Plant-Microbe Symbiosis
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Workshop: Non-Seed Plants (Plant and Animal Genome XXI Conference)

Origin of the molecular "toolkit" for plant – microbe symbioses
Pierre-Marc Delaux, University of Wisconsin Madison

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Plant-Microbe Symbiosis
Beneficial associations between plants and microbes
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Rescooped by Jean-Michel Ané from The Plant Microbiome
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Host preference and network properties in biotrophic plant–fungal associations

Analytical methods can offer insights into the structure of biological networks, but mechanisms that determine the structure of these networks remain unclear. We conducted a synthesis based on 111 previously published datasets to assess a range of ecological and evolutionary mechanisms that may influence the plant-associated fungal interaction networks. We calculated the relative host effect on fungal community composition and compared nestedness and modularity among different mycorrhizal types and endophytic fungal guilds. We also assessed how plant-fungal network structure was related to host phylogeny, environmental and sampling properties. Orchid mycorrhizal fungal communities responded most strongly to host identity, but the effect of host was similar among all other fungal guilds. Community nestedness, which did not differ among fungal guilds, declined significantly with increasing mean annual precipitation on a global scale. Orchid and ericoid mycorrhizal fungal communities were more modular than ectomycorrhizal and root endophytic communities, with arbuscular mycorrhizal fungi in an intermediate position. Network properties among a broad suite of plant-associated fungi were largely comparable and generally unrelated to phylogenetic distance among hosts. Instead, network metrics were predominantly affected by sampling and matrix properties, indicating the importance of study design in properly inferring ecological patterns.


Via Stéphane Hacquard
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Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi

Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi | Plant-Microbe Symbiosis | Scoop.it
Arbuscular mycorrhizal fungi (AMF) are a group of soil microorganisms that establish symbioses with the vast majority of land plants. To date, generation of AMF coding information has been limited to model genera that grow well axenically; Rhizoglomus and Gigaspora. Meanwhile, data on the functional gene repertoire of most AMF families is non-existent. Here, we provide primary large-scale transcriptome data from eight poorly studied AMF species (Acaulospora morrowiae, Diversispora versiforme, Scutellospora calospora, Racocetra castanea, Paraglomus brasilianum, Ambispora leptoticha, Claroideoglomus claroideum and Funneliformis mosseae) using ultra-low input ribonucleic acid (RNA)-seq approaches. Our analyses reveals that quiescent spores of many AMF species harbour a diverse functional diversity and solidify known evolutionary relationships within the group. Our findings demonstrate that RNA-seq data obtained from low-input RNA are reliable in comparison to conventional RNA-seq experiments. Thus, our methodology can potentially be used to deepen our understanding of fungal microbial function and phylogeny using minute amounts of RNA material.

Via Francis Martin, Jessie Uehling
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Francis Martin's curator insight, December 4, 11:16 AM
A nice piece of work!
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Nodule-Enriched GRETCHEN HAGEN 3 Enzymes Have Distinct Substrate Specificities and Are Important for Proper Soybean Nodule Development

Nodule-Enriched GRETCHEN HAGEN 3 Enzymes Have Distinct Substrate Specificities and Are Important for Proper Soybean Nodule Development | Plant-Microbe Symbiosis | Scoop.it
Legume root nodules develop as a result of a symbiotic relationship between the plant and nitrogen-fixing rhizobia bacteria in soil. Auxin activity is detected in different cell types at different stages of nodule development; as well as an enhanced sensitivity to auxin inhibits, which could affect nodule development. While some transport and signaling mechanisms that achieve precise spatiotemporal auxin output are known, the role of auxin metabolism during nodule development is unclear. Using a soybean root lateral organ transcriptome data set, we identified distinct nodule enrichment of three genes encoding auxin-deactivating GRETCHEN HAGEN 3 (GH3) indole-3-acetic acid (IAA) amido transferase enzymes: GmGH3-11/12, GmGH3-14 and GmGH3-15. In vitro enzymatic assays showed that each of these GH3 proteins preferred IAA and aspartate as acyl and amino acid substrates, respectively. GmGH3-15 showed a broad substrate preference, especially with different forms of auxin. Promoter:GUS expression analysis indicated that GmGH3-14 acts primarily in the root epidermis and the nodule primordium where as GmGH3-15 might act in the vasculature. Silencing the expression of these GH3 genes in soybean composite plants led to altered nodule numbers, maturity, and size. Our results indicate that these GH3s are needed for proper nodule maturation in soybean, but the precise mechanism by which they regulate nodule development remains to be explained.
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Good job, Sen!

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Previous crop and rotation history effects on maize seedling health and associated rhizosphere microbiome

Previous crop and rotation history effects on maize seedling health and associated rhizosphere microbiome | Plant-Microbe Symbiosis | Scoop.it
To evaluate crop rotation effects on maize seedling performance and its associated microbiome, maize plants were grown in the greenhouse in soils preceded by either maize, pea, soybean or sunflower. Soils originated from a replicated field experiment evaluating different four-year rotation combinations. In the greenhouse, a stressor was introduced by soil infestation with western corn rootworm (WCR) or Fusarium graminearum. Under non-infested conditions, maize seedlings grown in soils preceded by sunflower or pea had greater vigor. Stress with WCR or F. graminearum resulted in significant root damage. WCR root damage was equivalent for seedlings regardless of soil provenance; whereas F. graminearum root damage was significantly lower in maize grown in soils preceded by sunflower. Infestation with WCR affected specific microbial taxa (Acinetobacter, Smaragdicoccus, Aeromicrobium, Actinomucor). Similarly, F. graminearum affected fungal endophytes including Trichoderma and Endogone. In contrast to the biological stressors, rotation sequence had a greater effect on rhizosphere microbiome composition, with larger effects observed for fungi compared to bacteria. In particular, relative abundance of Glomeromycota was significantly higher in soils preceded by sunflower or maize. Defining the microbial players involved in crop rotational effects in maize will promote selection and adoption of favorable crop rotation sequences.

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Compatible bacterial mixture, tolerant to desiccation, improves maize plant growth

Compatible bacterial mixture, tolerant to desiccation, improves maize plant growth | Plant-Microbe Symbiosis | Scoop.it
Plant growth-promoting rhizobacteria (PGPR) increase plant growth and crop productivity. The inoculation of plants with a bacterial mixture (consortium) apparently provides greater benefits to plant growth than inoculation with a single bacterial strain. In the present work, a bacterial consortium was formulated containing four compatible and desiccation-tolerant strains with potential as PGPR. The formulation had one moderately (Pseudomonas putida KT2440) and three highly desiccation-tolerant (Sphingomonas sp. OF178, Azospirillum brasilense Sp7 and Acinetobacter sp. EMM02) strains. The four bacterial strains were able to adhere to seeds and colonize the rhizosphere of plants when applied in both mono-inoculation and multi-inoculation treatments, showing that they can also coexist without antagonistic effects in association with plants. The effects of the bacterial consortium on the growth of blue maize were evaluated. Seeds inoculated with either individual bacterial strains or the bacterial consortium were subjected to two experimental conditions before sowing: normal hydration or desiccation. In general, inoculation with the bacterial consortium increased the shoot and root dry weight, plant height and plant diameter compared to the non-inoculated control or mono-inoculation treatments. The bacterial consortium formulated in this work had greater benefits for blue maize plants even when the inoculated seeds underwent desiccation stress before germination, making this formulation attractive for future field applications.

Via Ryohei Thomas Nakano
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Bacterial Endophyte Colonization and Distribution within Plants

Bacterial Endophyte Colonization and Distribution within Plants | Plant-Microbe Symbiosis | Scoop.it
Abstract: The plant endosphere contains a diverse group of microbial communities. There is general consensus that these microbial communities make significant contributions to plant health. Both recently adopted genomic approaches and classical microbiology techniques continue to develop the science of plant-microbe interactions. Endophytes are microbial symbionts residing within the plant for the majority of their life cycle without any detrimental impact to the host plant. The use of these natural symbionts offers an opportunity to maximize crop productivity while reducing the environmental impacts of agriculture. Endophytes promote plant growth through nitrogen fixation, phytohormone production, nutrient acquisition, and by conferring tolerance to abiotic and biotic stresses. Colonization by endophytes is crucial for providing these benefits to the host plant. Endophytic colonization refers to the entry, growth and multiplication of endophyte populations within the host plant. Lately, plant microbiome research has gained considerable attention but the mechanism allowing plants to recruit endophytes is largely unknown. This review summarizes currently available knowledge about endophytic colonization by bacteria in various plant species, and specifically discusses the colonization of maize plants by Populus endophytes.
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Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi

Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi | Plant-Microbe Symbiosis | Scoop.it
Many heritable mutualisms, in which beneficial symbionts are transmitted vertically between host generations, originate as antagonisms with parasite dispersal constrained by the host. Only after the parasite gains control over its transmission is the symbiosis expected to transition from antagonism to mutualism. Here, we explore this prediction in the mutualism between the fungus Rhizopus microsporus (Rm, Mucoromycotina) and a beta-proteobacterium Burkholderia, which controls host asexual reproduction. We show that reproductive addiction of Rm to endobacteria extends to mating, and is mediated by the symbiont gaining transcriptional control of the fungal ras2 gene, which encodes a GTPase central to fungal reproductive development. We also discover candidate G-protein-coupled receptors for the perception of trisporic acids, mating pheromones unique to Mucoromycotina. Our results demonstrate that regulating host asexual proliferation and modifying its sexual reproduction are sufficient for the symbiont’s control of its own transmission, needed for antagonism-to-mutualism transition in heritable symbioses. These properties establish the Rm-Burkholderia symbiosis as a powerful system for identifying reproductive genes in Mucoromycotina.

Via Francis Martin
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Wow.... nice!

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Dharanipathi's curator insight, November 30, 8:45 AM
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Synima: a Synteny imaging tool for annotated genome assemblies

Synima: a Synteny imaging tool for annotated genome assemblies | Plant-Microbe Symbiosis | Scoop.it

Background
Ortholog prediction and synteny visualization across whole genomes are valuable methods for detecting and representing a range of evolutionary processes such as genome expansion, chromosomal rearrangement, and chromosomal translocation. Few standalone methods are currently available to visualize synteny across any number of annotated genomes.

Results
Here, I present a Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima – and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License.

Conclusions
Synima should be a valuable tool for visualizing synteny between two or more annotated genome assemblies.


Via Ronny Kellner, Matt Agler, Jessie Uehling, Francis Martin, IPM Lab
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Cool!

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Glomeromycotina: what is a species and why should we care?

A workshop at the recent International Conference on Mycorrhiza was focused on species recognition in Glomeromycotina and parts of their basic biology that define species. The workshop was motivated by the paradigm-shifting evidence derived from genomic data for sex and for the lack of heterokaryosis, and by published exchanges in Science that were based on different species concepts and have led to differing views of dispersal and endemism in these fungi. Although a lively discussion ensued, there was general agreement that species recognition in the group is in need of more attention, and that many basic assumptions about the biology of these important fungi including sexual or clonal reproduction, similarity or dissimilarity of nuclei within an individual, and species boundaries need to be re-examined and scrutinized with current techniques.
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A MUST read!

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Molecular Mechanism of Plant Recognition of Extracellular ATP

Adenosine 5′-triphosphate (ATP), a ubiquitously dispersed biomolecule, is not only a major source of biochemical energy for living cells, but also acts as a critical signaling molecule through inter-cellular communication. Recent studies have clearly shown that extracellular ATP is involved in various physiological processes in plants, including root growth, stomata movement, pollen tube development, gravitropism, and abiotic/biotic stress responses. The first plant purinergic receptor for extracellular ATP, DORN1 (the founding member of the P2K family of purinergic receptors), was identified in Arabidopsis thaliana by a forward genetic screen. DORN1 consists of an extracellular lectin domain, transmembrane domain, and serine/threonine kinase, intracellular domain. The predicted structure of the DORN1 extracellular domain revealed putative key ATP binding residues but an apparent lack of sugar binding. In this chapter, we summarize recent studies on the molecular mechanism of plant recognition of extracellular ATP with specific reference to the role of DORN1.

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Nitrogen limitation impairs plant control over the arbuscular mycorrhizal symbiosis in response to phosphorus and shading in two European sand dune species

The symbiosis of plants with arbuscular mycorrhizal fungi (AMF) may become parasitic if the cost:benefit ratio (carbon:phosphorus ratio) increases. In case of mycorrhizal parasitism, a plant may prevent growth depression through the reduction of root colonization as a form of control over the symbiosis. In this greenhouse study, we attempted to manipulate the cost:benefit ratio of the arbuscular mycorrhizal symbiosis by shading and/or phosphorus (P) fertilization in the differentially mycotrophic plant species Hieracium pilosella and Corynephorus canescens. By repeated sampling of soil cores, we assessed the temporal progress of plant investment towards mycorrhizal structures as a measure of plant control over the AMF. Unexpectedly, we found no obvious treatment effects on mycorrhizal growth dependency (MGD), most likely caused by constant N-limitation in AM plants being enhanced by P-fertilization and shade probably not exacerbating plant C-budget for AMF. This highlights the importance of N:P:C stoichiometry for the outcome of the symbiosis. Nevertheless, we found possible control mechanisms in shaded H. pilosella, with considerably higher resource investments into root than into hyphal growth, while root colonization was only marginally suppressed. This control only manifested after 4 weeks of growth under potentially detrimental conditions, emphasizing the importance of time in plant control over the arbuscular mycorrhizal symbiosis. In contrast, the less mycotrophic C. canescens did not exhibit obvious changes in mycorrhizal investments in reaction to shading and P-fertilization, possibly because the low mycotrophy and AMF colonization already imposes a functioning control mechanism in this species. Our study suggests that highly mycotrophic plants may have a stronger need to keep AMF in check than less mycotrophic plants, which may have implications for the role of mycotrophy in the outcome of symbiotic interactions in natural situations.

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Isolation and molecular identification of endophytic diazotrophs from seeds and stems of three cereal crops

Isolation and molecular identification of endophytic diazotrophs from seeds and stems of three cereal crops | Plant-Microbe Symbiosis | Scoop.it
Ten strains of endophytic diazotroph were isolated and identified from the plants collected from three different agricultural crop species, wheat, rice and maize, using the nitrogen-free selective isolation conditions. The nitrogen-fixing ability of endophytic diazotroph was verified by the nifH-PCR assay that showed positive nitrogen fixation ability. These identified strains were classified by 879F-RAPD and 16S rRNA sequence analysis. RAPD analyses revealed that the 10 strains were clustered into seven 879F-RAPD groups, suggesting a clonal origin. 16S rRNA sequencing analyses allowed the assignment of the 10 strains to known groups of nitrogen-fixing bacteria, including organisms from the genera Paenibacillus, Enterobacter, Klebsiella and Pantoea. These representative genus are not endophytic diazotrophs in the conventional sense. They may have obtained nitrogen fixation ability through lateral gene transfer, however, the evolutionary forces of lateral gene transfer are not well known. Molecular identification results from 16S rRNA analyses were also confirmed by morphological and biochemical data. The test strains SH6A and MZB showed positive effect on the growth of plants.

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Variation in the bacteriome of the tropical liverwort, Marchantia inflexa, between the sexes and across habitats

Plant-microbe interactions impact ecosystem function through nutrient cycling, community interactions, and individual costs/benefits to the organisms involved. However, information on the establishment, diversity, and function of plant-microbe interactions remains limited, especially for non-vascular plants. We hypothesized that variation in the environment and sex of a host plant, impact the composition and diversity of associated microbial communities. To test this hypothesis, we characterized the bacteriome of the non-vascular plant, Marchantia inflexa, in both males and females across multiple habitats by targeted sequencing of the bacterial 16S rRNA gene. We describe the bacteriome for M. inflexa, and find that it is abundant and diverse, showing some similarities with other non-vascular plant lineages. Using these data, we detected a habitat specific component of the bacteriome, and sex differences in the bacteriome under common garden conditions. On the basis of known microbial functions, our analyses suggest that the specific taxonomic assemblages of bacteria detected in particular habitat types may serve functional roles; allowing plants to better acclimate to their local environment, and that sex differences in the bacteriome may correspond to subtle differences in the physiology and morphology of the sexes. Our initial characterization of variation in bacteriome composition of this tropical liverwort lineage provides valuable information for better understanding the patterns of plant-microbe interactions across land plants.

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Mycorrhizal Love

Jean-Michel Ané's insight:

I love it!

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Bob Reeves's curator insight, December 6, 3:54 PM
Get out the marshmallows - it's time to get folksy with our Fungal Friends!
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Comprehensive genome-wide classification reveals that many plant-specific transcription factors evolved in streptophyte algae

Plant genomes encode many lineage-specific, unique transcription factors. Expansion of such gene families has been previously found to coincide with the evolution of morphological complexity, although comparative analyses have been hampered by severe sampling bias. Here, we make use of the recently increased availability of plant genomes. We have updated and expanded previous rule sets for domain-based classification of transcription associated proteins (TAPs), comprising transcription factors and transcriptional regulators. The genome-wide annotation of these protein families has been analyzed and made available via the novel TAPscan web interface. We find that many TAP families previously thought to be specific for land plants actually evolved in streptophyte (charophyte) algae; 26 out of 36 TAP family gains are inferred to have occurred in the common ancestor of the Streptophyta (uniting the land plants – Embryophyta – with their closest algal relatives). In contrast, expansions of TAP families were found to occur throughout streptophyte evolution. 17 out of 76 expansion events were found to be common to all land plants and thus probably evolved concomitant with the water-to-land-transition.
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Check out this website: https://plantcode.online.uni-marburg.de/tapscan/species.php

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Development of a GAL4-VP16/UAS trans-activation system for tissue specific expression in Medicago truncatula

Development of a GAL4-VP16/UAS trans-activation system for tissue specific expression in Medicago truncatula | Plant-Microbe Symbiosis | Scoop.it
Promoters with tissue-specific activity are very useful to address cell-autonomous and non cell autonomous functions of candidate genes. Although this strategy is widely used in Arabidopsis thaliana, its use to study tissue-specific regulation of root symbiotic interactions in legumes has only started recently. Moreover, using tissue specific promoter activity to drive a GAL4-VP16 chimeric transcription factor that can bind short upstream activation sequences (UAS) is an efficient way to target and enhance the expression of any gene of interest. Here, we developed a collection of promoters with different root cell layers specific activities in Medicago truncatula and tested their abilities to drive the expression of a chimeric GAL4-VP16 transcription factor in a trans-activation UAS: β-Glucuronidase (GUS) reporter gene system. By developing a binary vector devoted to modular Golden Gate cloning together with a collection of adapted tissue specific promoters and coding sequences we could test the activity of four of these promoters in trans-activation GAL4/UAS systems and compare them to “classical” promoter GUS fusions. Roots showing high levels of tissue specific expression of the GUS activity could be obtained with this trans-activation system. We therefore provide the legume community with new tools for efficient modular Golden Gate cloning, tissue specific expression and a trans-activation system. This study provides the ground work for future development of stable transgenic lines in Medicago truncatula.

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The Brassicaceae family displays divergent, shoot-skewed NLR resistance gene expression

Nucleotide-binding site leucine-rich repeat resistance genes (NLRs) allow plants to detect microbial effectors. We hypothesized that NLR expression patterns could reflect organ-specific differences in effector challenge and tested this by carrying out a meta-analysis of expression data for 1,235 NLRs from 9 plant species. We found stable NLR root/shoot expression ratios within species, suggesting organ-specific hardwiring of NLR expression patterns in anticipation of distinct challenges. Most monocot and dicot plant species preferentially expressed NLRs in roots. In contrast, Brassicaceae species, including oilseed rape and the model plant Arabidopsis thaliana, were unique in showing NLR expression skewed towards the shoot across multiple phylogenetically distinct groups of NLRs. The Brassicaceae are also outliers in the sense that they have lost the common symbiosis signaling pathway, which enables intracellular infection by root symbionts. While it is unclear if these two events are related, the NLR expression shift identified here suggests that the Brassicaceae may have evolved unique PRRs and antimicrobial root metabolites to substitute for NLR protection. Such innovations in root protection could potentially be exploited in crop rotation schemes or for enhancing root defense systems of non-Brassicaceae crops.

Jean-Michel Ané's insight:

Too bad they have not looked at other clades that have lost the common symbiosis signaling pathway... I'd love to do that :-)

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Dynamics of Lotus japonicus ethylene production in response to compatible Nod factor

Establishment of symbiotic nitrogen-fixation in legumes is regulated by the plant hormone ethylene, but it has remained unclear whether and how its biosynthesis is regulated by the symbiotic pathway. We established a sensitive ethylene detection system for Lotus japonicus and found that ethylene production increased as early as six hours after inoculation with Mesorhizobium loti. This ethylene response was dependent on Nod factor production by compatible rhizobia. Analyses of nodulation mutants showed that perception of Nod factor was required for ethylene emission, while downstream transcription factors including CYCLOPS, NIN and ERN1 were not required for this response. Activation of the nodulation signalling pathway in spontaneously nodulating mutants was also sufficient to elevate ethylene production. Ethylene signalling is controlled by EIN2, which is duplicated in L. japonicus. We obtained a L. japonicus Ljein2a Ljein2b double mutant which exhibits complete ethylene insensitivity and confirms that these two genes act redundantly in ethylene signalling. Consistent with this redundancy, both LjEin2a and LjEin2b are required for negative regulation of nodulation and Ljein2a Ljein2b double mutants are hypernodulating and hyperinfected. We also identified an unexpected role for ethylene in the onset of nitrogen fixation, with the Ljein2a Ljein2b double mutant showing severely reduced nitrogen fixation These results demonstrate that ethylene production is an early and sustained nodulation response which acts at multiple stages to regulate infection, nodule organogenesis and nitrogen fixation in L. japonicus.
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Functional Diversity of Mycorrhizal Fungi Has Differential Effects on Salinity Tolerance of Acacia seyal (Del.) Seedlings

Acacia seyal is a leguminous plant that plays an important role in the ecosystem of Sahelian zone by producing gum, wood and fodder. The growth of A. seyal is subject to many constraints as salinity which can affect the development of this tree. Therefore, soil microorganisms can help A. seyal to better tolerate the effects of negative environmental stresses. The contribution of arbuscular mycorrhizal fungi (AMF) to the salt tolerance of A. seyal, was evaluated by testing the effects of eight different arbuscular mycorrhizal fungi (AMF) isolates in the performance of A. seyal seedlings subjected to different levels of salinity (0, 340 and 680 mM). The results based on growth parameters of shoot and root parts, shoot mineral N, P, K and Na content as well as survival rates and mycorrhization showed that AMF improved mineral nutrition of A. seyal seedlings during salt stress. The combination between AMF and salinity provided evidence that the efficiency of AMF isolates were variable in improving mineral nutrition and mortality rate for A. seyal seedlings related to the level of salt stress. However, the effects of inoculation were variable depending to the AMF isolate associated with seedlings and the level of salinity, suggesting that interactions between plants and AMF can be modulated by both AMF diversity and the type and level of abiotic factors. Rhizophagus intraradices was more efficient at 680 mM NaCl in plant growth and mineral uptake while Glomus deserticola did not promote a better plant development than most of the other species inoculated to seedlings.
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Medicago truncatula GRAS protein RAD1 supports arbuscular mycorrhiza symbiosis and Phytophthora palmivora susceptibility 

Medicago truncatula  GRAS protein RAD1 supports arbuscular mycorrhiza symbiosis and  Phytophthora palmivora  susceptibility  | Plant-Microbe Symbiosis | Scoop.it
The roots of most land plants are colonized by symbiotic arbuscular mycorrhiza (AM) fungi. To facilitate this symbiosis, plant genomes encode a set of genes required for microbial perception and accommodation. However, the extent to which infection by filamentous root pathogens also relies on some of these genes remains an open question. Here, we used genome-wide association mapping to identify genes contributing to colonization of Medicago truncatula roots by the pathogenic oomycete Phytophthora palmivora. Single-nucleotide polymorphism (SNP) markers most significantly associated with plant colonization response were identified upstream of RAD1, which encodes a GRAS transcription regulator first negatively implicated in root nodule symbiosis and recently identified as a positive regulator of AM symbiosis. RAD1 transcript levels are up-regulated both in response to AM fungus and, to a lower extent, in infected tissues by P. palmivora where its expression is restricted to root cortex cells proximal to pathogen hyphae. Reverse genetics showed that reduction of RAD1 transcript levels as well as a rad1 mutant are impaired in their full colonization by AM fungi as well as by P. palmivora. Thus, the importance of RAD1 extends beyond symbiotic interactions, suggesting a general involvement in M. truncatula microbe-induced root development and interactions with unrelated beneficial and detrimental filamentous microbes.

Via Christophe Jacquet
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Tracking plant preference for higher-quality mycorrhizal symbionts under varying CO2 conditions over multiple generations.

Abstract: The symbiosis between plants and root-colonizing arbuscular mycorrhizal (AM) fungi is one of the most ecologically important examples of interspecific cooperation in the world. AM fungi provide benefits to plants; in return plants allocate carbon resources to fungi, preferentially allocating more resources to higher-quality fungi. However, preferential allocations from plants to symbionts may vary with environmental context, particularly when resource availability affects the relative value of symbiotic services. We ask how differences in atmospheric CO2-levels influence root colonization dynamics between AMF species that differ in their quality as symbiotic partners. We find that with increasing CO2-conditions and over multiple plant generations, the more beneficial fungal species is able to achieve a relatively higher abundance. This suggests that increasing atmospheric carbon supply enables plants to more effectively allocate carbon to higher-quality mutualists, and over time helps reduce lower-quality AM abundance. Our results illustrate how environmental context may affect the extent to which organisms structure interactions with their mutualistic partners and have potential implications for mutualism stability and persistence under global change.

Keywords: context-dependence global change mutualism rewards sanction

Via Ronald Noë
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Very interesting 

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Ronald Noë's curator insight, November 24, 6:05 AM
Not a test of BMT per se, but a test of the effect of partner choice by plants when in interaction with two mycorrhizal fungi that are known to have different beneficial effects on plants, under different CO2-levels. The interesting aspect of this study is that the fungi were inoculated, single or in a mix, on three successive generations of plants, revealing subtle effects that would not necessarily be measurable over a single growth cycle of an annual plant. This obviously cannot show any evolutionary effects, neither on the plants nor on the fungi, but shows that the species composition of a community can be influenced by partner choice and that the result depends on environmental factors, such as the CO2 level.
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Mycorrhizal Symbioses and Pedogenesis Throughout Earth’s History

Mycorrhizal Symbioses and Pedogenesis Throughout Earth’s History | Plant-Microbe Symbiosis | Scoop.it
The evolution of land plants and of their symbiosis with soil fungi to form mycorrhiza-like associations were pivotal steps in Earth's history. They enabled the establishment of terrestrial ecosystems in which plants of increasing biomass, rooting depth, nutrient demand, and ability to capture and convert solar energy into chemical energy helped to drive mineral weathering and soil formation. Here we review evidence of the coevolutionary history of land plants and mycorrhizal symbioses, placing particular emphasis on their likely impacts upon silicate weathering, pedogenesis, and the resulting interlinked changes in the biogeochemical cycles of carbon, silicon, calcium and phosphorus. These, in turn, affect atmospheric carbon dioxide concentrations, ocean productivity, and climate over geological time. We conclude that, over time, coevolutionary advances in plants and fungi have increased photosynthate fluxes through mycorrhizas into soils, intensifying pedogenic processes, and mineral weathering, thereby strengthening the biosphere–geosphere–ocean–atmosphere interactions that regulate the Earth’s climate.

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Diverse peptide hormones affecting root growth identified in the Medicago truncatula secreted peptidome

Multigene families encoding diverse secreted peptide hormones play important roles in plant development. A need exists to efficiently elucidate the structures and post-translational modifications of these difficult-to-isolate peptide hormones in planta so that their biological functions can be determined. A mass spectrometry and bioinformatics approach was developed to comprehensively analyse the secreted peptidome of Medicago hairy root cultures and xylem sap. We identified 759 spectra corresponding to the secreted products of twelve peptide hormones including four CEP (C-TERMINALLY ENCODED PEPTIDE), two CLE (CLV3/ENDOSPERM SURROUNDING REGION RELATED) and six XAP (XYLEM SAP ASSOCIATED PEPTIDE) peptides. The MtCEP1, MtCEP2, MtCEP5 and MtCEP8 peptides identified differed in post-translational-modifications. Most were hydroxylated at conserved proline residues but some MtCEP1 derivatives were triarabinosylated. In addition, many CEP peptides possessed unexpected N- and C-terminal extensions. The pattern of these extensions suggested roles for endo- and exoproteases in CEP peptide maturation. Longer than expected, hydroxylated and homogeneously modified mono- and tri-arabinosylated CEP peptides corresponding to their in vivo structures were chemically synthesised to probe the effect of these post-translational-modifications on function. The ability of CEP peptides to elevate root nodule number was increased by hydroxylation at key positions. MtCEP1 peptides with N-terminal extensions or with triarabinosylation modification, however, were unable to impart increased nodulation. The MtCLE5 and MtCLE17 peptides identified were of precise size, and inhibited main root growth and increased lateral root number. Six XAP peptides, each beginning with a conserved DY sulfation motif, were identified including MtXAP1a, MtXAP1b, MtXAP1c, MtXAP3, MtXAP5 and MtXAP7. MtXAP1a and MtXAP5 inhibited lateral root emergence. Transcriptional analyses demonstrated peptide hormone gene expression in the root vasculature and tip. Since hairy roots can be induced on many plants, their corresponding root cultures may represent ideal source materials to efficiently identify diverse peptide hormones in vivo in a broad range of species.

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RNA sequencing and analysis of three Lupinus nodulomes provide new insights into specific host-symbiont relationships with compatible and incompatible Bradyrhizobium strains

RNA sequencing and analysis of three Lupinus nodulomes provide new insights into specific host-symbiont relationships with compatible and incompatible Bradyrhizobium strains | Plant-Microbe Symbiosis | Scoop.it
Nitrogen fixation in the legume root-nodule symbiosis has a critical importance in natural and agricultural ecosystems and depends on the proper choice of the symbiotic partners. However, the genetic determinism of symbiotic specificity remains unclear. To study this process, we inoculated three Lupinus species (L. albus, L. luteus, L. mariae-josephae), belonging to the under-investigated tribe of Genistoids, with two Bradyrhizobium strains (B. japonicum, B. valentinum) presenting contrasted degrees of symbiotic specificity depending on the host. We produced the first transcriptomes (RNA-Seq) from lupine nodules in a context of symbiotic specificity. For each lupine species, we compared gene expression between functional and non-functional interactions and determined differentially expressed (DE) genes. This revealed that L. luteus and L. mariae-josephae (nodulated by only one of the Bradyrhizobium strains) specific nodulomes were richest in DE genes than L. albus (nodulation with both microsymbionts, but non-functional with B. valentinum) and share a higher number of these genes between them than with L. albus. In addition, a functional analysis of DE genes highlighted the central role of the genetic pathways controlling infection and nodule organogenesis, hormones, secondary, carbon and nitrogen metabolisms, as well as the implication of plant defence in response to compatible or incompatible Bradyrhizobium strains.
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New method for the identification of arbuscular mycorrhizal fungi by proteomic-based biotyping of spores using MALDI-TOF-MS

New method for the identification of arbuscular mycorrhizal fungi by proteomic-based biotyping of spores using MALDI-TOF-MS | Plant-Microbe Symbiosis | Scoop.it
Arbuscular mycorrhizal fungi (AMF, Glomeromycota) are mutualistic symbionts associated with majority of land plants. These fungi play an important role in plant growth, but their taxonomic identification remains a challenge for academic research, culture collections and inoculum producers who need to certify their products. Identification of these fungi was traditionally performed based on their spore morphology. DNA sequence data have successfully been used to study the evolutionary relationships of AMF, develop molecular identification tools and assess their diversity in the environment. However, these methods require considerable expertise and are not well-adapted for “routine” quality control of culture collections and inoculum production. Here, we show that Matrix-Assisted Laser Desorption Ionisation Time of Flight Mass Spectrometry proteomic-based biotyping is a highly efficient approach for AMF identification. Nineteen isolates belonging to fourteen species, seven genera and five families were clearly differentiated by MALDI biotyping at the species level, and intraspecific differentiation was achieved for the majority. AMF identification by MALDI biotyping could be highly useful, not only for research but also in agricultural and environmental applications. Fast, accurate and inexpensive molecular mass determination and the possibility of automation make MALDI-TOF-MS a real alternative to conventional morphological and molecular methods for AMF identification.

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