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Facility-Specific “House” Microbiome Drives Microbial Landscapes of Artisan Cheesemaking Plants

Facility-Specific “House” Microbiome Drives Microbial Landscapes of Artisan Cheesemaking Plants | MycorWeb Plant-Microbe Interactions | Scoop.it

Cheese fermentations involve the growth of complex microbial consortia, which often originate in the processing environment and drive the development of regional product qualities. However, the microbial milieus of cheesemaking facilities are largely unexplored and the true nature of the fermentation-facility relationship remains nebulous. Thus, a high-throughput sequencing approach was employed to investigate the microbial ecosystems of two artisanal cheesemaking plants, with the goal of elucidating how the processing environment influences microbial community assemblages. Results demonstrate that fermentation-associated microbes dominated most surfaces, primarilyDebaryomyces and Lactococcus, indicating that establishment of these organisms on processing surfaces may play an important role in microbial transfer, beneficially directing the course of sequential fermentations. Environmental organisms detected in processing environments dominated the surface microbiota of washed-rind cheeses maturing in both facilities, demonstrating the importance of the processing environment for populating cheese microbial communities, even in inoculated cheeses. Spatial diversification within both facilities reflects the functional adaptations of microbial communities inhabiting different surfaces and the existence of facility-specific “house” microbiota, which may play a role in shaping site-specific product characteristics.

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Genome sequence and comparative analysis of clavicipitaceous insect-pathogenic fungus Aschersonia badia with Metarhizium spp.

Background
Aschersonia badia [(Ab) Teleomorph: Hypocrella siamensis] is an entomopathogenic fungus that specifically infects scale insects and whiteflies. We present the whole genome sequence of Ab and its comparison with two clavicipitaceous fungi Metarhizium robertsii (MR: generalist entomopathogen) and M. acridum (MAC: acridid-specific entomopathogen) that exhibit variable host preferences. Here, through comparative analysis of pathogen-host interacting genes, carbohydrate active enzymes, secondary metabolite biosynthesis genes, and sexuality genes, we explore the proteins with possible virulence functions in clavicipitaceous fungi. Comprehensive overview of GH18 family chitinases has been provided to decipher the role of chitinases in claviceptaceous fungi that are either host specific or generalists.

Results
We report the 28.8 Mb draft genome of Ab and its comparative genome analysis with MR and MAC. The comparative analyses suggests expansion in pathogen-host interacting gene families and carbohydrate active enzyme families in MR, whilst their contraction in Ab and MAC genomes. The multi-modular NRPS gene (dtxS1) responsible for biosynthesis of the secondary metabolite destruxin in MR is not conserved in Ab, similar to the specialist pathogen MAC. An additional siderophore biosynthetic gene responsible for acquisition of iron was identified in MR. Further, the domain survey of chitinases suggest that the CBM50 (LysM) domains, which participate in chitin-binding functions, were not observed in MAC, but were present in Ab and MR. However, apparent differences in frequency of CBM50 domains associated with chitinases of Ab and MR was identified, where MR chitinases displayed a higher proportion of associated CBM50 domains than Ab chitinases.

Conclusions
This study suggests differences in distribution of dtxS1 and chitinases in specialists (Ab and MAC) and generalists (MR) fungi. Our analysis also suggests the presence of a siderophore biosynthetic gene in the MR genome which perhaps aids in enhanced virulence potential and host range. The variation in association of CBMs, being higher in generalists (MR) and lower in specialists (Ab and MAC) fungi may further be responsible for the differences in host affiliation.
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Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens

Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens | MycorWeb Plant-Microbe Interactions | Scoop.it
High-throughput sequencing (HTS) has become a standard technique for genomics, metagenomics and taxonomy, but these analyses typically require large amounts of high-quality DNA that is difficult to obtain from uncultivable organisms including fungi with no living culture or fruit-body representatives. By using 1 ng DNA and low coverage Illumina HiSeq HTS, we evaluated the usefulness of genomics and metagenomics tools to recover fungal barcoding genes from old and problematic specimens of fruit-bodies and ectomycorrhizal (EcM) root tips. Ribosomal DNA and single-copy genes were successfully recovered from both fruit-body and EcM specimens typically <10 years old (maximum, 17 years). Samples with maximum obtained DNA concentration <0.2 ng µl-1 were sequenced poorly. Fungal rDNA molecules assembled from complex mock community and soil revealed a large proportion of chimeras and artefactual consensus sequences of closely related taxa. Genomics and metagenomics tools enable recovery of fungal genomes from very low initial amounts of DNA from fruit-bodies and ectomycorrhizas, but these genomes include a large proportion of prokaryote and other eukaryote DNA. Nonetheless, the recovered scaffolds provide an important source for phylogenetic and phylogenomic analyses and mining of functional genes.
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Fungi Sailing the Arctic Ocean: Speciose Communities in North Atlantic Driftwood as Revealed by High-Throughput Amplicon Sequencing

Fungi Sailing the Arctic Ocean: Speciose Communities in North Atlantic Driftwood as Revealed by High-Throughput Amplicon Sequencing | MycorWeb Plant-Microbe Interactions | Scoop.it
High amounts of driftwood sail across the oceans and provide habitat for organisms tolerating the rough and saline environment. Fungi have adapted to the extremely cold and saline conditions which driftwood faces in the high north. For the first time, we applied high-throughput sequencing to fungi residing in driftwood to reveal their taxonomic richness, community composition, and ecology in the North Atlantic. Using pyrosequencing of ITS2 amplicons obtained from 49 marine logs, we found 807 fungal operational taxonomic units (OTUs) based on clustering at 97 % sequence similarity cut-off level. The phylum Ascomycota comprised 74 % of the OTUs and 20 % belonged to Basidiomycota. The richness of basidiomycetes decreased with prolonged submersion in the sea, supporting the general view of ascomycetes being more extremotolerant. However, more than one fourth of the fungal OTUs remained unassigned to any fungal class, emphasising the need for better DNA reference data from the marine habitat. Different fungal communities were detected in coniferous and deciduous logs. Our results highlight that driftwood hosts a considerably higher fungal diversity than currently known. The driftwood fungal community is not a terrestrial relic but a speciose assemblage of fungi adapted to the stressful marine environment and different kinds of wooden substrates found in it.
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Secretion of small proteins is species-specific within Aspergillus sp

Small secreted proteins (SSP) have been defined as proteins containing a signal peptide and a sequence of less than 300 amino acids. In this analysis, we have compared the secretion pattern of SSPs among eight aspergilli species in the context of plant biomass degradation and have highlighted putative interesting candidates that could be involved in the degradative process or in the strategies developed by fungi to resist the associated stress that could be due to the toxicity of some aromatic compounds or reactive oxygen species released during degradation. Among these candidates, for example, some stress-related superoxide dismutases or some hydrophobic surface binding proteins (HsbA) are specifically secreted according to the species . Since these latter proteins are able to recruit lytic enzymes to the surface of hydrophobic solid materials and promote their degradation, a synergistic action of HsbA with the degradative system may be considered and need further investigations. These SSPs could have great applications in biotechnology by optimizing the efficiency of the enzymatic systems for biomass degradation.
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Scientists use people power to find disease-resistant ash trees

Scientists use people power to find disease-resistant ash trees | MycorWeb Plant-Microbe Interactions | Scoop.it
Walkers and other members of the public will be asked to help create new generation of healthy plants
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Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges

Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges | MycorWeb Plant-Microbe Interactions | Scoop.it
Microorganisms have shaped our planet and its inhabitants for over 3.5 billion years. Humankind has had a profound influence on the biosphere, manifested as global climate and land use changes, and extensive urbanization in response to a growing population. The challenges we face to supply food, energy, and clean water while maintaining and improving the health of our population and ecosystems are significant. Given the extensive influence of microorganisms across our biosphere, we propose that a coordinated, cross-disciplinary effort is required to understand, predict, and harness microbiome function. From the parallelization of gene function testing to precision manipulation of genes, communities, and model ecosystems and development of novel analytical and simulation approaches, we outline strategies to move microbiome research into an era of causality. These efforts will improve prediction of ecosystem response and enable the development of new, responsible, microbiome-based solutions to significant challenges of our time.
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America's New Plan to Zoom In on the Planet's Microbes

America's New Plan to Zoom In on the Planet's Microbes | MycorWeb Plant-Microbe Interactions | Scoop.it
Today, the White House is announcing the launch of the National Microbiome Initiative (NMI)—an ambitious plan to better understand the microbes that live in humans, other animals, crops, soils, oceans, and more. These miniscule organisms are attracting mammoth budgets: federal agencies are committing $121 million to the NMI over the next two years, while more than 100 universities, non-profits, and companies are chipping in another $400 million.

Essentially, America has decided to point half a billion microscopes at the planet, and look through them.

Note the “planet” bit. There’s a tendency of read “microbiome” and automatically see “human” before it. But that’s a narcissistic view.
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Soil metaproteomics reveals an inter-kingdom stress response to the presence of black truffles

Soil metaproteomics reveals an inter-kingdom stress response to the presence of black truffles | MycorWeb Plant-Microbe Interactions | Scoop.it
For some truffle species of the Tuber genus, the symbiotic phase is often associated with the presence of an area of scant vegetation, commonly known as the brûlé, around the host tree. Previous metagenomics studies have identified the microorganisms present inside and outside the brûlé of a Tuber melanosporum truffle-ground, but the molecular mechanisms that operate in this ecological niche remain to be clarified. To elucidate the metabolic pathways present in the brûlé, we conducted a metaproteomics analysis on the soil of a characterized truffle-ground and cross-referenced the resulting proteins with a database we constructed, incorporating the metagenomics data for the organisms previously identified in this soil. The soil inside the brûlé contained a larger number of proteins and, surprisingly, more proteins from plants, compared with the soil outside the brûlé. In addition, Fisher’s Exact Tests detected more biological processes inside the brûlé; these processes were related to responses to multiple types of stress. Thus, although the brûlé has a reduced diversity of plant and microbial species, the organisms in the brûlé show strong metabolic activity. Also, the combination of metagenomics and metaproteomics provides a powerful tool to reveal soil functioning.
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Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi

Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
Although cell cycle control is an ancient, conserved, and essential process, some core animal and fungal cell cycle regulators share no more sequence identity than non-homologous proteins. Here, we show that evolution along the fungal lineage was punctuated by the early acquisition and entrainment of the SBF transcription factor through horizontal gene transfer. Cell cycle evolution in the fungal ancestor then proceeded through a hybrid network containing both SBF and its ancestral animal counterpart E2F, which is still maintained in many basal fungi. We hypothesize that a virally-derived SBF may have initially hijacked cell cycle control by activating transcription via the cis-regulatory elements targeted by the ancestral cell cycle regulator E2F, much like extant viral oncogenes. Consistent with this hypothesis, we show that SBF can regulate promoters with E2F binding sites in budding yeast.
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Comparative genomics reveals genes significantly associated with woody hosts in the plant pathogen Pseudomonas syringae

Comparative genomics reveals genes significantly associated with woody hosts in the plant pathogen Pseudomonas syringae | MycorWeb Plant-Microbe Interactions | Scoop.it
The diversification of lineages within Pseudomonas syringae has involved a number of adaptive shifts from herbaceous hosts onto various species of tree, resulting in the emergence of highly destructive diseases such as bacterial canker of kiwi and bleeding canker of horse chestnut. This diversification has involved a high level of gene gain and loss, and these processes are likely to play major roles in the adaptation of individual lineages onto their host plants. In order to better understand the evolution of P. syringae onto woody plants, we have generated de novo genome sequences for 26 strains from the P. syringae species complex that are pathogenic on a range of woody species, and have looked for statistically significant associations between gene presence and host type (i.e., woody or herbaceous) across a phylogeny of 64 strains. We find evidence for a common set of genes associated with strains that are able to colonise woody plants, suggesting that divergent lineages have acquired similarities of genome composition that may form the genetic basis of their adaptation to woody hosts. We also describe in detail the gain, loss, and rearrangement of specific loci that may be functionally important in facilitating this adaptive shift. Overall, our analyses allow for a greater understanding of how gene gain and loss may contribute to adaptation in P. syringae. This article is protected by copyright. All rights reserved.
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Comparative Genomic Analysis of Drechmeria coniospora Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes

Comparative Genomic Analysis of  Drechmeria coniospora  Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes | MycorWeb Plant-Microbe Interactions | Scoop.it
Drechmeria coniospora is an obligate fungal pathogen that infects nematodes via the adhesion of specialized spores to the host cuticle. D. coniospora is frequently found associated with Caenorhabditis elegans in environmental samples. It is used in the study of the nematode’s response to fungal infection. Full understanding of this bi-partite interaction requires knowledge of the pathogen’s genome, analysis of its gene expression program and a capacity for genetic engineering. The acquisition of all three is reported here. A phylogenetic analysis placed D. coniospora close to the truffle parasite Tolypocladium ophioglossoides, and Hirsutella minnesotensis, another nematophagous fungus. Ascomycete nematopathogenicity is polyphyletic; D. coniospora represents a branch that has not been molecularly characterized. A detailed in silico functional analysis, comparing D. coniospora to 11 fungal species, revealed genes and gene families potentially involved in virulence and showed it to be a highly specialized pathogen. A targeted comparison with nematophagous fungi highlighted D. coniospora-specific genes and a core set of genes associated with nematode parasitism. A comparative gene expression analysis of samples from fungal spores and mycelia, and infected C. elegans, gave a molecular view of the different stages of the D. coniospora lifecycle. Transformation of D. coniospora allowed targeted gene knock-out and the production of fungus that expresses fluorescent reporter genes. It also permitted the initial characterisation of a potential fungal counter-defensive strategy, involving interference with a host antimicrobial mechanism. This high-quality annotated genome for D. coniospora gives insights into the evolution and virulence of nematode-destroying fungi. Coupled with genetic transformation, it opens the way for molecular dissection of D. coniospora physiology, and will allow both sides of the interaction between D. coniospora and C. elegans, as well as the evolutionary arms race that exists between pathogen and host, to be studied.
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Press release: When foes become friends

Because of their sedentary life, plants have to make the most of their surroundings. To do so, they take advantage of hitherto unknown molecular mechanisms to determine what benefits them and what harms them. They also grant microorganisms access to their roots in exchange for essential nutrients in the soil. The soil fungus Colletotrichum tofieldiae serves the model plant Arabidopsis as such a subtenant when required. The plant accepts the fungus as a phosphate supplier in situations where it has no access to those minerals itself, but rejects the fungus if it is able to tap phosphate supplies on its own. Thus, the plant very accurately weighs the demands of its environment to which it must respond. In the process, the plant’s immune system plays a key role. Stéphane Hacquard, Paul Schulze-Lefert and Richard O'Connell of the Max Planck Institute for Plant Breeding Research in Cologne are addressing the question of what changes are responsible for ensuring that Colletotrichum tofieldiae no longer has to contend with the full brunt of the plant’s immune system under certain conditions. They have found that just a few changes in the genome are sufficient to turn a pathogen into a partner.

Via Stéphane Hacquard
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Refining the origins of wood-rotting mechanisms - DOE Joint Genome Institute

Refining the origins of wood-rotting mechanisms - DOE Joint Genome Institute | MycorWeb Plant-Microbe Interactions | Scoop.it
Comparative genomics analysis uses newly-sequenced white rot and brown rot fungi to refine timeline for enzymatic origins of lignocellulose decomposition.
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Sebacinales – one thousand and one interactions with land plants

Sebacinales – one thousand and one interactions with land plants | MycorWeb Plant-Microbe Interactions | Scoop.it
Root endophytism and mycorrhizal associations are complex derived traits in fungi that shape plant physiology. Sebacinales (Agaricomycetes, Basidiomycota) display highly diverse interactions with plants. Although early-diverging Sebacinales lineages are root endophytes and/or have saprotrophic abilities, several more derived clades harbour obligate biotrophs forming mycorrhizal associations. Sebacinales thus display transitions from saprotrophy to endophytism and to mycorrhizal nutrition within one fungal order. This review discusses the genomic traits possibly associated with these transitions. We also show how molecular ecology revealed the hyperdiversity of Sebacinales and their evolutionary diversification into two sister families: Sebacinaceae encompasses mainly ectomycorrhizal and early-diverging saprotrophic species; the second family includes endophytes and lineages that repeatedly evolved ericoid, orchid and ectomycorrhizal abilities. We propose the name Serendipitaceae for this family and, within it, we transfer to the genus Serendipita the endophytic cultivable species Piriformospora indica and P. williamsii. Such cultivable Serendipitaceae species provide excellent models for root endophytism, especially because of available genomes, genetic tractability, and broad host plant range including important crop plants and the model plant Arabidopsis thaliana. We review insights gained with endophytic Serendipitaceae species into the molecular mechanisms of endophytism and of beneficial effects on host plants, including enhanced resistance to abiotic and pathogen stress.
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The changing ethnoecological cobweb of white truffle (Tuber magnatum Pico) gatherers in South Piedmont, NW Italy

The changing ethnoecological cobweb of white truffle (Tuber magnatum Pico) gatherers in South Piedmont, NW Italy | MycorWeb Plant-Microbe Interactions | Scoop.it

Traditional Environmental Knowledge (TEK) related to truffles represents an under-investigated area of research in ethnobiology. Nevertheless, truffles, in a few southern European areas, and notably in South Piedmont, represent a crucial component of the local economy and cultural heritage.

Thirty-four white truffle (Tuber magnatum Pico) gatherers, locally known as trifulau, aged between 35 and 75 years and living in a few villages and small towns of the Langhe and Roero areas (South Piedmont, NW Italy), were interviewed in-depth during the years 2010-2014 regarding their ecological perceptions, truffle gathering techniques, and the socio-ecological changes that have occurred during the past several decades.

A very sophisticated ethnoecological knowledge of the trees, soils, and climatic conditions considered ideal for searching for and finding white truffles was recorded. Moreover, a very intimate connection between gatherers and their dogs plays a fundamental role in the success of the truffle search. However, according to the informants, this complex ethnoecological cobweb among men, truffles, dogs, and the environment has been heavily threatened in the past few decades by major changes: climate change, in which the summer has become a very hot and dry season; social changes, due to a more market-oriented attitude of younger gatherers; and especially environmental and macro-economic dynamics, which followed the remarkable expansion of viticulture in the study area.

The TEK of white truffle gatherers indicates the urgent need for fostering sustainable gastronomy-centred initiatives, aimed at increasing the awareness of consumers and food entrepreneurs regarding the co-evolution that has inextricably linked locals, truffles, and their natural environment during the past three centuries.

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The potential of single-cell profiling in plants

The potential of single-cell profiling in plants | MycorWeb Plant-Microbe Interactions | Scoop.it
Single-cell transcriptomics has been employed in a growing number of animal studies, but the technique has yet to be widely used in plants. Nonetheless, early studies indicate that single-cell RNA-seq protocols developed for animal cells produce informative datasets in plants. We argue that single-cell transcriptomics has the potential to provide a new perspective on plant problems, such as the nature of the stem cells or initials, the plasticity of plant cells, and the extent of localized cellular responses to environmental inputs. Single-cell experimental outputs require different analytical approaches compared with pooled cell profiles and new tools tailored to single-cell assays are being developed. Here, we highlight promising new single-cell profiling approaches, their limitations as applied to plants, and their potential to address fundamental questions in plant biology.
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Towards a multidimensional root trait framework: a tree root review

Towards a multidimensional root trait framework: a tree root review | MycorWeb Plant-Microbe Interactions | Scoop.it
The search for a root economics spectrum (RES) has been sparked by recent interest in trait-based plant ecology. By analogy with the one-dimensional leaf economics spectrum (LES), fine-root traits are hypothesised to match leaf traits which are coordinated along one axis from resource acquisitive to conservative traits. However, our literature review and meta-level analysis reveal no consistent evidence of an RES mirroring an LES. Instead the RES appears to be multidimensional. We discuss three fundamental differences contributing to the discrepancy between these spectra. First, root traits are simultaneously constrained by various environmental drivers not necessarily related to resource uptake. Second, above- and belowground traits cannot be considered analogues, because they function differently and might not be related to resource uptake in a similar manner. Third, mycorrhizal interactions may offset selection for an RES. Understanding and explaining the belowground mechanisms and trade-offs that drive variation in root traits, resource acquisition and plant performance across species, thus requires a fundamentally different approach than applied aboveground. We therefore call for studies that can functionally incorporate the root traits involved in resource uptake, the complex soil environment and the various soil resource uptake mechanisms – particularly the mycorrhizal pathway – in a multidimensional root trait framework.
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Ectomycorrhizal fungal spore bank recovery after a severe forest fire: some like it hot

Ectomycorrhizal fungal spore bank recovery after a severe forest fire: some like it hot | MycorWeb Plant-Microbe Interactions | Scoop.it
After severe wildfires, pine recovery depends on ectomycorrhizal (ECM) fungal spores surviving and serving as partners for regenerating forest trees. We took advantage of a large, severe natural forest fire that burned our long-term study plots to test the response of ECM fungi to fire. We sampled the ECM spore bank using pine seedling bioassays and high-throughput sequencing before and after the California Rim Fire. We found that ECM spore bank fungi survived the fire and dominated the colonization of in situ and bioassay seedlings, but there were specific fire adapted fungi such as Rhizopogon olivaceotinctus that increased in abundance after the fire. The frequency of ECM fungal species colonizing pre-fire bioassay seedlings, post-fire bioassay seedlings and in situ seedlings were strongly positively correlated. However, fire reduced the ECM spore bank richness by eliminating some of the rare species, and the density of the spore bank was reduced as evidenced by a larger number of soil samples that yielded uncolonized seedlings. Our results show that although there is a reduction in ECM inoculum, the ECM spore bank community largely remains intact, even after a high-intensity fire. We used advanced techniques for data quality control with Illumina and found consistent results among varying methods. Furthermore, simple greenhouse bioassays can be used to determine which fungi will colonize after fires. Similar to plant seed banks, a specific suite of ruderal, spore bank fungi take advantage of open niche space after fires.
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Fungal Genomics Challenges the Dogma of Name-Based Biosecurity

Fungal Genomics Challenges the Dogma of Name-Based Biosecurity | MycorWeb Plant-Microbe Interactions | Scoop.it
Microorganisms have inadvertently been spread via the global movement and trade of their substrates, such as animals, plants, and soil. This intercontinental exchange in the current era of globalisation has given rise to significant increases in the distribution of known pests and pathogens. Importantly, it has also resulted in many novel, emerging, infectious diseases. Biosecurity and quarantine, which aim to prevent the establishment of foreign or harmful organisms in a non-native area, are under significant pressure due to the massive increases in travel and trade.

Traditionally, quarantine regulations have been implemented based on pathogens that already cause significant disease problems on congener hosts in other parts of the world (e.g., Q-bank, available at http://www.q-bank.eu). Well-known pathogens are described, named, and studied to determine their disease cycle, epidemiology, and impact. Their importance is assessed based on their risk of infection, establishment, and economic or environmental consequences. This then shapes phytosanitary practices.

The central dogma of biosecurity proportions risk and focuses resources on known and named pathogens. This practice overlooks emerging pests and diseases that are increasingly spread around the world. Challenging this central dogma for biosecurity of fungi and fungal-like organisms is long overdue for the following reasons.
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New Phytologist: The Sphagnum microbiome: new insights from an ancient plant lineage

New Phytologist: The Sphagnum microbiome: new insights from an ancient plant lineage | MycorWeb Plant-Microbe Interactions | Scoop.it
Peat mosses of the genus Sphagnum play a major role in global carbon storage and dominate many northern peatland ecosystems, which are currently being subjected to some of the most rapid climate changes on Earth. A rapidly expanding database indicates that a diverse community of microorganisms is intimately associated with Sphagnum, inhabiting the tissues and surface of the plant. Here we summarize the current state of knowledge regarding the Sphagnum microbiome and provide a perspective for future research directions. Although the majority of the microbiome remains uncultivated and its metabolic capabilities uncharacterized, prokaryotes and fungi have the potential to act as mutualists, symbionts, or antagonists of Sphagnum. For example, methanotrophic and nitrogen-fixing bacteria may benefit the plant host by providing up to 20–30% of Sphagnum carbon and nitrogen, respectively. Next-generation sequencing approaches have enabled the detailed characterization of microbiome community composition in peat mosses. However, as with other ecologically or economically important plants, our knowledge of Sphagnum–microbiome associations is in its infancy. In order to attain a predictive understanding of the role of the microbiome in Sphagnum productivity and ecosystem function, the mechanisms of plant–microbiome interactions and the metabolic potential of constituent microbial populations must be revealed.

Via Stéphane Hacquard
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Steve Marek's curator insight, May 15, 8:59 PM
Elucidating the plant comprising the peat mined for plant growth media
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Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes | MycorWeb Plant-Microbe Interactions | Scoop.it
Over 20% of Earth/'s terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils and a rapid shift in functional gene composition during short-term thaw experiments. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales. Here we use the combination of several molecular /`omics/' approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.
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Hijacked cell division helped fuel rise of fungi: Research could point to new antifungals that stop cell growth in fungi but not in their plant or animal hosts

Hijacked cell division helped fuel rise of fungi: Research could point to new antifungals that stop cell growth in fungi but not in their plant or animal hosts | MycorWeb Plant-Microbe Interactions | Scoop.it
The more than 90,000 known species of fungi may owe their abilities to spread and even cause disease to an ancient virus that hijacked their cell division machinery, researchers report. Over a billion years ago, a viral protein invaded the fungal genome, generating a family of proteins that now play key roles in fungal growth. The research could point to new antifungals that inhibit cell division in fungi but not in their plant or animal hosts.
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Overlapping Podospora anserina Transcriptional Responses to Bacterial and Fungal Non Self Indicate a Multilayered Innate Immune Response

Overlapping Podospora anserina Transcriptional Responses to Bacterial and Fungal Non Self Indicate a Multilayered Innate Immune Response | MycorWeb Plant-Microbe Interactions | Scoop.it
Recognition and response to non self is essential to development and survival of all organisms. It can occur between individuals of the same species or between different organisms. Fungi are established models for conspecific non self recognition in the form of vegetative incompatibility (VI), a genetically controlled process initiating a programmed cell death (PCD) leading to the rejection of a fusion cell between genetically different isolates of the same species. In Podospora anserina VI is controlled by members of the hnwd gene family encoding for proteins analogous to NOD Like Receptors (NLR) immune receptors in eukaryotes. It was hypothesized that the hnwd controlled VI reaction was derived from the fungal innate immune response. Here we analyze the P. anserina transcriptional responses to two bacterial species, Serratia fonticola to which P. anserina survives and S. marcescens to which P. anserina succumbs, and compare these to the transcriptional response induced under VI conditions. Transcriptional responses to both bacteria largely overlap, however the number of genes regulated and magnitude of regulation is more important when P. anserina survives. Transcriptional responses to bacteria also overlap with the VI reaction for both up or down regulated gene sets. Genes up regulated tend to be clustered in the genome, and display limited phylogenetic distribution. In all three responses we observed genes related to autophagy to be up-regulated. Autophagy contributes to the fungal survival in all three conditions. Genes encoding for secondary metabolites and histidine kinase signaling are also up regulated in all three conditions. Transcriptional responses also display differences. Genes involved in response to oxidative stress, or encoding small secreted proteins are essentially expressed in response to bacteria, while genes encoding NLR proteins are expressed during VI. Most functions encoded in response to bacteria favor survival of the fungus while most functions up regulated during VI would lead to cell death. These differences are discussed in the frame of a multilayered response to non self in fungi
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MycoDB, a global database of plant response to mycorrhizal fungi

MycoDB, a global database of plant response to mycorrhizal fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi alter plant productivity. Over 10 years with nearly 80 collaborators, we compiled data on the response of plant biomass to mycorrhizal fungal inoculation, including meta-analysis metrics and 24 additional explanatory variables that describe the biotic and abiotic context of each study. We also include phylogenetic trees for all plants and fungi in the database. To our knowledge, MycoDB is the largest ecological meta-analysis database. We aim to share these data to highlight significant gaps in mycorrhizal research and encourage synthesis to explore the ecological and evolutionary generalities that govern mycorrhizal functioning in ecosystems.

Via Jean-Michel Ané
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Rescooped by Francis Martin from Plant & Evolution
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Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
The sessile nature of plants forced them to evolve mechanisms to prioritize their responses to simultaneous stresses, including colonization by microbes or nutrient starvation. Here, we compare the genomes of a beneficial root endophyte, Colletotrichum tofieldiae and its pathogenic relative C. incanum, and examine the transcriptomes of both fungi and their plant host Arabidopsis during phosphate starvation. Although the two species diverged only 8.8 million years ago and have similar gene arsenals, we identify genomic signatures indicative of an evolutionary transition from pathogenic to beneficial lifestyles, including a narrowed repertoire of secreted effector proteins, expanded families of chitin-binding and secondary metabolism-related proteins, and limited activation of pathogenicity-related genes in planta. We show that beneficial responses are prioritized in C. tofieldiae-colonized roots under phosphate-deficient conditions, whereas defense responses are activated under phosphate-sufficient conditions. These immune responses are retained in phosphate-starved roots colonized by pathogenic C. incanum, illustrating the ability of plants to maximize survival in response to conflicting stresses.

Via Pierre-Marc Delaux
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