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Effector-Mediated Communication of Filamentous Plant Pathogens With Their Hosts

Effector-Mediated Communication of Filamentous Plant Pathogens With Their Hosts | symbiosis | Scoop.it
Pathogenic fungi and oomycetes can establish intimate associations with plants. These interactions underlie a molecular dialogue that leads to the successful colonization of host tissues. Major questions driving research in plant pathology these last decades are how pathogenic microorganisms circumvent preformed or induced defences and how pathogens manipulate host physiology to promote virulence. One key actor in this dialogue relies on a class of molecules secreted by pathogens termed effectors. Effectors perturb host processes by targeting a variety of host functions either in the apoplast or in the cytosol of host cells. This chapter focuses on fungal and oomycetal cytoplasmic effectors by reviewing methods to predict and to characterize effectors as well as their activities and role during infection. We provide current knowledge regarding their evolution and their putative role in the shaping of plant-associated microbial communities.
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Transcriptomic analysis of Sinorhizobium meliloti and Medicago truncatula symbiosis using nitrogen fixation deficient nodules

Transcriptomic analysis of Sinorhizobium meliloti and Medicago truncatula symbiosis using nitrogen fixation deficient nodules | symbiosis | Scoop.it
The bacterium Sinorhizobium meliloti interacts symbiotically with legume plant hosts such as Medicago truncatula to form nitrogen-fixing root nodules. During symbiosis, plant and bacterial cells differentiate in a coordinated manner, resulting in specialized plant cells that contain nitrogen-fixing bacteroids. Both plant and bacterial genes are required at each developmental stage of symbiosis. We analyzed gene expression in nodules formed by wild type bacteria on six plant mutants with defects in nitrogen fixation (dnf). We observed differential expression of 482 S. meliloti genes with functions in cell envelope homeostasis, cell division, stress response, energy metabolism and nitrogen fixation. We simultaneously analyzed gene expression in M. truncatula and observed differential regulation of host processes that may trigger bacteroid differentiation and control bacterial infection. Our analyses of developmentally arrested plant mutants indicate that plants use distinct means to control bacterial infection during early and late symbiotic stages.

Via Chang Fu Tian
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Virus-Based MicroRNA Silencing in Plants

MicroRNAs (miRNAs) play pivotal roles in various biological processes across kingdoms. Many plant miRNAs have been experimentally identified or predicted by bioinformatics mining of small RNA databases. However, the functions of these miRNAs remain largely unknown due to the lack of effective genetic tools. Here, we report a virus-based microRNA silencing (VbMS) system that can be used for functional analysis of plant miRNAs. VbMS is performed through tobacco rattle virus-based expression of miRNA target mimics to silence endogenous miRNAs. VbMS of either miR172 or miR165/166 caused developmental defects in Nicotiana benthamiana. VbMS of miR319 reduced the complexity of tomato (Solanum lycopersicum) compound leaves. These results demonstrate that tobacco rattle virus-based VbMS is a powerful tool to silence endogenous miRNAs and to dissect their functions in different plant species. 


Via Guogen Yang
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Evolutionary Dynamics of Nitrogen Fixation in the Legume–Rhizobia Symbiosis

Evolutionary Dynamics of Nitrogen Fixation in the Legume–Rhizobia Symbiosis | symbiosis | Scoop.it

The stabilization of host–symbiont mutualism against the emergence of parasitic individuals is pivotal to the evolution of cooperation. One of the most famous symbioses occurs between legumes and their colonizing rhizobia, in which rhizobia extract nutrients (or benefits) from legume plants while supplying them with nitrogen resources produced by nitrogen fixation (or costs). Natural environments, however, are widely populated by ineffective rhizobia that extract benefits without paying costs and thus proliferate more efficiently than nitrogen-fixing cooperators. How and why this mutualism becomes stabilized and evolutionarily persists has been extensively discussed. To better understand the evolutionary dynamics of this symbiosis system, we construct a simple model based on the continuous snowdrift game with multiple interacting players. We investigate the model using adaptive dynamics and numerical simulations. We find that symbiotic evolution depends on the cost–benefit balance, and that cheaters widely emerge when the cost and benefit are similar in strength. In this scenario, the persistence of the symbiotic system is compatible with the presence of cheaters. This result suggests that the symbiotic relationship is robust to the emergence of cheaters, and may explain the prevalence of cheating rhizobia in nature. In addition, various stabilizing mechanisms, such as partner fidelity feedback, partner choice, and host sanction, can reinforce the symbiotic relationship by affecting the fitness of symbionts in various ways. This result suggests that the symbiotic relationship is cooperatively stabilized by various mechanisms. In addition, mixed nodule populations are thought to encourage cheater emergence, but our model predicts that, in certain situations, cheaters can disappear from such populations. These findings provide a theoretical basis of the evolutionary dynamics of legume–rhizobia symbioses, which is extendable to other single-host, multiple-colonizer systems


Via Ryohei Thomas Nakano, IvanOresnik, Jean-Michel Ané
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Jean-Michel Ané's curator insight, September 22, 2014 10:56 PM

Wow... very nice modeling paper!

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Non-Additive Transcriptional Profiles Underlie Dikaryotic Superiority in Pleurotus ostreatus Laccase Activity

Non-Additive Transcriptional Profiles Underlie Dikaryotic Superiority in Pleurotus ostreatus Laccase Activity | symbiosis | Scoop.it

The basidiomycete Pleurotus ostreatus is an efficient producer of laccases, a group of enzymes appreciated for their use in multiple industrial processes. The aim of this study was to reveal the molecular basis of the superiority of laccase production by dikaryotic strains compared to their parental monokaryons.


Via Francis Martin
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Mutation of praR in Rhizobium leguminosarum enhances root biofilms, improving nodulation competitiveness by increased expression of attachment proteins

Mutation of praR in Rhizobium leguminosarum enhances root biofilms, improving nodulation competitiveness by increased expression of attachment proteins | symbiosis | Scoop.it

In Rhizobium leguminosarum bv. viciae, quorum-sensing is regulated by CinR, which induces the cinIS operon. CinI synthesises an AHL, whereas CinS inactivates PraR, a repressor. Mutation of praR enhanced biofilms in vitro. We developed a light (lux)-dependent assay of rhizobial attachment to roots and demonstrated that mutation of praR increased biofilms on pea roots. The praR mutant out-competed wild-type for infection of pea nodules in mixed inoculations. Analysis of gene expression by microarrays and promoter fusions revealed that PraR represses its own transcription and mutation of praR increased expression of several genes including those encoding secreted proteins (the adhesins RapA2, RapB and RapC, two cadherins and the glycanase PlyB), the polysaccharide regulator RosR, and another protein similar to PraR. PraR bound to the promoters of several of these genes indicating direct repression. Mutations in rapA2, rapB, rapC, plyB, the cadherins or rosR did not affect the enhanced root attachment or nodule competitiveness of the praR mutant. However combinations of mutations in rapA, rapB and rapC abolished the enhanced attachment and nodule competitiveness. We conclude that relief of PraR-mediated repression determines a lifestyle switch allowing the expression of genes that are important for biofilm formation on roots and the subsequent initiation of infection of legume roots.

 

Marijke Frederix, Anne Edwards, Anna Swiderska, Andrew Stanger, Ramakrishnan Karunakaran, Alan Williams, Pamela Abbruscato, Maria Sanchez-Contrera,, Philip S. Poole and J. Allan Downie (2014). Mol Microbiol  on line 7 MAY

 


Via IvanOresnik
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Abundance and Diversity of Soybean Nodulating Rhizobia in Black Soil are Impacted by Land Use and Crop Managements

To investigate the effects of land use and crop managements on the soybean rhizobia communities, 280 nodule isolates were trapped from 7 fields with different land use and culturing histories. Besides the known Bradyrhizobium japonicum, three novel genospecies were isolated from these fields. Grassland (GL) maintained higher diversity of soybean bradyrhizobia than the other cultivation systems. Two genospecies (Bradyrhizobium spp. I and III) distributed widely in all treatments, while Bradyrhizobium sp. II was only found in GL treatment. Cultivation with soybean increased the rhizobial abundance and diversity, except for the soybean-monoculture (S-S) treatment. In monoculture systems, soybean favored Bradyrhizobium sp. I, while maize and wheat favoredBradyrhizobium sp. III. Fertilization decreased the rhizobial diversity indexes, but did not change the species composition. The content of organic carbon (OC), available phosphorus (AP) and pH were the main soil parameters positively correlated with the distribution of Bradyrhizobium spp. I, II and B. japonicum, and negatively correlated with Bradyrhizobium sp. III. These results revealed that different land use and crop managements could not only alter the diversity and abundance of soybean rhizobia, but also change interactions between rhizobia and plants of legumes or non-legumes, which offered novel information for the biogeography of rhizobia.


Via Jean-Michel Ané
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The Medicago truncatula hypermycorrhizal B9 mutant displays an altered response to phosphate and is more susceptible to Aphanomyces euteiches

The Medicago truncatula hypermycorrhizal B9 mutant displays an altered response to phosphate and is more susceptible to Aphanomyces euteiches | symbiosis | Scoop.it

Inorganic phosphate (Pi) plays a key role in the development of arbuscular mycorrhizal (AM) symbiosis, which is favoured when Pi is limiting in the environment. We have characterized the Medicago truncatula hypermycorrhizal B9 mutant for its response to limiting (P/10) and replete (P2) Pi. On P2, mycorrhization was significantly higher in B9 plants than in wild-type (WT). The B9 mutant displayed hallmarks of Pi-limited plants, including higher levels of anthocyanins and lower concentrations of Pi in shoots than WT plants. Transcriptome analyses of roots of WT and B9 plants cultivated on P2 or on P/10 confirmed the Pi-limited profile of the mutant on P2 and highlighted its altered response to Pi on P/10. Furthermore, the B9 mutant displayed a higher expression of defence/stress-related genes and was more susceptible to infection by the root oomycete pathogen Aphanomyces euteiches than WT plants. We propose that the hypermycorrhizal phenotype of the B9 mutant is linked to its Pi-limited status favouring AM symbiosis in contrast to WT plants in Pi-replete conditions, and discuss the possible links between the altered response of the B9 mutant to Pi, mycorrhization and infection by A. euteiches.


Via Jean-Michel Ané
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Jean-Michel Ané's curator insight, June 2, 2014 3:57 PM

Very interesting...

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The oxidative environment: a mediator of interspecies communication that drives symbiosis evolution

The oxidative environment: a mediator of interspecies communication that drives symbiosis evolution | symbiosis | Scoop.it

Symbiotic interactions are ubiquitous in nature and play a major role in driving the evolution of life. Interactions between partners are often mediated by shared signalling pathways, which strongly influence both partners' biology and the evolution of the association in various environments. As an example of ‘common language’, the regulation of the oxidative environment plays an important role in driving the evolution of symbiotic associations. Such processes have been occurring for billions of years, including the increase in Earth's atmospheric oxygen and the subsequent evolution of mitochondria. The effect of reactive oxygen species and reactive nitrogen species (RONS) has been characterized functionally, but the molecular dialogue between partners has not been integrated within a broader evolutionary context yet. Given the pleiotropic role of RONS in cell–cell communication, development and immunity, but also their associated physiological costs, we discuss here how their regulation can influence the establishment, the maintenance and the breakdown of various symbiotic associations. By synthesizing recent developments in redox biology, we aim to provide an interdisciplinary understanding of the influence of such mediators of interspecies communication on the evolution and stability of symbioses, which in turn can shape ecosystems and play a role in health and disease.


Via Jean-Michel Ané
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Jean-Michel Ané's curator insight, May 14, 2014 4:05 PM

Great review Natacha!

Rescooped by Yuanchun Wang from Publications
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Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization, Evolution and Expression of the Nitrogen Fixation Genes. PLoS Genetics 2014

Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization, Evolution and Expression of the Nitrogen Fixation Genes. PLoS Genetics 2014 | symbiosis | Scoop.it

We provide here a comparative genome analysis of 31 strains within the genus Paenibacillusincluding 11 new genomic sequences of N2-fixing strains. The heterogeneity of the 31 genomes (15 N2-fixing and 16 non-N2-fixing Paenibacillus strains) was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. Large numbers of transposable elements might be related to the heterogeneity. We discovered that a minimal and compact nif cluster comprising nine genes nifB, nifH, nifD, nifK, nifE, nifN, nifX,hesA and nifV encoding Mo-nitrogenase is conserved in the 15 N2-fixing strains. The nif cluster is under control of a σ70-depedent promoter and possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe–S] cluster is highly conserved in N2-fixing and non-N2-fixing strains. Furthermore, we demonstrate that the nif cluster enabled Escherichia coli JM109 to fix nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that Paenibacillus andFrankia are sister groups. Phylogeny of the concatenated 275 single-copy core genes suggests that the ancestral Paenibacillus did not fix nitrogen. The N2-fixing Paenibacillus strains were generated by acquiring the nif cluster via horizontal gene transfer (HGT) from a source related to Frankia. During the history of evolution, the nif cluster was lost, producing some non-N2-fixing strains, and vnf encoding V-nitrogenase or anf encoding Fe-nitrogenase was acquired, causing further diversification of some strains. In addition, some N2-fixing strains have additional nif and nif-like genes which may result from gene duplications. The evolution of nitrogen fixation in Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnfgenes. This study not only reveals the organization and distribution of nitrogen fixation genes inPaenibacillus, but also provides insight into the complex evolutionary history of nitrogen fixation.


Via Chang Fu Tian
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A positive regulator of nodule organogenesis, NODULE INCEPTION, acts as a negative regulator of rhizobial infection in Lotus japonicus.

Legume–rhizobium symbiosis occurs in specialized root organs called nodules. To establish the symbiosis, two major genetically controlled events, rhizobial infection and organogenesis, must be occur. For a successful symbiosis, it is essential that the two phenomena simultaneously proceed in different root tissues. Although several symbiotic genes have been identified during genetic screening of non-symbiotic mutants, most of the mutants harbor defects in both infection and organogenesis pathways, leading to experimental difficulty in investigating the molecular genetic relationships between the pathways. In this study we isolated a novel non-nodulation mutant, daphne, in Lotus japonicus, that shows complete loss of nodulation but a dramatically increased number of infection threads. Characterization of the locus responsible for these phenotypes revealed a chromosomal translocation upstream of NODULE INCEPTION (NIN) in daphne. Genetic analysis using a known nin mutant revealed that daphne is a novel nin mutant allele. Although the daphne mutant showed reduced induction of NIN after rhizobial infection, the spatial expression pattern of NIN in epidermal cells was broader than that in the wild type. Over-expression of NIN strongly suppressed hyper-infection in daphne, and daphne phenotypes were partially rescued by cortical expression of NIN. These observations suggested that daphne mutation enhanced the role of NIN in the infection pathway due to a specific loss of the role of NIN in nodule organogenesis. Based on the results, we provide evidence that a bifunctional transcription factor NIN negatively regulates infection but positively regulates nodule organogenesis during the course of the symbiosis.


Via Chang Fu Tian
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Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization, Evolution and Expression of the Nitrogen Fixation Genes. PLoS Genetics 2014

Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization, Evolution and Expression of the Nitrogen Fixation Genes. PLoS Genetics 2014 | symbiosis | Scoop.it

We provide here a comparative genome analysis of 31 strains within the genus Paenibacillusincluding 11 new genomic sequences of N2-fixing strains. The heterogeneity of the 31 genomes (15 N2-fixing and 16 non-N2-fixing Paenibacillus strains) was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. Large numbers of transposable elements might be related to the heterogeneity. We discovered that a minimal and compact nif cluster comprising nine genes nifB, nifH, nifD, nifK, nifE, nifN, nifX,hesA and nifV encoding Mo-nitrogenase is conserved in the 15 N2-fixing strains. The nif cluster is under control of a σ70-depedent promoter and possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe–S] cluster is highly conserved in N2-fixing and non-N2-fixing strains. Furthermore, we demonstrate that the nif cluster enabled Escherichia coli JM109 to fix nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that Paenibacillus andFrankia are sister groups. Phylogeny of the concatenated 275 single-copy core genes suggests that the ancestral Paenibacillus did not fix nitrogen. The N2-fixing Paenibacillus strains were generated by acquiring the nif cluster via horizontal gene transfer (HGT) from a source related to Frankia. During the history of evolution, the nif cluster was lost, producing some non-N2-fixing strains, and vnf encoding V-nitrogenase or anf encoding Fe-nitrogenase was acquired, causing further diversification of some strains. In addition, some N2-fixing strains have additional nif and nif-like genes which may result from gene duplications. The evolution of nitrogen fixation in Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnfgenes. This study not only reveals the organization and distribution of nitrogen fixation genes inPaenibacillus, but also provides insight into the complex evolutionary history of nitrogen fixation.


Via Chang Fu Tian
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Rescooped by Yuanchun Wang from Symbiosis & Evolution
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RbohB, a Phaseolus vulgaris NADPH oxidase gene, enhances symbiosome number, bacteroid size, and nitrogen fixation in nodules and impairs mycorrhizal colonization -

RbohB, a Phaseolus vulgaris NADPH oxidase gene, enhances symbiosome number, bacteroid size, and nitrogen fixation in nodules and impairs mycorrhizal colonization - | symbiosis | Scoop.it

Via Chang Fu Tian
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EPPO and Pest Risk Analysis

EPPO and Pest Risk Analysis | symbiosis | Scoop.it

This e-journal on 'Pest Risk Analysis' is maintained by the Secretariat of the European and Mediterranean Plant Protection Organization (EPPO) and its aim is to share information collected on the Internet on pest risk analyses and on PRA tools.

 

EPPO is an intergovernmental organization created in 1951 which currently has 50 member countries. EPPO is responsible for harmonization and cooperation among the National Plant Protection Organizations (official authorities) of its member countries. EPPO helps its members in their efforts to protect plant health in agriculture, forestry and the uncultivated environment (standard-setting activities and exchange of information).

 

On its official website, EPPO also provides:

- all PRAs conducted by EPPO Expert Working Groups: http://www.eppo.int/QUARANTINE/Pest_Risk_Analysis/PRA_intro.htm

- working documents on Pest Risk Analysis which have been presented to various EPPO Panels: http://www.eppo.int/QUARANTINE/Pest_Risk_Analysis/PRA_documents.htm

- the EPPO Alert List (early warning on emerging pests which could present a risk for the Euro-Mediterranean region):
www.eppo.int/QUARANTINE/Alert_List/alert_list.htm

 

Read more on EPPO work on PRA on http://www.eppo.int/QUARANTINE/Pest_Risk_Analysis/PRA_intro.htm.

 

Visit the official EPPO website: www.eppo.int


Via Muriel Suffert
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Muriel Suffert's curator insight, January 9, 2013 9:01 AM

You can also follow updates on this page via twitter (@MurielSuffert)

Mehmet Levent's comment, August 4, 2014 7:40 AM
good
Neohouse's comment, July 27, 2017 6:02 AM
Woa bài viết rấy hay . Mong nhận được nhiều bài viết từ bạn
Rescooped by Yuanchun Wang from Plant-Microbe Symbiosis
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Benefits of Legumes in Agriculture and Crop Rotation

Benefits of Legumes in Agriculture and Crop Rotation | symbiosis | Scoop.it
Most legumes, as we know, contain symbiotic bacteria called rhizobia. To be “symbiotic” is to have long-term, usually mutualistic, interactions with other species. After legume seeds germinate, rhizobia in the soil invade the root hairs and move towards the root of the legume. The bacteria multiply quickly in the root, causing the inflation of root cells to create nodules.
These rhizobia are located within the root nodules of the legume’s root system. These bacteria have the extremely unique ability to fix nitrogen – which cannot be readily used by many microbial organisms – from the atmosphere, or from molecular nitrogen, into ammonia. The ammonia can then be converted into its usable form, ammonium.
With this arrangement, the plant’s root nodules become an excellent source of nitrogen for the legume. Nitrogen is a key element in crop productivity and protein production. With this being said, legumes tend to be highly rich in protein.
In crop rotation, or the practice of growing many different types of crop species in the same area for many seasons, legumes are often utilized. By alternating between legumes and non-legumes, the soil gains sufficient amounts of usable nitrogen exerted from the legumes to better the livelihood of the non-legumes. On the other hand, when a non-legume is harvested and removed from the soil, all of the crop’s nutrients leave with it, leaving the soil with less nutrients.

Via Jean-Michel Ané
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NODULE INCEPTION creates a long-distance negative feedback loop involved in homeostatic regulation of nodule organ production

NODULE INCEPTION creates a long-distance negative feedback loop involved in homeostatic regulation of nodule organ production | symbiosis | Scoop.it
Significance

Long-range organ-to-organ communications are important for the coordination of development and environmental adaptation in multicellular organisms, particularly plants that continuously produce postembryonic lateral organs in various environmental conditions. The substance of homeostatic regulation of organ development via long-distance signals has not yet been identified, however. Legumes use an autoregulatory negative-feedback system involving root–shoot communication to maintain optimal numbers of nodules by systemically suppressing nodulation. We show that a transcription factor, NODULE INCEPTION (NIN), an essential inducer for nodule primordium formation, directly activates genes encoding small peptides that act as root-derived long-distance mobile signals, leading to repression of endogenous NIN though the root–shoot communication and resulting in systemic suppression of nodulation. We demonstrate that an autoregulatory negative-feedback loop homeostatically regulates nodule production via this long-range signaling.
Abstract

Autoregulatory negative-feedback loops play important roles in fine-balancing tissue and organ development. Such loops are composed of short-range intercellular signaling pathways via cell–cell communications. On the other hand, leguminous plants use a long-distance negative-feedback system involving root–shoot communication to control the number of root nodules, root lateral organs that harbor symbiotic nitrogen-fixing bacteria known as rhizobia. This feedback system, known as autoregulation of nodulation (AON), consists of two long-distance mobile signals: root-derived and shoot-derived signals. Two Lotus japonicus CLAVATA3/ENDOSPERM SURROUNDING REGION (CLE)-related small peptides, CLE ROOT SIGNAL1 (CLE-RS1) and CLE-RS2, function as root-derived signals and are perceived by a shoot-acting AON factor, the HYPERNODULATION ABERRANT ROOT FORMATION1 (HAR1) receptor protein, an ortholog of Arabidopsis CLAVATA1, which is responsible for shoot apical meristem homeostasis. This peptide–receptor interaction is necessary for systemic suppression of nodulation. How the onset of nodulation activates AON and how optimal nodule numbers are maintained remain unknown, however. Here we show that an RWP-RK–containing transcription factor, NODULE INCEPTION (NIN), which induces nodule-like structures without rhizobial infection when expressed ectopically, directly targets CLE-RS1 and CLE-RS2. Roots constitutively expressing NIN systemically repress activation of endogenous NIN expression in untransformed roots of the same plant in a HAR1-dependent manner, leading to systemic suppression of nodulation and down-regulation of CLE expression. Our findings provide, to our knowledge, the first molecular evidence of a long-distance autoregulatory negative-feedback loop that homeostatically regulates nodule organ formation.
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Proteomic analysis of free-living Bradyrhizobium diazoefficiens: highlighting potential determinants of a successful symbiosis

Proteomic analysis of free-living Bradyrhizobium diazoefficiens: highlighting potential determinants of a successful symbiosis | symbiosis | Scoop.it

Strain CPAC 7 (=SEMIA 5080) was recently reclassified into the new species Bradyrhizobium diazoefficiens; due to its outstanding efficiency in fixing nitrogen, it has been used in commercial inoculants for application to crops of soybean [Glycine max (L.) Merr.] in Brazil and other South American countries. Although the efficiency of B. diazoefficiens inoculant strains is well recognized, few data on their protein expression are available.

Results

We provided a two-dimensional proteomic reference map of CPAC 7 obtained under free-living conditions, with the successful identification of 115 spots, representing 95 different proteins. The results highlighted the expression of molecular determinants potentially related to symbiosis establishment (e.g. inositol monophosphatase, IMPase), fixation of atmospheric nitrogen (N2) (e.g. NifH) and defenses against stresses (e.g. chaperones). By using bioinformatic tools, it was possible to attribute probable functions to ten hypothetical proteins. For another ten proteins classified as "NO related COG" group, we analyzed by RT-qPCR the relative expression of their coding-genes in response to the nodulation-gene inducer genistein. Six of these genes were up-regulated, including blr0227, which may be related to polyhydroxybutyrate (PHB) biosynthesis and competitiveness for nodulation.

Conclusions

The proteomic map contributed to the identification of several proteins of B. diaozoefficiens under free-living conditions and our approach--combining bioinformatics and gene-expression assays--resulted in new information about unknown genes that might play important roles in the establishment of the symbiosis with soybean.


Via IvanOresnik
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David Kuykendall's curator insight, August 24, 2014 7:57 AM

This new species includes strain USDA110, an agriculturally superb soybean inoculant strain. The study seems to suggest new pathways of efficient symbiotic nitrogen fixation heretofor uncharacterized. I like it, I like it very much.

Rescooped by Yuanchun Wang from Plant-Microbe Symbiosis
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Mechanisms of physiological adjustment of N2 fixation in Cicer arietinum L. (chickpea) during early stages of water deficit: single or multi-factor controls

Drought negatively impacts symbiotic nitrogen fixation (SNF) in Cicer arietinum L. (chickpea), thereby limiting yield potential. Understanding how drought affects chickpea nodulation will enable the development of strategies to biotechnologically engineer chickpea varieties with enhanced SNF under drought conditions. By analyzing carbon and nitrogen metabolism, we studied the mechanisms of physiological adjustment of nitrogen fixation in chickpea plants nodulated with Mesorhizobium ciceri during both drought stress and subsequent recovery. The nitrogenase activity, levels of several key carbon (in nodules) and nitrogen (in both nodules and leaves) metabolites and antioxidant compounds, as well as the activity of related nodule enzymes were examined in M. ciceri-inoculated chickpea plants under early drought stress and subsequent recovery. Results indicated that drought reduced nitrogenase activity, and that this was associated with a reduced expression of the nifK gene. Furthermore, drought stress promoted an accumulation of amino acids, mainly asparagine in nodules (but not in leaves), and caused a cell redox imbalance in nodules. An accumulation of organic acids, especially malate, in nodules, which coincided with the decline of nodulated root respiration, was also observed under drought stress. Taken together, our findings indicate that reduced nitrogenase activity occurring at early stages of drought stress involves, at least, the inhibition of respiration, nitrogen accumulation and an imbalance in cell redox status in nodules. The results of this study demonstrate the potential that the genetic engineering-based improvement of SNF efficiency could be applied to reduce the impact of drought on the productivity of chickpea, and perhaps other legume crops.


Via Jean-Michel Ané
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Rescooped by Yuanchun Wang from Rhizobium Research
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Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field

Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field | symbiosis | Scoop.it

Highly diverse communities of bacteria inhabiting soybean rhizospheres play pivotal roles in plant growth and crop production; however, little is known about the changes that occur in these communities during growth. We used both culture-dependent physiological profiling and culture independent DNA-based approaches to characterize the bacterial communities of the soybean rhizosphere during growth in the field. The physiological properties of the bacterial communities were analyzed by a community-level substrate utilization assay with BioLog Eco plates, and the composition of the communities was assessed by gene pyrosequencing. Higher metabolic capabilities were found in rhizosphere soil than in bulk soil during all stages of the BioLog assay. Pyrosequencing analysis revealed that differences between the bacterial communities of rhizosphere and bulk soils at the phylum level; i.e., Proteobacteria were increased, while Acidobacteria and Firmicutes were decreased in rhizosphere soil during growth. Analysis of operational taxonomic units showed that the bacterial communities of the rhizosphere changed significantly during growth, with a higher abundance of potential plant growth promoting rhizobacteria, including Bacillus, Bradyrhizobium, and Rhizobium, in a stage-specific manner. These findings demonstrated that rhizosphere bacterial communities were changed during soybean growth in the field.

  Sugiyama A, Ueda Y, Zushi T, Takase H, Yazaki K (2014). PLoS One. Jun 23;9(6):e100709.


Via IvanOresnik
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Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean

Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean | symbiosis | Scoop.it

Background The soybean-Bradyrhizobium symbiosis can be highly efficient in fixing nitrogen, but few genomic sequences of elite inoculant strains are available. Here we contribute with information on the genomes of two commercial strains that are broadly applied to soybean crops in the tropics. B. japonicum CPAC 15 (=SEMIA 5079) is outstanding in its saprophytic capacity and competitiveness, whereas B. diazoefficiens CPAC 7 (=SEMIA 5080) is known for its high efficiency in fixing nitrogen. Both are well adapted to tropical soils. The genomes of CPAC 15 and CPAC 7 were compared to each other and also to those of B. japonicum USDA 6T and B. diazoefficiens USDA 110T. Results Differences in genome size were found between species, with B. japonicum having larger genomes than B. diazoefficiens. Although most of the four genomes were syntenic, genome rearrangements within and between species were observed, including events in the symbiosis island. In addition to the symbiotic region, several genomic islands were identified. Altogether, these features must confer high genomic plasticity that might explain adaptation and differences in symbiotic performance. It was not possible to attribute known functions to half of the predicted genes. About 10% of the genomes was composed of exclusive genes of each strain, but up to 98% of them were of unknown function or coded for mobile genetic elements. In CPAC 15, more genes were associated with secondary metabolites, nutrient transport, iron-acquisition and IAA metabolism, potentially correlated with higher saprophytic capacity and competitiveness than seen with CPAC 7. In CPAC 7, more genes were related to the metabolism of amino acids and hydrogen uptake, potentially correlated with higher efficiency of nitrogen fixation than seen with CPAC 15. Conclusions Several differences and similarities detected between the two elite soybean-inoculant strains and between the two species of Bradyrhizobium provide new insights into adaptation to tropical soils, efficiency of N2 fixation, nodulation- and competitiveness.


Via Stéphane Hacquard, Jean-Michel Ané
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Deletions of the SACPD-C locus elevate seed stearic acid levels but also result in fatty acid and morphological alterations in nitrogen fixing nodules

Deletions of the SACPD-C locus elevate seed stearic acid levels but also result in fatty acid and morphological alterations in nitrogen fixing nodules | symbiosis | Scoop.it

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Background

Soybean (Glycine max) seeds are the primary source of edible oil in the United States. Despite its widespread utility, soybean oil is oxidatively unstable. Until recently, the majority of soybean oil underwent chemical hydrogenation, a process which also generates trans fats. An alternative to chemical hydrogenation is genetic modification of seed oil through identification and introgression of mutant alleles. One target for improvement is the elevation of a saturated fat with no negative cardiovascular impacts, stearic acid, which typically constitutes a minute portion of seed oil (~3%).

Results

We examined radiation induced soybean mutants with moderately increased stearic acid (10-15% of seed oil, ~3-5 X the levels in wild-type soybean seeds) via comparative whole genome hybridization and genetic analysis. The deletion of one SACPD isoform encoding gene (SACPD-C) was perfectly correlated with moderate elevation of seed stearic acid content. However, SACPD-C deletion lines were also found to have altered nodule fatty acid composition and grossly altered morphology. Despite these defects, overall nodule accumulation and nitrogen fixation were unaffected, at least under laboratory conditions.

Conclusions

Although no yield penalty has been reported for moderate elevated seed stearic acid content in soybean seeds, our results demonstrate that genetic alteration of seed traits can have unforeseen pleiotropic consequences. We have identified a role for fatty acid biosynthesis, and SACPD activity in particular, in the establishment and maintenance of symbiotic nitrogen fixation.

 

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Rescooped by Yuanchun Wang from Plant-Microbe Symbiosis
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Effect of shoot removal on remobilization of carbon and nitrogen during regrowth of nitrogen-fixing alfalfa

The contribution of carbon and nitrogen reserves to regrowth following shoot removal has been studied in the past. However, important gaps remain in understanding the effect of shoot cutting on nodule performance and its relevance during regrowth. In this study, isotopic labelling was conducted at root and canopy levels with both 15 N2 and 13C-depleted CO2 on exclusively nitrogen fixing alfalfa plants. As expected, our results indicate that the roots were the main sink organs before shoots were removed. Seven days after regrowth the carbon and nitrogen stored in the roots was invested in shoot biomass formation and partitioned to the nodules. The large depletion in nodule carbohydrate availability suggests that root-derived carbon compounds were delivered towards nodules in order to sustain respiratory activity. In addition to the limited carbohydrate availability, the up-regulation of nodule peroxidases showed that oxidative stress was also involved during poor nodule performance. Fourteen days after cutting, and as a consequence of the stimulated photosynthetic and N2-fixing machinery, availability of Cnew and Nnew strongly diminished in the plants due to their replacement by C and N assimilated during the post-labelling period. In summary, our study indicated that during the first week of regrowth, root-derived C and N remobilization did not overcome C- and N-limitation in nodules and leaves. However, fourteen days after cutting, leaf and nodule performance were re-established.


Via Jean-Michel Ané
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Rescooped by Yuanchun Wang from Symbiosis & Evolution
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The Role of Symbiotic Nitrogen Fixation in Sustainable Production of Biofuels

With the ever-increasing population of the world (expected to reach 9.6 billion by 2050), and altered life style, comes an increased demand for food, fuel and fiber. However, scarcity of land, water and energy accompanied by climate change means that to produce enough to meet the demands is getting increasingly challenging. Today we must use every avenue from science and technology available to address these challenges. The natural process of symbiotic nitrogen fixation, whereby plants such as legumes fix atmospheric nitrogen gas to ammonia, usable by plants can have a substantial impact as it is found in nature, has low environmental and economic costs and is broadly established. Here we look at the importance of symbiotic nitrogen fixation in the production of biofuel feedstocks; how this process can address major challenges, how improving nitrogen fixation is essential, and what we can do about it.

Via Chang Fu Tian
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Chang Fu Tian's curator insight, May 11, 2014 3:12 AM

Yes, what we can do about it

Rescooped by Yuanchun Wang from Publications
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Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization, Evolution and Expression of the Nitrogen Fixation Genes. PLoS Genetics 2014

Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization, Evolution and Expression of the Nitrogen Fixation Genes. PLoS Genetics 2014 | symbiosis | Scoop.it

We provide here a comparative genome analysis of 31 strains within the genus Paenibacillusincluding 11 new genomic sequences of N2-fixing strains. The heterogeneity of the 31 genomes (15 N2-fixing and 16 non-N2-fixing Paenibacillus strains) was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. Large numbers of transposable elements might be related to the heterogeneity. We discovered that a minimal and compact nif cluster comprising nine genes nifB, nifH, nifD, nifK, nifE, nifN, nifX,hesA and nifV encoding Mo-nitrogenase is conserved in the 15 N2-fixing strains. The nif cluster is under control of a σ70-depedent promoter and possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe–S] cluster is highly conserved in N2-fixing and non-N2-fixing strains. Furthermore, we demonstrate that the nif cluster enabled Escherichia coli JM109 to fix nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that Paenibacillus andFrankia are sister groups. Phylogeny of the concatenated 275 single-copy core genes suggests that the ancestral Paenibacillus did not fix nitrogen. The N2-fixing Paenibacillus strains were generated by acquiring the nif cluster via horizontal gene transfer (HGT) from a source related to Frankia. During the history of evolution, the nif cluster was lost, producing some non-N2-fixing strains, and vnf encoding V-nitrogenase or anf encoding Fe-nitrogenase was acquired, causing further diversification of some strains. In addition, some N2-fixing strains have additional nif and nif-like genes which may result from gene duplications. The evolution of nitrogen fixation in Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnfgenes. This study not only reveals the organization and distribution of nitrogen fixation genes inPaenibacillus, but also provides insight into the complex evolutionary history of nitrogen fixation.


Via Chang Fu Tian
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Rescooped by Yuanchun Wang from Plant-Microbe Interaction
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Science: Paired Plant Immune Receptors (2014)

Science: Paired Plant Immune Receptors (2014) | symbiosis | Scoop.it

Plants are constantly interpreting microbial signals from potential pathogens and potential commensals or mutualists. Because plants have no circulating cells dedicated to this task, every plant cell must, in principle, recognize any microbe as friend, foe, or irrelevant bystander. That tall order is mediated by an array of innate immune system receptors: pattern-recognition receptors outside the plant cell and nucleotide-binding oligomerization domain (NOD)–like receptors (NLRs) inside the cell. Despite their importance for plant health, how NLRs function mechanistically has remained obscure. On page 299 of this issue, Williams et al. (1) reveal a role for heterodimerization between NLRs and show how the rather limited NLR repertoire of any plant genome might be enhanced by combinatorial diversity.

 

Marc T. Nishimura, Jeffery L. Dangl


Via Nicolas Denancé, Guogen Yang
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