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Horizontal Gene Transfer in Eukaryotic Plant Pathogens - Annu Rev Phytopath

Horizontal Gene Transfer in Eukaryotic Plant Pathogens - Annu Rev Phytopath | MycorWeb Plant-Microbe Interactions | Scoop.it

Gene transfer has been identified as a prevalent and pervasive phenomenon and an important source of genomic innovation in bacteria. The role of gene transfer in microbial eukaryotes seems to be of a reduced magnitude but in some cases can drive important evolutionary innovations, such as new functions that underpin the colonization of different niches. The aim of this review is to summarize published cases that support the hypothesis that horizontal gene transfer (HGT) has played a role in the evolution of phytopathogenic traits in fungi and oomycetes. Our survey of the literature identifies 46 proposed cases of transfer of genes that have a putative or experimentally demonstrable phytopathogenic function. When considering the life-cycle steps through which a pathogen must progress, the majority of the HGTs identified are associated with invading, degrading, and manipulating the host. Taken together, these data suggest HGT has played a role in shaping how fungi and oomycetes colonize plant hosts.

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Evolution and disorder

Evolution and disorder | MycorWeb Plant-Microbe Interactions | Scoop.it

The evolution of disordered proteins or regions of proteins differs from that of ordered proteins because of the differences in their sequence composition, intramolecular contacts, and function. Recent assessments of disordered protein evolution at the sequence, structural, and functional levels support this hypothesis. Disordered proteins have a different pattern of accepted point mutations, exhibit higher rates of insertions and deletions, and generally, but not always, evolve more rapidly than ordered proteins. Even with these high rates of sequence evolution, a few examples have shown that disordered proteins maintain their flexibility under physiological conditions, and it is hypothesized that they maintain specific structural ensembles.

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Cell Research - A DELLA protein complex controls the arbuscular mycorrhizal symbiosis in plants

Plants establish beneficial symbiotic associations with arbuscular mycorrhizal fungi, which colonize the root cortex, building specialized structures called arbuscules that facilitate nutrient exchange. The association occurs following plant recognition of lipochitooligosaccharides (LCOs) from mycorrhizal fungi, which activates the symbiosis signaling pathway prior to mycorrhizal colonization. Here we show that SLR1/DELLA, a repressor of gibberellic acid (GA) signaling, and its interacting partner protein are required for the mycorrhizal symbiosis. GA treatment inhibits mycorrhizal colonization and leads to the degradation of DELLAs. Consistently, rice lines mutated in DELLA are unable to be colonized by mycorrhizal fungi. DELLAs are members of the GRAS family of transcription factors. We further show that rice DELLA interacts with a second GRAS protein, DIP1 (DELLA Interacting Protein 1). DIP1 is also required for mycorrhizal colonization and in turn interacts with a previously characterized mycorrhizal GRAS protein, RAM1, that has been shown to directly regulate mycorrhizal-associated gene expression. We conclude that a complex of GRAS proteins, including DELLAs, is necessary for regulation of mycorrhizal-associated gene expression and thus colonization.

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Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis

Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis | MycorWeb Plant-Microbe Interactions | Scoop.it

The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade-offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions.


Via Christophe Jacquet, Stéphane Hacquard
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Gibbon genome and the fast karyotype evolution of small apes : Nature

Gibbon genome and the fast karyotype evolution of small apes : Nature | MycorWeb Plant-Microbe Interactions | Scoop.it

Gibbons are small arboreal apes that display an accelerated rate of evolutionary chromosomal rearrangement and occupy a key node in the primate phylogeny between Old World monkeys and great apes. Here we present the assembly and analysis of a northern white-cheeked gibbon (Nomascus leucogenys) genome. We describe the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage. We further show that the gibbon genera (Nomascus, Hylobates, Hoolock andSymphalangus) experienced a near-instantaneous radiation ~5 million years ago, coincident with major geographical changes in southeast Asia that caused cycles of habitat compression and expansion. Finally, we identify signatures of positive selection in genes important for forelimb development (TBX5) and connective tissues (COL1A1) that may have been involved in the adaptation of gibbons to their arboreal habitat.

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The role of forest trees and their mycorrhizal fungi in carbonate rock weathering and its significance for global carbon cycling

The role of forest trees and their mycorrhizal fungi in carbonate rock weathering and its significance for global carbon cycling | MycorWeb Plant-Microbe Interactions | Scoop.it

On million-year timescales, carbonate rock weathering exerts no net effect on atmospheric CO2 concentration. However, on timescales of decades-to-centuries it can contribute to sequestration of anthropogenic CO2 and increase land-ocean alkalinity flux, counteracting ocean acidification. Historical evidence indicates this flux is sensitive to land-use change, and recent experimental evidence suggests that trees and their associated soil microbial communities are major drivers of continental mineral weathering. Here, we review key physical and chemical mechanisms by which the symbiotic mycorrhizal fungi of forest tree roots potentially enhance carbonate rock weathering. Evidence from our ongoing field study at the UK's national pinetum confirms increased weathering of carbonate rocks by a wide range of gymnosperm and angiosperm tree species that form arbuscular (AM) or ectomycorrhizal (EM) fungal partnerships. We demonstrate that calcite-containing rock grains under EM tree species weather significantly faster than those under AM trees, an effect linked to greater soil acidification by EM trees. Weathering and corresponding alkalinity export is likely to increase with rising atmospheric CO2 and associated climate change. Our analyses suggest that strategic planting of fast growing EM angiosperm taxa on calcite-and dolomite rich terrain might accelerate the transient sink for atmospheric CO2 and slow rates of ocean acidification.


Via Christophe Jacquet
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Microbes ride the current

Microbes ride the current | MycorWeb Plant-Microbe Interactions | Scoop.it

How do differences in marine bacterial populations arise in the ocean? On page 1346 of this Science issue, Hellweger et al. (1) investigate this question with a model based on ocean currents, parameterized with data from the most ubiquitous and abundant ocean bacterium, Pelagibacter. The model assumes that mutations are neutral—that is, they cause no change in the fitness of organisms, so that selection cannot act on them. The results show that neutral processes are enough to generate biogeographical patterns in marine bacteria without any adaptive evolution taking place.

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The Ins and Outs of Rust Haustoria

The Ins and Outs of Rust Haustoria | MycorWeb Plant-Microbe Interactions | Scoop.it

Rust diseases caused by fungi of the order Pucciniales afflict a wide range of plants, including cereals, legumes, ornamentals, and fruit trees, and pose a serious threat to cropping systems and global food security. The obligate parasitic lifestyle of these fungi and their complex life cycles, often involving alternate hosts for the sexual and asexual stages, also make this group of pathogens of great biological interest. One of the most remarkable adaptations of rust fungi is the specialized infection structure that underpins the sustained biotrophic association with hosts; the haustorium (Figure 1A and C). This organ forms after penetration of the wall of a live host cell, expanding on the inner side of the cell wall while invaginating the surrounding host plasma membrane (Figure 1C). Through haustoria, the pathogen derives nutrients from the host and secretes virulence proteins called effectors, which are believed to be the key players that manipulate the physiological and immune responses of host cells [1]–[4]. Analogous terminal feeding structures have independently evolved in other organisms such as the haustorium in powdery mildews (ascomycetes) and downy mildews (oomycetes, not true fungi), and the arbuscules in arbuscular mycorrhizae, suggesting that such architecture represents a successful adaptation of these organisms to interact with their respective host plants [5], [6].

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Convergent Targeting of a Common Host Protein-Network by Pathogen Effectors from Three Kingdoms of Life

Convergent Targeting of a Common Host Protein-Network by Pathogen Effectors from Three Kingdoms of Life | MycorWeb Plant-Microbe Interactions | Scoop.it

While conceptual principles governing plant immunity are becoming clear, its systems-level organization and the evolutionary dynamic of the host-pathogen interface are still obscure. We generated a systematic protein-protein interaction network of virulence effectors from the ascomycete pathogen Golovinomyces orontii andArabidopsis thaliana host proteins. We combined this data set with corresponding data for the eubacterial pathogen Pseudomonas syringae and the oomycete pathogen Hyaloperonospora arabidopsidis. The resulting network identifies host proteins onto which intraspecies and interspecies pathogen effectors converge. Phenotyping of 124 Arabidopsis effector-interactor mutants revealed a correlation between intraspecies and interspecies convergence and several altered immune response phenotypes. Several effectors and the most heavily targeted host protein colocalized in subnuclear foci. Products of adaptively selected Arabidopsis genes are enriched for interactions with effector targets. Our data suggest the existence of a molecular host-pathogen interface that is conserved across Arabidopsis accessions, while evolutionary adaptation occurs in the immediate network neighborhood of effector targets.

  
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MPMI: The genome of the saprophytic fungus Verticillium tricorpus reveals a complex effector repertoire resembling that of its pathogenic relatives (2014)

MPMI: The genome of the saprophytic fungus Verticillium tricorpus reveals a complex effector repertoire resembling that of its pathogenic relatives (2014) | MycorWeb Plant-Microbe Interactions | Scoop.it

Vascular wilts caused by Verticillium spp. are destructive plant diseases, affecting hundreds of hosts. Only few Verticillium spp. are causal agents of vascular wilt diseases, of which V. dahliae is the most notorious pathogen, and several V. dahliae genomes are available. In contrast, V. tricorpus is mainly known as saprophyte and causal agent of opportunistic infections. Based on a hybrid approach that combines second and third generation sequencing, a near-gapless V. tricorpus genome assembly was obtained. With comparative genomics, we aimed to identify genomic features in V. dahliae that confer the ability to cause vascular wilt disease. Unexpectedly, both species encode similar effector repertoires and share a genomic structure with genes encoding secreted proteins clustered in genomic islands. Intriguingly, V. tricorpus contains significantly less repetitive elements and an extended spectrum of secreted carbohydrate-active enzymes when compared with V. dahliae. In conclusion, we highlight the technical advances of a hybrid sequencing and assembly approach and reveal that the saprophyte V. tricorpus shares many hallmark features with V. dahliae.


Via Kamoun Lab @ TSL
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Biology Letters: The dawn of symbiosis between plants and fungi (2011)

Biology Letters: The dawn of symbiosis between plants and fungi (2011) | MycorWeb Plant-Microbe Interactions | Scoop.it

The colonization of land by plants relied on fundamental biological innovations, among which was symbiosis with fungi to enhance nutrient uptake. Here we present evidence that several species representing the earliest groups of land plants are symbiotic with fungi of the Mucoromycotina. This finding brings up the possibility that terrestrialization was facilitated by these fungi rather than, as conventionally proposed, by members of the Glomeromycota. Since the 1970s it has been assumed, largely from the observation that vascular plant fossils of the early Devonian (400 Ma) show arbuscule-like structures, that fungi of the Glomeromycota were the earliest to form mycorrhizas, and evolutionary trees have, until now, placed Glomeromycota as the oldest known lineage of endomycorrhizal fungi. Our observation that Endogone-like fungi are widely associated with the earliest branching land plants, and give way to glomeromycotan fungi in later lineages, raises the new hypothesis that members of the Mucoromycotina rather than the Glomeromycota enabled the establishment and growth of early land colonists.


Via Kamoun Lab @ TSL
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Metatranscriptomic analysis of ectomycorrhizal roots reveal genes associated with Piloderma-Pinus symbiosis: Improved methodologies for assessing gene expression in situ

Metatranscriptomic analysis of ectomycorrhizal roots reveal genes associated with Piloderma-Pinus symbiosis: Improved methodologies for assessing gene expression in situ | MycorWeb Plant-Microbe Interactions | Scoop.it

Ectomycorrhizal (EM) fungi form symbiotic associations with plant roots that regulate nutrient exchange between forest plants and soil. Environmental metagenomics approaches that employ next-generation sequencing show great promise for studying EM symbioses, however, metatranscriptomic studies have been constrained by the inherent difficulties associated with isolation and sequencing of RNA from mycorrhizae. Here we apply an optimized method for combined DNA/RNA extraction using field-collected EM fungal-pine root clusters, together with protocols for taxonomic identification of expressed ribosomal RNA, and inference of EM function based on plant and fungal metatranscriptomics. We used transcribed portions of ribosomal RNA genes to identify several transcriptionally dominant fungal taxa associated with loblolly pine including Amphinema, Russula, and Piloderma spp. One taxon, Piloderma croceum, has a publically available genome that allowed us to identify patterns of gene content and transcript abundance. Over 1500 abundantly expressed Piloderma genes were detected from mycorrhizal roots, including genes for protein metabolism, cell signaling, electron transport, terpene synthesis, and other extracellular activities. In contrast, Piloderma gene encoding an ammonia transporter showed highest transcript abundance in soil samples. Our methodology highlights the potential of metatranscriptomics to identify genes associated with symbiosis and ecosystem function using field-collected samples.

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A wake-up call with coffee

A wake-up call with coffee | MycorWeb Plant-Microbe Interactions | Scoop.it

The captain of the starship Voyager from one of the latter-dayStar Trek television series expressed the sentiments of many by stating: “Coffee, the finest organic suspension ever devised.” On page 1181, Denoeud et al. present a draft genome of the diploidCoffea canephora (1), one of the two founder species of the tetraploid crop Coffea arabica. Coffee, the plant bearing the irresistible bean that delivers the most widely consumed psychoactive drug in the world—caffeine—joins a long list of crop species that have been sequenced using ever-improving genomic hardware and assembly software (2). High-quality genome assemblies facilitate the resequencing of many cultivated varieties, landraces (local ecotypes), and sometimes wild, crop-related species. The challenge now is to translate these decoded genomes into new and improved tools for plant breeding; there is a need for a better balance of research priorities, with greater emphasis on crop phenotypes.

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Temperature sensitivity of soil respiration rates enhanced by microbial community response : Nature

Temperature sensitivity of soil respiration rates enhanced by microbial community response : Nature | MycorWeb Plant-Microbe Interactions | Scoop.it
Soils store about four times as much carbon as plant biomass, and soil microbial respiration releases about 60 petagrams of carbon per year to the atmosphere as carbon dioxide. Short-term experiments have shown that soil microbial respiration increases exponentially with temperature. This information has been incorporated into soil carbon and Earth-system models, which suggest that warming-induced increases in carbon dioxide release from soils represent an important positive feedback loop that could influence twenty-first-century climate change. The magnitude of this feedback remains uncertain, however, not least because the response of soil microbial communities to changing temperatures has the potential to either decrease or increase warming-induced carbon losses substantially. Here we collect soils from different ecosystems along a climate gradient from the Arctic to the Amazon and investigate how microbial community-level responses control the temperature sensitivity of soil respiration. We find that the microbial community-level response more often enhances than reduces the mid- to long-term (90 days) temperature sensitivity of respiration. Furthermore, the strongest enhancing responses were observed in soils with high carbon-to-nitrogen ratios and in soils from cold climatic regions. After 90 days, microbial community responses increased the temperature sensitivity of respiration in high-latitude soils by a factor of 1.4 compared to the instantaneous temperature response. This suggests that the substantial carbon stores in Arctic and boreal soils could be more vulnerable to climate warming than currently predicted.
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What’s for dinner? Undescribed species of porcini in a commercial packet

What’s for dinner? Undescribed species of porcini in a commercial packet | MycorWeb Plant-Microbe Interactions | Scoop.it
Accurate diagnosis of the components of our food and a standard lexicon for clear communication is essential for regulating global food trade and identifying food frauds. Reliable identification of wild collected foods can be particularly difficult, especially when they originate in under-documented regions or belong to poorly known groups such as Fungi. Porcini, one of the most widely traded wild edible mushrooms in the world, are large and conspicuous and they are used as a food both on their own and in processed food products. China is a major exporter of porcini, most of it ending up in Europe. We used DNA-sequencing to identify three species of mushroom contained within a commercial packet of dried Chinese porcini purchased in London. Surprisingly, all three have never been formally described by science and required new scientific names. This demonstrates the ubiquity of unknown fungal diversity even in widely traded commercial food products from one of the most charismatic and least overlooked groups of mushrooms. Our rapid analysis and description makes it possible to reliably identify these species, allowing their harvest to be monitored and their presence tracked in the food chain.
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PLoS Genetics: Trans-kingdom Cross-Talk: Small RNAs on the Move

PLoS Genetics: Trans-kingdom Cross-Talk: Small RNAs on the Move | MycorWeb Plant-Microbe Interactions | Scoop.it

This review focuses on the mobility of small RNA (sRNA) molecules from the perspective of trans-kingdom gene silencing. Mobility of sRNA molecules within organisms is a well-known phenomenon, facilitating gene silencing between cells and tissues. sRNA signals are also transmitted between organisms of the same species and of different species. Remarkably, in recent years many examples of RNA-signal exchange have been described to occur between organisms of different kingdoms. These examples are predominantly found in interactions between hosts and their pathogens, parasites, and symbionts. However, they may only represent the tip of the iceberg, since the emerging picture suggests that organisms in biological niches commonly exchange RNA-silencing signals. In this case, we need to take this into account fully to understand how a given biological equilibrium is obtained. Despite many observations of trans-kingdom RNA signal transfer, several mechanistic aspects of these signals remain unknown. Such RNA signal transfer is already being exploited for practical purposes, though. Pathogen genes can be silenced by plant-produced sRNAs designed to affect these genes. This is also known as Host-Induced Genes Silencing (HIGS), and it has the potential to become an important disease-control method in the future.


Via Stéphane Hacquard
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Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest | MycorWeb Plant-Microbe Interactions | Scoop.it

The phyllosphere—the aerial surfaces of plants, including leaves—is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density–growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant–microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function.

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The cryptic role of biodiversity in the emergence of host–microbial mutualisms

The cryptic role of biodiversity in the emergence of host–microbial mutualisms | MycorWeb Plant-Microbe Interactions | Scoop.it

The persistence of mutualisms in host-microbial – or holobiont – systems is difficult to explain because microbial mutualists, who bear the costs of providing benefits to their host, are always prone to being competitively displaced by non-mutualist ‘cheater’ species. This disruptive effect of competition is expected to be particularly strong when the benefits provided by the mutualists entail costs such as reduced competitive ability. Using a metacommunity model, we show that competition between multiple cheaters within the host's microbiome, when combined with the spatial structure of host–microbial interactions, can have a constructive rather than a disruptive effect by allowing the emergence and maintenance of mutualistic microorganisms within the host. These results indicate that many of the microorganisms inhabiting a host's microbiome, including those that would otherwise be considered opportunistic or even potential pathogens, play a cryptic yet critical role in promoting the health and persistence of the holobiont across spatial scales.


Via Jean-Michel Ané
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Biogeographic patterns in ocean microbes emerge in a neutral agent-based model

Biogeographic patterns in ocean microbes emerge in a neutral agent-based model | MycorWeb Plant-Microbe Interactions | Scoop.it

A key question in ecology and evolution is the relative role of natural selection and neutral evolution in producing biogeographic patterns. We quantify the role of neutral processes by simulating division, mutation, and death of 100,000 individual marine bacteria cells with full 1 million–base-pair genomes in a global surface ocean circulation model. The model is run for up to 100,000 years and output is analyzed using BLAST (Basic Local Alignment Search Tool) alignment and metagenomics fragment recruitment. Simulations show the production and maintenance of biogeographic patterns, characterized by distinct provinces subject to mixing and periodic takeovers by neighbors (coalescence), after which neutral evolution reestablishes the province and the patterns reorganize. The emergent patterns are substantial (e.g., down to 99.5% DNA identity between North and Central Pacific provinces) and suggest that microbes evolve faster than ocean currents can disperse them. This approach can also be used to explore environmental selection.

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Evidence for land plant cell wall biosynthetic mechanisms in charophyte green algae

Evidence for land plant cell wall biosynthetic mechanisms in charophyte green algae | MycorWeb Plant-Microbe Interactions | Scoop.it

 

Abstract

Background and Aims The charophyte green algae (CGA) are thought to be the closest living relatives to the land plants, and ancestral CGA were unique in giving rise to the land plant lineage. The cell wall has been suggested to be a defining structure that enabled the green algal ancestor to colonize land. These cell walls provide support and protection, are a source of signalling molecules, and provide developmental cues for cell differentiation and elongation. The cell wall of land plants is a highly complex fibre composite, characterized by cellulose cross-linked by non-cellulosic polysaccharides, such as xyloglucan, embedded in a matrix of pectic polysaccharides. How the land plant cell wall evolved is currently unknown: early-divergent chlorophyte and prasinophyte algae genomes contain a low number of glycosyl transferases (GTs), while land plants contain hundreds. The number of GTs in CGA is currently unknown, as no genomes are available, so this study sought to give insight into the evolution of the biosynthetic machinery of CGA through an analysis of available transcriptomes.

Methods Available CGA transcriptomes were mined for cell wall biosynthesis GTs and compared with GTs characterized in land plants. In addition, gene cloning was employed in two cases to answer important evolutionary questions.

Key Results Genetic evidence was obtained indicating that many of the most important core cell wall polysaccharides have their evolutionary origins in the CGA, including cellulose, mannan, xyloglucan, xylan and pectin, as well as arabino-galactan protein. Moreover, two putative cellulose synthase-like D family genes (CSLDs) from the CGA speciesColeochaete orbicularis and a fragment of a putative CSLA/K-like sequence from a CGA Spirogyra species were cloned, providing the first evidence that all the cellulose synthase/-like genes present in early-divergent land plants were already present in CGA.

Conclusions The results provide new insights into the evolution of cell walls and support the notion that the CGA were pre-adapted to life on land by virtue of the their cell wall biosynthetic capacity. These findings are highly significant for understanding plant cell wall evolution as they imply that some features of land plant cell walls evolved prior to the transition to land, rather than having evolved as a result of selection pressures inherent in this transition.


Via Pierre-Marc Delaux
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Deep-biosphere consortium of fungi and prokaryotes in Eocene subseafloor basalts

Deep-biosphere consortium of fungi and prokaryotes in Eocene subseafloor basalts | MycorWeb Plant-Microbe Interactions | Scoop.it

The deep biosphere of the subseafloor crust is believed to contain a significant part of Earth's biomass, but because of the difficulties of directly observing the living organisms, its composition and ecology are poorly known. We report here a consortium of fossilized prokaryotic and eukaryotic micro-organisms, occupying cavities in deep-drilled vesicular basalt from the Emperor Seamounts, Pacific Ocean, 67.5 m below seafloor (mbsf). Fungal hyphae provide the framework on which prokaryote-like organisms are suspended like cobwebs and iron-oxidizing bacteria form microstromatolites (Frutexites). The spatial inter-relationships show that the organisms were living at the same time in an integrated fashion, suggesting symbiotic interdependence. The community is contemporaneous with secondary mineralizations of calcite partly filling the cavities. The fungal hyphae frequently extend into the calcite, indicating that they were able to bore into the substrate through mineral dissolution. A symbiotic relationship with chemoautotrophs, as inferred for the observed consortium, may be a pre-requisite for the eukaryotic colonization of crustal rocks. Fossils thus open a window to the extant as well as the ancient deep biosphere.

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Frontiers | Control of arbuscular mycorrhiza development by nutrient signals | Plant Physiology

Inorganic phosphate (Pi), the main form of phosphorus used by plants, is one of the most important limiting factors for plant growth. In the soil soluble Pi that is readily available for uptake, occurs at very low concentrations (Schachtman et al., 1998). One adaptation of plants to low Pi availability is the symbiosis with arbuscular mycorrhiza fungi (AMF) of the phylum Glomeromycota. The fungi efficiently take up phosphate and other mineral nutrients and deliver them to the host, in exchange for carbohydrates. Thereby, arbuscular-mycorrhiza compatible plants have two Pi uptake pathways, which are defined by different sets of phosphate transporters: a direct uptake pathway through the epidermis and root hairs, and a symbiotic uptake pathway for the Pi provided by the fungus (Smith and Smith, 2011).

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Storify: #NPW10 Origin and evolution of plants and their interactions with fungi. 9–10 September 2014


Via Kamoun Lab @ TSL, Pierre-Marc Delaux
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10th New Phytologist Workshop: Origin and evolution of plants and their interactions with fungi, 9–10 September 2014, Natural History Museum, London, UK

10th New Phytologist Workshop: Origin and evolution of plants and their interactions with fungi, 9–10 September 2014, Natural History Museum, London, UK | MycorWeb Plant-Microbe Interactions | Scoop.it

Our overall goal is to understand how plants and their eukaryotic symbionts (fungi and fungi-like microorganisms, especially oomycetes) co-evolved during the early development of terrestrial ecosystems. Several diverse and rapidly developing disciplines are relevant to addressing this goal. Our workshop is designed to bringing together experts from across these disciplines to learn about recent developments, understand the range of approaches and to explore potential cross disciplinary collaborations.

 

1. We will bring together a multidisciplinary group of specialists in the biology and phylogenetics of living bryophytes and of fungi, experts on the evolution of plant-­‐fungal interactions (biochemical/physiological/ecological) and specialists on the early fossil record. Our focus will be to determine how expertise in these diverse disciplines could be harnessed to investigate the early evolution of key events, metabolic pathways, and symbiotic associations.

 

2. We will identify themes which cut across the different disciplines and how best to harness collaboration. For example, recent genomic and molecular clock analyses indicate that the origin of lignin decomposition coincided with the end of the Carboniferous Period. A carefully constructed investigation of Palaeozoic Era fossil plants (e.g. evidence of white rots) and analyses of sediment geochemistry documenting could test these hypotheses. A second area of interest is arbuscular mycorrhizal symbioses, where much remains to be learned about the early evolution of the trait. This would benefit from focused discussion by experts on living bryophyte/fungal systems, developmental biologists and palaeontologists. A third area of interest is the early evolution and development of soil ecosystems, in which the identification and characterisation of modern analogues could greatly assist interpretation of sediments in the early fossil record.

 

3. The proposed workshop is a first step in community collaboration. We will look for ways to develop and strengthen collaboration at an international level. We envisage building a scheme of communication and knowledge sharing through laboratory exchange visits, and to take the field forward we intend to explore the possibility of developing multidisciplinary research networks/consortia.

 
Via Kamoun Lab @ TSL
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eLIFE: Active invasion of bacteria into living fungal cells

eLIFE: Active invasion of bacteria into living fungal cells | MycorWeb Plant-Microbe Interactions | Scoop.it

The rice seedling blight fungus Rhizopus microsporus and its endosymbiont Burkholderia rhizoxinica form an unusual, highly specific alliance to produce the highly potent antimitotic phytotoxin rhizoxin. Yet, it has remained a riddle how bacteria invade into the fungal cells. Genome mining for potential symbiosis factors and functional analyses revealed that a type 2 secretion system (T2SS) of the bacterial endosymbiont is required for the formation of the endosymbiosis. Comparative proteome analyses show that the T2SS releases chitinolytic enzymes (chitinase, chitosanase) and chitin-binding proteins. The genes responsible for chitinolytic proteins and T2SS components are highly expressed during infection. Through targeted gene knock-outs, sporulation assays and microscopic investigations we found that chitinase is essential for bacteria to enter hyphae. Unprecedented snapshots of the traceless bacterial intrusion were obtained using cryo-electron microscopy. Beyond unveiling the pivotal role of chitinolytic enzymes in the active invasion of a fungus by bacteria, these findings grant unprecedented insight into the fungal cell wall penetration and symbiosis formation.


Via Stéphane Hacquard
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The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis | MycorWeb Plant-Microbe Interactions | Scoop.it

Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.

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