Plant-Microbe Symbiosis
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Arbuscular Mycorrhizal Symbiosis, extraradical CARBON flow 1 (Live Imaging)

Rice (Oryza sativa) + Arbuscular mycorrhizal fungi (Glomus intraradices). Green: rice phosphate transporter PT11-GFP, Red: Nile Red.
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Plant-Microbe Symbiosis
Beneficial associations between plants and microbes
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CNRS, CEA, Inserm... Leurs dirigeants soutiennent la Marche pour les sciences

CNRS, CEA, Inserm... Leurs dirigeants soutiennent la Marche pour les sciences | Plant-Microbe Symbiosis | Scoop.it

D'Alain Fuchs (CNRS) à Yves Lévy (Inserm) en passant par Philippe Mauguin (INRA) et Daniel Verwaerde, ces grands dirigeants d'institutions scientifiques françaises annoncent leur soutien à la "Marche pour la science" du 22 avril 2017


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Influence of nutrient signals and carbon allocation on the expression of phosphate and nitrogen transporter genes in winter wheat (Triticum aestivum L.) roots colonized by arbuscular mycorrhizal fungi

Influence of nutrient signals and carbon allocation on the expression of phosphate and nitrogen transporter genes in winter wheat (Triticum aestivum L.) roots colonized by arbuscular mycorrhizal fungi | Plant-Microbe Symbiosis | Scoop.it
Arbuscular mycorrhizal (AM) colonization of plant roots causes the down-regulation of expression of phosphate (Pi) or nitrogen (N) transporter genes involved in direct nutrient uptake pathways. The mechanism of this effect remains unknown. In the present study, we sought to determine whether the expression of Pi or N transporter genes in roots of winter wheat colonized by AM fungus responded to (1) Pi or N nutrient signals transferred from the AM extra-radical hyphae, or (2) carbon allocation changes in the AM association. A three-compartment culture system, comprising a root compartment (RC), a root and AM hyphae compartment (RHC), and an AM hyphae compartment (HC), was used to test whether the expression of Pi or N transporter genes responded to nutrients (Pi, NH4+ and NO3-) added only to the HC. Different AM inoculation density treatments (roots were inoculated with 0, 20, 50 and 200 g AM inoculum) and light regime treatments (6 hours light and 18 hours light) were established to test the effects of carbon allocation on the expression of Pi or N transporter genes in wheat roots. The expression of two Pi transporter genes (TaPT4 and TaPHT1.2), five nitrate transporter genes (TaNRT1.1, TaNRT1.2, TaNRT2.1, TaNRT2.2, and TaNRT2.3), and an ammonium transporter gene (TaAMT1.2) was quantified using real-time polymerase chain reaction. The expression of TaPT4, TaNRT2.2, and TaAMT1.2 was down-regulated by AM colonization only when roots of host plants received Pi or N nutrient signals. However, the expression of TaPHT1.2, TaNRT2.1, and TaNRT2.3 was down-regulated by AM colonization, regardless of whether there was nutrient transfer from AM hyphae. The expression of TaNRT1.2 was also down-regulated by AM colonization even when there was no nutrient transfer from AM hyphae. The present study showed that an increase in carbon consumption by the AM fungi did not necessarily result in greater down-regulation of expression of Pi or N transporter genes.

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Great paper. I love it.

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Community matters: A history of Biological Nitrogen Fixation and Nodulation research, 1965 to 1995

Community matters: A history of Biological Nitrogen Fixation and Nodulation research, 1965 to 1995
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Great dissertation for those interested in the history of this field.

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Merriam-Webster Welcomes 'Microbiome' To The English Language

Merriam-Webster Welcomes 'Microbiome' To The English Language | Plant-Microbe Symbiosis | Scoop.it
This week, Merriam-Webster added “microbiome” to the English dictionary, defining the noun as “a community of microorganisms (such as bacteria, fungi, and viruses) that inhabit a particular environment and especially the collection of microorganisms living in or on the human body.” 
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And, by the way, it seems that it is not in the French Larousse dictionary yet  :-)

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Evolutionary asymmetry in the arbuscular mycorrhizal symbiosis: conservatism in fungal morphology does not predict host plant growth

Although arbuscular mycorrhizal (AM) fungi are obligate symbionts that can influence plant growth, the magnitude and direction of these effects are highly variable within fungal genera and even among isolates within species, as well as among plant taxa.
To determine whether variability in AM fungal morphology and growth is correlated with AM fungal effects on plant growth, we established a common garden experiment with 56 AM fungal isolates comprising 17 genera and six families growing with three plant host species.
Arbuscular mycorrhizal fungal morphology and growth was highly conserved among isolates of the same species and among species within a family. By contrast, plant growth response to fungal inoculation was highly variable, with the majority of variation occurring among different isolates of the same AM fungal species.
Our findings show that host performance cannot be predicted from AM fungal morphology and growth traits. Divergent effects on plant growth among isolates within an AM fungal species may be caused by coevolution between co-occurring fungal and plant populations.
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Marchantia liverworts as a proxy to plants basal microbiomes.

Microbiomes influence plant development, establishment, nutrient acquisition, pathogen defense, and the myriad of roles that ultimately impacts plant health. Plants microbiome are shaped through interactions between the microbes (ranging from cooperative functions to chemical warfare) and a selection process entailed by the host plants that distinguishes between pathogens, commensals, symbionts and transient bacteria. The soil is a primary source for microbes colonizing plants, along with other environmental sources including rain and interactions with other organisms. In this work, we explore the microbiomes through massive sequencing of the 16S rRNA gene in the eldest terrestrial plants: Marchantia liverworts. We compared microbiomes from M. polymorpha, and M. paleacea plants collected in the wild and their soils, all together luckily in the same geographical location (sympatric) thus reducing geographic effects; and also from plants grown in vitro and established from gemmae obtained from the same population of wild plants. Qualitative and quantitative microbiome analysis allowed us to identify microbes conserved in both native and in vitro Marchantia species. While M. polymorpha native plants microbiomes richness is reduced about M. paleacea, containing almost half of the Operative Taxonomic Units (OTUs) observed in M. paleacea, M. polymorpha grown in vitro exhibits larger OTUs. This diversity differences might be the result of impairment to recognize their microbial partners and being an open niche for opportunistic bacteria. The main OTUs in Marchantia microbiomes were assigned to the genera: Methylobacterium, Rhizobium, Paenibacillus, Lysobacter, Pirellula, Steroidobacter, and Bryobacter. The assigned genera correspond to bacteria capable of plant-growth promotion, complex exudates degradation, nitrogen fixation, methylotrophs, and disease-suppressive bacteria, all hosted in the relatively simple anatomy of the plant that provides refuge on their surfaces, rhizoids, and multiple gas chambers that work as specialized niches for different bacterial groups. Marchantia is a promising model to study not only long-term relationships between plants and their microbes but also the transgenerational impact of microbiomes because of Marchantia long 450 million years under climate change conditions testing microbiome configurations.


Via Pierre-Marc Delaux
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Microbiome by looking only at 16S.... hum...

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Effects of jasmonic acid signalling on the wheat microbiome differ between body sites

Effects of jasmonic acid signalling on the wheat microbiome differ between body sites | Plant-Microbe Symbiosis | Scoop.it

Jasmonic acid (JA) signalling helps plants to defend themselves against necrotrophic pathogens and herbivorous insects and has been shown to influence the root microbiome of Arabidopsis thaliana. In this study, we determined whether JA signalling influences the diversity and functioning of the wheat (Triticum aestivum) microbiome and whether these effects are specific to particular parts of the plant. Activation of the JA pathway was achieved via exogenous application of methyl jasmonate and was confirmed by significant increases in the abundance of 10 JA-signalling-related gene transcripts. Phylogenetic marker gene sequencing revealed that JA signalling reduced the diversity and changed the composition of root endophytic but not shoot endophytic or rhizosphere bacterial communities. The total enzymatic activity and substrate utilisation profiles of rhizosphere bacterial communities were not affected by JA signalling. Our findings indicate that the effects of JA signalling on the wheat microbiome are specific to individual plant compartments.


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Soil networks become more connected and take up more carbon as nature restoration progresses

Soil networks become more connected and take up more carbon as nature restoration progresses | Plant-Microbe Symbiosis | Scoop.it
Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered.

Via Francis Martin, Stéphane Hacquard
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Arbuscular mycorrhizal fungi alter Hg root uptake and ligand environment as studied by X-ray absorption fine structure

Arbuscular mycorrhizal fungi alter Hg root uptake and ligand environment as studied by X-ray absorption fine structure | Plant-Microbe Symbiosis | Scoop.it
Publication date: January 2017
Source:Environmental and Experimental Botany, Volume 133
Author(s): Alojz Kodre, Iztok Arčon, Marta Debeljak, Mateja Potisek, Matevž Likar, Katarina Vogel-Mikuš
Mercury (Hg) – plant – fungal interactions are only poorly studied. Hg speciation and ligand environment in maize roots inoculated with arbuscular mycorrhizal (AM) fungi were investigated in order to better understand the role of AM in Hg soil to root transfer. The maize plants were grown in Hg polluted substrate (50μgg−1 as dissolved HgCl2) and inoculated with AM fungi originating from: a) highly Hg polluted environment of a former Hg smelting site in Idrija, Slovenia, (Glomus sp. – sample AmI), and b) non-polluted environment (commercial AM inoculum Symbivit® – sample AmC). Hg speciation and ligand environment in maize roots was studied by Hg-L3 XANES and EXAFS with emphasis on XAS methodology – modelling and fitting the XAFS spectra to extract in a reliable way as much information on Hg coordination as possible. The AmI plants developed more arbuscules and less vesicles than the AmC plants, and also accumulated more Hg in the roots. A clear difference in Hg coordination between the AM (AmC & AmI) and the control (ConC & ConI) plants is recognized in Hg L3-edge EXAFS analysis: in the ConC & ConI maize roots 73–80% of Hg is attached between two sulphur atoms at the distance of 2.34Å. The remaining ligand is nitrogen at 2.04Å. In AmI & AmC roots another Hg-S attachment encompassing four thiol groups at the S-distance of ∼2.50Å are identified, accounting for 21–26%. AM fungi can modify Hg ligand environment in plant roots, thus playing an important role in biogeochemical cycling of Hg in terrestrial ecosystems.
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How Plant-Soil Feedback Affects Ecological Diversity | The Scientist Magazine®

How Plant-Soil Feedback Affects Ecological Diversity | The Scientist Magazine® | Plant-Microbe Symbiosis | Scoop.it
Researchers examine how underground microbes and nutrients affect plant populations.
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The Role of Plant Innate Immunity in the Legume-Rhizobium Symbiosis

The Role of Plant Innate Immunity in the Legume-Rhizobium Symbiosis | Plant-Microbe Symbiosis | Scoop.it
A classic view of the evolution of mutualism is that it derives from a pathogenic relationship that attenuated over time to a situation in which both partners can benefit. If this is the case for rhizobia, then one might uncover features of the symbiosis that reflect this earlier pathogenic state. For example, as with plant pathogens, it is now generally assumed that rhizobia actively suppress the host immune response to allow infection and symbiosis establishment. Likewise, the host has retained mechanisms to control the nutrient supply to the symbionts and the number of nodules so that they do not become too burdensome. The open question is whether such events are strictly ancillary to the central symbiotic nodulation factor signaling pathway or are essential for rhizobial host infection. Subsequent to these early infection events, plant immune responses can also be induced inside nodules and likely play a role in, for example, nodule senescence. Thus, a balanced regulation of innate immunity is likely required throughout rhizobial infection, symbiotic establishment, and maintenance. In this review, we discuss the significance of plant immune responses in the regulation of symbiotic associations with rhizobia, as well as rhizobial evasion of the host immune system.

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Physiological responses and gene co-expression network of mycorrhizal roots under K+ deprivation

Physiological responses and gene co-expression network of mycorrhizal roots under K+ deprivation | Plant-Microbe Symbiosis | Scoop.it
Arbuscular mycorrhizal (AM) associations enhance the phosphorous and nitrogen nutrition of host plants, but little is known about their role in potassium (K+) nutrition. Medicago truncatula plants were co-cultured with the AM fungus Rhizophagus irregularis under high and low K+ regimes for six weeks. We determined how K+ deprivation affects plant development, mineral acquisition, and how these negative effects are tempered by the AM colonization. The transcriptional response of AM roots under K+ deficiency was analyzed by whole genome RNA-seq. K+ deprivation decreased root biomass, external K+ uptake, and modulated oxidative stress gene expression in M. truncatula roots. AM colonization induced specific transcriptional responses to K+ deprivation that seem to temper these negative effects. A gene network analysis revealed putative key regulators of these responses. This study confirmed that AM associations provide some tolerance to K+ deprivation to host plants, revealed that AM symbiosis modulates the expression of specific root genes to cope with this nutrient stress, and identified putative regulators participating in these tolerance mechanisms.
 

Via Kevin Garcia
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Here is the latest paper from our lab!

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Arbuscular mycorrhizal fungi inoculation mediated changes in rhizosphere bacterial community structure while promoting revegetation in a semiarid ecosystem

Arbuscular mycorrhizal fungi inoculation mediated changes in rhizosphere bacterial community structure while promoting revegetation in a semiarid ecosystem | Plant-Microbe Symbiosis | Scoop.it
The main goal of this study was to assess the effect of the inoculation of four autochthonous shrub species with the arbuscular mycorrhizal (AM) fungus Rhizophagus intraradices on the rhizosphere bacterial community and to ascertain whether such an effect is dependent on the host plant species. Additionally, analysis of rhizosphere soil chemical and biochemical properties was performed to find relationships between them and the rhizosphere bacterial communities. Non-metric multidimensional scaling analysis and subsequent permutational multivariate analysis of variance revealed differences in bacterial community composition and structure between non-inoculated and inoculated rhizospheres. Moreover, an influence of the plant species was observed. Different bacterial groups were found to be indicator taxonomic groups of non-inoculated and inoculated rhizospheres, Gemmatimonadetes and Anaerolineaceae, respectively, being the most notable indicators. As shown by distance based redundancy analysis, the shifts in bacterial community composition and structure mediated by the inoculation with the AM fungus were mainly related to changes in plant nutrients and growth parameters, such as the shoot phosphorus content. Our findings suggest that the AM fungal inoculum was able to modify the rhizosphere bacterial community assemblage while improving the host plant performance.

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Influence of nutrient signals and carbon allocation on the expression of phosphate and nitrogen transporter genes in winter wheat (Triticum aestivum L.) roots colonized by arbuscular mycorrhizal fungi

Influence of nutrient signals and carbon allocation on the expression of phosphate and nitrogen transporter genes in winter wheat (Triticum aestivum L.) roots colonized by arbuscular mycorrhizal fungi | Plant-Microbe Symbiosis | Scoop.it
Arbuscular mycorrhizal (AM) colonization of plant roots causes the down-regulation of expression of phosphate (Pi) or nitrogen (N) transporter genes involved in direct nutrient uptake pathways. The mechanism of this effect remains unknown. In the present study, we sought to determine whether the expression of Pi or N transporter genes in roots of winter wheat colonized by AM fungus responded to (1) Pi or N nutrient signals transferred from the AM extra-radical hyphae, or (2) carbon allocation changes in the AM association. A three-compartment culture system, comprising a root compartment (RC), a root and AM hyphae compartment (RHC), and an AM hyphae compartment (HC), was used to test whether the expression of Pi or N transporter genes responded to nutrients (Pi, NH4+ and NO3-) added only to the HC. Different AM inoculation density treatments (roots were inoculated with 0, 20, 50 and 200 g AM inoculum) and light regime treatments (6 hours light and 18 hours light) were established to test the effects of carbon allocation on the expression of Pi or N transporter genes in wheat roots. The expression of two Pi transporter genes (TaPT4 and TaPHT1.2), five nitrate transporter genes (TaNRT1.1, TaNRT1.2, TaNRT2.1, TaNRT2.2, and TaNRT2.3), and an ammonium transporter gene (TaAMT1.2) was quantified using real-time polymerase chain reaction. The expression of TaPT4, TaNRT2.2, and TaAMT1.2 was down-regulated by AM colonization only when roots of host plants received Pi or N nutrient signals. However, the expression of TaPHT1.2, TaNRT2.1, and TaNRT2.3 was down-regulated by AM colonization, regardless of whether there was nutrient transfer from AM hyphae. The expression of TaNRT1.2 was also down-regulated by AM colonization even when there was no nutrient transfer from AM hyphae. The present study showed that an increase in carbon consumption by the AM fungi did not necessarily result in greater down-regulation of expression of Pi or N transporter genes.

Via Francis Martin
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Great paper. I love it.

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international Molecular Mycorrhiza Meeting 2017

iMMM2017 Research into the molecular basis of symbiosis between plant roots and fungi has achieved major breakthroughs in recent years. The international Molecular Mycorrhiza Meeting (iMMM) is a response to the perceived need for a specialized meeting series covering the molecular mechanistic aspects of mycorrhizal symbioses including yet non-categorised endophytic root fungus interactions. After the success of the two first editions in Munich (2012) and Cambridge (2015), the 3rd international Molecular Mycorrhiza Meeting will be held in Toulouse in 2017. To keep the meeting highly interactive, the participant number will be limited to 150 people.

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Teaching Computers to Recognize Unhealthy Guts

Teaching Computers to Recognize Unhealthy Guts | Plant-Microbe Symbiosis | Scoop.it
A new proof-of-concept study by researchers from the University of California San Diego has succeeded in training computers to “learn” what a healthy versus an unhealthy gut microbiome looks like based on its genetic makeup. Since this can be done by genetically sequencing fecal samples, the research suggests there is great promise for new diagnostic tools that are, unlike blood draws, non-invasive.

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Commonalities in Symbiotic Plant-Microbe Signalling

Commonalities in Symbiotic Plant-Microbe Signalling | Plant-Microbe Symbiosis | Scoop.it
Plants face the problem that they have to discriminate symbionts from a diverse pool of soil microbes, including pathogens. Studies on different symbiotic systems revealed commonalities in plant-microbe signalling. In this chapter we focus on four intimate symbiotic interactions: two mycorrhizal ones, with arbuscular- and ectomycorrhizal fungi, and two nitrogen-fixing ones, with rhizobium and Frankia bacteria. Comparing these systems uncovered commonalities in the way plants attract their symbiotic partners. Especially flavonoids, and in a lesser extent strigolactones, are pivotal plant signals that are perceived by the microsymbiont. In response, signal molecules are exuded by the microbes to trigger symbiotic responses in their host plant. Strikingly, microbes that establish an endosymbiotic relation with their host plant, namely arbuscular mycorrhizal fungi, rhizobium and Frankia bacteria, make use of a symbiotic signalling network that is highly conserved in plants. The use of flavonoids as attractants for symbiotic microbes, in combination with the use of a common plant signalling network to establish endosymbioses, raises questions about how plants manage to discriminate their microbial partners.

Via Jonathan Plett
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Excellent review.

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The receptor kinase FER is a RALF-regulated scaffold controlling plant immune signaling

The receptor kinase FER is a RALF-regulated scaffold controlling plant immune signaling | Plant-Microbe Symbiosis | Scoop.it
“ RALFs (rapid alkalinization factors), a family of small peptides in plants, are produced in response to rapidly changing conditions. Stegmann et al. studied the agility and diversity built into this signaling network. Some RALFs, such as RALF23 and its relative RALF33, are activated by proteolytic cleavage. Others, such as RALF32, are not. RALF23 and RALF33 are called into play after a pathogen triggers immune responses. RALF32, on the other hand, regulates seedling growth. All three of these RALFs use the same receptor kinase, which can interact with other signaling components. Thus, plant responses can be fine-tuned by rapid release of peptides. Science , this issue p. [287][1] [1]: /lookup/doi/10.1126/science.aal2541”
Via Tatsuya Nobori, Xiefang lab, Jennifer Mach
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Prospects for Biological Soilborne Disease Control: Application of Indigenous Versus Synthetic Microbiomes | Phytopathology

Prospects for Biological Soilborne Disease Control: Application of Indigenous Versus Synthetic Microbiomes | Phytopathology | Plant-Microbe Symbiosis | Scoop.it
Biological disease control of soilborne plant diseases has traditionally employed the biopesticide approach whereby single strains or strain mixtures are introduced into production systems through inundative/inoculative release. The approach has significant barriers that have long been recognized, including a generally limited spectrum of target pathogens for any given biocontrol agent and inadequate colonization of the host rhizosphere, which can plague progress in the utilization of this resource in commercial field-based crop production systems. Thus, although potential exists, this model has continued to lag in its application. New omics’ tools have enabled more rapid screening of microbial populations allowing for the identification of strains with multiple functional attributes that may contribute to pathogen suppression. Similarly, these technologies also enable the characterization of consortia in natural systems which provide the framework for construction of synthetic microbiomes for disease control. Harnessing the potential of the microbiome indigenous to agricultural soils for disease suppression through application of specific management strategies has long been a goal of plant pathologists. Although this tactic also possesses limitation, our enhanced understanding of functional attributes of suppressive soil systems through application of community and metagenomic analysis methods provide opportunity to devise effective resource management schemes. As these microbial communities in large part are fostered by the resources endemic to soil and the rhizosphere, substrate mediated recruitment of disease-suppressive microbiomes constitutes a practical means to foster their establishment in crop production systems.

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Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments

Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments | Plant-Microbe Symbiosis | Scoop.it

The microbiomes of rhizocompartments (nodule endophytes, root endophytes, rhizosphere and root zone) in soybean and alfalfa were analyzed using high-throughput sequencing to investigate the interactions among legume species, microorganisms and soil types. A clear hierarchical filtration of microbiota by plants was observed in the four rhizocompartments—the nodule endosphere, root endosphere, rhizosphere and root zone—as demonstrated by significant variations in the composition of the microbial community in the different compartments. The rhizosphere and root zone microbial communities were largely influenced by soil type, and the nodule and root endophytes were primarily determined by plant species. Diverse microbes inhabited the root nodule endosphere, and the corresponding dominant symbiotic rhizobia belonged to Ensifer for alfalfa and Ensifer-Bradyrhizobium for soybean. The non-symbiotic nodule endophytes were mainly Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The variation in root microbial communities was also affected by the plant growth stage. In summary, this study demonstrated that the enrichment process of nodule endophytes follows a hierarchical filtration and that the bacterial communities in nodule endophytes vary according to the plant species.The microbiomes of rhizocompartments (nodule endophytes, root endophytes, rhizosphere and root zone) in soybean and alfalfa were analyzed using high‐throughput sequencing to investigate th


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NSF awards $3 million for plant and animal microbiome and phenomics research | NSF - National Science Foundation

NSF awards $3 million for plant and animal microbiome and phenomics research | NSF - National Science Foundation | Plant-Microbe Symbiosis | Scoop.it
NSF's mission is to advance the progress of science, a mission accomplished by funding proposals for research and education made by scientists, engineers, and educators from across the country.
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Fritz Haber

Fritz Haber | Plant-Microbe Symbiosis | Scoop.it
Fritz Haber (1868-1934), the German scientist who won the Nobel Prize for Chemistry in 1918, is best known as the father of chemical warfare. He won the prize not for that but for the Haber-Bosch process, which allows fertilizer to be made by fixing nitrogen from the air: "bread from air". Two out of five…
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Handelsman Brings Expansive Vision to WID’s Future | Wisconsin Institute for Discovery

Handelsman Brings Expansive Vision to WID’s Future | Wisconsin Institute for Discovery | Plant-Microbe Symbiosis | Scoop.it
Jo Handelsman began her tenure as Director of the Wisconsin Institute for Discovery on February 1. Shortly before her start date, we sat down with her to talk about the future of WID and the course she intends to set.

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Phylogenomic analysis of gene co‐expression networks reveals the evolution of functional modules

Phylogenomic analysis of gene co‐expression networks reveals the evolution of functional modules | Plant-Microbe Symbiosis | Scoop.it

Molecular evolutionary studies correlate genomic and phylogenetic information with the emergence of new traits of organisms. These traits are, however, the consequence of dynamic gene networks composed of functional modules, which might not be captured by genomic analyses. Here, we established a method, which combines large-scale genomic and phylogenetic data with gene co-expression networks, to extensively study the evolutionary make-up of modules in the moss Physcomitrella patens and in the angiosperms Arabidopsis thaliana and rice. We first show that younger genes are less annotated than older genes. By mapping genomic data onto the co-expression networks, we found that genes from the same evolutionary period tend to be connected, while old and young genes tend to be disconnected. Consequently, the analysis revealed modules that emerged at a specific time in plant evolution. To uncover the evolutionary relationships of the modules that are conserved across the plant kingdom, we added phylogenetic information which revealed duplication and speciation events on the module level. This combined analysis revealed an independent duplication of cell wall modules in bryophytes and angiosperms, suggesting a parallel evolution of cell wall pathways in land plants. We provide an online tool allowing plant researchers to perform these analyses at www.gene2function.de.


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Nitrogen: At the Nexus Between Food Security and Sustainability - A Virtual Symposium - March 8th and 9th, 2017

Nitrogen: At the Nexus Between Food Security and Sustainability - A Virtual Symposium - March 8th and 9th, 2017 | Plant-Microbe Symbiosis | Scoop.it

A Virtual Symposium
March 8th and 9th, 2017
FREE REGISTRATION!

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Free event and great speakers!

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