MycorWeb Plant-Microbe Interactions
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DOE Joint Genome Institute - My submission for the DOE Joint Genome Institute Poetry…

DOE Joint Genome Institute - My submission for the DOE Joint Genome Institute Poetry… | MycorWeb Plant-Microbe Interactions | Scoop.it
ENERGY IN THE TREES

Poplar tree growing fast and tall:
how do your genes make your cell walls?

Enzymes string together sugars into rows,
to make straight fibers you know as cellulose;

Reverse this process during cell wall degradation,
and you get sugars for biofuel creation!

Alas there’s also lignin, an amorphous beast;
lignin linked to cellulose blocks sugar release.

To solve this recalcitrance, the genome holds the key,
let’s make better poplar — for sustainable energy!
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Poem by Kelsey Wood was inspired in part by a talk by Gerald Tuskan (Oak Rigde) at JGI 2014 User's Meeting and is 10 lines long to mark a decade of the Community Science Program.

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Wood decay rates of 13 temperate tree species in relation to wood properties, enzyme activities and organismic diversities

Wood decay rates of 13 temperate tree species in relation to wood properties, enzyme activities and organismic diversities | MycorWeb Plant-Microbe Interactions | Scoop.it
Deadwood decay is an important ecosystem process in forest ecosystems, but the relative contribution of specific wood properties of tree species, activities of wood-degrading enzymes, and decomposer communities such as fungi and insects is unclear. We ask whether wood properties, in particular differences between angiosperms and gymnosperms, and organismic diversity of colonizers contribute to wood decomposition. To test this, we exposed deadwood logs of 13 tree species, covering four gymnosperms and nine angiosperm species, in 30 plots under different forest management in three regions in Germany. After a decomposition time of 6.5 years Carpinus betulus and Fagus sylvatica showed the highest decay rates. We found a positive correlation of decay rate with enzyme activities, chemical wood properties (S, K concentration) and organismic diversity, while, heartwood character, lignin content, extractive concentration and phenol content were negatively correlated with decay rate across all 13 tree species. By applying a multi-model inference approach we found that the activity of the wood-degrading enzymes laccase and endocellulase, beetle diversity, heartwood presence, wood ray height and fungal diversity were the most important predictor variables for wood decay. Although we were not able to identify direct cause and effect relations by our approach, we conclude that enzyme activity and organismic diversity are the main drivers of wood decay rate, which greatly differed among tree species. Maintaining high tree species diversity will therefore result in high structural deadwood diversity in terms of decay rate and decay stage.
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The theory of island biogeography applies to ectomycorrhizal fungi in subalpine tree “islands” at a fine scale

The theory of island biogeography applies to ectomycorrhizal fungi in subalpine tree “islands” at a fine scale | MycorWeb Plant-Microbe Interactions | Scoop.it
The theory of island biogeography, which predicts that species richness is a function of island size and distance from the mainland, is well tested with macro-fauna and flora. Yet, in many ways, microbes are more appropriate for testing this and other ecological theories due to their small size and short generation times that translate to an ease of replication. We used a natural experimental system of isolated “host islands” to test the generality of the theory of island biogeography. Specifically, we tested whether ectomycorrhizal fungal (EMF) richness increased with tree size and decreased with distance from forest in a subalpine basin in Yosemite National Park for two congeneric pine species, Pinus albicaulis and Pinus contorta. We determined EMF richness with next-generation sequencing, measured the size and age of each tree island (n = 40), and calculated geographic distances from each tree to the nearest forest edge. We found that EMF richness increased with island size (as measured by tree volume) and tree age for both pine species and decreased with distance from forest edge for P. albicaulis. Thus, we show the applicability of the theory to microbial symbionts in harsh, dry, and likely non-equilibrium systems. In addition, we found that despite the fact that our tree islands had a mean age of 65 yr, a pioneer community of EMF dominated. We interpret this as evidence that water stress interacts with succession to create a sustained period of early-stage fungi even in mature trees.
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Exploring new horizons

Exploring new horizons | MycorWeb Plant-Microbe Interactions | Scoop.it
Historically, bacteria have been thought of as simple cells whose only aim is to replicate. However, research over the past two decades has revealed that many types of bacteria are able to develop into communities that contain several types of cells, with different cell types performing particular roles (Kuchina et al., 2011). These communities are of interest in scientific fields as diverse as petroleum engineering and bacterial pathogenesis.

Streptomyces were perhaps the first bacteria to be recognized as having a multicellular lifestyle (Waksman and Henrici, 1943). In fact, this lifestyle led to them being classified as fungi when they were first isolated from soil at the beginning of the last century (Hopwood, 2007). This case of mistaken identity stemmed from the fuzzy texture of Streptomyces colonies (see Figure 1A), which resembles many of the fungi we see growing on bread and other natural surfaces (Waksman, 1954).
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Oak protein profile alterations upon root colonization by an ectomycorrhizal fungus

Oak protein profile alterations upon root colonization by an ectomycorrhizal fungus | MycorWeb Plant-Microbe Interactions | Scoop.it
An increased knowledge on the real impacts of ectomycorrhizal symbiosis in forest species is needed to optimize forest sustainable productivity and thus to improve forest services and their capacity to act as carbon sinks. In this study, we investigated the response of an oak species to ectomycorrhizae formation using a proteomics approach complemented by biochemical analysis of carbohydrate levels. Comparative proteome analysis between mycorrhizal and nonmycorrhizal cork oak plants revealed no differences at the foliar level. However, the protein profile of 34 unique oak proteins was altered in the roots. Consistent with the results of the biochemical analysis, the proteome analysis of the mycorrhizal roots suggests a decreasing utilization of sucrose for the metabolic activity of mycorrhizal roots which is consistent with an increased allocation of carbohydrates from the plant to the fungus in order to sustain the symbiosis. In addition, a promotion of protein unfolding mechanisms, attenuation of defense reactions, increased nutrient mobilization from the plant-fungus interface (N and P), as well as cytoskeleton rearrangements and induction of plant cell wall loosening for fungal root accommodation in colonized roots are also suggested by the results. The suggested improvement in root capacity to take up nutrients accompanied by an increase of root biomass without apparent changes in aboveground biomass strongly re-enforces the potential of mycorrhizal inoculation to improve cork oak forest resistance capacity to cope with coming climate change.

Via Christophe Jacquet
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The pangenome of hexaploid bread wheat - Montenegro - The Plant Journal - Wiley Online Library

The pangenome of hexaploid bread wheat - Montenegro - The Plant Journal - Wiley Online Library | MycorWeb Plant-Microbe Interactions | Scoop.it
There is an increasing understanding that gene presence absence variation plays an important role in the heritability of agronomic traits, however there have been relatively few studies on gene presence absence variation in crop species. Hexaploid wheat is one of the most important food crops in the world and intensive breeding has reduced the genetic diversity of elite cultivars. Major efforts have produced draft genome assemblies for the cultivar Chinese Spring, but it is unknown how well this represents the genome diversity found in current modern elite cultivars. In this study we build an improved reference for Chinese Spring and explore gene diversity across 18 wheat cultivars. We predict a pangenome size of 140,500 +/- 102 genes, a core genome of 81,070 +/- 1,631 genes, and an average of 128,656 genes in each cultivar. Functional annotation of the variable gene set suggests that it is enriched for genes that may be associated with important agronomic traits. In addition to gene presence variation, more than 36 million intervarietal SNPs were identified across the pangenome. This study of the wheat pangenome provides insight into elite wheat genome diversity as a basis for genomics based improvement of this important crop. A wheat pangenome Gbrowse is available at http://appliedbioinformatics.com.au/cgi-bin/gb2/gbrowse/WheatPan/, and data is available for download from http://wheatgenome.info/wheat_genome_databases.php.
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Towards a whole-genome sequence for rye (Secale cereale L.)

Towards a whole-genome sequence for rye (Secale cereale L.) | MycorWeb Plant-Microbe Interactions | Scoop.it
We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.
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Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics

Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics | MycorWeb Plant-Microbe Interactions | Scoop.it
Tree disease epidemics are a global problem, impacting food security, biodiversity and national economies. The potential for conservation and breeding in trees is hampered by complex genomes and long lifecycles, with most species lacking genomic resources. The European Ash tree Fraxinus excelsior is being devastated by the fungal pathogen Hymenoscyphus fraxineus, which causes ash dieback disease. Taking this system as an example and utilizing Associative Transcriptomics for the first time in a plant pathology study, we discovered gene sequence and gene expression variants across a genetic diversity panel scored for disease symptoms and identified markers strongly associated with canopy damage in infected trees. Using these markers we predicted phenotypes in a test panel of unrelated trees, successfully identifying individuals with a low level of susceptibility to the disease. Co-expression analysis suggested that pre-priming of defence responses may underlie reduced susceptibility to ash dieback.
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Phylogenetic relatedness explains highly interconnected and nested symbiotic networks of woody plants and arbuscular mycorrhizal fungi in a Chinese subtropical forest

Phylogenetic relatedness explains highly interconnected and nested symbiotic networks of woody plants and arbuscular mycorrhizal fungi in a Chinese subtropical forest | MycorWeb Plant-Microbe Interactions | Scoop.it

Elucidating symbiotic relationships between arbuscular mycorrhizal fungi (AMF) and plants contributes to a better understanding of their reciprocally dependent co-existence and community assembly. However, the main drivers of plant and AMF community assembly remain unclear. In this study, we examined AMF communities from 166 root samples of 17 woody plant species from 10 quadrats in a Chinese subtropical forest using 454 pyrosequencing of 18S rRNA gene to describe symbiotic AMF-plant association. Our results show the woody plant-AMF networks to be highly interconnected and nested, but in anti-modular and anti-specialized manners. The non-random pattern in the woody plant-AMF network was explained by plant and AMF phylogenies, with a tendency for a stronger phylogenetic signal by plant than AMF phylogeny. This study suggests that the phylogenetic niche conservatism in woody plants and their AMF symbionts could contribute to interdependent AMF and plant community assembly in this subtropical forest ecosystem.


Via Jonathan Plett
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Getting at the “what” and the “how” in symbiosis

Getting at the “what” and the “how” in symbiosis | MycorWeb Plant-Microbe Interactions | Scoop.it
Symbioses are ubiquitous and have had a tremendous impact on the evolution of life on the planet. Indeed, endosymbiosis lead to the generation of the first eukaryotic cell and from that point onwards, eukaryotes have interacted with the other domains of life, sometimes forming persistent and necessary relationships that span generations. However, because the majority of hosts and symbionts are not easily manipulated, the intricate details of these symbioses, an understanding of the molecular underpinnings of these interactions, have not been elucidated. It is difficult to ask questions about the details of a host-microbe symbiosis if either member cannot be cultured, genetically manipulated, or even housed in a laboratory. Several technological advances in recent years may address these difficulties, making it easier for researchers to ask mechanistic questions in symbiotic systems.
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Spatial distribution of aquatic marine fungi across the western Arctic and sub-arctic

Spatial distribution of aquatic marine fungi across the western Arctic and sub-arctic | MycorWeb Plant-Microbe Interactions | Scoop.it
Fungi are important parasites of primary producers and nutrient cyclers in aquatic ecosystems. In the Pacific-Arctic domain, fungal parasitism is linked to light intensities and algal stress that can elevate disease incidence on algae and reduce diatom concentrations. Fungi are vastly understudied in the marine realm and knowledge of their function is constrained by the current understanding of fungal distribution and drivers on global scales. To investigate the spatial distribution of fungi in the western Arctic and sub-Arctic, we used high throughput methods to sequence 18S rRNA, cloned and sequenced 28S rRNA and microscopically counted chytrid-infected diatoms. We identified a broad distribution of fungal taxa predominated by Chytridiomycota and Dikarya. Phylogenetic analysis of our Chytridiomycota clones placed Arctic marine fungi sister to the order Lobulomycetales. This clade of fungi predominated in fungal communities under ice with low snowpack. Microscopic examination of fixed seawater and sea ice samples revealed chytrids parasitizing diatoms collected across the Arctic that notably infected 25% of a single diatom species in the Bering Sea. The Pezizomycotina comprised > 95% of eukaryotic sequence reads in Greenland, providing preliminary evidence for osmotrophs being a substitute for algae as the base of food webs.
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Dissection of genomic features and variations of three pathotypes of Puccinia striiformis through whole genome sequencing

Dissection of genomic features and variations of three pathotypes of Puccinia striiformis through whole genome sequencing | MycorWeb Plant-Microbe Interactions | Scoop.it
Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici, is one of the important diseases of wheat. We used NGS technologies to generate a draft genome sequence of two highly virulent (46S 119 and 31) and a least virulent (K) pathotypes of P. striiformis from the Indian subcontinent. We generated ~24,000–32,000 sequence contigs (N50;7.4–9.2 kb), which accounted for ~86X–105X sequence depth coverage with an estimated genome size of these pathotypes ranging from 66.2–70.2 Mb. A genome-wide analysis revealed that pathotype 46S 119 might be highly evolved among the three pathotypes in terms of year of detection and prevalence. SNP analysis revealed that ~47% of the gene sets are affected by nonsynonymous mutations. The extracellular secreted (ES) proteins presumably are well conserved among the three pathotypes, and perhaps purifying selection has an important role in differentiating pathotype 46S 119 from pathotypes K and 31. In the present study, we decoded the genomes of three pathotypes, with 81% of the total annotated genes being successfully assigned functional roles. Besides the identification of secretory genes, genes essential for pathogen-host interactions shall prove this study as a huge genomic resource for the management of this disease using host resistance.
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The impact of third generation genomic technologies on plant genome assembly

The impact of third generation genomic technologies on plant genome assembly | MycorWeb Plant-Microbe Interactions | Scoop.it
Since the introduction of next generation sequencing, plant genome assembly projects do not need to rely on dedicated research facilities or community-wide consortia anymore, even individual research groups can sequence and assemble the genomes they are interested in. However, such assemblies are typically not based on the entire breadth of genomic technologies including genetic and physical maps and their contiguities tend to be low compared to the full-length gold standard reference sequences. Recently emerging third generation genomic technologies like long-read sequencing or optical mapping promise to bridge this quality gap and enable simple and cost-effective solutions for chromosomal-level assemblies.
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Verticillium dahliae manipulates plant immunity by glycoside hydrolase 12 proteins in conjuction with carbohydrate‐binding module 1

Verticillium dahliae manipulates plant immunity by glycoside hydrolase 12 proteins in conjuction with carbohydrate‐binding module 1 | MycorWeb Plant-Microbe Interactions | Scoop.it
Glycoside hydrolase 12 (GH12) proteins act as virulence factors and pathogen-associated molecular patterns (PAMPs) in oomycetes. However, the pathogenic mechanisms of fungal GH12 proteins have not been characterized. In this study, we demonstrated that two of the six GH12 proteins produced by the fungus Verticillium dahliae Vd991, VdEG1 and VdEG3 acted as PAMPs to trigger cell death and PAMP-triggered immunity (PTI) independent of their enzymatic activity in Nicotiana benthamiana. A 63-amino-acid peptide of VdEG3 was sufficient for cell death-inducing activity, but this was not the case for the corresponding peptide of VdEG1. Further study indicated that VdEG1 and VdEG3 trigger PTI in different ways: BAK1 is required for VdEG1- and VdEG3-triggered immunity, while SOBIR1 is specifically required for VdEG1-triggered immunity in N. benthamiana. Unlike oomycetes, which employ RXLR effectors to suppress host immunity, a carbohydrate-binding module family 1 (CBM1) protein domain suppressed GH12 protein-induced cell death. Furthermore, during infection of N. benthamiana and cotton, VdEG1 and VdEG3 acted as PAMPs and virulence factors, respectively indicative of host-dependent molecular functions. These results suggest that VdEG1 and VdEG3 associate differently with BAK1 and SOBIR1 receptor-like kinases to trigger immunity in N. benthamiana, and together with CBM1-containing proteins manipulate plant immunity. This article is protected by copyright. All rights reserved.

Via Christophe Jacquet
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Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees

Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees | MycorWeb Plant-Microbe Interactions | Scoop.it

Background

The plant microbiome represents one of the key determinants of plant health and productivity by providing a plethora of functional capacities such as access to low-abundance nutrients, suppression of phytopathogens, and resistance to biotic and/or abiotic stressors. However, a robust understanding of the structural composition of the bacterial microbiome present in different plant microenvironments and especially the relationship between below-ground and above-ground communities has remained elusive. In this work, we addressed hypotheses regarding microbiome niche differentiation and structural stability of the bacterial communities within different ecological plant niches.


Methods

We sampled the rhizosphere soil, root, stem, and leaf endosphere of field-grown poplar trees (Populus tremula × Populus alba) and applied 16S rRNA amplicon pyrosequencing to unravel the bacterial communities associated with the different plant habitats.


Results

We found that the structural variability of rhizosphere microbiomes in field-grown poplar trees (P. tremula × P. alba) is much lower than that of the endosphere microbiomes. Furthermore, our data not only confirm microbiome niche differentiation reports at the rhizosphere soil–root interface but also clearly show additional fine-tuning and adaptation of the endosphere microbiome in the stem and leaf compartment. Each plant compartment represents an unique ecological niche for the bacterial communities. Finally, we identified the core bacterial microbiome associated with the different ecological niches of Populus.


Conclusions
Understanding the complex host–microbe interactions of Populus could provide the basis for the exploitation of the eukaryote–prokaryote associations in phytoremediation applications, sustainable crop production (bio-energy efficiency), and/or the production of secondary metabolites.

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Unearthing diversity in fungal dark matter

Unearthing diversity in fungal dark matter | MycorWeb Plant-Microbe Interactions | Scoop.it
To be born an orchid is a most unlikely thing. First your parents must be pollinated, which is difficult. Orchids are both rare, and rarely pollinated due to the bizarre and dishonest means by which they go about attracting pollinators. Added to that, orchids often rely on a single species of pollinator to do the job.

Let’s say, however, that your orchid parents do manage to achieve fertilization. Your orchid mother will produce many thousands of tiny dust-like seed, which will be jettisoned into the wind. Unlike most seeds, you have no maternal energy investment to power your germination and first days as a seedling. Instead, you must rely on blind luck to land you within reaching distance of a strand of soil fungus. This fungus is the wet nurse to bring you into the world, invading the seed coat and hooking the young orchid up to a network of fungal strands that pervade the soil. Tapping into this network provides you with the first sips of carbohydrate and nutrient you need in order to build your first green leaf and begin to stand on your own roots. But it is not enough to land near any fungus. Many orchid species require fungal partnership with a specific species of fungus for this to occur at all. Multiplied together, it is a wonder that orchids ever overcome these odds to propagate themselves into the next generation.

The southwest of Western Australia is rightly famous as a global biodiversity hotspot. The area is particularly rich in orchids, and the spider orchids (Caladenia) are some of the most impressive and diverse of the region’s main orchid groups. In 1967, University of Adelaide researcher John Warcup discovered in association with Caladenia a new genus of fungi. Today those fungi are called Serendipita, and although we have known of them for around 60 years, there have been less than a handful of species discovered and described.
Francis Martin's insight:
A nice introduction to orchid mycorrhizal symbiosis with great orchid pics
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Direct conversion of root primordium into shoot meristem relies on timing of stem cell niche development

Direct conversion of root primordium into shoot meristem relies on timing of stem cell niche development | MycorWeb Plant-Microbe Interactions | Scoop.it
To understand how the identity of an organ can be switched, we studied the transformation of lateral root primordia (LRP) into shoot meristems in Arabidopsis root segments. In this system, the cytokinin-induced conversion does not involve the formation of callus-like structures. Detailed analysis showed that the conversion sequence starts with a mitotic pause and is concomitant with the differential expression of regulators of root and shoot development. The conversion requires the presence of apical stem cells and only LRP at stages VI or VII can be switched. It is engaged as soon as cell divisions resume because their position and orientation differ in the converting organ compared to the undisturbed emerging LRP. By alternating auxin and cytokinin treatments, we showed that the root and shoot organogenetic programs are remarkably plastic because the status of the same plant stem cell niche can be reversed repeatedly within a set developmental window. Thus, the networks at play in the meristem of a root can morph in the span of a couple cell division cycles into those of a shoot, and back, through transdifferentiation.

Via Loïc Lepiniec
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Genomic dissection of host–microbe and microbe–microbe interactions for advanced plant breeding

Genomic dissection of host–microbe and microbe–microbe interactions for advanced plant breeding | MycorWeb Plant-Microbe Interactions | Scoop.it
Highlights



Sequencing plants and microbiota has identified mechanisms of communal interactions.


Identification of host traits, responsible for microbial community structure.


Plant microbiota members evolve at multiple speeds and vary in host specificity.


Niche formation is involved in the structuring of the host associated microbiome.


Niche customization for beneficial microbes is an important plant breeding trait.

Agriculture faces many emerging challenges to sustainability, including limited nutrient resources, losses from diseases caused by current and emerging pathogens and environmental degradation. Microorganisms have great importance for plant growth and performance, including the potential to increase yields, nutrient uptake and pathogen resistance. An urgent need is therefore to understand and engineer plants and their associated microbial communities. Recent massive genomic sequencing of host plants and associated microbes offers resources to identify novel mechanisms of communal assembly mediated by the host. For example, host–microbe and microbe–microbe interactions are involved in niche formation, thereby contributing to colonization. By leveraging genomic resources, genetic traits underlying those mechanisms will become important resources to design plants selecting and hosting beneficial microbial communities.

Via Christophe Jacquet, Elsa Ballini
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Genetic and genomic evidence of niche partitioning and adaptive radiation in mountain pine beetle fungal symbionts

Genetic and genomic evidence of niche partitioning and adaptive radiation in mountain pine beetle fungal symbionts | MycorWeb Plant-Microbe Interactions | Scoop.it
Bark beetles form multipartite symbiotic associations with blue stain fungi (Ophiostomatales, Ascomycota). These symbionts play an important role during the beetle's life cycle by providing nutritional supplementation, overcoming tree defenses and modifying host tissues to favor brood development. The maintenance of stable multipartite symbioses with seemingly less competitive symbionts in similar habitats is of fundamental interest to ecology and evolution. We tested the hypothesis that the coexistence of three fungal species associated with the mountain pine beetle is the result of niche partitioning and adaptive radiation using SNP genotyping coupled with genotype-environment association analysis and phenotypic characterization of growth rate under different temperatures. We found that genetic variation and population structure within each species is best explained by distinct spatial and environmental variables. We observed both common (temperature seasonality and the host species) and distinct (drought, cold stress, precipitation) environmental and spatial factors that shaped the genomes of these fungi resulting with contrasting outcomes. Phenotypic intraspecific variations in Grosmannia clavigera and Leptographium longiclavatum, together with high heritability, suggest potential for adaptive selection in these species. By contrast, Ophiostoma montium displayed narrower intraspecific variation but greater tolerance to extreme high temperatures. Our study highlights unique phenotypic and genotypic characteristics in these symbionts that are consistent with our hypothesis. By maintaining this multipartite relationship, the beetles increase the likelihood of obtaining the benefits afforded by the fungi and reduce the risk of being left aposymbiotic. Complementarity among species could facilitate colonization of new habitats and survival under adverse conditions.


Via Steve Marek
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Ecological networks to unravel the routes to horizontal transposon transfers

Ecological networks to unravel the routes to horizontal transposon transfers | MycorWeb Plant-Microbe Interactions | Scoop.it
Transposable elements (TEs) represent the single largest component of numerous eukaryotic genomes, and their activity and dispersal constitute an important force fostering evolutionary innovation. The horizontal transfer of TEs (HTT) between eukaryotic species is a common and widespread phenomenon that has had a profound impact on TE dynamics and, consequently, on the evolutionary trajectory of many species' lineages. However, the mechanisms promoting HTT remain largely unknown. In this article, we argue that network theory combined with functional ecology provides a robust conceptual framework and tools to delineate how complex interactions between diverse organisms may act in synergy to promote HTTs.
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Welcome to Ash tree genomes | The British Ash Tree Genome Project

Welcome to Ash tree genomes | The British Ash Tree Genome Project | MycorWeb Plant-Microbe Interactions | Scoop.it
This website hosts ash genome data to assist scientists in the search for genes that may confer resistance to ash dieback (Hymenoscyphus fraxinea) and the emerald ash borer (Agrilus planipennis).

Scientists at Queen Mary, University of London (QMUL) in Richard Buggs' lab have sequenced the genome of the European ash tree (Fraxinus excelsior), funded by an urgency grant awarded by the Natural Environment Research Council in 2013. The ash genome and associated data have now been published in Nature. The paper is available open access here.

The tree sequenced was the result of self-pollination of a tree growing in woodland in Oxfordshire. The controlled self-pollination of the parent tree was carried out by Dr David Boshier of Oxford University. The offspring from this self-pollination are growing at Paradise Wood in Oxfordshire, owned by the Earth Trust, and managed by Jo Clark. Tissue was collected from one of these trees in January 2013 and DNA was extracted from it by Jasmin Zohren (funded by MSC ITN "Intercrossing") at QMUL. Using flow cytometry, we estimated the 1C genome size of the tree to be 877 Mbp.

Raw DNA sequence data for the British ash genome were generated by Eurofins, and the data was assembled by Lizzy Sollars (funded by MSC ITN "Intercrossing") and Richard Buggs at QMUL, in collaboration with CLCbio, using open access and proprietary software. Assembly and analysis of the genome is being carried out on the QMUL-High Performance Computing MidPlus cluster, and servers at CLCbio.

Since 2014 we have collaborated with The Genome Analysis Centre in Norwich to improve and annotate the genome assembly. Full structural annotations are available for the latest assembly under the "Data" tab.

We are currently sequencing the genomes of 30 other ash species from around the world. Some preliminary data from this as yet unpublished work is available on this website. This work is funded by the LWEC Tree Health and Plant Biosecurity Initiative Phase 2 Grant, BB/L012162/1 funded jointly by a grant from BBSRC, Defra, ESRC, the Forestry Commission, NERC and the Scottish Government.
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Genome Sequence of the Basidiomycete White-Rot Fungus Trametes pubescens FBCC735

Here, we report the genome sequence of the basidiomycete white-rot fungus Trametes pubescens FBCC735, isolated from Finland. The 39.67-Mb genome containing 14,451 gene models is typical among saprobic wood-rotting species.
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New horizons in geomycology

New horizons in geomycology | MycorWeb Plant-Microbe Interactions | Scoop.it
Geomycology can be simply defined as the roles and significance of fungi in processes of relevance to geology, and as such is part of the more general area of geomicrobiology (Gadd, 2010). Rock and mineral bioweathering, metal transformations, mineral formation and cycling of the elements, all of which are involved in mineral soil formation, are the most obvious geomicrobial processes under this heading. In the case of fungi, their additional significance as major decomposers of organic material underlines their important role in the cycling of major elements such as C, H, N, O, P, S, as well all other elements that may be associated with organic matter. The majority of stable elements can be found in living organisms, including metal pollutants, and the release of these in decomposition can result in further interaction with environmental components resulting in mineral formation for example. There are therefore clear connections between organic and inorganic components of geomicrobial processes, and between the aerobic and anaerobic domains of life. This is not always appreciated in geomicrobiology where to some the ‘geo’ prefix is equated with chemolithotrophy and anaerobiosis in certain prokaryotes.

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Influence of nutrient signals and carbon allocation on the expression of phosphate and nitrogen transporter genes in winter wheat (Triticum aestivum L.) roots colonized by arbuscular mycorrhizal fungi

Influence of nutrient signals and carbon allocation on the expression of phosphate and nitrogen transporter genes in winter wheat (Triticum aestivum L.) roots colonized by arbuscular mycorrhizal fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
Arbuscular mycorrhizal (AM) colonization of plant roots causes the down-regulation of expression of phosphate (Pi) or nitrogen (N) transporter genes involved in direct nutrient uptake pathways. The mechanism of this effect remains unknown. In the present study, we sought to determine whether the expression of Pi or N transporter genes in roots of winter wheat colonized by AM fungus responded to (1) Pi or N nutrient signals transferred from the AM extra-radical hyphae, or (2) carbon allocation changes in the AM association. A three-compartment culture system, comprising a root compartment (RC), a root and AM hyphae compartment (RHC), and an AM hyphae compartment (HC), was used to test whether the expression of Pi or N transporter genes responded to nutrients (Pi, NH4+ and NO3-) added only to the HC. Different AM inoculation density treatments (roots were inoculated with 0, 20, 50 and 200 g AM inoculum) and light regime treatments (6 hours light and 18 hours light) were established to test the effects of carbon allocation on the expression of Pi or N transporter genes in wheat roots. The expression of two Pi transporter genes (TaPT4 and TaPHT1.2), five nitrate transporter genes (TaNRT1.1, TaNRT1.2, TaNRT2.1, TaNRT2.2, and TaNRT2.3), and an ammonium transporter gene (TaAMT1.2) was quantified using real-time polymerase chain reaction. The expression of TaPT4, TaNRT2.2, and TaAMT1.2 was down-regulated by AM colonization only when roots of host plants received Pi or N nutrient signals. However, the expression of TaPHT1.2, TaNRT2.1, and TaNRT2.3 was down-regulated by AM colonization, regardless of whether there was nutrient transfer from AM hyphae. The expression of TaNRT1.2 was also down-regulated by AM colonization even when there was no nutrient transfer from AM hyphae. The present study showed that an increase in carbon consumption by the AM fungi did not necessarily result in greater down-regulation of expression of Pi or N transporter genes.
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Jean-Michel Ané's curator insight, February 22, 9:37 AM

Great paper. I love it.

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Identification of effector-like proteins in Trichoderma spp. and role of a hydrophobin in the plant-fungus interaction and mycoparasitism

Identification of effector-like proteins in Trichoderma spp. and role of a hydrophobin in the plant-fungus interaction and mycoparasitism | MycorWeb Plant-Microbe Interactions | Scoop.it

Background. Trichoderma spp. can establish beneficial interactions with plants by promoting plant growth and defense systems, as well as, antagonizing fungal phytopathogens in mycoparasitic interactions. Such interactions depend on signal exchange between both participants and can be mediated by effector proteins that alter the host cell structure and function, allowing the establishment of the relationship. The main purpose of this work was to identify, using computational methods, candidates of effector proteins from T. virens, T. atroviride and T. reesei, validate the expression of some of the genes during a beneficial interaction and mycoparasitism and to define the biological function for one of them.

Results. We defined a catalogue of putative effector proteins from T. virens, T. atroviride and T. reesei. We further validated the expression of 16 genes encoding putative effector proteins from T. virens and T. atroviride during the interaction with the plant Arabidopsis thaliana, and with two anastomosis groups of the phytopathogenic fungus Rhizoctonia solani. We found genes which transcript levels are modified in response to the presence of both plant fungi, as well as genes that respond only to either a plant or a fungal host. Further, we show that overexpression of the gene tvhydii1, a Class II hydrophobin family member, enhances the antagonistic activity of T. virens against R. solani AG2. Further, deletion of tvhydii1 results in reduced colonization of plant roots, while its overexpression increases it.


Conclusions. Our results show that Trichoderma is able to respond in different ways to the presence of a plant or a fungal host, and it can even distinguish between different strains of fungi of a given species. The putative effector proteins identified here may play roles in preventing perception of the fungus by its hosts, favoring host colonization or protecting it from the host’s defense response. Finally, the novel effector protein TVHYDII1 plays a role in plant root colonization by T, virens, and participates in its antagonistic activity against R. solani.

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Verticillium dahliae manipulates plant immunity by glycoside hydrolase 12 proteins in conjuction with carbohydrate-binding module 1

Verticillium dahliae manipulates plant immunity by glycoside hydrolase 12 proteins in conjuction with carbohydrate-binding module 1 | MycorWeb Plant-Microbe Interactions | Scoop.it
Glycoside hydrolase 12 (GH12) proteins act as virulence factors and pathogen-associated molecular patterns (PAMPs) in oomycetes. However, the pathogenic mechanisms of fungal GH12 proteins have not been characterized. In this study, we demonstrated that two of the six GH12 proteins produced by the fungus Verticillium dahliae Vd991, VdEG1 and VdEG3 acted as PAMPs to trigger cell death and PAMP-triggered immunity (PTI) independent of their enzymatic activity in Nicotiana benthamiana. A 63-amino-acid peptide of VdEG3 was sufficient for cell death-inducing activity, but this was not the case for the corresponding peptide of VdEG1. Further study indicated that VdEG1 and VdEG3 trigger PTI in different ways: BAK1 is required for VdEG1- and VdEG3-triggered immunity, while SOBIR1 is specifically required for VdEG1-triggered immunity in N. benthamiana. Unlike oomycetes, which employ RXLR effectors to suppress host immunity, a carbohydrate-binding module family 1 (CBM1) protein domain suppressed GH12 protein-induced cell death. Furthermore, during infection of N. benthamiana and cotton, VdEG1 and VdEG3 acted as PAMPs and virulence factors, respectively indicative of host-dependent molecular functions. These results suggest that VdEG1 and VdEG3 associate differently with BAK1 and SOBIR1 receptor-like kinases to trigger immunity in N. benthamiana, and together with CBM1-containing proteins manipulate plant immunity. This article is protected by copyright. All rights reserved.
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