MycorWeb Plant-Microbe Interactions
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Small RNAs: A New Paradigm in Plant-Microbe Interactions -

Small RNAs: A New Paradigm in Plant-Microbe Interactions - | MycorWeb Plant-Microbe Interactions | Scoop.it

A never-ending arms race drives coevolution between pathogens and hosts. In plants, pathogen attacks invoke multiple layers of host immune responses. Many pathogens deliver effector proteins into host cells to suppress host immunity, and many plants have evolved resistance proteins to recognize effectors and trigger robust resistance. Here, we discuss findings on noncoding small RNAs (sRNAs) from plants and pathogens, which regulate host immunity and pathogen virulence. Recent discoveries have unveiled the role of noncoding sRNAs from eukaryotic pathogens and bacteria in pathogenicity in both plant and animal hosts. The discovery of fungal sRNAs that are delivered into host cells to suppress plant immunity added sRNAs to the list of pathogen effectors. Similar to protein effector genes, many of these sRNAs are generated from transposable element (TE) regions, which are likely to contribute to rapidly evolving virulence and host adaptation. We also discuss RNA silencing that occurs between organisms.


Via Christophe Jacquet
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How the truffle got its mate: insights from genetic structure in spontaneous and planted Mediterranean populations of Tuber melanosporum

How the truffle got its mate: insights from genetic structure in spontaneous and planted Mediterranean populations of Tuber melanosporum | MycorWeb Plant-Microbe Interactions | Scoop.it
The life cycles and dispersal of edible fungi are still poorly known, thus limiting our understanding of their evolution and domestication. The prized Tuber melanosporum produces fruitbodies (fleshy organs where meiospores mature) gathered in natural, spontaneously inoculated forests or harvested in plantations of nursery-inoculated trees. Yet, how fruitbodies are formed remains unclear, thus limiting yields, and how current domestication attempts affect population genetic structure is overlooked. Fruitbodies result from mating between two haploid individuals: the maternal parent forms the flesh and the meiospores, while the paternal parent only contributes to the meiospores. We analyzed the genetic diversity of T. melanosporum comparatively in spontaneous forests versus plantations, using SSR polymorphism of 950 samples from South-East France. All populations displayed strong genetic isolation by distance at the metric scale, possibly due to animal dispersal, meiospore persistence in soil, and/or exclusion of unrelated individuals by vegetative incompatibility. High inbreeding was consistently found, suggesting that parents often develop from meiospores produced by the same fruitbody. Unlike maternal genotypes, paternal mycelia contributed to few fruitbodies each, did not persist over years, and were undetectable on tree mycorrhizae. Thus, we postulate that germlings from the soil spore bank act as paternal partners. Paternal genetic diversity and outbreeding were higher in plantations than in spontaneous truffle-grounds, perhaps because truffle growers disperse fruitbodies to maintain inoculation in plantations. However, planted and spontaneous populations were not genetically isolated, so that T. melanosporum illustrates an early step of domestication where genetic structure remains little affected.
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Root-hair endophyte stacking in finger millet creates a
physicochemical barrier to trap the fungal pathogen Fusarium
graminearum

The ancient African crop, finger millet, has broad resis tance to pathogens including the toxigenic fungus Fusa rium gr ami nearum . Here, we report the discovery of a novel plant defence mechanism resulting from an unusual symbiosis between finger millet and a root-inhabiting bacterial endophyte, M6 (Enterobacter sp.). Seed-coated M6 swarms towards root-invading Fusarium and is associated with the growth of root hairs, which then bend parallel to the root axis, subsequently forming biofilm-mediated microcolonies, resulting in a remarkable, multilayer root-hair endophyte stack (RHESt). The RHESt results in a physical barrier that prev ents entry and/or traps F. graminearum, which is then killed . M6 thus creates its own specialize d kil ling microhabita t. Tn5-mutagenesis shows tha t M6 kill ing requir es c-di-GMP- dependent sig nalling, diverse fungicid es and r esistance to a Fusarium-derived antibiotic. Further mol ecular evidence suggests long-term hos t–endo phyte– pathogen co-ev olution. The end result of this remarkable symbiosis is reduced deoxyniv alenol mycotoxin, potentially benefiting milli ons of subsistence farmers and livestock. F urther r esults suggest tha t the anti-Fusarium activity of M6 may be transferable to maize and wheat. RHESt demonstra tes the value of exploring ancient, orphan crop micr obiomes.
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Citizen science data reveal ecological, historical and evolutionary factors shaping interactions between woody hosts and wood-inhabiting fungi

Citizen science data reveal ecological, historical and evolutionary factors shaping interactions between woody hosts and wood-inhabiting fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
Woody plants host diverse communities of associated organisms, including wood-inhabiting fungi. In this group, host effects on species richness and interaction network structure are not well understood, especially not at large geographical scales. We investigated ecological, historical and evolutionary determinants of fungal species richness and network modularity, that is, subcommunity structure, across woody hosts in Denmark, using a citizen science data set comprising > 80 000 records of > 1000 fungal species on 91 genera of woody plants. Fungal species richness was positively related to host size, wood pH, and the number of species in the host genus, with limited influence of host frequency and host history, that is, time since host establishment in the area. Modularity patterns were unaffected by host history, but largely reflected host phylogeny. Notably, fungal communities differed substantially between angiosperm and gymnosperm hosts. Host traits and evolutionary history appear to be more important than host frequency and recent history in structuring interactions between hosts and wood-inhabiting fungi. High wood acidity appears to act as a stress factor reducing fungal species richness, while large host size, providing increased niche diversity, enhances it. In some fungal groups that are known to interact with live host cells in the establishment phase, host selectivity is common, causing a modular community structure.
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High-quality reference transcript datasets hold the key to transcript-specific RNA-sequencing analysis in plants

High-quality reference transcript datasets hold the key to transcript-specific RNA-sequencing analysis in plants | MycorWeb Plant-Microbe Interactions | Scoop.it
Re-programming of the transcriptome involves both transcription and alternative splicing (AS). Some genes are regulated only at the AS level with no change in expression at the gene level. AS data must be incorporated as an essential aspect of the regulation of gene expression. RNA-sequencing (RNA-seq) can deliver both transcriptional and AS information, but accurate methods to analyse the added complexity in RNA-seq data are needed. The construction of a comprehensive reference transcript dataset (RTD) for a specific plant species, variety or accession, from all available sequence data, will immediately allow more robust analysis of RNA-seq data. RTDs will continually evolve and improve, a process that will be more efficient if resources across a community are shared and pooled.
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An assay for entry of secreted fungal effectors into plant cells

An assay for entry of secreted fungal effectors into plant cells | MycorWeb Plant-Microbe Interactions | Scoop.it
Successful colonization of plants by prokaryotic and eukaryotic pathogens requires active effector-mediated suppression of defense responses and host tissue reprogramming. Secreted effector proteins can either display their activity in the apoplast or translocate into host cells and function therein. Although characterized in bacteria, the molecular mechanisms of effector delivery by fungal phytopathogens remain elusive. Here we report the establishment of an assay that is based on biotinylation of effectors in the host cytoplasm as hallmark of uptake. The assay exploits the ability of the bacterial biotin ligase BirA to biotinylate any protein that carries a short peptide (Avitag). It is based on the stable expression of BirA in the cytoplasm of maize plants and on engineering of Ustilago maydis strains to secrete Avitagged effectors. We demonstrate translocation of a number of effectors in the U. maydis–maize system and show data that suggest that the uptake mechanism could be rather nonspecific The assay promises to be a powerful tool for the classification of effectors as well as for the functional study of effector uptake mechanism not only in the chosen system but more generally for systems where biotrophic interactions are established.
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The Plant Microbiota: Systems-Level Insights and Perspectives

Plants do not grow as axenic organisms in nature, but host a diverse community of microorganisms, termed the plant microbiota. There is an increasing awareness that the plant microbiota plays a role in plant growth and can provide protection from invading pathogens. Apart from intense research on crop plants, Arabidopsis is emerging as a valuable model system to investigate the drivers shaping stable bacterial communities on leaves and roots and as a tool to decipher the intricate relationship among the host and its colonizing microorganisms. Gnotobiotic experimental systems help establish causal relationships between plant and microbiota genotypes and phenotypes and test hypotheses on biotic and abiotic perturbations in a systematic way. We highlight major recent findings in plant microbiota research using comparative community profiling and omics analyses, and discuss these approaches in light of community establishment and beneficial traits like nutrient acquisition and plant health.

Via Jean-Michel Ané
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Radiocarbon constraints imply reduced carbon uptake by soils during the 21st century

Radiocarbon constraints imply reduced carbon uptake by soils during the 21st century | MycorWeb Plant-Microbe Interactions | Scoop.it
Soil is the largest terrestrial carbon reservoir and may influence the sign and magnitude of carbon cycle–climate feedbacks. Many Earth system models (ESMs) estimate a significant soil carbon sink by 2100, yet the underlying carbon dynamics determining this response have not been systematically tested against observations. We used 14C data from 157 globally distributed soil profiles sampled to 1-meter depth to show that ESMs underestimated the mean age of soil carbon by a factor of more than six (430 ± 50 years versus 3100 ± 1800 years). Consequently, ESMs overestimated the carbon sequestration potential of soils by a factor of nearly two (40 ± 27%). These inconsistencies suggest that ESMs must better represent carbon stabilization processes and the turnover time of slow and passive reservoirs when simulating future atmospheric carbon dioxide dynamics.
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Too much or not enough: Reflection on two contrasting perspectives on soil biodiversity

Too much or not enough: Reflection on two contrasting perspectives on soil biodiversity | MycorWeb Plant-Microbe Interactions | Scoop.it
Soil biodiversity has become a major area of research over the last decade, and the literature on the topic has expanded tremendously in recent years, so much so that a huge number of publications now deal with soil biodiversity every year. This article does not attempt the formidable task of drawing a general picture of where the field is at the moment, but it zeroes in instead on two perspectives that seem to have gathered momentum over time and raise concern about future progress. The first perspective involves the implicit assumption that to make sense of either the species-, genetic-, or functional biodiversity of soils, it is not necessary to consider in detail the features of (micro)habitats provided by soils to organisms, and that analysis of the information provided by extracted DNA or RNA suffices. The second perspective is associated with research on the effect of the physical and chemical characteristics of microhabitats on the activity of microorganisms. It basically hypothesizes that all microorganisms behave similarly, and therefore that observations made mostly with bacteria can be extended readily to all organisms, ignoring taxonomic biodiversity. To illustrate both perspectives, we provide a number of illustrative examples from the relevant literature and analyze them briefly. We argue that these two perspectives, if they spread, will hinder progress in our understanding of soil biodiversity at any level, and especially of its impact on soil processes. In order to return to a more fruitful middle ground, where both a variety of organisms and the characteristics of the microhabitats where they reside are carefully considered, several routes can be envisaged, but our experience suggests that an emphasis on genuinely interdisciplinary research is crucial.
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Convergent local adaptation to climate in distantly related conifers

Convergent local adaptation to climate in distantly related conifers | MycorWeb Plant-Microbe Interactions | Scoop.it
When confronted with an adaptive challenge, such as extreme temperature, closely related species frequently evolve similar phenotypes using the same genes. Although such repeated evolution is thought to be less likely in highly polygenic traits and distantly related species, this has not been tested at the genome scale. We performed a population genomic study of convergent local adaptation among two distantly related species, lodgepole pine and interior spruce. We identified a suite of 47 genes, enriched for duplicated genes, with variants associated with spatial variation in temperature or cold hardiness in both species, providing evidence of convergent local adaptation despite 140 million years of separate evolution. These results show that adaptation to climate can be genetically constrained, with certain key genes playing nonredundant roles.
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New Phytologist - Comparative phylogenomics of symbiotic associations

New Phytologist - Comparative phylogenomics of symbiotic associations | MycorWeb Plant-Microbe Interactions | Scoop.it
Understanding the genetic bases of complex traits has been a main challenge in biology for decades. Comparative phylogenomics offers an opportunity to identify candidate genes associated with these complex traits. This approach initially developed in prokaryotes consists in looking at shared coevolution between genes and traits. It thus requires a precise reconstruction of the trait evolution, a large genomic sampling in the clades of interest and an accurate definition of orthogroups. Recently, with the growing body of sequenced plant genomes, comparative genomics has been successfully applied to plants to study the widespread arbuscular mycorrhizal symbiosis. Here I will use these findings to illustrate the main principles of comparative phylogenomic approaches and propose directions to improve our understanding of symbiotic associations.

Via LRSV, Christophe Jacquet, Stéphane Hacquard
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Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures

Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures | MycorWeb Plant-Microbe Interactions | Scoop.it
Biological activity is a major factor in Earth’s chemical cycles, including facilitating CO2 sequestration and providing climate feedbacks. Thus a key question in Earth’s evolution is when did life arise and impact hydrosphere–atmosphere–lithosphere chemical cycles? Until now, evidence for the oldest life on Earth focused on debated stable isotopic signatures of 3,800–3,700 million year (Myr)-old metamorphosed sedimentary rocks and minerals1, 2 from the Isua supracrustal belt (ISB), southwest Greenland3. Here we report evidence for ancient life from a newly exposed outcrop of 3,700-Myr-old metacarbonate rocks in the ISB that contain 1–4-cm-high stromatolites—macroscopically layered structures produced by microbial communities. The ISB stromatolites grew in a shallow marine environment, as indicated by seawater-like rare-earth element plus yttrium trace element signatures of the metacarbonates, and by interlayered detrital sedimentary rocks with cross-lamination and storm-wave generated breccias. The ISB stromatolites predate by 220 Myr the previous most convincing and generally accepted multidisciplinary evidence for oldest life remains in the 3,480-Myr-old Dresser Formation of the Pilbara Craton, Australia4, 5. The presence of the ISB stromatolites demonstrates the establishment of shallow marine carbonate production with biotic CO2 sequestration by 3,700 million years ago (Ma), near the start of Earth’s sedimentary record. A sophistication of life by 3,700 Ma is in accord with genetic molecular clock studies placing life’s origin in the Hadean eon (>4,000 Ma)6.
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Genomic analyses inform on migration events during the peopling of Eurasia

Genomic analyses inform on migration events during the peopling of Eurasia | MycorWeb Plant-Microbe Interactions | Scoop.it
High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.
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The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations | MycorWeb Plant-Microbe Interactions | Scoop.it
Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.
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La dendrochronologie, l’art de lire dans les cernes des arbres

La dendrochronologie, l’art de lire dans les cernes des arbres | MycorWeb Plant-Microbe Interactions | Scoop.it
Les anneaux concentriques que l’on observe sur les souches nous en disent long sur la vie des arbres, tout particulièrement la manière dont ils réagissent aux changements climatiques.
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Phosphate uptake kinetics and tissue-specific transporter expression profiles in poplar ( Populus  ×  canescens ) at different phosphorus availabilities

Phosphate uptake kinetics and tissue-specific transporter expression profiles in poplar ( Populus  ×  canescens ) at different phosphorus availabilities | MycorWeb Plant-Microbe Interactions | Scoop.it

Background

Phosphorus (P) is a major plant nutrient. It is transported into and allocated inside plants by four families of phosphate transporters (PHT1 to PHT4) with high or low affinity to phosphate. Here, we studied whole-plant P uptake kinetics and expression profiles of members of the PHT families under high, intermediate and low P availability in the woody crop poplar (Populus × canescens) in relation to plant performance.


Results

Poplars exhibited strong growth reduction and increased P use efficiency in response to lower P availabilities. The relative P uptake rate increased with intermediate and decreased with low P availability. This decrease was not energy-limited because glucose addition could not rescue the uptake. The maximum P uptake rate was more than 13-times higher in P-starved than in well-supplied poplars. The Km for whole-root uptake ranged between 26 μM and 20 μM in poplars with intermediate and low P availability, respectively. In well-supplied plants, only low uptake rate was found. The minimum concentration for net P uptake from the nutrient solution was 1.1 μM. All PHT1 members studied showed significant up-regulation upon P starvation and were higher expressed in roots than leaves, with the exception of PtPHT1;3. PtPHT1;1 and PtPHT1;2 showed root- and P starvation-specific expression. Various members of the PHT2, PHT3 and PHT4 families showed higher expression in leaves than in roots, but were unresponsive to P deprivation. Other members (PtPHT3;1, PtPHT3;2, PtPHT3;6, PtPHT4;6 to PtPHT4;8) exhibited higher expression in roots than in leaves and were in most cases up-regulated in response to P deficiency.

Conclusions

Expression profiles of distinct members of the PHT families, especially those of PHT1 were linked with changes in P uptake and allocation at whole-plant level. The regulation was tissue-specific with lower P responsiveness in leaves than in roots. Uptake efficiency for P increased with decreasing P availability, but could not overcome a threshold of about 1 μM P in the nutrient solution. Because the P concentrations in soil solutions are generally in the lower micro-molar range, even below the apparent Km-values, our findings suggest that bare-rooted poplars are prone to suffer from P limitations in most environments.

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Change in soil fungal community structure driven by a decline in ectomycorrhizal fungi following a mountain pine beetle (Dendroctonus ponderosae) outbreak

Change in soil fungal community structure driven by a decline in ectomycorrhizal fungi following a mountain pine beetle (Dendroctonus ponderosae) outbreak | MycorWeb Plant-Microbe Interactions | Scoop.it
Western North American landscapes are rapidly being transformed by forest die-off caused by mountain pine beetle (Dendroctonus ponderosae), with implications for plant and soil communities. The mechanisms that drive changes in soil community structure, particularly for the highly prevalent ectomycorrhizal fungi in pine forests, are complex and intertwined. Critical to enhancing understanding will be disentangling the relative importance of host tree mortality from changes in soil chemistry following tree death. Here, we used a recent bark beetle outbreak in lodgepole pine (Pinus contorta) forests of western Canada to test whether the effects of tree mortality altered the richness and composition of belowground fungal communities, including ectomycorrhizal and saprotrophic fungi. We also determined the effects of environmental factors (i.e. soil nutrients, moisture, and phenolics) and geographical distance, both of which can influence the richness and composition of soil fungi. The richness of both groups of soil fungi declined and the overall composition was altered by beetle-induced tree mortality. Soil nutrients, soil phenolics and geographical distance influenced the community structure of soil fungi; however, the relative importance of these factors differed between ectomycorrhizal and saprotrophic fungi. The independent effects of tree mortality, soil phenolics and geographical distance influenced the community composition of ectomycorrhizal fungi, while the community composition of saprotrophic fungi was weakly but significantly correlated with the geographical distance of plots. Taken together, our results indicate that both deterministic and stochastic processes structure soil fungal communities following landscape-scale insect outbreaks and reflect the independent roles tree mortality, soil chemistry and geographical distance play in regulating the community composition of soil fungi.
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Fungal diversity and seasonal succession in ash leaves infected by the invasive ascomycete Hymenoscyphus fraxineus

Fungal diversity and seasonal succession in ash leaves infected by the invasive ascomycete Hymenoscyphus fraxineus | MycorWeb Plant-Microbe Interactions | Scoop.it
High biodiversity is regarded as a barrier against biological invasions. We hypothesized that the invasion success of the pathogenic ascomycete Hymenoscyphus fraxineus threatening common ash in Europe relates to differences in dispersal and colonization success between the invader and the diverse native competitors. Ash leaf mycobiome was monitored by high-throughput sequencing of the fungal internal transcribed spacer region (ITS) and quantitative PCR profiling of H. fraxineus DNA. Initiation of ascospore production by H. fraxineus after overwintering was followed by pathogen accumulation in asymptomatic leaves. The induction of necrotic leaf lesions coincided with escalation of H. fraxineus DNA levels and changes in proportion of biotrophs, followed by an increase of ubiquitous endophytes with pathogenic potential. H. fraxineus uses high propagule pressure to establish in leaves as quiescent thalli that switch to pathogenic mode once these thalli reach a certain threshold – the massive feedback from the saprophytic phase enables this fungus to challenge host defenses and the resident competitors in mid-season when their density in host tissues is still low. Despite the general correspondence between the ITS-1 and ITS-2 datasets, marker biases were observed, which suggests that multiple barcodes provide better overall representation of mycobiomes.
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Giving back to the community: microbial mechanisms of plant–soil interactions

Giving back to the community: microbial mechanisms of plant–soil interactions | MycorWeb Plant-Microbe Interactions | Scoop.it
The role of both plants and soil microbes on ecosystem functioning has been long recognized, but the precise feedback mechanisms between them are more elusive. Definition of these interactions is critical if we aim to achieve an integral understanding of ecosystem functioning, and ultimately explain natural, agricultural and synthetic systems.
Advances in genomic technologies and the development of more appropriate statistical, mathematical and computational frameworks enable researchers to almost fully describe and measure the diversity of microbial communities in soil, rhizosphere and plant tissues. Under the scaffold of community ecology, we integrate the observed patterns of microbial diversity with current mechanistic understanding of plant–microbe mutualistic and pathogenic interactions, and propose a model in which plant microbial communities are shaped by different ecological forces differentially through the plant life cycle.
The same genomic technologies, applied on natural and reconstructed systems, establish that plant genotype has a small, but significant, effect on the microbial community composition in, on and around plant organs. Despite these advances, technical limitations are still important and only a handful of studies exist where a precise genetic element definitively participates in these interactions.
Studies at the field or ecosystem level are dominated by agricultural settings, examining microbial species and communities effects on plant productivity; and conversely, that plant genetics and agricultural practices can potentially impose selective pressures on specific microbes and microbial communities.
Revitalized interest in plant–soil microbial feedbacks requires researchers to systematically pose and evaluate more complex hypotheses with increasingly more realistic microbial settings. Despite the advances reviewed here, most studies focus on one aspect of plant, microbe and soil interactions. Experiments that simultaneously and methodically manipulate multiple components are necessary to establish the ecological principles, and molecular mechanisms, which drive microbially mediated plant–soil interactions. This knowledge will be critical to predict how environmental changes affect microbial and plant diversity, and will guide efforts to improve agricultural and conservation practices.
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Root Development and Endosymbioses: DELLAs Lead the Orchestra

Root Development and Endosymbioses: DELLAs Lead the Orchestra | MycorWeb Plant-Microbe Interactions | Scoop.it
The plasticity of the root system development is crucial for plant adaptation to changing soil environments. External cues control root growth and differentiation as well as beneficial plant–microorganism symbiotic associations. Arbuscular mycorrhizal (AM) and rhizobial endosymbioses are mutualistic interactions respectively formed between most Angiosperms and Glomeromycota soil fungi under nutrient (e.g., phosphorus) starvation, and between legume (Fabacae) plants and soil bacteria collectively referred to as Rhizobia when soil nitrogen availability is limiting. In both cases, microorganisms colonize host roots depending on related signaling pathways, and in the rhizobial symbiosis, the plant additionally forms nodule organs allowing nitrogen fixation.

DELLA proteins are GRAS transcriptional regulators whose accumulation highly depends on the GA hormonal pool [1. Indeed, GAs promote a targeted degradation of DELLA proteins mediated by the SCF/26S proteasome. As a result of their capacity to interact with multiple transcription factors from diverse families [1, 2], DELLA proteins are emerging as integrators of transcriptional networks associated with various signaling pathways, and notably controlling root growth and endosymbiotic associations.

Via Christophe Jacquet
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Tian Zeng's curator insight, September 27, 12:00 PM
della showed central role in development and symbiosis
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Differential Communications between Fungi and Host Plants Revealed by Secretome Analysis of Phylogenetically Related Endophytic and Pathogenic Fungi

Differential Communications between Fungi and Host Plants Revealed by Secretome Analysis of Phylogenetically Related Endophytic and Pathogenic Fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
During infection, both phytopathogenic and endophytic fungi form intimate contact with living plant cells, and need to resist or disable host defences and modify host metabolism to adapt to their host. Fungi can achieve these changes by secreting proteins and enzymes. A comprehensive comparison of the secretomes of both endophytic and pathogenic fungi can improve our understanding of the interactions between plants and fungi. Although Magnaporthe oryzae , Gaeumannomyces graminis , and M . poae are economically important fungal pathogens, and the related species Harpophora oryzae is an endophyte, they evolved from a common pathogenic ancestor. We used a pipeline analysis to predict the H . oryzae , M . oryzae , G . graminis , and M . poae secretomes and identified 1142, 1370, 1001, and 974 proteins, respectively. Orthologue gene analyses demonstrated that the M . oryzae secretome evolved more rapidly than those of the other three related species, resulting in many species-specific secreted protein-encoding genes, such as avirulence genes. Functional analyses highlighted the abundance of proteins involved in the breakdown of host plant cell walls and oxidation-reduction processes. We identified three novel motifs in the H . and M . oryzae secretomes, which may play key roles in the interaction between rice and H . oryzae . Furthermore, we found that expression of the H . oryzae secretome involved in plant cell wall degradation was downregulated, but the M . oryzae secretome was upregulated with many more upregulated genes involved in oxidation-reduction processes. The divergent in planta expression patterns of the H . and M . oryzae secretomes reveal differences that are associated with mutualistic and pathogenic interactions, respectively.

Via Yogesh Gupta
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Researchers discover key genes for climate adaptation shared between distantly related trees

Researchers discover key genes for climate adaptation shared between distantly related trees | MycorWeb Plant-Microbe Interactions | Scoop.it
Despite 140 million years of independent evolution, two types of coniferous trees use the same small set of 47 genes to rapidly adapt to varying climates, an international team of forestry researchers have found in a new study, published today in Science.

Using the same genes suggests Mother Nature is limited in the way she can help western Canadian lodgepole pine and interior spruce trees survive in the sometimes-harsh climates of their home range.

“Evolution is constrained in how many different ways it can solve the same problem,” said Sally Aitken, a University of British Columbia forestry professor and the study’s senior author.

When faced with drought or cold, trees decide to turn thousands of genes on or off to deal with changes in temperature and moisture. This suggests there may be multiple different ways trees in a region can adapt to local climate.

But after sequencing the DNA of 23,000 specific genes from hundreds of pine and spruce trees in B.C. and Alberta, the researchers discovered that the two tree species used DNA variation in 47 of the same genes to adapt to low or high temperatures. This, despite the trees evolving as separate species for roughly as long as humans and kangaroos.

The fact that these two distantly-related types of trees use variation within many of the same genes to brave the elements reveals some limits to successful climate adaptation, but also sheds light on ways scientists can help trees adapt quickly.
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Experimental Evolution as an Underutilized Tool for Studying Beneficial Animal–Microbe Interactions

Experimental Evolution as an Underutilized Tool for Studying Beneficial Animal–Microbe Interactions | MycorWeb Plant-Microbe Interactions | Scoop.it
Microorganisms play a significant role in the evolution and functioning of the eukaryotes with which they interact. Much of our understanding of beneficial host–microbe interactions stems from studying already established associations; we often infer the genotypic and environmental conditions that led to the existing host–microbe relationships. However, several outstanding questions remain, including understanding how host and microbial (internal) traits, and ecological and evolutionary (external) processes, influence the origin of beneficial host–microbe associations. Experimental evolution has helped address a range of evolutionary and ecological questions across different model systems; however, it has been greatly underutilized as a tool to study beneficial host–microbe associations. In this review, we suggest ways in which experimental evolution can further our understanding of the proximate and ultimate mechanisms shaping mutualistic interactions between eukaryotic hosts and microbes. By tracking beneficial interactions under defined conditions or evolving novel associations among hosts and microbes with little prior evolutionary interaction, we can link specific genotypes to phenotypes that can be directly measured. Moreover, this approach will help address existing puzzles in beneficial symbiosis research: how symbioses evolve, how symbioses are maintained, and how both host and microbe influence their partner’s evolutionary trajectories. By bridging theoretical predictions and empirical tests, experimental evolution provides us with another approach to test hypotheses regarding the evolution of beneficial host–microbe associations
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EMBO practical course: Plant microbiota, 26 March-07 April, Cologne, Germany

EMBO practical course: Plant microbiota, 26 March-07 April, Cologne, Germany | MycorWeb Plant-Microbe Interactions | Scoop.it
Research on the plant microbiota has developed into a highly dynamic, distinctive and interdisciplinary research field during the last five years. This practical course will focus on microbial communities colonizing the model plant Arabidopsis thaliana grown in natural soils and aims to educate the participants to apply the knowledge gained to any other plant species. The course will educate students in (i) advanced quantitative methods to detect and profile both bacterial and fungal communities that live in intimate association with healthy plants in different compartments of leaves and roots (ii) establishing microbial culture collections of the microbiota by application of high-throughput culturing methods (iii) using gnotobiotic plant systems and synthetic microbial communities to test microbiota functions for plant health (iv) applying metagenomic approaches to identify microbial functionalities of plants grown in extreme environments, e.g. under malnutrition conditions (v) using plant mutants and synthetic microbial communities to dissect the role of the plant innate immune system and plant nutrient sensing on microbial community establishment and function(s) (vi) applying computational and a suite of statistical tools to interpret next generation DNA sequencing data that are key for plant microbiota research and for experimental design.

Via Stéphane Hacquard
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Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses | MycorWeb Plant-Microbe Interactions | Scoop.it
Ocean microbes drive biogeochemical cycling on a global scale1. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories2, 3. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known4. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions5, 6, and analyse the resulting ‘global ocean virome’ dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups7, 8). This roughly triples the number of known ocean viral populations4 and doubles the number of candidate bacterial and archaeal virus genera8, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.
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Late Pleistocene climate drivers of early human migration : Nature : Nature Research

Late Pleistocene climate drivers of early human migration : Nature : Nature Research | MycorWeb Plant-Microbe Interactions | Scoop.it
On the basis of fossil and archaeological data it has been hypothesized that the exodus of Homo sapiens out of Africa and into Eurasia between ~50–120 thousand years ago occurred in several orbitally paced migration episodes. Crossing vegetated pluvial corridors from northeastern Africa into the Arabian Peninsula and the Levant and expanding further into Eurasia, Australia and the Americas, early H. sapiens experienced massive time-varying climate and sea level conditions on a variety of timescales. Hitherto it has remained difficult to quantify the effect of glacial- and millennial-scale climate variability on early human dispersal and evolution. Here we present results from a numerical human dispersal model, which is forced by spatiotemporal estimates of climate and sea level changes over the past 125 thousand years. The model simulates the overall dispersal of H. sapiens in close agreement with archaeological and fossil data and features prominent glacial migration waves across the Arabian Peninsula and the Levant region around 106–94, 89–73, 59–47 and 45–29 thousand years ago. The findings document that orbital-scale global climate swings played a key role in shaping Late Pleistocene global population distributions, whereas millennial-scale abrupt climate changes, associated with Dansgaard–Oeschger events, had a more limited regional effect.
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