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Auxin perception is required for arbuscule development in arbuscular mycorrhizal symbiosis

Abstract

Most land plant species live in symbiosis with arbuscular mycorrhizal (AM) fungi. These fungi differentiate essential functional structures called arbuscules in root cortical cells from which mineral nutrients are released to the plant. We investigated the role of miR393, a microRNA that targets several auxin receptors, in AM root colonization. Expression of the precursors of the miR393 was down-regulated during mycorrhization in three different plant species: Solanum lycopersicum (Solanaceae), Medicago truncatula (Fabaceae) and Oryza sativa (Poaceae). Treatment of S. lycopersicum, M. truncatula and O. sativa roots with concentration of synthetic auxin analogs that did not affect root development, stimulated mycorrhization, particularly arbuscule formation. DR5-GUS, a reporter for auxin response, was preferentially expressed in root cells containing arbuscules. Finally, overexpression of miR393 in root tissues resulted in downregulation of auxin receptor genes (TIR1, AFB) and in under-developed arbuscules in all three plant species. These results support the conclusion that miR393 is a negative regulator of arbuscule formation by hampering auxin perception in arbuscule-containing cells.


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Pierre-Marc Delaux's curator insight, August 5, 2014 2:06 PM

Tomato, Medicago and Rice... nice job!

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The Beaker phenomenon and the genomic transformation of northwest Europe

The Beaker phenomenon and the genomic transformation of northwest Europe | MycorWeb Plant-Microbe Interactions | Scoop.it

From around 2750 to 2500 BC, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 BC. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain’s gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.

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Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation

Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation | MycorWeb Plant-Microbe Interactions | Scoop.it
In recent years, copy number (CN) variation has emerged as a new and significant source of genetic polymorphisms contributing to the phenotypic diversity of populations. CN variants are defined as genetic loci that, due to duplication and deletion, vary in their number of copies across individuals in a population. CN variants range in size from 50 base pairs to whole chromosomes, can influence gene activity, and are associated with a wide range of phenotypes in diverse organisms, including the budding yeast Saccharomyces cerevisiae. In this review, we introduce CN variation, discuss the genetic and molecular mechanisms implicated in its generation, how they can contribute to genetic and phenotypic diversity in fungal populations, and consider how CN variants may influence wine yeast adaptation in fermentation-related processes. In particular, we focus on reviewing recent work investigating the contribution of changes in CN of fermentation-related genes in yeast wine strains and offer notable illustrations of such changes, including the high levels of CN variation among the CUP genes, which confer resistance to copper, a metal with fungicidal properties, and the preferential deletion and duplication of the MAL1 and MAL3 loci, respectively, which are responsible for metabolizing maltose and sucrose. Based on the available data, we propose that CN variation is a substantial dimension of yeast genetic diversity that occurs largely independent of single nucleotide polymorphisms. As such, CN variation harbors considerable potential for understanding and manipulating yeast strains in the wine fermentation environment and beyond.
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Root-Associated Bacterial and Fungal Community Profiles of Arabidopsis thaliana Are Robust Across Contrasting Soil P Levels

Root-Associated Bacterial and Fungal Community Profiles of Arabidopsis thaliana Are Robust Across Contrasting Soil P Levels | MycorWeb Plant-Microbe Interactions | Scoop.it
Plant survival depends on the ability of roots to sense and acquire nutrients in soils, which harbor a rich diversity of microbes. A subset of this microcosm interacts with plant roots and collectively forms root-associated microbial communities, termed the root microbiota. Under phosphorus-limiting conditions, some plants can engage in mutualistic interactions, for example with arbuscular mycorrhizal fungi. Here, we describe how Arabidopsis thaliana, which lacks the genetic capacity for establishing the aforementioned symbiosis, interacts with soil-resident bacteria and fungi in soil from a long-term phosphorus fertilization trial. Long-term, contrasting fertilization regimes resulted in an ∼6-fold and ∼2.4-fold disparity in bioavailable and total phosphorous, respectively, which may explain differences in biomass of A. thaliana plants. Sequencing of marker genes enabled us to characterize bacterial and fungal communities present in the bulk soil, rhizosphere, and root compartments. Phosphorus had little effect on alpha- or beta-diversity indices, but more strongly influences bacterial and fungal community shifts in plant-associated compartments compared with bulk soil. The significant impact of soil P abundance could only be resolved at operational taxonomic unit level, and these subtle differences are more pronounced in the root compartment. We conclude that despite decades of different fertilization, both bacterial and fungal soil communities remained unexpectedly stable in soils tested, suggesting that the soil biota is resilient over time to nutrient supplementation. Conversely, low-abundance, root-associated microbes, which collectively represent 2 to 3% of the relative abundance of bacteria and fungi in the roots, exhibited a subtle

Via Stéphane Hacquard
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The soil microbiome — from metagenomics to metaphenomics

The soil microbiome — from metagenomics to metaphenomics | MycorWeb Plant-Microbe Interactions | Scoop.it
Soil microorganisms carry out important processes, including support of plant growth and cycling of carbon and other nutrients. However, the majority of soil microbes have not yet been isolated and their functions are largely unknown. Although metagenomic sequencing reveals microbial identities and functional gene information, it includes DNA from microbes with vastly varying physiological states. Therefore, metagenomics is only predictive of community functional potential. We posit that the next frontier lies in understanding the metaphenome, the product of the combined genetic potential of the microbiome and available resources. Here we describe examples of opportunities towards gaining understanding of the soil metaphenome.

Via Stéphane Hacquard
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Mycorrhizal symbioses influence the trophic structure of the Serengeti

Mycorrhizal symbioses influence the trophic structure of the Serengeti | MycorWeb Plant-Microbe Interactions | Scoop.it
It is known that tropical grasslands such as Serengeti host large populations of arbuscular mycorrhizal (AM) fungi and that they respond to abiotic and biotic factors. It is also known that AM symbioses are important for the uptake of essential plant nutrients, which, in turn, influences the biomass and nutritional quality of herbivores and their predators. The purpose of this study was to investigate the influence of AM symbioses on the biomass of different trophic levels of an ecosystem. To do this, we first measured the neutral lipid fatty acid biomarker 16:1ω5 to estimate the biomass of AM fungi in a long-term grazing exclusion experiment. Then, we used model selection of Bayesian linear regressions to infer the primary factors that influence AM fungal biomass. Using model selection of different combinations of soil characteristics, we selected the best model using the leave-one-out cross-validation information criterion. Finally, we used the Madingley model to simulate the influence of AM fungi on higher trophic levels. We combined spatially explicit information about soil phosphorus and AM fungal biomass to explore the emergent patterns of the Serengeti resulting from AM symbioses. Our Bayesian analysis indicated that total soil phosphorus was the strongest predictor of AM fungal biomass, and there were significant interactions with grazing. Arbuscular mycorrhizal fungal biomass is lowest in soil where phosphorus is limited and increases with increasing phosphorus concentration. Biomass was also significantly higher in plots that were not grazed. The Madingley model indicated that nutritional benefits of AM symbioses maintain a substantial proportion of the biomass across all trophic levels. Synthesis. Our analysis shows that inputs of phosphorus through arbuscular mycorrhizal symbioses substantially increase the ability of plants to grow and maintain nutritional quality, cascading through the biomass of consumers and predators in the ecosystem. Although they account for less than 1% of the total modelled biomass, the predicted nutritional benefit provided by arbuscular mycorrhizal fungi increased the biomass of macro-organisms in the Serengeti by 48%. When considering the management of biodiversity, future ecosystem models should account for the influence of arbuscular mycorrhizal fungi on all trophic levels.
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Timing of mutualist arrival has a greater effect on Pinus muricata seedling growth than interspecific competition

Timing of mutualist arrival has a greater effect on Pinus muricata seedling growth than interspecific competition | MycorWeb Plant-Microbe Interactions | Scoop.it
Interactions with symbiotic microbes, such as mycorrhizal fungi, have the potential to greatly influence plant growth, but it is unclear whether field variation in symbiont availability is common and, if so, sufficient to influence interspecific plant competition. In a greenhouse experiment using natural field soils, I varied the timing of ectomycorrhizal inoculation and the presence of an arbuscular mycorrhizal plant competitor, and measured their effects on pine seedling growth. I found that ectomycorrhizal colonization was absent in some field soils, and that in soils without mycorrhizal inoculum, delayed arrival of ectomycorrhizal spores progressively reduced pine seedling growth and favoured growth of the competitor. Competition had significant negative effects on pine seedling growth, but the competition effect was much smaller than the effect of delayed mutualist arrival. Synthesis. The importance of mycorrhizal spore arrival time on pine growth suggests that plants may experience mutualist limitation more frequently than previously expected, and the relative magnitude of seedling responses to mycorrhizal fungi and competing plants show that in some systems mutualism is likely of equal or greater importance compared with interspecific competition in affecting plant community assembly.
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Fungal community shifts underpin declining mycelial production and turnover across a Pinus sylvestris chronosequence

Fungal community shifts underpin declining mycelial production and turnover across a Pinus sylvestris chronosequence | MycorWeb Plant-Microbe Interactions | Scoop.it
Fungi play critical roles in ecosystem processes such as decomposition and nutrient cycling, but have also been highlighted as significant contributors to organic matter build-up in boreal forest soils. Ectomycorrhizal (ECM) mycelial biomass and necromass dynamics have recently been highlighted as essential for regulating build-up of soil organic matter. Understanding the extent to which shifts in mycelial community or growth trait composition cause changes in mycelial production and turnover over ecological gradients would aid a mechanistic understanding of these important processes at an ecosystem scale. Here, we test the hypotheses that shifting species and mycelial trait (exploration type) composition within the mycelial community underpin changes in biomass turnover with increasing forest age. We quantified mycelial turnover and assessed fungal community composition in a chronosequence of eight, 12- to 158-year-old, managed Pinus sylvestris forests. Turnover was estimated by determining mycelial biomass (ergosterol) in a sequence of ingrowth mesh bags and applying mathematical models. Fungal communities in the bags were identified using Pacific Biosciences sequencing of fungal ITS2 amplicons. To evaluate the accuracy of this method to represent all ECM fungi, community composition in bags was followed over time and compared with communities in soil. Mycelial communities changed with stand age, but we found no evidence that there were concurrent shifts in mycelial exploration types. Forest age and turnover were significantly correlated with ECM mycelial community composition and collectively explained 39.4% of total variation. The similarity between fungal communities in mesh bags and in soil was strongly forest age dependent, with communities in mesh bags diverging from soil communities in stands older than 60 years. However, in all stands, when bag incubation time exceeded 75 days, communities became more similar to soil communities. Synthesis. Our results support the idea that shifts in fungal community composition underpin the forest age-related decrease in mycelial turnover; however, since ingrowth mesh bags exclude some mycorrhizal species in older forests, it remains a possibility that turnover estimates were not reflecting the entire community. While we found no evidence that mycelial exploration types of fungi changed systematically with forest age, we suggest that other traits that relate to biomass turnover and necromass degradation require further study, as they may explain the extent to which ectomycorrhizal fungi regulate and contribute to soil organic matter accumulation.
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Melanization of mycorrhizal fungal necromass structures microbial decomposer communities - Fernandez - 2018 - Journal of Ecology - Wiley Online Library

Melanization of mycorrhizal fungal necromass structures microbial decomposer communities - Fernandez - 2018 - Journal of Ecology - Wiley Online Library | MycorWeb Plant-Microbe Interactions | Scoop.it
Mycorrhizal fungal necromass is increasingly recognized as an important contributor to soil organic carbon pools, particularly in forest ecosystems. While its decomposition rate is primarily determined by biochemical composition, how traits such as melanin content affect the structure of necromass decomposer communities remains poorly understood. To assess the role of biochemical traits on microbial decomposer community composition and functioning, we incubated melanized and non-melanized necromass of the mycorrhizal fungus Meliniomyces bicolor in Pinus- and Quercus-dominated forests in Minnesota, USA and then assessed the associated fungal and bacterial decomposer communities after 1, 2 and 3 months using high-throughput sequencing. Melanized necromass decomposed significantly slower than non-melanized necromass in both forests. The structure of the microbial decomposer communities depended significantly on necromass melanin content, although the effect was stronger for fungi than bacteria. On non-melanized necromass, fungal communities were dominated by r-selected ascomycete and mucoromycete microfungi early and then replaced by basidiomycete ectomycorrhizal fungi, while on melanized necromass these groups were co-dominant throughout the incubation. Bacterial communities were dominated by both specialist mycophageous and generalist taxa. Synthesis. Our results indicate that necromass biochemistry not only strongly affects rates of decomposition but also the structure of the associated decomposer communities. Furthermore, the observed colonization patterns suggest that fungi, and particularly ectomycorrhizal fungi, may play a more important role in necromass decomposition than previously recognized.
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PLOS Pathogens: Tricked or trapped—Two decoy mechanisms in host–pathogen interactions (2018)

PLOS Pathogens: Tricked or trapped—Two decoy mechanisms in host–pathogen interactions (2018) | MycorWeb Plant-Microbe Interactions | Scoop.it

Antagonistic interactions between hosts and pathogens frequently result in arms races. The host attempts to recognise the pathogen and inhibit its growth and spread, whereas the pathogen tries to subvert recognition and suppress host responses. These antagonistic interactions drive the evolution of ‘decoys’ in both hosts and pathogens. In host–pathogen interactions, the term decoy describes molecules that mimic a component at the host–pathogen interface that is manipulated during infection. Decoys undergo the same manipulation as the component they mimic, but they serve the opposite role, either by preventing manipulation of the component they mimic or by triggering a molecular recognition event. At least three different types of decoy have been defined, described in detail below. However, these different decoy models cause confusion on how they function mechanistically. Here, we discuss the three different types of decoys with examples and classify them according to two distinct mechanisms.


Via Kamoun Lab @ TSL
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The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte

The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte | MycorWeb Plant-Microbe Interactions | Scoop.it

Highlights Summary The evolutionary emergence of land plant body plans transformed the planet. However, our understanding of this formative episode is mired in the uncertainty associated with the phylogenetic relationships among bryophytes (hornworts, liverworts, and mosses) and tracheophytes (vascular plants). Here we attempt to clarify this problem by analyzing a large transcriptomic dataset with models that allow for compositional heterogeneity between sites. Zygnematophyceae is resolved as sister to land plants, but we obtain several distinct relationships between bryophytes and tracheophytes. Concatenated sequence analyses that can explicitly accommodate site-specific compositional heterogeneity give more support for a mosses-liverworts clade, “Setaphyta,” as the sister to all other land plants, and weak support for hornworts as the sister to all other land plants. Bryophyte monophyly is supported by gene concatenation analyses using models explicitly accommodating lineage-specific compositional heterogeneity and analyses of gene trees. Both maximum-likelihood analyses that compare the fit of each gene tree to proposed species trees and Bayesian supertree estimation based on gene trees support bryophyte monophyly. Of the 15 distinct rooted relationships for embryophytes, we reject all but three hypotheses, which differ only in the position of hornworts. Our results imply that the ancestral embryophyte was more complex than has been envisaged based on topologies recognizing liverworts as the sister lineage to all other embryophytes. This requires many phenotypic character losses and transformations in the liverwort lineage, diminishes inconsistency between phylogeny and the fossil record, and prompts re-evaluation of the phylogenetic affinity of early land plant fossils, the majority of which are considered stem tracheophytes.


Via Pierre-Marc Delaux
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The giant mycoheterotrophic orchid Erythrorchis altissima is associated mainly with a divergent set of wood-decaying fungi

The climbing orchid Erythrorchis altissima is the largest mycoheterotroph in the world. Although previous in vitro work suggests that E. altissima has a unique symbiosis with wood-decaying fungi, little is known about how this giant orchid meets its carbon and nutrient demands exclusively via mycorrhizal fungi. In this study, the mycorrhizal fungi of E. altissima were molecularly identified using root samples from 26 individuals. Furthermore, in vitro symbiotic germination with five fungi and stable isotope compositions in five E. altissima at one site were examined. In total, 37 fungal operational taxonomic units (OTUs) belonging to nine orders in Basidiomycota were identified from the orchid roots. Most of the fungal OTUs were wood-decaying fungi, but underground roots had ectomycorrhizal Russula. Two fungal isolates from mycorrhizal roots induced seed germination and subsequent seedling development in vitro. Measurement of carbon and nitrogen stable isotope abundances revealed that E. altissima is a full mycoheterotroph whose carbon originates mainly from wood-decaying fungi. All of the results show that E. altissima is associated with a wide range of wood- and soil-inhabiting fungi, the majority of which are wood-decaying taxa. This generalist association enables E. altissima to access a large carbon pool in woody debris and has been key to the evolution of such a large mycoheterotroph.
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Interactions among decaying leaf litter, root litter and soil organic matter vary with mycorrhizal type

Interactions among decaying leaf litter, root litter and soil organic matter vary with mycorrhizal type | MycorWeb Plant-Microbe Interactions | Scoop.it

"Root-derived inputs are increasingly viewed as primary controls of soil organic matter (SOM) formation; however, we have a limited understanding of how root decay rates depend on soil factors, and how decaying roots influence the breakdown of leaf litter and SOM.
We incubated root and leaf litter (alone and in combination) from arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) trees in soils collected from forest plots dominated by AM and ECM trees in a factorial design. In each microcosm, we quantified litter decay rates and the effects of decaying litters on soil C balance. We hypothesized that (1) AM root litters would decompose faster than ECM root litters, (2) root litter decay would be greatest when decomposed in “home” soils (e.g. AM litters in AM soils and ECM litters in ECM soils) and (3) root and leaf litters would decompose faster when decaying in the same microcosms than when decaying in separate microcosms, resulting in the largest CO2 losses.
Overall, AM root litter decomposed faster than ECM root litter, and the magnitude of this effect depended on soil origin. AM litters decayed fastest in AM soils, but ECM and mixed AM–ECM litters were unaffected by soil origin. Decaying roots increased leaf litter mass loss, but only in microcosms containing soils of the same origin (e.g. AM litters in AM soils; mixed litters in mixed soils).
Carbon losses were dominated by microbial respiration, and the magnitude of this flux depended on litter type and soil origin. When leaves and roots decayed together, respiratory losses exceeded those from microcosms containing leaves and roots alone, with the largest losses occurring in each litters' “home” soil. In AM soils, elevated losses were driven by roots accelerating leaf decay, while in ECM soils, elevated losses resulted from roots and leaves accelerating the decay of SOM; in mixed soils, root-induced increases in leaf and SOM decay contributed to elevated C losses.
Our results suggest that root, leaf and SOM decay are intertwined, and that measurements of these processes in isolation may lead to incorrect estimates of the magnitude and source of C losses from soils."


Via Gabriel R. Smith
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Frontiers | Secretome Analysis from the Ectomycorrhizal Ascomycete Cenococcum geophilum | Microbiology

Frontiers | Secretome Analysis from the Ectomycorrhizal Ascomycete Cenococcum geophilum | Microbiology | MycorWeb Plant-Microbe Interactions | Scoop.it
Cenococcum geophilum is an ectomycorrhizal fungus with global distribution in numerous habitats and associates with a large range of host species including gymnosperm and angiosperm trees. Moreover, C. geophilum is the unique ectomycorrhizal species within the clade Dothideomycetes, the largest class of Ascomycetes containing predominantly saprotrophic and many devastating phytopathogenic fungi. Recent studies highlight that mycorrhizal fungi, as pathogenic ones, use effectors in form of Small Secreted Proteins (SSPs) as molecular keys to promote symbiosis. In order to better understand the biotic interaction of C. geophilum with its host plants, the goal of this work was to characterize mycorrhiza-induced small-secreted proteins (MiSSPs) that potentially play a role in the ectomycorrhiza formation and functioning of this ecologically very important species. We combined different approaches such as gene expression profiling, genome localization and conservation of MiSSP genes in different C. geophilum strains and closely related species as well as protein subcellular localization studies of potential targets of MiSSPs in interacting plants using in tobacco leaf cells. Gene expression analyses of C. geophilum interacting with Pinus sylvestris (pine) and Populus tremula × Populus alba (poplar) showed that similar sets of genes coding for secreted proteins were up-regulated and only few were specific to each host. Whereas pine induced more carbohydrate active enzymes (CAZymes), the interaction with poplar induced the expression of specific SSPs. We identified a set of 22 MiSSPs, which are located in both, gene-rich, repeat-poor or gene-sparse, repeat-rich regions of the C. geophilum genome, a genome showing a bipartite architecture as seen for some pathogens but not yet for an ectomycorrhizal fungus. Genome re-sequencing data of 15 C. geophilum strains and two close relatives Glonium stellatum and Lepidopterella palustris were used to study sequence conservation of MiSSP-encoding genes. The 22 MiSSPs showed a high presence-absence polymorphism among the studied C. geophilum strains suggesting an evolution through gene gain/gene loss. Finally, we showed that six CgMiSSPs target four distinct sub-cellular compartments such as endoplasmic reticulum, plasma membrane, cytosol and tonoplast. Overall, this work presents a comprehensive analysis of secreted proteins and MiSSPs in different genetic level of C. geophilum opening a valuable resource to future functional analysis.
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The genomic history of southeastern Europe

The genomic history of southeastern Europe | MycorWeb Plant-Microbe Interactions | Scoop.it
Farming was first introduced to Europe in the mid-seventh millennium BC, and was associated with migrants from Anatolia who settled in the southeast before spreading throughout Europe. Here, to understand the dynamics of this process, we analysed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12000 and 500 BC. We document a west–east cline of ancestry in indigenous hunter-gatherers and, in eastern Europe, the early stages in the formation of Bronze Age steppe ancestry. We show that the first farmers of northern and western Europe dispersed through southeastern Europe with limited hunter-gatherer admixture, but that some early groups in the southeast mixed extensively with hunter-gatherers without the sex-biased admixture that prevailed later in the north and west. We also show that southeastern Europe continued to be a nexus between east and west after the arrival of farmers, with intermittent genetic contact with steppe populations occurring up to 2,000 years earlier than the migrations from the steppe that ultimately replaced much of the population of northern Europe.
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Transcription factors network in root endosymbiosis establishment and development

Root endosymbioses are mutualistic interactions between plants and the soil microorganisms (Fungus, Frankia or Rhizobium) that lead to the formation of nitrogen-fixing root nodules and/or arbuscular mycorrhiza. These interactions enable many species to survive in different marginal lands to overcome the nitrogen-and/or phosphorus deficient environment and can potentially reduce the chemical fertilizers used in agriculture which gives them an economic, social and environmental importance. The formation and the development of these structures require the mediation of specific gene products among which the transcription factors play a key role. Three of these transcription factors, viz., CYCLOPS, NSP1 and NSP2 are well conserved between actinorhizal, legume, non-legume and mycorrhizal symbioses. They interact with DELLA proteins to induce the expression of NIN in nitrogen fixing symbiosis or RAM1 in mycorrhizal symbiosis. Recently, the small non coding RNA including micro RNAs (miRNAs) have emerged as major regulators of root endosymbioses. Among them, miRNA171 targets NSP2, a TF conserved in actinorhizal, legume, non-legume and mycorrhizal symbioses. This review will also focus on the recent advances carried out on the biological function of others transcription factors during the root pre-infection/pre-contact, infection or colonization. Their role in nodule formation and AM development will also be described.


Via Jean-Michel Ané
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The timescale of early land plant evolution

The timescale of early land plant evolution | MycorWeb Plant-Microbe Interactions | Scoop.it
Establishing the timescale of early land plant evolution is essential to testing hypotheses on the coevolution of land plants and Earth’s System. Here, we establish a timescale for early land plant evolution that integrates over competing hypotheses on bryophyte−tracheophyte relationships. We estimate land plants to have emerged in a middle Cambrian–Early Ordovocian interval, and vascular plants to have emerged in the Late Ordovician−Silurian. This timescale implies an early establishment of terrestrial ecosystems by land plants that is in close accord with recent estimates for the origin of terrestrial animal lineages. Biogeochemical models that are constrained by the fossil record of early land plants, or attempt to explain their impact, must consider a much earlier, middle Cambrian–Early Ordovician, origin.

Establishing the timescale of early land plant evolution is essential for testing hypotheses on the coevolution of land plants and Earth’s System. The sparseness of early land plant megafossils and stratigraphic controls on their distribution make the fossil record an unreliable guide, leaving only the molecular clock. However, the application of molecular clock methodology is challenged by the current impasse in attempts to resolve the evolutionary relationships among the living bryophytes and tracheophytes. Here, we establish a timescale for early land plant evolution that integrates over topological uncertainty by exploring the impact of competing hypotheses on bryophyte−tracheophyte relationships, among other variables, on divergence time estimation. We codify 37 fossil calibrations for Viridiplantae following best practice. We apply these calibrations in a Bayesian relaxed molecular clock analysis of a phylogenomic dataset encompassing the diversity of Embryophyta and their relatives within Viridiplantae. Topology and dataset sizes have little impact on age estimates, with greater differences among alternative clock models and calibration strategies. For all analyses, a Cambrian origin of Embryophyta is recovered with highest probability. The estimated ages for crown tracheophytes range from Late Ordovician to late Silurian. This timescale implies an early establishment of terrestrial ecosystems by land plants that is in close accord with recent estimates for the origin of terrestrial animal lineages. Biogeochemical models that are constrained by the fossil record of early land plants, or attempt to explain their impact, must consider the implications of a much earlier, middle Cambrian–Early Ordovician, origin.
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Specialized plant biochemistry drives gene clustering in fungi

Specialized plant biochemistry drives gene clustering in fungi | MycorWeb Plant-Microbe Interactions | Scoop.it

The fitness and evolution of prokaryotes and eukaryotes are affected by the organization of their genomes. In particular, the physical clustering of genes can coordinate gene expression and can prevent the breakup of co-adapted alleles. Although clustering may thus result from selection for phenotype optimization and persistence, the impact of environmental selection pressures on eukaryotic genome organization has rarely been systematically explored. Here, we investigated the organization of fungal genes involved in the degradation of phenylpropanoids, a class of plant-produced secondary metabolites that mediate many ecological interactions between plants and fungi. Using a novel gene cluster detection method, we identified 1110 gene clusters and many conserved combinations of clusters in a diverse set of fungi. We demonstrate that congruence in genome organization over small spatial scales is often associated with similarities in ecological lifestyle. Additionally, we find that while clusters are often structured as independent modules with little overlap in content, certain gene families merge multiple modules into a common network, suggesting they are important components of phenylpropanoid degradation strategies. Together, our results suggest that phenylpropanoids have repeatedly selected for gene clustering in fungi, and highlight the interplay between genome organization and ecological evolution in this ancient eukaryotic lineage.

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Association of ectomycorrhizal trees with high carbon-to-nitrogen ratio soils across temperate forests is driven by smaller nitrogen not larger carbon stocks 

Association of ectomycorrhizal trees with high carbon-to-nitrogen ratio soils across temperate forests is driven by smaller nitrogen not larger carbon stocks  | MycorWeb Plant-Microbe Interactions | Scoop.it
The distribution of mycorrhizal associations across biomes parallels a distinct gradient of soil carbon (C) and nitrogen (N) stocks, raising the question of how mycorrhizal traits relate to ecosystem properties. Arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) hosts and fungi employ contrasting strategies for N acquisition, which may manifest in differences in soil C and N pools and/or soil C:N. However, cross-biome comparisons are confounded with climatic and edaphic gradients as well as phylogenetic and functional trait distributions of component plant species. Here, we test emerging hypotheses that soil C, N and C:N are related to the dominance of EM trees within a temperate forest region where AM and EM trees largely coexist but vary in local abundance.
To determine the importance of mycorrhizal type on soil C and N, we analysed data from c. 1,000 forest inventory plots in the eastern United States. For each plot, we quantified the dominance of trees with different mycorrhizal associations and accounted for potentially confounding variables including phylogeny (angiosperm or gymnosperm), leaf N, soil clay content and climate. We used hierarchical Bayesian models to determine how these variables explained the patterns of soil C and N in the forest floor and mineral soil layers.
Increasing EM dominance was associated with higher C:N across all soil layers. This relationship remained even after accounting for tree phylogeny, leaf N content, soil clay content, temperature and precipitation, which were all important for explaining soil C:N. However, this mycorrhizal pattern of soil C:N was not related to increases in soil C content; rather, increasing EM dominance was associated with reductions in soil N.
Synthesis. Our findings are consistent with the proposition that mycorrhizal associations are related to terrestrial ecosystem properties. The mycorrhizal effect on soil C:N may result from differences in how arbuscular mycorrhizal and ectomycorrhizal plants interact with their fungal symbionts, decomposers and organic matter, to sustain differential cycling of C and N. Alternatively, these patterns could arise from differential success of the two mycorrhizal types in contrasting soil conditions; both processes may occur simultaneously, leading to a self-reinforcing positive feedback.
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Interactions among decaying leaf litter, root litter and soil organic matter vary with mycorrhizal type

Interactions among decaying leaf litter, root litter and soil organic matter vary with mycorrhizal type | MycorWeb Plant-Microbe Interactions | Scoop.it
Root-derived inputs are increasingly viewed as primary controls of soil organic matter (SOM) formation; however, we have a limited understanding of how root decay rates depend on soil factors, and how decaying roots influence the breakdown of leaf litter and SOM. We incubated root and leaf litter (alone and in combination) from arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) trees in soils collected from forest plots dominated by AM and ECM trees in a factorial design. In each microcosm, we quantified litter decay rates and the effects of decaying litters on soil C balance. We hypothesized that (1) AM root litters would decompose faster than ECM root litters, (2) root litter decay would be greatest when decomposed in “home” soils (e.g. AM litters in AM soils and ECM litters in ECM soils) and (3) root and leaf litters would decompose faster when decaying in the same microcosms than when decaying in separate microcosms, resulting in the largest CO2 losses. Overall, AM root litter decomposed faster than ECM root litter, and the magnitude of this effect depended on soil origin. AM litters decayed fastest in AM soils, but ECM and mixed AM–ECM litters were unaffected by soil origin. Decaying roots increased leaf litter mass loss, but only in microcosms containing soils of the same origin (e.g. AM litters in AM soils; mixed litters in mixed soils). Carbon losses were dominated by microbial respiration, and the magnitude of this flux depended on litter type and soil origin. When leaves and roots decayed together, respiratory losses exceeded those from microcosms containing leaves and roots alone, with the largest losses occurring in each litters' “home” soil. In AM soils, elevated losses were driven by roots accelerating leaf decay, while in ECM soils, elevated losses resulted from roots and leaves accelerating the decay of SOM; in mixed soils, root-induced increases in leaf and SOM decay contributed to elevated C losses. Synthesis. Our results suggest that root, leaf and SOM decay are intertwined, and that measurements of these processes in isolation may lead to incorrect estimates of the magnitude and source of C losses from soils.
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Arbuscular mycorrhizal fungi as mediators of ecosystem responses to nitrogen deposition: A trait-based predictive framework

Arbuscular mycorrhizal fungi as mediators of ecosystem responses to nitrogen deposition: A trait-based predictive framework | MycorWeb Plant-Microbe Interactions | Scoop.it
Anthropogenic nitrogen (N) deposition is exposing plants and their arbuscular mycorrhizal fungi (AMFs) to elevated N availability, often leading to shifts in communities of AMF. However, physiological trade-offs among AMF taxa in their response to N enrichment vs the ability to acquire other soil nutrients could have negative effects on plant and ecosystem productivity. It follows that information on the functional traits of AMF taxa can be used to generate predictions of their potential role in mediating ecosystem responses to N enrichment. Arbuscular mycorrhizal fungi taxa that produce extensive networks of external hyphae should forage for N and phosphorus (P) more effectively, but these services incur greater carbon (C) costs to the plant. If N enrichment ameliorates plant nutrient limitation, then plants may reduce C available for AMF, which in turn could eliminate AMF taxa with large extensive external hyphae from the soil community. As a result, the remaining AMF taxa may confer less P benefit to their host plants. Using a synthesis of data from the literature, we found that the ability of a taxon to persist in the face of increasing soil N availability was particularly high in isolates from the genus Glomus, but especially low among the Gigasporaceae. Across AMF genera, our data support the prediction that AMF with a tolerance for high soil N may confer a lower P benefit to their host plant. Relationships between high N tolerance and production of external hyphae were mixed. Synthesis. If the relationship between N tolerance and plant P benefit is widespread, then shifts in arbuscular mycorrhizal fungi communities associated with N deposition could have negative consequences for the ability of plants to acquire P and possibly other nutrients via a mycorrhizal pathway. Based on this relationship, we predict that arbuscular mycorrhizal fungi responses could constrain net primary productivity in P-limited ecosystems exposed to N enrichment. This prediction could be tested in future empirical and modelling studies.
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Rescooped by Francis Martin from Plant-Microbe Symbiosis
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Land plants arose earlier than thought—and may have had a bigger impact on the evolution of animals

Land plants arose earlier than thought—and may have had a bigger impact on the evolution of animals | MycorWeb Plant-Microbe Interactions | Scoop.it
We have land plants to thank for the oxygen we breathe. And now we have a better idea of when they took to land in the first place. While the oldest known fossils of land plants are 420 million years old, researchers have now determined that pond scum first made landfall almost 100 million years earlier.
 
 “[This] study has important global implications, because we know early plants cooled the climate and increased the oxygen level in the Earth’s atmosphere,” conditions that supported the expansion of terrestrial animal life, says Tim Lenton, an earth system scientist at the University of Exeter, United Kingdom who was not involved with the work. 

For decades biologists have been trying to come up with a reliable birth date for land plants. Lacking backbones and hard shells, plants leave relatively little behind in the fossil record, so researchers suspect even the oldest plant fossils don't represent the first flora. 

Via Jean-Michel Ané
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A Comprehensive and Dated Phylogenomic Analysis of Butterflies

A Comprehensive and Dated Phylogenomic Analysis of Butterflies | MycorWeb Plant-Microbe Interactions | Scoop.it

Butterflies (Papilionoidea), with over 18,000 described species [1], have captivated naturalists and scientists for centuries. They play a central role in the study of speciation, community ecology, biogeography, climate change, and plant-insect interactions and include many model organisms and pest species [2, 3]. However, a robust higher-level phylogenetic framework is lacking. To fill this gap, we inferred a dated phylogeny by analyzing the first phylogenomic dataset, including 352 loci (> 150,000 bp) from 207 species representing 98% of tribes, a 35-fold increase in gene sampling and 3-fold increase in taxon sampling over previous studies [4]. Most data were generated with a new anchored hybrid enrichment (AHE) [5] gene kit (BUTTERFLY1.0) that includes both new and frequently used (e.g., [6]) informative loci, enabling direct comparison and future dataset merging with previous studies. Butterflies originated around 119 million years ago (mya) in the late Cretaceous, but most extant lineages diverged after the Cretaceous-Paleogene (K-Pg) mass-extinction 65 mya. Our analyses support swallowtails (Papilionidae) as sister to all other butterflies, followed by skippers (Hesperiidae) + the nocturnal butterflies (Hedylidae) as sister to the remainder, indicating a secondary reversal from diurnality to nocturnality. The whites (Pieridae) were strongly supported as sister to brush-footed butterflies (Nymphalidae) and blues + metalmarks (Lycaenidae and Riodinidae). Ant association independently evolved once in Lycaenidae and twice in Riodinidae. This study overturns prior notions of the taxon’s evolutionary history, as many long-recognized subfamilies and tribes are para- or polyphyletic. It also provides a much-needed backbone for a revised classification of butterflies and for future comparative studies including genome evolution and ecology.

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NanoSIMS and tissue autoradiography reveal symbiont carbon fixation and organic carbon transfer to giant ciliate host

NanoSIMS and tissue autoradiography reveal symbiont carbon fixation and organic carbon transfer to giant ciliate host | MycorWeb Plant-Microbe Interactions | Scoop.it

The giant colonial ciliate Zoothamnium niveum harbors a monolayer of the gammaproteobacteria Cand. Thiobios zoothamnicoli on its outer surface. Cultivation experiments revealed maximal growth and survival under steady flow of high oxygen and low sulfide concentrations. We aimed at directly demonstrating the sulfur-oxidizing, chemoautotrophic nature of the symbionts and at investigating putative carbon transfer from the symbiont to the ciliate host. We performed pulse-chase incubations with 14C- and 13C-labeled bicarbonate under varying environmental conditions. A combination of tissue autoradiography and nanoscale secondary ion mass spectrometry coupled with transmission electron microscopy was used to follow the fate of the radioactive and stable isotopes of carbon, respectively. We show that symbiont cells fix substantial amounts of inorganic carbon in the presence of sulfide, but also (to a lesser degree) in the absence of sulfide by utilizing internally stored sulfur. Isotope labeling patterns point to translocation of organic carbon to the host through both release of these compounds and digestion of symbiont cells. The latter mechanism is also supported by ultracytochemical detection of acid phosphatase in lysosomes and in food vacuoles of ciliate cells. Fluorescence in situ hybridization of freshly collected ciliates revealed that the vast majority of ingested microbial cells were ectosymbionts.


Via Jonathan Plett
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Frontiers | Recent Insights on Biological and Ecological Aspects of Ectomycorrhizal Fungi and Their Interactions | Microbiology

Frontiers | Recent Insights on Biological and Ecological Aspects of Ectomycorrhizal Fungi and Their Interactions | Microbiology | MycorWeb Plant-Microbe Interactions | Scoop.it
The roots of most terrestrial plants are colonized by mycorrhizal fungi. They play a key role in terrestrial environments influencing soil structure and ecosystem functionality. Around them a peculiar region, the mycorrhizosphere, develops. This is a very dynamic environment where plants, soil and microorganisms interact. Interest in this fascinating environment has increased over the years. For a long period the knowledge of the microbial populations in the rhizosphere has been limited, because they have always been studied by traditional culture-based techniques. These methods, which only allow the study of cultured microorganisms, do not allow the characterization of most organisms existing in nature. The introduction in the last few years of methodologies that are independent of culture techniques has bypassed this limitation. This together with the development of high-throughput molecular tools has given new insights into the biology, evolution, and biodiversity of mycorrhizal associations, as well as, the molecular dialog between plants and fungi. The genomes of many mycorrhizal fungal species have been sequenced so far allowing to better understanding the lifestyle of these fungi, their sexual reproduction modalities and metabolic functions. The possibility to detect the mycelium and the mycorrhizae of heterothallic fungi has also allowed to follow the spatial and temporal distributional patterns of strains of different mating types. On the other hand, the availability of the genome sequencing from several mycorrhizal fungi with a different lifestyle, or belonging to different groups, allowed to verify the common feature of the mycorrhizal symbiosis as well as the differences on how different mycorrhizal species interact and dialog with the plant. Here, we will consider the aspects described before, mainly focusing on ectomycorrhizal fungi and their interactions with plants and other soil microorganisms.
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A comprehensive review of mycorrhizal biology and ecology
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Rescooped by Francis Martin from Fungi - Organisms to Ecosystems
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Timing of mutualist arrival has a greater effect on Pinus muricata seedling growth than interspecific competition

Timing of mutualist arrival has a greater effect on Pinus muricata seedling growth than interspecific competition | MycorWeb Plant-Microbe Interactions | Scoop.it

Interactions with symbiotic microbes, such as mycorrhizal fungi, have the potential to greatly influence plant growth, but it is unclear whether field variation in symbiont availability is common and, if so, sufficient to influence interspecific plant competition.
In a greenhouse experiment using natural field soils, I varied the timing of ectomycorrhizal inoculation and the presence of an arbuscular mycorrhizal plant competitor, and measured their effects on pine seedling growth. I found that ectomycorrhizal colonization was absent in some field soils, and that in soils without mycorrhizal inoculum, delayed arrival of ectomycorrhizal spores progressively reduced pine seedling growth and favoured growth of the competitor. Competition had significant negative effects on pine seedling growth, but the competition effect was much smaller than the effect of delayed mutualist arrival. The importance of mycorrhizal spore arrival time on pine growth suggests that plants may experience mutualist limitation more frequently than previously expected, and the relative magnitude of seedling responses to mycorrhizal fungi and competing plants show that in some systems mutualism is likely of equal or greater importance compared with interspecific competition in affecting plant community assembly.


Via Gabriel R. Smith
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