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Rescooped by Francis Martin from Plant-Microbe Symbioses
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Carbon and nitrogen fluxes between beech and their ectomycorrhizal assemblage

To determine the exchange of nitrogen and carbon between ectomycorrhiza and host plant, young beech (Fagus sylvatica) trees from natural regeneration in intact soil cores were labelled for one growing season in a greenhouse with 13CO2 and 15NO3 15NH4. The specific enrichments of 15N and13C were higher in ectomycorrhizas (EMs) than in any other tissue. The enrichments of 13C and 15N were also higher in the fine-root segments directly connected with the EM (mainly second-order roots) than that in bulk fine or coarse roots. A strict, positive correlation was found between the specific 15N enrichment in EM and the attached second-order roots. This finding indicates that strong N accumulators provide more N to their host than low N accumulators. A significant correlation was also found for the specific 13C enrichment in EM and the attached second-order roots. However, the specific enrichments for 15N and 13C in EM were unrelated showing that under long-term conditions, C and N exchange between host and EMs are uncoupled. These findings suggest that EM-mediated N flux to the plant is not the main control on carbon flux to the fungus, probably because EMs provide many different services to their hosts in addition to N provision in their natural assemblages.


Via Jean-Michel Ané
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Jean-Michel Ané's curator insight, April 26, 2014 1:14 PM

Very interesting results

Rescooped by Francis Martin from Plant-Microbe Symbioses
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An improved genome release (version Mt4.0) for the model legume Medicago truncatula

Background

Medicago truncatula, a close relative of alfalfa, is a preeminent model for studying nitrogen fixation, symbiosis, and legume genomics. The Medicago sequencing project began in 2003 with the goal to decipher sequences originated from the euchromatic portion of the genome. The initial sequencing approach was based on a BAC tiling path, culminating in a BAC-based assembly (Mt3.5) as well as an in-depth analysis of the genome published in 2011.

Results

Here we describe a further improved and refined version of the M. truncatula genome (Mt4.0) based on de novo whole genome shotgun assembly of a majority of Illumina and 454 reads using ALLPATHS-LG. The ALLPATHS-LG scaffolds were anchored onto the pseudomolecules on the basis of alignments to both the optical map and the genotyping-by-sequencing (GBS) map. The Mt4.0 pseudomolecules encompass ~360 Mb of actual sequences spanning 390 Mb of which ~330 Mb align perfectly with the optical map, presenting a drastic improvement over the BAC-based Mt3.5 which only contained 70% sequences (~250 Mb) of the current version. Most of the sequences and genes that previously resided on the unanchored portion of Mt3.5 have now been incorporated into the Mt4.0 pseudomolecules, with the exception of ~28 Mb of unplaced sequences. With regard to gene annotation, the genome has been re-annotated through our gene prediction pipeline, which integrates EST, RNA-seq, protein and gene prediction evidences. A total of 50,894 genes (31,661 high confidence and 19,233 low confidence) are included in Mt4.0 which overlapped with ~82% of the gene loci annotated in Mt3.5. Of the remaining genes, 14% of the Mt3.5 genes have been deprecated to an "unsupported" status and 4% are absent from the Mt4.0 predictions.

Conclusions

Mt4.0 and its associated resources, such as genome browsers, BLAST-able datasets and gene information pages, can be found on the JCVI Medicago web site (http://www.jcvi.org/medicago). The assembly and annotation has been deposited in GenBank (BioProject: PRJNA10791). The heavily curated chromosomal sequences and associated gene models of Medicago will serve as a better reference for legume biology and comparative genomics.


Via Jean-Michel Ané
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Sequencing the Tree of Life

Sequencing the Tree of Life | MycorWeb Plant-Microbe Interactions | Scoop.it

Charting the progress of the various large-scale genome-sequencing projects as researchers working separately on their chosen species begin to pool analytical resources.

“We are still in the developmental stage, where every consortium focuses on a specific domain and is building up their own data and making sure it’s in good enough shape,” said Igor Grigoriev, head of the fungal genomics program at the US Department of Energy (DOE) Joint Genome Insitute (JGI) in Walnut Creek, California, and part of the 1,000 Fungal Genomes project. “Some dialog between the consortia is happening but grand-scale data integration remains to happen.”

Francis Martin's insight:

Gustav Klimt’s “The Tree of Life,” 1909 (Wikimedia)

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Beautiful and unusual trees

Beautiful and unusual trees | MycorWeb Plant-Microbe Interactions | Scoop.it
I think that I shall never see A poem lovely as a tree. - Joyce Kilmer In the hands of a skilled photographer, a tree can look magisterial, menacing, or otherworldly. When better than National Arbor Day to highlight some amazing images shared on Flickr? Enjoy their work. And if you don’t, feel free to make like a tree and get out of here! Do you have a photo of a beloved or unique tree? Post it in the comments below using the format: [Flickr photo page URL]
Francis Martin's insight:

Photo: Trees in the Mist-Blue de welshio

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Rescooped by Francis Martin from Forest health
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Drunken Trees: Dramatic Signs of Climate Change

Drunken Trees: Dramatic Signs of Climate Change | MycorWeb Plant-Microbe Interactions | Scoop.it

As the permafrost melts in the north, forests no longer grow straight.


Via Richard Hamelin
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Comparative Genomic and Transcriptomic Analysis of Wangiella dermatitidis, A Major Cause of Phaeohyphomycosis and a Model Black Yeast Human Pathogen

Comparative Genomic and Transcriptomic Analysis of Wangiella dermatitidis, A Major Cause of Phaeohyphomycosis and a Model Black Yeast Human Pathogen | MycorWeb Plant-Microbe Interactions | Scoop.it

Black or dark brown (phaeoid) fungi cause cutaneous, subcutaneous, and systemic infections in humans. Black fungi thrive in stressful conditions such as intense light, high radiation, and very low pH. Wangiella (Exophiala) dermatitidis is arguably the most studied phaeoid fungal pathogen of humans. Here, we report our comparative analysis of the genome of W. dermatitidis and the transcriptional response to low pH stress. This revealed that W. dermatitidis has lost the ability to synthesize alpha-glucan, a cell wall compound many pathogenic fungi use to evade the host immune system. In contrast, W. dermatitidis contains a similar profile of chitin synthase genes as related fungi and strongly induces genes involved in cell wall synthesis in response to pH stress. The large portfolio of transporters may provide W. dermatitidis with an enhanced ability to remove harmful products as well as to survive on diverse nutrient sources. The genome encodes three independent pathways for producing melanin, an ability linked to pathogenesis; these are active during pH stress, potentially to produce a barrier to accumulated oxidative damage that might occur under stress conditions. In addition, a full set of fungal light-sensing genes is present, including as part of a carotenoid biosynthesis gene cluster. Finally, we identify a two-gene cluster involved in nucleotide sugar metabolism conserved with a subset of fungi and characterize a horizontal transfer event of this cluster between fungi and algal viruses. This work reveals how W. dermatitidis has adapted to stress and survives in diverse environments, including during human infections.

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Rescooped by Francis Martin from Plant-Microbe Symbioses
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Amplicon –Based Metagenomic Analysis of Mixed Fungal Samples Using Proton Release Amplicon Sequencing

Amplicon –Based Metagenomic Analysis of Mixed Fungal Samples Using Proton Release Amplicon Sequencing | MycorWeb Plant-Microbe Interactions | Scoop.it
Next generation sequencing technology has revolutionised microbiology by allowing concurrent analysis of whole microbial communities. Here we developed and verified similar methods for the analysis of fungal communities using a proton release sequencing platform with the ability to sequence reads of up to 400 bp in length at significant depth. This read length permits the sequencing of amplicons from commonly used fungal identification regions and thereby taxonomic classification. Using the 400 bp sequencing capability, we have sequenced amplicons from the ITS1, ITS2 and LSU fungal regions to a depth of approximately 700,000 raw reads per sample. Representative operational taxonomic units (OTUs) were chosen by the USEARCH algorithm, and identified taxonomically through nucleotide blast (BLASTn). Combination of this sequencing technology with the bioinformatics pipeline allowed species recognition in two controlled fungal spore populations containing members of known identity and concentration. Each species included within the two controlled populations was found to correspond to a representative OTU, and these OTUs were found to be highly accurate representations of true biological sequences. However, the absolute number of reads attributed to each OTU differed among species. The majority of species were represented by an OTU derived from all three genomic regions although in some cases, species were only represented in two of the regions due to the absence of conserved primer binding sites or due to sequence composition. It is apparent from our data that proton release sequencing technologies can deliver a qualitative assessment of the fungal members comprising a sample. The fact that some fungi cannot be amplified by specific “conserved” primer pairs confirms our recommendation that a multi-region approach be taken for other amplicon-based metagenomic studies.

Via Jean-Michel Ané
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Håvard Kauserud's curator insight, April 17, 2014 3:24 AM

Should not refer to this as metagenomics..

Rescooped by Francis Martin from Plant-Microbe Symbioses
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Genet dynamics and ecological functions of the pioneer ectomycorrhizal fungi Laccaria amethystina and Laccaria laccata in a volcanic desert on Mount Fuji

Genet dynamics and ecological functions of the pioneer ectomycorrhizal fungi Laccaria amethystina and Laccaria laccata in a volcanic desert on Mount Fuji | MycorWeb Plant-Microbe Interactions | Scoop.it

To understand the reproduction of the pioneer ectomycorrhizal fungi Laccaria amethystina andLaccaria laccata in a volcanic desert on Mount Fuji, Japan, the in situ genet dynamics of sporocarps were analysed. Sporocarps of the two Laccaria species were sampled at fine and large scales for 3 and 2 consecutive years, respectively, and were genotyped using microsatellite markers. In the fine-scale analysis, we found many small genets, the majority of which appeared and disappeared annually. The high densities and annual renewal of Laccaria genets indicate frequent turnover by sexual reproduction via spores. In the large-scale analysis, we found positive spatial autocorrelations in the shortest distance class. An allele-clustering analysis also showed that several alleles were distributed in only a small, localised region. These results indicate that Laccaria spores contributing to sexual reproduction may be dispersed only short distances from sporocarps that would have themselves been established via rare, long-distance spore dispersal. This combination of rare, long-distance and frequent, short-distance Laccaria spore dispersal is reflected in the establishment pattern of seeds of their host, Salix reinii.


Via Jean-Michel Ané
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Rescooped by Francis Martin from How microbes emerge
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PLOS Genetics: Interspecific Sex in Grass Smuts and the Genetic Diversity of Their Pheromone-Receptor System (2011)

PLOS Genetics: Interspecific Sex in Grass Smuts and the Genetic Diversity of Their Pheromone-Receptor System (2011) | MycorWeb Plant-Microbe Interactions | Scoop.it

The grass smuts comprise a speciose group of biotrophic plant parasites, so-called Ustilaginaceae, which are specifically adapted to hosts of sweet grasses, the Poaceae family. Mating takes a central role in their life cycle, as it initiates parasitism by a morphological and physiological transition from saprobic yeast cells to pathogenic filaments. As in other fungi, sexual identity is determined by specific genomic regions encoding allelic variants of a pheromone-receptor (PR) system and heterodimerising transcription factors. Both operate in a biphasic mating process that starts with PR–triggered recognition, directed growth of conjugation hyphae, and plasmogamy of compatible mating partners. So far, studies on the PR system of grass smuts revealed diverse interspecific compatibility and mating type determination. However, many questions concerning the specificity and evolutionary origin of the PR system remain unanswered. Combining comparative genetics and biological approaches, we report on the specificity of the PR system and its genetic diversity in 10 species spanning about 100 million years of mating type evolution. We show that three highly syntenic PR alleles are prevalent among members of the Ustilaginaceae, favouring a triallelic determination as the plesiomorphic characteristic of this group. Furthermore, the analysis of PR loci revealed increased genetic diversity of single PR locus genes compared to genes of flanking regions. Performing interspecies sex tests, we detected a high potential for hybridisation that is directly linked to pheromone signalling as known from intraspecies sex. Although the PR system seems to be optimised for intraspecific compatibility, the observed functional plasticity of the PR system increases the potential for interspecific sex, which might allow the hybrid-based genesis of newly combined host specificities.


Via Kamoun Lab @ TSL, Niklaus Grunwald
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Transcription factor-dependent nuclear localization of a transcriptional repressor in jasmonate hormone signaling

Transcription factor-dependent nuclear localization of a transcriptional repressor in jasmonate hormone signaling | MycorWeb Plant-Microbe Interactions | Scoop.it

The plant hormone jasmonate (JA) plays an important role in regulating growth, development and immunity. A key step in JA signaling is ligand-dependent assembly of a coreceptor complex consisting of the F-box protein COI1 and JAZ transcriptional repressors. Assembly of this receptor complex results in proteasome-mediated degradation of JAZ repressors, which at resting state bind to and repress the MYC transcription factors. Although the JA receptor complex is believed to function within the nucleus, how this receptor complex enters the nucleus and, more generally, the cell biology of jasmonate signaling are not well understood. In this study, we conducted mutational analysis of the C termini (containing the conserved Jas motif) of two JAZ repressors, JAZ1 and JAZ9. These analyses unexpectedly revealed different subcellular localization patterns of JAZ1ΔJas and JAZ9ΔJas, which were associated with differential interaction of JAZ1ΔJas and JAZ9ΔJas with MYC2 and differential repressor activity in vivo. Importantly, physical interaction with MYC2 appears to play an active role in the nuclear targeting of JAZ1 and JAZ9, and the nuclear localization of JAZ9 was compromised in myc2 mutant plants. We identified a highly conserved arginine residue in the Jas motif that is critical for coupling MYC2 interaction with nuclear localization of JAZ9 and JAZ9 repressor function in vivo. Our results suggest a model for explaining why some JAZΔJas proteins, but not others, confer constitutive JA-insensitivity when overexpressed in plants. Results also provide evidence for a transcription factor-dependent mechanism for nuclear import of a cognate transcriptional repressor JAZ9 in plants.

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Rescooped by Francis Martin from Plants and Microbes
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New Phytologist: Virtual Special Issue on phytopathogen effector proteins (2014)

New Phytologist: Virtual Special Issue on phytopathogen effector proteins (2014) | MycorWeb Plant-Microbe Interactions | Scoop.it

Upon analysis of phytopathogen genomes it turned out that phytopathogenic microbes typically express dozens (bacteria; Collmer et al., 2009) to hundreds (oomycetes and fungi; Schmidt & Panstruga, 2011) of effector proteins. They often do not share any considerable sequence relatedness to known proteins and therefore can be considered as ‘pioneer proteins’, which renders their functional analysis a formidable task. Nevertheless, owing to the key role effector proteins play in plant–microbe interactions, their molecular analysis lately became very popular and is a flourishing research field. This development, which is evidenced by the substantial increase in literature devoted to ‘effectors’ during the last decade (Fig. 1), has also been appreciated by New Phytologist as documented by the organization of two symposia, in 2009 and 2012, with an emphasis on effectors in plant–microbe interactions (22nd New Phytologist Symposium and 30th New Phytologist Symposium; Lee et al., 2013). Besides proteinaceous effectors, secreted small molecules can also exhibit effector activity. Prominent examples from the phytopathogenic bacterium Pseudomonas syringae comprise syringolin (a proteasome inhibitor) and coronatine (a mimic of the phytohormone jasmonic acid), but also fungal secondary metabolites can have defense-suppressing activities (e.g. host-selective toxins; Tsuge et al., 2013).


In this Virtual Special Issue we compile a number of papers that were published recently in New Phytologist which all deal with various aspects of effector biology, ranging from bacterial to oomycete and fungal as well as nematode effectors. These papers cover effector functions related to suppression of plant immune responses as well as nutrient acquisition and the identification of plant effector targets.


Via Kamoun Lab @ TSL
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Whole Genome and Global Gene Expression Analyses of the Model Mushroom Flammulina velutipes Reveal a High Capacity for Lignocellulose Degradation

Whole Genome and Global Gene Expression Analyses of the Model Mushroom Flammulina velutipes Reveal a High Capacity for Lignocellulose Degradation | MycorWeb Plant-Microbe Interactions | Scoop.it

Flammulina velutipes is a fungus with health and medicinal benefits that has been used for consumption and cultivation in East Asia. F. velutipes is also known to degrade lignocellulose and produce ethanol. The overlapping interests of mushroom production and wood bioconversion make F. velutipes an attractive new model for fungal wood related studies. Here, we present the complete sequence of the F. velutipes genome. This is the first sequenced genome for a commercially produced edible mushroom that also degrades wood. The 35.6-Mb genome contained 12,218 predicted protein-encoding genes and 287 tRNA genes assembled into 11 scaffolds corresponding with the 11 chromosomes of strain KACC42780. The 88.4-kb mitochondrial genome contained 35 genes. Well-developed wood degrading machinery with strong potential for lignin degradation (69 auxiliary activities, formerly FOLymes) and carbohydrate degradation (392 CAZymes), along with 58 alcohol dehydrogenase genes were highly expressed in the mycelium, demonstrating the potential application of this organism to bioethanol production. Thus, the newly uncovered wood degrading capacity and sequential nature of this process in F. velutipes, offer interesting possibilities for more detailed studies on either lignin or (hemi-) cellulose degradation in complex wood substrates. The mutual interest in wood degradation by the mushroom industry and (ligno-)cellulose biomass related industries further increase the significance of F. velutipes as a new model.

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Mapping the Cellular Response to Small Molecules Using Chemogenomic Fitness Signatures

Mapping the Cellular Response to Small Molecules Using Chemogenomic Fitness Signatures | MycorWeb Plant-Microbe Interactions | Scoop.it

Genome-wide characterization of the in vivo cellular response to perturbation is fundamental to understanding how cells survive stress. Identifying the proteins and pathways perturbed by small molecules affects biology and medicine by revealing the mechanisms of drug action. We used a yeast chemogenomics platform that quantifies the requirement for each gene for resistance to a compound in vivo to profile 3250 small molecules in a systematic and unbiased manner. We identified 317 compounds that specifically perturb the function of 121 genes and characterized the mechanism of specific compounds. Global analysis revealed that the cellular response to small molecules is limited and described by a network of 45 major chemogenomic signatures. Our results provide a resource for the discovery of functional interactions among genes, chemicals, and biological processes.

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Rescooped by Francis Martin from Plant-Microbe Symbioses
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The importance of individuals: intraspecific diversity of mycorrhizal plants and fungi in ecosystems

The importance of individuals: intraspecific diversity of mycorrhizal plants and fungi in ecosystems | MycorWeb Plant-Microbe Interactions | Scoop.it

A key component of biodiversity is the number and abundance of individuals (i.e. genotypes), and yet such intraspecific diversity is rarely considered when investigating the effects of biodiversity of mycorrhizal plants and fungi on ecosystem processes. Within a species, individuals vary considerably in important reproductive and functional attributes, including carbon fixation, mycelial growth and nutrient utilization, but this is driven by both genetic and environmental (including climatic) factors. The interactions between individual plants and mycorrhizal fungi can have important consequences for the maintenance of biodiversity and regulation of resource transfers in ecosystems. There is also emerging evidence that assemblages of genotypes may affect ecosystem processes to a similar extent as assemblages of species. The application of whole-genome sequencing and population genomics to mycorrhizal plants and fungi will be crucial to determine the extent to which individual variation in key functional attributes is genetically based. We argue the need to unravel the importance of the diversity (especially assemblages of different evenness and richness) of individuals of both mycorrhizal plants and fungi, and the need to take a ‘community genetics’ approach to better understand the functional significance of the biodiversity of mycorrhizal symbioses.


Via Jean-Michel Ané
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Jean-Michel Ané's curator insight, April 27, 2014 12:49 PM

A bit old but still very interesting review.

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New Phytol: Fungal associations in Horneophyton ligneri from the Rhynie Chert (c. 407 million year old) closely resemble those in extant lower land plants (2014)

New Phytol: Fungal associations in Horneophyton ligneri from the Rhynie Chert (c. 407 million year old) closely resemble those in extant lower land plants (2014) | MycorWeb Plant-Microbe Interactions | Scoop.it

Fungi (Eumycota) form close associations with plants, with which they have co-existed since the dawn of life on land, but their diversity in early terrestrial ecosystems is still poorly understood.We studied petrographic sections of exceptionally well-preserved petrified plants from the 407 million yr-old Rhynie Chert (Scotland, UK). For comparative purposes, we illustrate fungal associations in four extant lower land plants.We document two new endophytes in the plant Horneophyton lignieri: Palaeoglomus boullardii (sp. nov. Glomeromycota) colonizes parenchyma in a discontinuous zone of the outer cortex of the aerial axes, forming arbuscule-like structures, vesicles and spores; Palaeoendogone gwynne-vaughaniae (gen. nov., sp. nov. Mucoromycotina) colonizes parenchyma in the basal part of the plant, where it is present in intercellular spaces and as intracellular coils but absent from rhizoids.Critical comparisons between the newly discovered Horneophyton endophytes, fungi previously described from the Rhynie Chert and fungal colonization in extant lower land plants reveal several features characteristic of both Mucoromycotina and Glomeromycota. A reappraisal of fungal associations in early land plants indicates that they are more diverse than assumed hitherto, overturning the long-held paradigm that the early endophytes were exclusively Glomeromycota.


Via Christophe Jacquet, Kamoun Lab @ TSL
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Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation | MycorWeb Plant-Microbe Interactions | Scoop.it

Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e.grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.

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N-Glycosylation of Effector Proteins by an α-1,3-Mannosyltransferase Is Required for the Rice Blast Fungus to Evade Host Innate Immunity

N-Glycosylation of Effector Proteins by an α-1,3-Mannosyltransferase Is Required for the Rice Blast Fungus to Evade Host Innate Immunity | MycorWeb Plant-Microbe Interactions | Scoop.it

Plant pathogenic fungi deploy secreted effectors to suppress plant immunity responses. These effectors operate either in the apoplast or within host cells, so they are putatively glycosylated, but the posttranslational regulation of their activities has not been explored. In this study, the ASPARAGINE-LINKED GLYCOSYLATION3 (ALG3)-mediated N-glycosylation of the effector, Secreted LysM Protein1 (Slp1), was found to be essential for its activity in the rice blast fungus Magnaporthe oryzae. ALG3 encodes an α-1,3-mannosyltransferase for protein N-glycosylation. Deletion of ALG3 resulted in the arrest of secondary infection hyphae and a significant reduction in virulence. We observed that Δalg3 mutants induced massive production of reactive oxygen species in host cells, in a similar manner to Δslp1 mutants, which is a key factor responsible for arresting infection hyphae of the mutants. Slp1 sequesters chitin oligosaccharides to avoid their recognition by the rice (Oryza sativa) chitin elicitor binding protein CEBiP and the induction of innate immune responses, including reactive oxygen species production. We demonstrate that Slp1 has three N-glycosylation sites and that simultaneous Alg3-mediated N-glycosylation of each site is required to maintain protein stability and the chitin binding activity of Slp1, which are essential for its effector function. These results indicate that Alg3-mediated N-glycosylation of Slp1 is required to evade host innate immunity.


Via Wheat Pathogenomics
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Wheat Pathogenomics's curator insight, April 20, 2014 12:58 PM

Ecp6 homologue in Magnaporthe requires N-glycosylation for efficient binding to chitin.

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Synthetic biology approaches to engineering the nitrogen symbiosis in cereals

Synthetic biology approaches to engineering the nitrogen symbiosis in cereals | MycorWeb Plant-Microbe Interactions | Scoop.it

Nitrogen is abundant in the earth’s atmosphere but, unlike carbon, cannot be directly assimilated by plants. The limitation this places on plant productivity has been circumvented in contemporary agriculture through the production and application of chemical fertilizers. The chemical reduction of nitrogen for this purpose consumes large amounts of energy and the reactive nitrogen released into the environment as a result of fertilizer application leads to greenhouse gas emissions, as well as widespread eutrophication of aquatic ecosystems. The environmental impacts are intensified by injudicious use of fertilizers in many parts of the world. Simultaneously, limitations in the production and supply of chemical fertilizers in other regions are leading to low agricultural productivity and malnutrition. Nitrogen can be directly fixed from the atmosphere by some bacteria and Archaea, which possess the enzyme nitrogenase. Some plant species, most notably legumes, have evolved close symbiotic associations with nitrogen-fixing bacteria. Engineering cereal crops with the capability to fix their own nitrogen could one day address the problems created by the over- and under-use of nitrogen fertilizers in agriculture. This could be achieved either by expression of a functional nitrogenase enzyme in the cells of the cereal crop or through transferring the capability to form a symbiotic association with nitrogen-fixing bacteria. While potentially transformative, these biotechnological approaches are challenging; however, with recent advances in synthetic biology they are viable long-term goals. This review discusses the possibility of these biotechnological solutions to the nitrogen problem, focusing on engineering the nitrogen symbiosis in cereals.

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Structural Basis for Assembly and Function of a Heterodimeric Plant Immune Receptor

Structural Basis for Assembly and Function of a Heterodimeric Plant Immune Receptor | MycorWeb Plant-Microbe Interactions | Scoop.it

Cytoplasmic plant immune receptors recognize specific pathogen effector proteins and initiate effector-triggered immunity. In Arabidopsis, the immune receptors RPS4 and RRS1 are both required to activate defense to three different pathogens. We show that RPS4 and RRS1 physically associate. Crystal structures of the N-terminal Toll–interleukin-1 receptor/resistance (TIR) domains of RPS4 and RRS1, individually and as a heterodimeric complex (respectively at 2.05, 1.75, and 2.65 angstrom resolution), reveal a conserved TIR/TIR interaction interface. We show that TIR domain heterodimerization is required to form a functional RRS1/RPS4 effector recognition complex. The RPS4 TIR domain activates effector-independent defense, which is inhibited by the RRS1 TIR domain through the heterodimerization interface. Thus, RPS4 and RRS1 function as a receptor complex in which the two components play distinct roles in recognition and signaling.

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The 8th International Symbiosis Congress will convene at the University of Lisbon, in Portugal

The 8th International Symbiosis Congress will convene at the University of Lisbon, in Portugal | MycorWeb Plant-Microbe Interactions | Scoop.it

The University of Lisbon (ULisboa; http://www.ulisboa.pt/) was created in 2013 based on the union of university institutions, which date back to the 13th century. We hope that this symbiosis between new and old will create the perfect environment to host the Symbiosis Congress in 2015. We welcome all researchers, educators, and students who work in the many diverse fields which involve symbioses.

Held every three years and organized by the International Symbiosis Society, the Congress is focused on a concept - symbiosis. Long viewed as an exception, a curiosity on the margins of biology, symbiosis is today considered ubiquitous and one of the main characteristics of the biological systems, which involves networking at distinct levels through molecular, physical, or physiological communication and allows evolution and adaptation. The theme and the spirit of the meeting, “Symbiotic lifestyle”, is an invitation to innovation and creativity and aims at opening horizons and creating avenues of knowledge in a multidisciplinary environment.

We hope that this meeting will be an ideal venue for discussion, exchange and transfer of knowledge, helping to create new and foster existing collaborations and symbioses between researchers.

We hope you enjoy it,

 

The organizing committee:

Silvana Munzi (Faculdade de Ciências da Universidade de Lisboa)

Cristina Cruz (Faculdade de Ciências da Universidade de Lisboa)

Rusty Rodriguez (Adaptive Symbiotic Technologies)

 


Via Jean-Michel Ané
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The new symbiont on the block?

The new symbiont on the block? | MycorWeb Plant-Microbe Interactions | Scoop.it

When you step back and look at the field of symbiosis research (see Mary Beth Saffo’s recent blog post for the ISS), one can see that the rapid growth and appreciation of our field is staggering. Perhaps we do not rival other research fields with respect to number of scientists per unit effort, but scientists and non-scientists alike are finally beginning to comprehend the true magnitude and importance of microbial symbiosis.  A Grand Challenge Article (GCA) for the recently established journal Frontiers in Microbial Symbiosis highlighted how we are increasingly seeing the terms ‘holobiont’, ‘metaorganism’ and ‘microbiome’ used by researchers from a range of scientific disciplines. However, despite this recent progress in appreciating the importance and ubiquity of microbial symbioses, many scientists still tend to view symbiotic partners as separate individuals, thereby limiting our ability to assess interactive mechanisms (including synergism and pathogenesis) within these systems.  As researchers we desperately need to overcome this perception of individualism to truly understand the ecology and evolution of microbial symbioses.  And whilst Mary Beth highlighted the need for clarity and consistency regarding the definition of “symbiosis,” it is equally important to recognize that the concept of symbiosis needs to remain fluid. The subcategories of “symbiosis” (pathogenic, mutualistic and commensal) are ultimately just idealized interaction states; whereas the actualized state may wander across these defined boundaries depending on evolutionary processes, changes in environmental conditions and/or health state of the host/symbiont. For example, the cnidarian-algal mutualism, a partnership where most of the symbiont transmission is horizontal (and should therefore theoretically favour parasitism) highlights the complexity of symbiotic interactions. A study by Sachs and Wilcox (2006) used sequential horizontal transmission to demonstrate that after only a few forced horizontal transmissions, the Cassiopea–Symbiodinium partnership began to display parasitic rather than mutualistic characteristics.


Via Jean-Michel Ané
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Endemism and functional convergence across the North American soil mycobiome

Endemism and functional convergence across the North American soil mycobiome | MycorWeb Plant-Microbe Interactions | Scoop.it

Identifying the ecological processes that structure communities and the consequences for ecosystem function is a central goal of ecology. The recognition that fungi, bacteria, and viruses control key ecosystem functions has made microbial communities a major focus of this field. Because many ecological processes are apparent only at particular spatial or temporal scales, a complete understanding of the linkages between microbial community, environment, and function requires analysis across a wide range of scales. Here, we map the biological and functional geography of soil fungi from local to continental scales and show that the principal ecological processes controlling community structure and function operate at different scales. Similar to plants or animals, most soil fungi are endemic to particular bioregions, suggesting that factors operating at large spatial scales, like dispersal limitation or climate, are the first-order determinants of fungal community structure in nature. By contrast, soil extracellular enzyme activity is highly convergent across bioregions and widely differing fungal communities. Instead, soil enzyme activity is correlated with local soil environment and distribution of fungal traits within the community. The lack of structure–function relationships for soil fungal communities at continental scales indicates a high degree of functional redundancy among fungal communities in global biogeochemical cycles.

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Ectomycorrhizal Cortinarius species participate in enzymatic oxidation of humus in northern forest ecosystems

Ectomycorrhizal Cortinarius species participate in enzymatic oxidation of humus in northern forest ecosystems | MycorWeb Plant-Microbe Interactions | Scoop.it

In northern forests, belowground sequestration of nitrogen (N) in complex organic pools restricts nutrient availability to plants. Oxidative extracellular enzymes produced by ectomycorrhizal fungi may aid plant N acquisition by providing access to N in macromolecular complexes. We test the hypotheses that ectomycorrhizal Cortinarius species produce Mn-dependent peroxidases, and that the activity of these enzymes declines at elevated concentrations of inorganic N.In a boreal pine forest and a sub-arctic birch forest, Cortinarius DNA was assessed by 454-sequencing of ITS amplicons and related to Mn-peroxidase activity in humus samples with- and without previous N amendment. Transcription of Cortinarius Mn-peroxidase genes was investigated in field samples. Phylogenetic analyses of Cortinarius peroxidase amplicons and genome sequences were performed.We found a significant co-localization of high peroxidase activity and DNA from Cortinarius species. Peroxidase activity was reduced by high ammonium concentrations. Amplification of mRNA sequences indicated transcription of Cortinarius Mn-peroxidase genes under field conditions. The Cortinarius glaucopus genome encodes 11 peroxidases – a number comparable to many white-rot wood decomposers.These results support the hypothesis that some ectomycorrhizal fungi – Cortinarius species in particular – may play an important role in decomposition of complex organic matter, linked to their mobilization of organically bound N.


Via Christophe Jacquet, Jean-Michel Ané
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Genome-wide Comparative Analysis of the GRAS Gene Family in Populus, Arabidopsis and Rice

GRAS genes belong to a gene family of transcription regulators that function in the regulation of plant growth and development. Our knowledge about the expansion and diversification of this gene family in flowering plants is presently limited to the herbaceous species Arabidopsis and rice. Numerous aspects, including the phylogenetic history, expansion, functional divergence and adaptive evolution await further study, especially in woody tree species. Based on the latest genome assemblies, we found 106, 34 and 60 putative GRAS genes in Populus, Arabidopsis and rice, respectively. Phylogenetic analysis revealed that GRAS proteins could be divided into at least 13 subfamilies. Tandem and segmental duplications are the most common expansion mechanisms of this gene family, and their frequent joint action may explain the rapid expansion in Populus. Site-specific shifts in evolutionary rates might be the main force driving subfamily-specific functional diversification. Adaptive evolution analysis revealed that GRAS genes have evolved mainly under purifying selection after duplication, suggesting that strong functional constraints have a bearing on the evolution of GRAS genes. Both expressed sequence tags (EST) and microarray data revealed that GRAS genes in Populus have broad expression patterns across a variety of organs/tissues. Expression divergence analyses between paralogous pairs of GRAS genes suggested that the retention of GRAS genes after duplication could be mainly attributed to substantial functional novelty such as neo-functionalization or sub-functionalization. Our study highlights the expansion and diversification of the GRAS gene family in Populus and provides the first comprehensive analysis of this gene family in the Populus genome.


Via Jean-Michel Ané
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Botany: Special issue: The microbiota of plants

In this Special Issue, we have tried to capture the diversity of plant–microbe research that is on-going, and that might not normally be marketed under the banner of “plant microbiome research”. Nevertheless, it belongs under this banner and we highlight some of this research here, including a variety of plant “habitats” such as roots, leaves, and floral parts, as well as a variety of microbes, from bacteria and arbuscular mycorrhizal fungi to dark septate fungi. Of course, the field is broader than what we are able present in a single issue, but we hope that it inspires researchers of overlooked aspects of plant microbiota research to get in on the game, and contribute to a more complete picture of this complex “ecosystem”.


Via Stéphane Hacquard
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