Plant-Microbe Symbiosis
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Comparative analysis of mitochondrial genomes of Rhizophagus irregularis – syn. Glomus irregulare – reveals a polymorphism induced by variability generating elements

Comparative analysis of mitochondrial genomes of Rhizophagus irregularis – syn. Glomus irregulare – reveals a polymorphism induced by variability generating elements | Plant-Microbe Symbiosis | Scoop.it

Arbuscular mycorrhizal (AM) fungi are involved in one of the most widespread plant–fungus interactions. A number of studies on the population dynamics of AM fungi have used mitochondrial (mt) DNA sequences, and yet mt AM fungus genomes are poorly known. To date, four mt genomes of three species of AM fungi are available, among which are two from Rhizophagus irregularis.
In order to study intra- and interstrain mt genome variability of R. irregularis, we sequenced and de novo assembled four additional mt genomes of this species. We used 454 pyrosequencing and Illumina technologies to directly sequence mt genomes from total genomic DNA.
The mt genomes are unique within each strain. Interstrain divergences in genome size, as a result of highly polymorphic intergenic and intronic sequences, were observed. The polymorphism is brought about by three types of variability generating element (VGE): homing endonucleases, DNA polymerase domain-containing open reading frames and small inverted repeats. Based on VGE positioning, mt sequences and nuclear markers, two subclades of R. irregularis were characterized.
The discovery of VGEs highlights the great intraspecific plasticity of the R. irregularis mt genome. VGEs allow the design of powerful mt markers for the typing and monitoring of R. irregularis strains in genetic and population studies.

 

 

Damien Formey, Marion Molès, Alexandra Haouy, Bruno Savelli, Olivier Bouchez, Guillaume Bécard, Christophe Roux

Volume 196, Issue 4, pages 1217–1227, December 2012

 

DOI: 10.1111/j.1469-8137.2012.04283.x


Via Stefano Ghignone
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Plant-Microbe Symbiosis
Beneficial associations between plants and microbes
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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 | Plant-Microbe Symbiosis | 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
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The systemic nodule number regulation kinase SUNN in Medicago truncatula interacts with MtCLV2 and MtCRN

Autoregulation of nodulation (AON), a systemic signaling pathway in legumes, limits the number of nodules formed by the legume in its symbiosis with rhizobia. Recent research suggests a model for the systemic regulation in Medicago truncatula in which root signaling peptides are translocated to the shoot where they bind to a shoot receptor complex containing the leucine-rich repeat receptor-like kinase SUNN, triggering signal transduction which terminates nodule formation in roots. Here we show that a tagged SUNN protein capable of rescuing the sunn-4 phenotype is localized to the plasma membrane and is associated with the plasmodesmata. Using bimolecular fluorescence complementation analysis we show that, like its sequence ortholog Arabidopsis CLV1, SUNN interacts with homologous CLV1-interacting proteins MtCLAVATA2 and MtCORYNE. All three proteins were also able to form homomers and MtCRN and MtCLV2 also interact with each other. A crn Tnt1 insertion mutant of M. truncatula displayed a shoot controlled increased nodulation phenotype, similar to the clv2 mutants of pea and Lotus japonicus. Together these data suggest that legume AON signaling could occur through a multi-protein complex and that both MtCRN and MtCLV2 may play roles in AON together with SUNN.
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Microbe-ID: an open source toolbox for microbial genotyping and species identification

Microbe-ID: an open source toolbox for microbial genotyping and species identification | Plant-Microbe Symbiosis | Scoop.it
Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.

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M. Philip Oliver's curator insight, August 20, 2:30 PM

Thank God! I was waiting for this..

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Without oxygen from ancient moss you wouldn’t be alive today

Without oxygen from ancient moss you wouldn’t be alive today | Plant-Microbe Symbiosis | Scoop.it
Earth’s air is only breathable today because of moss-like plants that colonised the land 470 million years ago.

The moss enriched the atmosphere with oxygen and triggered a cycle that maintained its levels, paving the way to complex life.

Oxygen in its current form first appeared on Earth 2.4 billion years ago in what has become known as the Great Oxidation Event.

But it was not until around 400 million years ago that oxygen in the atmosphere approached present day levels. Scientists have long debated what caused this shift, without which humans could not have evolved.
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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 | Plant-Microbe Symbiosis | 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.

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Arbuscular Mycorrhizal Fungi in Wetland Habitats and Their Application in Constructed Wetland: A Review

Over the last three decades, the presence and functional roles of arbuscular mycorrhizal (AM) fungi in wetland habitats have received increasing attention. This review summarized the mycorrhizal status in wetlands and the effect of flooding on AM fungal colonization. Plants of 99 families living in 31 different habitats have been found to be associated with AM fungi, even including submerged aquatic plants and several plant species that were thought to be nonmycorrhizal (Cyperaceae, Chenopodiaceae, and Plumbaginaceae). The functions of AM fungi in wetland ecological systems could be concluded as their influences on the composition, succession, and diversity of the wetland plant community, and the growth and nutrition of wetland plants. Affecting the composition, succession, and diversity of the wetland plant community, AM fungi have positive, negative, or neutral effects on the performance of different wetland species under different conditions. The factors that affect the application effect of AM fungi in constructed wetland (CW) include flooding, phosphorus, plant species, aerenchyma, salinity, CW types, operation modes of CW, and wastewater quality. The generalist AM fungi strains can be established spontaneously, rapidly, and extensively in wastewater bioremediation technical installations; therefore, AM fungi can be considered ideal inhabitants of technical installations for the plant-based bioremediation of groundwater contaminated by organic pollutants or other contaminants. In the future, roles of AM fungi and factors that affect the purifying capacity of AM-CW system must be understood to optimize CW ecosystem.

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New insights into Nod factor biosynthesis: Analyses of chitooligomers and lipo-chitooligomers of Rhizobium sp. IRBG74 mutants

New insights into Nod factor biosynthesis: Analyses of chitooligomers and lipo-chitooligomers of Rhizobium sp. IRBG74 mutants | Plant-Microbe Symbiosis | Scoop.it
Soil-dwelling, nitrogen-fixing rhizobia signal their presence to legume hosts by secreting lipo-chitooligomers (LCOs) that are decorated with a variety of chemical substituents. It has long been assumed, but never empirically shown, that the LCO backbone is synthesized first by NodC, NodB, and NodA, followed by addition of one or more substituents by other Nod proteins. By analyzing a collection of in-frame deletion mutants of key nod genes in the bacterium Rhizobium sp. IRBG74 by mass spectrometry, we were able to shed light on the possible substitution order of LCO decorations, and we discovered that the prevailing view is probably erroneous. We found that most substituents could be transferred to a short chitin backbone prior to acylation by NodA, which is probably one of the last steps in LCO biosynthesis. The existence of substituted, short chitin oligomers offers new insights into symbiotic plant–microbe signaling.
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Latest paper from our lab!

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Decoding molecular interactions in microbial communities

Decoding molecular interactions in microbial communities | Plant-Microbe Symbiosis | Scoop.it
Microbial communities govern numerous fundamental processes on earth. Discovering and tracking molecular interactions among microbes is critical for understanding how single species and complex communities impact their associated host or natural environment. While recent technological developments in DNA sequencing and functional imaging have led to new and deeper levels of understanding, we are limited now by our inability to predict and interpret the intricate relationships and interspecies dependencies within these communities. In this review, we highlight the multifaceted approaches investigators have taken within their areas of research to decode interspecies molecular interactions that occur between microbes. Understanding these principles can give us greater insight into ecological interactions in natural environments and within synthetic consortia.

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We've Been Wrong About Lichen For 150 Years

We've Been Wrong About Lichen For 150 Years | Plant-Microbe Symbiosis | Scoop.it

Hundreds of millions of years ago, a tiny green microbe joined forces with a fungus, and together they conquered the world. It’s a tale of two cross-kingdom organisms, one providing food and the one other shelter, and it’s been our touchstone example of symbiosis for 150 years. Trouble is, that story is nowhere near complete.

 

A sweeping genetic analysis of lichen has revealed a third symbiotic organism, hiding in plain sight alongside the familiar two, that has eluded scientists for decades. The stowaway is another fungus, a basidiomycete yeast. It’s been found in 52 genera of lichen across six continents, indicating that it is an extremely widespread, if not ubiquitous, part of the symbiosis. And according to molecular dating, it’s probably been along for the ride since the beginning.

 

“I think this will require some rewriting of the textbooks,” said Catharine Aime, a mycologist at Purdue University and co-author on the study published today in Science.


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Peter Buckland's curator insight, July 23, 4:14 AM
A fascinating discovery
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Grasses suppress shoot-borne roots to conserve water during drought

Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree of root initiation from the belowground basal nodes of the shoot, termed the crown. Although this postembryonic shoot-borne root system represents the major conduit for water uptake, little is known about the effect of water availability on its development. Here we demonstrate that in the model C4 grass Setaria viridis, the crown locally senses water availability and suppresses postemergence crown root growth under a water deficit. This response was observed in field and growth room environments and in all grass species tested. Luminescence-based imaging of root systems grown in soil-like media revealed a shift in root growth from crown-derived to primary root-derived branches, suggesting that primary root-dominated architecture can be induced in S. viridis under certain stress conditions. Crown roots of Zea mays and Setaria italica, domesticated relatives of teosinte and S. viridis, respectively, show reduced sensitivity to water deficit, suggesting that this response might have been influenced by human selection. Enhanced water status of maize mutants lacking crown roots suggests that under a water deficit, stronger suppression of crown roots actually may benefit crop productivity.

Via Pierre-Marc Delaux
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Multiplex amplicon sequencing for microbe identification in community-based culture collections

Multiplex amplicon sequencing for microbe identification in community-based culture collections | Plant-Microbe Symbiosis | Scoop.it
Microbiome analysis using metagenomic sequencing has revealed a vast microbial diversity associated with plants. Identifying the molecular functions associated with microbiome-plant interaction is a significant challenge concerning the development of microbiome-derived technologies applied to agriculture. An alternative to accelerate the discovery of the microbiome benefits to plants is to construct microbial culture collections concomitant with accessing microbial community structure and abundance. However, traditional methods of isolation, cultivation, and identification of microbes are time-consuming and expensive. Here we describe a method for identification of microbes in culture collections constructed by picking colonies from primary platings that may contain single or multiple microorganisms, which we named community-based culture collections (CBC). A multiplexing 16S rRNA gene amplicon sequencing based on two-step PCR amplifications with tagged primers for plates, rows, and columns allowed the identification of the microbial composition regardless if the well contains single or multiple microorganisms. The multiplexing system enables pooling amplicons into a single tube. The sequencing performed on the PacBio platform led to recovery near-full-length 16S rRNA gene sequences allowing accurate identification of microorganism composition in each plate well. Cross-referencing with plant microbiome structure and abundance allowed the estimation of diversity and abundance representation of microorganism in the CBC.

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Root signals that mediate mutualistic interactions in the rhizosphere

Root signals that mediate mutualistic interactions in the rhizosphere | Plant-Microbe Symbiosis | Scoop.it
A recent boom in research on belowground ecology is rapidly revealing a multitude of fascinating interactions, in particular in the rhizosphere. Many of these interactions are mediated by photo-assimilates that are excreted by plant roots. Root exudates are not mere waste products, but serve numerous functions to control abiotic and biotic processes. These functions range from changing the chemical and physical properties of the soil, inhibiting the growth of competing plants, combatting herbivores, and regulating the microbial community. Particularly intriguing are root-released compounds that have evolved to serve mutualistic interactions with soil-dwelling organisms. These mutually beneficial plant-mediated signals are not only of fundamental ecological interest, but also exceedingly important from an agronomical perspective. Here, we attempt to provide an overview of the plant-produced compounds that have so far been implicated in mutualistic interactions. We propose that these mutualistic signals may have evolved from chemical defenses and we point out that they can be (mis)used by specialized pathogens and herbivores. We speculate that many more signals and interactions remain to be uncovered and that a good understanding of the mechanisms and ecological implications can be the basis for exploitation and manipulation of the signals for crop improvement and protection.

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Everything you own could one day be made from mushrooms

Everything you own could one day be made from mushrooms | Plant-Microbe Symbiosis | Scoop.it
Most people look at mushrooms as an ingredient in risotto or a one-way ticket to a psychedelic wonderland. Sophia Wang sees a different future for fungi.

Sitting on the back porch of a San Francisco coffee shop, she fans a piece of worn, indigo-colored leather made from fungi grown in her company's lab.

"It's a new thing in the world," Wang, CEO and cofounder of MycoWorks, says of the mushroom-like material.
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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 | Plant-Microbe Symbiosis | 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.

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Plant peptides – taking them to the next level

Plant growth, development, reproduction and environmental stress responses are tightly regulated by a complex network of signalling pathways. Plant hormones – including salicylic acid, ethylene, jasmonic acid, auxins, gibberellins, cytokinins, abscisic acid and brassinosteroids – have long been considered the major signalling molecules during those processes. However, the discovery that many different (secreted) peptides are involved in signalling has stimulated intensive research, and this special issue reflects the latest developments in this dynamic field.
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A putative molybdate transporter LjMOT1 is required for molybdenum transport in Lotus japonicus

Molybdenum (Mo) is an essential micronutrient that is required in plant growth and development, and it affects the formation of root nodules and nitrogen fixation in legumes. In this study, Lotus japonicus was grown on MS solid media containing 0 nmol · L−1 (−Mo), 103 nmol · L−1 (+Mo) and 1030 nmol · L−1 (10 × Mo) of Mo. The phenotypes of plants growing on the three different media showed no obvious differences after 15 days, but the plants growing on –Mo for 45 days presented typical symptoms of Mo depletion, such as a short taproot, few lateral roots, and yellowing leaves. A Mo transporter gene, LjMOT1, was isolated from L. japonicus. It encoded 468 amino acids, including two conserved motifs, and was predicted to locate to chromosome 3 of the L. japonicus genome. A homology comparison indicated that LjMOT1 had high similarities to other MOT1 proteins and was closely related to GmMOT1. Subcellular localization indicated that LjMOT1 is localized to the plasma membrane. qRT-PCR analyses showed that increasing Mo concentrations regulated the relative expression level of LjMOT1. Moreover, the Mo concentration in shoots was positively correlated to the expression of LjMOT1, but there was no such evident correlation in the roots. In addition, changes in the nitrate reductase activity were coincident with changes in the Mo concentration. These results suggest that LjMOT1 may be involved in the transport of Mo and provide a theoretical basis for further understanding of the mechanism of Mo transport in higher plants.

Via Kevin Garcia
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Evaluation of the role of the LysM receptor-like kinase, OsNFR5/OsRLK2 for AM symbiosis in rice

In legume-specific rhizobial symbiosis, host plants perceive rhizobial signal molecules, Nod factors, by a couple of LysM receptor like kinases, NFR1/LYK3 and NFR5/NFP, and activate symbiotic responses through the downstream signaling components required also for arbuscular mycorrhizal (AM) symbiosis. Recently, rice NFR1/LYK3 ortholog, OsCERK1, was shown to play crucial roles for AM symbiosis. On the other hand, the roles of NFR5/NFP ortholog in rice have not been elucidated, while it has been shown that NFR5/NFP orthologs, Parasponia PaNFR5 and tomato SlRLK10, engage in AM symbiosis.

OsCERK1 also triggers immune responses in combination with a receptor partner, OsCEBiP, against fungal or bacterial infection, thus regulating opposite responses against symbiotic and pathogenic microbes. However, it has not been elucidated how OsCERK1 switches these opposite functions. Here, we analyzed the function of rice NFR5/NFP ortholog, OsNFR5/OsRLK2, as a possible candidate of the OsCERK1 partner for symbiotic signaling.

Inoculation of AM fungi induced the expression of OsNFR5 in the rice root and the chimeric receptor consisting of the extracellular domain of LjNFR5 and the intracellular domain of OsNFR5 complemented Ljnfr5 mutant for rhizobial symbiosis, indicating that the intracellular kinase domain of OsNFR5 could activate symbiotic signaling in L. japonicus. Although these data suggested the possible involvement of OsNFR5 in AM symbiosis, osnfr5 knockout mutants were colonized by AM fungi similar to the wild-type rice. These observations suggested several possibilities including the presence of functionally redundant genes other than OsNFR5 or involvement of novel ligands, which do not require OsNFR5 for recognition.

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Genetic Control of Lateral Root Formation in Cereals

Cereals form complex root systems composed of different root types. Lateral root formation is a major determinant of root architecture and is instrumental for the efficient uptake of water and nutrients. Positioning and patterning of lateral roots and cell types involved in their formation are unique in monocot cereals. Recent discoveries advanced the molecular understanding of the intrinsic genetic control of initiation and elongation of lateral roots in cereals by distinct, in part root-type-specific genetic programs. Moreover, molecular networks modulating the plasticity of lateral root formation in response to water and nutrient availability and arbuscular mycorrhizal fungal colonization have been identified. These novel discoveries provide a better mechanistic understanding of postembryonic lateral root development in cereals.

Via Pierre-Marc Delaux
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Advancing Crop Transformation in the Era of Genome Editing

Advancing Crop Transformation in the Era of Genome Editing | Plant-Microbe Symbiosis | Scoop.it
Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than 30 years of technological advances. Genome editing provides novel opportunities to enhance crop productivity but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Here, we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimization of time in culture. Currently, specialized facilities exist for crop transformation. Single-cell and robotic techniques should be developed for high-throughput genomic screens. Plant genes involved in developmental reprogramming, wound response, and/or homologous recombination should be used to boost the recovery of transformed plants. Engineering universal Agrobacterium tumefaciens strains and recruiting other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized.

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The physiology and habitat of the last universal common
ancestor

The physiology and habitat of the last universal common<br/>                    ancestor | Plant-Microbe Symbiosis | Scoop.it
A phylogenetic approach was used to illuminate the physiology of the last universal common ancestor, supporting the theory that LUCA was an H2-dependent autotroph in a hydrothermal setting rich in hydrogen, carbon dioxide and iron.

Via Loïc Lepiniec
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LUCA was fixing nitrogen... I am excited to see that our ancestor was fixing nitrogen.

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Intraradical colonization by arbuscular mycorrhizal fungi triggers induction of a lipochitooligosaccharide receptor

Intraradical colonization by arbuscular mycorrhizal fungi triggers induction of a lipochitooligosaccharide receptor | Plant-Microbe Symbiosis | Scoop.it
Functional divergence of paralogs following gene duplication is one of the mechanisms leading to evolution of novel pathways and traits. Here we show that divergence of Lys11 and Nfr5 LysM receptor kinase paralogs of Lotus japonicus has affected their specificity for lipochitooligosaccharides (LCOs) decorations, while the innate capacity to recognize and induce a downstream signalling after perception of rhizobial LCOs (Nod factors) was maintained. Regardless of this conserved ability, Lys11 was found neither expressed, nor essential during nitrogen-fixing symbiosis, providing an explanation for the determinant role of Nfr5 gene during Lotus-rhizobia interaction. Lys11 was expressed in root cortex cells associated with intraradical colonizing arbuscular mycorrhizal fungi. Detailed analyses of lys11 single and nfr1nfr5lys11 triple mutants revealed a functional arbuscular mycorrhizal symbiosis, indicating that Lys11 alone, or its possible shared function with the Nod factor receptors is not essential for the presymbiotic phases of AM symbiosis. Hence, both subfunctionalization and specialization appear to have shaped the function of these paralogs where Lys11 acts as an AM-inducible gene, possibly to fine-tune later stages of this interaction.

Via Ryohei Thomas Nakano
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Grasses suppress shoot-borne roots to conserve water during drought

Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree of root initiation from the belowground basal nodes of the shoot, termed the crown. Although this postembryonic shoot-borne root system represents the major conduit for water uptake, little is known about the effect of water availability on its development. Here we demonstrate that in the model C4 grass Setaria viridis, the crown locally senses water availability and suppresses postemergence crown root growth under a water deficit. This response was observed in field and growth room environments and in all grass species tested. Luminescence-based imaging of root systems grown in soil-like media revealed a shift in root growth from crown-derived to primary root-derived branches, suggesting that primary root-dominated architecture can be induced in S. viridis under certain stress conditions. Crown roots of Zea mays and Setaria italica, domesticated relatives of teosinte and S. viridis, respectively, show reduced sensitivity to water deficit, suggesting that this response might have been influenced by human selection. Enhanced water status of maize mutants lacking crown roots suggests that under a water deficit, stronger suppression of crown roots actually may benefit crop productivity.

Via Pierre-Marc Delaux
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Phytochemicals induced in chickpea roots selectively and non-selectively stimulate and suppress fungal endophytes and pathogens

Phytochemicals induced in chickpea roots selectively and non-selectively stimulate and suppress fungal endophytes and pathogens | Plant-Microbe Symbiosis | Scoop.it
Aims

Plant roots shape the structure of the soil microbiome by producing a wide array of phytochemicals, which in turn impact plant growth and health. The synthesis of root metabolites is a dynamic process that is modulated by interactions with soil microorganisms. This study explored the regulation of soil-borne fungal endophytes and pathogens by the production of phytochemicals in chickpea (Cicer arietinum L.) roots colonized or not colonized by the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis.

Methods

Proteins and low-molecular-mass phytochemicals were extracted from chickpea roots and fractionated by flash chromatography and high pressure liquid chromatography (HPLC). The effects of these metabolites on the soil-borne fungal endophytes Trichoderma harzianum and Geomyces vinaceus and on the pathogens Fusarium oxysporum and Rhizoctonia solani were tested in 96-well plate assays.

Results

One protein fraction from the AM roots, which contained an apparent 34 KDa chitinase/chitin-binding domain and 24 KDa non-specific lipid transfer protein, non-selectively repressed the fungal endophytes and pathogens. By contrast to the protein fraction, the low-molecular-mass fractions were often selective. Eighteen fractions stimulated specific fungal species and seven fractions inhibited others.

Conclusions

Several protein and low-molecular-mass phytochemicals in chickpea roots influence fungal endophytes. The difference in the response of fungal species to the phytochemicals suggests that these metabolites could be involved in the so called host ‘preference’ of fungal endophytes or ‘resistance’ to pathogens. This research reveals that the majority of the bioactive root metabolites could be involved in the selective association of chickpea and fungal endophytes while a few compounds provided resistance by suppressing the pathogenic species.
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The elusive predisposition to mycoheterotrophy in Ericaceae

The elusive predisposition to mycoheterotrophy in Ericaceae | Plant-Microbe Symbiosis | Scoop.it
The rise and diversification of land plants was accompanied by mycorrhizal symbiosis, from their emergence to their adaptation to various biomes and ecological situations (Selosse et al., 2015). In most mycorrhizal associations, fungi provide soil minerals to the plant, in exchange for sugars derived from photosynthesis (Smith & Read, 2008; van der Heijden et al., 2015). However, several plant species adapted to shaded forest conditions by secondarily reversing this exchange of carbohydrates: they became achlorophyllous thanks to carbon provided by the fungus. This so-called mycoheterotrophic nutrition is described in over 400 species and evolved at least 40 times independently (Merckx, 2013), raising the question of what predispositions underlie these convergences.
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Frontiers | “Omics” Tools for Better Understanding the Plant–Endophyte Interactions | Plant Biotic Interactions

Frontiers | “Omics” Tools for Better Understanding the Plant–Endophyte Interactions | Plant Biotic Interactions | Plant-Microbe Symbiosis | Scoop.it
Endophytes, which mostly include bacteria, fungi and actinomycetes, are the endosymbionts that reside asymptomatically in plants for at least a part of their life cycle. They have emerged as a valuable source of novel metabolites, industrially important enzymes and as stress relievers of host plant, but still many aspects of endophytic biology are unknown. Functions of individual endophytes are the result of their continuous and complex interactions with the host plant as well as other members of the host microbiome. Understanding plant microbiomes as a system allows analysis and integration of these complex interactions. Modern genomic studies involving metaomics and comparative studies can prove to be helpful in unraveling the gray areas of endophytism. A deeper knowledge of the mechanism of host infestation and role of endophytes could be exploited to improve the agricultural management in terms of plant growth promotion, biocontrol and bioremediation. Genome sequencing, comparative genomics, microarray, next gen sequencing, metagenomics, metatranscriptomics are some of the techniques that are being used or can be used to unravel plant–endophyte relationship. The modern techniques and approaches need to be explored to study endophytes and their putative role in host plant ecology. This review highlights “omics” tools that can be explored for understanding the role of endophytes in the plant microbiome.

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