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Mycena lamprocephala, a new luminescent species from the Brazilian Amazon
Abstract
A luminescent fungus growing on decaying leaves and sticks was collected in terra-firme forest at the upper Cuieiras river, Amazonas, Brazil. Morphological study and phylogenetic analysis (based on ITS+LSU data) confirmed it as a new species of Mycena. Mycena lamprocephala sp. nov. is characterized macroscopically by small, thin, basidiomata with an olivaceous brown pileus and glutinous stipe, and microscopically by diverticulate pleurocystidia, ramose cheilocystidia, and thin, diverticulate and branching pileipellis hyphae. The luminescence of the pileus and of the mycelium in the substrate is typically green and sometimes pulsating. This is the third luminescent species of Mycenaceae described from the Amazon Forest.
... Brownish Mycena, characterized by a yellowish-brown, grayish-brown to dark brown pileus or stipe, predominantly inhabit the northern temperate zone, with fewer occurrences in tropical and subtropical areas [11,12,[20][21][22][23][24][25][26][27]. They are categorized into at least nine sections, namely: sect. ...
... In recent years, the species diversity of Mycena has received heightened attention, leading to the publication of many new species, and marking substantial advances in research [13][14][15]26,27,[30][31][32]. However, brownish Mycena have remained relatively underexplored, with their phylogenetic relationships still unclear and a considerable number of species unknown. ...
Within the genus Mycena, species exhibiting brownish basidiomata present considerable challenges in identification due to similar coloration. This study underscores the significance of pileipellis types and cheilocystidia characteristics as critical in delimiting brownish Mycena species. To clarify the principal taxonomic characters and their utility in distinguishing between brownish Mycena species, a morphological taxonomy and phylogenetic analysis were performed. Five new species from China were introduced and characterized through a comprehensive morphological anatomy and phylogenetic substantiation: M. campanulatihemisphaerica sp. nov., M. digitifurcata sp. nov., M. kunyuensis sp. nov., M. limitis sp. nov., and M. oryzifluens sp. nov. Discussions of these taxa are supplemented with morphological illustrations. The phylogenetic relationships were inferred using Bayesian Inference and Maximum Likelihood methods based on sequences from the internal transcribed spacer and the large subunit regions of nuclear ribosomal RNA. With the addition of these five new species, the worldwide count of brownish Mycena increases to 94, and a key to the 29 known species of brownish Mycena from China is presented.
The mystery phenomenon of fungal bioluminescence has always captivated human curiosity, although more attempts need to be made, particularly to bring the new species to the surface. In this study, we devoted considerable space to the taxonomy of these fungi while discussing their biogeography, evolution, bioluminescence mechanism, and potential ecological roles. We provide a detailed explanation of how these fungi produce light, including the role of the enzyme luciferase and luciferin. We also discussed their applications. Here, we presented an updated list of 122 bioluminescent fungi identified from five distinct evolutionary lineages viz. Armillaria, Eoscyphella, Lucentipes, Mycenoid, and Omphalotus worldwide, mainly in tropical and subtropical areas. The bioluminescent fungi descended from the last common ancestor of the mycenoid and the marasmioid clades of Agaricales, which have been maintained for at least 160 million years of evolution. We highlighted the need for further research to understand the ecological role of bioluminescent fungi. Applying bioluminescent fungi in various areas (e.g., environmental and medicinal) demonstrates their validity.
During nocturnal field expeditions in the Brazilian Atlantic Rainforest, an unexpected bioluminescent fungus with reduced form was found. Based on morphological data, the taxon was first identified as belonging to the cyphelloid genus Maireina, but in our phylogenetic analyses, Maireina was recovered and confirmed as a paraphyletic group related to genera Merismodes and Cyphellopsis. Maireina filipendula, Ma. monacha, and Ma. subsphaerospora are herein transferred to Merismodes. Based upon morphological and molecular characters, the bioluminescent cyphelloid taxon is described as the new genus Eoscyphella, characterized by a vasiform to urceolate basidiomata, subglobose to broadly ellipsoid basidiospores, being pigmented, weakly to densely encrusted external hyphae, regularly bi-spored basidia, unclamped hyphae, and an absence of both conspicuous long external hairs and hymenial cystidia. Phylogenetic analyses based on ITS rDNA and LSU rDNA support the proposal of the new genus and confirm its position in Cyphellopsidaceae. Eoscyphella luciurceolata represents a new lineage of bioluminescent basidiomycetes with reduced forms.
Mycena section Calodontes is macromorphologically distinguished by the collybioid or mycenoid basidiome, which is pink, purple, or violet, and, rarely, reddish-brown or yellowish. It is further characterized by the presence of oxalate crystals in the basal mycelium. The section comprises approximately 40 taxa, of which only five species and one variety exhibit bioluminescence. As part of an extensive study on Mycena sect. Calodontes in Mexico, specimens belonging to this section were collected and subjected to morphological analysis. Sequences from the nuclear internal transcribed spacer (ITS) of nuclear ribosomal DNA, RNA polymerase II large subunit Rpb1 (rpb1), and translation elongation factor-1α (Tef-1α) were generated to infer the relationships within Mycena sect. Calodontes using maximum likelihood and Bayesian inference. The phylogenetic evidence, along with the macro- and micromorphological features, supported the recognition of five new bioluminescent species within Mycena sect. Calodontes. Detailed macro- and micromorphological descriptions, line-drawing illustrations, and light and dark photographs of the new species are provided.
Luminous fungi have long attracted public attention in Japan, from old folklore and fiction to current tourism, children’s toys, games, and picture books. At present, 25 species of luminous fungi have been discovered in Japan, which correspond to approximately one-fourth of the globally recognized species. This species richness is arguably due to the abundant presence of mycophiles looking to find new mushroom species and a tradition of night-time activities, such as firefly watching, in Japan. Bioluminescence, a field of bioscience focused on luminous organisms, has long been studied by many Japanese researchers, including the biochemistry and chemistry of luminous fungi. A Japanese Nobel Prize winner, Osamu Shimomura (1928–2018), primarily focused on the bioluminescence system of luminous fungi in the latter part of his life, and total elucidation of the mechanism was finally accomplished by an international research team with representatives from Russia, Brazil, and Japan in 2018. In this review, we focused on multiple aspects related to luminous fungi of Japan, including myth, taxonomy, and modern sciences.
Mycena subpiligera, a new taxon in sect. Fragilipedes that can strongly enhance the germination efficiency of Gastrodia elata seeds, was discovered in subtropical areas of China. As revealed by a morphological comparison with related Mycena species as well as maximum likelihood (ML) and Bayesian phylogenetic analyses based on sequences of the internal transcribed spacer (ITS) and the large subunit (LSU) regions of nuclear ribosomal RNA, the new taxon can be distinguished from phenotypically similar and phylogenetically related species. Optimal cultural conditions for M. subpiligera basidiomata are reported, and the germination rate of the new species is compared with that of M. citrinomarginata.
A new luminescent lignicolous fungal species, Mycena cristinae sp. nov., is proposed from the Central Amazon forest. This is unique and supported by morphological evaluation along with LSU- and ITS-based phylogenetic analyses. The basidiomata have mostly fuscous olivaceous brown pileus, adnate to subdecurrent and distant lamellae, and stipe with slightly bulbous base (basal mycelium absent). It also has inamyloid and/or weakly amyloid basidiospores, ramose cheilocystidia and a pileipellis composed of an aerated tangle of slender, diverticulate hyphae forming a coralloid pellicle overlaying the hypodermium. The luminescence is evident in the basidiomata (especially the stipe) and in the mycelium on the substrate. The LSU phylogenetic trees reveal that M. cristinae is sister to M. coralliformis within the Mycenaceae clade. In the ITS trees, it forms a unique lineage grouping with undetermined Mycena taxa. Morphological data support M. cristinae as a different species compared to previously described taxa.
Bioluminescence is the emission of of perceptible cold light from organisms; therefore, they are recognized as living lights. Bioluminescent organisms are present everywhere on the earth predominately in the ocean. The terrestrial bioluminescent organism includes very well‐known Fireflies; microorganisms like bacteria; insects like flies and springtails. Mushrooms, earthworms, snail, centipedes, millipedes and beetles are some other terrestrial bioluminescent organisms. Attracting prey, intraspecies visual communication and escape from a predator are some major significance of bioluminescence in living organisms. Bioluminescent organisms produce light by the chemical reaction; therefore, it is known as chemiluminescence. Luciferase catalyzes the chemical oxidation of the substrate (luciferin) which leads to the emission of light. About 40 bioluminescence systems have been reported on the earth in which D‐luciferin, coelenterazine and Cypridina luciferin‐based systems are well studied. About 81 known species of bioluminescent fungi are recorded worldwide. These fungi belong to four dissimilar lineages – Omphalotus, Armillaria, mycenoid and Lucentipes. Lightening, monitoring biological process, clinical diagnosis, drug discovery, cancer research, biosensor development and immunoassays are the future scope of bioluminescence technology. Future lighting is the most exciting scope of bioluminescence technology. Recently, eukaryotic yeast cell autonomously glowed after the transfer of a genetically encoded system of bioluminescent fungus Neonothopanus nambi . The bioluminescence system of the same fungus was used to produce an engineered tobacco plant that also has the self glowing property. The fungal bioluminescence system was also successfully used as a biosensor for the environmental monitoring of mercury, copper and zinc. The virulence and growth of some fungi like Candida albicans, Aspergillus fumigatus and Cryptococcus neoformans were real‐time monitored using bioluminescence‐based non‐invasive method in vivo. It is known as bioluminescence imaging (BLI) that allows the temporal and spatial progression of disease in living beings. So, the present chapter aims to give insights about bioluminescence in fungi, its mechanism and future scope.
Significance
We present the genomes of five new bonnet mushroom Mycena species, formerly the last fungal bioluminescent lineage lacking reference genomes. These genome-scale datasets allowed us to construct an evolutionary model pinpointing all possible changes in the luciferase cluster across all fungi and additional genes involved in bioluminescence. We show that luciferase clusters were differentially lost in different fungal lineages and in particular a substantial loss was observed in the mycenoid lineage. This can be attributed to genome regions of Mycena that underwent different evolutionary dynamics. Our findings offer insights into the evolution of how a gene cluster emerged 160 million years ago and was frequently lost or maintained due to differences in genome plasticity.
Based on morphological and molecular phylogenetic analyses, the new genus Chrysomycena is described for the species C. perplexa which shows a peculiar combination of features within the Porotheleaceae family: a mycenoid habitus, a pileipellis structured as an ixocutis with some pileocystidioid elements, slightly amyloid spores and basidia, long lageniform to flagellate (flagelliform) cheilocystidia, abundant clamp-connections and sarcodimitic tissues.
A ocorrência dos fungos do filo Basidiomycota é encontrada com maior frequência na floresta, agindo como principais decompositores da matéria orgânica. Com isso, esta pesquisa teve como objetivo realizar um levantamento de basidiomicetos, permitindo assim e sistematizar informações da diversidade de fungos encontradas na Reserva Natural de Palmari, localizada no município de Atalaia do Norte-AM. Em uma das trilhas pré-existentes da Reserva, foram marcados, a cada 200m, quatro transectos dispostos de 40m x 10m, totalizando quatro equidistantes pontos, onde se procuraram os macrofungos em todos os substratos. Foram encontrados 948 espécimes de fungos, totalizando 31 espécies, distribuídas em oito famílias, sendo que a ordem Agaricales apresentou maior índice de riqueza de espécimes. A área estudada é um centro de diversidade e abriga expressiva diversidade de fungos decompositores de matéria orgânica, configurando uma área de grande importância ecológica para a conservação do ecossistema, além de apresentar espécies comestíveis e medicinais.
The rare gilled fungus Mycena clavata is reported from the Czech Republic for the first time. It was found on large fallen trunks of Picea abies in Boubínský prales virgin forest, the best preserved montane old-growth forest in the country. The basidiomata occurred in the lower half of the trunks, either on their upper or lateral sides, on bark covered by mosses, on bare bark, or directly on wood covered by mosses, in wet times of the year. Descriptions and photographs of macro- and microcharacters are provided and data on the distribution and ecology of M. clavata are summarised. The species was sequenced for the first time. ITS-LSU rDNA sequences confirmed the species‘ distinct position and showed that M. clavata belongs to a moderately supported clade consisting of various Mycena and Hemimycena species, some of them recently transferred to the vaguely delimited genus Phloeomana.
The book describes and illustrates a total of 35 species surveyed, and 20 are new species that were collected from the southwestern region of Japan focusing on the Nansei Islands and Kyushu region.
A pedological study of the most common "latossolos amarelos, alicos, argilosos" (heavy yellow clay latossols) was made on the plateau of the ZF 2 region. The "initial reference state" under the primary forest is characterized by the presence of a medium horizon that is porous and contains strong micro-agregates between two less porous horizons. This soil is also characterized by a uniform and deeply distributed organic matter content. Soil under young secondary regrowth showed a different distribution of pores and organic matter. However with time, these evolve towards the former situation under the initial forest. Mechanically cultivated soils have a low porosity in the surface and progressively less organic matter down to 45cm.
Mycena margarita, a widespread agaric in the Caribbean region and recently recognized as frequently luminescent, is reported for the first time in Brazil, occurring on decaying wood in the Araripe National Forest, municipality of Crato, Ceará state. This species is fully described and illustrated and the description is accompanied by color photographs of fresh basidiomata. Comments on the taxonomy and ecology of the species are presented.
Mycena viscidocruenta is presently known only from the Antipodes. Collections from far eastern Russia were shown to be closely related both by morphology and by sequence homology. Phylogenetic analyses based on ribosomal LSU and ITS sequences show that the M. viscidocruenta clade is sister to Panellus stypticus and Panellus (Dictyopanus) pusillus, two laterally stipitate taxa, in the panelloid clade. Resinomycena rhododendri, the type species of Resinomycena is basal to this group. A new genus, Cruentomycena, is proposed to accommodate C. viscidocruenta (typus generis) and a new species, C. kedrovayae. Introduction Mycena viscidocruenta is a small (cap 7–11 mm), bright red agaric with a very slimy stem and cap. Fruiting on leaves and small woody debris, it has been reported from the southeastern Australian mainland and Tasmania (Grgurinovic 2002; Fungimap, Australia: http://fungimap.rbg.vic.gov.au), and from the North and South Islands of New Zealand (McKenzie et al. 2000, on Nothofagus debris; Segedin & Pennycook 2001; E. Horak, pers. com.). An LSU rDNA sequence of Tasmanian material was used by Moncalvo et al. (2002), who showed that collection to belong to the panelloid clade (denoted as /panelloid). That paper further noted that a relationship among Resinomycena rhododendri (typus generis), Mycena viscidocruenta, Panellus (pleurotoid, lamellate) and Dictyopanus (pleurotoid, poroid) had not previously been reported (Singer 1986), but did not discuss morphological circumscription of M. viscidocruenta or the proposed merger of Dictyopanus and Panellus (Burdsall & Miller 1975).
Fifteen bioluminescent fungi recently collected from Peninsular Malaysia are analysed herein. The phylogeny of the Malaysian bioluminescent fungi and closely related taxa were evaluated with molecular data from the nuclear ribosom-al large subunit (LSU), RNA polymerase 2 second largest subunit (RPB2) and internal transcribed spacers (ITS) gene regions. DNA sequences data support the circumscription of species based on the morphological species concept, but was unable to fully support the current sectional delimitation of genus Mycena. Of the 15 taxa analysed here, four are novel species described herein, viz. Mycena gombakensis, M. nocticaelum, M. coralliformis and Panellus luxfilamentus; while four taxa of Mycena sect. Calodontes were recently described as new. One species (M. noctilucens) represents a new distribution record to Peninsular Malaysia, and six spe-cies (Neonothopanus nambi, Filoboletus manipularis, P. luminescens, Roridomyces pruinosoviscidus, M. chlorophos and M. illuminans) have been previously reported. Roridomyces pruinosoviscidus is accepted as a new combina-tion based on morphological and phylogenetic data. Culture morphology data indicate its potential for taxon delimitation as axenic cultures of each species produced unique and dis-tinguishable characteristics. Comprehensive descriptions, il-lustrations and photographs are provided on basidiome and culture morphology. A key to aid in species identification, comparisons with allied species and data on basidiome and mycelium luminescence are also provided. This study gives the first report on mycelial luminescence for M. noctilucens, P. luminescens, R. pruinosoviscidus as well as all new species described herein. The reports in this study bring the total known luminescent fungi worldwide to 81 species.
Three new species and one new variety of bioluminescent Mycena collected from Peninsular Malaysia are described herein. All new species belong to Mycena sect. Calodontes in what is known as the Mycena pura complex. Comprehensive descriptions, photographs, illustrations and comparisons with phenetically similar species are provided. Molecular sequences data from the nuclear internal transcribed spacers (ITS-1 and ITS-2, including the 5.8S rRNA) were used to infer relationships within sect. Calodontes. Axenic cultures were obtained to provide data on culture morphology. This is the first published photographic documentation of bioluminescent basidiomes of members of Mycena sect. Calodontes. Also, this addition brings the total known bioluminescent fungi to 77 species.
Summary — A new agaric species, Mycena moconensis, is described from Paranaense Rain Forest Argentina. This species is characterized by a small basidomata, yellow, orange yellow to golden pileus and magent to purple stipe, pip shaped spores and diverticulate cheilocystidia.
Two lignicolous species ofMycena (Agaricales, Basidiomycetes) are described and illustrated from eastern, Japan:Mycena auricoma sp. nov., forming ephemeral coprinoid basidiomata and belonging to sectionRadiatae, was found on a dead fallen twig ofQuercus serrata. It appears to close to a Malaysian species,“Trogia” crinipelliformis. Mycena spinosissima in sectionSacchariferae, new to Japan, was collected from dead bark ofAphananthe aspera, a dead fallen inflorescence ofCryptomeria japonica, and a dead fallen twig ofQuercus serrata.
An epitype specimen is designated for Pleurotus cornucopiae. Morphological examination of Mexican material and the type specimen of P. opuntiae showed that the distribution of this species includes North Africa and the highlands of Mexico. The type specimen of Lentinus (Pleurotus) eugrammus reveals that Singer based his proposal of Nothopanus on a mistaken interpretation of L. eugrammus, and that the concept of Nothopanus requires a new name and type species. Neonothopanus is proposed to solve this problem. Morphological reports are supplemented with data on mating systems.
Mycena lacrimans (Agaricales, Mycenaceae) is redescribed from material collected recently near the type locality and is for the first time reported as bioluminescent. A comprehensive description, illustrations, photographs, comparison with phenetically similar species, and discussion of phylogenetic relationships are provided.
Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data.Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.Contact:
peter@biomatters.com
Since the early 20th century, many researchers have attempted to determine how fungi are able to emit light. The first successful experiment was obtained using the classical luciferin-luciferase test that consists of mixing under controlled conditions hot (substrate/luciferin) and cold (enzyme/luciferase) water extracts prepared from bioluminescent fungi. Failures by other researchers to reproduce those experiments using different species of fungi lead to the hypothesis of a non-enzymatic luminescent pathway. Only recently, the involvement of a luciferase in this system was proven, thus confirming its enzymatic nature. Of the 100 000 described species in Kingdom Fungi, only 71 species are known to be luminescent and they are distributed unevenly amongst four distantly related lineages. The question we address is whether the mechanism of bioluminescence is the same in all four evolutionary lineages suggesting a single origin of luminescence in the Fungi, or whether each lineage has a unique mechanism for light emission implying independent origins. We prepared hot and cold extracts of numerous species representing the four bioluminescent fungal lineages and performed cross-reactions (luciferin × luciferase) in all possible combinations using closely related non-luminescent species as controls. All cross-reactions with extracts from luminescent species yielded positive results, independent of lineage, whereas no light was emitted in cross-reactions with extracts from non-luminescent species. These results support the hypothesis that all four lineages of luminescent fungi share the same type of luciferin and luciferase, that there is a single luminescent mechanism in the Fungi, and that fungal luciferin is not a ubiquitous molecule in fungal metabolism.
Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
The bioluminescent agaric, Agaricus gardneri Berk., was rediscovered recently in central Brazil. The new combination, Neonothopanus gardneri, is proposed for this long-forgotten taxon supported by morphological and molecular data.
Bioluminescence spans all oceanic dimensions and has evolved many times--from bacteria to fish--to powerfully influence behavioral and ecosystem dynamics. New methods and technology have brought great advances in understanding of the molecular basis of bioluminescence, its physiological control, and its significance in marine communities. Novel tools derived from understanding the chemistry of natural light-producing molecules have led to countless valuable applications, culminating recently in a related Nobel Prize. Marine organisms utilize bioluminescence for vital functions ranging from defense to reproduction. To understand these interactions and the distributions of luminous organisms, new instruments and platforms allow observations on individual to oceanographic scales. This review explores recent advances, including the chemical and molecular, phylogenetic and functional, community and oceanographic aspects of bioluminescence.
This study provides a first broad systematic treatment of the euagarics as they have recently emerged in phylogenetic systematics. The sample consists of 877 homobasidiomycete taxa and includes approximately one tenth (ca. 700 species) of the known number of species of gilled mushrooms that were traditionally classified in the order Agaricales. About 1000 nucleotide sequences at the 5(') end of the nuclear large ribosomal subunit gene (nLSU) were produced for each taxon. Phylogenetic analyses of nucleotide sequence data employed unequally weighted parsimony and bootstrap methods. Clades revealed by the analyses support the recognition of eight major groups of homobasidiomycetes that cut across traditional lines of classification, in agreement with other recent phylogenetic studies. Gilled fungi comprise the majority of species in the euagarics clade. However, the recognition of a monophyletic euagarics results in the exclusion from the clade of several groups of gilled fungi that have been traditionally classified in the Agaricales and necessitates the inclusion of several clavaroid, poroid, secotioid, gasteroid, and reduced forms that were traditionally classified in other basidiomycete orders. A total of 117 monophyletic groups (clades) of euagarics can be recognized on the basis on nLSU phylogeny. Though many clades correspond to traditional taxonomic groups, many do not. Newly discovered phylogenetic affinities include for instance relationships of the true puffballs (Lycoperdales) with Agaricaceae, of Panellus and the poroid fungi Dictyopanus and Favolaschia with Mycena, and of the reduced fungus Caripia with Gymnopus. Several clades are best supported by ecological, biochemical, or trophic habits rather than by morphological similarities.
An overview of the phylogeny of the Agaricales is presented based on a multilocus analysis of a six-gene region supermatrix. Bayesian analyses of 5611 nucleotide characters of rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S ribosomal RNA genes recovered six major clades, which are recognized informally and labeled the Agaricoid, Tricholomatoid, Marasmioid, Pluteoid, Hygrophoroid and Plicaturopsidoid clades. Each clade is discussed in terms of key morphological and ecological traits. At least 11 origins of the ectomycorrhizal habit appear to have evolved in the Agaricales, with possibly as many as nine origins in the Agaricoid plus Tricholomatoid clade alone. A family-based phylogenetic classification is sketched for the Agaricales, in which 30 families, four unplaced tribes and two informally named clades are recognized.
Agarics (gilled mushrooms) and the order Agaricales include some of the best‐known and most charismatic fungi. However, neither group has had its constituent genera exhaustively compiled in a modern phylogenetic context. To provide that framework, we identified and analyzed 1383 names of genera of agarics (regardless of taxonomic placement) and the Agaricales (regardless of morphology), compiling various data for each name. Including 590 accepted names, the other 793 listed with reasons explaining their disuse, this compendium is intended to be comprehensive at present and phylogenetically up‐to‐date. Data we gathered included type species, continents from which type species were described, accepted synonyms of those species, current family placements, gross macromorphological categories, and sequenced loci (for type specimens, type species, and each genus as a whole). Index Fungorum provided a basis for the data, but much was manually confirmed, augmented, or corrected based on recent literature. Among accepted gilled genera, 82% belonged to the Agaricales; among accepted genera of Agaricales, 67% were gilled. Based on automated searches of GenBank and MycoCosm, 7% of generic names had DNA sequences of their type specimens, 68% had sequences of their type species, and 87% had sequences representing their genus. This leaves an estimated 103 accepted genera entirely lacking molecular data. Some subsets of genera have been sequenced relatively thoroughly (e.g., nidularioid genera and genera described from Europe); others relatively poorly (e.g., cyphelloid genera and genera described from Africa and tropical Asia). We also list nomenclaturally threatened and taxonomically doubtful genus and family names.
The taxonomy and phylogeny of the hydropoid clade (genera Clitocybula s.l., Megacollybia, Leucoinocybe gen. nov., Hydropus, Trogia, Gerronema, Porotheleum and Lignomphalia gen. nov.)in Europe is studied using morphological and molecular approaches; the first three genera in detail including all known European species. Only two European species remain in Clitocybula s.str., Clitocybula lacerata and Clitocybula familia. The European C. lacerata is a species complex which should be treated as C. lacerata agg. at the current state of knowledge. A neotype originating from type area was designated to fix the application of the name. The presence of American species Clitocybula abundans in Europe is insufficiently proved. “Clitocybula dryadicola ˮ belongs to the genus Hydropus, and Clitocybula tilieti has an unclear systematic position. The results showed that Megacollybia and Leucoinocybe represent independent genera separated from Clitocybula. The genus Leucoinocybe is validly published with two European species, Leucoinocybe lenta and Leucoinocybe taniae. “Clitocybula flavoaurantia” proved to be conspecific with the latter species. The genus Lignomphalia is published for “Pseudoomphalina lignicola”, a lignicolous omphalinoid species. The Indian “Clitocybula sulcata” is transferred to Leucoinocybe and “Clitocybula atrialba” to Gerronema. The first European records of Megacollybia marginata are published.
Omphalotaceae is the family of widely distributed and morphologically diverse marasmioid and gymnopoid agaric genera. Phylogenetic studies have included the family in Agaricales, grouping many traditionally and recently described genera of saprotrophic or parasitic mushroom-producing fungi. However, some genera in Omphalotaceae have not reached a stable concept that reflects monophyletic groups with identifiable morphological circumscription. This is the case of Gymnopus and Marasmiellus, which have been the target of two opposing views: (1) a more inclusive Gymnopus encompassing Marasmiellus, or (2) a more restricted Gymnopus (s. str.) while Marasmiellus remains a distict genus; both genera still await a more conclusive phylogenetic hypothesis coupled with morphological recognition. Furthermore, some new genera or undefined clades need more study. In the present paper, a phylogenetic study was conducted based on nrITS and nrLSU in single and multilocus analyses including members of the Omphalotaceae, more specifically of the genera belonging to the /letinuloid clade. The resulting trees support the view of a more restricted Gymnopus and a distinct Marasmiellus based on monophyletic and strongly supported clades on which their morphological circumscriptions and taxonomic treatments are proposed herein. The results also provide evidence for the description of two new genera: Paragymnopus and Pusillomyces. Pusillomyces manuripioides sp. nov. (type species of the genus) is described with morphological description, taxonomic and ecological remarks, and illustrations.
Limited research has been published on the mushroom-forming basidiomycetous fungi of the oceanic islands São Tomé and Príncipe, West Africa. Based on field work in April 2006 and 2008, which generated 24 specimens of mycenoid fungi, we recognize 14 species of Mycena, and 5 species belonging to the allied genera Clitocybula, Filoboletus, Hydropus and “Trogia”. Of these, 9 species are recognized herein as new to science, viz., Mycena antennae, M. brunneoviolacea, M. longinqua, M. oboensis, M. phaeonox, M. solis, Clitocybula intervenosa, Hydropus globosporus, and H. murinus; an additional 10 species are new distribution reports for São Tomé and Príncipe. Species delimitations are based on comprehensive morphological descriptions and molecular sequence (nLSU, ITS) data. Line drawings of salient micromorphological features, colour photographs of basidiomata, comparisons with allied taxa, a key to aid in identification, and phylogenetic inferences are provided.
Six species of bioluminescent agarics are described and illustrated from a single site in primary Atlantic Forest habitat in the Parque Estadual Turístico do Alto Ribeira, São Paulo State, Brazil. These include two new taxa of Mycena, viz. M. asterina and M. lucentipes. Luminescence in Mycena fera, M. singeri and M. discobasis is reported for the first time. In addition an undeterminable luminescent Mycena species is described and additional specimens of Gerronema viridilucens are documented. An accounting of known bioluminescent species of Mycena and a discussion of why they luminesce are presented.
Four species of mycenoid fungi are reported as luminescent (or putatively luminescent) on the basis of specimens collected from São Paulo State, Brazil. Two of them represent new species (Mycena oculisnymphae, Resinomycena petarensis), and two represent new reports of luminescence in previously described species (M. deformis, M. globulispora). Comprehensive descriptions, illustrations, photographs, and comparisons with phenetically similar species are provided. Sequences of nuc rDNA internal transcribed spacer regions were generated for barcoding purposes and for comparisons with similar species.
The enormity of the breadth and depth of specimens held within the world's biological collections offers unparalleled opportunities to capture genomic data from across the entire range of known biological diversity. Such a task would take many lifetimes to complete if we could rely only on fresh samples. High-throughput sequencing provides a technical solution to the long-term problems of recalcitrant and degraded DNA typical of museum specimens, suggesting that we may be on the verge of a major collections-based revolution. Although the potential is great, the feasibility of using preserved collections for large-scale, taxonomically comprehensive phylogenomic studies remains unknown. In the present study, we demonstrate the continued relevance of fungarium collections in the genomic era by analyzing a genomic dataset composed of 39 genomes representing 26 family-level clades, including 14 newly generated draft genomes derived from short-read shotgun sequencing of preserved specimens, frozen and freeze-dried material, representing most of the known families of Agaricales. We predicted homologues of 210 putative single copy genes in the newly generated draft genome assemblies, of which 208 were used for phylogenetic reconstruction. Our analyses resulted in a robust and, for the first time, fully supported phylogeny of the Agaricales, enabling the recognition of seven suborders and providing a resource for testing hypotheses of the evolution of mushrooms. Our analysis of optimal combinations of ranked genes using an information theory-based method provides guidance on gene selection for future studies, enabling efficient application of high-throughput sequencing techniques toward unlocking the potential of collections-based research in the genomic era.
Bioluminescence, the creation and emission of light by organisms, affords insight into the lives of organisms doing it. Luminous living things are widespread and access diverse mechanisms to generate and control luminescence [1-5]. Among the least studied bioluminescent organisms are phylogenetically rare fungi-only 71 species, all within the ∼9,000 fungi of the temperate and tropical Agaricales order-are reported from among ∼100,000 described fungal species [6, 7]. All require oxygen [8] and energy (NADH or NADPH) for bioluminescence and are reported to emit green light (λmax 530 nm) continuously, implying a metabolic function for bioluminescence, perhaps as a byproduct of oxidative metabolism in lignin degradation. Here, however, we report that bioluminescence from the mycelium of Neonothopanus gardneri is controlled by a temperature-compensated circadian clock, the result of cycles in content/activity of the luciferase, reductase, and luciferin that comprise the luminescent system. Because regulation implies an adaptive function for bioluminescence, a controversial question for more than two millennia [8-15], we examined interactions between luminescent fungi and insects [16]. Prosthetic acrylic resin "mushrooms," internally illuminated by a green LED emitting light similar to the bioluminescence, attract staphilinid rove beetles (coleopterans), as well as hemipterans (true bugs), dipterans (flies), and hymenopterans (wasps and ants), at numbers far greater than dark control traps. Thus, circadian control may optimize energy use for when bioluminescence is most visible, attracting insects that can in turn help in spore dispersal, thereby benefitting fungi growing under the forest canopy, where wind flow is greatly reduced.
Copyright © 2015 Elsevier Ltd. All rights reserved.
Bioluminescence is widely recognized among white-spored species of Basidiomycota. Most reports of fungal bioluminescence are based upon visual light perception. When instruments such as photomultipliers have been used to measure fungal luminescence, more taxa have been discovered to produce light, albeit at a range of magnitudes. The present studies were undertaken to determine the prevalence of bioluminescence among North American Armillaria species. Consistent, constitutive bioluminescence was detected for the first time for mycelia of Armillaria calvescens, Armillaria cepistipes, Armillaria gemina, Armillaria nabsnona, and Armillaria sinapina and confirmed for mycelia of Armillaria gallica, Armillaria mellea, Armillaria ostoyae, and Armillaria tabescens. Emission spectra of mycelia representing all species had maximum intensity in the range 515-525 nm confirming that emitted light was the result of bioluminescence rather than chemiluminescence. Time series analysis of 1000 consecutive luminescence measurements revealed a highly significant departure from random variation. Mycelial luminescence of eight species exhibited significant, stable shifts in magnitude in response to a series of mechanical disturbance treatments, providing one mechanism for generating observed luminescence variation.
Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.
