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Pairwise Transcriptomic Analysis of the Interactions Between the Ectomycorrhizal Fungus Laccaria bicolor S238N and Three Beneficial, Neutral and Antagonistic Soil Bacteria

Pairwise Transcriptomic Analysis of the Interactions Between the Ectomycorrhizal Fungus Laccaria bicolor S238N and Three Beneficial, Neutral and Antagonistic Soil Bacteria | MycorWeb Plant-Microbe Interactions | Scoop.it

Ectomycorrhizal fungi are surrounded by bacterial communities with which they interact physically and metabolically during their life cycle. These bacteria can have positive or negative effects on the formation and the functioning of ectomycorrhizae. However, relatively little is known about the mechanisms by which ectomycorrhizal fungi and associated bacteria interact. To understand how ectomycorrhizal fungi perceive their biotic environment and the mechanisms supporting interactions between ectomycorrhizal fungi and soil bacteria, we analysed the pairwise transcriptomic responses of the ectomycorrhizal fungus Laccaria bicolor(Basidiomycota: Agaricales) when confronted with beneficial, neutral or detrimental soil bacteria. Comparative analyses of the three transcriptomes indicated that the fungus reacted differently to each bacterial strain. Similarly, each bacterial strain produced a specific and distinct response to the presence of the fungus. Despite these differences in responses observed at the gene level, we found common classes of genes linked to cell–cell interaction, stress response and metabolic processes to be involved in the interaction of the four microorganisms.

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Peaceful ant-plant partnerships lead to genomic arms races

Peaceful ant-plant partnerships lead to genomic arms races | MycorWeb Plant-Microbe Interactions | Scoop.it
It’s well known that humans—and our antibiotics—are in an evolutionary arms race with the bacteria that make us sick. As fast as we rev up a strong defense, they change to evade those defenses, upping the ante for either our bodies or our drugs. This arms race has been called the Red Queen hypothesis after the Alice in Wonderland character who told Alice that in looking-glass land, she would have to run as fast as she could just to stay in the same place.

But what about friendly alliances—such as those between us and the beneficial microbes that naturally inhabit our guts and other tissues and help us digest food and stave off other infections? Researchers have often assumed that once such a mutualistic partnership arose, both sides would be stable gene-wise—they would have no need to keep evolving to match each other. A decade ago, this idea was dubbed the Red King hypothesis. But a new study in ants finds that even partners known to be engaged in mutually beneficial associations have rapidly evolving genomes, apparently to keep those partnerships intact.

To find out how quickly friendly partners evolve, Corrie Moreau, an evolutionary biologist at the Field Museum of Natural History in Chicago, Illinois, and her graduate student Benjamin Rubin sequenced the genomes of seven ant species. Three survive by partnering with just one plant: the acacia tree, the Japanese knotweed, or a tropical tree called Tachigali. In the case of the acacia, Pseudomyrmex flavicornis defends the tree from elephants and other grazers in return for a special acacia-produced sugar and the hollow spines in which it nests. The duo also sequenced the genomes of three nonspecialist species—each closely related to one of the specialists—and one very distantly related ant species. All seven were in the Pseudomyrmex genus.
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Uncovering Earth’s virome : Nature

Uncovering Earth’s virome : Nature | MycorWeb Plant-Microbe Interactions | Scoop.it
Viruses are the most abundant biological entities on Earth, but challenges in detecting, isolating, and classifying unknown viruses have prevented exhaustive surveys of the global virome. Here we analysed over 5 Tb of metagenomic sequence data from 3,042 geographically diverse samples to assess the global distribution, phylogenetic diversity, and host specificity of viruses. We discovered over 125,000 partial DNA viral genomes, including the largest phage yet identified, and increased the number of known viral genes by 16-fold. Half of the predicted partial viral genomes were clustered into genetically distinct groups, most of which included genes unrelated to those in known viruses. Using CRISPR spacers and transfer RNA matches to link viral groups to microbial host(s), we doubled the number of microbial phyla known to be infected by viruses, and identified viruses that can infect organisms from different phyla. Analysis of viral distribution across diverse ecosystems revealed strong habitat-type specificity for the vast majority of viruses, but also identified some cosmopolitan groups. Our results highlight an extensive global viral diversity and provide detailed insight into viral habitat distribution and host–virus interactions.
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Genomic insights into the origin of farming in the ancient Near East : Nature

Genomic insights into the origin of farming in the ancient Near East : Nature | MycorWeb Plant-Microbe Interactions | Scoop.it
We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter–gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter–gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter–gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.
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Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality : Nature

Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality : Nature | MycorWeb Plant-Microbe Interactions | Scoop.it
Many experiments have shown that loss of biodiversity reduces the capacity of ecosystems to provide the multiple services on which humans depend1, 2. However, experiments necessarily simplify the complexity of natural ecosystems and will normally control for other important drivers of ecosystem functioning, such as the environment or land use. In addition, existing studies typically focus on the diversity of single trophic groups, neglecting the fact that biodiversity loss occurs across many taxa3, 4 and that the functional effects of any trophic group may depend on the abundance and diversity of others5, 6. Here we report analysis of the relationships between the species richness and abundance of nine trophic groups, including 4,600 above- and below-ground taxa, and 14 ecosystem services and functions and with their simultaneous provision (or multifunctionality) in 150 grasslands. We show that high species richness in multiple trophic groups (multitrophic richness) had stronger positive effects on ecosystem services than richness in any individual trophic group; this includes plant species richness, the most widely used measure of biodiversity. On average, three trophic groups influenced each ecosystem service, with each trophic group influencing at least one service. Multitrophic richness was particularly beneficial for ‘regulating’ and ‘cultural’ services, and for multifunctionality, whereas a change in the total abundance of species or biomass in multiple trophic groups (the multitrophic abundance) positively affected supporting services. Multitrophic richness and abundance drove ecosystem functioning as strongly as abiotic conditions and land-use intensity, extending previous experimental results7, 8 to real-world ecosystems. Primary producers, herbivorous insects and microbial decomposers seem to be particularly important drivers of ecosystem functioning, as shown by the strong and frequent positive associations of their richness or abundance with multiple ecosystem services. Our results show that multitrophic richness and abundance support ecosystem functioning, and demonstrate that a focus on single groups has led to researchers to greatly underestimate the functional importance of biodiversity.
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Apiculture: Telling the bees : Nature

Apiculture: Telling the bees : Nature | MycorWeb Plant-Microbe Interactions | Scoop.it
Skill, orderliness, productivity and, most of all, industry lie at the heart of bee mythology. Hence, for example, this image in philosopher Bernard de Mandeville's The Fable of the Bees (1714):

 A Spacious Hive well stockt with Bees,
 That liv'd in Luxury and Ease;
 And yet as fam'd for Laws and Arms,
 As yielding large and early Swarms;
 Was counted the great Nursery
 Of Sciences and Industry.

As the Industrial Revolution unfolded, this anthropomorphic and mechanistic view of bees as little machines of honey production came to obscure their importance as the means through which more than 30% of our food crops and 90% of the world's wild flora survive. “Every third bite of food you take, you can thank a bee or other pollinator for,” as biologist E. O. Wilson, doyen of the social insect, notes in his introduction to Stephen Buchmann and Gary Nabhan's The Forgotten Pollinators (Island, 2012).
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New Primers for Discovering Fungal Diversity Using Nuclear Large Ribosomal DNA

New Primers for Discovering Fungal Diversity Using Nuclear Large Ribosomal DNA | MycorWeb Plant-Microbe Interactions | Scoop.it

Barcoding has become an important tool in the discovery of biodiversity, including fungi, which are the second most speciose group of eukaryotes, with diverse and important ecological roles in terrestrial ecosystems. We have designed and tested new PCR primers that target the D1 variable region of nuclear large subunit (LSU) ribosomal DNA; one set that targets the phylum Ascomycota and another that recovers all other fungal phyla. The primers yield amplicons compatible with the Illumina MiSeq platform, which is cost-effective and has a lower error rate than other high throughput sequencing platforms. The new primer set LSU200A-F/LSU476A-R (Ascomycota) yielded 95–98% of reads of target taxa from environmental samples, and primers LSU200-F/LSU481-R (all other fungi) yielded 72–80% of target reads. Both primer sets have fairly low rates of data loss, and together they cover a wide variety of fungal taxa. We compared our results with these primers by amplifying and sequencing a subset of samples using the previously described ITS3_KYO2/ITS4_KYO3 primers, which amplify the internal transcribed spacer 2 (ITS2) of Ascomycota and Basidiomycota. With approximately equivalent read depth, our LSU primers recovered a greater number and phylogenetic diversity of sequences than the ITS2 primers. For instance, ITS3_KYO2/ITS4_KYO3 primers failed to pick up any members of Eurotiales, Mytilinidiales, Pezizales, Saccharomycetales, or Venturiales within Ascomycota, or members of Exobasidiomycetes, Microbotryomycetes, Pucciniomycetes, or Tremellomycetes within Basidiomycota, which were retrieved in good numbers from the same samples by our LSU primers. Among the OTUs recovered using the LSU primers were 127 genera and 28 species that were not obtained using the ITS2 primers, although the ITS2 primers recovered 10 unique genera and 16 species that were not obtained using either of the LSU primers These features identify the new primer sets developed in this study as useful complements to other universal primers for the study of fungal diversity and community composition.


Via Steve Marek, Niklaus Grunwald
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Metal induction of a Pisolithus albus metallothionein and its potential involvement in heavy metal tolerance during mycorrhizal symbiosis

Metal induction of a Pisolithus albus metallothionein and its potential involvement in heavy metal tolerance during mycorrhizal symbiosis | MycorWeb Plant-Microbe Interactions | Scoop.it
Metallothioneins (MTs) are small, cysteine-rich peptides involved in intracellular sequestration of heavy metals in eukaryotes. We examined the role in metal homeostasis and detoxification of an MT from the ectomycorrhizal fungus Pisolithus albus (PaMT1). PaMT1 encodes a 35 amino acid-long polypeptide, with 7 cysteine residues; most of them part of a C-x-C motif found in other known basidiomycete MTs. The expression levels of PaMT1 increased as a function of increased external Cu and Cd concentrations and were higher with Cu than with Cd. Heterologous complementation assays in metal-sensitive yeast mutants indicated that PaMT1 encodes a polypeptide capable of conferring higher tolerance to both Cu and Cd. Eucalyptus tereticornis plantlets colonized with P. albus grown in the presence of Cu and Cd showed better growth compared with those with non-mycorrhizal plants. Higher PaMT1 expression levels were recorded in mycorrhizal plants grown in the presence of Cu and Cd compared with those in control mycorrhizal plants not exposed to heavy metals. These data provide the first evidence to our knowledge that fungal MTs could protect ectomycorrhizal fungi from heavy metal stress and in turn help the plants to establish in metal-contaminated sites.
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Comparative genomics of biotechnologically important yeasts

Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.
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Vertical and seasonal dynamics of fungal communities in boreal Scots pine forest soil

Vertical and seasonal dynamics of fungal communities in boreal Scots pine forest soil | MycorWeb Plant-Microbe Interactions | Scoop.it
Fungal communities are important for carbon (C) transformations in boreal forests that are one of the largest C pools in terrestrial ecosystems, warranting thus further investigation of fungal community dynamics in time and space. We investigated fungal diversity and community composition seasonally and across defined soil horizons in boreal Scots pine forest in Finland using 454-pyrosequencing. We collected a total of 120 samples from five vertical soil horizons monthly from March to October; in March, under snow. Boreal forest soil generally harbored diverse fungal communities across soil horizons. The communities shifted drastically and rapidly over time. In late winter, saprotrophs dominated the community and were replaced by ectomycorrhizal fungi during the growing season. Our studies are among the first to dissect the spatial and temporal dynamics in boreal forest ecosystems and highlights the ecological importance of vertically distinct communities and their rapid seasonal dynamics. As climate change is predicted to result in warmer and longer snow-free winter seasons, as well as increase the rooting depth of trees in boreal forest, the seasonal and vertical distribution of fungal communities may change. These changes are likely to affect the organic matter decomposition by the soil-inhabiting fungi and thus alter organic C pools.
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Uniting species- and community-oriented approaches to understand arbuscular mycorrhizal fungal diversity

Uniting species- and community-oriented approaches to understand arbuscular mycorrhizal fungal diversity | MycorWeb Plant-Microbe Interactions | Scoop.it
Arbuscular mycorrhizal fungi (AMF) occur in the majority of terrestrial, and some aquatic, habitats worldwide. They are important for the functioning of individual plants and of entire ecosystems. Here, we review trends in research on species- (species recognition, phylogenetic relationships, autecology) and community-level AMF diversity patterns and aim to identify ways of improving the complementarity of these approaches. Research into many aspects of AMF diversity has flourished in parallel with the increasing availability of molecular biology techniques. However, despite their shared goal of understanding AMF biodiversity, species- and community-level perspectives, and the morphological and molecular approaches that underpin them, currently have limited capacity for information exchange. We indicate critical research gaps in AMF species and community characterisation and outline important research directions. We propose steps that could link research using different methods and targeting different aspects of diversity, in order to maximise our understanding of AMF.
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Ectomycorrhizal fungal diversity and saprotrophic fungal diversity are linked to different tree community attributes in a field-based tree experiment

Ectomycorrhizal fungal diversity and saprotrophic fungal diversity are linked to different tree community attributes in a field-based tree experiment | MycorWeb Plant-Microbe Interactions | Scoop.it
Exploring the link between above- and belowground biodiversity has been a major theme of recent ecological research, due in large part to the increasingly well-recognized role that soil microorganisms play in driving plant community processes. In this study, we utilized a field-based tree experiment in Minnesota, USA, to assess the effect of changes in plant species richness and phylogenetic diversity on the richness and composition of both ectomycorrhizal and saprotrophic fungal communities. We found that ectomycorrhizal fungal species richness was significantly positively influenced by increasing plant phylogenetic diversity, while saprotrophic fungal species richness was significantly affected by plant leaf nitrogen content, specific root length and standing biomass. The increasing ectomycorrhizal fungal richness associated with increasing plant phylogenetic diversity was driven by the combined presence of ectomycorrhizal fungal specialists in plots with both gymnosperm and angiosperm hosts. Although the species composition of both the ectomycorrhizal and saprotrophic fungal communities changed significantly in response to changes in plant species composition, the effect was much greater for ectomycorrhizal fungi. In addition, ectomycorrhizal but not saprotrophic fungal species composition was significantly influenced by both plant phylum (angiosperm, gymnosperm, both) and origin (Europe, America, both). The phylum effect was caused by differences in ectomycorrhizal fungal community composition, while the origin effect was attributable to differences in community heterogeneity. Taken together, this study emphasizes that plant-associated effects on soil fungal communities are largely guild-specific and provides a mechanistic basis for the positive link between plant phylogenetic diversity and ectomycorrhizal fungal richness
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DELLA proteins are common components of symbiotic rhizobial and mycorrhizal signalling pathways

DELLA proteins are common components of symbiotic rhizobial and mycorrhizal signalling pathways | MycorWeb Plant-Microbe Interactions | Scoop.it
Legumes form symbiotic associations with either nitrogen-fixing bacteria or arbuscular mycorrhizal fungi. Formation of these two symbioses is regulated by a common set of signalling components that act downstream of recognition of rhizobia or mycorrhizae by host plants. Central to these pathways is the calcium and calmodulin-dependent protein kinase (CCaMK)–IPD3 complex which initiates nodule organogenesis following calcium oscillations in the host nucleus. However, downstream signalling events are not fully understood. Here we show that Medicago truncatula DELLA proteins, which are the central regulators of gibberellic acid signalling, positively regulate rhizobial symbiosis. Rhizobia colonization is impaired in della mutants and we provide evidence that DELLAs can promote CCaMK–IPD3 complex formation and increase the phosphorylation state of IPD3. DELLAs can also interact with NSP2–NSP1 and enhance the expression of Nod-factor-inducible genes in protoplasts. We show that DELLA is able to bridge a protein complex containing IPD3 and NSP2. Our results suggest a transcriptional framework for regulation of root nodule symbiosis.

Via Pierre-Marc Delaux
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New role for a CEP peptide and its receptor: complex control of lateral roots

New role for a CEP peptide and its receptor: complex control of lateral roots | MycorWeb Plant-Microbe Interactions | Scoop.it
Optimized root system deployment should enable more-efficient nutrient acquisition and increased crop yields. C-TERMINALLY ENCODED PEPTIDE (CEP) hormones and their receptors, which regulate root growth, could be important in research with this aim. Roberts et al. (pages 4889–4899 in this issue) suggest that the full extent of CEP function and signalling is highly complex, and we emerge with a picture of CEPs and their known receptors being involved in long-distance and possibly more local regulatory networks.

Via Christophe Jacquet
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Draft Genome Sequence of the Deep-Sea Ascomycetous Filamentous Fungus Cadophora malorum Mo12 from the Mid-Atlantic Ridge Reveals Its Biotechnological Potential

Draft Genome Sequence of the Deep-Sea Ascomycetous Filamentous Fungus Cadophora malorum Mo12 from the Mid-Atlantic Ridge Reveals Its Biotechnological Potential | MycorWeb Plant-Microbe Interactions | Scoop.it
Cadophora malorum Mo12 was isolated from the Rainbow hydrothermal site on the Mid-Atlantic Ridge. We present the draft genome sequence of this filamentous fungal strain, which has high biotechnological potentials as revealed by the presence of genes encoding biotechnologically important enzymes and genes involved in the synthesis of secondary metabolites.
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Reconciling the evolutionary origin of bread wheat (Triticum aestivum)

Reconciling the evolutionary origin of bread wheat (Triticum aestivum) | MycorWeb Plant-Microbe Interactions | Scoop.it
The origin of bread wheat (Triticum aestivum; AABBDD) has been a subject of controversy and of intense debate in the scientific community over the last few decades. In 2015, three articles published in New Phytologist discussed the origin of hexaploid bread wheat (AABBDD) from the diploid progenitors Triticum urartu (AA), a relative of Aegilops speltoides (BB) and Triticum tauschii (DD). Access to new genomic resources since 2013 has offered the opportunity to gain novel insights into the paleohistory of modern bread wheat, allowing characterization of its origin from its diploid progenitors at unprecedented resolution. We propose a reconciled evolutionary scenario for the modern bread wheat genome based on the complementary investigation of transposable element and mutation dynamics between diploid, tetraploid and hexaploid wheat. In this scenario, the structural asymmetry observed between the A, B and D subgenomes in hexaploid bread wheat derives from the cumulative effect of diploid progenitor divergence, the hybrid origin of the D subgenome, and subgenome partitioning following the polyploidization events.
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Addition of multiple limiting resources reduces grassland diversity : Nature

Addition of multiple limiting resources reduces grassland diversity : Nature | MycorWeb Plant-Microbe Interactions | Scoop.it
Niche dimensionality provides a general theoretical explanation for biodiversity—more niches, defined by more limiting factors, allow for more ways that species can coexist1. Because plant species compete for the same set of limiting resources, theory predicts that addition of a limiting resource eliminates potential trade-offs, reducing the number of species that can coexist2. Multiple nutrient limitation of plant production is common and therefore fertilization may reduce diversity by reducing the number or dimensionality of belowground limiting factors. At the same time, nutrient addition, by increasing biomass, should ultimately shift competition from belowground nutrients towards a one-dimensional competitive trade-off for light3. Here we show that plant species diversity decreased when a greater number of limiting nutrients were added across 45 grassland sites from a multi-continent experimental network4. The number of added nutrients predicted diversity loss, even after controlling for effects of plant biomass, and even where biomass production was not nutrient-limited. We found that elevated resource supply reduced niche dimensionality and diversity and increased both productivity5 and compositional turnover. Our results point to the importance of understanding dimensionality in ecological systems that are undergoing diversity loss in response to multiple global change factors.
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Multiple mutualist effects on genome-wide expression in the tripartite association between Medicago truncatula, nitrogen-fixing bacteria, and mycorrhizal fungi

Multiple mutualist effects on genome-wide expression in the tripartite association between Medicago truncatula, nitrogen-fixing bacteria, and mycorrhizal fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
While all species interact with multiple mutualists, the fitness consequences and molecular mechanisms underlying these interactions remain largely unknown. We combined factorial ecological experiments with genome-wide expression analyses to examine the phenotypic and transcriptomic responses of model legume Medicago truncatula to rhizobia and mycorrhizal fungi. We found synergistic effects of these mutualists on plant performance and examined unique features of plant gene expression responses to multiple mutualists. There were genome-wide signatures of mutualists and multiple mutualists on expression, with partners often affecting unique sets of genes. Mycorrhizal fungi had stronger effects on plant expression than rhizobia, with 70% of differentially expressed genes affected by fungi. Fungal and bacterial mutualists had joint effects on 10% of differentially expressed genes, including unexpected, non-additive effects on some genes with important functions such as nutrient metabolism. For a subset of genes, interacting with multiple mutualists even led to reversals in the direction of expression (shifts from up to down regulation) compared to interacting with single mutualists. Rhizobia also affected the expression of several mycorrhizal genes, including those involved in nutrient transfer to host plants, indicating that partner species can also impact each other's molecular phenotypes. Collectively, these data illustrate the diverse molecular mechanisms and transcriptional responses associated with the synergistic benefits of multiple mutualists.

Via Ryohei Thomas Nakano, Jean-Michel Ané
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Les éponges, une écologie complexe au fond des mers

Les éponges, une écologie complexe au fond des mers | MycorWeb Plant-Microbe Interactions | Scoop.it
Récemment, dans un article publié dans Scientific Reports (Groupe Nature), nous avons mis en évidence une deuxième fonctionnalité des crambescines et crambescidines ; la communication. Cette communication chimique au sein de la mer s’apparente à ce qui se passe en milieu terrestre : comme pour une fleur qui pour compenser son immobilité, distille son parfum dans l’air par le biais de métabolites volatiles qui auront pour effet de signaler sa présence. Les caractéristiques chimiques des métabolites de communication intervenant en milieu marin sont différentes de celles rencontrées en milieu terrestre du seul fait de la nature de l’eau par rapport à l’air (plus visqueuse, hautement réactive).

Grâce à des mesures chimiques précises nous avons mis en évidence la présence d’un halo de crambescines et crambescidines autour de l’éponge C. crambe dans son milieu naturel. Ce halo est généré par l’expulsion constante de petites cellules d’éponges – les cellules sphéruleuses – qui contiennent chacune une vingtaine de vésicules renfermant jusqu’à 136 000 molécules toxiques. Ces cellules sont expulsées de l’éponge par ses canaux exhalant puis les vésicules sont libérées dans l’eau de mer, ce qui conduira à la solubilisation d’une partie des composés toxiques autour de l’éponge. Ainsi, un halo chimique jouant le rôle de bouclier est continuellement réapprovisionné par l’éponge elle-même.
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The local environment determines the assembly of root endophytic fungi at a continental scale

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.
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Unveiled: Earth’s Viral Diversity - DOE Joint Genome Institute

Unveiled: Earth’s Viral Diversity - DOE Joint Genome Institute | MycorWeb Plant-Microbe Interactions | Scoop.it
DOE JGI researchers have uncovered over 125,000 partial and complete viral genomes, increasing the number of known viral genes by a factor of 16.
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Draft genome of the wheat rust pathogen (Puccinia triticina) unravels genome-wide structural variations during evolution

Draft genome of the wheat rust pathogen (Puccinia triticina) unravels genome-wide structural variations during evolution | MycorWeb Plant-Microbe Interactions | Scoop.it
Leaf rust is one of the most important diseases of wheat and is caused by Puccinia triticina, a highly variable rust pathogen prevalent worldwide. Decoding the genome of this pathogen will help in unraveling the molecular basis of its evolution and in the identification of genes responsible for its various biological functions. We generated high quality draft genome sequences (approximately 100- 106 Mb) of two races of P. triticina; the variable and virulent Race77 and the old, avirulent Race106. The genomes of races 77 and 106 had 33X and 27X coverage, respectively. We predicted 27678 and 26384 genes, with average lengths of 1,129 and 1,086 bases in races 77 and 106, respectively and found that the genomes consisted of 37.49% and 39.99% repetitive sequences. Genome wide comparative analysis revealed that Race77 differs substantially from Race106 with regard to segmental duplication (SD), repeat element, and SNP/InDel characteristics. Comparative analyses showed that Race 77 is a recent, highly variable and adapted Race compared with Race106. Further sequence analyses of 13 additional pathotypes of Race77 clearly differentiated the recent, active and virulent, from the older pathotypes. Average densities of 2.4 SNPs and 0.32 InDels per kb were obtained for all P. triticina pathotypes. Secretome analysis demonstrated that Race77 has more virulence factors than Race 106, which may be responsible for the greater degree of adaptation of this pathogen. We also found that genes under greater selection pressure were conserved in the genomes of both races, and may affect functions crucial for the higher levels of virulence factors in Race77. This study provides insights into the genome structure, genome organization, molecular basis of variation, and pathogenicity of P. triticina. The genome sequence data generated in this study have been submitted to public domain databases and will be an important resource for comparative genomics studies of the more than 4000 existing Puccinia species.

Via Yogesh Gupta
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Slowed decomposition in ectomycorrhizal ecosystems is independent of plant chemistry

Slowed decomposition in ectomycorrhizal ecosystems is independent of plant chemistry | MycorWeb Plant-Microbe Interactions | Scoop.it
Ecosystems dominated by plants in symbiosis with ectomycorrhizal fungi store more carbon in soils. There is increasing evidence that this may be due to competition between primary producers and microbial decomposers for soil nitrogen, mediated by ectomycorrhizal fungi. This competitive interaction inhibits decomposition and increases soil carbon storage. However, other work suggests elevated carbon storage is due to recalcitrant plant tissue chemistry in ectomycorrhizal ecosystems, rather than ectomycorrhizal competition for soil nitrogen. These two frameworks make similar predictions for soil carbon storage, making them difficult to distinguish empirically. Here I argue that the ectomycorrhizal-recalcitrance hypothesis is not well supported by recent developments in the understanding of soil carbon chemistry, or evolutionary relationships among ectomycorrhizal plants. Therefore, differences in input chemistry are not sufficient to discount alternative mechanisms of carbon stabilization in ectomycorrhizal ecosystems. Future work on EM-specific stabilization of soil C should focus on alternative mechanisms including competition for N, direct antagonistic interactions, and other microbial community driven mechanisms.
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Lytic Polysaccharide Monooxygenases: The Microbial Power Tool for Lignocellulose Degradation

Lytic Polysaccharide Monooxygenases: The Microbial Power Tool for Lignocellulose Degradation | MycorWeb Plant-Microbe Interactions | Scoop.it
Lytic polysaccharide monooxygenases (LPMOs) are copper-enzymes that catalyze oxidative cleavage of glycosidic bonds. These enzymes are secreted by many microorganisms to initiate infection and degradation processes. In particular, the concept of fungal degradation of lignocellulose has been revised in the light of this recent finding. LPMOs require a source of electrons for activity, and both enzymatic and plant-derived sources have been identified. Importantly, light-induced electron delivery from light-harvesting pigments can efficiently drive LPMO activity. The possible implications of LPMOs in plant–symbiont and –pathogen interactions are discussed in the context of the very powerful oxidative capacity of these enzymes.
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Scooped by Francis Martin
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Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition

Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition | MycorWeb Plant-Microbe Interactions | Scoop.it
Microorganisms play a crucial role in the biological decomposition of plant litter in terrestrial ecosystems. Due to the permanently changing litter quality during decomposition, studies of both fungi and bacteria at a fine taxonomic resolution are required during the whole process. Here we investigated microbial community succession in decomposing leaf litter of temperate beech forest using pyrotag sequencing of the bacterial 16S and the fungal internal transcribed spacer (ITS) rRNA genes. Our results reveal that both communities underwent rapid changes. Proteobacteria, Actinobacteria and Bacteroidetes dominated over the entire study period, but their taxonomic composition and abundances changed markedly among sampling dates. The fungal community also changed dynamically as decomposition progressed, with ascomycete fungi being increasingly replaced by basidiomycetes. We found a consistent and highly significant correlation between bacterial richness and fungal richness (R = 0.76, P < 0.001) and community structure (RMantel = 0.85, P < 0.001), providing evidence of coupled dynamics in the fungal and bacterial communities. A network analysis highlighted nonrandom co-occurrences among bacterial and fungal taxa as well as a shift in the cross-kingdom co-occurrence pattern of their communities from the early to the later stages of decomposition. During this process, macronutrients, micronutrients, C:N ratio and pH were significantly correlated with the fungal and bacterial communities, while bacterial richness positively correlated with three hydrolytic enzymes important for C, N and P acquisition. Overall, we provide evidence that the complex litter decay is the result of a dynamic cross-kingdom functional succession.
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Rescooped by Francis Martin from Forest microbiome
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Fungi associated with decomposing deadwood in a natural beech-dominated forest

Fungi associated with decomposing deadwood in a natural beech-dominated forest | MycorWeb Plant-Microbe Interactions | Scoop.it
Deadwood represents a specific habitat of particular importance in natural, unmanaged forests where wood is not harvested. Here, we characterized the basic wood chemistry, enzyme activity, fungal biomass content and community composition of Fagus sylvatica, Abies alba and Picea abies coarse woody debris decomposing for <5, 5–15, 16–38 and > 38 years in a natural temperate forest. The results indicate that coarse deadwood represents a highly diverse substratum in terms of the quality, fungal biomass content and, in particular, the composition of fungal communities whose properties change with time. Because sequences recovered from individual logs were typically dominated by one or few fungal species, which were rarely tree species-specific, the community assembly appeared to show a high level of stochasticity. Among the estimated variables, nitrogen content that increased with decay length was the most important candidate driver of fungal biomass content, community composition and enzyme activity.

Via Petr Baldrian
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