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Mining Novel Effector Proteins from the Esophageal Gland Cells of Meloidogyne incognita

Mining Novel Effector Proteins from the Esophageal Gland Cells of Meloidogyne incognita | MycorWeb Plant-Microbe Interactions | Scoop.it

Meloidogyne incognita is one of the most economically damaging plant pathogens in agriculture and horticulture. Identifying and characterizing the effector proteins which M. incognita secretes into its host plants during infection is an important step toward finding new ways to manage this pest. In this study, we have identified the cDNAs for 18 putative effectors (i.e., proteins that have the potential to facilitate M. incognitaparasitism of host plants). These putative effectors are secretory proteins that do not contain transmembrane domains and whose genes are specifically expressed in the secretory gland cells of the nematode, indicating that they are likely secreted from the nematode through its stylet. We have determined that, in the plant cells, these putative effectors are likely to localize to the cytoplasm. Furthermore, the transcripts of many of these novel effectors are specifically upregulated during different stages of the nematode's life cycle, indicating that they function at specific stages during M. incognita parasitism. The predicted proteins showed little to no homology to known proteins from free-living nematode species, suggesting that they evolved recently to support the parasitic lifestyle. On the other hand, several of the effectors are part of gene families within the M. incognita genome as well as that of M. hapla, which points to an important role that these putative effectors are playing in both parasites. With the discovery of these putative effectors, we have increased our knowledge of the effector repertoire utilized by root-knot nematodes to infect, feed on, and reproduce on their host plants. Future studies investigating the roles that these proteins play in planta will help mitigate the effects of this damaging pest.

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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

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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.
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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.
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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
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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.
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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.
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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).)
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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.

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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.
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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.

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Nature Plants: Epichloë grass endophytes in sustainable agriculture

Nature Plants: Epichloë grass endophytes in sustainable agriculture | MycorWeb Plant-Microbe Interactions | Scoop.it

There is an urgent need to create new solutions for sustainable agricultural practices that circumvent the heavy use of fertilizers and pesticides and increase the resilience of agricultural systems to environmental change. Beneficial microbial symbionts of plants are expected to play an important role in integrated pest management schemes over the coming decades. Epichloë endophytes, symbiotic fungi of many grass species, can protect plants against several stressors, and could therefore help to increase the productivity of forage grasses and the hardiness of turf grasses while reducing the use of synthetic pesticides. Indeed, Epichloë endophytes have successfully been developed and commercialized for agricultural use in the USA, Australia and New Zealand. Many of the host grass species originate from Europe, which is a biodiversity hotspot for both grasses and endophytes. However, intentional use of endophyte-enhanced grasses in Europe is virtually non-existent. We suggest that the diversity of European Epichloë endophytes and their host grasses should be exploited for the development of sustainable agricultural, horticultural and landscaping practices, and potentially for bioremediation and bioenergy purposes, and for environmental improvement.


Via Stéphane Hacquard
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Forest management not so hot at fighting warming

Forest management not so hot at fighting warming | MycorWeb Plant-Microbe Interactions | Scoop.it
Forest management practices in Europe have slightly worsened climate change, new research shows.
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Metagenomics uncovers gaps in amplicon-based detection of microbial diversity

Metagenomics uncovers gaps in amplicon-based detection of microbial diversity | MycorWeb Plant-Microbe Interactions | Scoop.it

Our view of microbial diversity has expanded greatly over the past 40 years, primarily through the wide application of PCR-based surveys of the small-subunit ribosomal RNA (SSU rRNA) gene. Yet significant gaps in knowledge remain due to well-recognized limitations of this method. Here, we systematically survey primer fidelity in SSU rRNA gene sequences recovered from over 6,000 assembled metagenomes sampled globally. Our findings show that approximately 10% of environmental microbial sequences might be missed from classical PCR-based SSU rRNA gene surveys, mostly members of the Candidate Phyla Radiation (CPR) and as yet uncharacterized Archaea. These results underscore the extent of uncharacterized microbial diversity and provide fruitful avenues for describing additional phylogenetic lineages.

 

 

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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.

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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.
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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.
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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.
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Daniel Wipf's curator insight, February 8, 2:03 AM

Our last T. aestivum paper by @Verzinie @UMRAgroecologie

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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.
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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.
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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.
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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.

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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.

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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
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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.

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Environmental Microbiology: The local environment determines the assembly of root endophytic fungi at a continental scale

Environmental Microbiology: The local environment determines the assembly of root endophytic fungi at a continental scale | MycorWeb Plant-Microbe Interactions | Scoop.it

Root endophytic fungi are found in a great variety of plants and ecosystems, but the ecological drivers of their biogeographic distribution are poorly understood. Here, we investigate the occurrence of root endophytes in the non-mycorrhizal plant genus Microthlaspi, and the effect of environmental factors and geographic distance in structuring their communities at a continental scale. We sampled 52 plant populations across the northern Mediterranean and central Europe and used a cultivation approach to study their endophytic communities. Cultivation of roots yielded 2601 isolates, which were grouped into 296 operational taxonomic units (OTUs) by internal transcribed spacer sequencing of 1998 representative colonies. Climatic and spatial factors were the best descriptors of the structure of endophytic communities, outweighing soil characteristics, host genotype and geographical distance. OTU richness was negatively affected by precipitation, and the composition of communities followed latitudinal gradients of precipitation and temperature. Only six widespread OTUs belonging to the orders Pleosporales, Hypocreales and Helotiales represented about 50% of all isolates. Assessments of their individual distribution revealed particular ecological preferences or a cosmopolitan occurrence. Our findings support a strong influence of the local environment in determining root endophytic communities, and show a different niche occupancy by individual endophytes.


Via Stéphane Hacquard
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Forests not equal when it comes to climate

Forests not equal when it comes to climate | MycorWeb Plant-Microbe Interactions | Scoop.it

Simply planting trees will not necessarily slow down climate change, an analysis of Europe's vegetation history shows. Although the continent's forests have expanded by 10% since 1750, timber harvesting and shifts to more commercially valuable tree species have resulted in a net release of carbon to the atmosphere, a Science paper published on 4 February concludes1. The changes have also had local effects, the analysis finds, raising surface temperatures by 0.12 °C by increasing the absorption and retention of heat.

“The current assumption is that all forest management and all forests contribute to climate mitigation,” says Kim Naudts, a postdoctoral ecologist at the Max Planck Institute for Meteorology in Hamburg, Germany. “We cannot say that is true, at least for Europe.” Naudts conducted the analysis with a team of colleagues while at the Laboratory of Climate Science and Environment in Gif-sur-Yvette, France.

The paper sounds a warning about potential limitations to the benefits of forest expansion, or afforestation, but does not come as a surprise, says Richard Houghton

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