Fungi in the Age of Extinction
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The mechanism of ascus firing – Merging biophysical and mycological viewpoints

The mechanism of ascus firing – Merging biophysical and mycological viewpoints | Fungi in the Age of Extinction | Scoop.it

The actively discharging ascus is the unique spore-bearing cell that is responsible to dispatch spores into the atmosphere. From a physical perspective, this type of ascus is a sophisticated pressure gun that reliably discharges the spores at an extremely high velocity, without breaking apart. We identify four essential steps in discharge of spores whose order and timing may vary across species. First, asci that fire are mature, so a cue must be present that prevents discharge of immature spores and signals maturity. Second, pressure within the ascus serves to propel the spores forward; therefore a mechanism should be present to pressurize the ascus. Third, in ostiolate fruiting bodies (e.g. perithecia), the ascus extends through an opening to fire spores into the air. The extension process is a relatively unique aspect of the ascus and must be structurally facilitated. Fourth, the ascus must open at its tip for spore release in a controlled rupture. Here we discuss each of these aspects in the context of understanding the process of ascus and fruiting body function. While there is great diversity among fungi, we focus on discharge in a few model species, and then discuss how this framework may vary in other fungi. Our goal is to tie the physiological and molecular studies of ascus function with concepts in engineering that dictate structure.


Via Alejandro Rojas
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Natural Constraints to Species Diversification

Natural Constraints to Species Diversification | Fungi in the Age of Extinction | Scoop.it

Identifying modes of species diversification is fundamental to our understanding of how biodiversity changes over evolutionary time. Diversification modes are captured in species phylogenies, but characterizing the landscape of diversification has been limited by the analytical tools available for directly comparing phylogenetic trees of groups of organisms. Here, we use a novel, non-parametric approach and 214 family-level phylogenies of vertebrates representing over 500 million years of evolution to identify major diversification modes, to characterize phylogenetic space, and to evaluate the bounds and central tendencies of species diversification. We identify five principal patterns of diversification to which all vertebrate families hold. These patterns, mapped onto multidimensional space, constitute a phylogenetic space with distinct properties. Firstly, phylogenetic space occupies only a portion of all possible tree space, showing family-level phylogenies to be constrained to a limited range of diversification patterns. Secondly, the geometry of phylogenetic space is delimited by quantifiable trade-offs in tree size and the heterogeneity and stem-to-tip distribution of branching events. These trade-offs are indicative of the instability of certain diversification patterns and effectively bound speciation rates (for successful clades) within upper and lower limits. Finally, both the constrained range and geometry of phylogenetic space are established by the differential effects of macroevolutionary processes on patterns of diversification. Given these properties, we show that the average path through phylogenetic space over evolutionary time traverses several diversification stages, each of which is defined by a different principal pattern of diversification and directed by a different macroevolutionary process. The identification of universal patterns and natural constraints to diversification provides a foundation for understanding the deep-time evolution of biodiversity.


Via Pierre Gladieux, Christian Schwarz
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Global Extinction Rates: Why Do Estimates Vary So Wildly? by Fred Pearce: Yale Environment 360

Global Extinction Rates: Why Do Estimates Vary So Wildly? by Fred Pearce: Yale Environment 360 | Fungi in the Age of Extinction | Scoop.it
Is it 150 species a day or 24 a day or far less than that? Prominent scientists cite dramatically different numbers when estimating the rate at which species are going extinct. Why is that?
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Phylogenomic analyses indicate that early fungi evolved digesting cell walls of algal ancestors of land plants

As decomposers, fungi are key players in recycling plant material in global carbon cycles. We hypothesized that genomes of early diverging fungi may have inherited pectinases from an ancestral species that had been able to extract nutrients from pectin-containing land plants and their algal allies (Streptophytes). We aimed to infer, based on pectinase gene expansions and on the organismal phylogeny, the geological timing of the plant-fungus association. We analyzed 40 fungal genomes, three of which, including Gonapodya prolifera, were sequenced for this study. In the organismal phylogeny from 136 housekeeping loci, Rozella diverged first from all other fungi. Gonapodya prolifera was included among the flagellated, predominantly aquatic fungal species in Chytridiomycota. Sister to the Chytridiomycota were the predominantly terrestrial fungi including zygomycota I and II, along with the ascomycetes and basidiomycetes that comprise Dikarya. The Gonapodya genome has 27 genes representing five of the seven classes of pectin-specific enzymes known from fungi. Most of these share a common ancestry with pectinases from Dikarya. Indicating functional as well as sequence similarity,Gonapodya, like many Dikarya, can use pectin as a carbon source for growth in pure culture. Shared pectinases of Dikarya and Gonapodyaprovide evidence that even ancient aquatic fungi had adapted to extract nutrients from the plants in the green lineage. This implies that 750 million years, the estimated maximum age of origin of the pectin-containing streptophytes represents a maximum age for the divergence of Chytridiomycota from the lineage including Dikarya.

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A peek into the world of fungi

A peek into the world of fungi | Fungi in the Age of Extinction | Scoop.it

From the time they inhabited the landmasses some 500 million years ago, fungi have played a fundamental role in Earth’s geochemical cycles. They are important ingredients for healthy and agriculturally viable soil as they decompose dead organic matter to provide necessary nutrients to plants. The balance of fungal communities can even directly affect the carbon cycle and, thereby, the pace of climate change. Yet, due to their concealed existence—most fungi are microscopic and live beneath the soil—we know very little of their global ecology.

In the recent past, several studies have sought to advance our understanding of fungal ecosystems and highlight the important role soil fungi play in sustainable soil management, forest preservation and climate change mitigation. Now, in a first-of-its-kind study, a team of scientists, led by Leho Tedersoo of the University of Tartu, Estonia, sampled the microbial life of the soil at 365 locations across six continents to know about the basic drivers of fungal biodiversity. They studied the distribution of fungal communities at each site along with soil pH, rainfall pattern, plant diversity and spatial variables.


Via Francis Martin
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New records of Dothideomycetes from Mexico: ingentaconnect

New records of Dothideomycetes from Mexico: ingentaconnect | Fungi in the Age of Extinction | Scoop.it

"Ten dothideomycetous species were studied. New records for the Mexican mycobiota include Heptameria obesa, Leptospora rubella, Macrovalsaria megalospora, and Psiloglonium clavisporum, and an extended distribution for rarely reported dothideomycetes in Mexico is reported for Anteaglonium abbreviatum, Astrosphaeriella trochus, Gloniopsis praelonga, Hysterobrevium mori, Oedohysterium insidens, and Rhytidhysteron rufulum. Observations and photographs on macro- and microscopic characters are provided."

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The Evolution of Fungal Metabolic Pathways

The Evolution of Fungal Metabolic Pathways | Fungi in the Age of Extinction | Scoop.it

Fungi contain a remarkable range of metabolic pathways, sometimes encoded by gene clusters, enabling them to digest most organic matter and synthesize an array of potent small molecules. Although metabolism is fundamental to the fungal lifestyle, we still know little about how major evolutionary processes, such as gene duplication (GD) and horizontal gene transfer (HGT), have interacted with clustered and non-clustered fungal metabolic pathways to give rise to this metabolic versatility. We examined the synteny and evolutionary history of 247,202 fungal genes encoding enzymes that catalyze 875 distinct metabolic reactions from 130 pathways in 208 diverse genomes. We found that gene clustering varied greatly with respect to metabolic category and lineage; for example, clustered genes in Saccharomycotina yeasts were overrepresented in nucleotide metabolism, whereas clustered genes in Pezizomycotina were more common in lipid and amino acid metabolism. The effects of both GD and HGT were more pronounced in clustered genes than in their non-clustered counterparts and were differentially distributed across fungal lineages; specifically, GD, which was an order of magnitude more abundant than HGT, was most frequently observed in Agaricomycetes, whereas HGT was much more prevalent in Pezizomycotina. The effect of HGT in some Pezizomycotina was particularly strong; for example, we identified 111 HGT events associated with the 15 Aspergillus genomes, which sharply contrasts with the 60 HGT events detected for the 48 genomes from the entire Saccharomycotina subphylum. Finally, the impact of GD within a metabolic category was typically consistent across all fungal lineages, whereas the impact of HGT was variable. These results indicate that GD is the dominant process underlying fungal metabolic diversity, whereas HGT is episodic and acts in a category- or lineage-specific manner. Both processes have a greater impact on clustered genes, suggesting that metabolic gene clusters represent hotspots for the generation of fungal metabolic diversity.


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Ordering microbial diversity into ecologically and genetically cohesive units

Ordering microbial diversity into ecologically and genetically cohesive units | Fungi in the Age of Extinction | Scoop.it

Abstract: 

We propose that microbial diversity must be viewed in light of gene flow and selection, which define units of genetic similarity, and of phenotype and ecological function, respectively. We discuss to what extent ecological and genetic units overlap to form cohesive populations in the wild, based on recent evolutionary modeling and on evidence from some of the first microbial populations studied with genomics. These show that if recombination is frequent and selection moderate, ecologically adaptive mutations or genes can spread within populations independently of their original genomic background (gene-specific sweeps). Alternatively, if the effect of recombination is smaller than selection, genome-wide selective sweeps should occur. In both cases, however, distinct units of overlapping ecological and genotypic similarity will form if microgeographic separation, likely involving ecological tradeoffs, induces barriers to gene flow. These predictions are supported by (meta)genomic data, which suggest that a ‘reverse ecology’ approach, in which genomic and gene flow information is used to make predictions about the nature of ecological units, is a powerful approach to ordering microbial diversity.

  


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High-Resolution Global Maps of 21st-Century Forest Cover Change

High-Resolution Global Maps of 21st-Century Forest Cover Change | Fungi in the Age of Extinction | Scoop.it

"Quantification of global forest change has been lacking despite the recognized importance of forest ecosystem services. In this study, Earth observation satellite data were used to map global forest loss (2.3 million square kilometers) and gain (0.8 million square kilometers) from 2000 to 2012 at a spatial resolution of 30 meters. The tropics were the only climate domain to exhibit a trend, with forest loss increasing by 2101 square kilometers per year. Brazil’s well-documented reduction in deforestation was offset by increasing forest loss in Indonesia, Malaysia, Paraguay, Bolivia, Zambia, Angola, and elsewhere. Intensive forestry practiced within subtropical forests resulted in the highest rates of forest change globally. Boreal forest loss due largely to fire and forestry was second to that in the tropics in absolute and proportional terms. These results depict a globally consistent and locally relevant record of forest change."

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This hits home as I embark on research aimed at uncovering fungal diversity in the disappearing tropical forests of the Neotropics.

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Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood

Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood | Fungi in the Age of Extinction | Scoop.it
"Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine wood. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of wood extractives were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea's extractives metabolism. These results contribute to our fundamental understanding of pioneer colonization of conifer wood and provide insight into the diverse chemistries employed by fungi in carbon cycling processes."
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Synthesis of phylogeny and taxonomy into a comprehensive tree of life

"Reconstructing the phylogenetic relationships that unite all biological lineages (the tree of life) is a grand challenge of biology. However, the paucity of readily available homologous character data across disparately related lineages renders direct phylogenetic inference currently untenable. Our best recourse towards realizing the tree of life is therefore the synthesis of existing collective phylogenetic knowledge available from the wealth of published primary phylogenetic hypotheses, together with taxonomic hierarchy information for unsampled taxa. We combined phylogenetic and taxonomic data to produce a draft tree of life?the Open Tree of Life?containing 2.3 million tips. Realization of this draft tree required the assembly of two resources that should prove valuable to the community: 1) a novel comprehensive global reference taxonomy, and 2) a database of published phylogenetic trees mapped to this common taxonomy. Our open source framework facilitates community comment and contribution, enabling a continuously updatable tree when new phylogenetic and taxonomic data become digitally available. While data coverage and phylogenetic conflict across the Open Tree of Life illuminates significant gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point from which we can continue to improve through community contributions. Having a comprehensive tree of life will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change studies, agriculture, and genomics."
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Taxonomy of the Truffles

Truffles are the hypogeous fruiting bodies of Ascomycete fungi that live in symbiosis with roots of trees such as oaks, hazels, poplar, etc. Due to limited morphological characters, these fungi are difficult to identify at species level. Molecular phylogenetic studies have recently demonstrated that morphological characters of hypogeous Ascomycetes can be unreliable.

Via Jean-Michel Ané
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Global diversity and geography of soil fungi

Global diversity and geography of soil fungi | Fungi in the Age of Extinction | Scoop.it

"Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macro ecological framework".

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Gates Foundation mandates open access for all the research it funds

Gates Foundation mandates open access for all the research it funds | Fungi in the Age of Extinction | Scoop.it
“Effective January 17, all research funded in whole or in part by the Bill and Melinda Gates Foundation must be published in journals that are immediately free-to-access, under a Creative Commons Attribution-only license.”
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Origins of the terrestrial flora: A symbiosis with fungi?

Land phototrophs need to exploit both atmosphere (providing gas and light) and substrate (furnishing water and minerals). Yet, their algal ancestors were poorly pre-adapted to such a life at the interface. We review the paleontological evidence that fungal symbioses which can exploit substrate resources, helped adaptation to land constraints. Diverse structures dating back to the Devonian present convincing evidence for lichens, (symbioses between fungi and microscopic algae) but fossils remain scarce, so that early lichen abundance and ecological relevance remain questionable. Several enigmatic but abundant fossils from the Siluro-Devonian, such as Spongiophytonor the giant Prototaxites (Nematophytes), likely represent fungus-algal symbioses, which shaped early terrestrial ecosystems. Yet, these taxa are fully extinct, and do not have clear affinities with extant groups. Finally, terrestrialization of Embryophyta (land plants), which currently dominate land ecosystems, is linked to a symbiosis with Glomeromycetes. Today, these fungi form arbuscular mycorrhizae, which help most Embryophyta to exploit soil, and molecular data combined with paleontological evidence support the idea that this type of association is ancestral. The role of symbiotic Mucoromycetes during terrestrialization is not fully understood and mycorrhizal association diversified later in the evolution of Embryophyta. Fungal-algal symbioses thus recurrently contributed to terrestrialization of phototrophs.

Via Jean-Michel Ané
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Jean-Michel Ané's curator insight, September 1, 2015 11:25 AM

Another great review from Marc-André Selosse. A must read.

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Research shows catastrophic invertebrate extinction in Hawaiʻi and globally

Research shows catastrophic invertebrate extinction in Hawaiʻi and globally | Fungi in the Age of Extinction | Scoop.it
New study provides rigorous assessment of extinction of invertebrates in Hawaiʻi.
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Not exactly about fungi but relevant to the threats faced by organisms globally, including fungi.

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Entorrhizomycota: A New Fungal Phylum Reveals New Perspectives on the Evolution of Fungi

Entorrhizomycota: A New Fungal Phylum Reveals New Perspectives on the Evolution of Fungi | Fungi in the Age of Extinction | Scoop.it
by Robert Bauer, Sigisfredo Garnica, Franz Oberwinkler, Kai Riess, Michael Weiß, Dominik Begerow
Entorrhiza is a small fungal genus comprising 14 species that all cause galls on roots of Cyperaceae and Juncaceae.

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The importance of fungi and mycology for addressing major global challenges


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Phylogenetic diversity of true morels (Morchella), the main edible non-timber product from native Patagonian forests of Argentina

Phylogenetic diversity of true morels (Morchella), the main edible non-timber product from native Patagonian forests of Argentina | Fungi in the Age of Extinction | Scoop.it

"Morchella species are edible fungi in high demand and therefore command high prices in world markets. Phenotypic-based identification at the species-level remains inadequate because of their complex life cycles, minor differences and plasticity of morphological characteristics between species, and the lack of agreement between scientific and common names. In Patagonia–Argentina, morels are associated with native forests of Austrocedrus chilensis (Cordilleran or Chilean cypress) and Nothofagus antarctica (ñire) and several exotic conifers that were introduced from western North America. Little is known about their taxonomy and phylogenetic relationships with other species in the genus. This work focused on the identification of collections of Morchella from Patagonia and their phylogenetic relationships with other species from the Northern Hemisphere. The comparison was made by analysis of DNA sequences obtained from four loci: the nuclear ribosomal internal transcribed spacer region (ITS) and the partial RNA polymerase I gene (RPB1) for the complete collection; and ITS, RPB1, RNA polymerase II gene (RPB2), and translation elongation factor (EF1-α) for the species-rich Elata Subclade. Analyses of individual and combined data sets revealed that Patagonian morels belong to the Elata Clade and comprised three strongly supported species-level lineages from both Patagonian native forest, and exotic trees introduced from western North America. One lineage was identified as Morchella frustrata phylogenetic species Mel-2, which is known from the USA and Canada. The second lineage, which appeared to be ‘fire-adapted’, was identified as Morchella septimelata phylogenetic species (Mel-7), which is also known from the USA. This species was collected from burned native forests mainly composed of A. chilensis and N. antarctica but also Pseudotsuga menziesii (Mirb.) Blanco, which is native to western North America. The phylogenetic analyses suggested that the third species from Patagonia was nested within the species-rich Elata Subclade and represents a new species-level lineage (informally designated Mel-37) within Elata Clade. The present collections from Patagonia constitute the southernmost latitude from which Morchella has been reported to date. The identification of two Argentine morels as North American taxa is therefore a remarkable biogeographic pattern. In view of the hypothesis that the Elata Clade originated in western North America, we speculate that at least two of the lineages colonized South America from North America via long distance dispersal, migration or, more likely, they were introduced with the exotic tree species that they were collected near."

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Manfred Girbardt and Charles Bracker: outstanding pioneers in fungal microscopy : Nature Reviews Microbiology : Nature Publishing Group

Manfred Girbardt and Charles Bracker: outstanding pioneers in fungal microscopy : Nature Reviews Microbiology : Nature Publishing Group | Fungi in the Age of Extinction | Scoop.it
Midway through the twentieth century, the availability of new and improved optical and electronic microscopes facilitated rapid advances in the elucidation of the fine structure of fungal cells. In this Essay, I pay tribute to Manfred Girbardt (1919–1991) and Charles Bracker (1938–2012) — two individuals who, despite being separated by geography and the restrictions of the Cold War, both made equally fundamental discoveries in fungal cell ultrastructure and set high standards for specimen manipulation and image processing.

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Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests

Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests | Fungi in the Age of Extinction | Scoop.it
Boreal forest soils store a major proportion of the global terrestrial carbon (C) and below-ground inputs contribute as much as above-ground plant litter to the total C stored in the soil. A better understanding of the dynamics and drivers of root-associated fungal communities is essential to predict long-term soil C storage and climate feedbacks in northern ecosystems.
We used 454-pyrosequencing to identify fungal communities across fine-scaled soil profiles in a 5000 yr fire-driven boreal forest chronosequence, with the aim of pinpointing shifts in fungal community composition that may underlie variation in below-ground C sequestration.
In early successional-stage forests, higher abundance of cord-forming ectomycorrhizal fungi (such as Cortinarius and Suillus species) was linked to rapid turnover of mycelial biomass and necromass, efficient nitrogen (N) mobilization and low C sequestration. In late successional-stage forests, cord formers declined, while ericoid mycorrhizal ascomycetes continued to dominate, potentially facilitating long-term humus build-up through production of melanized hyphae that resist decomposition.
Our results suggest that cord-forming ectomycorrhizal fungi and ericoid mycorrhizal fungi play opposing roles in below-ground C storage. We postulate that, by affecting turnover and decomposition of fungal tissues, mycorrhizal fungal identity and growth form are critical determinants of C and N sequestration in boreal forests.

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Diagnosis and discovery of fungal viruses using deep sequencing of ... - PubMed - NCBI

Diagnosis and discovery of fungal viruses using deep sequencing of ... - PubMed - NCBI | Fungi in the Age of Extinction | Scoop.it

"Analysis of virus-derived small RNAs with high-throughput sequencing has been successful for detecting novel viruses in plants and invertebrates. However, the applicability of this method has not been demonstrated in fungi, although fungi were among the first organisms reported to utilize RNA silencing. Here, we used virus-infected isolates of the fungal species complex Heterobasidion annosum sensu lato as a model system to test whether mycovirus genome segments can be detected with small RNA deep sequencing. Species of Heterobasidion are some of the most devastating forest pathogens in boreal forests. These fungi cause wood decay and are commonly infected with species of Partitiviridae and the yet unassigned virus species Heterobasidion RNA virus 6 (HetRV6). Small RNA deep sequencing allowed the simultaneous detection of all eight double-stranded RNA virus strains known to be present in the tested samples and one putative mitovirus species (family Narnaviridae) with a single-stranded RNA genome, designated here as Heterobasidion mitovirus 1. Prior to this study, no members of the family Narnaviridae had been described as infecting species of Heterobasidion. Quantification of viral double- and single-stranded RNA with quantitative PCR indicated that co-infecting viral species and viruses with segmented genomes can be detected with small RNA deep sequencing despite vast differences in the amount of RNA. This is the first study demonstrating the usefulness of this method for detecting fungal viruses. Moreover, the results suggest that viral genomes are processed into small RNAs by different species of Heterobasidion."

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The mechanism of ascus firing – Merging biophysical and mycological viewpoints

The mechanism of ascus firing – Merging biophysical and mycological viewpoints | Fungi in the Age of Extinction | Scoop.it

The actively discharging ascus is the unique spore-bearing cell that is responsible to dispatch spores into the atmosphere. From a physical perspective, this type of ascus is a sophisticated pressure gun that reliably discharges the spores at an extremely high velocity, without breaking apart. We identify four essential steps in discharge of spores whose order and timing may vary across species. First, asci that fire are mature, so a cue must be present that prevents discharge of immature spores and signals maturity. Second, pressure within the ascus serves to propel the spores forward; therefore a mechanism should be present to pressurize the ascus. Third, in ostiolate fruiting bodies (e.g. perithecia), the ascus extends through an opening to fire spores into the air. The extension process is a relatively unique aspect of the ascus and must be structurally facilitated. Fourth, the ascus must open at its tip for spore release in a controlled rupture. Here we discuss each of these aspects in the context of understanding the process of ascus and fruiting body function. While there is great diversity among fungi, we focus on discharge in a few model species, and then discuss how this framework may vary in other fungi. Our goal is to tie the physiological and molecular studies of ascus function with concepts in engineering that dictate structure.


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BMC Research Notes: ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences

BMC Research Notes: ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences | Fungi in the Age of Extinction | Scoop.it
Studies on fungal diversity and ecology aim to identify fungi and to investigate their interactions with each other and with the environment. DNA sequence-based tools are essential for these studies because they can speed up the identification process and access greater fungal diversity than traditional methods. The nucleotide sequence encoding for the internal transcribed spacer (ITS) of the nuclear ribosomal RNA has recently been proposed as a standard marker for molecular identification of fungi and evaluation of fungal diversity. However, the analysis of large sets of ITS sequences involves many programs and steps, which makes this task intensive and laborious.

Via Stéphane Hacquard, Francis Martin
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Twenty‐first century mycology: a diverse, collaborative, and highly relevant science - Kennedy - 2014 - New Phytologist

Twenty‐first century mycology: a diverse, collaborative, and highly relevant science - Kennedy - 2014 - New Phytologist | Fungi in the Age of Extinction | Scoop.it

"In June 2014, over 250 researchers from a variety of national and international locations attended the annual meeting of the Mycological Society of America (MSA), which was held on the campus of Michigan State University in East Lansing, MI, USA. Talks, posters, and symposia covered an impressive breadth of fungal biology organized around four main research themes: cell biology/physiology, ecology/pathology, genetics/molecular biology, and systematics. The taxonomic diversity of the fungal kingdom was highlighted throughout the meeting, with presentations covering all of the major fungal lineages. While the core of the talks was on the fungi themselves, many emphasized interactions with other species, including a wide range of plants, animals, and bacteria. It was also clear that mycologists have adopted all the latest ‘–omics’ and next generation sequencing methodologies to ask cutting-edge questions about topics such as infectious disease, climate change, and bioremediation. At the same time, in the era where almost anyone can generate a fungal sequence, strong organism-based knowledge has become even more important (see in this issue of New Phytologist, Herr et al., pp. 27–31). Fortunately, this was on consistent display throughout the meeting and the MSA has long been a welcoming community to researchers from all disciplinary backgrounds. Below we summarize a handful of the many meeting highlights."

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Morphological and molecular characterization of three Agaricus species from tropical Asia (Pakistan, Thailand) reveals a new group in section Xanthodermatei

Morphological and molecular characterization of three Agaricus species from tropical Asia (Pakistan, Thailand) reveals a new group in section Xanthodermatei | Fungi in the Age of Extinction | Scoop.it

"The genus Agaricus is known for its medicinal and edible species but also includes toxic species that belong to section Xanthodermatei. Previous phylogenetic reconstruction for temperate species, based on sequence data of nuc rRNA gene (rDNA) internal transcribed spacers (ITS), has revealed two major groups in this section and a possible third lineage for A. pseudopratensis. Recent research in Agaricus has shown that classifications need improving with the addition of tropical taxa. In this study we add new tropical collections to section Xanthodermatei. We describe three species from collections made in Pakistan and Thailand and include them in a larger analysis using all available ITS data for section Xanthodermatei. Agaricus bisporiticus sp. nov. and A. fuscopunctatus sp. nov. are introduced based on molecular and morphological studies, whereas A. microvolvatulus is recorded for the first time in Asia. Specimens from Thailand however have a much larger pileus than the type specimens from Congo. In maximum likelihood (ML) and maximum parsimony (MP) phylogenetic analyses these three species cluster with A. pseudopratensis from the Mediterranean area and A. murinocephalus recently described from Thailand. In Agaricus section Xanthodermatei this new group is monophyletic and receives low bootstrap support whereas the two previously known groups receive strong support. Within the new group, the most closely related species share some traits, but we did not find any unifying morphological character; however the five species of the group share a unique short nucleotide sequence. Two putatively toxic species of section Xanthodermatei are now recognized in Pakistan and six in Thailand".

 
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