MycorWeb Plant-Mi...
Follow
Find
51.1K views | +98 today
 
Rescooped by Francis Martin from Plant pathogens and pests
onto MycorWeb Plant-Microbe Interactions
Scoop.it!

Mechanisms of Nutrient Acquisition and Utilization During Fungal Infections of Leaves

Mechanisms of Nutrient Acquisition and Utilization During Fungal Infections of Leaves | MycorWeb Plant-Microbe Interactions | Scoop.it

Foliar fungal pathogens challenge global food security, but how they optimize growth and development during infection is understudied. Despite adopting several lifestyles to facilitate nutrient acquisition from colonized cells, little is known about the genetic underpinnings governing pathogen adaption to host-derived nutrients. Homologs of common global and pathway-specific gene regulatory elements are likely to be involved, but their contribution to pathogenicity, and how they are connected to broader genetic networks, is largely unspecified. Here, we focus on carbon and nitrogen metabolism in foliar pathogens and consider what is known, and what is not known, about fungal exploitation of host nutrient and ask how common metabolic regulators have been co-opted to the plant-pathogenic lifestyle as well as how nutrients are utilized to drive infection.


Via Christophe Jacquet
more...
No comment yet.
MycorWeb Plant-Microbe Interactions
Your new post is loading...
Your new post is loading...
Scooped by Francis Martin
Scoop.it!

The big five of the monocot genomes

The big five of the monocot genomes | MycorWeb Plant-Microbe Interactions | Scoop.it
Monocots represent a monophyletic clade of the angiosperms that — based on fossil and molecular records — originated at around the Early Cretaceous from aquatic and wetland ancestors. Among their members are important crops including maize, wheat, rice, sorghum and barley, accounting for the major source for the daily calorie uptake by humans. Reflecting this importance, the partly large and complex genomes of these plants were major targets for ambitious and innovative sequencing projects, which will be discussed in this review article.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Mitochondrial comparative genomics and phylogenetic signal assessment of mtDNA among arbuscular mycorrhizal fungi

Mitochondrial comparative genomics and phylogenetic signal assessment of mtDNA among arbuscular mycorrhizal fungi | MycorWeb Plant-Microbe Interactions | Scoop.it

Mitochondrial (mt) genes, such as cytochrome C oxidase genes (cox), have been widely used for barcoding in many groups of organisms, although this approach has been less powerful in the fungal kingdom due to the rapid evolution of their mt genomes. The use of mt genes in phylogenetic studies of Dikarya has been met with success, while early diverging fungal lineages remain less studied, particularly the arbuscular mycorrhizal fungi (AMF). Advances in next-generation sequencing have substantially increased the number of publically available mtDNA sequences for the Glomeromycota. As a result, comparison of mtDNA across key AMF taxa can now be applied to assess the phylogenetic signal of individual mt coding genes, as well as concatenated subsets of coding genes. Here we show comparative analyses of publically available mt genomes of Glomeromycota, augmented with two mtDNA genomes that were newly sequenced for this study (Rhizophagus irregularis DAOM240159 and Glomus aggregatum DAOM240163), resulting in 16 complete mtDNA datasets. R. irregularis isolate DAOM240159 and G. aggregatum isolate DAOM240163 showed mt genomes measuring 72,293 bp and 69,505 bp with G + C contents of 37.1% and 37.3%, respectively. We assessed the phylogenies inferred from single mt genes and complete sets of coding genes, which are referred to as “supergenes” (16 concatenated coding genes), using Shimodaira–Hasegawa tests, in order to identify genes that best described AMF phylogeny. We found that rnl, nad5, cox1, and nad2 genes, as well as concatenated subset of these genes, provided phylogenies that were similar to the supergene set. This mitochondrial genomic analysis was also combined with principal coordinate and partitioning analyses, which helped to unravel certain evolutionary relationships in the Rhizophagus genus and for G. aggregatum within the Glomeromycota. We showed evidence to support the position of G. aggregatum within the R. irregularis ‘species complex’.

more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Ancient DNA and the rewriting of human history: be sparing with Occam’s razor

Ancient DNA and the rewriting of human history: be sparing with Occam’s razor | MycorWeb Plant-Microbe Interactions | Scoop.it
The human past on many timescales is of broad intrinsic interest, and genetics contributes to our understanding of it, as do paleontology, archaeology, linguistics and other disciplines. Geneticists have long studied present-day populations to glean information about their past, using models to infer past population events such as migrations or replacements, generally invoking Occam’s razor to favor the simplest model consistent with the data. But this is not the most straightforward approach to understanding such events: the obvious way to study any aspect of human genetic history is to analyze population samples from before, during and after the period of interest, and to simply catalogue the changes. Advances in ancient DNA (aDNA) technology are now beginning to make this more direct approach possible, facilitated by new sequencing technologies that are now capable of generating gigabases of data at moderate cost (Box 1). This abundance of data, combined with an understanding of the damage patterns indicative of authentic aDNA, greatly simplify the recognition and avoidance of the bugbear of the field: contamination.

Here, we review some of the key events in the peopling of the world in the light of recent aDNA findings, discussing new evidence for how migration, admixture and selection have shaped human populations.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Plankton networks driving carbon export in the oligotrophic ocean : Nature

Plankton networks driving carbon export in the oligotrophic ocean : Nature | MycorWeb Plant-Microbe Interactions | Scoop.it

The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.

more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

A symbiotic SNARE protein generated by alternative termination of transcription

A symbiotic SNARE protein generated by alternative termination of transcription | MycorWeb Plant-Microbe Interactions | Scoop.it
Many microbes interact with their hosts across a membrane interface, which is often distinct from existing membranes. Understanding how this interface acquires its identity has significant implications. In the symbiosis between legumes and rhizobia, the symbiosome encases the intracellular bacteria and receives host secretory proteins important for bacterial development. We show that the Medicago truncatula SYNTAXIN 132 (SYP132) gene undergoes alternative cleavage and polyadenylation during transcription, giving rise to two target-membrane soluble NSF attachment protein receptor (t-SNARE) isoforms. One of these isoforms, SYP132A, is induced during the symbiosis, is able to localize to the peribacteroid membrane, and is required for the maturation of symbiosomes into functional forms. The second isoform, SYP132C, has important functions unrelated to symbiosis. The SYP132A sequence is broadly found in flowering plants that form arbuscular mycorrhizal symbiosis, an ancestral mutualism between soil fungi and most land plants. SYP132A silencing severely inhibited arbuscule colonization, indicating that SYP132A is an ancient factor specifying plant–microbe interfaces.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

How plants interact with beneficial microbes in the soil

Scientists have wondered for years how legumes such as soybeans, whose roots host nitrogen-fixing bacteria that produce essential plant nutrients out of thin air, are able to recognize these bacteria as both friendly and distinct from their own cells, and how the host plant's specialized proteins find the bacteria and use the nutritional windfall.

Now a team of molecular biologists led by Dong Wang at the University of Massachusetts Amherst, working with the alfalfa-clover Medicago truncatula, has found how a gene in the host plant encodes a protein that recognizes the cell membrane surrounding the symbiotic bacteria, then directs other proteins to harvest the nutrients. Details appear online in the January edition of Nature Plants.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

SSR-based identification of genetic groups within European populations of Tuber aestivum

SSR-based identification of genetic groups within European populations of Tuber aestivum | MycorWeb Plant-Microbe Interactions | Scoop.it
Tuber species are ectomycorrhizal ascomycetes establishing relationships with different host trees and forming hypogeous fruiting bodies known as truffles. Among Tuber species, Tuber aestivum Vittad. has a wide distributional range being found naturally all over Europe. Here, we performed large-scale population genetic analyses in T. aestivum to (i) investigate its genetic diversity at the European scale, (ii) characterize its genetic structure and test for the presence of ecotypes and (iii) shed light into its demographic history. To reach these goals, 230 ascocarps from different populations were genotyped using 15 polymorphic simple sequence repeat markers. We identified 181 multilocus genotypes and four genetic groups which did not show a clear geographical separation; although, one of them was present exclusively in Southeast France, Italy and Spain. Fixation index values between pairs of genetic groups were generally high and ranged from 0.29 to 0.45. A significant deficit of heterozygosity indicated a population expansion instead of a recent population bottleneck, suggesting that T. aestivum is not endangered in Europe, not even in Mediterranean regions. Our study based on a large-scale population genetic analysis suggests that genetically distinct populations and likely ecotypes within T. aestivum are present. In turn, this study paves the way to future investigations aimed at addressing the biological and/or ecological factors that have concurred in shaping the population genetic structure of this species. Present results should also have implications for the truffle market since defining genetic markers are now possible at least for some specific T. aestivum genetic groups.
more...
Daniel Wipf's curator insight, February 8, 2:03 AM

Our last T. aestivum paper by @Verzinie @UMRAgroecologie

Scooped by Francis Martin
Scoop.it!

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis | MycorWeb Plant-Microbe Interactions | Scoop.it
Rapid advancements in sequencing technologies along with falling costs present widespread opportunities for microbiome studies across a vast and diverse array of environments. These impressive technological developments have been accompanied by a considerable growth in the number of methodological variables, including sampling, storage, DNA extraction, primer pairs, sequencing technology, chemistry version, read length, insert size, and analysis pipelines, amongst others. This increase in variability threatens to compromise both the reproducibility and the comparability of studies conducted. Here we perform the first reported study comparing both amplicon and shotgun sequencing for the three leading next-generation sequencing technologies. These were applied to six human stool samples using Illumina HiSeq, MiSeq and Ion PGM shotgun sequencing, as well as amplicon sequencing across two variable 16S rRNA gene regions. Notably, we found that the factor responsible for the greatest variance in microbiota composition was the chosen methodology rather than the natural inter-individual variance, which is commonly one of the most significant drivers in microbiome studies. Amplicon sequencing suffered from this to a large extent, and this issue was particularly apparent when the 16S rRNA V1-V2 region amplicons were sequenced with MiSeq. Somewhat surprisingly, the choice of taxonomic binning software for shotgun sequences proved to be of crucial importance with even greater discriminatory power than sequencing technology and choice of amplicon. Optimal N50 assembly values for the HiSeq was obtained for 10 million reads per sample, whereas the applied MiSeq and PGM sequencing depths proved less sufficient for shotgun sequencing of stool samples. The latter technologies, on the other hand, provide a better basis for functional gene categorisation, possibly due to their longer read lengths. Hence, in addition to highlighting methodological biases, this study demonstrates the risks associated with comparing data generated using different strategies. We also recommend that laboratories with particular interests in certain microbes should optimise their protocols to accurately detect these taxa using different techniques.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Rainforest regrowth boosts carbon capture, study shows - BBC News

Rainforest regrowth boosts carbon capture, study shows - BBC News | MycorWeb Plant-Microbe Interactions | Scoop.it
Secondary rainforests - if allowed to flourish in the right conditions - can absorb 11 times as much carbon as old-growth rainforests, a study shows.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

The mite that jumped, the bee that traveled, the disease that followed

The mite that jumped, the bee that traveled, the disease that followed | MycorWeb Plant-Microbe Interactions | Scoop.it
European honeybees are among the best-studied and most widely recognized insect species in the world. Originally kept for honey production, they have become the flagship species for pollination and large-scale agriculture. Since large colony losses were reported across the United States in 2006, researchers have investigated the myriad factors that contribute to the decline in honeybee populations. In particular, the aptly named Varroa destructor mite (see the photo) and the deformed wing virus (DWV) have been clearly linked to colony collapse (1). On page 594 of this issue, Wilfert et al. use a phylogeographic analysis to examine the evolutionary origin and mechanisms for the global spread of the DWV (2).

Based on molecular data from 17 countries and 32 geographical regions, the authors confirm that DWV is an endemic pathogen of the European honeybee, Apis mellifera (see the figure). Thus, the recent honeybee decline associated with DWV constitutes the reemergence of a previously existing disease of A. mellifera. This reemergence was facilitated by the spread of the new vector V. destructor and by human transport of honeybee colonies from Europe and North America to other geographical regions.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Europe’s forest management did not mitigate climate warming

Europe’s forest management did not mitigate climate warming | MycorWeb Plant-Microbe Interactions | Scoop.it

Afforestation and forest management are considered to be key instruments in mitigating climate change. Here we show that since 1750, in spite of considerable afforestation, wood extraction has led to Europe’s forests accumulating a carbon debt of 3.1 petagrams of carbon. We found that afforestation is responsible for an increase of 0.12 watts per square meter in the radiative imbalance at the top of the atmosphere, whereas an increase of 0.12 kelvin in summertime atmospheric boundary layer temperature was mainly caused by species conversion. Thus, two and a half centuries of forest management in Europe have not cooled the climate. The political imperative to mitigate climate change through afforestation and forest management therefore risks failure, unless it is recognized that not all forestry contributes to climate change mitigation.

more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Identification of genes regulated by histone acetylation during root development in Populus trichocarpa

Identification of genes regulated by histone acetylation during root development in Populus trichocarpa | MycorWeb Plant-Microbe Interactions | Scoop.it

Background

Histone deacetylases (HDACs) are key enzymes catalyzing the removal of acetyl groups from histones. HDACs act in concert with histone acetyltransferases (HATs) to regulate histone acetylation status, which modifies chromatin structure, affecting gene transcription and thus regulating multiple biological processes such as plant growth and development. Over a decade, certain HDACs in herbaceous plants have been deeply studied. However, functions of HDACs in woody plants are not well understood.


Results
Histone deacetylase specific inhibitor trichostatin A (TSA) was used to investigate the role of HDACs in organogenesis of roots and root development in Populus trochocarpa. The adventitious roots were regenerated and grown on medium supplemented with 0, 1, and 2.5 μM TSA. TSA treatment delayed root regeneration and inhibited primary root growth. To examine the genes modified by TSA in the regenerated roots, tag-based digital gene expression (DGE) analysis was performed using Illumina HiSeqTM 2000. Approximately 4.5 million total clean tags were mapped per library. The distinct clean tags for the three libraries corresponding to 0, 1 and 2.5 μM TSA treatment were 166167, 143103 and 153507, from which 38.45 %, 31.84 % and 38.88 % were mapped unambiguously to the unigene database, respectively. Most of the tags were expressed at similar levels, showing a < 5-fold difference after 1 μM and 2.5 μM TSA treatments and the maximum fold-change of the tag copy number was around 20. The expression levels of many genes in roots were significantly altered by TSA. A total of 36 genes were up-regulated and 1368 genes were down-regulated after 1 μM TSA treatment, while 166 genes were up-regulated and 397 genes were down-regulated after 2.5 μM TSA treatment. Gene ontology (GO) and pathway analyses indicated that the differentially expressed genes were related to many kinds of molecular functions and biological processes. The genes encoding key enzymes catalyzing gibberellin biosynthesis were significantly down-regulated in the roots exposed to 2.5 μM TSA and their expression changes were validated by using real-time PCR.


Conclusions
HDACs were required for de novo organogenesis and normal growth of populus roots. DGE data provides the gene profiles in roots probably regulated by histone acetylation during root growth and development, which will lead to a better understanding of the mechanism controlling root development.

more...
No comment yet.
Rescooped by Francis Martin from The Plant Microbiome
Scoop.it!

Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes

Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes | MycorWeb Plant-Microbe Interactions | Scoop.it

Given the recently appreciated complexity of symbioses among hosts and their microbes, significant rethinking in biology is occurring today. Scientists and philosophers are asking questions at new biological levels of hierarchical organization - What is a holobiont and hologenome? When should this vocabulary and associated concepts apply? Are these points of view a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Legitimate questions, advancements and revisions are warranted at this nascent stage of the field. However, a productive and meaningful discourse can only commence when skeptics and proponents alike use the same definitions and constructs. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not necessarily the primary unit of selection is not synonymous with arguing that it is not a unit of selection in general. Here, we succinctly deconstruct and clarify these recent misconceptions. Holobionts (hosts and their microbes) and hologenomes (all genomes of the holobiont) are multipartite entities that result from ecological, evolutionary and genetic processes. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome. We invite the community to consider these new perspectives in biology.


Via Stéphane Hacquard
more...
Ryohei Thomas Nakano's curator insight, February 3, 3:46 AM

[ For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not necessarily the primary unit of selection is not synonymous with arguing that it is not a unit of selection in general. ]

 

Absolutely.

Scooped by Francis Martin
Scoop.it!

The effector candidate repertoire of the arbuscular mycorrhizal fungus Rhizophagus clarus

The effector candidate repertoire of the arbuscular mycorrhizal fungus Rhizophagus clarus | MycorWeb Plant-Microbe Interactions | Scoop.it

Background

Arbuscular mycorrhizal fungi (AMF) form an ecologically important symbiosis with more than two thirds of studied land plants. Recent studies of plant-pathogen interactions showed that effector proteins play a key role in host colonization by controlling the plant immune system. We hypothesise that also for symbiotic-plant interactions the secreted effectome of the fungus is a major component of communication and the conservation level of effector proteins between AMF species may be indicative whether they play a fundamental role.

 

Results
In this study, we used a bioinformatics pipeline to predict and compare the effector candidate repertoire of the two AMF species, Rhizophagus irregularis and Rhizophagus clarus. Our in silico pipeline revealed a list of 220 R. irregularis candidate effector genes that create a valuable information source to elucidate the mechanism of plant infection and colonization by fungi during AMF symbiotic interaction. While most of the candidate effectors show no homologies to known domains or proteins, the candidates with homologies point to potential roles in signal transduction, cell wall modification or transcription regulation. A remarkable aspect of our work is presence of a large portion of the effector proteins involved in symbiosis, which are not unique to each fungi or plant species, but shared along the Glomeromycota phylum. For 95 % of R. irregularis candidates we found homologs in a R. clarus genome draft generated by Illumina high-throughput sequencing. Interestingly, 9 % of the predicted effectors are at least as conserved between the two Rhizophagus species as proteins with housekeeping functions (similarity > 90 %). Therefore, we state that this group of highly conserved effector proteins between AMF species may play a fundamental role during fungus-plant interaction.

 

Conclusions
We hypothesise that in symbiotic interactions the secreted effectome of the fungus might be an important component of communication. Identification and functional characterization of the primary AMF effectors that regulate symbiotic development will help in understanding the mechanisms of fungus-plant interaction.

more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Le berger du Haut-Languedoc nous écrit une lettre émouvante

Le berger du Haut-Languedoc nous écrit une lettre émouvante | MycorWeb Plant-Microbe Interactions | Scoop.it
A la suite du portrait que nous lui avions consacré, son ânesse et son ânon ont été empoisonnés. Il songe désormais à arrêter son métier.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Genomic insights into the Ixodes scapularis tick vector of Lyme disease : Nature Communications

Genomic insights into the Ixodes scapularis tick vector of Lyme disease : Nature Communications | MycorWeb Plant-Microbe Interactions | Scoop.it

Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ~57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick–host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host ‘questing’, prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent

more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Real-time, portable genome sequencing for Ebola surveillance : Nature

Real-time, portable genome sequencing for Ebola surveillance : Nature | MycorWeb Plant-Microbe Interactions | Scoop.it
The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths. Genome sequencing in viral outbreaks is desirable to characterize the infectious agent and determine its evolutionary rate. Genome sequencing also allows the identification of signatures of host adaptation, identification and monitoring of diagnostic targets, and characterization of responses to vaccines and treatments. The Ebola virus (EBOV) genome substitution rate in the Makona strain has been estimated at between 0.87 × 10−3 and 1.42 × 10−3 mutations per site per year. This is equivalent to 16–27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions. Genomic surveillance during the epidemic has been sporadic owing to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities. To address this problem, here we devise a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. We present sequence data and analysis of 142 EBOV samples collected during the period March to October 2015. We were able to generate results less than 24 h after receiving an Ebola-positive sample, with the sequencing process taking as little as 15–60 min. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Comparative transcriptomic analyses of Zymoseptoria tritici strains show complex lifestyle transitions and intraspecific variability in transcription profiles

Comparative transcriptomic analyses of Zymoseptoria tritici strains show complex lifestyle transitions and intraspecific variability in transcription profiles | MycorWeb Plant-Microbe Interactions | Scoop.it
Zymoseptoria tritici causes Septoria tritici blotch (STB) on wheat. The disease interaction is characterized by clearly defined temporal phases of infection, ultimately resulting in the death of host tissue. Zymoseptoria tritici is a highly polymorphic species with significant intraspecific variation in virulence profiles. We generated a deep transcriptomic sequencing dataset spanning the entire time course of an infection using a previously uncharacterized, highly virulent Z. tritici strain isolated from a Swiss wheat field. We found that seven clusters of gene transcription profiles explained the progression of the infection. The earliest highly up-regulated genes included chloroperoxidases, which may help the fungus cope with plant defences. The onset of necrotrophy was characterized by a concerted up-regulation of proteases, plant cell wall-degrading enzymes and lipases. Functions related to nutrition and growth characterized late necrotrophy and the transition to saprotrophic growth on dead plant tissue. We found that the peak up-regulation of genes essential for mating coincided with the necrotrophic phase. We performed an intraspecies comparative transcriptomics analysis using a comparable time course infection experiment of the genome reference isolate IPO323. Major components of the fungal infection transcriptome were conserved between the two strains. However, individual small, secreted proteins, proteases and cell wall-degrading enzymes showed strongly differentiated transcriptional profiles between isolates. Our analyses illustrate that successful STB infections involve complex transcriptomic remodelling to up-regulate distinct gene functions. Heterogeneity in transcriptomes among isolates may explain some of the considerable variation in virulence and host specialization found within the species.
more...
No comment yet.
Rescooped by Francis Martin from Plant-Microbe Symbiosis
Scoop.it!

Dead fungal mycelium in forest soil represents a decomposition hotspot and a habitat for a specific microbial community

Turnover of fungal biomass in forest litter and soil represents an important process in the environment. To date, knowledge of mycelial decomposition has been derived primarily from short-term studies, and the guild of mycelium decomposers has been poorly defined.
Here, we followed the fate of the fruiting bodies of an ectomycorrhizal fungus in litter and soil of a temperate forest over 21 wk. The community of associated microbes and enzymatic processes in this specific substrate were described.
The decomposition of fungal fruiting bodies exhibited biphasic kinetics. The rapid initial phase, which included the disappearance of DNA, was followed by a slower turnover of the recalcitrant fraction. Compared with the surrounding litter and soil, the mycelium represented a hotspot of activity of several biopolymer-degrading enzymes and high bacterial biomass. Specific communities of bacteria and fungi were associated with decomposing mycelium. These communities differed between the initial and late phases of decomposition. The bacterial community associated with decomposing mycelia typically contained the genera Pedobacter, Pseudomonas, Variovorax, Chitinophaga, Ewingella and Stenotrophomonas, whereas the fungi were mostly nonbasidiomycetous r-strategists of the genera Aspergillus, Penicillium, Mortierella, Cladosporium and several others.
Decomposing ectomycorrhizal fungal mycelium exhibits high rates of decomposition and represents a specific habitat supporting a specific microbial community.

Via Jean-Michel Ané
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Convergence in Multispecies Interactions: Trends in Ecology & Evolution

Convergence in Multispecies Interactions: Trends in Ecology & Evolution | MycorWeb Plant-Microbe Interactions | Scoop.it
The concepts of convergent evolution and community convergence highlight how selective pressures can shape unrelated organisms or communities in similar ways. We propose a related concept, convergent interactions, to describe the independent evolution of multispecies interactions with similar physiological or ecological functions. A focus on convergent interactions clarifies how natural selection repeatedly favors particular kinds of associations among species. Characterizing convergent interactions in a comparative context is likely to facilitate prediction of the ecological roles of organisms (including microbes) in multispecies interactions and selective pressures acting in poorly understood or newly discovered multispecies systems. We illustrate the concept of convergent interactions with examples: vertebrates and their gut bacteria; ectomycorrhizae; insect–fungal–bacterial interactions; pitcher-plant food webs; and ants and ant–plants.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Biomass resilience of Neotropical secondary forests

Biomass resilience of Neotropical secondary forests | MycorWeb Plant-Microbe Interactions | Scoop.it
Land-use change occurs nowhere more rapidly than in the tropics, where the imbalance between deforestation and forest regrowth has large consequences for the global carbon cycle. However, considerable uncertainty remains about the rate of biomass recovery in secondary forests, and how these rates are influenced by climate, landscape, and prior land use. Here we analyse aboveground biomass recovery during secondary succession in 45 forest sites and about 1,500 forest plots covering the major environmental gradients in the Neotropics. The studied secondary forests are highly productive and resilient. Aboveground biomass recovery after 20 years was on average 122 megagrams per hectare (Mg ha−1), corresponding to a net carbon uptake of 3.05 Mg C ha−1 yr−1, 11 times the uptake rate of old-growth forests. Aboveground biomass stocks took a median time of 66 years to recover to 90% of old-growth values. Aboveground biomass recovery after 20 years varied 11.3-fold (from 20 to 225 Mg ha−1) across sites, and this recovery increased with water availability (higher local rainfall and lower climatic water deficit). We present a biomass recovery map of Latin America, which illustrates geographical and climatic variation in carbon sequestration potential during forest regrowth. The map will support policies to minimize forest loss in areas where biomass resilience is naturally low (such as seasonally dry forest regions) and promote forest regeneration and restoration in humid tropical lowland areas with high biomass resilience.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

The fate and age of carbon – insights into the storage and remobilization dynamics in trees

The fate and age of carbon – insights into the storage and remobilization dynamics in trees | MycorWeb Plant-Microbe Interactions | Scoop.it
The fate and age of carbon (C) in trees. An overview of the estimated age/turnover time (colour code) of structural carbon (SC) and nonstructural carbon (NSC) in trees. The arrows indicate transported sugars, in roots and leaves the age of SC is indicated. The inflated trunk section indicates the age of the SC of the tree ring and the NSC in the parenchyma ray (starch and sugars) and in the phloem (sugars). For clarity the size of the parenchyma rays has been strongly increased and does not represent the real scale. (From data from Muhr et al. (2016, this issue of New Phytologist, pp. 1410–1416), Richardson et al. (2015) and Gaudinski et al. (2009).)
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Biophysical climate impacts of recent changes in global forest cover

Biophysical climate impacts of recent changes in global forest cover | MycorWeb Plant-Microbe Interactions | Scoop.it

Changes in forest cover affect the local climate by modulating the land-atmosphere fluxes of energy and water. The magnitude of this biophysical effect is still debated in the scientific community and currently ignored in climate treaties. Here we present an observation-driven assessment of the climate impacts of recent forest losses and gains, based on Earth observations of global forest cover and land surface temperatures. Our results show that forest losses amplify the diurnal temperature variation and increase the mean and maximum air temperature, with the largest signal in arid zones, followed by temperate, tropical, and boreal zones. In the decade 2003–2012, variations of forest cover generated a mean biophysical warming on land corresponding to about 18% of the global biogeochemical signal due to CO2 emission from land-use change.

more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Fungal Melanin: What do We Know About Structure?

Fungal Melanin: What do We Know About Structure? | MycorWeb Plant-Microbe Interactions | Scoop.it
The production of melanin significantly enhances the virulence of many important human pathogenic fungi. Despite fungal melanin’s importance in human disease, as well as melanin’s contribution to the ability of fungi to survive in diverse hostile environments, the structure of melanin remains unsolved. Nevertheless, ongoing research efforts have progressively revealed several notable structural characteristics of this enigmatic pigment, which will be the focus of this review. These compositional and organizational insights could further our ability to develop novel therapeutic approaches to combat fungal disease and enhance our understanding of how melanin is inserted into the cell wall.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

The genome of newly classified Ochroconi mirabilis: Insights into fungal adaptation t different living conditions

The genome of newly classified Ochroconi mirabilis: Insights into fungal adaptation t different living conditions | MycorWeb Plant-Microbe Interactions | Scoop.it

Background

Ochroconis mirabilis, a recently introduced water-borne dematiaceous fungus, is occasionally isolated from human skin lesions and nails. We identified an isolate of O. mirabilis from a skin scraping with morphological and molecular studies. Its genome was then sequenced and analysed for genetic features related to classification and biological characteristics.

 

Results
UM 578 was identified as O. mirabilis based on morphology and internal transcribed spacer (ITS)-based phylogeny. The 34.61 Mb assembled genome with 13,435 predicted genes showed less efficiency of this isolate in plant cell wall degradation. Results from the peptidase comparison analysis with reported keratin-degrading peptidases from dermatophytes suggest that UM 578 is very unlikely to be utilising these peptidases to survive in the host. Nevertheless, we have identified peptidases from M10A, M12A and S33 families that may allow UM 578 to invade its host via extracellular matrix and collagen degradation. Furthermore, the lipases in UM 578 may have a role in supporting the fungus in host invasion. This fungus has the potential ability to synthesise melanin via the 1,8-dihydroxynaphthalene (DHN)-melanin pathway and to produce mycotoxins. The mating ability of this fungus was also inspected in this study and a mating type gene containing alpha domain was identified. This fungus is likely to produce taurine that is required in osmoregulation. The expanded gene family encoding the taurine catabolism dioxygenase TauD/TdfA domain suggests the utilisation of taurine under sulfate starvation. The expanded glutathione-S-transferase domains and RTA1-like protein families indicate the selection of genes in UM 578 towards adaptation in hostile environments.


Conclusions
The genomic analysis of O. mirabilis UM 578 provides a better understanding of fungal survival tactics in different habitats.

more...
No comment yet.