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Rescooped by Francis Martin from Plant hormones
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The Characterization Of Six Auxin-Induced Tomato GH3 Genes Uncovers A Member, SlGH3.4, Strongly Responsive To Arbuscular Mycorrhizal Symbiosis

In plants, GH3 gene family is widely considered to be involved in a broad range of plant physiological processes, through modulation of hormonal homeostasis. Multiple GH3 genes have been functionally characterized in several plant species, however to date, limited works to study the GH3 genes in tomato have been reported. Here, we characterize the expression and regulatory profiles of six tomato GH3 genes, SlGH3.2, SlGH3.3, SlGH3.4, SlGH3.7, SlGH3.9 and SlGH3.15 in response to different phytohormone applications and arbuscular mycorrhizal (AM) fungal colonization. All the six GH3 genes showed inducible responses to external indole-3-acetic acid (IAA), and three members were significantly upregulated in response to AM symbiosis. Particularly, SlGH3.4, of which the transcripts were barely detectable under normal growth condition, was strongly activated in the IAA-treated and AM fungal-colonized roots. A comparison of the SlGH3.4 expression in wild-type plants and M161, a mutant with defection in AM symbiosis confirmed that the SlGH3.4 expression is highly correlated to mycorrhizal colonization. Histochemical staining demonstrated that a 2258-bp SlGH3.4 promoter fragment could drive the GUS expression strongly in root tips, steles and cortical cells of IAA-treated roots, but predominantly in the fungal-colonized cells of mycorrhizal roots. A truncated promoter with 654 bp in length failed to direct the GUS expression in IAA-treated roots, but maintained the symbiosis-induced activity in mycorrhizal roots. In summary, our results propose that a mycorrhizal signaling pathway that is at least partially independent to the auxin signaling pathway have been evolved in the co-regulation of the auxin- and mycorrhiza-activated GH3 genes in plants.

Via Jean-Michel Ané, Christophe Jacquet
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Sequencing the genome of Marssonina brunnea reveals fungus-poplar co-evolution

Sequencing the genome of Marssonina brunnea reveals fungus-poplar co-evolution | MycorWeb Plant-Microbe Interactions | Scoop.it
We sequence the genome of M. brunnea with a size of 52 Mb assembled into 89 scaffolds, representing the first sequenced Dermateaceae genome. By inoculating this fungus onto a poplar hybrid clone, we investigate how M. brunnea interacts and co-evolves with its host to colonize poplar leaves. While a handful of virulence genes in M. brunnea, mostly from the LysM family, are detected to up-regulate during infection, the poplar down-regulates its resistance genes, such as nucleotide binding site domains and leucine rich repeats, in response to infection. From 10,027 predicted proteins of M. brunnea in a comparison with those from poplar, we identify four poplar transferases that stimulate the host to resist M. brunnea. These transferas-encoding genes may have driven the co-evolution of M. brunnea and Populus during the process of infection and anti-infection.
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The past, present and future of secondary metabolite research in the Dothideomycetes

The past, present and future of secondary metabolite research in the Dothideomycetes | MycorWeb Plant-Microbe Interactions | Scoop.it
The Dothideomycetes represents a large and diverse array of fungi in which prominent plant pathogens are over-represented. Species within the Cochliobolus, Alternaria, Pyrenophora and Mycosphaerella (amongst others) all cause diseases that threaten food security in many parts of the world. Significant progress has been made over the past decade in understanding how some of these pathogens cause disease at a molecular level. It is reasonable to suggest that much of this progress can be attributed to the increased availability of genome sequences. However, together with revealing mechanisms of pathogenicity, these genome sequences have also highlighted the capacity of the Dothideomycetes to produce an extensive array of secondary metabolites, far greater than originally thought. Indeed, it is now clear that we appear to have only scratched the surface to date in terms of the identification of secondary metabolites produced by these fungi. In the first half of this review, we examine the current status of secondary metabolite research in the Dothideomycetes and highlight the diversity of the molecules discovered thus far, in terms of both structure and biological activity. In the second part of this review, we survey the emerging techniques and technologies that will be required to shed light on the vast array of secondary metabolite potential that is encoded within these genomes. Experimental design, analytical chemistry and synthetic biology are all discussed in the context of how they will contribute to this field.
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Rhizobium–legume symbioses: the crucial role of plant immunity: Trends in Plant Science

Rhizobium–legume symbioses: the crucial role of plant immunity: Trends in Plant Science | MycorWeb Plant-Microbe Interactions | Scoop.it
Highlights


•Nod factors that elicit legume nodule organogenesis also suppress plant immunity.
•The rhizobial type III secretion system (T3SS) can influence host range.
•Resistance gene-mediated immunity can impact upon rhizobial host range.
•Management of host defenses is also important for the maintenance of symbiosis.
•The plant growth environment can impact upon plant defense and symbiosis.
New research results have significantly revised our understanding of the rhizobium–legume infection process. For example, Nod factors (NFs), previously thought to be absolutely essential for this symbiosis, were shown to be dispensable under particular conditions. Similarly, an NF receptor, previously considered to be solely involved in symbiosis, was shown to function during plant pathogen infections. Indeed, there is a growing realization that plant innate immunity is a crucial component in the establishment and maintenance of symbiosis. We review here the factors involved in the suppression of plant immunity during rhizobium–legume symbiosis, and we attempt to place this information into context with the most recent and sometimes surprising research results.


Via Suayib Üstün, Rey Thomas, Christophe Jacquet
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The Fungus, the Witches’ Broom, and the Chocolate Tree: Deciphering the Molecular Interplay between Moniliophthora perniciosa and Theobroma cacao

The Fungus, the Witches’ Broom, and the Chocolate Tree: Deciphering the Molecular Interplay between Moniliophthora perniciosa and Theobroma cacao | MycorWeb Plant-Microbe Interactions | Scoop.it
As American cartoonist Charles Schulz once put it: “All you need is love. But a little chocolate now and then doesn’t hurt.” An aggressive and intractable hemibiotrophic fungus, Moniliophthora perniciosa, is ravaging chocolate tree (Theobroma cacao) plantations in many American countries, threatening livelihoods and the billion dollar cacao industry, and jeopardizing the world’s most beloved treat. M. perniciosa is the causal agent of witches’ broom disease, which results in yield reductions of 50 to 90% in infected regions (Meinhardt et al., 2008). Once the fungus enters a susceptible tree through stomata or wounds, it slowly grows between living plant cells. A key feature of the biotrophic stage of the disease is that the infected shoots lose apical dominance and morph into swollen structures called green brooms (see figure), which divert the plant’s energy from effective growth. Two to three months after infection, the disease enters the necrotrophic stage of development (Evans, 1980). The brooms become brown and eventually perish, giving rise to small, pink basidiocarps, which release millions of fungal spores capable of repeating the cycle in neighboring trees. M. perniciosa can tolerate high levels of fungicides, and there is no known treatment for witches’ broom disease.
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New Phytol: Temporal patterns of orchid mycorrhizal fungi in meadows and forests as revealed by 454 pyrosequencing

New Phytol: Temporal patterns of orchid mycorrhizal fungi in meadows and forests as revealed by 454 pyrosequencing | MycorWeb Plant-Microbe Interactions | Scoop.it

Orchid mycorrhizal (OrM) symbionts play a key role in the growth of orchids, but the temporal variation and habitat partitioning of these fungi in roots and soil remain unclear.
Temporal changes in root and rhizosphere fungal communities of Cypripedium calceolus, Neottia ovata and Orchis militaris were studied in meadow and forest habitats over the vegetation period by using 454 pyrosequencing of the full internal transcribed spacer (ITS) region.
The community of typical OrM symbionts differed by plant species and habitats. The root fungal community of N. ovata changed significantly in time, but this was not observed in C. calceolus and O. militaris. The rhizosphere community included a low proportion of OrM symbionts that exhibited a slight temporal turnover in meadow habitats but not in forests. Habitat differences in OrM and all fungal associates are largely attributable to the greater proportion of ectomycorrhizal fungi in forests.
Temporal changes in OrM fungal communities in roots of certain species indicate selection of suitable fungal species by plants. It remains to be elucidated whether these shifts depend on functional differences inside roots, seasonality, climate or succession.


Via Stéphane Hacquard
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The ecology and evolution of non-domesticated Saccharomyces species

The ecology and evolution of non-domesticated Saccharomyces species | MycorWeb Plant-Microbe Interactions | Scoop.it
Yeast researchers need model systems for ecology and evolution, but the model yeast Saccharomyces cerevisiae is not ideal because its evolution has been affected by domestication. Instead, ecologists and evolutionary biologists are focusing on close relatives of S. cerevisiae, the seven species in the genus Saccharomyces. The best-studied Saccharomyces yeast, after S. cerevisiae, is S. paradoxus, an oak tree resident throughout the northern hemisphere. In addition, several more members of the genus Saccharomyces have recently been discovered. Some Saccharomyces species are only found in nature, while others include both wild and domesticated strains. Comparisons between domesticated and wild yeasts have pinpointed hybridization, introgression and high phenotypic diversity as signatures of domestication. But studies of wild Saccharomyces natural history, biogeography and ecology are only beginning. Much remains to be understood about wild yeasts' ecological interactions and life cycles in nature. We encourage researchers to continue to investigate Saccharomyces yeasts in nature, both to place S. cerevisiae biology into its ecological context and to develop the genus Saccharomyces as a model clade for ecology and evolution
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Life in a World without Microbes

How many times have we started proposals, manuscripts, or presentations with compelling statements about the critical roles that microorganisms play in sustaining life? How often has the possibility of a world without microbes been explored in our introductory microbiology classes? Within the human microbiome research community, entire fields explore the interdependence of humans and their microbial counterparts.

But what would happen in a world without microbes?

In order to promote discussion about the value of microbial services supporting life on this planet, we explore the opportunities and challenges of a microbe-free existence. Our discussion begins by considering life without the human gut microbiome, follows with a hypothetical scenario of a world without Bacteria and Archaea, and concludes with the implications of a world without all microbes, including microbial eukaryotes and viruses. We do not include the organelles, such as mitochondria and chloroplasts, as microbes in our discussion, simply because most eukaryotic life would cease instantly in their absence.

We argue that despite myriad fundamental roles that microorganisms contribute to human and environmental function, it would be false to claim that macroscopic life cannot exist without microbes. However, although life would persist in the absence of microbes, both the quantity and quality of life would be reduced drastically.
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The Evolution of Fungal Metabolic Pathways

The Evolution of Fungal Metabolic Pathways | MycorWeb Plant-Microbe Interactions | Scoop.it

Fungi contain a remarkable range of metabolic pathways, sometimes encoded by gene clusters, enabling them to digest most organic matter and synthesize an array of potent small molecules. Although metabolism is fundamental to the fungal lifestyle, we still know little about how major evolutionary processes, such as gene duplication (GD) and horizontal gene transfer (HGT), have interacted with clustered and non-clustered fungal metabolic pathways to give rise to this metabolic versatility. We examined the synteny and evolutionary history of 247,202 fungal genes encoding enzymes that catalyze 875 distinct metabolic reactions from 130 pathways in 208 diverse genomes. We found that gene clustering varied greatly with respect to metabolic category and lineage; for example, clustered genes in Saccharomycotina yeasts were overrepresented in nucleotide metabolism, whereas clustered genes in Pezizomycotina were more common in lipid and amino acid metabolism. The effects of both GD and HGT were more pronounced in clustered genes than in their non-clustered counterparts and were differentially distributed across fungal lineages; specifically, GD, which was an order of magnitude more abundant than HGT, was most frequently observed in Agaricomycetes, whereas HGT was much more prevalent in Pezizomycotina. The effect of HGT in some Pezizomycotina was particularly strong; for example, we identified 111 HGT events associated with the 15 Aspergillus genomes, which sharply contrasts with the 60 HGT events detected for the 48 genomes from the entire Saccharomycotina subphylum. Finally, the impact of GD within a metabolic category was typically consistent across all fungal lineages, whereas the impact of HGT was variable. These results indicate that GD is the dominant process underlying fungal metabolic diversity, whereas HGT is episodic and acts in a category- or lineage-specific manner. Both processes have a greater impact on clustered genes, suggesting that metabolic gene clusters represent hotspots for the generation of fungal metabolic diversity.

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Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies | MycorWeb Plant-Microbe Interactions | Scoop.it
Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process.
Francis Martin's insight:

Good that JGI is using RNA-Seq to support gene prediction of our fungal genomes.

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Ectomycorrhizal fungi – potential organic matter decomposers, yet not saprotrophs

Ectomycorrhizal fungi – potential organic matter decomposers, yet not saprotrophs | MycorWeb Plant-Microbe Interactions | Scoop.it
Although hypothesized for many years, the involvement of ectomycorrhizal fungi in decomposition of soil organic matter remains controversial and has not yet been fully acknowledged as an important factor in the regulation of soil carbon (C) storage. Here, we review recent findings, which support the view that some ectomycorrhizal fungi have the capacity to oxidize organic matter, either by ‘brown-rot’ Fenton chemistry or using ‘white-rot’ peroxidases. We propose that ectomycorrhizal fungi benefit from organic matter decomposition primarily through increased nitrogen mobilization rather than through release of metabolic C and question the view that ectomycorrhizal fungi may act as facultative saprotrophs. Finally, we discuss how mycorrhizal decomposition may influence organic matter storage in soils and mediate responses of ecosystem C sequestration to environmental changes.

Via Jean-Michel Ané
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Overexpression of Laccaria bicolor aquaporin JQ585595 alters root water transport properties in ectomycorrhizal white spruce (Picea glauca) seedlings

Overexpression of Laccaria bicolor aquaporin JQ585595 alters root water transport properties in ectomycorrhizal white spruce (Picea glauca) seedlings | MycorWeb Plant-Microbe Interactions | Scoop.it
The contribution of hyphae to water transport in ectomycorrhizal (ECM) white spruce (Picea glauca) seedlings was examined by altering expression of a major water-transporting aquaporin in Laccaria bicolor.
Picea glauca was inoculated with wild-type (WT), mock transgenic or L. bicolor aquaporin JQ585595-overexpressing (OE) strains and exposed to root temperatures ranging from 5 to 20°C to examine the root water transport properties, physiological responses and plasma membrane intrinsic protein (PIP) expression in colonized plants.
Mycorrhization increased shoot water potential, transpiration, net photosynthetic rates, root hydraulic conductivity and root cortical cell hydraulic conductivity in seedlings. At 20°C, OE plants had higher root hydraulic conductivity compared with WT plants and the increases were accompanied by higher expression of P. glauca PIP GQ03401_M18.1 in roots. In contrast to WT L. bicolor, the effects of OE fungi on root and root cortical cell hydraulic conductivities were abolished at 10 and 5°C in the absence of major changes in the examined transcript levels of P. glauca root PIPs.
The results provide evidence for the importance of fungal aquaporins in root water transport of mycorrhizal plants. They also demonstrate links between hyphal water transport, root aquaporin expression and root water transport in ECM plants.
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First evidence of mutualism between ancient plant lineages (Haplomitriopsida liverworts) and Mucoromycotina fungi and its response to simulated Palaeozoic changes in atmospheric CO2

First evidence of mutualism between ancient plant lineages (Haplomitriopsida liverworts) and Mucoromycotina fungi and its response to simulated Palaeozoic changes in atmospheric CO2 | MycorWeb Plant-Microbe Interactions | Scoop.it

The discovery that Mucoromycotina, an ancient and partially saprotrophic fungal lineage, associates with the basal liverwort lineage Haplomitriopsida casts doubt on the widely held view that Glomeromycota formed the sole ancestral plant–fungus symbiosis. Whether this association is mutualistic, and how its functioning was affected by the fall in atmospheric CO2 concentration that followed plant terrestrialization in the Palaeozoic, remains unknown.We measured carbon-for-nutrient exchanges between Haplomitriopsida liverworts and Mucoromycotina fungi under simulated mid-Palaeozoic (1500 ppm) and near-contemporary (440 ppm) CO2 concentrations using isotope tracers, and analysed cytological differences in plant–fungal interactions. Concomitantly, we cultured both partners axenically, resynthesized the associations in vitro, and characterized their cytology.We demonstrate that liverwort–Mucoromycotina symbiosis is mutualistic and mycorrhiza-like, but differs from liverwort–Glomeromycota symbiosis in maintaining functional efficiency of carbon-for-nutrient exchange between partners across CO2 concentrations. Inoculation of axenic plants with Mucoromycotina caused major cytological changes affecting the anatomy of plant tissues, similar to that observed in wild-collected plants colonized by Mucoromycotina fungi.By demonstrating reciprocal exchange of carbon for nutrients between partners, our results provide support for Mucoromycotina establishing the earliest mutualistic symbiosis with land plants. As symbiotic functional efficiency was not compromised by reduced CO2, we suggest that other factors led to the modern predominance of the Glomeromycota symbiosis.

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Tasmania's giant ash trees may be world's tallest

Tasmania's giant ash trees may be world's tallest | MycorWeb Plant-Microbe Interactions | Scoop.it

In the southern hemisphere grow trees that may be secret record-breaker.

 

Stephen Sillett's laboratory is dangling 90 metres above the ground. It is an intricate web of ropes and instruments strung up in the branches of a tree. And in the windy conditions that plague Tasmania's forests, it can be distinctly precarious.

"You can hear big gusts come through like freight trains pounding along their way toward you," says Sillett, a forest ecologist at Humboldt State University in Arcata, California. "As the gust hits, then the whole tree top just lays over and there's big old blows. It's amazing."

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Discovery of a novel small secreted protein family with conserved N-terminal IGY motif in Dikarya fungi

Discovery of a novel small secreted protein family with conserved N-terminal IGY motif in Dikarya fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
A novel fungal SSP family consisting of 107 members was identified in the poplar tree fungal pathogen Marssonina brunnea, which accounts for over 17% of its secretome. We named these proteins IGY proteins (IGYPs) based on the conserved three amino acids at the N-terminus. In spite of overall low sequence similarity among IGYPs; they showed conserved N- and C-terminal motifs and a unified gene structure. By RT-PCR-seq, we analyzed the IGYP gene models and validated their expressions as active genes during infection. IGYP homologues were also found in 25 other Dikarya fungal species, all of which shared conserved motifs and the same gene structure. Furthermore, 18 IGYPs from 11 fungi also shared similar genomic contexts. Real-time RT-PCR showed that 8 MbIGYPs were highly expressed in the biotrophic stage. Interestingly, transient assay of 12 MbIGYPs showed that the MbIGYP13 protein induced cell death in resistant poplar clones.
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Spatio-Temporal Dynamic of Tuber magnatum Mycelium in Natural Truffle Grounds

Spatio-Temporal Dynamic of Tuber magnatum Mycelium in Natural Truffle Grounds | MycorWeb Plant-Microbe Interactions | Scoop.it
Tuber magnatum produces the world's most expensive truffle. This fungus produces very rare ectomycorrhizas which are difficult or even impossible to detect in the field. A “real-time” PCR assay was recently developed to quantify and to track T. magnatum mycelium in soil. Here, this technique was used to investigate the spatial distribution of T. magnatum extra-radical mycelium in soil productive patches and its dynamic across seasons. This study was carried out in four different natural T. magnatum truffle grounds located in different Italian regions. During the fruiting seasons, the amount of T. magnatum mycelium was significantly higher around the fruiting points and decreased going farther away from them. Moreover, T. magnatum mycelium inside the productive patches underwent seasonal fluctuations. In early spring, the amount of T. magnatum mycelium was significantly higher than in summer. In summer, probably due to the hot and dry season, T. magnatum mycelium significantly decreased, whereas in autumn it increased again and was concentrated at the putative fruiting points. These results give new insights on T. magnatum ecology and are useful to plan the most appropriate sampling strategy for evaluating the management of a truffle ground.
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High-Resolution Transcript Profiling of the Atypical Biotrophic Interaction between Theobroma cacao and the Fungal Pathogen Moniliophthora perniciosa

High-Resolution Transcript Profiling of the Atypical Biotrophic Interaction between Theobroma cacao and the Fungal Pathogen Moniliophthora perniciosa | MycorWeb Plant-Microbe Interactions | Scoop.it
Witches’ broom disease (WBD), caused by the hemibiotrophic fungus Moniliophthora perniciosa, is one of the most devastating diseases of Theobroma cacao, the chocolate tree. In contrast to other hemibiotrophic interactions, the WBD biotrophic stage lasts for months and is responsible for the most distinctive symptoms of the disease, which comprise drastic morphological changes in the infected shoots. Here, we used the dual RNA-seq approach to simultaneously assess the transcriptomes of cacao and M. perniciosa during their peculiar biotrophic interaction. Infection with M. perniciosa triggers massive metabolic reprogramming in the diseased tissues. Although apparently vigorous, the infected shoots are energetically expensive structures characterized by the induction of ineffective defense responses and by a clear carbon deprivation signature. Remarkably, the infection culminates in the establishment of a senescence process in the host, which signals the end of the WBD biotrophic stage. We analyzed the pathogen’s transcriptome in unprecedented detail and thereby characterized the fungal nutritional and infection strategies during WBD and identified putative virulence effectors. Interestingly, M. perniciosa biotrophic mycelia develop as long-term parasites that orchestrate changes in plant metabolism to increase the availability of soluble nutrients before plant death. Collectively, our results provide unique insight into an intriguing tropical disease and advance our understanding of the development of (hemi)biotrophic plant-pathogen interactions.
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New Phytol: Land-use intensity and host plant identity interactively shape communities of arbuscular mycorrhizal fungi in roots of grassland plants

New Phytol: Land-use intensity and host plant identity interactively shape communities of arbuscular mycorrhizal fungi in roots of grassland plants | MycorWeb Plant-Microbe Interactions | Scoop.it

We studied the effect of host plant identity and land-use intensity (LUI) on arbuscular mycorrhizal fungi (AMF, Glomeromycota) communities in roots of grassland plants. These are relevant factors for intraradical AMF communities in temperate grasslands, which are habitats where AMF are present in high abundance and diversity. In order to focus on fungi that directly interact with the plant at the time, we investigated root-colonizing communities.
Our study sites represent an LUI gradient with different combinations of grazing, mowing, and fertilization. We used massively parallel multitag pyrosequencing to investigate AMF communities in a large number of root samples, while being able to track the identity of the host.
We showed that host plants significantly differed in AMF community composition, while land use modified this effect in a plant species-specific manner. Communities in medium and low land-use sites were subsets of high land-use communities, suggesting a differential effect of land use on the dispersal of AMF species with different abundances and competitive abilities.
We demonstrate that in these grasslands, there is a small group of highly abundant, generalist fungi which represent the dominating species in the AMF community.


Via Stéphane Hacquard
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Analyses of Phlebiopsis gigantea genome reveal enzyme systems involved in the degradation of conifers

Analyses of  Phlebiopsis gigantea genome reveal enzyme systems involved in the degradation of conifers | MycorWeb Plant-Microbe Interactions | Scoop.it
Analyses of the Phlebiopsis gigantea genome reveal enzyme systems involved in the degradation of conifers.
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The ISME Journal - Dynamics in microbial communities: unraveling mechanisms to identify principles

The ISME Journal - Dynamics in microbial communities: unraveling mechanisms to identify principles | MycorWeb Plant-Microbe Interactions | Scoop.it
Diversity begets higher-order properties such as functional stability and robustness in microbial communities, but principles that inform conceptual (and eventually predictive) models of community dynamics are lacking. Recent work has shown that selection as well as dispersal and drift shape communities, but the mechanistic bases for assembly of communities and the forces that maintain their function in the face of environmental perturbation are not well understood. Conceptually, some interactions among community members could generate endogenous dynamics in composition, even in the absence of environmental changes. These endogenous dynamics are further perturbed by exogenous forcing factors to produce a richer network of community interactions and it is this ‘system’ that is the basis for higher-order community properties. Elucidation of principles that follow from this conceptual model requires identifying the mechanisms that (a) optimize diversity within a community and (b) impart community stability. The network of interactions between organisms can be an important element by providing a buffer against disturbance beyond the effect of functional redundancy, as alternative pathways with different combinations of microbes can be recruited to fulfill specific functions.
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Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history

Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history | MycorWeb Plant-Microbe Interactions | Scoop.it
Colobines are a unique group of Old World monkeys that principally eat leaves and seeds rather than fruits and insects. We report the sequencing at 146× coverage, de novo assembly and analyses of the genome of a male golden snub-nosed monkey (Rhinopithecus roxellana) and resequencing at 30× coverage of three related species (Rhinopithecus bieti, Rhinopithecus brelichi and Rhinopithecus strykeri). Comparative analyses showed that Asian colobines have an enhanced ability to derive energy from fatty acids and to degrade xenobiotics. We found evidence for functional evolution in the colobine RNASE1 gene, encoding a key secretory RNase that digests the high concentrations of bacterial RNA derived from symbiotic microflora. Demographic reconstructions indicated that the profile of ancient effective population sizes for R. roxellana more closely resembles that of giant panda rather than its congeners. These findings offer new insights into the dietary adaptations and evolutionary history of colobine primates
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Ten Simple Rules for Finishing Your PhD

Ten Simple Rules for Finishing Your PhD | MycorWeb Plant-Microbe Interactions | Scoop.it

After years of research and with completion in sight, the final year of the PhD often represents the most challenging time of a student's career, in which the ultimate reward is the PhD honor itself. A large investment in time, energy, and motivation is needed, with many tasks to be completed; concluding experiments must be carried out, results interpreted, and a research story mapped out in preparation for writing the final thesis. All the while, administrative obligations need attention (e.g., university credits and mandatory documents), papers may need to be published, students mentored, and due consideration paid to planning for the next career move. Without some form of strategic action plan and the employment of project management skills, students run the risk of becoming overwhelmed and run down or of not meeting their final deadlines. Personal time management and stress resilience are competences that can be developed and honed during this final period of the PhD.

Here, we present ten simple rules on how to deal with time issues and conflict situations when facing the last year of a PhD in science. The rules focus on defining research goals in advance and designing a plan of action. Moreover, we discuss the importance of managing relationships with supervisors and colleagues, as well as early career planning.

PLOS Computational Biology is an open-access
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Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood

Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood | MycorWeb Plant-Microbe Interactions | Scoop.it
Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine wood. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of wood extractives were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea's extractives metabolism. These results contribute to our fundamental understanding of pioneer colonization of conifer wood and provide insight into the diverse chemistries employed by fungi in carbon cycling processes.
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Whose truffle is this? Distribution patterns of ECM fungal diversity in Tuber melanosporum brûlés developed in multi-host Mediterranean plant communities

Whose truffle is this? Distribution patterns of ECM fungal diversity in Tuber melanosporum brûlés developed in multi-host Mediterranean plant communities | MycorWeb Plant-Microbe Interactions | Scoop.it
In the Mediterranean region, patches of vegetation recovering from disturbance and transiently dominated by shrubs produce one of the world's most prized fungi, the black truffle (Tuber melanosporum). In these successional plant communities, we have fragmentary knowledge of the distribution of T. melanosporum in space among ectomycorrhizal (ECM) host species and in time.

Molecular identification of hosts (RFLP) and fungi (ITS sequencing) and quantification of T. melanosporum mycelium (qPCR) were employed to evaluate the presence of T. melanosporum on four dominant ECM host species (Quercus ilex, Q. coccifera, Arbutus unedo, Cistus albidus) and the extent to which their respective ECM communities shared fungal diversity, over the course of development of truffle grounds, from recent unproductive brûlés to senescent ones where production has stopped.

We found that truffle grounds host rich communities in which multi-host fungal species dominate in frequency. When considering both ECM tips and soil mycelia, we documented a dynamic and spatially heterogeneous pattern of T. melanosporum distribution in soils and a presence of ECM tips restricted to Q. ilex roots.

This study advances our knowledge of the ecology of T. melanosporum, and provides insight into the extent of ECM fungal sharing among plant species that dominate Mediterranean landscapes.

Via Jean-Michel Ané
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Community assembly of ectomycorrhizal fungi along a subtropical secondary forest succession

Community assembly of ectomycorrhizal fungi along a subtropical secondary forest succession | MycorWeb Plant-Microbe Interactions | Scoop.it
Environmental selection and dispersal limitation are two of the primary processes structuring biotic communities in ecosystems, but little is known about these processes in shaping soil microbial communities during secondary forest succession.
We examined the communities of ectomycorrhizal (EM) fungi in young, intermediate and old forests in a Chinese subtropical ecosystem, using 454 pyrosequencing.
The EM fungal community consisted of 393 operational taxonomic units (OTUs), belonging to 21 EM fungal lineages, in which three EM fungal lineages and 11 EM fungal OTUs showed significantly biased occurrence among the young, intermediate and old forests. The EM fungal community was structured by environmental selection and dispersal limitation in old forest, but only by environmental selection in young, intermediate, and whole forests. Furthermore, the EM fungal community was affected by different factors in the different forest successional stages, and the importance of these factors in structuring EM fungal community dramatically decreased along the secondary forest succession series.
This study suggests that different assembly mechanisms operate on the EM fungal community at different stages in secondary subtropical forest succession.
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