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Altering the Cell Wall and Its Impact on Plant Disease: From Forage to Bioenergy

Altering the Cell Wall and Its Impact on Plant Disease: From Forage to Bioenergy | MycorWeb Plant-Microbe Interactions | Scoop.it

The individual sugars found within the major classes of plant cell wall polymers are dietary components of herbivores and are targeted for release in industrial processes for fermentation to liquid biofuels. With a growing understanding of the biosynthesis of the complex cell wall polymers, genetic modification strategies are being developed to target the cell wall to improve the digestibility of forage crops and to render lignocellulose less recalcitrant for bioprocessing. This raises concerns as to whether altering cell wall properties to improve biomass processing traits may inadvertently make plants more susceptible to diseases and pests. Here, we review the impacts of cell wall modification on plant defense, as assessed from studies in model plants utilizing mutants or transgenic modification and in crop plants specifically engineered for improved biomass or bioenergy traits. Such studies reveal that cell wall modifications can indeed have unintended impacts on plant defense, but these are not always negative.


Via Christophe Jacquet
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Infographic: European forests | www.foresteurope.org

Infographic: European forests | www.foresteurope.org | MycorWeb Plant-Microbe Interactions | Scoop.it
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EXO70I Is Required for Development of a Sub-domain of the Periarbuscular Membrane during Arbuscular Mycorrhizal Symbiosis

In eukaryotic cells, polarized secretion mediated by exocytotic fusion of membrane vesicles with the plasma membrane is essential for spatially restricted expansion of the plasma membrane and for the delivery of molecules to specific locations at the membrane and/or cell surface. The EXOCYST complex is central to this process, and in yeast, regulation of the EXO70 subunit influences exocytosis and cargo specificity [ 1, 2 ]. In contrast to yeast and mammalian cells, plants have upwards of 23 EXO70 genes with largely unknown roles [ 3–6 ]. During arbuscular mycorrhizal (AM) symbiosis, deposition of the plant periarbuscular membrane (PAM) around the fungal arbuscule creates an intracellular membrane interface between the symbionts. The PAM has two major membrane sub-domains, and symbiosis-specific transporter proteins are localized in the branch domain [ 7–11 ]. Currently, the mechanisms and cellular machinery involved in biogenesis of the PAM are largely unknown. Here, we identify an EXO70I protein present exclusively in plants forming AM symbiosis. Medicago truncatula exo70imutants are unable to support normal arbuscule development, and incorporation of two PAM-resident ABC transporters, STR and STR2, is limited. During arbuscule branching, EXO70I is located in spatially restricted zones adjacent to the PAM around the arbuscule hyphal tips where it interacts with Vapyrin [ 12–14 ], a plant-specific protein required for arbuscule development. We conclude that EXO70I provides a specific exocytotic capacity necessary for development of the main functional sub-domain of the PAM. Furthermore, in contrast to other eukaryotes, plant EXO70s have evolved distinct specificities and interaction partners to fulfill their specialized secretory requirements.


Via Pierre-Marc Delaux
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The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

Background. Accurate genome assembly and gene model annotation are critical for comparative species and gene functional analyses. Here we present the completed genome sequence and annotation of the reference strain PH-1 of Fusarium graminearum, the causal agent of head scab disease of small grain cereals which threatens global food security. Completion was achieved by combining (a) the BROAD Sanger sequenced draft, with (b) the gene predictions from Munich Information Services for Protein Sequences (MIPS) v3.2, with (c) de novo whole-genome shotgun re-sequencing, (d) re-annotation of the gene models using RNA-seq evidence and Fgenesh, Snap, GeneMark and Augustus prediction algorithms, followed by (e) manual curation.

 

Results. We have comprehensively completed the genomic 36,563,796 bp sequence by replacing unknown bases, placing supercontigs within their correct loci, correcting assembly errors, and inserting new sequences which include for the first time complete AT rich sequences such as centromere sequences, subtelomeric regions and the telomeres. Each of the four F. graminearium chromosomes was found to be submetacentric with respect to centromere positioning. The position of a potential neocentromere was also defined. A preferentially higher frequency of genetic recombination was observed at the end of the longer arm of each chromosome. Within the genome 1529 gene models have been modified and 412 new gene models predicted, with a total gene call of 14,164. The re-annotation impacts upon 69 entries held within the Pathogen-Host Interactions database (PHI-base) which stores information on genes for which mutant phenotypes in pathogen-host interactions have been experimentally tested, of which 59 are putative transcription factors, 8 kinases, 1 ATP citrate lyase (ACL1), and 1 syntaxin-like SNARE gene (GzSYN1). Although the completed F. graminearum contains very few transposon sequences, a previously unrecognised and potentially active gypsy-type long-terminal-repeat (LTR) retrotransposon was identified. In addition, each of the sub-telomeres and centromeres contained either a LTR or MarCry-1_FO element. The full content of the proposed ancient chromosome fusion sites has also been revealed and investigated. Regions with high recombination previously noted to be rich in secretome encoding genes were also found to be rich in tRNA sequences. This study has identified 741 F. graminearum species specific genes and provides the first complete genome assembly for a Sordariomycetes species.

 

Conclusions. This fully completed F. graminearum PH-1 genome and manually curated annotation, available at Ensembl Fungi, provides the optimum resource to perform interspecies comparative analyses and gene function studies.

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Symbiotic options for the conquest of land

Symbiotic options for the conquest of land | MycorWeb Plant-Microbe Interactions | Scoop.it

The domination of the landmasses of Earth by plants starting during the Ordovician Period drastically altered the development of the biosphere and the composition of the atmosphere, with far-reaching consequences for all life ever since. It is widely thought that symbiotic soil fungi facilitated the colonization of the terrestrial environment by plants. However, recent discoveries in molecular ecology, physiology, cytology, and paleontology have brought into question the hitherto-assumed identity and biology of the fungi engaged in symbiosis with the earliest-diverging lineages of extant land plants. Here, we reconsider the existing paradigm and show that the symbiotic options available to the first plants emerging onto the land were more varied than previously thought.

 
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Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function

Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function | MycorWeb Plant-Microbe Interactions | Scoop.it

Conifers have been understudied at the genomic level despite their worldwide ecological and economic importance but the situation is rapidly changing with the development of next generation sequencing (NGS) technologies. With NGS, genomics research has simultaneously gained in speed, magnitude and scope. In just a few years, genomes of 20–24 gigabases have been sequenced for several conifers, with several others expected in the near future. Biological insights have resulted from recent sequencing initiatives as well as genetic mapping, gene expression profiling and gene discovery research over nearly two decades. We review the knowledge arising from conifer genomics research emphasizing genome evolution and the genomic basis of adaptation, and outline emerging questions and knowledge gaps. We discuss future directions in three areas with potential inputs from NGS technologies: the evolutionary impacts of adaptation in conifers based on the adaptation-by-speciation model; the contributions of genetic variability of gene expression in adaptation; and the development of a broader understanding of genetic diversity and its impacts on genome function. These research directions promise to sustain research aimed at addressing the emerging challenges of adaptation that face conifer trees.

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New Phytologist: Standards for plant synthetic biology: a common syntax for exchange of DNA parts (2015)

New Phytologist: Standards for plant synthetic biology: a common syntax for exchange of DNA parts (2015) | MycorWeb Plant-Microbe Interactions | Scoop.it

Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering.


Via Kamoun Lab @ TSL
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Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays

Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays | MycorWeb Plant-Microbe Interactions | Scoop.it
Plant genomes encode numerous small secretory peptides (SSPs) whose functions have yet to be explored. Based on structural features that characterize SSP families known to take part in postembryonic development, this comparative genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication. Because genome annotation based on short sequence homology is difficult, the criteria for the de novo identification and aggregation of conserved SSP sequences were first benchmarked across five reference plant species. The resulting gene families were then extended to 32 genome sequences, including major crops. The global phylogenetic pattern common to the functionally characterized SSP families suggests that their apparition and expansion coincide with that of the land plants. The SSP families can be searched online for members, sequences and consensus (http://bioinformatics.psb.ugent.be/webtools/PlantSSP/). Looking for putative regulators of root development, Arabidopsis thaliana SSP genes were further selected through transcriptome meta-analysis based on their expression at specific stages and in specific cell types in the course of the lateral root formation. As an additional indication that formerly uncharacterized SSPs may control development, this study showed that root growth and branching were altered by the application of synthetic peptides matching conserved SSP motifs, sometimes in very specific ways. The strategy used in the study, combining comparative genomics, transcriptome meta-analysis and peptide functional assays in planta, pinpoints factors potentially involved in non-cell-autonomous regulatory mechanisms. A similar approach can be implemented in different species for the study of a wide range of developmental programmes.

Via Jean-Michel Ané
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Harnessing phytomicrobiome signaling for rhizosphere microbiome engineering

Harnessing phytomicrobiome signaling for rhizosphere microbiome engineering | MycorWeb Plant-Microbe Interactions | Scoop.it
The goal of microbiome engineering is to manipulate the microbiome toward a certain type of community that will optimize plant functions of interest. For instance, in crop production the goal is to reduce disease susceptibility, increase nutrient availability increase abiotic stress tolerance and increase crop yields. Various approaches can be devised to engineer the plant–microbiome, but one particularly promising approach is to take advantage of naturally evolved plant–microbiome communication channels. This is, however, very challenging as the understanding of the plant–microbiome communication is still mostly rudimentary and plant–microbiome interactions varies between crops species (and even cultivars), between individual members of the microbiome and with environmental conditions. In each individual case, many aspects of the plant–microorganisms relationship should be thoroughly scrutinized. In this article we summarize some of the existing plant–microbiome engineering studies and point out potential avenues for further research.

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We Want the Funk: The Ups and Downs of Wild Microbes in Beer - EveryONE

We Want the Funk: The Ups and Downs of Wild Microbes in Beer - EveryONE | MycorWeb Plant-Microbe Interactions | Scoop.it
Funky, floral, complex. No, this is not a description of a piece of vintage wallpaper. These are some of the words that are used to describe the enormous variety that exists within the world of beer. Whether you are enjoying … Continue reading »
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Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor

Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor | MycorWeb Plant-Microbe Interactions | Scoop.it
Microbial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for the existence of microbial communities in ~40° to 60°C sediment associated with lignite coal beds at ~1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis was indicated by the isotopic compositions of methane and carbon dioxide, biomarkers, cultivation data, and gas compositions. Concentrations of indigenous microbial cells below 1.5 km ranged from <10 to ~104 cells cm−3. Peak concentrations occurred in lignite layers, where communities differed markedly from shallower subseafloor communities and instead resembled organotrophic communities in forest soils. This suggests that terrigenous sediments retain indigenous community members tens of millions of years after burial in the seabed.
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Revolution in human evolution

Revolution in human evolution | MycorWeb Plant-Microbe Interactions | Scoop.it
ust 5 years ago, extracting and deciphering a single fossil's genome—and making sure the result was not muddied by contamination with modern DNA—was a titanic effort. Now, thanks to technological breakthroughs that have vastly accelerated sequencing and made the results more trustworthy, DNA researchers the world over are awash in data (see p. 359). The result is a series of revelations about humanity's past. Ancient DNA has led to the discovery of new types of ancient humans and revealed interbreeding between our ancestors and our archaic cousins, which left a genetic legacy that shapes our health and appearance today. And because investigators can now sequence entire ancient populations, as Reich's lab is doing, ancient DNA is adding layers of complexity to the story of how ancient populations migrated and mixed across the globe. “The whole field is exploding in terms of its impact,” says Christina Warinner of the University of Oklahoma, Norman. “The data that's coming out is completely rewriting what we know about human prehistory.”
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Lost worlds found

Lost worlds found | MycorWeb Plant-Microbe Interactions | Scoop.it
If time travel were possible, big game hunters would be clamoring to visit the Yukon during the last ice age. About 30,000 years ago, mammoths with 3-meter tusks and shaggy coats nosed about with bison, woolly rhinos, muskoxen, and small horses, while lions, short-faced bears, and scimitar-toothed cats lurked in the background. But the vast Pleistocene game park had vanished by 10,000 years ago. The great beasts were long gone, replaced by familiar elk and moose, with lynx and grizzlies as predators.

For decades, scientists have debated why these megafauna disappeared from the Arctic and much of the rest of the world. Did a fluctuating climate drive species to extinction? Or did humans, in their relentless expansion across the globe, kill off the big game in an ancient hunting spree?

Now, ancient DNA data have entered the fray, most recently in the form of molecules scooped directly from samples of soil or ice. By sequencing whatever DNA emerges from even a thimbleful of ancient soil, researchers are reconstructing ancient ecosystems as far back as 700,000 years ago with astonishing clarity. A single sample of so-called environmental DNA (eDNA), combining sequences from plant and animal detritus as well as microbes, can provide an inventory of ancient species, filling gaps in conventional fossil and pollen records. The method “could revolutionize our understanding of [ancient] ecosystems by giving us … a full picture of the food web from the ground up,” says geologist Fred Longstaffe of Western University in London, Canada.
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FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild | MycorWeb Plant-Microbe Interactions | Scoop.it

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

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Where Next for Genetics and Genomics?

Where Next for Genetics and Genomics? | MycorWeb Plant-Microbe Interactions | Scoop.it
The last few decades have utterly transformed genetics and genomics, but what might the next ten years bring? PLOS Biology asked eight leaders spanning a range of related areas to give us their predictions. Without exception, the predictions are for more data on a massive scale and of more diverse types. All are optimistic and predict enormous positive impact on scientific understanding, while a recurring theme is the benefit of such data for the transformation and personalization of medicine. Several also point out that the biggest changes will very likely be those that we don’t foresee, even now.
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Convergent evolution of strigolactone perception enabled host detection in parasitic plants

Obligate parasitic plants in the Orobanchaceae germinate after sensing plant hormones, strigolactones, exuded from host roots. In Arabidopsis thaliana, the α/β-hydrolase D14 acts as a strigolactone receptor that controls shoot branching, whereas its ancestral paralog, KAI2, mediates karrikin-specific germination responses. We observed that KAI2, but not D14, is present at higher copy numbers in parasitic species than in nonparasitic relatives. KAI2 paralogs in parasites are distributed into three phylogenetic clades. The fastest-evolving clade, KAI2d, contains the majority of KAI2 paralogs. Homology models predict that the ligand-binding pockets of KAI2d resemble D14. KAI2d transgenes confer strigolactone-specific germination responses to Arabidopsis thaliana. Thus, the KAI2 paralogs D14 and KAI2d underwent convergent evolution of strigolactone recognition, respectively enabling developmental responses to strigolactones in angiosperms and host detection in parasites.


Via Pierre-Marc Delaux
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The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal peptaibiotics

The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal peptaibiotics | MycorWeb Plant-Microbe Interactions | Scoop.it

Background. Two major mycoparasitic lineages, the family Hypocreaceae and the genus Tolypocladium, exist within the fungal order, Hypocreales. Peptaibiotics are a group of secondary metabolites almost exclusively described from Trichoderma species of Hypocreaceae. Peptaibiotics are produced by nonribosomal peptide synthetases (NRPSs) and have antibiotic and antifungal activities. Tolypocladium species are mainly truffle parasites, but a few species are insect pathogens.

 

Results. The draft genome sequence of the truffle parasite Tolypocladium ophioglossoides was generated and numerous secondary metabolite clusters were discovered, many of which have no known putative product. However, three large peptaibiotic gene clusters were identified using phylogenetic analyses. Peptaibiotic genes are absent from the predominantly plant and insect pathogenic lineages of Hypocreales, and are therefore exclusive to the largely mycoparasitic lineages. Using NRPS adenylation domain phylogenies and reconciliation of the domain tree with the organismal phylogeny, it is demonstrated that the distribution of these domains is likely not the product of horizontal gene transfer between mycoparasitic lineages, but represents independent losses in insect pathogenic lineages. Peptaibiotic genes are less conserved between species of Tolypocladium and are the product of complex patterns of lineage sorting and module duplication. In contrast, these genes are more conserved within the genus Trichoderma and consistent with diversification through speciation.

 

Conclusions. Peptaibiotic NRPS genes are restricted to mycoparasitic lineages of Hypocreales, based on current sampling. Phylogenomics and comparative genomics can provide insights into the evolution of secondary metabolite genes, their distribution across a broader range of taxa, and their possible function related to host specificity.

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Microsporidia: Eukaryotic Intracellular Parasites Shaped by Gene Loss and Horizontal Gene Transfers - Annual Review of Microbiology

Microsporidia are eukaryotic parasites of many animals that appear to have adapted to an obligate intracellular lifestyle by modifying the morphology and content of their cells. Living inside other cells, they have lost many, or all, metabolic functions, resulting in genomes that are always gene poor and often very small. The minute content of microsporidian genomes led many to assume that these parasites are biochemically static and uninteresting. However, recent studies have demonstrated that these organisms can be surprisingly complex and dynamic. In this review I detail the most significant recent advances in microsporidian genomics and discuss how these have affected our understanding of many biological aspects of these peculiar eukaryotic intracellular pathogens.
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How Trees Calm Us Down - The New Yorker

How Trees Calm Us Down - The New Yorker | MycorWeb Plant-Microbe Interactions | Scoop.it
How a leafy sidewalk or a forest scene can make us feel richer, younger, and more focussed.
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Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417

Background
Plant growth-promoting rhizobacteria (PGPR) can protect plants against pathogenic microbes through a diversity of mechanisms including competition for nutrients, production of antibiotics, and stimulation of the host immune system, a phenomenon called induced systemic resistance (ISR). In the past 30 years, the Pseudomonas spp. PGPR strains WCS358, WCS374 and WCS417 of the Willie Commelin Scholten (WCS) collection have been studied in detail in pioneering papers on the molecular basis of PGPR-mediated ISR and mechanisms of biological control of soil-borne pathogens via siderophore-mediated competition for iron.

Results
The genomes of the model WCS PGPR strains were sequenced and analyzed to unearth genetic cues related to biological questions that surfaced during the past 30 years of functional studies on these plant-beneficial microbes. Whole genome comparisons revealed important novel insights into iron acquisition strategies with consequences for both bacterial ecology and plant protection, specifics of bacterial determinants involved in plant-PGPR recognition, and diversity of protein secretion systems involved in microbe-microbe and microbe-plant communication. Furthermore, multi-locus sequence alignment and whole genome comparison revealed the taxonomic position of the WCS model strains within the Pseudomonas genus. Despite the enormous diversity of Pseudomonas spp. in soils, several plant-associated Pseudomonas spp. strains that have been isolated from different hosts at different geographic regions appear to be nearly isogenic to WCS358, WCS374, or WCS417. Interestingly, all these WCS look-a-likes have been selected because of their plant protective or plant growth-promoting properties.

Conclusions
The genome sequences of the model WCS strains revealed that they can be considered representatives of universally-present plant-beneficial Pseudomonas spp. With their well-characterized functions in the promotion of plant growth and health, the fully sequenced genomes of the WCS strains provide a genetic framework that allows for detailed analysis of the biological mechanisms of the plant-beneficial traits of these PGPR. Considering the increasing focus on the role of the root microbiome in plant health, functional genomics of the WCS strains will enhance our understanding of the diversity of functions of the root microbiome.

Via Jean-Michel Ané
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Oxalate secretion by ectomycorrhizal Paxillus involutus is mineral-specific and controls calcium weathering from minerals

Oxalate secretion by ectomycorrhizal Paxillus involutus is mineral-specific and controls calcium weathering from minerals | MycorWeb Plant-Microbe Interactions | Scoop.it

Trees and their associated rhizosphere organisms play a major role in mineral weathering driving calcium fluxes from the continents to the oceans that ultimately control long-term atmospheric CO2 and climate through the geochemical carbon cycle. Photosynthate allocation to tree roots and their mycorrhizal fungi is hypothesized to fuel the active secretion of protons and organic chelators that enhance calcium dissolution at fungal-mineral interfaces. This was tested using 14CO2 supplied to shoots of Pinus sylvestris ectomycorrhizal with the widespread fungus Paxillus involutus in monoxenic microcosms, revealing preferential allocation by the fungus of plant photoassimilate to weather grains of limestone and silicates each with a combined calcium and magnesium content of over 10 wt.%. Hyphae had acidic surfaces and linear accumulation of weathered calcium with secreted oxalate, increasing significantly in sequence: quartz, granite < basalt, olivine, limestone < gabbro. These findings confirmed the role of mineral-specific oxalate exudation in ectomycorrhizal weathering to dissolve calcium bearing minerals, thus contributing to the geochemical carbon cycle.

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Les mycorhizes

Les mycorhizes | MycorWeb Plant-Microbe Interactions | Scoop.it
Depuis la première édition de ce livre, en 2008, plus de 10000 nouvelles contributions à la connaissance des mycorhizes ont été publiées. Voilà pourquoi cette nouvelle édition augmentée et mise à jour a paru nécessaire.
Les mycorhizes sont formées par des champignons microscopiques qui font merveille en horticulture en travaillant en symbiose avec les racines des plantes. Les champignons aident les plantes à puiser des éléments nutritifs dans le sol et à s'adapter au milieu. En échange, les plantes fournissent aux champignons l'énergie qu'ils sont incapables de tirer eux-mêmes du soleil.
Au cours des dernières années, une multitude de travaux ont clairement démontré l'intérêt scientifique et pratique de ces symbioses pour l'ensemble des végétaux du monde entier, que ce soit dans les écosystèmes naturels ou ceux aménagés par l'homme. Pourtant, en dépit de ces preuves répétées et irréfutables, un grand nombre de praticiens en horticulture, en agriculture, en foresterie et en environnement comprennent encore mal l'importance concrète de ce phénomène. Les pratiques durables dans ces domaines d'application ont pourtant tout à gagner d'une utilisation judicieuse des symbioses mycorhiziennes.
C'est dans cet esprit que les auteurs – des sommités en matière de mycorhizes – ont préparé cette nouvelle édition d'un volume qui vise à la fois à faire comprendre la biologie des mycorhizes dans ce qu'elle a de plus fascinant et à montrer comment en tirer profit dans de très nombreux aspects de la culture des plantes et de leur protection, tout en assurant le maintien des équilibres naturels.

Via Jean-Michel Ané
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Marie Aizpuru's curator insight, July 29, 4:31 AM

Via les murs d'actualités thématiques de Jean-Michel Ané si bien documentés. Merci.

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Rice researchers redress retraction

Rice researchers redress retraction | MycorWeb Plant-Microbe Interactions | Scoop.it
As for how the retraction saga has altered working practices in her lab, Ronald now requires that three independent researchers validate new experimental approaches before publication. And all lab members now use electronic notebooks to make it easier to find data once members have left the lab.
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Evidence for archaic adaptive introgression in humans : Nature Reviews Genetics

Evidence for archaic adaptive introgression in humans : Nature Reviews Genetics | MycorWeb Plant-Microbe Interactions | Scoop.it
As modern and ancient DNA sequence data from diverse human populations accumulate, evidence is increasing in support of the existence of beneficial variants acquired from archaic humans that may have accelerated adaptation and improved survival in new environments — a process known as adaptive introgression. Within the past few years, a series of studies have identified genomic regions that show strong evidence for archaic adaptive introgression. Here, we provide an overview of the statistical methods developed to identify archaic introgressed fragments in the genome sequences of modern humans and to determine whether positive selection has acted on these fragments. We review recently reported examples of adaptive introgression, grouped by selection pressure, and consider the level of supporting evidence for each. Finally, we discuss challenges and recommendations for inferring selection on introgressed regions.
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New mystery for Native American origins

New mystery for Native American origins | MycorWeb Plant-Microbe Interactions | Scoop.it

The Americas were the last great frontier to be settled by humans, and their peopling remains one of the great mysteries for researchers. This week, two major studies of the DNA of living and ancient people try to settle the big questions about the early settlers: who they were, when they came, and how many waves arrived. But instead of converging on a single consensus picture, the studies, published online in Science and Nature, throw up a new mystery: Both detect in modern Native Americans a trace of DNA related to that of native people from Australia and Melanesia. The competing teams, neither of which knew what the other was up to until the last minute, are still trying to reconcile and make sense of each other's data.

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Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life

Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life | MycorWeb Plant-Microbe Interactions | Scoop.it

Sexual reproduction and clonality in eukaryotes are mostly seen as exclusive, the latter being rather exceptional. This view might be biased by focusing almost exclusively on metazoans. We analyze and discuss reproduction in the context of extant eukaryotic diversity, paying special attention to protists. We present results of phylogenetically extended searches for homologs of two proteins functioning in cell and nuclear fusion, respectively (HAP2 and GEX1), providing indirect evidence for these processes in several eukaryotic lineages where sex has not been observed yet. We argue that (i) the debate on the relative significance of sex and clonality in eukaryotes is confounded by not appropriately distinguishing multicellular and unicellular organisms; (ii) eukaryotic sex is extremely widespread and already present in the last eukaryotic common ancestor; and (iii) the general mode of existence of eukaryotes is best described by clonally propagating cell lines with episodic sex triggered by external or internal clues. However, important questions concern the relative longevity of true clonal species (i.e., species not able to return to sexual procreation anymore). Long-lived clonal species seem strikingly rare. We analyze their properties in the light of meiotic sex development from existing prokaryotic repair mechanisms. Based on these considerations, we speculate that eukaryotic sex likely developed as a cellular survival strategy, possibly in the context of internal reactive oxygen species stress generated by a (proto) mitochondrion. Thus, in the context of the symbiogenic model of eukaryotic origin, sex might directly result from the very evolutionary mode by which eukaryotic cells arose.

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