Fungal|Oomycete Biology
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Fungal|Oomycete Biology
Various topics on fungal and oomycete biology
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Species from within the Phytophthora cryptogea complex and related species, P. erythroseptica and P. sansomeana, readily hybridize

Species from within the Phytophthora cryptogea complex and related species, P. erythroseptica and P. sansomeana, readily hybridize | Fungal|Oomycete Biology | Scoop.it
During a study on the phylogenetic relationships between species in the Phytophthora cryptogea complex and related species, P. erythroseptica and P. sansomeana, 19 hybrid isolates with multiple polymorphisms in the nuclear sequences were observed. Molecular characterization of hybrids was achieved by sequencing three nuclear (internal transcribed spacers, ß-tubulin, heat shock protein 90) and two mitochondrial (cytochrome c oxidase subunit I, NADH dehydrogenase subunit I) gene regions and cloning of the single copy nuclear gene, ß-tubulin. Based on the molecular studies the hybrid isolates belonged to six distinct groups between P. cryptogea, P. erythroseptica, P. pseudocryptogea, P. sansomeana and P. sp. kelmania. In all cases, only a single cytochrome c oxidase subunit I and NADH dehydrogenase subunit I allele was detected and nuclear genes were biparentally inherited, suggesting that the hybrids arose from sexual recombination events. Colony morphology, growth rate, cardinal temperatures, breeding system, and morphology of sporangia, oogonia, oospores and antheridia were also determined. Some morphological differences between the hybrids and the parental species were noted; however, they were not sufficient to reliably distinguish the taxa and DNA markers from nuclear and mitochondrial genes will to be necessary for their identification. The parental species are all important pathogens of agricultural fields that have been transported globally. With the apparent ease of hybridization within this group there is ample opportunity for virulent hybrids to form, perhaps with extended host ranges.
Alejandro Rojas's insight:
It is really interesting since we also found P. sansomeana on corn and soybean, so what are the species of Phytophthora hybridizing in this host/environment? It could be P. cryptogea species complex since it is widely present (most often on tree species). 
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Hijacked cell division helped fuel rise of fungi: Research could point to new antifungals that stop cell growth in fungi but not in their plant or animal hosts

Hijacked cell division helped fuel rise of fungi: Research could point to new antifungals that stop cell growth in fungi but not in their plant or animal hosts | Fungal|Oomycete Biology | Scoop.it
The more than 90,000 known species of fungi may owe their abilities to spread and even cause disease to an ancient virus that hijacked their cell division machinery, researchers report. Over a billion years ago, a viral protein invaded the fungal genome, generating a family of proteins that now play key roles in fungal growth. The research could point to new antifungals that inhibit cell division in fungi but not in their plant or animal hosts.

Via Francis Martin
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Development and characterization of microsatellite markers for the oomyceta Aphanomyces euteiches

Development and characterization of microsatellite markers for the oomyceta Aphanomyces euteiches | Fungal|Oomycete Biology | Scoop.it
Aphanomyces euteiches Drechsler is a serious pathogen of leguminous crops that causes devastating root rot of pea worldwide. Given that A. euteiches is a diploid organism, robust, codominant markers are needed for population genetics studies. We have developed and screened a microsatellite-enriched small-insert genomic library for identification of A. euteiches SSR containing sequences. Fourteen out of the 48 primer pairs designed to amplify SSR, produced unambiguous polymorphic products in our test population of 94 isolates. The number of alleles at each locus ranged from one to four. The identification of new markers would enhance the ability to evaluate the genetic structure of A. euteiches populations, and pathogen evolution.
Aphanomyces euteiches Drechsler is a serious pathogen of leguminous crops that causes devastating root rot of pea worldwide. Given that A. euteiches is a diploid organism, robust, codominant markers are needed for population genetics studies. We have developed and screened a microsatellite-enriched small-insert genomic library for identification of A. euteiches SSR containing sequences. Fourteen out of the 48 primer pairs designed to amplify SSR, produced unambiguous polymorphic products in our test population of 94 isolates. The number of alleles at each locus ranged from one to four. The identification of new markers would enhance the ability to evaluate the genetic structure of A. euteiches populations, and pathogen evolution.
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FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild | Fungal|Oomycete Biology | Scoop.it
Fungi typically live in highly diverse communities composed of multiple ecological guilds. Although high-throughput sequencing has greatly increased the ability to quantify the diversity of fungi in environmental samples, researchers currently lack a simple and consistent way to sort large sequence pools into ecologically meaningful categories. We address this issue by introducing FUNGuild, a tool that can be used to taxonomically parse fungal OTUs by ecological guild independent of sequencing platform or analysis pipeline. Using a database and an accompanying bioinformatics script, we demonstrate the application of FUNGuild to three high-throughput sequencing datasets from different habitats: forest soils, grassland soils, and decomposing wood. We found that guilds characteristic of each habitat (i.e., saprotrophic and ectomycorrhizal fungi in forest soils, saprotrophic and arbuscular mycorrhizal fungi in grassland soils, saprotrophic, wood decomposer, and plant pathogenic fungi in decomposing wood) were each well represented. The example datasets demonstrate that while we could quickly and efficiently assign a large portion of the data to guilds, another large portion could not be assigned, reflecting the need to expand and improve the database as well as to gain a better understanding of natural history for many described and undescribed fungal species. As a community resource, FUNGuild is dependent on third-party annotation, so we invite researchers to populate it with new categories and records as well as refine those already in existence.
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Emergence and accumulation of novel pathogens suppress an invasive species - Stricker - 2016 - Ecology Letters - Wiley Online Library

Emergence and accumulation of novel pathogens suppress an invasive species - Stricker - 2016 - Ecology Letters - Wiley Online Library | Fungal|Oomycete Biology | Scoop.it
Emerging pathogens are a growing threat to human health, agriculture and the diversity of ecological communities but may also help control problematic species. Here we investigated the diversity, distribution and consequences of emerging fungal pathogens infecting an aggressive invasive grass that is rapidly colonising habitats throughout the eastern USA. We document the recent emergence and accumulation over time of diverse pathogens that are members of a single fungal genus and represent multiple, recently described or undescribed species. We also show that experimental suppression of these pathogens increased host performance in the field, demonstrating the negative effects of emerging pathogens on invasive plants. Our results suggest that invasive species can facilitate pathogen emergence and amplification, raising concerns about movement of pathogens among agricultural, horticultural, and wild grasses. However, one possible benefit of pathogen accumulation is suppression of aggressive invaders over the long term, potentially abating their negative impacts on native communities.

Via Niklaus Grunwald
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Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi

Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi | Fungal|Oomycete Biology | Scoop.it
 A genome-scale comparative study was conducted across 74 fungal genomes to identify clusters of orthologous genes unique to the three Magnaporthaceae species as well as species specific genes. We found 1149 clusters that were unique to the Magnaporthaceae family of fungi with 295 of those containing genes from all three species. Gene clusters involved in metabolic and enzymatic activities were highly represented in the Magnaporthaceae specific clusters. Also highly represented in the Magnaporthaceae specific clusters as well as in the species specific genes were transcriptional regulators. In addition, we examined the relationship between gene evolution and distance to repetitive elements found in the genome. No correlations between diversifying or purifying selection and distance to repetitive elements or an increased rate of evolution in secreted and small secreted proteins were observed.

Via Bradford Condon
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Characterization of Phytophthora spp. Isolated from Ornamental Plants in Florida — Plant Disease

Characterization of Phytophthora spp. Isolated from Ornamental Plants in Florida — Plant Disease | Fungal|Oomycete Biology | Scoop.it

This report investigates population structure and genetic variability of Phytophthora spp. isolated from botanically diverse plants in Florida. Internal transcribed spacer-based molecular phylogenetic analyses indicate that Phytophthora isolates recovered from ornamental plants in Florida represent a genetically diverse population and that a majority of the isolates belong to Phytophthora nicotianae (73.2%), P. palmivora(18.7%), P. tropicalis (4.9%), P. katsurae (2.4%), and P. cinnamomi (0.8%). Mating type analyses revealed that most isolates were heterothallic, consisting of both mating type A1 (25.2%) and mating type A2 (39.0%), and suggesting that they could outcross. Fungicide sensitivity assays determined that several isolates were moderate to completely insensitive to mefenoxam. In addition, several isolates were also moderately insensitive to additional fungicides with different modes of action. However, correlation analyses did not reveal occurrence of fungicide cross-resistance. These studies suggest that a genetically diverse Phytophthora population infects ornamental crops and the occurrence of mefenoxam-insensitive Phytophthora populations raises concerns about disease management in ornamentals. Mitigating fungicide resistance will require prudent management strategies, including tank mixes and rotation of chemicals with different modes of actions.


Via Niklaus Grunwald
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Genome-Enabled Analysis of Plant-Pathogen Migration - Annual Review of Phytopathology, 53(1):121

Genome-Enabled Analysis of Plant-Pathogen Migration - Annual Review of Phytopathology, 53(1):121 | Fungal|Oomycete Biology | Scoop.it

Trade in plant and plant products has profoundly affected the global distri- bution and diversity of plant pathogens. Identification of migration pathways can be used to monitor or manage pathogen movement for proactive dis- ease management or quarantine measures. Genomics-based genetic marker discovery is allowing unprecedented collection of population genetic data for plant pathogens. These data can be used for detailed analysis of the ancestry of population samples and therefore for analysis of migration. Re- construction of migration histories has confirmed previous hypotheses based on observational data and led to unexpected new findings on the origins of pathogens and source populations for past and recent migration. The choice of software for analysis depends on the type of migration being studied and the reproductive mode of the pathogen. Biased sampling and complex pop- ulation structures are potential challenges to accurate inference of migration pathways.


Via Ronny Kellner
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The two-speed genomes of filamentous pathogens: waltz with plants

The two-speed genomes of filamentous pathogens: waltz with plants | Fungal|Oomycete Biology | Scoop.it

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

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Serenella A Sukno's comment, January 20, 5:42 PM
not in Colletotrichum!
Steve Marek's comment, January 20, 5:52 PM
Interesting!
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Diversity of Foliar Phytophthora Species on Rhododendron in Oregon Nurseries — Plant Disease

Diversity of Foliar Phytophthora Species on Rhododendron in Oregon Nurseries — Plant Disease | Fungal|Oomycete Biology | Scoop.it

The genus Phytophthora contains some of the most notorious plant pathogens affecting nursery crops. Given the recent emergence of the sudden oak death pathogen Phytophthora ramorum, particularly in association with Rhododendron spp., characterization of Phytophthora communities associated with this host in nursery environments is prudent. Many taxa may present symptoms similar to P. ramorum but we do not necessarily know their identity, frequency, and importance. Here, we present a survey of Phytophthora taxa observed from seven nurseries in the U.S. state of Oregon. Incidence and diversity of Phytophthora communities differed significantly among nurseries and among seasons within nursery. The taxa P. syringae and P. plurivora were widespread and detected at most of the nurseries sampled. Nine other taxa were also detected but were found either in a single nursery or were shared among only a few nurseries. Characterization of the Phytophthora communities present in nurseries is an important step toward understanding the ecology of these organisms as well as an aid to nursery managers in determining what risks may be present when symptomatic plants are observed. This study builds on an increasing literature, which characterizes Phytophthora community structure in nurseries.


Via Niklaus Grunwald
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Response to Comment on “Global diversity and geography of soil fungi”

Response to Comment on “Global diversity and geography of soil fungi” | Fungal|Oomycete Biology | Scoop.it

Schadt and Rosling (Technical Comment, 26 June 2015, p. 1438) argue that primer-template mismatches neglected the fungal class Archaeorhizomycetes in a global soil survey. Amplicon-based metabarcoding of nine barcode-primer pair combinations and polymerase chain reaction (PCR)–free shotgun metagenomics revealed that barcode and primer choice and PCR bias drive the diversity and composition of microorganisms in general, but the Archaeorhizomycetes were little affected in the global study. We urge that careful choice of DNA markers and primers is essential for ecological studies using high-throughput sequencing for identification.


Via Francis Martin
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PNAS: Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping

PNAS: Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping | Fungal|Oomycete Biology | Scoop.it

Plants maintain microbial associations whose functions remain largely unknown. For the past 15 y, we have planted the annual postfire tobacco Nicotiana attenuata into an experimental field plot in the plant’s native habitat, and for the last 8 y the number of plants dying from a sudden wilt disease has increased, leading to crop failure. Inadvertently we had recapitulated the common agricultural dilemma of pathogen buildup associated with continuous cropping for this native plant. Plants suffered sudden tissue collapse and black roots, symptoms similar to a Fusarium–Alternaria disease complex, recently characterized in a nearby native population and developed into an in vitro pathosystem for N. attenuata. With this in vitro disease system, different protection strategies (fungicide and inoculations with native root-associated bacterial and fungal isolates), together with a biochar soil amendment, were tested further in the field. A field trial with more than 900 plants in two field plots revealed that inoculation with a mixture of native bacterial isolates significantly reduced disease incidence and mortality in the infected field plot without influencing growth, herbivore resistance, or 32 defense and signaling metabolites known to mediate resistance against native herbivores. Tests in a subsequent year revealed that a core consortium of five bacteria was essential for disease reduction. This consortium, but not individual members of the root-associated bacteria community which this plant normally recruits during germination from native seed banks, provides enduring resistance against fungal diseases, demonstrating that native plants develop opportunistic mutualisms with prokaryotes that solve context-dependent ecological problems.


Via Stéphane Hacquard
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bioRxiv: Successful asexual lineages of the Irish potato Famine pathogen are triploid (2015)

bioRxiv: Successful asexual lineages of the Irish potato Famine pathogen are triploid (2015) | Fungal|Oomycete Biology | Scoop.it

The oomycete Phytophthora infestans was the causal agent of the Irish Great Famine and is a recurring threat to global food security. The pathogen can reproduce both sexually and asexually and has a potential to adapt both abiotic and biotic environment. Although in many regions the A1 and A2 mating types coexist, the far majority of isolates belong to few clonal, asexual lineages. As other oomycetes, P. infestans is thought to be diploid during the vegetative phase of its life cycle, but it was observed that trisomy correlated with virulence and mating type locus and that polyploidy can occur in some isolates. It remains unknown about the frequency of polyploidy occurrence in nature and the relationship between ploidy level and sexuality. Here we discovered that the sexuality of P. infestans isolates correlates with ploidy by comparison of microsatellite fingerprinting, genome-wide polymorphism, DNA quantity, and chromosome numbers. The sexual progeny of P. infestans in nature are diploid, whereas the asexual lineages are mostly triploids, including successful clonal lineages US-1 and 13_A2. This study reveals polyploidization as an extra evolutionary risk to this notorious plant destroyer.


Via Kamoun Lab @ TSL
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Sequencing of the litchi downy blight pathogen reveals it is a Phytophthora species with downy mildew-like characteristics 

Sequencing of the litchi downy blight pathogen reveals it is a Phytophthora species with downy mildew-like characteristics  | Fungal|Oomycete Biology | Scoop.it
On the basis of its downy mildew-like morphology, the litchi downy blight pathogen was previously named Peronophythora litchii. Recently however, it was proposed to transfer this pathogen to Phytophthora clade 4. To better characterize this unusual oomycete species and important fruit pathogen, we obtained the genome sequence of Phytophthora litchii and compared it to those from other oomycete species. P. litchii has a small genome with tightly spaced genes. On the basis of a multilocus phylogenetic analysis, the placement of P. litchii in the genus Phytophthora is strongly supported. Effector proteins predicted included 245 RxLRs, 30 NLPs and 14 CRNs. The typical motifs, phylogenies and activities of these effectors were typical for a Phytophthora species. However, like the genome features of the analyzed downy mildews, P. litchii exhibited a streamlined genome with a relatively small number of genes in both core and species-specific protein families. The low GC content and slight codon preference of P. litchii sequences were similar to those of the analyzed downy mildews and a subset of Phytophthora species. Taken together, these observations suggest that P. litchii is a Phytophthora pathogen that is in the process of acquiring downy mildew-like genomic and morphological features. Thus P. litchii may provide a novel model for investigating morphological development and genomic adaptation in oomycete pathogens.
 
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Nuclear dynamics and genetic rearrangement in heterokaryotic colonies of Fusarium oxysporum

Nuclear dynamics and genetic rearrangement in heterokaryotic colonies of Fusarium oxysporum | Fungal|Oomycete Biology | Scoop.it
Recent studies have shown horizontal transfer of chromosomes to be a potential key contributor to genome plasticity in asexual fungal pathogens. However, the mechanisms behind horizontal chromosome transfer in eukaryotes are not well understood. Here we investigated the role of conidial anastomosis in heterokaryon formation between incompatible strains of Fusarium oxysporum and determined the importance of heterokaryons for horizontal chromosome transfer. Using live-cell imaging we demonstrate that conidial pairing of incompatible strains under carbon starvation can result in the formation of viable heterokaryotic hyphae in F. oxysporum. Nuclei of the parental lines presumably fuse at some stage as conidia with a single nucleus harboring both marker histones (GFP- and RFP-tagged) are produced. Upon colony formation, this hybrid offspring is subject to progressive and gradual genome rearrangement. The parental genomes appear to become spatially separated and RFP-tagged histones, deriving from one of the strains, Fol4287, are eventually lost. With a PCR-based method we showed that markers for most of the chromosomes of this strain are lost, indicating a lack of Fol4287 chromosomes. This leaves offspring with the genomic background of the other strain (Fo47), but in some cases together with one or two chromosomes from Fol4287, including the chromosome that confers pathogenicity towards tomato.
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Lotus Lofgren's curator insight, April 24, 10:22 PM
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Plant root pathogens over 120,000 years of temperate rainforest ecosystem development

Plant root pathogens over 120,000 years of temperate rainforest ecosystem development | Fungal|Oomycete Biology | Scoop.it

The role of pathogens, including oomycetes, in long-term ecosystem development has remained largely unknown, despite hypotheses that pathogens drive primary succession, determine mature ecosystem plant diversity, or dominate in retrogressive, nutrient-limited ecosystems. Using DNA sequencing from roots, we investigated the frequency and host relationships of oomycete communities along a 120 000 year glacial chronosequence. Oomycetes were frequent in early successional sites (5 - 70 yrs), occurring in 38 - 65% of plant roots, but rare (average 3%) in all older ecosystems (280 yrs and older). Oomycetes were highly host specific, and more frequent on plant species that declined most strongly in abundance between ecosystem ages. In contrast, oomycetes were not correlated with plant abundance or plant root traits associated with retrogression. The results support the importance of root pathogens in early succession, but not thereafter, suggesting root pathogen-driven dynamics may be important in driving succession but not long-term diversity maintenance.

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Development and characterization of microsatellite markers for Fusarium virguliforme and their utility within clade 2 of the Fusarium solani species complex

Development and characterization of microsatellite markers for Fusarium virguliforme and their utility within clade 2 of the Fusarium solani species complex | Fungal|Oomycete Biology | Scoop.it
Clade 2 of the Fusarium solani species complex contains plant pathogens including Fusarium virguliforme and closely related species Fusarium brasiliense, Fusarium crassistipitatum, Fusarium tucumaniae, which are the primary causal agents of soybean sudden death syndrome (SDS), a significant threat to soybean production. In this study, we developed microsatellite markers from a F. virguliforme genome sequence and applied them to a F. virguliforme population collection of 38 isolates from Michigan and four reference strains from other locations. Of the 225 detected microsatellite loci, 108 loci were suitable for primer design, and 12 of the microsatellite markers were determined to be highly polymorphic, amplifying on average 5.7 alleles per locus. Using these markers, F. virguliforme isolates were partitioned into three distinct clusters, but isolates were not grouped based on relatedness of sampling sites. In addition, 11 out of 12 markers were demonstrated to be highly transferrable to other closely related species.
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The power and promise of RNA-seq in ecology and evolution

The power and promise of RNA-seq in ecology and evolution | Fungal|Oomycete Biology | Scoop.it
Reference is regularly made to the power of new genomic sequencing approaches. Using powerful technology, however, is not the same as having the necessary power to address a research question with statistical robustness. In the rush to adopt new and improved genomic research methods, limitations of technology and experimental design may be initially neglected. Here, we review these issues with regard to RNA sequencing (RNA-seq). RNA-seq adds large-scale transcriptomics to the toolkit of ecological and evolutionary biologists, enabling differential gene expression (DE) studies in nonmodel species without the need for prior genomic resources. High biological variance is typical of field-based gene expression studies and means that larger sample sizes are often needed to achieve the same degree of statistical power as clinical studies based on data from cell lines or inbred animal models. Sequencing costs have plummeted, yet RNA-seq studies still underutilize biological replication. Finite research budgets force a trade-off between sequencing effort and replication in RNA-seq experimental design. However, clear guidelines for negotiating this trade-off, while taking into account study-specific factors affecting power, are currently lacking. Study designs that prioritize sequencing depth over replication fail to capitalize on the power of RNA-seq technology for DE inference. Significant recent research effort has gone into developing statistical frameworks and software tools for power analysis and sample size calculation in the context of RNA-seq DE analysis. We synthesize progress in this area and derive an accessible rule-of-thumb guide for designing powerful RNA-seq experiments relevant in eco-evolutionary and clinical settings alike.

Via Francis Martin
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Mildew-Omics: How Global Analyses Aid the Understanding of Life and Evolution of Powdery Mildews

Mildew-Omics: How Global Analyses Aid the Understanding of Life and Evolution of Powdery Mildews | Fungal|Oomycete Biology | Scoop.it
The common powdery mildew plant diseases are caused by ascomycete fungi of the order Erysiphales. Their characteristic life style as obligate biotrophs renders functional analyses in these species challenging, mainly because of experimental constraints to genetic manipulation. Global large-scale (“-omics”) approaches are thus particularly valuable and insightful for the characterisation of the life and evolution of powdery mildews. Here we review the knowledge obtained so far from genomic, transcriptomic and proteomic studies in these fungi. We consider current limitations and challenges regarding these surveys and provide an outlook on desired future investigations on the basis of the various –omics technologies

Via Francis Martin
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Microbial and Functional Diversity within the Phyllosphere of Espeletia sp. in an Andean High Mountain Ecosystem

Microbial and Functional Diversity within the Phyllosphere of Espeletia sp. in an Andean High Mountain Ecosystem | Fungal|Oomycete Biology | Scoop.it

Microbial populations residing in close contact with plants can be found in the rhizosphere, or in the phyllosphere as epiphytes on the surface, or endophytes inside plants. Here, we analyzed the microbiota associated with Espeletia plants, endemic to the Páramo environment of the Andes Mountains and a unique model for studying microbial populations and their adaptations to the adverse conditions of high-mountain neo-tropical ecosystems. Communities were analyzed using samples from the rhizosphere, necromass and young and mature leaves, the latter two analyzed separately as endophytes and epiphytes. The taxonomic composition performed by sequencing the V5-V6 region of the 16S rRNA gene indicated differences among populations of the leaf phyllosphere, the necromass and the rhizosphere, with predominance of some phyla but only few shared OTUs. Functional profiles predicted based on taxonomic affiliations differed from those obtained by GeoChip microarray analysis, which separated community functional capacity based on plant microenvironment. The identified metabolic pathways provided insight regarding microbial strategies for colonization and survival in these ecosystems. This study of novel plant phyllosphere microbiomes and their putative functional ecology is also the first step for future bioprospecting studies in search of enzymes, compounds or microorganisms relevant to industry or remediation efforts.

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Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta

Delineating microbial populations, discovering ecologically relevant phenotypes and identifying migrants, hybrids or admixed individuals have long proved notoriously difficult, thereby limiting our understanding of the evolutionary forces at play during the diversification of microbial species. However, recent advances in sequencing and computational methods have enabled an unbiased approach whereby incipient species and the genetic correlates of speciation can be identified by examining patterns of genomic variation within and between lineages. We present here a population genomic study of a phylogenetic species in the Neurospora discreta species complex, based on the resequencing of full genomes (~37 Mb) for 52 fungal isolates from nine sites in three continents. Population structure analyses revealed two distinct lineages in South–East Asia, and three lineages in North America/Europe with a broad longitudinal and latitudinal range and limited admixture between lineages. Genome scans for selective sweeps and comparisons of the genomic landscapes of diversity and recombination provided no support for a role of selection at linked sites on genomic heterogeneity in levels of divergence between lineages. However, demographic inference indicated that the observed genomic heterogeneity in divergence was generated by varying rates of gene flow between lineages following a period of isolation. Many putative cases of exchange of genetic material between phylogenetically divergent fungal lineages have been discovered, and our work highlights the quantitative importance of genetic exchanges between more closely related taxa to the evolution of fungal genomes. Our study also supports the role of allopatric isolation as a driver of diversification in saprobic microbes.
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Australasian Plant Pathology: Globalisation, the founder effect, hybrid Phytophthora species and rapid evolution: new headaches for biosecurity (2015)

Australasian Plant Pathology: Globalisation, the founder effect, hybrid Phytophthora species and rapid evolution: new headaches for biosecurity (2015) | Fungal|Oomycete Biology | Scoop.it

The oomycete genus Phytophthora contains a large number of plant pathogens that cause significant damage to natural and agricultural systems. Until recently species have been distinguished using a limited set of morphological characters. The development of DNA-based technologies has revealed much broader and more complex diversity than previously recognised, and has led to the recent description of many new species. This review looks at the underlying mechanisms for the generation of diversity within the genus. The intercontinental movement and transplantation of infected plant material partially explains the appearance of new species in unexpected places. However, it is also likely that novel species arise as a result of the hybridisation and rapid evolution of introduced species under episodic selection pressures. Hybrid progeny may possess equal or greater virulence than parent species, thereby posing an increasing risk to our natural environment and agricultural production systems. These discoveries amplify the threats posed by the introduction of plant pathogens into new environments, and expose a crucial weakness in current evidence-based biosecurity regimes. Further work is required to identify hybrids, anticipate and understand the occurrence of hybridisation, and to implement appropriate quarantine and risk management measures.


Via Kamoun Lab @ TSL, Niklaus Grunwald
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Eric Larson's curator insight, December 29, 2015 7:40 AM

New biosecurity challenges.

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Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi: Current Biology

Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi: Current Biology | Fungal|Oomycete Biology | Scoop.it
Highlights
•New HTRs are found in cheese fungi
•HTRs are flanked by specific transposable elements
•HTRs have spread in cheese-associated fungi through recent selective sweeps
•Experiments link two HTRs to growth and competitive advantages on cheese

Summary
Domestication is an excellent model for studies of adaptation because it involves recent and strong selection on a few, identified traits [ 1–5 ]. Few studies have focused on the domestication of fungi, with notable exceptions [ 6–11 ], despite their importance to bioindustry [ 12 ] and to a general understanding of adaptation in eukaryotes [ 5 ]. Penicillium fungi are ubiquitous molds among which two distantly related species have been independently selected for cheese making—P. roqueforti for blue cheeses like Roquefort and P. camemberti for soft cheeses like Camembert. The selected traits include morphology, aromatic profile, lipolytic and proteolytic activities, and ability to grow at low temperatures, in a matrix containing bacterial and fungal competitors [ 13–15 ]. By comparing the genomes of ten Penicillium species, we show that adaptation to cheese was associated with multiple recent horizontal transfers of large genomic regions carrying crucial metabolic genes. We identified seven horizontally transferred regions (HTRs) spanning more than 10 kb each, flanked by specific transposable elements, and displaying nearly 100% identity between distant Penicillium species. Two HTRs carried genes with functions involved in the utilization of cheese nutrients or competition and were found nearly identical in multiple strains and species of cheese-associated Penicillium fungi, indicating recent selective sweeps; they were experimentally associated with faster growth and greater competitiveness on cheese and contained genes highly expressed in the early stage of cheese maturation. These findings have industrial and food safety implications and improve our understanding of the processes of adaptation to rapid environmental changes.


Via Steve Marek
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Insights into Triticum aestivum seedling root rot caused by Fusarium graminearum

Insights into Triticum aestivum seedling root rot caused by Fusarium graminearum | Fungal|Oomycete Biology | Scoop.it

Fusarium graminearum (Fg) is one of the most common and potent fungal pathogens of wheat (Triticum aestivum), known for causing devastating spike infections and grain yield damage. Fg is a typical soil-borne pathogen that builds up during consecutive cereal cropping. Speculations on systemic colonisations of cereals by Fg root infection have existed for quite a while, but were not proven. We have assessed the Fusarium root rot disease macroscopically in a diverse set of 12 wheat genotypes, and microscopically in a comparative study of two genotypes with diverging responses. Here, we show a “new” aspect of Fg life-cycle: the head blight fungus uses a unique root infection strategy with an initial stage typical for root-pathogens and a later stage typical for spike infection. Root colonisation negatively affects seedling development and leads to systemic plant invasion by tissue-adapted fungal strategies. Another major outcome is the identification of partial resistance to root rot. Disease severity assessments and histological examinations both demonstrated three distinct disease phases which, however, proceeded differently in resistant and susceptible genotypes. Soil-borne inoculum and root infection are considered significant components of the Fg lifecycle with important implications for the development of new strategies of resistance breeding and disease control.

Alejandro Rojas's insight:

Great combination of classical tools with qPCR and CLS microscopy

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Rescooped by Alejandro Rojas from The Plant Microbiome
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PNAS: Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

Human activities have resulted in large increases in the availability of nutrients in terrestrial ecosystems worldwide. Although plant community responses to elevated nutrients have been well studied, soil microbial community responses remain poorly understood, despite their critical importance to ecosystem functioning. Using DNA-sequencing approaches, we assessed the response of soil microbial communities to experimentally added nitrogen and phosphorus at 25 grassland sites across the globe. Our results demonstrate that the composition of these communities shifts in consistent ways with elevated nutrient inputs and that there are corresponding shifts in the ecological attributes of the community members. This study represents an important step forward for understanding the connection between elevated nutrient inputs, shifts in soil microbial communities, and altered ecosystem functioning.


Via Stéphane Hacquard
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