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Novel Entries in a Fungal Biofilm Matrix Encyclopedia

Novel Entries in a Fungal Biofilm Matrix Encyclopedia | MycorWeb Plant-Microbe Interactions | Scoop.it

Virulence of Candida is linked with its ability to form biofilms. Once established, biofilm infections are nearly impossible to eradicate. Biofilm cells live immersed in a self-produced matrix, a blend of extracellular biopolymers, many of which are uncharacterized. In this study, we provide a comprehensive analysis of the matrix manufactured by Candida albicans both in vitro and in a clinical niche animal model. We further explore the function of matrix components, including the impact on drug resistance. We uncovered components from each of the macromolecular classes (55% protein, 25% carbohydrate, 15% lipid, and 5% nucleic acid) in the C. albicans biofilm matrix. Three individual polysaccharides were identified and were suggested to interact physically. Surprisingly, a previously identified polysaccharide of functional importance, β-1,3-glucan, comprised only a small portion of the total matrix carbohydrate. Newly described, more abundant polysaccharides included α-1,2 branched α-1,6-mannans (87%) associated with unbranched β-1,6-glucans (13%) in an apparent mannan-glucan complex (MGCx). Functional matrix proteomic analysis revealed 458 distinct activities. The matrix lipids consisted of neutral glycerolipids (89.1%), polar glycerolipids (10.4%), and sphingolipids (0.5%). Examination of matrix nucleic acid identified DNA, primarily noncoding sequences. Several of the in vitro matrix components, including proteins and each of the polysaccharides, were also present in the matrix of a clinically relevant in vivo biofilm. Nuclear magnetic resonance (NMR) analysis demonstrated interaction of aggregate matrix with the antifungal fluconazole, consistent with a role in drug impedance and contribution of multiple matrix components.

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Tree genotype influences ectomycorrhizal fungal community structure: Ecological and evolutionary implications

Tree genotype influences ectomycorrhizal fungal community structure: Ecological and evolutionary implications | MycorWeb Plant-Microbe Interactions | Scoop.it
Although the eco-evolutionary dynamics of multicellular organisms are intertwined with the microorganisms that colonize them, there is only a rudimentary understanding of how a host's genotype influences its microbiome. We utilize Populus angustifolia to test whether communities of essential symbionts, ectomycorrhizal fungi (EMF), vary among host genotypes. Further, we test whether EMF communities covary among tree genotypes with the chemistry of senescent leaves and aboveground biomass, traits important to tree fitness, and carbon and nutrient cycling. We found: 1) EMF composition, colonization and the Basidiomycota to Ascomycota ratio varied among tree genotypes (broad-sense heritability = 0.10–0.25). 2) EMF composition did not covary among genotypes with aboveground biomass but it did covary with senescent leaf chemistry (rho = 0.29), primarily due to a single genotype. These findings demonstrate a link between tree genotype and EMF communities, which has implications for fungal diversity, host-symbiont interactions and aboveground-belowground linkages in ecological and evolutionary contexts.
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Observed forest sensitivity to climate implies large changes in 21st century North American forest growth

Observed forest sensitivity to climate implies large changes in 21st century North American forest growth | MycorWeb Plant-Microbe Interactions | Scoop.it
Predicting long-term trends in forest growth requires accurate characterisation of how the relationship between forest productivity and climatic stress varies across climatic regimes. Using a network of over two million tree-ring observations spanning North America and a space-for-time substitution methodology, we forecast climate impacts on future forest growth. We explored differing scenarios of increased water-use efficiency (WUE) due to CO2-fertilisation, which we simulated as increased effective precipitation. In our forecasts: (1) climate change negatively impacted forest growth rates in the interior west and positively impacted forest growth along the western, southeastern and northeastern coasts; (2) shifting climate sensitivities offset positive effects of warming on high-latitude forests, leaving no evidence for continued ‘boreal greening’; and (3) it took a 72% WUE enhancement to compensate for continentally averaged growth declines under RCP 8.5. Our results highlight the importance of locally adapted forest management strategies to handle regional differences in growth responses to climate change.
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Intraradical colonization by arbuscular mycorrhizal fungi triggers induction of a lipochitooligosaccharide receptor

Intraradical colonization by arbuscular mycorrhizal fungi triggers induction of a lipochitooligosaccharide receptor | MycorWeb Plant-Microbe Interactions | Scoop.it
Functional divergence of paralogs following gene duplication is one of the mechanisms leading to evolution of novel pathways and traits. Here we show that divergence of Lys11 and Nfr5 LysM receptor kinase paralogs of Lotus japonicus has affected their specificity for lipochitooligosaccharides (LCOs) decorations, while the innate capacity to recognize and induce a downstream signalling after perception of rhizobial LCOs (Nod factors) was maintained. Regardless of this conserved ability, Lys11 was found neither expressed, nor essential during nitrogen-fixing symbiosis, providing an explanation for the determinant role of Nfr5 gene during Lotus-rhizobia interaction. Lys11 was expressed in root cortex cells associated with intraradical colonizing arbuscular mycorrhizal fungi. Detailed analyses of lys11 single and nfr1nfr5lys11 triple mutants revealed a functional arbuscular mycorrhizal symbiosis, indicating that Lys11 alone, or its possible shared function with the Nod factor receptors is not essential for the presymbiotic phases of AM symbiosis. Hence, both subfunctionalization and specialization appear to have shaped the function of these paralogs where Lys11 acts as an AM-inducible gene, possibly to fine-tune later stages of this interaction.

Via Ryohei Thomas Nakano, Jean-Michel Ané
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Reciprocal genomic evolution in the ant-fungus agricultural symbiosis : Nature Communications : Nature Research

Reciprocal genomic evolution in the ant-fungus agricultural symbiosis : Nature Communications : Nature Research | MycorWeb Plant-Microbe Interactions | Scoop.it
The attine ant–fungus agricultural symbiosis evolved over tens of millions of years, producing complex societies with industrial-scale farming analogous to that of humans. Here we document reciprocal shifts in the genomes and transcriptomes of seven fungus-farming ant species and their fungal cultivars. We show that ant subsistence farming probably originated in the early Tertiary (55–60 MYA), followed by further transitions to the farming of fully domesticated cultivars and leaf-cutting, both arising earlier than previously estimated. Evolutionary modifications in the ants include unprecedented rates of genome-wide structural rearrangement, early loss of arginine biosynthesis and positive selection on chitinase pathways. Modifications of fungal cultivars include loss of a key ligninase domain, changes in chitin synthesis and a reduction in carbohydrate-degrading enzymes as the ants gradually transitioned to functional herbivory. In contrast to human farming, increasing dependence on a single cultivar lineage appears to have been essential to the origin of industrial-scale ant agriculture.
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Comparing Fungal Secretions to Uncover Carbon Compound Degradation Pathways - DOE Joint Genome Institute

Comparing Fungal Secretions to Uncover Carbon Compound Degradation Pathways - DOE Joint Genome Institute | MycorWeb Plant-Microbe Interactions | Scoop.it
Fungal secretomes, those collections of all molecules secreted by a cell, contain enzymes that can break down plant cell wall components such as cellulose, hemicellulose and lignin. These capabilities make them of interest to bioenergy researchers looking for cost-effective ways to convert plant mass into sustainable, alternative transportation fuels. In a study published online July 19, 2016 in Plos ONE, a team led by researchers at Harvard University and Woods Hole Oceanographic Institution (WHOI) conducted a comparative analysis of the secretomes of four recently-isolated and sequenced filamentous Ascomycete fungi to learn more about the variety of pathways they deploy to break down carbon compounds.
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Early nitrogen-deprivation responses in Arabidopsis roots reveal distinct differences on transcriptome and (phospho-) proteome levels between nitrate and ammonium nutrition

Early nitrogen-deprivation responses in Arabidopsis roots reveal distinct differences on transcriptome and (phospho-) proteome levels between nitrate and ammonium nutrition | MycorWeb Plant-Microbe Interactions | Scoop.it
Plant roots acquire nitrogen predominantly as ammonium and nitrate, which besides serving as nutrients, also have signaling roles. Re-addition of nitrate to starved plants rapidly re-programs the metabolism and gene expression, but the earliest responses to nitrogen deprivation are unknown. Here, the early transcriptional and (phospho)proteomic responses of roots to nitrate or ammonium deprivation were analyzed. The rapid transcriptional repression of known nitrate-induced genes proceeded the tissue NO3- concentration drop, with the transcription factor genes LBD37/38 and HRS1/HHO1 among those with earliest significant change. Similar rapid transcriptional repression occurred in loss-of-function mutants of the nitrate response factor NLP7 and some transcripts were stabilized by nitrate. In contrast, an early transcriptional response to ammonium deprivation was almost completely absent. However, ammonium deprivation induced a rapid and transient perturbation of the proteome and a differential phosphorylation pattern in proteins involved in adjusting the pH and cation homeostasis, plasma membrane H+, NH4+, K+ and water fluxes. Fewer differential phosphorylation patterns in transporters, kinases and other proteins occurred with nitrate deprivation. The deprivation responses were not just opposite to the re-supply responses, but identified NO3--deprivation induced mRNA decay and signaling candidates potentially reporting the external nitrate status to the cell.

Via Kevin Garcia
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Misconceptions on the application of biological market theory to the mycorrhizal symbiosis

The symbiosis between plants and arbuscular mycorrhizal fungi has been described as a biological market based on evidence that plants supply more carbohydrates to fungal partners that provide more soil nutrients, and vice versa1,​2,​3,​4. A recent paper by Walder and van der Heijden challenges this view5. However, their challenge is based on misunderstandings of biological market theory, and evolutionary theory more generally.

First, their claim that biological market theory requires (or assumes) tightly coupled direct resource exchange is incorrect. All that is required is that individuals have a preference, on average, for interacting with more beneficial partners6,​7,​8,​9. Biological market theory makes no claim on understanding (proximate) mechanisms of transfer processes. Instead, the aim of biological market theory is to address ultimate questions such as why partnerships remain stable over evolutionary time, even in the presence of less beneficial partners. Its usefulness lies in predicting how these exchanges will be affected by context, such as varying environmental conditions7,8,10,​11,​12.
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Draft Genome Sequence of the Deep-Sea Basidiomycetous Yeast Cryptococcus sp. Strain Mo29 Reveals Its Biotechnological Potential

Cryptococcus sp. strain Mo29 was isolated from the Rainbow hydrothermal site on the Mid-Atlantic Ridge. Here, we present the draft genome sequence of this basidiomycetous yeast strain, which has highlighted its biotechnological potential as revealed by the presence of genes involved in the synthesis of secondary metabolites and biotechnologically important enzymes.
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Climate, decay, and the death of the coal forests: Current Biology

Climate, decay, and the death of the coal forests: Current Biology | MycorWeb Plant-Microbe Interactions | Scoop.it
The botanical origin of coal is not disputed, but the causal factors that determined the rate of Corg sequestration and that limited the extent of coal forests are matters of debate. One theory is that abiotic factors were solely responsible for shifts in rates of Corg burial. Under this view, the high rate of carbon sequestration during the Permo-Carboniferous was caused by unusually widespread mire environments with anoxic, waterlogged conditions, which inhibited decay, and contractions in coal forests were caused by climatic shifts toward drier conditions.

An alternative hypothesis, proposed by Robinson, introduced, in addition to geological and environmental factors, the concept that biological interactions among organisms might also be important in coal formation. Specifically, the dramatic accumulation of Corg in the Permo-Carboniferous occurred in part because the fungi that are able to efficiently decompose lignin (a recalcitrant, heterogeneous plant polymer) had yet to evolve and diversify. Robinson also suggested that coal-age spore-bearing plants had an unusually high lignin content compared with the seed plants that would eventually replace them as dominant forest trees. This hypothesis is based on a limited fossil record of fungi, with liberal extrapolation to extant taxa. Here, we evaluate the Robinson hypothesis by considering the diversity and evolution of fungal decay mechanisms, which can now be addressed through comparative genomics, as well as the evolution of plant cell walls (PCWs). Historical inferences based on living species must also be reconcilable with the paleobotanical record, and ultimately should both inform and be tested by increasingly sophisticated Earth System models.
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Agrobacterium-mediated insertional mutagenesis in the mycorrhizal fungus Laccaria bicolor

Agrobacterium-mediated insertional mutagenesis in the mycorrhizal fungus Laccaria bicolor | MycorWeb Plant-Microbe Interactions | Scoop.it
Agrobacterium-mediated gene transfer (AMT) is extensively employed as a tool in fungal functional genomics and accordingly, in previous studies we used AMT on a dikaryotic strain of the ectomycorrhizal basidiomycete Laccaria bicolor. The interest in this fungus derives from its capacity to establish a symbiosis with tree roots, thereby playing a major role in nutrient cycling of forest ecosystems. The ectomycorrhizal symbiosis is a highly complex interaction involving many genes from both partners. To advance in the functional characterization of fungal genes, AMT was used on a monokaryotic L. bicolor. A collection of over 1200 transgenic strains was produced, of which 200 randomly selected strains were analyzed for their genomic T-DNA insertion patterns. By means of insertional mutagenesis, a number of transgenic strains were obtained displaying differential growth features. Moreover, mating with a compatible strain resulted in dikaryons that retained altered phenotypic features of the transgenic monokaryon. The analysis of the T-DNA integration pattern revealed mostly similar results to those reported in earlier studies, confirming the usefulness of AMT on different genetic backgrounds of L. bicolor. Taken together, our studies display the great versatility and potentiality of AMT as a tool for the genetic characterization of L. bicolor.
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Host genotype and age shape the leaf and root microbiomes of a wild perennial plant

Host genotype and age shape the leaf and root microbiomes of a wild perennial plant | MycorWeb Plant-Microbe Interactions | Scoop.it
Bacteria living on and in leaves and roots influence many aspects of plant health, so the extent of a plant’s genetic control over its microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies, because they poorly simulate true environmental heterogeneity, may misestimate or totally miss the influence of certain host genes on the microbiome. Here we report a large-scale field experiment to disentangle the effects of genotype, environment, age and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta (Brassicaceae), a perennial wild mustard. Host genetic control of the microbiome is evident in leaves but not roots, and varies substantially among sites. Microbiome composition also shifts as plants age. Furthermore, a large proportion of leaf bacterial groups are shared with roots, suggesting inoculation from soil. Our results demonstrate how genotype-by-environment interactions contribute to the complexity of microbiome assembly in natural environments.
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Tree species, spatial heterogeneity, and seasonality drive soil fungal abundance, richness, and composition in Neotropical rainforests

Tree species, spatial heterogeneity, and seasonality drive soil fungal abundance, richness, and composition in Neotropical rainforests | MycorWeb Plant-Microbe Interactions | Scoop.it
Tropical ecosystems remain poorly understood and this is particularly true for belowground soil fungi. Soil fungi may respond to plant identity when, for example, plants differentially allocate resources belowground. However, spatial and temporal heterogeneity in factors such as plant inputs, moisture, or nutrients can also affect fungal communities and obscure our ability to detect plant effects in single time point studies or within diverse forests. To address this, we sampled replicated monocultures of four tree species and secondary forest controls sampled in the drier and wetter seasons over 2 years. Fungal community composition was primarily related to vegetation type and spatial heterogeneity in the effects of vegetation type, with increasing divergence partly reflecting greater differences in soil pH and soil moisture. Across wetter versus drier dates, fungi were 7% less diverse, but up to four-fold more abundant. The combined effects of tree species and seasonality suggest that predicted losses of tropical tree diversity and intensification of drought have the potential to cascade belowground to affect both diversity and abundance of tropical soil fungi.
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The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity

The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity | MycorWeb Plant-Microbe Interactions | Scoop.it
The unicellular ancestor of animals had a complex repertoire of genes linked to multicellular processes. This suggests that changes in the regulatory genome, rather than in gene innovation, were key to the origin of animals. Here, we carry out multiple functional genomic assays in Capsaspora owczarzaki, the unicellular relative of animals with the largest known gene repertoire for transcriptional regulation. We show that changing chromatin states, differential lincRNA expression, and dynamic cis-regulatory sites are associated with life cycle transitions in Capsaspora. Moreover, we demonstrate conservation of animal developmental transcription-factor networks and extensive network interconnection in this premetazoan organism. In contrast, however, Capsaspora lacks animal promoter types, and its regulatory sites are small, proximal, and lack signatures of animal enhancers. Overall, our results indicate that the emergence of animal multicellularity was linked to a major shift in genome cis-regulatory complexity, most notably the appearance of distal enhancer regulation.
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Root morphology and mycorrhizal symbioses together shape nutrient foraging strategies of temperate trees

Photosynthesis by leaves and acquisition of water and minerals by roots are required for plant growth, which is a key component of many ecosystem functions. Although the role of leaf functional traits in photosynthesis is generally well understood, the relationship of root functional traits to nutrient uptake is not. In particular, predictions of nutrient acquisition strategies from specific root traits are often vague. Roots of nearly all plants cooperate with mycorrhizal fungi in nutrient acquisition. Most tree species form symbioses with either arbuscular mycorrhizal (AM) or ectomycorrhizal (EM) fungi. Nutrients are distributed heterogeneously in the soil, and nutrient-rich “hotspots” can be a key source for plants. Thus, predicting the foraging strategies that enable mycorrhizal root systems to exploit these hotspots can be critical to the understanding of plant nutrition and ecosystem carbon and nutrient cycling. Here, we show that in 13 sympatric temperate tree species, when nutrient availability is patchy, thinner root species alter their foraging to exploit patches, whereas thicker root species do not. Moreover, there appear to be two distinct pathways by which thinner root tree species enhance foraging in nutrient-rich patches: AM trees produce more roots, whereas EM trees produce more mycorrhizal fungal hyphae. Our results indicate that strategies of nutrient foraging are complementary among tree species with contrasting mycorrhiza types and root morphologies, and that predictable relationships between below-ground traits and nutrient acquisition emerge only when both roots and mycorrhizal fungi are considered together.
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North American forests unlikely to save us from climate change, study finds - Scienmag

North American forests unlikely to save us from climate change, study finds - Scienmag | MycorWeb Plant-Microbe Interactions | Scoop.it
Forests take up 25 – 30 percent of human-caused emissions of carbon dioxide — a strong greenhouse gas — and are therefore considered to play a crucial role in mitigating the speed and magnitude of climate change. However, a new study that combines future climate model projections, historic tree-ring records across the entire continent of North America, and how the growth rates of trees may respond to a higher concentration of carbon dioxide in the atmosphere has shown that the mitigation effect of forests will likely be much smaller in the future than previously suggested.

Published in the journal Ecology Letters, the study is the first to reveal the possible impact of a changing climate on the growth rate of trees across all of North America, in other words, how their growth changes over time and in response to shifting environmental conditions. The result are detailed forecast maps for the entire North American continent that reveal how forest growth will be impacted by climate change.
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Basidiomycete yeasts in the cortex of ascomycete macrolichens

Basidiomycete yeasts in the cortex of ascomycete macrolichens | MycorWeb Plant-Microbe Interactions | Scoop.it
For over 140 years, lichens have been regarded as a symbiosis between a single fungus, usually an ascomycete, and a photosynthesizing partner. Other fungi have long been known to occur as occasional parasites or endophytes, but the one lichen–one fungus paradigm has seldom been questioned. Here we show that many common lichens are composed of the known ascomycete, the photosynthesizing partner, and, unexpectedly, specific basidiomycete yeasts. These yeasts are embedded in the cortex, and their abundance correlates with previously unexplained variations in phenotype. Basidiomycete lineages maintain close associations with specific lichen species over large geographical distances and have been found on six continents. The structurally important lichen cortex, long treated as a zone of differentiated ascomycete cells, appears to consistently contain two unrelated fungi.
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Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi

Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that synergistically drive litter decomposition in the environment. While secretome studies of model organisms such as Phanerochaete chrysosporium and Aspergillus species have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or conducted side-by-side comparisons of diverse species. Thus, the mechanisms of carbon degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of LC-MS/MS, genomic, and bioinformatic analyses to characterize and compare the protein composition of the secretomes of four recently isolated, cosmopolitan, Mn(II)-oxidizing Ascomycetes ( Alternaria alternata SRC1lrK2f, Stagonospora sp. SRC1lsM3a, Pyrenochaeta sp. DS3sAY3a, and Paraconiothyrium sporulosum AP3s5-JAC2a). We demonstrate that the organisms produce a rich yet functionally similar suite of extracellular enzymes, with species-specific differences in secretome composition arising from unique amino acid sequences rather than overall protein function. Furthermore, we identify not only a wide range of carbohydrate-active enzymes that can directly oxidize recalcitrant carbon, but also an impressive suite of redox-active accessory enzymes that suggests a role for Fenton-based hydroxyl radical formation in indirect, non-specific lignocellulose attack. Our findings highlight the diverse oxidative capacity of these environmental isolates and enhance our understanding of the role of filamentous Ascomycetes in carbon turnover in the environment.
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Cell Host & Microbe: Mechanisms Underlying Robustness and Tunability in a Plant Immune Signaling Network (2016)

Cell Host & Microbe: Mechanisms Underlying Robustness and Tunability in a Plant Immune Signaling Network (2016) | MycorWeb Plant-Microbe Interactions | Scoop.it
A predictive, dynamic PTI signaling network model with four major sectors was builtInhibition of the jasmonate sector by the ethylene sector was central to robustnessMAMP-specific patterns of multiple inputs can tune the network responseThe symmetrically placed jasmonate and PAD4 sectors may form a tetrastable switch

 

The plant immune signaling network needs to be robust against attack from fast-evolving pathogens and tunable to optimize immune responses. We investigated the basis of robustness and tunability in the signaling network controlling pattern-triggered immunity (PTI) in Arabidopsis. A dynamic network model containing four major signaling sectors, the jasmonate, ethylene, phytoalexin-deficient 4, and salicylate sectors, which together govern up to 80% of the PTI levels, was built using data for dynamic sector activities and PTI levels under exhaustive combinatorial sector perturbations. Our regularized multiple regression model had a high level of predictive power and captured known and unexpected signal flows in the network. The sole inhibitory sector in the model, the ethylene sector, contributed centrally to network robustness via its inhibition of the jasmonate sector. The model’s multiple input sites linked specific signal input patterns varying in strength and timing to different network response patterns, indicating a mechanism enabling tunability.


Via Kamoun Lab @ TSL
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Reply to ‘Misconceptions on the application of biological market theory to the mycorrhizal symbiosis’

The exchange of carbon for soil nutrients is thought to be the cornerstone of the arbuscular mycorrhizal (AM) symbiosis1,2. In our recent Review, we proposed that environmental conditions, functional diversity, competition for surplus resources, reciprocity and sink strength3 explain the outcome of resource exchange in the AM symbiosis. We also questioned the use of biological market theory as a universal framework to explain resource exchange in the AM symbiosis. In biological markets, interactions are viewed from an economic perspective, and the most beneficial partners are favoured in direct relation to the amount of resources received
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Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis | MycorWeb Plant-Microbe Interactions | Scoop.it
Transcriptome data sets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta-analysis of these samples has become routine in the plant research community, it is often hampered by a lack of metadata or differences in annotation styles of different labs. In this study, we carefully selected and integrated 6057 Arabidopsis microarray expression samples from 304 experiments deposited to the Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI). Metadata such as tissue type, growth conditions and developmental stage were manually curated for each sample. We then studied the global expression landscape of the integrated data set and found that samples of the same tissue tend to be more similar to each other than to samples of other tissues, even in different growth conditions or developmental stages. Root has the most distinct transcriptome, compared with aerial tissues, but the transcriptome of cultured root is more similar to the transcriptome of aerial tissues, as the cultured root samples lost their cellular identity. Using a simple computational classification method, we showed that the tissue type of a sample can be successfully predicted based on its expression profile, opening the door for automatic metadata extraction and facilitating the re-use of plant transcriptome data. As a proof of principle, we applied our automated annotation pipeline to 708 RNA-seq samples from public repositories and verified the accuracy of our predictions with sample metadata provided by the authors.
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Piriformospora indica Stimulates Root Metabolism of Arabidopsis thaliana

Piriformospora indica Stimulates Root Metabolism of Arabidopsis thaliana | MycorWeb Plant-Microbe Interactions | Scoop.it
Piriformospora indica is a root-colonizing fungus, which interacts with a variety of plants including Arabidopsis thaliana. This interaction has been considered as mutualistic leading to growth promotion of the host. So far, only indolic glucosinolates and phytohormones have been identified as key players. In a comprehensive non-targeted metabolite profiling study, we analyzed Arabidopsis thaliana’s roots, root exudates, and leaves of inoculated and non-inoculated plants by ultra performance liquid chromatography/electrospray ionization quadrupole-time-of-flight mass spectrometry (UPLC/(ESI)-QTOFMS) and gas chromatography/electron ionization quadrupole mass spectrometry (GC/EI-QMS), and identified further biomarkers. Among them, the concentration of nucleosides, dipeptides, oligolignols, and glucosinolate degradation products was affected in the exudates. In the root profiles, nearly all metabolite levels increased upon co-cultivation, like carbohydrates, organic acids, amino acids, glucosinolates, oligolignols, and flavonoids. In the leaf profiles, we detected by far less significant changes. We only observed an increased concentration of organic acids, carbohydrates, ascorbate, glucosinolates and hydroxycinnamic acids, and a decreased concentration of nitrogen-rich amino acids in inoculated plants. These findings contribute to the understanding of symbiotic interactions between plant roots and fungi of the order of Sebacinales and are a valid source for follow-up mechanistic studies, because these symbioses are particular and clearly different from interactions of roots with mycorrhizal fungi or dark septate endophytes

Via Jean-Michel Ané
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Laccase multigene families in Agaricomycetes

Laccase multigene families in Agaricomycetes | MycorWeb Plant-Microbe Interactions | Scoop.it
Here we present the results of the exploration of laccase multigene families (MGFs) in basidiomycetous fungi from different taxonomic groups using a next generation sequencing (NGS) technology. In our study, multiple laccase genes were identified in all of the investigated fungi (13 species) from Polyporaceae, Phanerochaetaceae, Meruliaceae, Pleurotaceae, Physalacriaceae, and Peniophoraceae families. It was shown that phylogenetic positioning of the newly identified sequences exhibit patterns of clusterization with respect to enzyme properties. This can be a potentially useful tool for selecting naturally existing laccases with different physicochemical characteristics relevant to different biotechnological applications. Moreover, the method developed in this study can be used in the screening of environmental samples and fast characterization of laccase MGFs in newly identified fungal species.
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Frontiers | Editorial: Transport in Plant Microbe Interactions | Plant Traffic and Transport

Frontiers | Editorial: Transport in Plant Microbe Interactions | Plant Traffic and Transport | MycorWeb Plant-Microbe Interactions | Scoop.it
The Editorial on the Research Topic
Transport in Plant Microbe Interactions

Plant–microbe interactions are omnipresent in terrestrial ecosystems and central to understand processes of individual growth, community assembly, and biogeochemical cycling. Plants and microbes interact above and below ground, and such interactions could theoretically include all combinations of positive (i.e., mycorrhizal and legume-rhizobia), negative (i.e., pathogenic interactions), or neutral effects. Many plant pathogenic and symbiotic microbes produce specialized structures that invade plant cells, but remain enveloped by plant-derived membranes. These intimate contacts between plant and microbial structures drive either bidirectional flows of nutrients as symbiotic (mycorrhizal or legume-rhizobia) or unidirectional flows as in pathogenic interactions. Whatever the biotrophic context (symbiotic vs. pathogenic), nutrients must pass several membrane barriers and the apoplastic interface before their assimilation by plant or microbial cells. Plant and microbial cells must be “re-programmed,” which includes differentiation and polarization of membrane transport functions to take up, to transfer or to exchange nutrients between partners of the biotrophic interaction. However, the mechanisms underlying the functioning and the dynamics of the transportome (the range of genes of an organism that encode proteins contributing to transport molecules across cellular membranes: membrane transporters, ions exchangers, and ion channels) at the biotrophic interface are still poorly understood. The transportome is a key player in nutrient uptake and exchange mechanisms and its regulation pattern is essential in determining the outcome of plant fungal interactions and in adapting to environmental changes.
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Les origines inattendues de la photosynthèse

Les origines inattendues de la photosynthèse | MycorWeb Plant-Microbe Interactions | Scoop.it
La conversion de la lumière du soleil en énergie chimique, un processus nommé photosynthèse, est l’un des plus importants processus biologiques sur Terre. La photosynthèse oxygénique entraîne la libération d’oxygène et la fixation de dioxyde de carbone (CO2), elle est réalisée par les végétaux terrestres, les algues et certaines bactéries appelées cyanobactéries du fait de leur coloration bleue.

Jusqu’à présent, on ignorait l’origine du processus de photosynthèse, apparu il y a 3,8 milliards d’années avec les premières cyanobactéries. Dans une récente publication scientifique, nous montrons qu’au cours de l’évolution, des organismes appartenant à deux domaines du vivant (une bactérie et une archéobactérie) ont contribué à la mise en place du système biologique sur lequel repose la fixation du CO2.
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High-resolution community profiling of arbuscular mycorrhizal fungi

High-resolution community profiling of arbuscular mycorrhizal fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
Community analyses of arbuscular mycorrhizal fungi (AMF) using ribosomal small subunit (SSU) or internal transcribed spacer (ITS) DNA sequences often suffer from low resolution or coverage. We developed a novel sequencing based approach for a highly resolving and specific profiling of AMF communities. We took advantage of previously established AMF-specific PCR primers that amplify a c. 1.5-kb long fragment covering parts of SSU, ITS and parts of the large ribosomal subunit (LSU), and we sequenced the resulting amplicons with single molecule real-time (SMRT) sequencing. The method was applicable to soil and root samples, detected all major AMF families and successfully discriminated closely related AMF species, which would not be discernible using SSU sequences. In inoculation tests we could trace the introduced AMF inoculum at the molecular level. One of the introduced strains almost replaced the local strain(s), revealing that AMF inoculation can have a profound impact on the native community. The methodology presented offers researchers a powerful new tool for AMF community analysis because it unifies improved specificity and enhanced resolution, whereas the drawback of medium sequencing throughput appears of lesser importance for low-diversity groups such as AMF.
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