Fungal population biology
771 views | +0 today
Follow
Your new post is loading...
Your new post is loading...
Rescooped by Kirk Broders from Adaptive Evolution and Speciation
Scoop.it!

The Soil-Borne Supremacy - Trends in Plant Science

The Soil-Borne Supremacy - Trends in Plant Science | Fungal population biology | Scoop.it
The rhizosphere microbiome plays an important role in plant growth, nutrition and health. Recent research unearthed that plant genotype-dependent navigation of microbial community composition in the rhizosphere is associated with fitness consequences for the host plant, providing great promise for breeding soil-borne supremacy traits into future crops.

Via Ronny Kellner
more...
No comment yet.
Rescooped by Kirk Broders from Microbe-Microbe Interactions and miscellaneous
Scoop.it!

Networks of energetic and metabolic interactions define dynamics in microbial communities

Networks of energetic and metabolic interactions define dynamics in microbial communities | Fungal population biology | Scoop.it
Microbial communities are critical to global carbon cycling and particularly important in oxygen-limited environments, such as sediments and parts of the human microbiome. However, the uncultured members of these communities often hinder the study of community composition and interspecies interactions at a deeper level. Here, we integrate metagenomic binning, metatranscriptomic analysis, and metabolic modeling to obtain quantitative information about interspecies interactions between individual species present in methanogenic communities. We found that these communities are defined by not only metabolic interactions but also additional interdependencies, such as amino acid auxotrophies. Strategic usage of antimicrobials by specific community members further reinforces this intricate interspecies network, thereby enforcing strong collaboration among community members.

Via Nina Dombrowski
more...
No comment yet.
Rescooped by Kirk Broders from Plant pathogenic fungi
Scoop.it!

Endophytic Epichloë species and their grass hosts: from evolution to applications - Springer

Endophytic Epichloë species and their grass hosts: from evolution to applications - Springer | Fungal population biology | Scoop.it
The closely linked fitness of the Epichloë symbiont and the host grass is presumed to align the coevolution of the species towards specialization and mutually beneficial cooperation. Ecological observations demonstrating that Epichloë-grass symbioses can modulate grassland ecosystems via both above- and belowground ecosystem processes support this. In many cases the detected ecological importance of Epichloë species is directly or indirectly linked to defensive mutualism attributable to alkaloids of fungal-origin. Now, modern genetic and molecular techniques enable the precise studies on evolutionary origin of endophytic Epichloë species, their coevolution with host grasses and identification the genetic variation that explains phenotypic diversity in ecologically relevant characteristics of Epichloë-grass associations. Here we briefly review the most recent findings in these areas of research using the present knowledge of the genetic variation that explains the biosynthetic pathways driving the diversity of alkaloids produced by the endophyte. These findings underscore the importance of genetic interplay between the fungus and the host in shaping their coevolution and ecological role in both natural grass ecosystems, and in the agricultural arena.

Via Steve Marek
more...
No comment yet.
Rescooped by Kirk Broders from Norwich rust group
Scoop.it!

Replacement of the European wheat yellow rust population by new races from the centre of diversity in the near-Himalayan region

Replacement of the European wheat yellow rust population by new races from the centre of diversity in the near-Himalayan region | Fungal population biology | Scoop.it

Isolates of recently spreading races of yellow rust from wheat and triticale in Europe were analysed using virulence phenotypic data of 2605 isolates sampled in twelve countries between 2000 and 2014. A subset of 239 isolates was investigated by microsatellite markers. At least three races of non-European origin, termed Warrior, Kranich, and Triticale aggressive, were identified in the post-2011 population. The ‘Warrior’ race was present in high frequencies already in the first year of detection in most European countries and replaced to a large extent the pre-2011 European population, whereas the two other exotic races were localized to certain regions and/or crop type. The presence of at least six multi-locus genotypes of the Warrior race and five genotypes of the Kranich race already in the first years of detection and across large areas is consistent with a hypothesis of aerial spread from genetically diverse source populations. The study illustrates the potential role of sexual P. striiformis populations as a reservoir for new races replacing distant clonal populations.


Via Norwich Rust Group
more...
No comment yet.
Rescooped by Kirk Broders from Plants and Microbes
Scoop.it!

New Phytologist: Comparative genomics of Fusarium oxysporum f. sp. melonis reveals the secreted protein recognized by the Fom-2 resistance gene in melon (2015)

New Phytologist: Comparative genomics of Fusarium oxysporum f. sp. melonis reveals the secreted protein recognized by the Fom-2 resistance gene in melon (2015) | Fungal population biology | Scoop.it
Development of resistant crops is the most effective way to control plant diseases to safeguard food and feed production. Disease resistance is commonly based on resistance genes, which generally mediate the recognition of small proteins secreted by invading pathogens. These proteins secreted by pathogens are called ‘avirulence’ proteins. Their identification is important for being able to assess the usefulness and durability of resistance genes in agricultural settings.We have used genome sequencing of a set of strains of the melon wilt fungus Fusarium oxysporum f. sp. melonis (Fom), bioinformatics-based genome comparison and genetic transformation of the fungus to identify AVRFOM2, the gene that encodes the avirulence protein recognized by the melon Fom-2 gene.Both an unbiased and a candidate gene approach identified a single candidate for the AVRFOM2 gene. Genetic complementation of AVRFOM2 in three different race 2 isolates resulted in resistance of Fom-2-harbouring melon cultivars. AvrFom2 is a small, secreted protein with two cysteine residues and weak similarity to secreted proteins of other fungi.The identification of AVRFOM2 will not only be helpful to select melon cultivars to avoid melon Fusarium wilt, but also to monitor how quickly a Fom population can adapt to deployment of Fom-2-containing cultivars in the field.
Via Kamoun Lab @ TSL
more...
No comment yet.
Rescooped by Kirk Broders from MycorWeb Plant-Microbe Interactions
Scoop.it!

Entorrhizomycota: A New Fungal Phylum Reveals New Perspectives on the Evolution of Fungi

Entorrhizomycota: A New Fungal Phylum Reveals New Perspectives on the Evolution of Fungi | Fungal population biology | Scoop.it
Entorrhiza is a small fungal genus comprising 14 species that all cause galls on roots of Cyperaceae and Juncaceae. Although this genus was established 130 years ago, crucial questions on the phylogenetic relationships and biology of this enigmatic taxon are still unanswered. In order to infer a robust hypothesis about the phylogenetic position of Entorrhiza and to evaluate evolutionary trends, multiple gene sequences and morphological characteristics of Entorrhiza were analyzed and compared with respective findings in Fungi. In our comprehensive five-gene analyses Entorrhiza appeared as a highly supported monophyletic lineage representing the sister group to the rest of the Dikarya, a phylogenetic placement that received but moderate maximum likelihood and maximum parsimony bootstrap support. An alternative maximum likelihood tree with the constraint that Entorrhiza forms a monophyletic group with Basidiomycota could not be rejected. According to the first phylogenetic hypothesis, the teliospore tetrads of Entorrhiza represent the prototype of the dikaryan meiosporangium. The alternative hypothesis is supported by similarities in septal pore structure, cell wall and spindle pole bodies. Based on the isolated phylogenetic position of Entorrhiza and its peculiar combination of features related to ultrastructure and reproduction mode, we propose a new phylum Entorrhizomycota, for the genus Entorrhiza, which represents an apparently widespread group of inconspicuous fungi.

Via Francis Martin
more...
No comment yet.
Rescooped by Kirk Broders from Plant-Microbe Symbiosis
Scoop.it!

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

Compact graphical representation of phylogenetic data and metadata with GraPhlAn | Fungal population biology | Scoop.it
The increased availability of genomic and metagenomic data poses challenges at multiple analysis levels, including visualization of very large-scale microbial and microbial community data paired with rich metadata. We developed GraPhlAn (Graphical Phylogenetic Analysis), a computational tool that produces high-quality, compact visualizations of microbial genomes and metagenomes. This includes phylogenies spanning up to thousands of taxa, annotated with metadata ranging from microbial community abundances to microbial physiology or host and environmental phenotypes. GraPhlAn has been developed as an open-source command-driven tool in order to be easily integrated into complex, publication-quality bioinformatics pipelines. It can be executed either locally or through an online Galaxy web application. We present several examples including taxonomic and phylogenetic visualization of microbial communities, metabolic functions, and biomarker discovery that illustrate GraPhlAn’s potential for modern microbial and community genomics.

Via Jean-Michel Ané
more...
No comment yet.
Rescooped by Kirk Broders from Plant pathogenic fungi
Scoop.it!

Discordant phylogenies suggest repeated host shifts in the Fusarium–Euwallacea ambrosia beetle mutualism

Discordant phylogenies suggest repeated host shifts in the Fusarium–Euwallacea ambrosia beetle mutualism | Fungal population biology | Scoop.it

Highlights
• The Fusarium–Euwallacea ambrosia beetle mutualism evolved ∼20 million years ago.
• Fusaria and the Euwallacea ambrosia beetles that farm them are both monophyletic.
• The mutualism was shaped more by multiple host shifts than diversifying coevolution.
• Several exotic Fusarium–Euwallacea mutualists threaten avocado production worldwide.
• Evidence exists consistent with hybrid introgression between Euwallacea species.


Via Steve Marek
more...
No comment yet.
Rescooped by Kirk Broders from MycorWeb Plant-Microbe Interactions
Scoop.it!

PLOS Pathogens: Advances and Challenges in Computational Prediction of Effectors from Plant Pathogenic Fungi

PLOS Pathogens: Advances and Challenges in Computational Prediction of Effectors from Plant Pathogenic Fungi | Fungal population biology | Scoop.it

With the rising number of sequenced pathogen genomes, computational prediction of effector proteins holds promise as a fast and economical technique to define candidates for subsequent laboratory work. Bacterial effectors delivered to the host via dedicated pathogen-derived delivery mechanisms, such as the type III secretion system, can be predicted using machine learning approaches based on protein sequence information. In oomycetes, consensus sequence motifs implicated in host translocation, such as RXLR, can be exploited for effector prediction. However, computational effector prediction in fungi is challenging due to a lack of known protein features that are common to fungal effectors and the low number of characterized effectors for individual species, which limits the use of machine learning approaches.


Via Bradford Condon, Francis Martin
more...
No comment yet.
Rescooped by Kirk Broders from The Plant Microbiome
Scoop.it!

Effort versus Reward: Preparing Samples for Fungal Community Characterization in High-Throughput Sequencing Surveys of Soils

Effort versus Reward: Preparing Samples for Fungal Community Characterization in High-Throughput Sequencing Surveys of Soils | Fungal population biology | Scoop.it
Next generation fungal amplicon sequencing is being used with increasing frequency to study fungal diversity in various ecosystems; however, the influence of sample preparation on the characterization of fungal community is poorly understood. We investigated the effects of four procedural modifications to library preparation for high-throughput sequencing (HTS). The following treatments were considered: 1) the amount of soil used in DNA extraction, 2) the inclusion of additional steps (freeze/thaw cycles, sonication, or hot water bath incubation) in the extraction procedure, 3) the amount of DNA template used in PCR, and 4) the effect of sample pooling, either physically or computationally. Soils from two different ecosystems in Minnesota, USA, one prairie and one forest site, were used to assess the generality of our results. The first three treatments did not significantly influence observed fungal OTU richness or community structure at either site. Physical pooling captured more OTU richness compared to individual samples, but total OTU richness at each site was highest when individual samples were computationally combined. We conclude that standard extraction kit protocols are well optimized for fungal HTS surveys, but because sample pooling can significantly influence OTU richness estimates, it is important to carefully consider the study aims when planning sampling procedures.

Via Francis Martin, Håvard Kauserud, Stéphane Hacquard
more...
No comment yet.
Rescooped by Kirk Broders from MycorWeb Plant-Microbe Interactions
Scoop.it!

Seven common mistakes in population genetics and how to avoid them

Since the data resulting from modern genotyping tools are astoundingly complex, genotyping studies require great care in the sampling design, genotyping, data analysis and interpretation. Such care is necessary because, with datasets containing thousands of loci, small biases can easily become strongly significant patterns. Such biases may already be present in routine tasks that are present in almost every genotyping study. Here, I discuss seven common mistakes that can be frequently encountered in the genotyping literature: (i) giving more attention to genotyping than to sampling; (ii) failing to perform or report experimental randomisation in the lab; (iii) equating geopolitical borders with biological borders; (iv) testing significance of clustering output; (v) misinterpreting Mantel's r statistic; (vi) only interpreting a single value of k; (vii) forgetting that only a small portion of the genome will be associated with climate. For every of those issues, I give some suggestions how to avoid these mistakes. Overall, I argue that genotyping studies would benefit from establishing a more rigorous experimental design, involving proper sampling design, randomisation and better distinction of a priori hypotheses and exploratory analyses.

Via Francis Martin
more...
No comment yet.
Rescooped by Kirk Broders from Molecular basis of fungicide resistance
Scoop.it!

QTL mapping of fungicide sensitivity reveals novel genes and pleiotropy with melanization in the pathogen Zymoseptoria tritici - Lendenmann et al - Fungal Genetics & Biology

QTL mapping of fungicide sensitivity reveals novel genes and pleiotropy with melanization in the pathogen Zymoseptoria tritici - Lendenmann et al - Fungal Genetics & Biology | Fungal population biology | Scoop.it

A major problem associated with the intensification of agriculture is the emergence of fungicide resistance. Azoles are ergosterol biosynthesis inhibitors that have been widely used in agriculture and medicine since the 1970s, leading to emergence of increasingly resistant fungal populations. The known genetic mechanisms underlying lower azole sensitivity include mutations affecting the CYP51 gene that encodes the target protein, but in many cases azole resistance is a more complex trait with an unknown genetic basis. We used quantitative trait locus (QTL) mapping to identify genes affecting azole sensitivity in two crosses of Zymoseptoria tritici, the most damaging wheat pathogen in Europe. Restriction site associated DNA sequencing (RADseq) was used to genotype 263 (cross 1) and 261 (cross 2) progeny at ∼8500 single nucleotide polymorphisms (SNP) and construct two dense linkage maps. Azole sensitivity was assessed using high-throughput digital image analysis of colonies growing on Petri dishes with or without the fungicide propiconazole. We identified three QTLs for azole sensitivity, including two that contained novel fungicide sensitivity genes. One of these two QTLs contained only 16 candidate genes, among which four most likely candidates were identified. The third QTL contained ERG6, encoding another protein involved in ergosterol biosynthesis. Known genes in QTLs affecting colony growth included CYP51 and PKS1, a gene affecting melanization in Z. tritici. PKS1 showed compelling evidence for pleiotropy, with a rare segregating allele that increased melanization while decreasing growth rate and propiconazole sensitivity. This study resolved the genetic architecture of an important agricultural trait and led to identification of novel genes that are likely to affect azole sensitivity in Z. tritici. It also provided insight into fitness costs associated with lowered azole sensitivity and suggests a novel fungicide mixture strategy.


Via Melvin Bolton
more...
No comment yet.
Scooped by Kirk Broders
Scoop.it!

The population biology of fungal invasions - Gladieux - 2015 - Molecular Ecology - Wiley Online Library

The population biology of fungal invasions - Gladieux - 2015 - Molecular Ecology - Wiley Online Library | Fungal population biology | Scoop.it
more...
No comment yet.
Rescooped by Kirk Broders from microbial pathogenesis and plant immunity
Scoop.it!

Nature Biotech: Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture (2016)

Nature Biotech: Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture (2016) | Fungal population biology | Scoop.it

Wild relatives of domesticated crop species harbor multiple, diverse, disease resistance (R) genes that could be used to engineer sustainable disease control. However, breeding R genes into crop lines often requires long breeding timelines of 5–15 years to break linkage between R genes and deleterious alleles (linkage drag). Further, when R genes are bred one at a time into crop lines, the protection that they confer is often overcome within a few seasons by pathogen evolution1. If several cloned R genes were available, it would be possible to pyramid R genes2 in a crop, which might provide more durable resistance1. We describe a three-step method (MutRenSeq)-that combines chemical mutagenesis with exome capture and sequencing for rapid R gene cloning. We applied MutRenSeq to clone stem rust resistance genes Sr22 and Sr45 from hexaploid bread wheat. MutRenSeq can be applied to other commercially relevant crops and their relatives, including, for example, pea, bean, barley, oat, rye, rice and maize.


Via The Sainsbury Lab, Kamoun Lab @ TSL, Jim Alfano
more...
The Sainsbury Lab's curator insight, April 26, 4:14 AM
Wild relatives of domesticated crop species harbor multiple, diverse, disease resistance (R) genes that could be used to engineer sustainable disease control. However, breeding R genes into crop lines often requires long breeding timelines of 5–15 years to break linkage between R genes and deleterious alleles (linkage drag). Further, when R genes are bred one at a time into crop lines, the protection that they confer is often overcome within a few seasons by pathogen evolution1. If several cloned R genes were available, it would be possible to pyramid R genes2 in a crop, which might provide more durable resistance1. We describe a three-step method (MutRenSeq)-that combines chemical mutagenesis with exome capture and sequencing for rapid R gene cloning. We applied MutRenSeq to clone stem rust resistance genes Sr22 and Sr45 from hexaploid bread wheat. MutRenSeq can be applied to other commercially relevant crops and their relatives, including, for example, pea, bean, barley, oat, rye, rice and maize.
Neelam Redekar's curator insight, April 29, 8:19 AM
Share your insight
Rescooped by Kirk Broders from Publications
Scoop.it!

bioRxiv: In planta expression screens of candidate effector proteins from the wheat yellow rust fungus reveal processing bodies as a pathogen-targeted plant cell compartment (2015)

bioRxiv: In planta expression screens of candidate effector proteins from the wheat yellow rust fungus reveal processing bodies as a pathogen-targeted plant cell compartment (2015) | Fungal population biology | Scoop.it

Rust fungal pathogens of wheat (Triticum spp.) affect crop yields worldwide. The molecular mechanisms underlying the virulence of these pathogens remain elusive, due to the limited availability of suitable molecular genetic research tools. Notably, the inability to perform high-throughput analyses of candidate virulence proteins (also known as effectors) impairs progress. We previously established a pipeline for the fast-forward screens of rust fungal effectors in the model plant Nicotiana benthamiana. This pipeline involves selecting candidate effectors in silico and performing cell biology and protein-protein interaction assays in planta to gain insight into the putative functions of candidate effectors. In this study, we used this pipeline to identify and characterize sixteen candidate effectors from the wheat yellow rust fungal pathogen Puccinia striiformis f sp tritici. Nine candidate effectors targeted a specific plant subcellular compartment or protein complex, providing valuable information on their putative functions in plant cells. One candidate effector, PST02549, accumulated in processing bodies (P-bodies), protein complexes involved in mRNA decapping, degradation, and storage. PST02549 also associates with the P-body-resident ENHANCER OF mRNA DECAPPING PROTEIN 4 (EDC4) from N. benthamiana and wheat. Our work identifies P-bodies as a novel plant cell compartment targeted by pathogen effectors.


Via Kamoun Lab @ TSL
more...
No comment yet.
Rescooped by Kirk Broders from Plant-Microbe Symbiosis
Scoop.it!

Root Microbiome Assemblage is Modulated by Plant Host Factors

Root Microbiome Assemblage is Modulated by Plant Host Factors | Fungal population biology | Scoop.it
In recent years, the term plant microbiome inhabiting the root interior of healthy plants, as well as the rhizosphere, has received substantial attention, since it influences nutrient availability, plant growth promotion and disease suppression. The community structure and diversity of plant-associated microbiome is well characterized in modern systems such as Arabidopsis, maize and rice using deep rRNA gene sequencing techniques. Increasing evidence indicates that composition of root exudates secreted by host plants can shape the soil microbiome. The molecular communication fluctuates according to the plant genotype, plant development stage, biotic/abiotic stress, proximity to neighbouring species, management techniques and many other factors which may shape the rhizospheric microbiome. Plants secretes blends of organic compounds that are differentially produced at distinct stages of development to help orchestrate rhizosphere microbiome assemblage. A comprehensive understanding of the mechanisms that govern selection and activity of microbial communities by plant roots will provide new opportunities to increase crop production. Hence, this chapter focuses mainly on existing knowledge based on the root microbiome, its functional importance and potential influence of host plant to the establishment of its rhizospheric associates.

Via Jean-Michel Ané
more...
No comment yet.
Rescooped by Kirk Broders from Plant-Microbe Symbiosis
Scoop.it!

Endophytic fungi: resource for gibberellins and crop abiotic stress resistance

Endophytic fungi: resource for gibberellins and crop abiotic stress resistance | Fungal population biology | Scoop.it
The beneficial effects of endophytes on plant growth are important for agricultural ecosystems because they reduce the need for fertilizers and decrease soil and water pollution while compensating for environmental perturbations. Endophytic fungi are a novel source of bioactive secondary metabolites; moreover, recently they have been found to produce physiologically active gibberellins as well. The symbiosis of gibberellins producing endophytic fungi with crops can be a promising strategy to overcome the adverse effects of abiotic stresses. The association of such endophytes has not only increased plant biomass but also ameliorated plant-growth during extreme environmental conditions. Endophytic fungi represent a trove of unexplored biodiversity and a frequently overlooked component of crop ecology. The present review describes the role of gibberellins producing endophytic fungi, suggests putative mechanisms involved in plant endophyte stress interactions and discusses future prospects in this field.

Via Jean-Michel Ané
more...
Steve Marek's curator insight, October 15, 2015 11:24 AM

Nice review on phytohormone producing endophytic fungi.

Not sure if structures shown in roots (e, above) are from Penicillium resedanum.  Look like chytrid resting spores.

Rescooped by Kirk Broders from Plant pathogenic fungi
Scoop.it!

Phylogenomics and evolution of secondary metabolism in plant-associated fungi

Phylogenomics and evolution of secondary metabolism in plant-associated fungi | Fungal population biology | Scoop.it

Highlights
• Secondary metabolites are small, bioactive molecules that function in fungal ecology.
• Genomic sequencing has revealed greater diversity of secondary metabolite clusters than previously detected.
• The modular nature of some secondary metabolite core genes promotes evolutionary and functional diversification.
• Duplication and divergence and module fusion are two major drivers of NRPS diversification.


Via Steve Marek
more...
No comment yet.
Rescooped by Kirk Broders from Plant-Microbe Symbiosis
Scoop.it!

Impact of plant domestication on rhizosphere microbiome assembly and functions

The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars that may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Here, we review how plants shape the rhizosphere microbiome and how domestication may have impacted rhizosphere microbiome assembly and functions via habitat expansion and via changes in crop management practices, root exudation, root architecture, and plant litter quality. We also propose a “back to the roots” framework that comprises the exploration of the microbiome of indigenous plants and their native habitats for the identification of plant and microbial traits with the ultimate goal to reinstate beneficial associations that may have been undermined during plant domestication.

Via Jean-Michel Ané
more...
No comment yet.
Scooped by Kirk Broders
Scoop.it!

Colonization History, Host Distribution, Anthropogenic Influence and Landscape Features Shape Populations of White Pine Blister Rust, an Invasive Alien Tree Pathogen

Colonization History, Host Distribution, Anthropogenic Influence and Landscape Features Shape Populations of White Pine Blister Rust, an Invasive Alien Tree Pathogen | Fungal population biology | Scoop.it
White pine blister rust is caused by the fungal pathogen Cronartium ribicola J.C. Fisch (Basidiomycota, Pucciniales). This invasive alien pathogen was introduced into North America at the beginning of the 20th century on pine seedlings imported from Europe and has caused serious economic and ecological impacts. In this study, we applied a population and landscape genetics approach to understand the patterns of introduction and colonization as well as population structure and migration of C . ribicola . We characterized 1,292 samples of C . ribicola from 66 geographic locations in North America using single nucleotide polymorphisms (SNPs) and evaluated the effect of landscape features, host distribution, and colonization history on the structure of these pathogen populations. We identified eastern and western genetic populations in North America that are strongly differentiated. Genetic diversity is two to five times higher in eastern populations than in western ones, which can be explained by the repeated accidental introductions of the pathogen into northeastern North America compared with a single documented introduction into western North America. These distinct genetic populations are maintained by a barrier to gene flow that corresponds to a region where host connectivity is interrupted. Furthermore, additional cryptic spatial differentiation was identified in western populations. This differentiation corresponds to landscape features, such as mountain ranges, and also to host connectivity. We also detected genetic differentiation between the pathogen populations in natural stands and plantations, an indication that anthropogenic movement of this pathogen still takes place. These results highlight the importance of monitoring this invasive alien tree pathogen to prevent admixture of eastern and western populations where different pathogen races occur.
more...
No comment yet.
Rescooped by Kirk Broders from MycorWeb Plant-Microbe Interactions
Scoop.it!

Demystifying computer science for molecular ecologists

Demystifying computer science for molecular ecologists | Fungal population biology | Scoop.it

In this age of data-driven science and high-throughput biology, computational thinking is becoming an increasingly important skill for tackling both new and long-standing biological questions. However, despite its obvious importance and conspicuous integration into many areas of biology, computer science is still viewed as an obscure field that has, thus far, permeated into only a few of the biology curricula across the nation. A national survey has shown that lack of computational literacy in environmental sciences is the norm rather than the exception [Valle & Berdanier (2012) Bulletin of the Ecological Society of America, 93, 373–389]. In this article, we seek to introduce a few important concepts in computer science with the aim of providing a context-specific introduction aimed at research biologists. Our goal was to help biologists understand some of the most important mainstream computational concepts to better appreciate bioinformatics methods and trade-offs that are not obvious to the uninitiated.


Via Francis Martin
more...
No comment yet.
Rescooped by Kirk Broders from Plant & Evolution
Scoop.it!

Rice responds to endophytic colonization which is independent of the common symbiotic signaling pathway

Rice responds to endophytic colonization which is independent of the common symbiotic signaling pathway | Fungal population biology | Scoop.it

As molecular interactions of plants with N2-fixing endophytes are largely uncharacterized, we investigated whether the common signaling pathway (CSP) shared by root nodule symbioses (RNS) and arbuscular mycorrhizal (AM) symbioses may have been recruited for the endophytic Azoarcus sp.–rice (Oryza sativa) interaction, and combined this investigation with global approaches to characterize rice root responses to endophytic colonization.Putative homologs of genes required for the CSP were analyzed for their putative role in endophytic colonization. Proteomic and suppressive subtractive hybridization (SSH) approaches were also applied, and a comparison of defense-related processes was carried out by setting up a pathosystem for flooded roots with Xanthomonas oryzae pv. oryzae strain PXO99 (Xoo).All tested genes were expressed in rice roots seedlings but not induced upon Azoarcus sp. inoculation, and the oscyclops andoscastor mutants were not impaired in endophytic colonization. Global approaches highlighted changes in rice metabolic activity and Ca2+-dependent signaling in roots colonized by endophytes, including some stress proteins. Marker genes for defense responses were induced to a lesser extent by the endophytes than by the pathogen, indicating a more compatible interaction.Our results thus suggest that rice roots respond to endophytic colonization by inducing metabolic shifts and signaling events, for which the CSP is not essential.


Via Pierre-Marc Delaux
more...
No comment yet.
Rescooped by Kirk Broders from Plants and Microbes
Scoop.it!

Nature: Phylogenetic structure and host abundance drive disease pressure in communities (2015)

Nature: Phylogenetic structure and host abundance drive disease pressure in communities (2015) | Fungal population biology | Scoop.it

 

Pathogens play an important part in shaping the structure and dynamics of natural communities, because species are not affected by them equally1, 2. A shared goal of ecology and epidemiology is to predict when a species is most vulnerable to disease. A leading hypothesis asserts that the impact of disease should increase with host abundance, producing a ‘rare-species advantage’3, 4, 5. However, the impact of a pathogen may be decoupled from host abundance, because most pathogens infect more than one species, leading to pathogen spillover onto closely related species6, 7. Here we show that the phylogenetic and ecological structure of the surrounding community can be important predictors of disease pressure. We found that the amount of tissue lost to disease increased with the relative abundance of a species across a grassland plant community, and that this rare-species advantage had an additional phylogenetic component: disease pressure was stronger on species with many close relatives. We used a global model of pathogen sharing as a function of relatedness between hosts, which provided a robust predictor of relative disease pressure at the local scale. In our grassland, the total amount of disease was most accurately explained not by the abundance of the focal host alone, but by the abundance of all species in the community weighted by their phylogenetic distance to the host. Furthermore, the model strongly predicted observed disease pressure for 44 novel host species we introduced experimentally to our study site, providing evidence for a mechanism to explain why phylogenetically rare species are more likely to become invasive when introduced8, 9. Our results demonstrate how the phylogenetic and ecological structure of communities can have a key role in disease dynamics, with implications for the maintenance of biodiversity, biotic resistance against introduced weeds, and the success of managed plants in agriculture and forestry.


Se also News & Views 

http://www.nature.com/nature/journal/v520/n7548/full/520446a.html


Via Kamoun Lab @ TSL
more...
No comment yet.
Rescooped by Kirk Broders from MycorWeb Plant-Microbe Interactions
Scoop.it!

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi | Fungal population biology | Scoop.it
Rapid development of high-throughput (HTS) molecular identification methods has revolutionized our knowledge about taxonomic diversity and ecology of fungi. However, PCR-based methods exhibit multiple technical shortcomings that may bias our understanding of the fungal kingdom. This study was initiated to quantify potential biases in fungal community ecology by comparing the relative performance of amplicon-free shotgun metagenomics and amplicons of nine primer pairs over seven nuclear ribosomal DNA (rDNA) regions often used in metabarcoding analyses. The internal transcribed spacer (ITS) barcodes ITS1 and ITS2 provided greater taxonomic and functional resolution and richness of operational taxonomic units (OTUs) at the 97% similarity threshold compared to barcodes located within the ribosomal small subunit (SSU) and large subunit (LSU) genes. All barcode-primer pair combinations provided consistent results in ranking taxonomic richness and recovering the importance of floristic variables in driving fungal community composition in soils of Papua New Guinea. The choice of forward primer explained up to 2.0% of the variation in OTU-level analysis of the ITS1 and ITS2 barcode data sets. Across the whole data set, barcode-primer pair combination explained 37.6–38.1% of the variation, which surpassed any environmental signal. Overall, the metagenomics data set recovered a similar taxonomic overview, but resulted in much lower fungal rDNA sequencing depth, inability to infer OTUs, and high uncertainty in identification. We recommend the use of ITS2 or the whole ITS region for metabarcoding and we advocate careful choice of primer pairs in consideration of the relative proportion of fungal DNA and expected dominant groups.

Via Francis Martin
more...
No comment yet.
Rescooped by Kirk Broders from How microbes emerge
Scoop.it!

Crop pathogen emergence and evolution in agro-ecological landscapes - Papaïx - 2015 - Evolutionary Applications - Wiley Online Library

Crop pathogen emergence and evolution in agro-ecological landscapes - Papaïx - 2015 - Evolutionary Applications - Wiley Online Library | Fungal population biology | Scoop.it

Remnant areas hosting natural vegetation in agricultural landscapes can impact the disease epidemiology and evolutionary dynamics of crop pathogens. However, the potential consequences for crop diseases of the composition, the spatial configuration and the persistence time of the agro-ecological interface – the area where crops and remnant vegetation are in contact – have been poorly studied. Here, we develop a demographic–genetic simulation model to study how the spatial and temporal distribution of remnant wild vegetation patches embedded in an agricultural landscape can drive the emergence of a crop pathogen and its subsequent specialization on the crop host. We found that landscape structures that promoted larger pathogen populations on the wild host facilitated the emergence of a crop pathogen, but such landscape structures also reduced the potential for the pathogen population to adapt to the crop. In addition, the evolutionary trajectory of the pathogen population was determined by interactions between the factors describing the landscape structure and those describing the pathogen life histories. Our study contributes to a better understanding of how the shift of land-use patterns in agricultural landscapes might influence crop diseases to provide predictive tools to evaluate management practices.


Via Niklaus Grunwald
more...
No comment yet.