arctoparmelia separata, T. lecanoricola on Lecanora rupicola, T. thelotrematis on Thelotrema, T. umbilicariae and T.
umbilicariicola on Umbilicaria, T. weberi on Thelotrema weberi), three new saprobic species (T. filamentosa on Salix, T.
ravenelii on Quercus, T. stilbosporoides on Salix caprea), and one new combination, T. arthoniae.
Most saprobic Taeniolella species are wood-inhabiting (on bark, decorticated trunks and twigs, rotten wood), whereas
lichenicolous species grow on thalli and fruiting bodies (mostly apothecia) of lichens, mostly without causing any evident
damage, but they are nevertheless confined to their host lichens, or they are obviously pathogenic and cause either disease
of the thalli (e.g., Taeniolella chrysothricis and T. delicata) or at least thallus discolorations or necroses (e.g., T. christiansenii, T.
chrysothricis, T. cladinicola, T. pseudocyphellariae, and T. strictae). Taeniolella atricerebrina and T. rolfii induce the formation of
distinct galls. The range of micro-morphological traits for taxonomic purposes is limited in Taeniolella species, but size, shape
and septation of conidiophores and conidia, including surface ornamentation, provided basic characters. Mycelium, stromata
and arrangement of conidiophores are less important for the differentiation of species. Lichenicolous species are widespread
on a wide range of lichens, with a focus in the northern hemisphere, mainly in northern temperate regions, including arcticsubartic
habitats (18 species, i.e., 62 % of the lichenicolous species). Eleven lichenicolous species, e.g., T. pseudocyphellariae,
T. santessonii, T. thelotrematis, T. umbilicariae, are also known from collections in non-temperate Asia, Australia and South
America (38 % of the species). Most collections deposited in herbaria are from northern temperate to arctic-subarctic regions,
which may reflect activities of lichenologists and mycologist dealing with lichenicolous fungi in general and Taeniolella in
particular. Most lichenicolous Taeniolella species are confined to hosts of a single lichen genus or few closely allied genera (26
species, i.e., 97 % of the lichenicolous species), but only three species, T. delicata, T. punctata, and T. verrucosa, have wider
hosts ranges.
Excluded, doubtful and insufficiently known species assigned to Taeniolella are listed at the end, discussed, described and
in some cases illustrated, including Talpapellis beschiana comb. nov. (≡ Taeniolella beschiana), Corynespora laevistipitata (≡
Taeniolella laevistipitata), Stanjehughesia lignicola comb. nov. (≡ Taeniolella lignicola), Sterigmatobotrys rudis (≡ Taeniolella
rudis), and Taeniolina scripta (≡ Taeniolella scripta).
Incorporating asexual genera in a natural classification system and proposing one name for pleomorphic genera are important topics in the current era of mycology. Recently, several polyphyletic genera have been restricted to a single family, linked with a single sexual morph or spilt into several unrelated genera. Thus, updating existing data bases and check lists is essential to stay abreast of these recent advanes. In this paper, we update the existing outline of asexual genera and provide taxonomic notes for asexual genera which have been introduced since 2012. Approximately, 320 genera have been reported or linked with a sexual morph, but most genera lack sexual morphs.
The order Phyllachorales (Pezizomycotina, Ascomycota) is a group of biotrophic, obligate plant parasitic fungi with a tropical distribution and high host specificity. Traditionally two families are recognised within this order: Phyllachoraceae and Phaeochoraceae, based mostly on morphological and host characteristics. Currently, the position of the order within the class Sordariomycetes is inconclusive, as well as the monophyly of the order, and its internal phylogenetic structure. Here we present a phylogeny of the order Phyllachorales based on sequence data of 29 species with a broad host range resulting from a wide geographical sampling. We inferred Maximum Likelihood and Bayesian phylogenies from data of five DNA regions: nrLSU rDNA, nrSSU rDNA, ITS rDNA, and the protein coding genes RPB2, and TEF1. We found that the order Phyllachorales is monophyletic and related to members of the subclass Sordariomycetidae within Sordariomycetes. Within the order, members of the family Phaeochoraceae form a monophyletic group, and the family Phyllachoraceae is split into two lineages. Maximum Likelihood ancestral state reconstructions indicate that the ancestor of Phyllachorales had a monocotyledonous host plant, immersed perithecia, and a black stroma. Alternative states of these characters evolved multiple times independently within the order. Based on our results we redefine the family Phyllachoraceae and propose the new family Telimenaceae with Telimena erythrinae as type species, resulting in three families in the order. Species of Telimena spp. occur in several monocotyledonous and eudicotyledonous host plants except Poaceae, and generally have enlarged black pseudostroma around the perithecia, a character not present in species of Phyllachoraceae. © 2017 Naturalis Biodiversity Center & Westerdijk Fungal Biodiversity Institute.
The odor emanating from sporocarps of Hygrophorus paupertinus is disagreeable and fecal-like. Solid phase microextraction (SPME) and analysis by gas chromatography-mass spectrometry (GC-MS) showed 1-octen-3-ol, indole and 3-chloroindole were responsible for the odor. This is the first case in which 3-chloroindole has been identified from a terrestrial organism.
Taeniolella is a genus of asexual ascomycetes with saprophytic, endophytic and lichenicolous life styles. A phylogeny of representative species of the genus is presented, with a focus on lichenicolous taxa. We obtained mtSSU and nuLSU sequence data from culture isolates of Taeniolella and from freshly collected specimens of other species. The genus Taeniolella is recovered as strongly polyphyletic with species distributed between the Dothideomycetes and the Sordariomycetes. The type species, Taeniolella exilis, is placed in the Kirschsteiniotheliaceae within Dothideomycetes. Other saprophytic/endophytic Taeniolella species previously assigned to the Sordariomycetes based on sequences were found to represent either contaminants or species that cannot be assigned to Taeniolella for morphological reasons. Lichenicolous species are restricted to the Asterotexiales (Dothideomycetes) where the sequenced species of Taeniolella do not form a monophyletic group, but are related to species of the genera Buelliella s. lat., Karschia, Labrocarpon, Melaspilea s. lat., and Stictographa. Molecular data are, however, not sufficient to reallocate the lichenicolous Taeniolella species to other genera so far. Anamorph-teleomorph relationships between these taxa and lichenicolous Taeniolella species are discussed but could not be demonstrated with the current data. Buelliella minimula, the type species of the genus Buelliella, is placed in the Asterotexiales, and the genus recovered as polyphyletic. Three new lichenicolous Taeniolella species are described, namely T. hawksworthiana, T. pyrenulae, and T. toruloides. Taeniolella rudis is transferred to Sterigmatobotrys, as S. rudis. In addition, the taxonomic part comprises detailed treatments of the generic type T. exilis and of T. punctata, which are both included in the phylogenetic trees.
The Didymellaceae was established in 2009 to accommodate Ascochyta, Didymella and Phoma, as well as several related phoma-like genera. The family contains numerous plant pathogenic, saprobic and endophytic species associated with a wide range of hosts. Ascochyta and Phoma are morphologically difficult to distinguish, and species from both genera have in the past been linked to Didymella sexual morphs. The aim of the present study was to clarify the generic delimitation in Didymellaceae by combing multi-locus phylogenetic analyses based on ITS, LSU, rpb2 and tub2, and morphological observations. The resulting phylogenetic tree revealed 17 well-supported monophyletic clades in Didymellaceae, leading to the introduction of nine genera, three species, two nomina nova and 84 combinations. Furthermore, 11 epitypes and seven neotypes were designated to help stabilise the taxonomy and use of names. As a result of these data, Ascochyta, Didymella and Phoma were delineated as three distinct genera, and the generic circumscriptions of Ascochyta, Didymella, Epicoccum and Phoma emended. Furthermore, the genus Microsphaeropsis, which is morphologically distinct from the members of Didymellaceae, grouped basal to the Didymellaceae, for which a new family Microsphaeropsidaceae was introduced.
A new species of Venturia (V. chinensis) is described and illustrated from the leaves of Lonicera praeflorens collected from Lesser Khingan Mountains, the northeast China. It is characterized by habitat saprobic; ascomata small-sized, solitary or scattered, superficial, subglobose to citriform, wall black, papillate, ostiolate, covered with setae; peridium thin; hamathecium evanescent in mature ascomata; asci 8-spored, bitunicate, fissitunicate, oblong to obclavate, with or without a short, knob-like pedicel; ascospores ellipsoidal, olivaceous pale brown, 1-septate, ascospore wall thin, smooth. Comparisons of V. chinensis with V. lonicerae (another species on Lonicera caerulea) and other species of Venturia lead to the conclusion that collected taxon is new. Its relationships with other species of Venturia are discussed based on morphology and 28S nrDNA and ITS nrDNA sequence comparisons.
Herbivore-induced volatile organic compounds prime non-attacked plant tissues to respond more strongly to subsequent attacks. However, the key volatiles that trigger this primed state remain largely unidentified. In maize, the release of the aromatic compound indole is herbivore-specific and occurs earlier than other induced responses. We therefore hypothesized that indole may be involved in airborne priming. Using indole-deficient mutants and synthetic indole dispensers, we show that herbivore-induced indole enhances the induction of defensive volatiles in neighbouring maize plants in a species-specific manner. Furthermore, the release of indole is essential for priming of mono- and homoterpenes in systemic leaves of attacked plants. Indole exposure markedly increases the herbivore-induced production of the stress hormones jasmonate-isoleucine conjugate and abscisic acid, which represents a
likely mechanism for indole-dependent priming. These results demonstrate that indole
functions as a rapid and potent aerial priming agent that prepares systemic tissues and
neighbouring plants for incoming attacks.
Glyphium encompasses species with erect, carbonaceous ligulate to dolabrate ascomata that are strongly laterally compressed and dehisce along a longitudinal slit. The five currently recognized members of the genus are separated primarily by whether the ascospores disassociate into part-spores within the ascus. Glyphium has traditionally been placed in Mytilinidiaceae (Mytilinidiales, Pleosporomycetidae, Dothideomycetes). The present study, based on freshly collected material of G. elatum and G. grisonense, was initiated to determine the phylogenetic placement of Glyphium. Phylogenies inferred from the analysis of sequences of six gene regions (nuLSU, nuSSU, mtSSU, TEF1, RPB1, RPB2) derived from six accessions indicate that Glyphium belongs to Patellariales (Pleosporomycetidae, Dothideomycetes). Our phylogenies also support the phylogenetic relationship of Patellaria and Hysteropatella within this order. The nomenclatural history of Glyphium is summarized and a key to species is provided.
Copyright © 2015, Mycologia.
An unusual wood-inhabiting fungus was found in northern Thailand. The combination of characters of this taxon, viz. setose, ostiolate ascomata, bitunicate asci, dark brown, wedge-shaped to clavate, muriform ascospores, and a hyphomycetous asexual state producing ellipsoidal, septate, highly constricted, holoblastic conidia is not found in any hitherto described genus of Dothideomycetes. An LSU phylogeny showed this taxon to be clearly placed in the family Sympoventuriaceae, Venturiales. The name Clavatispora thailandica gen. and sp. nov., is introduced to accommodate this taxon, which is described and illustrated and compared with other genera in this family.
A complilation of anamorphic names for both Ascomycota and Basidiomycota is provided which comprises 2895 genera. The genera are listed against a backbone of teleomorphic relationships where known. The study reveals that 73 genera and 95 anamorph-like genera are linked to teleomorphic genera names, 447 genera (three anamorph-like genera) are linked to teleomorph families, orders or classes, while for mor e than 1592 (55%) genera no teleomorph link is known. The links are based on the literature and often because fungi were found in association, but have not been proven by molecular data. Many are based on links with species other than the generic type and thus must be considered questionable for the genus. A considerable effort is needed to establish whether these links are correct.
Volatile flavor components, produced during the young (P-1), immature (P-2), mature (P-3) and old (P-4) growth stages, of shiitake mushrooms (Lentinus edodes), were extracted by simultaneous steam distillation and extraction (SDE), using a mixture of n-pentane and diethyl ether (1:1, v/v) as the extraction solvent. Analyses of the concentrates, by capillary gas chromatography (GC) and gas chromatography-mass spectrometry (GC/MS), led to the identification of 129, 129, 111 and 120 components in the P-1, 2, 3 and 4 stages, respectively. The major volatile compounds were l-octen-3-o1, 3-octanol, 3-octanone and 4-octen-3-one. Ethanol and ethyl acetate were also detected in large amounts. The characteristic volatile compounds found in shiitake mushrooms, such as dimethyl disulfide, dimethyl trisulfide and 1, 2, 4-thiolane, were at low concentrations in all samples. The amount of l-octen-3-o1 decreased as growth progressed, but concentrations of 3-octanone increased. The amount of 4-octen-3-ol decreased from P-1 to P-3, but was at a high concentrations in P-4. The concentration of 3-octanol gradually increased and reached its highest concentration in P-3, but decreased in P-4. The C8-compounds comprised 70.91, 64.09, 64.29 and 60.01 % in the P-1, 2, 3 and 4 stages, respectively, so decreased gradually with growth. The S-compounds were found in the highest concentrations in P-3.
Cortinarius lebre Garrido, a common edible mushroom from central Chile, is distinct from other Cortinarii by its strong, naphtalene-like smell. The relevant volatile compounds were detected by gas chromatography - mass spectrometry and identified as indole together with 1-octen-3-ol, octane-3-one, and octan-3-ol.
An enormous variety of volatile substances are released in distinctive blends by fungal substrates that should be recognisable for fungivores. Certain compounds dominate in most of the fungal species. Fungal oxylipins as the eight-carbon volatiles are the most prominent. This raises the question whether such are specific enough to qualify as appropriate host cues for a fungivore. We could demonstrate differentiated responses of the fungivorous beetle Bolitophagus reticulatus to eight-carbon volatiles: Nine eight-carbon volatiles were identified with GC–MS from its host fungus Fomes fomentarius. 1-Octen-3-ol, 3-octanone and 3-octanol induced contrasting behaviour of beetles in olfactometer bioassays. Electroantennographic experiments investigating the beetle olfactory sense revealed distinguishable antennal responses. Moreover, their individual release from F. fomentarius fruiting bodies changes not only considerably, but also independently over successive stages of beetle colonisation. Concentrations of attractive and repellent eight-carbon volatiles correlate to frequency of beetles in the field and further substantiate their relevance as host cues. Our results show that a specialist fungivore is able to differentiate the most common eight-carbon volatiles of fungi to assess host quality. Key roles and marked similarities of fungal to plant oxylipins suggest a comparable importance of eight-carbon volatiles to fungivores as green leaf volatiles have to herbivores.
Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.
I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available.
The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML.
Alexandros.Stamatakis@h-its.org.
The holotype of Tothia fuscella has been re-examined and is re-described and illustrated. An identical fresh specimen from Austria is used to designate an epitype with herbarium material and a living culture. Sequence analyses show T. fuscella to be most closely related to Venturiaceae and not Microthyriaceae, to which it was previously referred.
With special emphasis on Aphyllophorales, this study was carried out to verify hitherto
published phylogenies of Hymenomycetes by nuclear large subunit rDNA sequences and
comparative morphology. Preferably Aphyllophorales with dolipores having the imperforate
parenthesome-type were used to remedy the imbalance in taxa composition of former analyses.
The results support the hypothesis of a monophyletic origin of homobasidiomycetes
having dolipore parenthesomes perforated by many small holes, including gilled, non-gilled
mushrooms and gasteromycetes. Only a minor part of the formally settled orders or families
could be verified by this analysis in full respect. Especially the Agaricales ss Singer contain
many different related Aphyllophorales. A monophylum comprising non-gilled mushrooms
from certain Corticiaceae and Hymenochaetales, having solely dolipores with imperforate
parenthesomes is the sistergroup of the homobasidiomycetes having dolipores with perforated
parenthesomes. The borderline between heterobasidiomycetes and homobasidiomycetes was
detected to be unsharp, because of repeatedly loss of secondary ballistospores in a monophylum
nesting the Tulasnellales, Botryobasidiales and cantharelloid taxa. Ranks dealing with the
higher taxonomy of the Hymenomycetes are discussed. New terms circumscribing phylogenetic
entities are proposed to handle ranking problems involved with taxonomic nomenclature.
Cladosporium araliae is validated as Stenella araliae sp. nov., a fungus with the herbarium name Cladosporium betuligenum is described as Fusicladium betuligenum sp. nov., Septonema acicola nom. nov. and Passalora phalaridis sp. nov. on Phalaris arundinacea are introduced. The new combinations Fusicladium parasiticum, Passalora foveolicola, Stenella eriolobi and S. oxycocci are proposed and detailed descriptions, illustrations and comments are provided. Herbarium material deposited under the name Cladosporium callae proved to be a syntype of Cercospora callae, Cladosporium persicum (in herb.) is identical with Stenella persicae, and Cladosporium herbarum f. rubi has to be reduced to synonymy with Pseudocercospora rubi. Furthermore, a collection deposited as Cladosporium sp. proved to be conspecific with Passalora plucheae.
Survey of seven strains determined as Septonema ochraceum (Dothideomycetes, inc. sed.) isolated from pine litter or obtained from public collections revealed three new species, Fusicladium cordae, F. sicilianum (Venturiaceae), Cladophialophora matsushimae (Herpotrichiellaceae) and a cryptic species morphologically identical to Devriesia americana (Teratosphaeriaceae), but phylogenetically distinct. Morphological survey and phylogenetic analysis using nucleotide sequence data from the nuclear
ribosomal subunit genes indicate a close relationship within three species colonising pine litter needles, F. cordae, F. pini and F. ramoconidii. F. sicilianum is most related to F. rhodense. C. matsushimae represents a species belonging to one of the lineages of the polyphyletic genus Cladophialophora. None of the strains observed can be classified morphologically as S. ochraceum, of which the type material does not exist.
Keywords28S rDNA-ITS rDNA-Pine litter needles-Taxonomy
Quasiconcha reticulata is reported from roots of two species of conifers. Agar cultures from single ascospores produced a dark mycelium bearing chlamydospores. An anamorph similar to the form-genus Chalara developed only on sterile twigs and leaves of Pinus halapensis. Because the fungus was associated with the pine wood nematode on one occasion it was tested in culture as a food organism for the nematode and found to support growth and reproduction of the nematode at 20 and 24 C.
Three new chlorinated sesquiterpenes, named lepistatins A–C, were isolated from the culture broth of Basidiomycete Lepista sordida. The structures were determined by the analysis of spectroscopic data including HREIMS and 1D and 2D NMR. The absolute configuration of lepistatin B was determined by comparing the specific rotation and circular dichroism spectrum with those of known structurally related compounds bearing the same chiral carbon. The structures of lepistatins A–C feature the indanone core structure, but differ from other indanone-containing sesquiterpenes of fungal origin by the alkyl substitution pattern. This indicates that lepistatins A–C probably possess a new sesquiterpene scaffold derived from the common precursor, trans-humulyl cation, by an alternative cyclization.
The family Gloniaceae is represented by the genera Glonium (plant saprobes) and Cenococcum (ectomycorrhizae). This work adds to the knowledge of the family, by introducing a new taxon from dead scales of pine cones collected on the ground in Chiang Mai Province, Thailand. Analysis of a combined LSU, SSU, RPB2 and TEF1 sequence dataset matrix placed it in Gloniaceae and Purpurepithecium murisporum gen. et sp. nov. is introduced to accommodate the new taxon. The genus is characterized by erumpent to superficial, navicular hysterothecia, with a prominent longitudinal slit, branched pseudoparaphyses in a gel matrix, with a purple pigmented epithecium, hyaline to dark brown muriform ascospores and a Psiloglonium stygium-like asexual morph which is produced in culture. The new taxon is illustrated and compared with similar genera.
Covering: up to January 2017
This review gives a comprehensive overview of the production of fungal volatiles, including the history of the discovery of the first compounds and their distribution in the various investigated strains, species and genera, as unravelled by modern analytical methods. Biosynthetic aspects and the accumulated knowledge about the bioactivity and biological functions of fungal volatiles are also covered. A total number of 325 compounds is presented in this review, with 247 cited references.
Species of Coleophoma have been reported as plant pathogenic, saprobic or endophytic on a wide host range. The genus is characterised by having pycnidial conidiomata, phialidic conidiogenous cells intermingled among paraphyses, and cylindrical conidia. Coleophoma has had a confusing taxonomic history with numerous synonyms, and its phylogeny has remained unresolved. The aim of the present study was to use a polyphasic approach incorporating morphology, ecology and molecular data of the partial large subunit nrDNA (LSU), the internal transcribed spacer region with intervening 5.8S nrDNA (ITS), partial β-tubulin (tub2), and translation elongation factor 1-alpha (tef1) gene sequences to resolve its taxonomy and phylogeny. Based on these results the genus was found to be polyphyletic, with taxa tentatively identified as Coleophoma clustering in Dothideomycetes and Leotiomycetes. Species corresponding to the concept of Coleophoma s.str. (Dermateaceae, Helotiales, Leotiomycetes) were found to form a distinct clade, with five new species. Furthermore, Coleophoma was found to be linked to the newly established sexual genus, Parafabraea, which is reduced to synonymy. Isolates occurring on Ilex aquifolium in the Netherlands also clustered in Dermateaceae, representing a novel genus, Hawksworthomyces. In the Dothideomycetes, several taxa clustered in Dothiora (Dothioraceae, Dothideales), which is shown to have Dothichiza and hormonema-like asexual morphs, with four new species. Furthermore, Pseudocamaropycnis is introduced as a new genus (Mytilinidiaceae, Mytilinidiales), along with Briansuttonomyces (Didymellaceae, Pleosporales) and Dimorphosporicola (Pleosporaceae, Pleosporales).
Button mushroom slices were dehydrated using freeze drying (FD) or combined with microwave vacuum drying (FMVD), and the changes in volatile composition were investigated and compared by using headspace GC–MS and electronic nose (E-nose). The results showed that the content of C8 compounds decreased during FD/FMVD process, while more alkanes and heterocyclic compounds were generated in the latter drying periods. The content of original thermal volatile compounds in FMVD products were significantly lower compared to FD, and the same trent was observed on alkanes and heterocyclic compounds. Moreover, the volatile compounds of FMVD products were more similar with fresh ones according to cluster analysis, and the critical point of change of volatile compounds might be at the end of sublimation period. In addition, E-nose could clearly discriminate button mushroom samples subject to different drying periods, the result obtained by E-nose showed good identity compared with GC–MS.
During a north–south latitudinal survey of aquatic fungi on submerged wood and herbaceous material in streams in the Asian region, we collected several hyphomycetous taxa. This paper is part of a series where we provide illustrated accounts of these taxa and place them in a natural classification in the fungi. DNA sequence based phylogenies in recent literature have shown that Dendryphion, Sporidesmium and Torula-like species are polyphyletic in the phylum Ascomycota and their taxonomyhas been problematic due to a lack of understanding of the importance of morphological characters used to delimit taxa, as well as the lack of ex-type or reference strains. Based on multi-locus phylogenies together with morphology, we propose the novel family Distoseptisporaceae (Sordariomycetes) and three novel genera Neotorula (Pleosporales, Dothideomycetes), Distoseptispora (Sordariomycetes) and Pseudosporidesmium (Sordariomycetes). In addition, Dendryphion aquaticum, D. submersum, Distoseptispora fluminicola, D. aquatica, Kirschsteiniothelia submersa, Neotorula aquatica, Sporidesmium aquaticum, S. submersum and S. fluminicola are introduced as new species. Pseudosporidesmium knawiae comb. nov. is proposed to accommodate Sporidesmium knawiae in Sordariomycetes. The polyphyletic nature of Dendryphion, Sporidesmium and Torula-like species are partially resolved, but further sampling with fresh collections and molecular data of species are needed to obtain a natural classification.
Fungal volatile secondary metabolites play important roles in mediating antagonistic and beneficial interactions among organisms. The effects of eight strains of white-rot fungi cultured on potato waste against the mycelial growth of Botrytis cinerea, Fusarium oxysporum and Mucor miehei were investigated using a bi-compartmented Petri dish assay. The chemical composition of volatile organic compounds released from the strain with the highest inhibitory effect was also investigated by headspace solid-phase microextraction and gas chromatography/mass spectrometry analysis. Of the eight white-rot fungi evaluated, Anthracophyllum discolor. Sp4 showed a high inhibitory activity against M. miehei (approximately 76%) and B. cinerea (approximately 20%). F. oxysporum was inhibited to a lesser extent (approximately 10%) by A. discolor and T. versiscolor. The gas chromatography/mass spectrometry analysis showed nine main volatile compounds released from A. discolor Sp4, among them are the sesquiterpenesα-bisabolene and bulnesene, and the chlorinated aromatic compounds 1,5-dichloro-2,3-dimethoxybenzene, 3,5-dichloro-4-methoxybenzaldehyde and 3-chloro-4-methoxybenzaldehyde. Some of which have been reported previously with antimicrobial activity. The antifungal activity and volatile profile of A. discolor have not been previously reported.
The volatilomes of fresh and dried fruiting bodies of Calocybe gambosa were analyzed and compared in this study for the first time. Aroma compounds were extracted by means of liquid/liquid extraction, purified by solvent assisted flavor evaporation (SAFE), and identified by gas chromatography-mass spectrometry and olfactometry. An aroma extract dilution analysis (AEDA) was performed to identify the key flavor compounds, and the main volatiles were quantified by GC flame ionization detection. The key odor compound of fresh fruiting bodies of C. gambosa was (E)-non-2-enal, which, together with (E)-non-2-en-1-ol, was responsible for the characteristic flour- and cucumber-like odor. The aroma profile of commercially available dried fruiting bodies of C. gambosa showed a different pattern. In the dried fruiting bodies, odor compounds like 3-methylbutanoic acid were dominating, and (E)-non-2-enal was not detectable. Thus, the aroma quality of commercially available dried fruiting bodies of C. gambosa differs significantly from that of freshly collected specimens. © 2015, German Mycological Society and Springer-Verlag Berlin Heidelberg.
Young fresh fruiting bodies of wild Lentinus lepideus were harvested from downed old chestnut trees. The volatile compounds were isolated by continuous liquid–liquid extraction (CLLE) and investigated by high resolution gas chromatography-mass spectrometry (HRGC-MS) on two columns of different polarity (DB-5 and ZB-WAX), gas chromatography-atomic emission detector (GC-AED), high resolution-mass spectrometry (HR-MS), and gas chromatography-olfactometry (GC-O). A total of 43 major volatile compounds were identified and semi-quantified. 19 sesquiterpenoids including 11 unknowns were newly found in this fungus. A sulfur-containing sesquiterpenoid mintsulfide was identified for the first time in the fungal kingdom, and a main odorant, 2-vinyl malonic acid methyl propyl mixed ester, was proposed. Five odorous compounds
were responsible for the characteristic flavour of the young fruiting bodies: nonanal, (E)-2-nonenal, germacrene-D, 2-vinyl malonic acid methyl ester propyl ester, and nonanoic acid. The results showed that this wild variety of Lentinus lepideus formed a wide diversity of natural sesquiterpenoids, but lacked, in contrast to previous studies, from cinnamic acid derivatives and 1-octen-3-ol.
The aroma compounds of fruiting bodies of C. odorifer were extracted by means of liquid/liquid extraction and purified by solvent assisted flavour evaporation (SAFE). The odour active compounds were identified by gas chromatography-mass spectrometry and olfactometry on two columns of different polarity and described by sensory detection. The volatilom of C. odorifer is reported here for the first time. Additionally, an aroma extract dilution analysis (AEDA) was performed to identify the main flavour compounds. Finally, the volatiles were quantified by GC flame ionization detection (GC-FID). The main odour compound of C. odorifer was methyl p-anisate with an FD factor of 8,192 and a concentration of 120 mg kg-1. Methyl p-anisate was also the compound responsible for the characteristic anise-like odour of C. odorifer. Copyright © 2015 John Wiley & Sons, Ltd.
Despite a significant body of evidence in support of the close phylogenetic relationship of species of Capronia (Herpotrichiellaceae) and black yeasts belonging to or allied with the genus Exophiala questions concerning the taxonomic importance of features furnished by ascospore, stromal and anamorph characters have remained unanswered. In order to address these issues and to elucidate more fully relationships within the family, we have sequenced a portion of the nuclear large ribosomal RNA subunit (28S), the 5.8S gene, and the internal transcribed spacers (ITS1 and ITS2) of 15 species of Capronia and 19 black yeasts assigned to the form genera Cladosporium, Cladophialophora, Exophiala, Fonsecaea, Phaeococcomyces, Phialophora, Ramichloridium and Rhinocladiella. Cladistic analysis of these data confirmed the monophyly of the Herpotrichiellaceae but did not support the division of the genus Capronia on the basis of conidial ontogeny, pattern of ascospore septation, or the degree of stromal development. Homothallic species of Capronia with 8-spored asci, muriform ascospores and Exophiala anamorphs formed a well-supported lineage that included the medically important species Exophiala dermatitidis. Capronia mansonii and Capronia munkii, morphologically similar taxa isolated from the wood of Populus, were inferred as closely related but separate species. The clade comprising members of the Herpotrichiellaceae that possess Cladosporium-like and Phialophora anamorphs was also strongly supported. Available molecular evidence indicates that Dictyotrichiella semiimmersa and Phialophora americana are teleomorph and anamorph states of a single holomorph. Cladistic analysis also confirmed that the genera Cladophialophora and Ramichloridium are polyphyletic. The anamorphs of Capronia nigerrima and Dictyotmchiella semiimmersa are described and illustrated, and the combination Capronia semiimmersa is proposed.
This study is focused on the volatile oils from the fruiting bodies of Pleurotus salmoneostramineus (PS) and P. sajor-caju (PSC), which was extracted by hydrodistillation (HD) and solvent-assisted flavor evaporation (SAFE) methods. The oils are analyzed by gas chromatography-mass spectrometry (GC-MS), GC-olfactometry (GC-O), and aroma extract dilution analysis (AEDA). A total of 31, 31, 45, and 15 components were identified in PS (HD and SAFE) and PSC (HD and SAFE), representing about 80.3%, 92.2%, 88.9%, and 83.0% of the oils, respectively. Regarding the aroma-active components, 13, 12, 13, and 5 components were identified in PS (HD and SAFE) and PSC (HD and SAFE), respectively, by the GC-O analyses. The results of the sniffing test, odor activity value (OAV) and flavor dilution (FD) factor indicate that 1-octen-3-ol and 3-octanone are the main aroma-active components of PS oils. On the other hands, methional and 1-octen-3-ol were estimated as the main aroma-active components of PSC oils.
In this study, the characteristic odorants of the volatile oils from Pleurotus species (P. eryngii var. tuoliensis and P. cystidiosus) were extracted by hydrodistillation and analyzed by gas chromatography-mass spectrometry (GC-MS), gas chromatography-olfactometry (GC-O), and aroma extract dilution analysis (AEDA). A total of 52 and 54 components (P. eryngii var. tuoliensis and P. cystidiosus, respectively) were identified, representing about 98.8% and 85.1% of the volatile oils, respectively. The main components of the P. eryngii var. tuoliensis oil were palmitic acid (82, 38.0%), oleic acid (86, 25.0%) and linoleic acid (85, 9.7%). The main components of the P. cystidiosus oil, palmitic acid (82, 25.8%), indole (54, 9.1%) and myristic acid (77, 5.3%). Regarding the aroma components, 16 and 13 components were identified in the P. eryngii var. tuoliensis and P. cystidiosus oils respectively, by the GC-O analyses. The results of the sniffing test, odor activity value (OAV) and flavor dilution (FD) factor indicate that methional, 1-octen-3-ol and nonanal are the main aroma-active components of P. eryngii var. tuoliensis oil. On the other hands, dimethyl trisulfide and 1-octen-3-ol were estimated as the main aroma-active components of the P. cystidiosus oil.
Nearly 400 generic names and 1000 species names of microfungi, mostly Hyphomycetes, have been checked from the original publications. Access to type or authenticated material of most of them has resulted in some revisions. Seven generic names and 22 species names are shown to be nomina dubia or nomina confusa.
Ascoma morphologies have traditionally been used to classify filamentous ascomycete fungi. Phylogenies generated using DNA sequence data have since shown most of the previously identified groups not to be monophyletic. The relationships of hysterothecia‐bearing ascolocularous fungi have been unsettled for many years. Recent molecular studies have shown this group as currently circumscribed not to constitute natural groupings. This study targeted wide taxon sampling to assess the validity of the current classification in the group. A data set of 40 taxa was assembled including sequence data from nuclear large subunit rDNA and translation elongation factor 1 alpha for each taxon with 68 new sequences being generated for this study and aligned with 62 sequences obtained from GenBank. Parsimony, Bayesian and Maximum Likelihood analyses were performed on the data. Mytilinidiales was recovered as a strongly supported monophyletic clade, while a monophyletic Hysteriales was also recovered but with weak support. Gloniaceae (comprising the genus Glonium s. str. excluding Psiloglonium) was shown not to be monophyletic. This study established a monophyletic hysterothecial clade nested within Pleosporales, for which we proposed a new genus, Anteaglonium gen. nov. including two new species, A. globosum sp. nov. and A. latirostrum sp. nov. that are described. This relationship was strongly supported and most statistical analyses support the placement. The result of this study further indicates that the hysterothecial type of ascomata may have evolved several times within the ascolocularous fungi.
The history of Glyphium Lehmann is briefly reviewed. G. leptothecium (Earle) comb. nov. (≡Lophium leptothecium Earle) from North America, and G. schizosporum (Maire) Zogg from Europe are distinguished mainly by size and septation of fragmented ascospores. Conidial states, referable to Peynnelia Cif. & Frag., are correlated for each species and differences enumerated.
Numerous recent collections permit a clearer view of several British Hysteriales. The genera and species of Farlowiella, Gloniopsis, Hysterium, Hysterographium and Mytilidion are summarized below, and a revised key to British species is appended.
The naphthalene-like smell of Scytinostroma portentosum (Berk. & Curt.) Donk originates predominantly from indole (1) together with 3-chloroindole (3) and to a lesser extent of 1- octen-3-ol (9). Naphthalene (8) itself could not be detected.
Recently, it has been proposed that the type for Dothidea be formally conserved as Sphaeria sambuci Pers. (Dothidea sambuci (Pers.) Fr.:Fr.) and additionally that an epitype specimen be established for that species. A description, illustrations, and DNA sequence data are given based on the epitype. In a search for original or type specimens, a specimen labeled Dothidea sambuci was examined from Fries's Herbarium. It is a mixed collection of a few immature stromata morphologically similar to those of Dothidea sambuci and mature perithecia of Diaporthe spiculosa (Pers.:Fr.) Nitschke, which is described and illustrated with brief remarks on its nomenclature.Key words: Sambucus, Aureobasidium, Hormonema, Dothideomycetes, phylogeny.
Based on own collections, two species of cheirosporous hyphomycetes (anamorphic Pleosporales) have been reexamined by morphology and molecular analysis. Cheiromyces inflatus is a new record for England. Transfers of Ch. inflatus to Dictyosporium and of Cheiromoniliophora elegans to Pseudodictyosporium are proposed.
The components of the volatile oil from wild mushroom (Lactarius hatsudake), used in Japanese traditional food, were analysed and quantified for the first time by capillary GC and GC–MS. Seventy-six components were separated from the oil and of these 71 components were identified. The main components of the oil were oxidized sesquiterpenes [cis-isolongifolanone (624.9 μg/100 g), α-cedrene epoxide (578.7 μg/100 g), humulene epoxide III (453.9 μg/100 g), clovane (425.4 μg/100 g)], aliphatic acids [linoleic acid (585.9 μg/100 g) and palmitoleic acid (333.3 μg/100 g)]. Odour evaluation of the volatile oil from L. hatsudake was also carried out using GC–MS/olfactometry (GC–MS/O) and aroma extract dilution analysis (AEDA), from which it was found that hexanal, 4-dehydroviridiflorol, myliol and phenylacetaldehyde seem to contribute to the green, spicy and sweet odour of L. hatsudake. Copyright © 2010 John Wiley & Sons, Ltd.
The potency of odourants in foods is determined by aroma extract dilution analysis (AEDA) and by the calculation of odour activity values (OAVs). The application of these methods to olive oil, butter, Swiss cheese, heated beef, bread, beer, green tea, dill herb and to the off-flavours formed in lemon oil, soybean oil and boiled trout is reviewed. The results allow the conclusion that only a small fraction of the complex mixture of volatiles causes the characteristic odour of a distinct food.
Three genera of lignicolousHyphomycetes Septonema
Corda,Hormiactella
Saac. andLylea
Morgan-Jones are discussed. Illustrations and determination keys are provided. Five species ofSeptonema—S. fasciculare (Corda) Hughes,S. leptaleum (Ellis & Harkn.) Hughes,S. pinicola
Hol.-Jech.,S. secedens
Corda andS. laricium
Hol.-Jech.—and two species ofHormiactella—H. fusca (Preuss) Sacc. andH. asetosa
Hol.-Jech.—have been found in Czechoslovakia. A new speciesS. pseudobinum
Hol.-Jech. is described from Romania.Septonema tetracoilum (Corda Hughes is accommodated in the genusLylea
Morgan-Jones.
Lophiostoma and Lophiotrema share several morphological and ecological features. They have been regarded as closely related genera within the family
Lophiostomataceae, but their morphological circumscriptions have been uncertain. To clarify the generic definitions of Lophiostoma and Lophiotrema, we conducted phylogenetic analyses of 29 isolates of these genera based on the SSU and LSU nrDNA sequences, and also reevaluated
several key characters previously used for their generic characterization. Our results clearly confirmed that Lophiostoma and Lophiotrema are distinct genera belonging to different families; the ascus shape, including length of the ascus stipe, is a reliable
taxonomic indicator to allow discrimination between the genera. In Lophiostoma species, asci are clavate with relatively long stipes [mostly (10–) 15–30μm in length], whereas in Lophiotrema the asci are cylindrical with short stipes (up to 15μm long). A new family, Lophiotremataceae, is proposed to accommodate
species in the Lophiotrema clade that was distantly placed from the Lophiostomataceae within the Pleosporales. Lophiostoma quadrisporum, collected from twigs of Liriodendron tulipifera, is described as a new species with distinctive 4-spored asci. Lophiotrema vitigenum, which has clavate asci with long stipes, is transferred to Lophiostoma.
KeywordsAscomycota–Dothideomycetes–Lophiotremataceae–Pleosporales–Systematics