Fungal|Oomycete Biology
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New Phytologist: Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the aboveground vegetation

New Phytologist: Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the aboveground vegetation | Fungal|Oomycete Biology | Scoop.it

Soil conditions and microclimate are important determinants of the fine-scale distribution of plant species in the Arctic, creating locally heterogeneous vegetation. We hypothesize that root-associated fungal (RAF) communities respond to the same fine-scale environmental gradients as the aboveground vegetation, creating a coherent pattern between aboveground vegetation and RAF.
We explored how RAF communities of the ectomycorrhizal (ECM) plant Bistorta vivipara and aboveground vegetation structure of arctic plants were affected by biotic and abiotic variables at 0.3–3.0-m scales. RAF communities were determined using pyrosequencing. Composition and spatial structure of RAF and aboveground vegetation in relation to collected biotic and abiotic variables were analysed by ordination and semi-variance analyses.
The vegetation was spatially structured along soil C and N gradients, whereas RAF lacked significant spatial structure. A weak relationship between RAF community composition and the cover of two ECM plants, B. vivipara and S. polaris, was found, and RAF richness increased with host root length and root weight.
Results suggest that the fine-scale spatial structure of RAF communities of B. vivipara and the aboveground vegetation are driven by different factors. At fine spatial scales, neighbouring ECM plants may affect RAF community composition, whereas soil nutrients gradients structure the vegetation.


Via Stéphane Hacquard
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Fungal|Oomycete Biology
Various topics on fungal and oomycete biology
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Why did filamentous plant pathogens evolve the potential to secrete hundreds of effectors to enable disease? - Thordal-Christensen - 2018 - Molecular Plant Pathology -

Why did filamentous plant pathogens evolve the potential to secrete hundreds of effectors to enable disease? - Thordal-Christensen - 2018 - Molecular Plant Pathology - | Fungal|Oomycete Biology | Scoop.it
During the past decade, many genomes have been sequenced from fungal and oomycete pathogens that interact biotrophically with plants, i.e. they thrive at least initially on living plant tissue. This has revealed genomes that often encode hundreds of proteins predicted to be secreted on the basis of N-terminal signal peptides. Most of these proteins are unique or found only within restricted phylogenetic clades (Franceschetti et al., 2017). They are predicted to be ‘effectors’, i.e. proteins which, in some way, contribute to the virulence of the pathogen (see below). The fact that these filamentous microbes have hundreds of candidate effector genes is in stark contrast with bacterial pathogens, which typically have an order of magnitude fewer effector candidate genes. Although most of these hundreds of effectors currently lack evidence for significant roles in virulence, it is still striking that many of them appear to contribute measurably to virulence and that several of them seem to physically interact with numerous host proteins. In this Opinion Piece, we discuss these observations and attempt to address the apparent need for hundreds of effector candidate genes in these species. We suggest that this requirement reflects, in part, the need for effectors to target defence-unrelated susceptibility components. Many of these, in turn, may be monitored (‘guarded’) by resistance-triggering immune sensors. Potentially, pathogen success depends on additional sets of effectors dedicated to suppress this kind of surveillance.
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The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome | Microbiome | Full Text

The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome | Microbiome | Full Text | Fungal|Oomycete Biology | Scoop.it
Microorganisms serve important functions within numerous eukaryotic host organisms. An understanding of the variation in the plant niche-level microbiome, from rhizosphere soils to plant canopies, is imperative to gain a better understanding of how both the structural and functional processes of microbiomes impact the health of the overall plant holobiome. Using Populus trees as a model ecosystem, we characterized the archaeal/bacterial and fungal microbiome across 30 different tissue-level niches within replicated Populus deltoides and hybrid Populus trichocarpa × deltoides individuals using 16S and ITS2 rRNA gene analyses. Our analyses indicate that archaeal/bacterial and fungal microbiomes varied primarily across broader plant habitat classes (leaves, stems, roots, soils) regardless of plant genotype, except for fungal communities within leaf niches, which were greatly impacted by the host genotype. Differences between tree genotypes are evident in the elevated presence of two potential fungal pathogens, Marssonina brunnea and Septoria sp., on hybrid P. trichocarpa × deltoides trees which may in turn be contributing to divergence in overall microbiome composition. Archaeal/bacterial diversity increased from leaves, to stem, to root, and to soil habitats, whereas fungal diversity was the greatest in stems and soils. This study provides a holistic understanding of microbiome structure within a bioenergy relevant plant host, one of the most complete niche-level analyses of any plant. As such, it constitutes a detailed atlas or map for further hypothesis testing on the significance of individual microbial taxa within specific niches and habitats of Populus and a baseline for comparisons to other plant species.
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A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci

A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci | Fungal|Oomycete Biology | Scoop.it
Pleurotus tuoliensis (Bailinggu) is a commercially cultivated mushroom species with an increasing popularity in China and other Asian countries. Commercial profits are now low, mainly due to a low yield, long cultivation period and sensitivity to diseases. Breeding efforts are thus required to improve agronomical important traits. Developing saturated genetic linkage and physical maps is a start for applying genetic and molecular approaches to accelerate the precise breeding programs. Here we present a genetic linkage map for P. tuoliensis constructed by using 115 haploid monokaryons derived from a hybrid strain H6. One thousand one hundred and eighty-two SNP markers developed by 2b–RAD (type IIB restriction-site associated DNA) approach were mapped to 12 linkage groups. The map covers 1073 cM with an average marker spacing of 1.0 cM. The genome of P. tuoliensis was de novo sequenced as 40.8 Mb and consisted of 500 scaffolds (>500 bp), which showed a high level of colinearity to the genome of P. eryngii var. eryngii. A total of 97.4% SNP markers (1151) were physically localized on 78 scaffolds, and the physical length of these anchored scaffolds were 33.9 Mb representing 83.1% of the whole genome. Mating type loci A and B were mapped on separate linkage groups and identified physically on the assembled genomes. Five putative pheromone receptors and two putative pheromone precursors were identified for the mating type B locus. This study reported a first genetic linkage map integrated with physical mapping of the de novo sequenced genome and the mating type loci of an important cultivated mushroom in China, P. tuoliensis. The de novo sequenced and annotated genome, assembled using a 2b–RAD generated linkage map, provides a basis for marker-assisted breeding of this economic important mushroom species.

Via Francis Martin
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Pathogen recognition in compatible plant-microbe interactions

Pathogen recognition in compatible plant-microbe interactions | Fungal|Oomycete Biology | Scoop.it
Microbial infections in plant leaves remain a major challenge in agriculture. Hence an understanding of disease mechanisms at the molecular level is of paramount importance for identifying possible intervention points for their control. Whole-transcriptome changes during early disease stages in susceptible plant species are less well-documented than those of resistant ones. This study focuses on the differential transcriptional changes at 24 hours post inoculation (hpi) in tomato leaflets affected by three pathogens: (1) Phytophthora infestans, (2) Botrytis cinerea, and (3) Oidium neolycopersici. Grey mould (B. cinerea) was the disease that had progressed the most by 24 hpi, both in terms of visible symptoms as well as differential gene expression. By means of RNA-seq, we identified 50 differentially expressed tomato genes specifically induced by B. cinerea infection and 18 specifically induced by P. infestans infection at 24 hpi. Additionally, a set of 63 genes were differentially expressed during all three diseases when compared by a Bayesian approach to their respective mock infections. And Gene expression patterns were found to also depend on the inoculation technique. These findings suggest a specific and distinct transcriptional response in plant leaf tissue in reaction to B. cinerea and P. infestans invasion at 24 hpi, indicating that plants may recognize the attacking pathogen.

Via Jonathan Plett, Jessie Uehling
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Lifestyle, gene gain and loss, and transcriptional remodeling cause divergence in the transcriptomes of Phytophthora infestans and Pythium ultimum during potato tuber colonization

Lifestyle, gene gain and loss, and transcriptional remodeling cause divergence in the transcriptomes of Phytophthora infestans and Pythium ultimum during potato tuber colonization | Fungal|Oomycete Biology | Scoop.it
How pathogen genomes evolve to support distinct lifestyles is not well-understood. The oomycete Phytophthora infestans, the potato blight agent, is a largely biotrophic pathogen that feeds from living host cells, which become necrotic only late in infection. The related oomycete Pythium ultimum grows saprophytically in soil and as a necrotroph in plants, causing massive tissue destruction. To learn what distinguishes their lifestyles, we compared their gene contents and expression patterns in media and a shared host, potato tuber. Genes related to pathogenesis varied in temporal expression pattern, mRNA level, and family size between the species. A family’s aggregate expression during infection was not proportional to size due to transcriptional remodeling and pseudogenization. Ph. infestans had more stage-specific genes, while Py. ultimum tended towards more constitutive expression. Ph. infestans expressed more genes encoding secreted cell wall-degrading enzymes, but other categories such as secreted proteases and ABC transporters had higher transcript levels in Py. ultimum. Species-specific genes were identified including new Pythium genes, perforins, which may disrupt plant membranes. Genome-wide ortholog analyses identified substantial diversified expression, which correlated with sequence divergence. Pseudogenization was associated with gene family expansion, especially in gene clusters. This first large-scale analysis of transcriptional divergence within oomycetes revealed major shifts in genome composition and expression, including subfunctionalization within gene families. Biotrophy and necrotrophy seem determined by species-specific genes and the varied expression of shared pathogenicity factors, which may be useful targets for crop protection.
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Frontiers | Interactions of Root-Feeding Insects with Fungal and Oomycete Plant Pathogens | Plant Science

Soilborne fungal and oomycete pathogens are the causal agents of several important plant diseases. Infection frequently co-occurs with herbivory by root-feeding insects, facilitating tripartite interactions that modify plant performance and mortality. In an agricultural context, interactions between pathogens, herbivores and plants can have important consequences for yield protection. However, belowground interactions are inherently difficult to observe and are often overlooked. Here, we review the impact of direct and indirect interactions between root-associated insects, fungi, and oomycetes on the development of plant disease. We explore the relationship between insect feeding injury and pathogen infection, as well as the role of insects as vectors of fungal and oomycete pathogens. Synergistic interactions between insects and phytopathogens may be important in weed suppression, and we highlight several promising candidates for biocontrol. Bridging the gap between entomological and pathological research is a critical step in understanding how interactions between insects and microorganisms modify the community structure of the rhizosphere, and how this impacts plant functioning. Furthermore, the identification of belowground interactions is required to develop effective pest monitoring and management strategies.

Via Philip Carella, Steve Marek
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PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives - New Phytologist

PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives - New Phytologist | Fungal|Oomycete Biology | Scoop.it
Second-generation, high-throughput sequencing methods have greatly improved our understanding of the ecology of soil microorganisms, yet the short barcodes (< 500 bp) provide limited taxonomic and phylogenetic information for species discrimination and taxonomic assignment.
Here, we utilized the third-generation Pacific Biosciences (PacBio) RSII and Sequel instruments to evaluate the suitability of full-length internal transcribed spacer (ITS) barcodes and longer rRNA gene amplicons for metabarcoding Fungi, Oomycetes and other eukaryotes in soil samples.
Metabarcoding revealed multiple errors and biases: Taq polymerase substitution errors and mis-incorporating indels in sequencing homopolymers constitute major errors; sequence length biases occur during PCR, library preparation, loading to the sequencing instrument and quality filtering; primer–template mismatches bias the taxonomic profile when using regular and highly degenerate primers.
The RSII and Sequel platforms enable the sequencing of amplicons up to 3000 bp, but the sequence quality remains slightly inferior to Illumina sequencing especially in longer amplicons. The full ITS barcode and flanking rRNA small subunit gene greatly improve taxonomic identification at the species and phylum levels, respectively. We conclude that PacBio sequencing provides a viable alternative for metabarcoding of organisms that are of relatively low diversity, require > 500-bp barcode for reliable identification or when phylogenetic approaches are intended.

Via Ronny Kellner
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Phylogenomic analysis supports multiple instances of polyphyly in the oomycete peronosporalean lineage

Phylogenomic analysis supports multiple instances of polyphyly in the oomycete peronosporalean lineage | Fungal|Oomycete Biology | Scoop.it
The study of biological diversification of oomycetes has been a difficult task for more than a century. Pioneer researchers used morphological characters to describe this heterogeneous group, and physiological and genetic tools expanded knowledge of these microorganisms. However, research on oomycete diversification is limited by conflicting phylogenies. Using whole genomic data from 17 oomycete taxa, we obtained a dataset of 277 core orthologous genes shared among these genomes. Analyses of this dataset resulted in highly congruent and strongly supported estimates of oomycete phylogeny when we used concatenated maximum likelihood and coalescent-based methods; the one important exception was the position of Albugo. Our results supported the position of Phytopythium vexans (formerly in Pythium clade K) as a sister clade to the Phytophthora-Hyaloperonospora clade. The remaining clades comprising Pythium sensu lato formed two monophyletic groups. One group was composed of three taxa that correspond to Pythium clades A, B and C, and the other group contained taxa representing clades F, G and I, in agreement with previous Pythium phylogenies. However, the group containing Pythium clades F, G and I was placed as sister to the Phytophthora-Hyaloperonospora-Phytopythium clade, thus confirming the lack of monophyly of Pythium sensu lato. Multispecies coalescent methods revealed that the white blister rust, Albugo laibachii, could not be placed with a high degree of confidence. Our analyses show that genomic data can resolve the oomycete phylogeny and provide a phylogenetic framework to study the evolution of oomycete lifestyles.
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Transcriptomic and metabolomic analyses of cucumber fruit peels reveal a developmental increase in terpenoid glycosides associated with age-related resistance to Phytophthora capsici

Transcriptomic and metabolomic analyses of cucumber fruit peels reveal a developmental increase in terpenoid glycosides associated with age-related resistance to Phytophthora capsici | Fungal|Oomycete Biology | Scoop.it

The oomycete, Phytophthora capsici, infects cucumber (Cucumis sativus L.) fruit. An age-related resistance (ARR) to this pathogen was previously observed in fruit of cultivar ‘Vlaspik’ and shown to be associated with the peel. Young fruits are highly susceptible, but develop resistance at ~10–12 days post pollination (dpp). Peels from resistant (16 dpp) versus susceptible (8 dpp) age fruit are enriched with genes associated with defense, and methanolic extracts from resistant age peels inhibit pathogen growth. Here we compared developing fruits from ‘Vlaspik’ with those of ‘Gy14’, a line that does not exhibit ARR. Transcriptomic analysis of peels of the two lines at 8 and 16 dpp identified 80 genes that were developmentally upregulated in resistant ‘Vlaspik’ 16 dpp versus 8 dpp, but not in susceptible ‘Gy14’ at 16 dpp. A large number of these genes are annotated to be associated with defense and/or specialized metabolism, including four putative resistance (R) genes, and numerous genes involved in flavonoid and terpenoid synthesis and decoration. Untargeted metabolomic analysis was performed on extracts from 8 and 16 dpp ‘Vlaspik’ and ‘Gy14’ fruit peels using Ultra-Performance Liquid Chromatography and Quadrupole Time-of-Flight Mass Spectrometry. Multivariate analysis of the metabolomes identified 113 ions uniquely abundant in resistant ‘Vlaspik’ 16 dpp peel extracts. The most abundant compounds in this group had relative mass defects consistent with terpenoid glycosides. Two of the three most abundant ions were annotated as glycosylated nor-terpenoid esters. Together, these analyses reveal potential mechanisms by which ARR to P. capsici may be conferred.

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Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria

Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria | Fungal|Oomycete Biology | Scoop.it
BACKGROUND
Among the extensive cortège of plant-associated microorganisms (the so-called plant microbiota), mutualistic fungal and bacterial symbionts are striking examples of soil microorganisms that have successfully coevolved with their hosts since plants adapted to terrestrial ecosystems. They promote plant growth by facilitating the acquisition of scarce nutrients. In these associations, plant root colonization requires complex molecular cross-talk between symbiotic partners to activate a variety of host developmental pathways and specialized symbiotic tissues and organs. Despite the evolutionary distances that separate mycorrhizal and nitrogen-fixing symbioses, recent research has identified certain highly conserved features associated with early stages of root colonization. We focus on recent and emerging areas of investigation concerning these major mutualistic symbioses and discuss some of the molecular pathways and cellular mechanisms involved in their evolution and development.
ADVANCES
Phylogenomic analyses and divergence time estimates based on symbiotic plant fossils are shedding light on the evolution of mutualistic symbioses. The earliest land plants [~407 million years ago (Ma)] were associated with fungi producing mycorrhiza-like intracellular structures similar to extant symbioses involving Glomeromycotina and Mucoromycotina. Arbuscular mycorrhizal endosymbioses then diversified by the Late Carboniferous. Pinaceae species from the Late Jurassic and Early Cretaceous (~180 Ma) formed the first ectomycorrhizal associations involving Dikarya. More recently, certain angiosperms evolved a “predisposition” for the evolution of nitrogen-fixing root nodule symbioses (~100 Ma) with bacteria.

A conserved core module of the “common symbiotic signaling pathway” (CSSP) is shared by all host plants that establish endosymbioses, including arbuscular mycorrhizal, rhizobial, and actinorhizal associations. This striking conservation among widely divergent host species underlines the shared evolutionary origin for this ancient symbiotic signaling pathway. Furthermore, chitin-based signaling molecules secreted by both arbuscular mycorrhizal fungi and rhizobia activate the host CSSP after perception by related receptor-like kinases. Downstream signal transduction pathways then lead to the apoplastic intracellular infection modes that characterize the majority of these associations and, finally, to the coordinated development of sophisticated bidirectional symbiotic interfaces found in both arbuscules and nitrogen-fixing nodules. A common feature of all these mutualistic associations is phytohormone-associated modifications of root development, which lead to an increase in potential colonization sites as well as major structural and functional changes to the root during the establishment of symbiotic tissues.
OUTLOOK
Although we are at last beginning to understand how mutualistic microorganisms communicate with plants, how associated root developmental pathways are modulated, and how plant immune responses are successfully circumvented, many important questions remain. For example, little is currently known about more primitive modes of intercellular apoplastic colonization, whether for ectomycorrhizal fungi or for certain nitrogen-fixing symbioses. Neither do we know whether the CSSP has a key role in ectomycorrhizal associations, nor how host plants distinguish between structurally similar chitin-based “symbiotic” and “pathogenic” microbial signals. Answering these questions should contribute to our understanding of the underlying mechanisms that govern the relationships between plants and their entire microbiota. On a broader level, improved understanding of how environmental and genetic cues, together with plant metabolism, modulate microbial colonization will be crucial for the future exploitation of the microbiota for the benefit of sustainable plant growth.

Via Steve Marek
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Analysis of microsatellites from the transcriptome of downy mildew pathogens and their application for characterization of Pseudoperonospora populations

Analysis of microsatellites from the transcriptome of downy mildew pathogens and their application for characterization of Pseudoperonospora populations | Fungal|Oomycete Biology | Scoop.it
Downy mildew pathogens affect several economically important crops worldwide but, due to their obligate nature, few genetic resources are available for genomic and population analyses. Draft genomes for emergent downy mildew pathogens such as the oomycete Pseudoperonospora cubensis, causal agent of cucurbit downy mildew, have been published and can be used to perform comparative genomic analysis and develop tools such as microsatellites to characterize pathogen population structure. We used bioinformatics to identify 2,738 microsatellites in the P. cubensis predicted transcriptome and evaluate them for transferability to the hop downy mildew pathogen, Pseudoperonospora humuli, since no draft genome is available for this species. We also compared the microsatellite repertoire of P. cubensis to that of the model organism Hyaloperonospora arabidopsidis, which causes downy mildew in Arabidopsis. Although trends in frequency of motif-type were similar, the percentage of SSRs identified from P. cubensis transcripts differed significantly from H. arabidopsidis. The majority of a subset of microsatellites selected for laboratory validation (92%) produced a product in P. cubensis isolates, and 83 microsatellites demonstrated transferability to P. humuli. Eleven microsatellites were found to be polymorphic and consistently amplified in P. cubensis isolates. Analysis of Pseudoperonospora isolates from diverse hosts and locations revealed higher diversity in P. cubensis compared to P. humuli isolates. These microsatellites will be useful in efforts to better understand relationships within Pseudoperonospora species and P. cubensis on a population level.
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Ericaceous plant–fungus network in a harsh alpine–subalpine environment

Ericaceous plant–fungus network in a harsh alpine–subalpine environment | Fungal|Oomycete Biology | 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 data set, 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 association 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.

Via Francis Martin
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Developing educational resources for population genetics in R: an open and collaborative approach

Developing educational resources for population genetics in R: an open and collaborative approach | Fungal|Oomycete Biology | Scoop.it
The R computing and statistical language community has developed a myriad of resources for conducting populations genetic analyses. However, resources for learning how to carry out population genetic analyses in R are scattered and often incomplete, which can make acquiring this skill unnecessarily difficult and time-consuming. To address this gap, we developed an online community resource with guidance and working demonstrations for conducting population genetic analyses in R. The resource is freely available at http://popgen.nescent.org, and includes material for both novices and advanced users of R for population genetics. To facilitate continued maintenance and growth of this resource, we developed a toolchain, process, and conventions designed to (1) minimize financial and labor costs of upkeep; (2) to provide a low barrier to contribution; and (3) to ensure strong quality assurance. The toolchain includes automatic integration testing of every change and rebuilding of the website when new vignettes or edits are accepted. The process and conventions largely follow a common, distributed version control-based contribution workflow, which is used to provide and manage open peer review by designated website editors. The online resources include detailed documentation of this process, including video tutorials. We invite the community of population geneticists working in R to contribute to this resource, whether for a new use-case of their own, or as one of the vignettes from the “wish list” we maintain, or by improving existing vignettes.
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This is a great resource! Indirectly related to the focus on this scoop.it, but quite valuable for those digging into the population genetics of plant associated fungi and oomycetes!
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Ericoid plant species and Pinus sylvestris shape fungal communities in their roots and surrounding soil

Ericoid plant species and Pinus sylvestris shape fungal communities in their roots and surrounding soil | Fungal|Oomycete Biology | Scoop.it

Root-colonizing fungi can form mycorrhizal or endophytic associations with plant roots, the type of association depending on the host. We investigated the differences and similarities of the fungal communities of three boreal ericoid plants and one coniferous tree, and identified the community structure of fungi utilizing photosynthates from the plants studied. The fungal communities of roots and soils of Vaccinium myrtillus, Vaccinium vitis-idaea, Calluna vulgaris and Pinus sylvestris were studied in an 18-month-long experiment where the plants were grown individually in natural substrate. Photosynthates utilizing fungi were detected with DNA stable-isotope probing using 13CO2 (13C-DNA-SIP). The results indicated that the plants studied provide different ecological niches preferred by different fungal species. Those fungi which dominated the community in washed roots had also the highest 13C-uptake. In addition, a common root endophyte without confirmed mycorrhizal status also obtained 13C from all the plants, indicating close plant-association of this fungal species. We detect several fungal species inhabiting the roots of both ericoid mycorrhizal and ectomycorrhizal plants. Our results highlight that the ecological role of co-occurrence of fungi with different life styles (e.g. mycorrhizal or endophytic) in plant root systems should be further investigated.


Via Petr Baldrian
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Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes

Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes | Fungal|Oomycete Biology | Scoop.it

Most studies of bacterial motility have examined small-scale (micrometer–centimeter) cell dispersal in monocultures. However, bacteria live in multispecies communities, where interactions with other microbes may inhibit or facilitate dispersal. Here, we demonstrate that motile bacteria in cheese rind microbiomes use physical networks created by filamentous fungi for dispersal, and that these interactions can shape microbial community structure. Serratia proteamaculans and other motile cheese rind bacteria disperse on fungal networks by swimming in the liquid layers formed on fungal hyphae. RNA-sequencing, transposon mutagenesis, and comparative genomics identify potential genetic mechanisms, including flagella-mediated motility, that control bacterial dispersal on hyphae. By manipulating fungal networks in experimental communities, we demonstrate that fungal-mediated bacterial dispersal can shift cheese rind microbiome composition by promoting the growth of motile over non-motile community members. Our single-cell to whole-community systems approach highlights the interactive dynamics of bacterial motility in multispecies microbiomes.


Via Stéphane Hacquard
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Molecular tools for gene manipulation in filamentous fungi - App. Microbiology and Biotechnology

Molecular tools for gene manipulation in filamentous fungi - App. Microbiology and Biotechnology | Fungal|Oomycete Biology | Scoop.it
Functional genomics of filamentous fungi has gradually uncovered gene information for constructing ‘cell factories’ and controlling pathogens. Available gene manipulation methods of filamentous fungi include random integration methods, gene targeting technology, gene editing with artificial nucleases and RNA technology. This review describes random gene integration constructed by restriction enzyme-mediated integration (REMI); Agrobacterium-mediated transformation (AMT); transposon-arrayed gene knockout (TAGKO); gene targeting technology, mainly about homologous recombination; and modern gene editing strategies containing transcription activator-like effector nucleases (TALENs) and a clustered regularly interspaced short palindromic repeat/associated protein system (CRISPR/Cas) developed in filamentous fungi and RNA technology including RNA interference (RNAi) and ribozymes. This review describes historical and modern gene manipulation methods in filamentous fungi and presents the molecular tools available to researchers investigating filamentous fungi. The biggest difference of this review from the previous ones is the addition of successful application and details of the promising gene editing tool CRISPR/Cas9 system in filamentous fungi.

Via Ronny Kellner
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Carbon allocation and partitioning in Populus tremuloides are modulated by ectomycorrhizal fungi under phosphorus limitation | Tree Physiology | Oxford Academic

Carbon allocation and partitioning in  Populus tremuloides  are modulated by ectomycorrhizal fungi under phosphorus limitation | Tree Physiology | Oxford Academic | Fungal|Oomycete Biology | Scoop.it

The fate of carbon (C) captured by forest trees during photosynthesis is influenced by the supply of other resources. Fixed C may be partitioned among biomolecules within the leaf and/or allocated throughout the tree to growth, storage and maintenance activities. Phosphorus (P) availability often limits tree productivity due to its high biological demand and strong interactions with soil minerals. As ectomycorrhizal (ECM) fungi play critical roles in enhancing phosphate (Pi) acquisition by their hosts, these symbioses will influence the fate of C within trees and forested ecosystems. Using Populus tremuloides Michx. (trembling aspen) in symbiosis with Laccaria bicolor (Marie) P.D. Orton or Paxillus involutus (Batsch) Fr., we assessed C acquisition, allocation and partitioning under Pi limitation, specifically focusing on primary and secondary C compounds. Both ECM fungi moderated the effects of low P on photosynthesis and C partitioning among carbohydrates and secondary metabolites by sustaining Pi uptake and translocation in P. tremuloides under Pi limitation. As leaf P declined, reductions in photosynthesis were accompanied by significant shifts in C partitioning from nonstructural carbohydrates (NSCs) to phenolic glycosides and tannins. Carbon partitioning in roots exhibited more complex patterns, with distinct increases in NSCs in nonmycorrhizal (NM) plants under Pi limitation that were not evident in plants colonized by either ECM symbiont. In general, aspen colonized by L. bicolor exhibited C partitioning patterns intermediate between those of NM and P. involutus aspen. The C cost of symbiosis was pronounced for plants supporting P. involutus, where ECM plants exhibited maintenance of photosynthesis yet reduced biomass in comparison with NM and L. bicolor aspen under Pi replete conditions. Our results indicate that the ECM symbiosis affects the disposition of C in forest trees in part by altering the acquisition of other limiting resources from soils, but also through ECM species-specific influences on host physiology. This modulation of C partitioning will have broad implications for forest ecosystem C capture, storage and cycling where nutrient resources may be limited.


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Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition

Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition | Fungal|Oomycete Biology | Scoop.it
Most land plants live in association with arbuscular mycorrhizal (AM) fungi and rely on this symbiosis to scavenge phosphorus (P) from soil. The ability to establish this partnership has been lost in some plant lineages like the Brassicaceae, which raises the question of what alternative nutrition strategies such plants have to grow in P-impoverished soils. To understand the contribution of plant–microbiota interactions, we studied the root-associated fungal microbiome of Arabis alpina (Brassicaceae) with the hypothesis that some of its components can promote plant P acquisition. Using amplicon sequencing of the fungal internal transcribed spacer 2, we studied the root and rhizosphere fungal communities of A. alpina growing under natural and controlled conditions including low-P soils and identified a set of 15 fungal taxa consistently detected in its roots. This cohort included a Helotiales taxon exhibiting high abundance in roots of wild A. alpina growing in an extremely P-limited soil. Consequently, we isolated and subsequently reintroduced a specimen from this taxon into its native P-poor soil in which it improved plant growth and P uptake. The fungus exhibited mycorrhiza-like traits including colonization of the root endosphere and P transfer to the plant. Genome analysis revealed a link between its endophytic lifestyle and the expansion of its repertoire of carbohydrate-active enzymes. We report the discovery of a plant–fungus interaction facilitating the growth of a nonmycorrhizal plant under native P-limited conditions, thus uncovering a previously underestimated role of root fungal microbiota in P cycling.

Via Stéphane Hacquard, Ronny Kellner
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Frontiers | Oomycete Communities Associated with Reed Die-Back Syndrome | Plant Science

Frontiers | Oomycete Communities Associated with Reed Die-Back Syndrome | Plant Science | Fungal|Oomycete Biology | Scoop.it
Phragmites australis (Cav.) Trin. ex Steud. die-back is a widely-studied phenomenon that was first discovered in northern Europe and that, until recently, was almost unknown in the Mediterranean basin. It has been described as a complex syndrome affecting reed populations leading to their retreat and decline, with significant impacts on valuable ecosystem services. Among the factors that cause the decline, soil-living microorganisms can be crucial. The aims of this study were to analyse the diversity of oomycetes communities associated with reed stands, and to understand whether they could play a key role in the decline. Variations in the structure of oomycetes communities were studied by metabarcoding of the internal transcribed spacer (ITS) 1 region of ribosomal DNA, from the sediments of five Italian freshwater ecosystems. They were chosen to cover a large variability in terms of surface area, water depth, microclimate and presence of documented reed retreat. From 96 samples collected from reed roots, rhizosphere, and bulk soil, we assembled 207661 ITS1 reads into 523 OTUs. We demonstrated that oomycete communities were structured by several factors, among which the most important was die-back occurrence. Our study also indicates that Pythiogeton spp. could be potentially involved in the development of die-back. The role of heavy metals in the soil was also explored, and cadmium concentration was shown to affect oomycetes distribution. This study represents a significant step forward for the characterization of microbial communities associated with reed die-back syndrome and helps to gain knowledge of the complexity of these important wet ecosystems.
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High‐resolution community profiling of arbuscular mycorrhizal fungi - New Phytologist

High‐resolution community profiling of arbuscular mycorrhizal fungi - New Phytologist | Fungal|Oomycete Biology | Scoop.it
Community analyses of arbuscular mycorrhizal fungi (AMF) using ribosomal small subunit (SSU) or internal transcribed spacer (ITS) DNA sequences often suffer from low resolution or coverage. We developed a novel sequencing based approach for a highly resolving and specific profiling of AMF communities.
We took advantage of previously established AMF-specific PCR primers that amplify a c. 1.5-kb long fragment covering parts of SSU, ITS and parts of the large ribosomal subunit (LSU), and we sequenced the resulting amplicons with single molecule real-time (SMRT) sequencing.
The method was applicable to soil and root samples, detected all major AMF families and successfully discriminated closely related AMF species, which would not be discernible using SSU sequences. In inoculation tests we could trace the introduced AMF inoculum at the molecular level. One of the introduced strains almost replaced the local strain(s), revealing that AMF inoculation can have a profound impact on the native community.
The methodology presented offers researchers a powerful new tool for AMF community analysis because it unifies improved specificity and enhanced resolution, whereas the drawback of medium sequencing throughput appears of lesser importance for low-diversity groups such as AMF.

Via Ronny Kellner, Niklaus Grunwald
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Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits

Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits | Fungal|Oomycete Biology | Scoop.it
Plant domestication was a pivotal accomplishment in human history, but also led to a reduction in genetic diversity of crop species compared to their wild ancestors. How this reduced genetic diversity affected plant–microbe interactions belowground is largely unknown. Here, we investigated the genetic relatedness, root phenotypic traits and rhizobacterial community composition of modern and wild accessions of common bean (Phaseolus vulgaris) grown in agricultural soil from the highlands of Colombia, one of the centers of common bean diversification. Diversity Array Technology-based genotyping and phenotyping of local common bean accessions showed significant genetic and root architectural differences between wild and modern accessions, with a higher specific root length for the wild accessions. Canonical Correspondence Analysis indicated that the divergence in rhizobacterial community composition between wild and modern bean accessions is associated with differences in specific root length. Along the bean genotypic trajectory, going from wild to modern, we observed a gradual decrease in relative abundance of Bacteroidetes, mainly Chitinophagaceae and Cytophagaceae, and an increase in relative abundance of Actinobacteria and Proteobacteria, in particular Nocardioidaceae and Rhizobiaceae, respectively. Collectively, these results establish a link between common bean domestication, specific root morphological traits and rhizobacterial community assembly.

Via Stéphane Hacquard
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Best practices for population genetic analyses | Phytopathology

Best practices for population genetic analyses | Phytopathology | Fungal|Oomycete Biology | Scoop.it
Population genetic analysis is a powerful tool to understand how pathogens emerge and adapt. However, determining the genetic structure of populations requires complex knowledge on a range of subtle skills that are often not explicitly stated in book chapters or review articles on population genetics. What is a good sampling strategy? How many isolates should I sample? How do I include positive and negative controls in my molecular assays? What marker system should I use? This review will attempt to address many of these practical questions that are often not readily answered from reading books or reviews on the topic, but emerge from discussions with colleagues and from practical experience. A further complication for microbial or pathogen populations is the frequent observation of clonality or partial clonality. Clonality invariably makes analyses of population data difficult because many assumptions underlying the theory from which analysis methods were derived are often violated. This review provides practical guidance on how to navigate through the complex web of data analyses of pathogens that may violate typical population genetics assumptions. We also provide resources and examples for analysis in the R programming environment.

Via Niklaus Grunwald, Steve Marek
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A Phylogenetic Method To Perform Genome-Wide Association Studies In Microbes That Accounts For Population Structure And Recombination

A Phylogenetic Method To Perform Genome-Wide Association Studies In Microbes That Accounts For Population Structure And Recombination | Fungal|Oomycete Biology | Scoop.it
Genome-Wide Association Studies (GWAS) in microbial organisms have the potential to vastly improve the way we understand, manage, and treat infectious diseases. Yet, GWAS methods established thus far remain insufficiently able to capitalise on the growing wealth of bacterial and viral genetic sequence data. Facing clonal population structure and homologous recombination, existing GWAS methods struggle to achieve both the precision necessary to reject spurious findings and the power required to detect associations in microbes. In this paper, we introduce a novel phylogenetic approach that has been tailor-made for microbial GWAS, which is applicable to organisms ranging from purely clonal to frequently recombining, and to both binary and continuous phenotypes. Our approach is robust to the confounding effects of both population structure and recombination, while maintaining high statistical power to detect associations. Thorough testing via application to simulated data provides strong support for the power and specificity of our approach and demonstrates the advantages offered over alternative cluster-based and dimension-reduction methods. Two applications to Neisseria meningitidis illustrate the versatility and potential of our method, confirming previously-identified penicillin resistance loci and resulting in the identification of both well-characterised and novel drivers of invasive disease. Our method is implemented as an open-source R package called treeWAS which is freely available at https://github.com/caitiecollins/treeWAS.

Via Ryohei Thomas Nakano
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Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen

Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen | Fungal|Oomycete Biology | Scoop.it

Genomic plasticity enables adaptation to changing environments, which is especially relevant for pathogens that engage in “arms races” with their hosts. In many pathogens, genes mediating virulence cluster in highly variable, transposon-rich, physically distinct genomic compartments. However, understanding of the evolution of these compartments, and the role of transposons therein, remains limited. Here, we show that transposons are the major driving force for adaptive genome evolution in the fungal plant pathogen Verticillium dahliae. We show that highly variable lineage-specific (LS) regions evolved by genomic rearrangements that are mediated by erroneous double-strand repair, often utilizing transposons. We furthermore show that recent genetic duplications are enhanced in LS regions, against an older episode of duplication events. Finally, LS regions are enriched in active transposons, which contribute to local genome plasticity. Thus, we provide evidence for genome shaping by transposons, both in an active and passive manner, which impacts the evolution of pathogen virulence.


Via Pierre Gladieux
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Rescooped by Alejandro Rojas from Adaptive Evolution and Speciation
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Fungal identification biases in microbiome projects - Environmental Microbiology Reports

Fungal identification biases in microbiome projects - Environmental Microbiology Reports | Fungal|Oomycete Biology | Scoop.it
Fungi are the key players in ecosystems as well as in plant and human health. High-throughput molecular identification of fungi has greatly progressed our understanding about the diversity of mutualists, saprotrophs, and pathogens. We argue that the methods promoted by the microbiome consortia are suboptimal for detection of the most important fungal pathogens and ecologically important degraders. We recommend several sets of optimized primers for analysis of fungi or all eukaryote groups based on either short or long amplicons that cover the ITS region as well as part of 18S and 28S rDNA.

Via Ronny Kellner
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