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Altering the Cell Wall and Its Impact on Plant Disease: From Forage to Bioenergy

Altering the Cell Wall and Its Impact on Plant Disease: From Forage to Bioenergy | MycorWeb Plant-Microbe Interactions | Scoop.it

The individual sugars found within the major classes of plant cell wall polymers are dietary components of herbivores and are targeted for release in industrial processes for fermentation to liquid biofuels. With a growing understanding of the biosynthesis of the complex cell wall polymers, genetic modification strategies are being developed to target the cell wall to improve the digestibility of forage crops and to render lignocellulose less recalcitrant for bioprocessing. This raises concerns as to whether altering cell wall properties to improve biomass processing traits may inadvertently make plants more susceptible to diseases and pests. Here, we review the impacts of cell wall modification on plant defense, as assessed from studies in model plants utilizing mutants or transgenic modification and in crop plants specifically engineered for improved biomass or bioenergy traits. Such studies reveal that cell wall modifications can indeed have unintended impacts on plant defense, but these are not always negative.


Via Christophe Jacquet
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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 | MycorWeb Plant-Microbe Interactions | 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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Missing checkerboards? An absence of competitive signal in Alnus-associated ectomycorrhizal fungal communities

Missing checkerboards? An absence of competitive signal in Alnus-associated ectomycorrhizal fungal communities | MycorWeb Plant-Microbe Interactions | Scoop.it


A number of recent studies suggest that interspecific competition plays a key role in determining the structure of ectomycorrhizal (ECM) fungal communities. Despite this growing consensus, there has been limited study of ECM fungal community dynamics in abiotically stressful environments, which are often dominated by positive rather than antagonistic interactions. In this study, we examined the ECM fungal communities associated with the host genus Alnus, which live in soils high in both nitrate and acidity. The nature of ECM fungal species interactions (i.e., antagonistic, neutral, or positive) was assessed using taxon co-occurrence and DNA sequence abundance correlational analyses. ECM fungal communities were sampled from root tips or mesh in-growth bags in three monodominant A. rubra plots at a site in Oregon, USA and identified using Illumina-based amplification of the ITS1 gene region. We found a total of 175 ECM fungal taxa; 16 of which were closely related to known Alnus-associated ECM fungi. Contrary to previous studies of ECM fungal communities, taxon co-occurrence analyses on both the total and Alnus-associated ECM datasets indicated that the ECM fungal communities in this system were not structured by interspecific competition. Instead, the co-occurrence patterns were consistent with either random assembly or significant positive interactions. Pair-wise correlational analyses were also more consistent with neutral or positive interactions. Taken together, our results suggest that interspecific competition does not appear to determine the structure of all ECM fungal communities and that abiotic conditions may be important in determining the specific type of interaction occurring among ECM fungi.

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Was cool to edit this paper for PeerJ!

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Novel interactions between non-native mammals and fungi facilitate establishment of invasive pines

Novel interactions between non-native mammals and fungi facilitate establishment of invasive pines | MycorWeb Plant-Microbe Interactions | Scoop.it
The role of novel ecological interactions between mammals, fungi and plants in invaded ecosystems remains unresolved, but may play a key role in the widespread successful invasion of pines and their ectomycorrhizal fungal associates, even where mammal faunas originate from different continents to trees and fungi as in New Zealand.We examine the role of novel mammal associations in dispersal of ectomycorrhizal fungal inoculum of North American pines (Pinus contorta, Pseudotsuga menziesii), and native beech trees (Lophozonia menziesii) using faecal analyses, video monitoring and a bioassay experiment.Both European red deer (Cervus elaphus) and Australian brushtail possum (Trichosurus vulpecula) pellets contained spores and DNA from a range of native and non-native ectomycorrhizal fungi.Faecal pellets from both animals resulted in ectomycorrhizal infection of pine seedlings with fungal genera Rhizopogon and Suillus, but not with native fungi or the invasive fungus Amanita muscaria, despite video and DNA evidence of consumption of these fungi.Native L. menziesii seedlings never developed any ectomycorrhizal infection from faecal pellet inoculation.Synthesis. Our results show that introduced mammals from Australia and Europe facilitate the co-invasion of invasive North American trees and Northern Hemisphere fungi in New Zealand, while we find no evidence that introduced mammals benefit native trees or fungi. This novel tripartite ‘invasional meltdown’, comprising taxa from three kingdoms and three continents, highlights unforeseen consequences of global biotic homogenization.
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A Flock of Bird Data Comes to Roost

A Flock of Bird Data Comes to Roost | MycorWeb Plant-Microbe Interactions | Scoop.it
In the long history of humankind (and animal kind too) those who learned to collaborate and improvise most effectively have prevailed.
—Attributed to Charles Darwin
In 1839 Charles Darwin published his famous account of the 5-year second voyage of the HMS Beagle, describing the flora and fauna he encountered surveying South America and circumnavigating the globe, including the famous Galápagos finches that helped develop much his theory of evolution. Providing his descriptions of these species
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Widespread polycistronic transcripts in mushroom-forming fungi revealed by single-molecule long-read mRNA sequencing

Widespread polycistronic transcripts in mushroom-forming fungi revealed by single-molecule long-read mRNA sequencing | MycorWeb Plant-Microbe Interactions | Scoop.it
Genes in prokaryotic genomes are often arranged into clusters and co-transcribed into polycistronic RNAs. Isolated examples of polycistronic RNAs were also reported in some eukaryotes but their presence was generally considered rare. Here we developed a long-read sequencing strategy to identify polycistronic transcripts in several mushroom forming fungal species including Plicaturopsis crispa, Phanerochaete chrysosporium, Trametes versicolor and Gloeophyllum trabeum1. We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, and it involves up to 8% of the transcribed genes. Unlike polycistronic mRNAs in prokaryotes, these co-transcribed genes are also independently transcribed, and upstream transcription may interfere downstream transcription. Further comparative genomic analysis indicates that polycistronic transcription is likely a feature unique to these fungi. In addition, we also systematically demonstrated that short-read assembly is insufficient for mRNA isoform discovery, especially for isoform-rich loci. In summary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a subset of fungi. Futhermore, our long-read sequencing approach combined with bioinformatics pipeline is a generic powerful tool for precise characterization of complex transcriptomes.
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36th New Phytologist Symposium: Cell biology at the plant–microbe interface, Munich, Germany 29 Nov – 1 Dec 2015

36th New Phytologist Symposium: Cell biology at the plant–microbe interface, Munich, Germany 29 Nov – 1 Dec 2015 | MycorWeb Plant-Microbe Interactions | Scoop.it

Symposium aim - We aim to organize a cutting edge meeting focused on the application of cell biology approaches to understand the mechanisms that diverse microbes use to manipulate plant cells to benefit their life styles. The meeting will bring together researchers working on a broad spectrum of microbes across different taxa (bacteria, fungi, oomycetes) that form a variety of different interactions (pathogenic, symbiotic) with plant organs/tissues (leaves, roots). With the explosion in microbial/host genome sequences and the identification of genes/proteins involved in these interactions, the focus of the field is moving rapidly towards using cell and molecular biology techniques and new imaging technologies to understand the molecular dialogue between plants and their microbial pathogens/symbionts. The need for a conference on this topic, the first of its type, is evidenced by the growing prominence of cell biology in the literature. Students and scientists in this field face many challenges in the application and interpretation of cell biology data and would greatly benefit from a specialized conference on this topic. The symposium will bring together a broad representation of researchers focussing on different cell biology aspects and will allow researchers across the different disciplines to present and exchange their recent advances in this important topic of plant biology.

Symposium rationale and scope - Plant organs are subject to colonisation and manipulation by microbes, and this requires reprogramming of host cell biology to accommodate microbial structures within tissues/cells and to mediate responses for proper immunity or for symbiosis. Host cell biology changes during microbial invasion were first reported more than 100 years ago based on microscopy studies revealing that many microbes project structures (haustoria, arbuscules) into plant cells that are enveloped with a specialized plant-­derived membrane and evidence now suggests an intimate molecular exchange takes place across these membrane interfaces. However, recent identification of some of the molecular players in these interactions is only now providing appropriate tools to analyse these events. The symposium will focus on advances in understanding the molecular interactions that occur between a microbe and its host at a cellular and subcellular level, such as:

how root and leaf cells accommodate microbial structures through biogenesis of specialized plant derived membranes, microbial invasion and spreading strategies (via stomata, roots, vasculature, plasmodesmata), the dynamic localization of cell surface and cytosolic receptors recognizing microbial signals the reprogramming of host membrane trafficking (focal accumulation, secretion), the delivery of microbial molecules from fungal and oomycete species into plant cells.

With recent advances in high resolution/throughput bioimaging we are gaining new insights into the cell biology mechanisms and pathways of plant cell interactions with diverse microbes. Therefore the symposium provides a timely and important opportunity to overview the application of these technologies to plant–microbe interactions, and to discuss recent discoveries emerging from diverse host–microbe interactions illustrating common underlying principles and differences of strategies used by the microbes to gain access to plant tissues/cells. The symposium will certainly trigger a wealth of discussions, exchange of findings and methodologies, and will promote new lines of research and ideas in this rapidly expanding field.


Via Kamoun Lab @ TSL
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An integrative approach to understanding bird origins

An integrative approach to understanding bird origins | MycorWeb Plant-Microbe Interactions | Scoop.it
Recent discoveries of spectacular dinosaur fossils overwhelmingly support the hypothesis that birds are descended from maniraptoran theropod dinosaurs, and furthermore, demonstrate that distinctive bird characteristics such as feathers, flight, endothermic physiology, unique strategies for reproduction and growth, and a novel pulmonary system originated among Mesozoic terrestrial dinosaurs. The transition from ground-living to flight-capable theropod dinosaurs now probably represents one of the best-documented major evolutionary transitions in life history. Recent studies in developmental biology and other disciplines provide additional insights into how bird characteristics originated and evolved. The iconic features of extant birds for the most part evolved in a gradual and stepwise fashion throughout archosaur evolution. However, new data also highlight occasional bursts of morphological novelty at certain stages particularly close to the origin of birds and an unavoidable complex, mosaic evolutionary distribution of major bird characteristics on the theropod tree. Research into bird origins provides a premier example of how paleontological and neontological data can interact to reveal the complexity of major innovations, to answer key evolutionary questions, and to lead to new research directions. A better understanding of bird origins requires multifaceted and integrative approaches, yet fossils necessarily provide the final test of any evolutionary model.
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Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs | MycorWeb Plant-Microbe Interactions | Scoop.it

To provide context for the diversification of archosaurs—the group that includes crocodilians, dinosaurs, and birds—we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.

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Comparative genomics reveals insights into avian genome evolution and adaptation

Comparative genomics reveals insights into avian genome evolution and adaptation | MycorWeb Plant-Microbe Interactions | Scoop.it
Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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A novel bioinformatics pipeline to discover genes related to arbuscular mycorrhizal symbiosis based on their evolutionary conservation pattern among higher plants

Genes involved in arbuscular mycorrhizal (AM) symbiosis have been identified primarily by mutant screens, followed by identification of the mutated genes (forward genetics). In addition, a number of AM-related genes has been identified by their AM-related expression patterns, and their function has subsequently been elucidated by knock-down or knock-out approaches (reverse genetics). However, genes that are members of functionally redundant gene families, or genes that have a vital function and therefore result in lethal mutant phenotypes, are difficult to identify. If such genes are constitutively expressed and therefore escape differential expression analyses, they remain elusive. The goal of this study was to systematically search for AM-related genes with a bioinformatics strategy that is insensitive to these problems. The central element of our approach is based on the fact that many AM-related genes are conserved only among AM-competent species.
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The population biology of fungal invasions

The population biology of fungal invasions | MycorWeb Plant-Microbe Interactions | Scoop.it
Fungal invasions are increasingly recognized as a significant component of global changes, threatening ecosystem health and damaging food production. Invasive fungi also provide excellent models to evaluate the generality of results based on other eukaryotes. We first consider here the reasons why fungal invasions have long been overlooked: they tend to be inconspicuous and inappropriate methods have been used for species recognition. We then review the information available on the patterns and mechanisms of fungal invasions. We examine the biological features underlying invasion success of certain fungal species. We review population structure analyses, revealing native source populations and strengths of bottlenecks. We highlight the documented ecological and evolutionary changes in invaded regions, including adaptation to temperature, increased virulence, hybridization, shifts to clonality and association with novel hosts. We discuss how the huge census size of most fungi allows adaptation even in bottlenecked, clonal invaders. We also present new analyses of the invasion of the anther smut pathogen on white campion in North America, as a case study illustrating how an accurate knowledge of species limits and phylogeography of fungal populations can be used to decipher the origin of invasions. This case study shows that successful invasions can occur even when life-history traits are particularly unfavorable to long-distance dispersal and even with a strong bottleneck. We conclude that fungal invasions are valuable models to contribute to our view of biological invasions, in particular by providing insights into the traits as well as ecological and evolutionary processes allowing successful introductions.

Via Jean-Michel Ané
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Contribution of oak lignans to wine taste: chemical identification, sensory characterization and quantification

Contribution of oak lignans to wine taste: chemical identification, sensory characterization and quantification | MycorWeb Plant-Microbe Interactions | Scoop.it

The modification of wine taste during oak ageing is due to the release of non-volatile compounds from wood. Among these molecules, some lignans have been previously described as exhibiting bitterness. However, the lack of knowledge concerning this class of compounds in oak wood led us to explore both their structural diversity and their sensory properties. Nine lignans were isolated from extracts of Quercus petraea oak heartwood. Among them, one new compound called quercoresinol was identified and four other molecules were described for the first time in Quercus genus. The presence of these lignans in oaked wine was then established and their gustatory properties were evaluated. Lyoniresinol was the bitterest compound with a detection threshold of 1.5 mg/L. An LC–HRMS quantitative method was performed to study the influence of oenological practices on lyoniresinol concentration in wine.

 

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Virtual Issues: Mycorrhizal networks in ecosystem structure and functioning - Functional Ecology

Virtual Issues: Mycorrhizal networks in ecosystem structure and functioning - Functional Ecology | MycorWeb Plant-Microbe Interactions | Scoop.it
The vast majority of land plants (> 80%) form mutualistic symbioses with soil-dwelling fungi known as mycorrhizas. Such symbioses typically involve the reciprocal exchange of fungal-acquired nutrients for plant-fixed carbohydrates (Smith and Read 2008). As mycorrhizal fungi tend to be non-specific in their choice of hosts, many plants can be linked through fungal hyphae in a common mycelial network (CMN). These networks can be enormous, with around 200m of mycorrhizal fungal hyphae present in a single gram of typical forest soil (Dickie, 2006). The flow of nutrients between plants and mycorrhiza and the resulting redistribution of nutrients throughout a community is an area of much recent research with important contributions having been made by publications in Functional Ecology. This Virtual Issue highlights those contributions covering three major themes in mycorrhizal research, namely; the movement of plant-fixed carbon, reciprocal exchange of nutrients, and the wider impacts on biodiversity and ecosystem function.
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Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales

Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales | MycorWeb Plant-Microbe Interactions | Scoop.it
Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333 Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates.
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Local-scale biogeography and spatiotemporal variability in communities of mycorrhizal fungi

Local-scale biogeography and spatiotemporal variability in communities of mycorrhizal fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
Knowledge of spatiotemporal patterns in species distribution is fundamental to understanding the ecological and evolutionary processes shaping communities. The emergence of DNA-based tools has expanded the geographic and taxonomic scope of studies examining spatial and temporal distribution of mycorrhizal fungi. However, the nature of spatiotemporal patterns documented and subsequent interpretation of ecological processes can vary significantly from study to study. In order to look for general patterns we synthesize the available data across different sampling scales and mycorrhizal types. The results of this analysis shed light on the relative importance of space, time and vertical soil structure on community variability across different mycorrhizal types. Although we found no significant trend in spatiotemporal variation among mycorrhizal types, the vertical community variation was distinctly greater than the spatial and temporal variability in mycorrhizal fungal communities. Both spatial and temporal variability of communities was greater in topsoil compared with lower horizons, suggesting that greater environmental heterogeneity drives community variation on a fine scale. This further emphasizes the importance of both niche differentiation and environmental filtering in maintaining diverse fungal communities.
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Forest stand growth dynamics in Central Europe have accelerated since 1870

Forest stand growth dynamics in Central Europe have accelerated since 1870 | MycorWeb Plant-Microbe Interactions | Scoop.it
Forest ecosystems have been exposed to climate change for more than 100 years, whereas the consequences on forest growth remain elusive. Based on the oldest existing experimental forest plots in Central Europe, we show that, currently, the dominant tree species Norway spruce and European beech exhibit significantly faster tree growth (+32 to 77%), stand volume growth (+10 to 30%) and standing stock accumulation (+6 to 7%) than in 1960. Stands still follow similar general allometric rules, but proceed more rapidly through usual trajectories. As forest stands develop faster, tree numbers are currently 17–20% lower than in past same-aged stands. Self-thinning lines remain constant, while growth rates increase indicating the stock of resources have not changed, while growth velocity and turnover have altered. Statistical analyses of the experimental plots, and application of an ecophysiological model, suggest that mainly the rise in temperature and extended growing seasons contribute to increased growth acceleration, particularly on fertile sites.
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Structural basis of diverse membrane target recognitions by ankyrins

Structural basis of diverse membrane target recognitions by ankyrins | MycorWeb Plant-Microbe Interactions | Scoop.it
Ankyrin adaptors together with their spectrin partners coordinate diverse ion channels and cell adhesion molecules within plasma membrane domains and thereby promote physiological activities including fast signaling in the heart and nervous system. Ankyrins specifically bind to numerous membrane targets through their 24 ankyrin repeats (ANK repeats), although the mechanism for the facile and independent evolution of these interactions has not been resolved. Here we report the structures of ANK repeats in complex with an inhibitory segment from the C-terminal regulatory domain and with a sodium channel Nav1.2 peptide, respectively, showing that the extended, extremely conserved inner groove spanning the entire ANK repeat solenoid contains multiple target binding sites capable of accommodating target proteins with very diverse sequences via combinatorial usage of these sites. These structures establish a framework for understanding the evolution of ankyrins' membrane targets, with implications for other proteins containing extended ANK repeat domains.
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Medicago truncatula symbiosis mutants affected in the interaction with a biotrophic root pathogen - Rey - 2014 - New Phytologist -

Medicago truncatula symbiosis mutants affected in the interaction with a biotrophic root pathogen - Rey - 2014 - New Phytologist - | MycorWeb Plant-Microbe Interactions | Scoop.it
Understanding how plants balance between enabling microbial symbionts and fending off pathogens has direct implications both for basic plant biology and optimal use of crop plants in agriculture. The degree to which the processes associated with these two types of interactions overlap is poorly known. Recent studies revealed that symbiotic and pathogenic filamentous microbes require common plant genetic elements to establish colonization (Wang et al., 2012; Rey et al., 2013), supporting the long-held view that plants have evolved the ability to accommodate microbes (Parniske, 2000) and that pathogens have exploited these pathways. However, the extent to which plant genes implicated in fungal or bacterial symbioses are involved in interactions with biotrophic pathogens is unknown and research has been hampered by the lack of suitable common host experimental systems.

Via Christophe Jacquet
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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 | MycorWeb Plant-Microbe Interactions | 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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Bird genomes give new perches to old friends

Bird genomes give new perches to old friends | MycorWeb Plant-Microbe Interactions | Scoop.it
With chicks that have claws on their wings and a digestive system that resembles a cow's, the pheasantsized hoatzin that roams the Amazon has always puzzled those trying to place it within the avian family tree. But now researchers believe they have pinned down the odd bird's relatives—just one of the many findings revealed this week from a massive international project analyzing the sequenced genomes of 48 bird species representing nearly every order of bird. The fruits of this effort—eight papers this week in Science and more than 20 additional reports in several other journals—represent the biggest advance in avian biology in decades. “This has not been done for any other organism before,” says Per Ericson, an evolutionary biologist at the Swedish Museum of Natural History in Stockholm. “It's mind-blowing.”

The effort, involving 200 people from 80 labs and several months of supercomputer time, has yielded the most definitive avian family tree yet. It has also pinpointed gene networks underlying the traits that make birds birds, such as feathers and beaks instead of teeth. In one provocative finding, a team has identified the gene network that underlies complex singing in birds—and found that the same network operates in humans, where it is presumably crucial to language.
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Whole-genome analyses resolve early branches in the tree of life of modern birds

Whole-genome analyses resolve early branches in the tree of life of modern birds | MycorWeb Plant-Microbe Interactions | Scoop.it
To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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A flock of genomes

A flock of genomes | MycorWeb Plant-Microbe Interactions | Scoop.it

Characterization of genomic biodiversity through comprehensive species sampling has the potential to change our understanding of evolution. To study evolution across a major vertebrate class, dissect the genomics of complex traits, and resolve a centuries-old debate on the avian species tree, we formed a consortium focused on the sequencing and analyses of at least one genome per avian order. The resulting data set of 48 consistently annotated bird genomes spans 32 of the 35 recently proposed avian orders,* including all 30 neognath orders, and thus represents a wide range of avian evolutionary diversity. Our consortium's analyses have resulted in eight papers published today in Science, as well as 20 papers in other journals [avian.genomics.cn/en]. These include two flagship papers: one exploiting genomic-scale data to generate a highly supported avian order phylogeny that resolves many debates on the timing and topology of their radiation; the other a comparative genomic analysis exploring avian genome evolution and the genetic basis of complex traits. Other studies in Science describe convergent brain regions and gene expression for avian song learning and human speech, the singing activated genome in songbirds, complex evolutionary trajectories of avian sex chromosomes, a single loss of teeth in the ancestor of modern birds, the genomes of their closest extant outgroup (crocodilians) and inferred dinosaur ancestor, and computational methods developed for large-scale genomic analyses. Studies in companion papers explore the genomic adaptations of penguins, genomics of nearly extinct species, lineage-specific selection in birds, paleoviral infiltration in bird genomes, and many other questions. Thus, this study of a major vertebrate class highlights the future promise of large-scale comparative genomics, and we hope sets the stage for an approach for sequencing and analyses of many more genomes of birds and other vertebrate lineages.

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Subcellular Nutrient Element Localization and Enrichment in Ecto- and Arbuscular Mycorrhizas of Field-Grown Beech and Ash Trees Indicate Functional Differences

Subcellular Nutrient Element Localization and Enrichment in Ecto- and Arbuscular Mycorrhizas of Field-Grown Beech and Ash Trees Indicate Functional Differences | MycorWeb Plant-Microbe Interactions | Scoop.it
Mycorrhizas are the chief organ for plant mineral nutrient acquisition. In temperate, mixed forests, ash roots (Fraxinus excelsior) are colonized by arbuscular mycorrhizal fungi (AM) and beech roots (Fagus sylvatica) by ectomycorrhizal fungi (EcM). Knowledge on the functions of different mycorrhizal species that coexist in the same environment is scarce. The concentrations of nutrient elements in plant and fungal cells can inform on nutrient accessibility and interspecific differences of mycorrhizal life forms. Here, we hypothesized that mycorrhizal fungal species exhibit interspecific differences in mineral nutrient concentrations and that the differences correlate with the mineral nutrient concentrations of their associated root cells. Abundant mycorrhizal fungal species of mature beech and ash trees in a long-term undisturbed forest ecosystem were the EcM Lactarius subdulcis, Clavulina cristata and Cenococcum geophilum and the AM Glomus sp. Mineral nutrient subcellular localization and quantities of the mycorrhizas were analysed after non-aqueous sample preparation by electron dispersive X-ray transmission electron microscopy. Cenococcum geophilum contained the highest sulphur, Clavulina cristata the highest calcium levels, and Glomus, in which cations and P were generally high, exhibited the highest potassium levels. Lactarius subdulcis-associated root cells contained the highest phosphorus levels. The root cell concentrations of K, Mg and P were unrelated to those of the associated fungal structures, whereas S and Ca showed significant correlations between fungal and plant concentrations of those elements. Our results support profound interspecific differences for mineral nutrient acquisition among mycorrhizas formed by different fungal taxa. The lack of correlation between some plant and fungal nutrient element concentrations may reflect different retention of mineral nutrients in the fungal part of the symbiosis. High mineral concentrations, especially of potassium, in Glomus sp. suggest that the well-known influence of tree species on chemical soil properties may be related to their mycorrhizal associates.

Via Jean-Michel Ané
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Suppression of xylan endotransglycosylase PtxtXyn10A affects cellulose microfibril angle in secondary wall in aspen wood

Suppression of xylan endotransglycosylase PtxtXyn10A affects cellulose microfibril angle in secondary wall in aspen wood | MycorWeb Plant-Microbe Interactions | Scoop.it
Certain xylanases from family GH10 are highly expressed during secondary wall deposition, but their function is unknown. We carried out functional analyses of the secondary-wall specific PtxtXyn10A in hybrid aspen (Populus tremula × tremuloides).
PtxtXyn10A function was analysed by expression studies, overexpression in Arabidopsis protoplasts and by downregulation in aspen.
PtxtXyn10A overexpression in Arabidopsis protoplasts resulted in increased xylan endotransglycosylation rather than hydrolysis. In aspen, the enzyme was found to be proteolytically processed to a 68 kDa peptide and residing in cell walls. Its downregulation resulted in a corresponding decrease in xylan endotransglycosylase activity and no change in xylanase activity. This did not alter xylan molecular weight or its branching pattern but affected the cellulose-microfibril angle in wood fibres, increased primary growth (stem elongation, leaf formation and enlargement) and reduced the tendency to form tension wood. Transcriptomes of transgenic plants showed downregulation of tension wood related genes and changes in stress-responsive genes.
The data indicate that PtxtXyn10A acts as a xylan endotransglycosylase and its main function is to release tensional stresses arising during secondary wall deposition. Furthermore, they suggest that regulation of stresses in secondary walls plays a vital role in plant development.
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Do Differences in Chemical Composition of Stem and Cap of Amanita muscaria Fruiting Bodies Correlate with Topsoil Type?

Do Differences in Chemical Composition of Stem and Cap of Amanita muscaria Fruiting Bodies Correlate with Topsoil Type? | MycorWeb Plant-Microbe Interactions | Scoop.it
Fly agaric (Amanita muscaria) was investigated using a 1H NMR-based metabolomics approach. The caps and stems were studied separately, revealing different metabolic compositions. Additionally, multivariate data analyses of the fungal basidiomata and the type of soil were performed. Compared to the stems, A. muscaria caps exhibited higher concentrations of isoleucine, leucine, valine, alanine, aspartate, asparagine, threonine, lipids (mainly free fatty acids), choline, glycerophosphocholine (GPC), acetate, adenosine, uridine, 4-aminobutyrate, 6-hydroxynicotinate, quinolinate, UDP-carbohydrate and glycerol. Conversely, they exhibited lower concentrations of formate, fumarate, trehalose, α- and β-glucose. Six metabolites, malate, succinate, gluconate, N-acetylated compounds (NAC), tyrosine and phenylalanine, were detected in whole A. muscaria fruiting bodies but did not show significant differences in their levels between caps and stems (P value>0.05 and/or OPLS-DA loading correlation coefficient <0.4). This methodology allowed for the differentiation between the fruiting bodies of A. muscaria from mineral and mineral-organic topsoil. Moreover, the metabolomic approach and multivariate tools enabled to ascribe the basidiomata of fly agaric to the type of topsoil. Obtained results revealed that stems metabolome is more dependent on the topsoil type than caps. The correlation between metabolites and topsoil contents together with its properties exhibited mutual dependences.
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