MycorWeb Plant-Microbe Interactions
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Functional soil microbiome: Belowground solutions to an aboveground problem

Functional soil microbiome: Belowground solutions to an aboveground problem | MycorWeb Plant-Microbe Interactions | Scoop.it

There is considerable evidence in the literature that beneficial rhizospheric microbes can alter plant morphology, enhance plant growth, and increase mineral content. Of late, there is a surge to understand the impact of the microbiome on plant health. Recent research shows the utilization of novel sequencing techniques to identify the microbiome in model systems such as Arabidopsis and Maize. However, it is not known how the community of microbes identified may play a role to improve plant health and fitness. There are very few detailed studies with isolated beneficial microbes showing the importance of the functional microbiome in plant fitness and disease protection. Some recent work on the cultivated microbiome in rice shows a wide diversity of bacterial species is associated with the roots of field-grown rice plants. However, biological significance and potential effects of the microbiome on the host plants are completely unknown. Work performed with isolated strains showed various genetic pathways that are involved in recognition of host-specific factors that are involved in the beneficial host-microbe interactions. The composition of the microbiome in plants is dynamic and controlled by multiple factors. In the case of the rhizosphere, temperature, pH, and the presence of chemical signals from bacteria, plants, and nematodes all shape the environment and influence which organisms will flourish. This provides a basis for plants and their microbiomes to selectively associate with one another. This update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security.


Via Christophe Jacquet, Stéphane Hacquard
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Refining the origins of wood-rotting mechanisms - DOE Joint Genome Institute

Refining the origins of wood-rotting mechanisms - DOE Joint Genome Institute | MycorWeb Plant-Microbe Interactions | Scoop.it
Comparative genomics analysis uses newly-sequenced white rot and brown rot fungi to refine timeline for enzymatic origins of lignocellulose decomposition.
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Aquaporin-mediated long-distance polyphosphate translocation directed towards the host in arbuscular mycorrhizal symbiosis: application of virus-induced gene silencing

Aquaporin-mediated long-distance polyphosphate translocation directed towards the host in arbuscular mycorrhizal symbiosis: application of virus-induced gene silencing | MycorWeb Plant-Microbe Interactions | Scoop.it
Arbuscular mycorrhizal fungi translocate polyphosphate through hyphae over a long distance to deliver to the host. More than three decades ago, suppression of host transpiration was found to decelerate phosphate delivery of the fungal symbiont, leading us to hypothesize that transpiration provides a primary driving force for polyphosphate translocation, probably via creating hyphal water flow in which fungal aquaporin(s) may be involved. The impact of transpiration suppression on polyphosphate translocation through hyphae of Rhizophagus clarus was evaluated. An aquaporin gene expressed in intraradical mycelia was characterized and knocked down by virus-induced gene silencing to investigate the involvement of the gene in polyphosphate translocation. Rhizophagus clarus aquaporin 3 (RcAQP3) that was most highly expressed in intraradical mycelia encodes an aquaglyceroporin responsible for water transport across the plasma membrane. Knockdown of RcAQP3 as well as the suppression of host transpiration decelerated polyphosphate translocation in proportion to the levels of knockdown and suppression, respectively. These results provide the first insight into the mechanism underlying long-distance polyphosphate translocation in mycorrhizal associations at the molecular level, in which host transpiration and the fungal aquaporin play key roles. A hypothetical model of the translocation is proposed for further elucidation of the mechanism.

Via Pierre-Marc Delaux
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Jessie Uehling's curator insight, May 3, 12:56 PM
 Long-distance polyphosphate translocation in mycorrhizal symbioses mediated by fungal host transpiration and aquaporins 
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Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl

Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl | MycorWeb Plant-Microbe Interactions | Scoop.it
Nuclear disasters at Chernobyl and Fukushima provide examples of effects of acute ionizing radiation on mutations that can affect the fitness and distribution of species. Here, we investigated the prevalence of Microbotryum lychnidis-dioicae, a pollinator-transmitted fungal pathogen of plants causing anther-smut disease in Chernobyl, its viability, fertility and karyotype variation, and the accumulation of non-synonymous mutations in its genome. We collected diseased flowers of Silene latifolia from locations ranging by more than two orders of magnitude in background radiation, from 0.05 to 21.03 μSv/h. Disease prevalence decreased significantly with increasing radiation level, possibly due to lower pollinator abundance and altered pollinator behaviour. Viability and fertility, measured as the budding rate of haploid sporidia following meiosis from the diploid teliospores, did not vary with increasing radiation levels and neither did karyotype overall structure and level of chromosomal size heterozygosity. We sequenced the genomes of twelve samples from Chernobyl and of four samples collected from uncontaminated areas and analysed alignments of 6,068 predicted genes, corresponding to 1.04x107 base pairs. We found no dose-dependent differences in substitution rates (neither dN, dS, nor dN/dS). Thus, we found no significant evidence of increased deleterious mutation rates at higher levels of background radiation in this plant pathogen. We even found lower levels of non-synonymous substitution rates in contaminated areas compared to control regions, suggesting that purifying selection was stronger in contaminated than uncontaminated areas. We briefly discuss the possibilities for a mechanistic basis of radio-resistance in this non-melanised fungus.
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Moonlighting transcriptional activation function of a fungal sulfur metabolism enzyme

Moonlighting transcriptional activation function of a fungal sulfur metabolism enzyme | MycorWeb Plant-Microbe Interactions | Scoop.it
Moonlighting proteins, including metabolic enzymes acting as transcription factors (TF), are present in a variety of organisms but have not been described in higher fungi so far. In a previous genome-wide analysis of the TF repertoire of the plant-symbiotic fungus Tuber melanosporum, we identified various enzymes, including the sulfur-assimilation enzyme phosphoadenosine-phosphosulfate reductase (PAPS-red), as potential transcriptional activators. A functional analysis performed in the yeast Saccharomyces cerevisiae, now demonstrates that a specific variant of this enzyme, PAPS-red A, localizes to the nucleus and is capable of transcriptional activation. TF moonlighting, which is not present in the other enzyme variant (PAPS-red B) encoded by the T. melanosporum genome, relies on a transplantable C-terminal polypeptide containing an alternating hydrophobic/hydrophilic amino acid motif. A similar moonlighting activity was demonstrated for six additional proteins, suggesting that multitasking is a relatively frequent event. PAPS-red A is sulfur-state-responsive and highly expressed, especially in fruitbodies, and likely acts as a recruiter of transcription components involved in S-metabolism gene network activation. PAPS-red B, instead, is expressed at low levels and localizes to a highly methylated and silenced region of the genome, hinting at an evolutionary mechanism based on gene duplication, followed by epigenetic silencing of this non-moonlighting gene variant.
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Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system

Background

The exponential growth of genomic data from next generation technologies renders traditional manual expert curation effort unsustainable. Many genomic systems have included community annotation tools to address the problem. Most of these systems adopted a “Wiki-based” approach to take advantage of existing wiki technologies, but encountered obstacles in issues such as usability, authorship recognition, information reliability and incentive for community participation.
Results

Here, we present a different approach, relying on tightly integrated method rather than “Wiki-based” method, to support community annotation and user collaboration in the Integrated Microbial Genomes (IMG) system. The IMG approach allows users to use existing IMG data warehouse and analysis tools to add gene, pathway and biosynthetic cluster annotations, to analyze/reorganize contigs, genes and functions using workspace datasets, and to share private user annotations and workspace datasets with collaborators. We show that the annotation effort using IMG can be part of the research process to overcome the user incentive and authorship recognition problems thus fostering collaboration among domain experts. The usability and reliability issues are addressed by the integration of curated information and analysis tools in IMG, together with DOE Joint Genome Institute (JGI) expert review.
Conclusion

By incorporating annotation operations into IMG, we provide an integrated environment for users to perform deeper and extended data analysis and annotation in a single system that can lead to publications and community knowledge sharing as shown in the case studies.
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Sunday Sitdown: Clark prof David Hibbett studies fungi, genetics

Sunday Sitdown: Clark prof David Hibbett studies fungi, genetics | MycorWeb Plant-Microbe Interactions | Scoop.it
WORCESTER - David S. Hibbett grew up next to a pond and, by his own account, was always out in the woods. After majoring in botany at the University of Massachusetts at Amherst, he planned to focus on plants during graduate school at Duke University. His project fell apart, however, and he turned to fungi.

At Clark University, his lab features whimsical mushroom pottery and research that looks at mushrooms at the genetic level. In a recent article in the prestigious journal Science, he pointed out an intriguing result of the DNA age: Scientists using modern tools to analyze soil and water are finding the genes of thousands of fungi never before cataloged. But scientific rules say those newly discovered species cannot be given names unless someone finds the actual fungi. No mushroom, no name. It's a situation that Mr. Hibbett would like to see changed.
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Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota)

Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota) | MycorWeb Plant-Microbe Interactions | Scoop.it
Empty dCommunities of litter saprotrophic and root-associated fungi are vertically separated within boreal forest soil profiles. It is unclear whether this depth partitioning is maintained exclusively by substrate-mediated niche partitioning (i.e. distinct fundamental niches), or by competition for space and resources (i.e. distinct realised niches). Improved understanding of the mechanisms driving spatial partitioning of these fungal guilds is critical, as they modulate carbon and nutrient cycling in different ways. Under field settings, we tested the effects of substrate quality and the local fungal species pool at various depths in determining the potential of saprotrophic and mycorrhizal fungi to colonize and exploit organic matter. Natural substrates of three qualities – fresh or partly decomposed litter or humus – were incubated in the corresponding organic layers in a boreal forest soil profile in a fully factorial design. After one and two growing seasons, fungal community composition in the substrates was determined by 454-pyrosequencing and decomposition was analysed. Fungal community development during the course of the experiment was determined to similar degrees by vertical location of the substrates (24% of explained variation) and by substrate quality (20%), indicating that interference competition is a strong additional driver of the substrate-dependent depth partitioning of fungal guilds in the system. During the first growing season, litter substrates decomposed slower when colonized by root-associated communities than when colonized by communities of litter saprotrophs, whereas humus was only slightly decomposed by both fungal guilds. During the second season, however, certain basidiomycetes from both guilds were particularly efficient in localizing and exploiting their native organic substrates although displaced in the vertical profile, validating that fungal community composition, rather than microclimatic factors, were responsible for observed depth-related differences in decomposer activities during the first season. In conclusion, our results suggest that saprotrophic and root-associated fungal guilds have overlapping fundamental niches with respect to colonizing substrates of different qualities, and that their substrate-dependent depth partitioning in soils of ectomycorrhiza-dominated ecosystems is reinforced by interference competition. Through competitive interactions mycorrhizal fungi can thus indirectly regulate litter decomposition rates by restraining activities of more efficient litter saprotrophs.escription
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Non, Tchernobyl n’est pas devenu une réserve naturelle

Non, Tchernobyl n’est pas devenu une réserve naturelle | MycorWeb Plant-Microbe Interactions | Scoop.it
Quels sont les effets à long terme des accidents nucléaires sur la biodiversité ? Des travaux menés en Ukraine et au Japon détaillent les dommages causés aux mammifères, oiseaux et insectes.
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Genomes and Evolution of Charophytes, Bryophytes, Lycophytes and Ferns, 1st Edition | Stefan Rensing

Genomes and Evolution of Charophytes, Bryophytes, Lycophytes and Ferns, 1st Edition | Stefan Rensing | MycorWeb Plant-Microbe Interactions | Scoop.it
The 78th volume of this series features in-depth and up-to-date reviews by recognized experts on a range of topics related to the genomes and evolution of charophytes, bryophytes, lycophytes, and ferns, discussing how the sequencing of genomes of various species in both the animal and plant kingdoms has greatly informed our understanding of evolution.

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Analysis of single root tip microbiomes suggests that distinctive bacterial communities are selected by Pinus sylvestris roots colonized by different ectomycorrhizal fungi

Analysis of single root tip microbiomes suggests that distinctive bacterial communities are selected by Pinus sylvestris roots colonized by different ectomycorrhizal fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
Symbiotic ectomycorrhizal tree roots represent an important niche for interaction with bacteria since the fungi colonizing them have a large surface area and receive a direct supply of photosynthetically derived carbon. We examined individual root tips of Pinus sylvestris at defined time points between 5 days and 24 weeks, identified the dominant fungi colonizing each root tip using Sanger sequencing and the bacterial communities colonizing individual root tips by 454 pyrosequencing. Bacterial colonization was extremely dynamic with statistically significant variation in time and increasing species richness until week 16 (3477 operational taxonomic units). Bacterial community structure of roots colonized by Russula sp. 6 GJ-2013b, Piloderma spp., Meliniomyces variabilis and Paxillus involutus differed significantly at weeks 8 and 16 but diversity declined and significant differences were no longer apparent at week 24. The most common genera were Burkholderia, Sphingopyxsis, Dyella, Pseudomonas, Acinetobacter, Actinospica, Aquaspirillum, Acidobacter Gp1, Sphingomonas, Terriglobus, Enhydrobacter, Herbaspirillum and Bradyrhizobium. Many genera had high initial abundance at week 8, declining with time but Dyella and Terriglobus increased in abundance at later time points. In roots colonized by Piloderma spp. several other bacterial genera, such as Actinospica, Bradyrhizobium, Acidobacter Gp1 and Rhizomicrobium appeared to increase in abundance at later sampling points.
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Jessie Uehling's curator insight, April 28, 11:52 AM
Individual root tips on a single root axis wit their own ECM fungi, and ECM fungi with their own bacterial communities, fleas on fleas 
Jean-Michel Ané's curator insight, April 29, 10:38 AM

Very nice!

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Evolution of plant genome architecture

Evolution of plant genome architecture | MycorWeb Plant-Microbe Interactions | Scoop.it
We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements; and (3) that various classes of small RNAs help shape genomic architecture and function. We illustrate ways in which understanding these organism-level and molecular genetic processes can be used for crop plant improvement.
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The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut | MycorWeb Plant-Microbe Interactions | Scoop.it
Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ~2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaensis). We show that these genomes are similar to cultivated peanut's A and B subgenomes and use them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut's subgenomes. On the basis of remarkably high DNA identity of the A. ipaensis genome and the B subgenome of cultivated peanut and biogeographic evidence, we conclude that A. ipaensis may be a direct descendant of the same population that contributed the B subgenome to cultivated peanut.
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A multi-omic future for microbiome studies

A multi-omic future for microbiome studies | MycorWeb Plant-Microbe Interactions | Scoop.it
Integration of multiple ‘omics’ technologies will allow researchers to gain a more complete picture of the constituents and functions of microbial communities and provide far richer information for predictive modelling of community phenotypes.
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The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of nonstructural polyphenols

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of nonstructural polyphenols | MycorWeb Plant-Microbe Interactions | Scoop.it
The Persian walnut (Juglans regia L.) a diploid species native to the mountainous regions of Central Asia, is the major walnut species cultivated for nut production and is one of the most widespread tree nut species in the world. The high nutritional value of J. regia nuts is associated with a rich array of polyphenolic compounds, whose complete biosynthetic pathways are still unknown. A J. regia genome sequence was obtained from the cultivar Chandler to discover target genes and additional unknown genes. The 667 Mbp genome was assembled using two different methods (SOAPdenovo2 and MaSuRCA), with a N50 scaffold size of 464,955 bp (based on a 606 Mbp genome size), 221,640 contigs and 37% GC content. Annotation with MAKER-P and other genomic resources yielded 32,498 gene models. Previous studies in walnut relying on tissue-specific methods have only identified a single PPO gene (JrPPO1). Enabled by the J. regia genome sequence, a second homolog of PPO (JrPPO2) was discovered. In addition, ~130 genes in the large GGT superfamily were detected. Specifically, two genes, JrGGT1 and JrGGT2, were significantly homologous to the GGT from Quercus robur (QrGGT), which is involved in the synthesis of 1-O-galloyl-β-D-glucose, a precursor for the synthesis of hydrolysable tannins. The reference genome for J. regia provides meaningful insight into the complex pathways required for the synthesis of polyphenols. The walnut genome sequence provides important tools and methods to accelerate breeding and to facilitate the genetic dissection of complex traits.

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Ericaceous plant–fungus network in a harsh alpine–subalpine environment

Ericaceous plant–fungus network in a harsh alpine–subalpine environment | MycorWeb Plant-Microbe Interactions | Scoop.it
In terrestrial ecosystems, plant species and diverse root-associated fungi form complex networks of host–symbiont associations. Recent studies have revealed that structures of those below-ground plant–fungus networks differ between arbuscular mycorrhizal and ectomycorrhizal symbioses. Nonetheless, we still remain ignorant of how ericaceous plant species, which dominate arctic and alpine tundra, constitute networks with their root-associated fungi. Based on a high-throughput DNA sequencing dataset, we characterized the statistical properties of a network involving 16 ericaceous plant species and more than 500 fungal taxa in the alpine–subalpine region of Mt. Tateyama, central Japan. While all the 16 ericaceous species were associated mainly with fungi in the order Helotiales, they varied remarkably in associations with fungi in other orders such as Sebacinales, Atheliales, Agaricales, Russulales, and Thelephorales. The ericaceous plant–fungus network was characterized by high symbiont/host preferences. Moreover, the network had a characteristic structure called “anti-nestedness”, which has been previously reported in ectomycorrhizal plant–fungus networks. The results lead to the hypothesis that ericaceous plants in harsh environments can host unexpectedly diverse root-associated fungal taxa, constituting networks whose structures are similar to those of previously reported ectomycorrhizal networks but not to those of arbuscular mycorrhizal ones.
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Carbon Nanofiber Arrays: A Novel Tool for Microdelivery of Biomolecules to Plants

Effective methods for delivering bioprobes into the cells of intact plants are essential for investigating diverse biological processes. Increasing research on trees, such as Populus spp., for bioenergy applications is driving the need for techniques that work well with tree species. This report introduces vertically aligned carbon nanofiber (VACNF) arrays as a new tool for microdelivery of labeled molecules to Populus leaf tissue and whole plants. We demonstrated that VACNFs penetrate the leaf surface to deliver sub-microliter quantities of solution containing fluorescent or radiolabeled molecules into Populus leaf cells. Importantly, VACNFs proved to be gentler than abrasion with carborundum, a common way to introduce material into leaves. Unlike carborundum, VACNFs did not disrupt cell or tissue integrity, nor did they induce production of hydrogen peroxide, a typical wound response. We show that femtomole to picomole quantities of labeled molecules (fluorescent dyes, small proteins and dextran), ranging from 0.5–500 kDa, can be introduced by VACNFs, and we demonstrate the use of the approach to track delivered probes from their site of introduction on the leaf to distal plant regions. VACNF arrays thus offer an attractive microdelivery method for the introduction of biomolecules and other probes into trees and potentially other types of plants.
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Extracellular electron transfer systems fuel cellulose oxidative degradation

Ninety percent of lignocellulose-degrading fungi contain genes encoding lytic polysaccharide monooxygenases (LPMOs). These enzymes catalyze the initial oxidative cleavage of recalcitrant polysaccharides after activation by an electron donor. Understanding the source of electrons is fundamental to fungal physiology and will also help exploit LPMOs for biomass processing. Using genome data and biochemical methods, we characterized and compared different extracellular electron sources for LPMO: cellobiose dehydrogenase, phenols procured from plant biomass or produced by fungi, and GMC oxidoreductases that regenerate LPMO-reducing diphenols. These data demonstrate that all three electron transfer systems are functional and that their relative importance during cellulose degradation depends on fungal lifestyle. The availability of extracellular electron donors is obligatory to activate fungal oxidative attack on polysaccharides.
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Sex-specific responses of Populus deltoides to Glomus intraradices colonization and Cd pollution

Sex-specific responses of Populus deltoides to Glomus intraradices colonization and Cd pollution | MycorWeb Plant-Microbe Interactions | Scoop.it
The positive effects of arbuscular mycorrhizal fungi (AM) on the survival, growth and physiology of plants under various stress conditions have been widely recognized. However, whether sex-dependent susceptibility to AM colonization exists, which can induce a differential tolerance between the sexes to stress conditions, is still unclear. In this study, we investigated the effects of Glomus intraradices on Cd-stressed males and females of Populus deltoides (spiked with 10 mg Cd per kg dry substrate) in terms of morphology, physiology, biochemistry, ultrastructure, and toxin storage and translocation. Exposure to Cd promoted the colonization by G. intraradices in males, but not in females. Generally, females suffered more impairments than males in response to Cd stress, reflected by leaf symptoms, the extent of lipid peroxidation, and integrity of the cellular ultrastructure, whether they were inoculated or not. Inoculation with G. intraradices alleviated the phytotoxic effects of Cd in females by stimulating antioxidant enzymes, decreasing levels of reactive oxygen species (ROS) and restricting Cd transfer to the shoots. In contrast, these beneficial effects induced by AM were not detected in mycorrhizal males compared to non-mycorrhizal males, based on thiobarbituric acid-reactive substances (TBARS) and cellular ultrastructure. Inoculation with AM promoted Cd accumulation in males but not in females, and caused the sequestration of more toxic Cd in the root systems in both sexes. Therefore, our results suggest that inoculated males of P. deltoides are suitable candidates for phytostabilization in Cd-polluted soils, due to their higher accumulation ability and greater tolerance relative to inoculated females.

Via Jean-Michel Ané
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Jean-Michel Ané's curator insight, May 1, 11:24 PM

Crazy...

Marcus Jansen's curator insight, May 2, 3:32 AM
Plant interactions with fungi drive plant phenotypes.
Jessie Uehling's curator insight, May 2, 9:17 AM
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Nematode-trapping fungi and fungus-associated bacteria interactions: The role of bacterial diketopiperazines and biofilms on Arthrobotrys oligospora surface in hyphal morphogenesis - Li - 2016 - En...

In soil, nematode-trapping fungi and bacteria often share microhabitats and interact with each other, but effects of fungus-associated bacteria on its trap formation are underestimated. We have ascertained the presence of Stenotrophomonas and Rhizobium genera associated with A. oligospora GJ-1. After A. oligospora GJ-1 without associated bacteria (cured Arthrobotrys) was co-cultivated with Stenotrophomonas and its supernatant extract, microscopic study of hyphae from co-cultivation indicated that bacterial biofilm formation on hyphae was related to trap formation in fungi and Stenotrophomonas supernatant extract. Four diketopiperazines (DKPs) were purified from Stenotrophomonas supernatant extract that could not induce traps in the cured Arthrobotrys. When cured Arthrobotrys was cultured with Stenotrophomonas and one of DKPs, polar attachment, bacterial biofilms on hyphae and trap formation in fungi were observed. After cured Arthrobotrys with bacterial biofilms was consecutively transferred several times on nutrient poor medium, trap formation disappeared with the disappearance of bacterial biofilms on hyphae. DKPs could facilitate chemotaxis of Stenotrophomonas towards fungal extract which was suggested to contribute to bacterial biofilms on hyphae. Furthermore, when cured Arthrobotrys was cultured with Stenotrophomonas and DKPs in soil, trap formation in fungi and bacterial biofilms on hyphae were also observed, and the fungal activity against nematode was enhanced. This article is protected by copyright. All rights reserved.

Via Ryohei Thomas Nakano, Stéphane Hacquard
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Mycorrhizal and saprotrophic fungal guilds compete for the same organic substrates but affect decomposition differently

Mycorrhizal and saprotrophic fungal guilds compete for the same organic substrates but affect decomposition differently | MycorWeb Plant-Microbe Interactions | Scoop.it
Communities of litter saprotrophic and root-associated fungi are vertically separated within boreal forest soil profiles. It is unclear whether this depth partitioning is maintained exclusively by substrate-mediated niche partitioning (i.e. distinct fundamental niches), or by competition for space and resources (i.e. distinct realised niches). Improved understanding of the mechanisms driving spatial partitioning of these fungal guilds is critical, as they modulate carbon and nutrient cycling in different ways. Under field settings, we tested the effects of substrate quality and the local fungal species pool at various depths in determining the potential of saprotrophic and mycorrhizal fungi to colonize and exploit organic matter. Natural substrates of three qualities – fresh or partly decomposed litter or humus – were incubated in the corresponding organic layers in a boreal forest soil profile in a fully factorial design. After one and two growing seasons, fungal community composition in the substrates was determined by 454-pyrosequencing and decomposition was analysed. Fungal community development during the course of the experiment was determined to similar degrees by vertical location of the substrates (24% of explained variation) and by substrate quality (20%), indicating that interference competition is a strong additional driver of the substrate-dependent depth partitioning of fungal guilds in the system. During the first growing season, litter substrates decomposed slower when colonized by root-associated communities than when colonized by communities of litter saprotrophs, whereas humus was only slightly decomposed by both fungal guilds. During the second season, however, certain basidiomycetes from both guilds were particularly efficient in localizing and exploiting their native organic substrates although displaced in the vertical profile, validating that fungal community composition, rather than microclimatic factors, were responsible for observed depth-related differences in decomposer activities during the first season. In conclusion, our results suggest that saprotrophic and root-associated fungal guilds have overlapping fundamental niches with respect to colonizing substrates of different qualities, and that their substrate-dependent depth partitioning in soils of ectomycorrhiza-dominated ecosystems is reinforced by interference competition. Through competitive interactions mycorrhizal fungi can thus indirectly regulate litter decomposition rates by restraining activities of more efficient litter saprotrophs.
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Cross-species comparisons of host genetic associations with the microbiome

Cross-species comparisons of host genetic associations with the microbiome | MycorWeb Plant-Microbe Interactions | Scoop.it
Recent studies in human populations and mouse models reveal notable congruences in gut microbial taxa whose abundances are partly regulated by host genotype. Host genes associating with these taxa are related to diet sensing, metabolism, and immunity. These broad patterns are further validated in similar studies of nonmammalian microbiomes. The next generation of genome-wide association studies will expand the size of the data sets and refine the microbial phenotypes to fully capture these intriguing signatures of host-microbiome coevolution.
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The two-speed genomes of filamentous pathogens: waltz with plants

The two-speed genomes of filamentous pathogens: waltz with plants | MycorWeb Plant-Microbe Interactions | Scoop.it
Fungi and oomycetes include deep and diverse lineages of eukaryotic plant pathogens. The last 10 years have seen the sequencing of the genomes of a multitude of species of these so-called filamentous plant pathogens. Already, fundamental concepts have emerged. Filamentous plant pathogen genomes tend to harbor large repertoires of genes encoding virulence effectors that modulate host plant processes. Effector genes are not randomly distributed across the genomes but tend to be associated with compartments enriched in repetitive sequences and transposable elements. These findings have led to the ‘two-speed genome’ model in which filamentous pathogen genomes have a bipartite architecture with gene sparse, repeat rich compartments serving as a cradle for adaptive evolution. Here, we review this concept and discuss how plant pathogens are great model systems to study evolutionary adaptations at multiple time scales. We will also introduce the next phase of research on this topic.

Via Christophe Jacquet
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How does the tree root microbiome assemble? Influence of ectomycorrhizal species on Pinus sylvestris root bacterial communities

How does the tree root microbiome assemble? Influence of ectomycorrhizal species on Pinus sylvestris root bacterial communities | MycorWeb Plant-Microbe Interactions | Scoop.it
Roots take on several key functions for trees such as anchoring, storing of nutrients and foraging for water and inorganic nutrients. This last part is actually mainly assumed by symbiotic ectomycorrhizal (EcM) fungi that associate with the short roots of most trees from boreal and temperate forests. Thanks to their very dense network of hyphae, EcM fungi explore large volumes of soil from which they uptake water and nutrients that they later transfer to the roots of their host tree. In exchange, trees provide EcM fungi with carbohydrates that are transferred to the fungal component of the ectomycorriza, i.e. the symbiotic organ formed by tree roots and fungal mycelium. This particular interface connects tree roots to the surrounding soil and supports intensive nutrient fluxes. Ectomycorrhizae are heavily colonized by complex microbial communities (Timonen et al., 1998; Johansson et al., 2004; Uroz et al., 2013). Up to 20% of the carbon fixed by trees is transferred below ground and is shared with EcM fungi and their associated microbial communities, thus giving them an important role in carbon cycling in forest ecosystems (Högberg et al., 2001). In addition to their participation in tree nutrition, nutrient cycling and soil fertility, EcM fungi and their microbial associates are involved in the protection of their host against pathogens (Barea et al., 2002). Giving the importance of EcM fungi and their microbial associates for the biology of trees and for nutrient cycling in forest soils, it is crucial for the management of forest ecosystems to identify the factors that drive the diversity and structure of tree root microbial communities.
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Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes

Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes | MycorWeb Plant-Microbe Interactions | Scoop.it
Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization—what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that the hologenome concept has always embraced multilevel selection. Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome.
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Fungi use the SakA (HogA) pathway for phytochrome-dependent light
signalling

Fungi use the SakA (HogA) pathway for phytochrome-dependent light<br/>                    signalling | MycorWeb Plant-Microbe Interactions | Scoop.it
Stress-sensing in fungi depends on a signalling cascade comprised of a two-component phosphorylation relay plus a subsequent MAP kinase cascade to trigger gene expression. Besides osmotic or oxidative stress, fungi sense many other environmental factors, one of which is light1,2. Light controls morphogenetic pathways but also the production of secondary metabolites such as penicillin. Here we show that phytochrome-dependent light signalling in Aspergillus nidulans involves the stress-sensing and osmosensing signalling pathway. In a screening for ‘blind’ mutants, the MAP kinase SakA (also known as HogA) was identified by whole-genome sequencing. The phytochrome FphA physically interacted with the histidine-containing phosphotransfer protein YpdA and caused light-dependent phosphorylation of the MAP kinase SakA and its shuttling into nuclei. In the absence of phytochrome, SakA still responded to osmotic stress but not to light. The SakA pathway thus integrates several stress factors and can be considered to be a hub for environmental signals.
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