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Pairwise Transcriptomic Analysis of the Interactions Between the Ectomycorrhizal Fungus Laccaria bicolor S238N and Three Beneficial, Neutral and Antagonistic Soil Bacteria

Pairwise Transcriptomic Analysis of the Interactions Between the Ectomycorrhizal Fungus Laccaria bicolor S238N and Three Beneficial, Neutral and Antagonistic Soil Bacteria | MycorWeb Plant-Microbe Interactions | Scoop.it

Ectomycorrhizal fungi are surrounded by bacterial communities with which they interact physically and metabolically during their life cycle. These bacteria can have positive or negative effects on the formation and the functioning of ectomycorrhizae. However, relatively little is known about the mechanisms by which ectomycorrhizal fungi and associated bacteria interact. To understand how ectomycorrhizal fungi perceive their biotic environment and the mechanisms supporting interactions between ectomycorrhizal fungi and soil bacteria, we analysed the pairwise transcriptomic responses of the ectomycorrhizal fungus Laccaria bicolor(Basidiomycota: Agaricales) when confronted with beneficial, neutral or detrimental soil bacteria. Comparative analyses of the three transcriptomes indicated that the fungus reacted differently to each bacterial strain. Similarly, each bacterial strain produced a specific and distinct response to the presence of the fungus. Despite these differences in responses observed at the gene level, we found common classes of genes linked to cell–cell interaction, stress response and metabolic processes to be involved in the interaction of the four microorganisms.

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Rescooped by Francis Martin from Plants and Microbes
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Current Biology: A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor (2015)

Current Biology: A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor (2015) | MycorWeb Plant-Microbe Interactions | Scoop.it

Gall-forming arthropods are highly specialized herbivores that, in combination with their hosts, produce extended phenotypes with unique morphologies [1]. Many are economically important, and others have improved our understanding of ecology and adaptive radiation [2]. However, the mechanisms that these arthropods use to induce plant galls are poorly understood. We sequenced the genome of the Hessian fly (Mayetiola destructor; Diptera: Cecidomyiidae), a plant parasitic gall midge and a pest of wheat (Triticumspp.), with the aim of identifying genic modifications that contribute to its plant-parasitic lifestyle. Among several adaptive modifications, we discovered an expansive reservoir of potential effector proteins. Nearly 5% of the 20,163 predicted gene models matched putative effector gene transcripts present in the M. destructor larval salivary gland. Another 466 putative effectors were discovered among the genes that have no sequence similarities in other organisms. The largest known arthropod gene family (family SSGP-71) was also discovered within the effector reservoir. SSGP-71 proteins lack sequence homologies to other proteins, but their structures resemble both ubiquitin E3 ligases in plants and E3-ligase-mimicking effectors in plant pathogenic bacteria. SSGP-71 proteins and wheat Skp proteins interact in vivo. Mutations in different SSGP-71 genes avoid the effector-triggered immunity that is directed by the wheat resistance genes H6 and H9. Results point to effectors as the agents responsible for arthropod-induced plant gall formation.


Via Kamoun Lab @ TSL
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Draft Genome Sequences of Symbiotic and Nonsymbiotic Rhizopus microsporus Strains CBS 344.29 and ATCC 62417

Specific Rhizopus microsporus pathovars harbor bacterial endosymbionts (Burkholderia rhizoxinica) for the production of a phytotoxin. Here, we present the draft genome sequences of two R. microsporus strains, one symbiotic (ATCC 62417), and one endosymbiont-free (CBS 344.29). The gene predictions were supported by RNA sequencing (RNA-seq) data. The functional annotation sets the basis for comparative analyses.

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Key genes for symbiosis between mycorrhiza fungi and trees evolved several times

Key genes for symbiosis between mycorrhiza fungi and trees evolved several times | MycorWeb Plant-Microbe Interactions | Scoop.it
Champenoux/ Halle(Saale)/ Leipzig. The life style of ectomycorrhiza fungi is some 100 million years younger than the one of their ancestors within white and brown rot fungi. The key genome adaptation enabling fungi to associate to roots for establishing a symbiosis evolved a repeatedly amount of time. This conclusion was drawn by an international team of researchers who performed the first comprehensive comparative phylogenomic analysis on mycorrhiza fungi, now appearing in the reputed scientific journal Nature Genetics. These sequences provide crucial information on how the symbiosis between fungi and trees evolved.

Via Jean-Michel Ané
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The Diverse Microbiome of the Hunter-Gatherer : Nature

The Diverse Microbiome of the Hunter-Gatherer : Nature | MycorWeb Plant-Microbe Interactions | Scoop.it
We tend to forget that modern humanity is largely sheltered from the last vestiges of wild untamed Earth and that our way of life bears little resemblance to how our ancestors lived during 90 percent of human history. We have lost nearly all trace of these former selves—and, worse, have marginalized the few remaining humans who retain their hunter-gatherer identity. In Tanzania, tribes of wandering foragers called the Hadza, who have lived for thousands of years in the East African Rift Valley ecosystem, tell us an immense and precious story about how humans, together with their microbial evolutionary partners, are adapted to live and thrive in a complex natural environment.
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Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield

Spatial patterns of microbial communities have been extensively surveyed in well-developed soils, but few studies investigated the vertical distribution of micro-organisms in newly developed soils after glacier retreat. We used 454-pyrosequencing to assess whether bacterial and fungal community structures differed between stages of soil development (SSD) characterized by an increasing vegetation cover from barren (vegetation cover: 0%/age: 10 years), sparsely vegetated (13%/60 years), transient (60%/80 years) to vegetated (95%/110 years) and depths (surface, 5 and 20 cm) along the Damma glacier forefield (Switzerland). The SSD significantly influenced the bacterial and fungal communities. Based on indicator species analyses, metabolically versatile bacteria (e.g. Geobacter) and psychrophilic yeasts (e.g. Mrakia) characterized the barren soils. Vegetated soils with higher C, N and root biomass consisted of bacteria able to degrade complex organic compounds (e.g. Candidatus Solibacter), lignocellulolytic Ascomycota (e.g. Geoglossum) and ectomycorrhizal Basidiomycota(e.g. Laccaria). Soil depth only influenced bacterial and fungal communities in barren and sparsely vegetated soils. These changes were partly due to more silt and higher soil moisture in the surface. In both soil ages, the surface was characterized by OTUs affiliated to Phormidium and Sphingobacteriales. In lower depths, however, bacterial and fungal communities differed between SSD. Lower depths of sparsely vegetated soils consisted of OTUs affiliated to Acidobacteria and Geoglossum, whereas depths of barren soils were characterized by OTUs related to Gemmatimonadetes. Overall, plant establishment drives the soil microbiota along the successional gradient but does not influence the vertical distribution of microbiota in recently deglaciated soils.

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Microbial dynamics in glacier forefield soils show succession is not just skin deep

Microbial dynamics in glacier forefield soils show succession is not just skin deep | MycorWeb Plant-Microbe Interactions | Scoop.it
All over the world, glaciers are receding. One key consequence of glacier area loss is the creation of new terrestrial habitats. This presents an experimental opportunity to study both community formation and the implications of glacier loss for terrestrial ecosystems. In this issue of Molecular Ecology, Rime et al. (2015) describe how microbial communities are structured according to soil depth and development in the forefield of Damma glacier in Switzerland. The study provides insights into the contrasting structures of microbial communities at different stages of soil development. An important strength of the study is the integration of soil depth into the paradigm of primary succession, a feature which has rarely been considered by other studies. These findings underscore the importance of studying the interactions between microbial communities and glaciers at a time when Earth's glacial systems are experiencing profound change.
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A maize wall-associated kinase confers quantitative resistance to head smut : Nature Genetics

A maize wall-associated kinase confers quantitative resistance to head smut : Nature Genetics | MycorWeb Plant-Microbe Interactions | Scoop.it

Head smut is a systemic disease in maize caused by the soil-borne fungus Sporisorium reilianum that poses a grave threat to maize production worldwide. A major head smut quantitative resistance locus, qHSR1, has been detected on maize chromosome bin2.09. Here we report the map-based cloning of qHSR1 and the molecular mechanism of qHSR1-mediated resistance. Sequential fine mapping and transgenic complementation demonstrated that ZmWAK is the gene within qHSR1 conferring quantitative resistance to maize head smut. ZmWAK spans the plasma membrane, potentially serving as a receptor-like kinase to perceive and transduce extracellular signals. ZmWAK was highly expressed in the mesocotyl of seedlings where it arrested biotrophic growth of the endophytic S. reilianum. Impaired expression in the mesocotyl compromised ZmWAK-mediated resistance. Deletion of the ZmWAK locus appears to have occurred after domestication and spread among maize germplasm, and the ZmWAK kinase domain underwent functional constraints during maize evolution.

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Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists : Nature Genetics

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists : Nature Genetics | MycorWeb Plant-Microbe Interactions | Scoop.it
Francis Martin and colleagues report genome sequences for 18 species of mycorrhizal fungi and a phylogenomic analysis including 32 other fungal genomes. The study identifies cell wall-degradation genes lost in all true ectomycorrhizal species and, using gene expression data, finds candidate genes for the establishment of symbiosis.
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Max-Bernhard Rudnick's comment, February 24, 2:35 AM
really nice work!
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Frontiers | Evolution and Conservation of Plant NLR Functions

In plants and animals, nucleotide-binding domain and leucine-rich repeats (NLR)–containing proteins play pivotal roles in innate immunity. Despite their similar biological functions and protein architecture, comparative genome-wide analyses of NLRs and genes encoding NLR-like proteins suggest that plant and animal NLRs have independently arisen in evolution. Furthermore, the demonstration of interfamily transfer of plant NLR functions from their original species to phylogenetically distant species implies evolutionary conservation of the underlying immune principle across plant taxonomy. In this review we discuss plant NLR evolution and summarise recent insights into plant NLR signalling mechanisms, which might constitute evolutionarily conserved NLR-mediated immune mechanisms.
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The interaction of Arabidopsis with Piriformospora indica shifts from initial transient stress induced by fungus-released chemical mediators to a mutualistic interaction after physical contact of t...

Background Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of many plant species including Arabidopsis thaliana. The symbiotic interaction promotes plant performance, growth and resistance/tolerance against abiotic and biotic stress. Results We demonstrate that exudated compounds from the fungus activate stress and defense responses in the Arabidopsis roots and shoots before the two partners are in physical contact. They induce stomata closure, stimulate reactive oxygen species (ROS) production, stress-related phytohormone accumulation and activate defense and stress genes in the roots and/or shoots. Once a physical contact is established, the stomata re-open, ROS and phytohormone levels decline, and the number and expression level of defense/stress-related genes decreases. Conclusions We propose that exudated compounds from P. indica induce stress and defense responses in the host. Root colonization results in the down-regulation of defense responses and the activation of genes involved in promoting plant growth, metabolism and performance.

Via Jean-Michel Ané
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Topology of tree-mycorrhizal fungus interaction networks in xeric and mesic Douglas-fir forests

Topology of tree-mycorrhizal fungus interaction networks in xeric and mesic Douglas-fir forests | MycorWeb Plant-Microbe Interactions | Scoop.it

1.From the phytocentric perspective, a mycorrhizal network (MN) is formed when the roots of two or more plants are colonized by the same fungal genet. MNs can be modelled as interaction networks with plants as nodes and fungal genets as links. The potential effects of MNs on facilitation or competition between plants are increasingly recognized, but their network topologies remain largely unknown. This information is needed to understand the ecological significance of MN functional traits.

2.The objectives of this study were to describe the interaction network topologies of MNs formed between two ectomycorrhizal fungal species, Rhizopogon vesiculosus and R. vinicolor, and interior Douglas-fir trees at the forest stand scale, identify factors leading to this structure and to contrast MN structures between forest plots with xeric versus mesic soil moisture regimes.

3.Tuberculate mycorrhizas were sampled in six 10 x 10 m plots with either xeric or mesic soil moisture regimes. Microsatellite DNA markers were used to identify tree and fungal genotypes isolated from mycorrhizas and for comparison with reference tree boles above-ground.

4.In all six plots, trees and fungal genets were highly interconnected. Size asymmetries between different tree cohorts led to non-random MN topologies, while differences in size and connectivity between Rhizopogon species-specific sub-network components contributed towards MN nestedness. Large mature trees acted as network hubs with a significantly higher node degree compared to smaller trees. MNs representing trees linked by R. vinicolor genets were mostly nested within larger, more highly connected R. vesiculosus-linked MNs.

5.Attributes of network nodes showed that hub trees were more important to MN topology on xeric than mesic sites, but the emergent structures of MNs were similar in the two soil moisture regimes.

6.Synthesis: This study suggests MNs formed between interior Douglas-fir trees and R. vesiculosus and R. vinicolor genets are resilient to the random loss of participants, and to soil water stress, but may be susceptible to the loss of large trees or fungal genets. Our results regarding the topology of MNs contribute to the understanding of forest stand dynamics and the resilience of forests to stress or disturbance.

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The draft genome of Primula veris yields insights into the molecular basis of heterostyly

The draft genome of Primula veris yields insights into the molecular basis of heterostyly | MycorWeb Plant-Microbe Interactions | Scoop.it
Background
The flowering plant Primula veris is a common spring blooming perennial that is widely cultivated throughout Europe. This species is an established model system in the study of the genetics, evolution, and ecology of heterostylous floral polymorphisms. Despite the long history of research focused on this and related species, the continued development of this system has been restricted due the absence of genomic and transcriptomic resources.

Results
We present here a de novo draft genome assembly of P. veris covering 301.8 Mb, or approximately 63% of the estimated 479.22 Mb genome, with an N50 contig size of 9.5 Kb, an N50 scaffold size of 164 Kb, and containing an estimated 19,507 genes. The results of a RADseq bulk segregant analysis allow for the confident identification of four genome scaffolds that are linked to the P. veris S-locus. RNAseq data from both P. veris and the closely related species P. vulgaris allow for the characterization of 113 candidate heterostyly genes that show significant floral morph-specific differential expression. One candidate gene of particular interest is a duplicated GLOBOSA homolog that may be unique to Primula (PveGLO2), and is completely silenced in L-morph flowers.

Conclusions
The P. veris genome represents the first genome assembled from a heterostylous species, and thus provides an immensely important resource for future studies focused on the evolution and genetic dissection of heterostyly. As the first genome assembled from the Primulaceae, the P. veris genome will also facilitate the expanded application of phylogenomic methods in this diverse family and the eudicots as a whole.
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Rescooped by Francis Martin from The Plant Microbiome
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PNAS: Root surface as a frontier for plant microbiome research

Plants associate—analogous to animals or us humans—with a multitude of microorganisms, which collectively function as a microbiome. A major discovery of the last decade is that numerous organisms of a microbiome (aka microbiota) are not unpretentious background actors. Instead, some microbiota members influence host processes including behavior, appetite, and health in animals (1) and contribute to nutrition and health of plants (2–4). Recently, the compositions of the plant root-associated microbiota from numerous plant species, including major crops, were revealed using high-throughput DNA sequencing. Factors such as soil type or host genotype influence the root-associated microbiota. However, the processes that determine the acquisition of the root microbiota, its resistance to stress, and its ecological function remain poorly understood. Edwards et al. (5) present the third publication in a recent series of PNAS articles about the bacterial microbiota associated with plant roots of maize (6), related Brassicaceae (7), and now Oryza sativa (rice). It comprises a comprehensive characterization of three microbial habitats that are in the proximity of, on, and inside plant roots, which are named rhizosphere, rhizoplane, and root endosphere (Fig. 1).


Via Stéphane Hacquard
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Draft Genome Sequence of the Cellulolytic Fungus Chaetomium globosum

Chaetomium globosum is a filamentous fungus typically isolated from cellulosic substrates. This species also causes superficial infections of humans and, more rarely, can cause cerebral infections. Here, we report the genome sequence of C. globosum isolate CBS 148.51, which will facilitate the study and comparative analysis of this fungus.
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Retracing the roots of fungal symbioses

Retracing the roots of fungal symbioses | MycorWeb Plant-Microbe Interactions | Scoop.it
With apologies to the poet John Donne, and based on recent work from the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, it can be said that no plant is an island, entire of itself. Unseen by the human eye, plants interact with many species of fungi and other microbes in the surrounding environment, and these exchanges can impact the plant's health and tolerance to stressors such as drought or disease, as well as the global carbon cycle.

Via Jean-Michel Ané
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The Microbiome of Pinus muricata Ectomycorrhizae: Community Assemblages, Fungal Species Effects, and Burkholderia as Important Bacteria in Multipartnered Symbioses

The Microbiome of Pinus muricata Ectomycorrhizae: Community Assemblages, Fungal Species Effects, and Burkholderia as Important Bacteria in Multipartnered Symbioses | MycorWeb Plant-Microbe Interactions | Scoop.it

Bacteria have been observed to grow with fungi, and those that associate with ectomycorrhizal fungi have often been thought of as symbionts that may either increase or decrease ectomycorrhizal formation rate or provide other unaccounted benefits. To explore this symbiosis from a community ecology perspective, we sampled ectomycorrhizal root tips over a 3-year period and used 454 pyrosequencing to identify the bacteria that live inside the ectomycorrhizal root tips. The results showed that fungal community composition within the same soil core and fungal taxonomic identity had a stronger effect on bacterial community composition than sample year or site. Members of the Burkholderiales and Rhizobiales were most highly represented, reflecting many previous reports of these bacteria in association with fungi. The repeated occurrences of these two bacterial orders suggest that they may be symbiotic with their fungal hosts, although the nature of such mechanisms, be it symbiotic diazotrophy or otherwise, remains to be thoroughly tested.


Via Kemen Lab, Jean-Michel Ané
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Jean-Michel Ané's curator insight, February 25, 11:44 AM

Burkholderiales and Rhizobiales... again the same culprits :-)

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The Microbes Within : Nature

The Microbes Within : Nature | MycorWeb Plant-Microbe Interactions | Scoop.it
Antony van Leeuwenhoek wrote to the Royal Society of London in a letter dated September 17, 1683, describing “very little animalcules, very prettily a-moving,” which he had seen under a microscope in plaque scraped from his teeth. For more than three centuries after van Leeuwenhoek's observation, the human “microbiome”—the 100 trillion or so microbes that live in various nooks and crannies of the human body—remained largely unstudied, mainly because it is not so easy to extract and culture them in a laboratory. A decade ago the advent of sequencing technologies finally opened up this microbiological frontier. The Human Microbiome Project reference database, established in 2012, revealed in unprecedented detail the diverse microbial community that inhabits our bodies.
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Two widespread green Neottia species (Orchidaceae) show mycorrhizal preference for Sebacinales in various habitats and ontogenetic stages

Two widespread green Neottia species (Orchidaceae) show mycorrhizal preference for Sebacinales in various habitats and ontogenetic stages | MycorWeb Plant-Microbe Interactions | Scoop.it
Plant dependence on fungal carbon (mycoheterotrophy) evolved repeatedly. In orchids, it is connected with a mycorrhizal shift from rhizoctonia to ectomycorrhizal fungi and a high natural 13C and 15N abundance. Some green relatives of mycoheterotrophic species show identical trends, but most of these remain unstudied, blurring our understanding of evolution to mycoheterotrophy. We analysed mycorrhizal associations and 13C and 15N biomass content in two green species, Neottia ovata and N. cordata (tribe Neottieae), from a genus comprising green and nongreen (mycoheterotrophic) species. Our study covered 41 European sites, including different meadow and forest habitats and orchid developmental stages. Fungal ITS barcoding and electron microscopy showed that both Neottia species associated mainly with nonectomycorrhizal Sebacinales Clade B, a group of rhizoctonia symbionts of green orchids, regardless of the habitat or growth stage. Few additional rhizoctonias from Ceratobasidiaceae and Tulasnellaceae, and ectomycorrhizal fungi were detected. Isotope abundances did not detect carbon gain from the ectomycorrhizal fungi, suggesting a usual nutrition of rhizoctonia-associated green orchids. Considering associations of related partially or fully mycoheterotrophic species such as Neottia camtschatea or N. nidus-avis with ectomycorrhizal Sebacinales Clade A, we propose that the genus Neottia displays a mycorrhizal preference for Sebacinales and that the association with nonectomycorrhizal Sebacinales Clade B is likely ancestral. Such a change in preference for mycorrhizal associates differing in ecology within the same fungal taxon is rare among orchids. Moreover, the existence of rhizoctonia-associated Neottia spp. challenges the shift to ectomycorrhizal fungi as an ancestral pre-adaptation to mycoheterotrophy in the whole Neottieae.
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Integrated genome sequence and linkage map of physic nut (Jatropha curcas L.), a biodiesel plant

Integrated genome sequence and linkage map of physic nut (Jatropha curcas L.), a biodiesel plant | MycorWeb Plant-Microbe Interactions | Scoop.it

The family Euphorbiaceae includes some of the most efficient biomass accumulators. Whole genome sequencing and the development of genetic maps of these species are important components in molecular breeding and genetic improvement. Here we report the draft genome of physic nut (Jatropha curcas L.), a biodiesel plant. The assembled genome has a total length of 320.5 Mbp and contains 27 172 putative protein-coding genes. We established a linkage map containing 1208 markers and anchored the genome assembly (81.7%) to this map to produce 11 pseudochromosomes. After gene family clustering, 15 268 families were identified, of which 13 887 existed in the castor bean genome. Analysis of the genome highlighted specific expansion and contraction of a number of gene families during the evolution of this species, including the ribosome-inactivating proteins and oil biosynthesis pathway enzymes. The genomic sequence and linkage map provide a valuable resource not only for fundamental and applied research on physic nut but also for evolutionary and comparative genomics analysis, particularly in the Euphorbiaceae.

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New insight into a complex plant-fungal pathogen interaction : Nature Genetics

New insight into a complex plant-fungal pathogen interaction : Nature Genetics | MycorWeb Plant-Microbe Interactions | Scoop.it
The coevolution of plants and microbes has shaped plant mechanisms that detect and repel pathogens. A newly identified plant gene confers partial resistance to a fungal pathogen not by preventing initial infection but by limiting its spread through the plant.
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Distribution and mixing of old and new nonstructural carbon in two temperate trees

Distribution and mixing of old and new nonstructural carbon in two temperate trees | MycorWeb Plant-Microbe Interactions | Scoop.it
We know surprisingly little about whole-tree nonstructural carbon (NSC; primarily sugars and starch) budgets. Even less well understood is the mixing between recent photosynthetic assimilates (new NSC) and previously stored reserves. And, NSC turnover times are poorly constrained.We characterized the distribution of NSC in the stemwood, branches, and roots of two temperate trees, and we used the continuous label offered by the radiocarbon (carbon-14, 14C) bomb spike to estimate the mean age of NSC in different tissues.NSC in branches and the outermost stemwood growth rings had the 14C signature of the current growing season. However, NSC in older aboveground and belowground tissues was enriched in 14C, indicating that it was produced from older assimilates. Radial patterns of 14C in stemwood NSC showed strong mixing of NSC across the youngest growth rings, with limited ‘mixing in’ of younger NSC to older rings.Sugars in the outermost five growth rings, accounting for two-thirds of the stemwood pool, had a mean age < 1 yr, whereas sugars in older growth rings had a mean age > 5 yr. Our results are thus consistent with a previously-hypothesized two-pool (‘fast’ and ‘slow’ cycling NSC) model structure. These pools appear to be physically distinct.
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A peek into the world of fungi

A peek into the world of fungi | MycorWeb Plant-Microbe Interactions | 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.

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Steppe migration rekindles debate on language origin

Steppe migration rekindles debate on language origin | MycorWeb Plant-Microbe Interactions | Scoop.it
From Icelanders to Sri Lankans, some 3 billion people speak the more than 400 languages and dialects that belong to the Indo-European family. Two fresh studies — one of ancient human DNA, the other a newly constructed genealogical ‘tree’ of languages — point to the steppes of Ukraine and Russia as the origin of this major language family, rekindling a long-standing debate.

Scholars have long recognized an Indo-European language group that includes Germanic, Slavic and Romance languages as well as classical Sanskrit and other languages of the south Asian subcontinent. Yet the origins of this family of tongues are mired in controversy.
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Moth Outbreaks Alter Root-Associated Fungal Communities in Subarctic Mountain Birch Forests

Moth Outbreaks Alter Root-Associated Fungal Communities in Subarctic Mountain Birch Forests | MycorWeb Plant-Microbe Interactions | Scoop.it
Climate change has important implications on the abundance and range of insect pests in forest ecosystems. We studied responses of root-associated fungal communities to defoliation of mountain birch hosts by a massive geometrid moth outbreak through 454 pyrosequencing of tagged amplicons of the ITS2 rDNA region. We compared fungal diversity and community composition at three levels of moth defoliation (intact control, full defoliation in one season, full defoliation in two or more seasons), replicated in three localities. Defoliation caused dramatic shifts in functional and taxonomic community composition of root-associated fungi. Differentially defoliated mountain birch roots harbored distinct fungal communities, which correlated with increasing soil nutrients and decreasing amount of host trees with green foliar mass. Ectomycorrhizal fungi (EMF) abundance and richness declined by 70–80 % with increasing defoliation intensity, while saprotrophic and endophytic fungi seemed to benefit from defoliation. Moth herbivory also reduced dominance of Basidiomycota in the roots due to loss of basidiomycete EMF and increases in functionally unknown Ascomycota. Our results demonstrate the top-down control of belowground fungal communities by aboveground herbivory and suggest a marked reduction in the carbon flow from plants to soil fungi following defoliation. These results are among the first to provide evidence on cascading effects of natural herbivory on tree root-associated fungi at an ecosystem scale.
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A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.
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