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

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

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

 

 

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

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

 

DOI: 10.1111/j.1469-8137.2012.04283.x


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Plant-Microbe Symbioses
Symbiotic associations between plants and microbes
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Plants That Practice Genetic Engineering

Plants That Practice Genetic Engineering | Plant-Microbe Symbioses | Scoop.it
Long ago, a new paper suggests, a fern took a useful gene from a neighboring hornwort, an acquisition that allowed ferns to thrive in shade.
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Not on microbial symbioses but... pretty cool anyway.

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How to say: "NODULATION" in English

This video teaches you how to say "NODULATION" in English.
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Just in case you never tried to say it before :-)

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Christophe Jacquet's comment, Today, 5:54 AM
C'est gentil de t'occuper de notre accent, y en a besoin, c'est sûr!;-)
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Feeding 9 Billion - National Geographic

Feeding 9 Billion - National Geographic | Plant-Microbe Symbioses | Scoop.it
When we think about threats to the environment, we tend to picture cars and smokestacks, not dinner. But the truth is, our need for food poses one of the biggest dangers to the planet.
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Beautiful images to illustrate what is, in my opinion, one of the most important challenge that our World is facing. How will we be able to feed 9 billion people by 2050 in a sustainable manner without damaging our planet irreversibly?

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The 8th International Symbiosis Congress will convene at the University of Lisbon, in Portugal

The 8th International Symbiosis Congress will convene at the University of Lisbon, in Portugal | Plant-Microbe Symbioses | Scoop.it

The University of Lisbon (ULisboa; http://www.ulisboa.pt/) was created in 2013 based on the union of university institutions, which date back to the 13th century. We hope that this symbiosis between new and old will create the perfect environment to host the Symbiosis Congress in 2015. We welcome all researchers, educators, and students who work in the many diverse fields which involve symbioses.

Held every three years and organized by the International Symbiosis Society, the Congress is focused on a concept - symbiosis. Long viewed as an exception, a curiosity on the margins of biology, symbiosis is today considered ubiquitous and one of the main characteristics of the biological systems, which involves networking at distinct levels through molecular, physical, or physiological communication and allows evolution and adaptation. The theme and the spirit of the meeting, “Symbiotic lifestyle”, is an invitation to innovation and creativity and aims at opening horizons and creating avenues of knowledge in a multidisciplinary environment.

We hope that this meeting will be an ideal venue for discussion, exchange and transfer of knowledge, helping to create new and foster existing collaborations and symbioses between researchers.

We hope you enjoy it,

 

The organizing committee:

Silvana Munzi (Faculdade de Ciências da Universidade de Lisboa)

Cristina Cruz (Faculdade de Ciências da Universidade de Lisboa)

Rusty Rodriguez (Adaptive Symbiotic Technologies)


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The new symbiont on the block?

The new symbiont on the block? | Plant-Microbe Symbioses | Scoop.it

When you step back and look at the field of symbiosis research (see Mary Beth Saffo’s recent blog post for the ISS), one can see that the rapid growth and appreciation of our field is staggering. Perhaps we do not rival other research fields with respect to number of scientists per unit effort, but scientists and non-scientists alike are finally beginning to comprehend the true magnitude and importance of microbial symbiosis.  A Grand Challenge Article (GCA) for the recently established journal Frontiers in Microbial Symbiosis highlighted how we are increasingly seeing the terms ‘holobiont’, ‘metaorganism’ and ‘microbiome’ used by researchers from a range of scientific disciplines. However, despite this recent progress in appreciating the importance and ubiquity of microbial symbioses, many scientists still tend to view symbiotic partners as separate individuals, thereby limiting our ability to assess interactive mechanisms (including synergism and pathogenesis) within these systems.  As researchers we desperately need to overcome this perception of individualism to truly understand the ecology and evolution of microbial symbioses.  And whilst Mary Beth highlighted the need for clarity and consistency regarding the definition of “symbiosis,” it is equally important to recognize that the concept of symbiosis needs to remain fluid. The subcategories of “symbiosis” (pathogenic, mutualistic and commensal) are ultimately just idealized interaction states; whereas the actualized state may wander across these defined boundaries depending on evolutionary processes, changes in environmental conditions and/or health state of the host/symbiont. For example, the cnidarian-algal mutualism, a partnership where most of the symbiont transmission is horizontal (and should therefore theoretically favour parasitism) highlights the complexity of symbiotic interactions. A study by Sachs and Wilcox (2006) used sequential horizontal transmission to demonstrate that after only a few forced horizontal transmissions, the Cassiopea–Symbiodinium partnership began to display parasitic rather than mutualistic characteristics.

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Genomic analysis of cyclic-di-GMP-related genes in rhizobial type strains and functional analysis in Rhizobium etli

Genomic analysis of cyclic-di-GMP-related genes in rhizobial type strains and functional analysis in Rhizobium etli | Plant-Microbe Symbioses | Scoop.it

teria that can fix nitrogen in symbiosis with leguminous plants or exist free living in the rhizosphere. Crucial to their complex lifestyle is the ability to sense and respond to diverse environmental stimuli, requiring elaborate signaling pathways. In the majority of bacteria, the nucleotide-based second messenger cyclic diguanosine monophosphate (c-di-GMP) is involved in signal transduction. Surprisingly, little is known about the importance of c-di-GMP signaling in rhizobia. We have analyzed the genome sequences of six well-studied type species (Bradyrhizobium japonicum, Mesorhizobium loti, Rhizobium etli,Rhizobium leguminosarum, Sinorhizobium fredii, and Sinorhizobium meliloti) for proteins possibly involved in c-di-GMP signaling based on the presence of four domains: GGDEF (diguanylate cyclase), EAL and HD-GYP (phosphodiesterase), and PilZ (c-di-GMP sensor). We find that rhizobia possess a high number of these proteins. Conservation analysis suggests that c-di-GMP signaling proteins modulate species-specific pathways rather than ancient rhizobia-specific processes. Two hybrid GGDEF-EAL proteins were selected for functional analysis, R. etli RHE_PD00105 (CdgA) and RHE_PD00137 (CdgB). Expression of cdgA and cdgBis repressed by the alarmone (p)ppGpp. cdgB is significantly expressed on plant roots and free living. Mutation of cdgA, cdgB, or both does not affect plant root colonization, nitrogen fixation capacity, biofilm formation, motility, and exopolysaccharide production. However, heterologous expression of the individual GGDEF and EAL domains of each protein in Escherichia coli strongly suggests that CdgA and CdgB are bifunctional proteins, possessing both diguanylate cyclase and phosphodiesterase activities. Taken together, our results provide a platform for future studies of c-di-GMP signaling in rhizobia.

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EMBO has become a sponsor of the 11th European Nitrogen Fixation Conference.

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Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR

ween rhizobial microbes and host plants involves the coordinated expression of multiple genes, which leads to nodule formation and nitrogen fixation. As part of the transcriptional machinery for nodulation and symbiosis across a range of Rhizobium, NolR serves as a global regulatory protein. Here, we present the X-ray crystal structures of NolR in the unliganded form and complexed with two different 22-base pair (bp) double-stranded operator sequences (oligos AT and AA). Structural and biochemical analysis of NolR reveals protein–DNA interactions with an asymmetric operator site and defines a mechanism for conformational switching of a key residue (Gln56) to accommodate variation in target DNA sequences from diverse rhizobial genes for nodulation and symbiosis. This conformational switching alters the energetic contributions to DNA binding without changes in affinity for the target sequence. Two possible models for the role of NolR in the regulation of different nodulation and symbiosis genes are proposed. To our knowledge, these studies provide the first structural insight on the regulation of genes involved in the agriculturally and ecologically important symbiosis of microbes and plants that leads to nodule formation and nitrogen fixation.

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Postdoctoral Researcher Position at the University of Wisconsin - Madison

Job Description

A postdoctoral position is available in the department of Agronomy at the University of Wisconsin – Madison.  The postdoctoral researcher will study and engineer interactions between cereals and nitrogen-fixing bacteria. He/she will use a wide range of genomic, molecular and cellular and phylogenetic techniques to study and manipulate these associations. The postdoctoral researcher will be involved in interdisciplinary collaborations nationally and internationally. This is a two-year position (with possible extension) starting on September 1, 2014. This is a full-time position.

 

Job Requirements

A Ph.D. in Plant Molecular and Cellular Biology, Molecular Microbiology, Plant Pathology, or related fields is required. An experienced postdoctoral scientist is needed to study interactions between nitrogen-fixing bacteria and cereals.  The successful candidate will have co-authored one or more peer-reviewed publications in reputable international journals in plant-microbe interactions, and will be familiar with plant molecular and cellular biology as well as microbial genetics. Candidates with prior experience in maize are especially encouraged to apply. Excellent oral and written communication skills in English, and the ability to work well in a collaborative environment are essential.

 

How to Apply: Please send a cover letter, a CV and at least 3 references by email to Jean-Michel Ané (jane@wisc.edu).

 

Application deadline: Applications will be accepted until a suitable candidate is identified.

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Phenotypic characterization of Astragalus glycyphyllos symbionts and their phylogeny based on the 16S rDNA sequences and RFLP of 16S rRNA gene

Phenotypic characterization of Astragalus glycyphyllos symbionts and their phylogeny based on the 16S rDNA sequences and RFLP of 16S rRNA gene | Plant-Microbe Symbioses | Scoop.it

In this study, the nitrogen fixing Astragalus glycyphyllos symbionts were characterized by phenotypic properties, restriction fragment length polymorphism (RFLP), and sequences of 16S rDNA. The generation time of A. glycyphyllos rhizobia in yeast extract mannitol medium was in the range 4–6 h. The studied isolates exhibited a low resistance to antibiotics, a moderate tolerance to NaCl, assimilated di- and trisaccharides, and produced acid in medium containing mannitol as a sole carbon source. In the cluster analysis, based on 86 phenotypic properties of A. glycyphyllossymbionts and the reference rhizobia, examined isolates and the genus Mesorhizobium strains were placed on a single branch, clearly distinct from other lineages of rhizobial genera. By the comparative analysis of 16S rRNA gene sequences and 16S rDNA–RFLP, A. glycyphyllosnodulators were also identified as the members of the genus Mesorhizobium. On the 16S rDNA sequence phylogram, the representatives of A. glycyphyllos nodule isolates formed a robust, monophyletic cluster together with the Mesorhizobium species at 16S rDNA sequence similarity of these bacteria between 95 and 99 %. Similarly, the cluster analysis of the combined RFLP–16S rDNA patterns, obtained with seven restriction endonucleases, showed that A. glycyphyllos rhizobia are closely related to the genus Mesorhizobium bacteria. The taxonomic approaches used in this paper allowed us to classify the studied bacteria into the genus Mesorhizobium.

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Phosphate concentration alters the effective bacterial quorum in the symbiosis of Medicago truncatula-Sinorhizobium meliloti

The symbiosis of Medicago truncatula-Sinorhizobium meliloti is affected by phosphate (P) deficiency in the environment. Quorum sensing (QS) is a regulatory pathway in S. meliloti that controls various functions of free-living and symbiotic bacteria in response to phosphate availability and regulation is mediated by a periplasmic protein PstS, and also bacterial density. The quorum sensing pathway ofS. meliloti, involves three genes named sinI, sinR and expR and also some bacterial auto-inducers such as N-acyl homoserine lactones (AHLs). In the current study, the expression of the different genes of quorum sensing and pstS were evaluated under 0.1, 0.5 and 2 mM P. The qRT-PCR results showed an increased expression of pstS and also the quorum sensing genes sinI and sinR but notexpR, following phosphate starvation. Indeed, the enhanced level of sinR induces the expression ofsinI that is responsible for the N-acyl homoserine lactones (AHL) production in S. meliloti. The different response of expR may be due to its negative control on sinR expression. In the symbiosis ofM. truncatula-S. meliloti, it was shown that the concentration of phosphate in the medium alters the effective inoculating bacterial quorum (density). By increasing the phosphate concentration in the medium from 0.1 to 0.5 and 2 mM, considering the optimal plant growth and pink nodule (nitrogen-fixing) formation, the effective inoculating bacterial densities were 105, 107 and 109 CFU ml−1, respectively. Therefore, low phosphate concentrations can compensate for a low bacterial density by inducing the quorum sensing pathway and establishing a symbiosis. Conversely, bacterial density plays the main role in the formation of symbiosis at high phosphate concentrations.

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Soybean Ureases, but Not That of Bradyrhizobium japonicum, Are Involved in the Process of Soybean Root Nodulation.

Ureases are abundant in plants, bacteria, and in the soil, but their role in signaling between soybean and soil microorganisms has not been investigated. The bacterium Bradyrhizobium japonicum forms nitrogen-fixing nodules on soybean roots. Here, we evaluated the role(s) of ureases in the process of soybean nodulation. Chemotaxis assays demonstrated that soybean and jack bean ureases were more chemotactic toward bacterial cells than the corresponding plant lectins. The eu1-a,eu4 soybean, deficient in urease isoforms, formed fewer but larger nodules than the wild-type, regardless of the bacterial urease phenotype. Leghemoglobin production in wild-type plants was higher and peaked earlier than in urease-deficient plants. Inhibition of urease activity in wild-type plants did not result in the alterations seen in mutated plants. We conclude that soybean urease(s) play(s) a role in the soybean-B. japonicum symbiosis, which is independent of its ureolytic activity. Bacterial urease does not play a role in nodulation.
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Botany: Special issue: The microbiota of plants

In this Special Issue, we have tried to capture the diversity of plant–microbe research that is on-going, and that might not normally be marketed under the banner of “plant microbiome research”. Nevertheless, it belongs under this banner and we highlight some of this research here, including a variety of plant “habitats” such as roots, leaves, and floral parts, as well as a variety of microbes, from bacteria and arbuscular mycorrhizal fungi to dark septate fungi. Of course, the field is broader than what we are able present in a single issue, but we hope that it inspires researchers of overlooked aspects of plant microbiota research to get in on the game, and contribute to a more complete picture of this complex “ecosystem”.


Via Stéphane Hacquard
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Mycorrhizal Associations: Introduction

Mycorrhizal Associations: Introduction | Plant-Microbe Symbioses | Scoop.it

This site was developed as an online textbook to provide current information about mycorrhizal associations. Information about this site, instructions, acknowledgements and site history information is provided in Section 13.

 
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One of the best websites dedicated to mycorrhizal associations.

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A Synthetic Community Approach Reveals Plant Genotypes Affecting the Phyllosphere Microbiota

A Synthetic Community Approach Reveals Plant Genotypes Affecting the Phyllosphere Microbiota | Plant-Microbe Symbioses | Scoop.it

The identity of plant host genetic factors controlling the composition of the plant microbiota and the extent to which plant genes affect associated microbial populations is currently unknown. Here, we use a candidate gene approach to investigate host effects on the phyllosphere community composition and abundance. To reduce the environmental factors that might mask genetic factors, the model plant Arabidopsis thaliana was used in a gnotobiotic system and inoculated with a reduced complexity synthetic bacterial community composed of seven strains representing the most abundant phyla in the phyllosphere. From a panel of 55 plant mutants with alterations in the surface structure, cell wall, defense signaling, secondary metabolism, and pathogen recognition, a small number of single host mutations displayed an altered microbiota composition and/or abundance. Host alleles that resulted in the strongest perturbation of the microbiota relative to the wild-type were lacs2 and pec1. These mutants affect cuticle formation and led to changes in community composition and an increased bacterial abundance relative to the wild-type plants, suggesting that different bacteria can benefit from a modified cuticle to different extents. Moreover, we identified ein2, which is involved in ethylene signaling, as a host factor modulating the community's composition. Finally, we found that different Arabidopsis accessions exhibited different communities, indicating that plant host genetic factors shape the associated microbiota, thus harboring significant potential for the identification of novel plant factors affecting the microbiota of the communities.


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Amplicon –Based Metagenomic Analysis of Mixed Fungal Samples Using Proton Release Amplicon Sequencing

Amplicon –Based Metagenomic Analysis of Mixed Fungal Samples Using Proton Release Amplicon Sequencing | Plant-Microbe Symbioses | Scoop.it
Next generation sequencing technology has revolutionised microbiology by allowing concurrent analysis of whole microbial communities. Here we developed and verified similar methods for the analysis of fungal communities using a proton release sequencing platform with the ability to sequence reads of up to 400 bp in length at significant depth. This read length permits the sequencing of amplicons from commonly used fungal identification regions and thereby taxonomic classification. Using the 400 bp sequencing capability, we have sequenced amplicons from the ITS1, ITS2 and LSU fungal regions to a depth of approximately 700,000 raw reads per sample. Representative operational taxonomic units (OTUs) were chosen by the USEARCH algorithm, and identified taxonomically through nucleotide blast (BLASTn). Combination of this sequencing technology with the bioinformatics pipeline allowed species recognition in two controlled fungal spore populations containing members of known identity and concentration. Each species included within the two controlled populations was found to correspond to a representative OTU, and these OTUs were found to be highly accurate representations of true biological sequences. However, the absolute number of reads attributed to each OTU differed among species. The majority of species were represented by an OTU derived from all three genomic regions although in some cases, species were only represented in two of the regions due to the absence of conserved primer binding sites or due to sequence composition. It is apparent from our data that proton release sequencing technologies can deliver a qualitative assessment of the fungal members comprising a sample. The fact that some fungi cannot be amplified by specific “conserved” primer pairs confirms our recommendation that a multi-region approach be taken for other amplicon-based metagenomic studies.
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Håvard Kauserud's curator insight, April 17, 3:24 AM

Should not refer to this as metagenomics..

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Bienvenue au Café des Spores - restaurant - Spécialité champignons et vins - Bruxelles - Saint-Gilles

Bienvenue au Café des Spores - restaurant - Spécialité champignons et vins - Bruxelles - Saint-Gilles | Plant-Microbe Symbioses | Scoop.it
Le Café des Spores - Restaurant spécialité champignons et vins nature à Bruxelles! Venez-nous rendre visite!!!
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A good one in French for my mycologist friends... the "Spore Coffee"... a restaurant in Belgium entirely around the theme of wine and fungi. 

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First International Workshop on Plant Synthetic Biology | May 17-18, 2014 at MIT Stata Center, Cambridge, MA USA

The First International Workshop on Plant Synthetic Biology aims to advance the harnessing of plant proficiencies for use in agriculture, as an energy source, and in any way that benefits the planet. Members of the synthetic biology community will join together with plant researchers in academia and industry, as well as representatives of funding agencies, to share current capabilities and identify pressing needs. The goal is to generate new research ventures, including the development of synthetic biology tools, methodologies, and safeguards specific to plants.

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Genet dynamics and ecological functions of the pioneer ectomycorrhizal fungi Laccaria amethystina and Laccaria laccata in a volcanic desert on Mount Fuji

Genet dynamics and ecological functions of the pioneer ectomycorrhizal fungi Laccaria amethystina and Laccaria laccata in a volcanic desert on Mount Fuji | Plant-Microbe Symbioses | Scoop.it

To understand the reproduction of the pioneer ectomycorrhizal fungi Laccaria amethystina andLaccaria laccata in a volcanic desert on Mount Fuji, Japan, the in situ genet dynamics of sporocarps were analysed. Sporocarps of the two Laccaria species were sampled at fine and large scales for 3 and 2 consecutive years, respectively, and were genotyped using microsatellite markers. In the fine-scale analysis, we found many small genets, the majority of which appeared and disappeared annually. The high densities and annual renewal of Laccaria genets indicate frequent turnover by sexual reproduction via spores. In the large-scale analysis, we found positive spatial autocorrelations in the shortest distance class. An allele-clustering analysis also showed that several alleles were distributed in only a small, localised region. These results indicate that Laccaria spores contributing to sexual reproduction may be dispersed only short distances from sporocarps that would have themselves been established via rare, long-distance spore dispersal. This combination of rare, long-distance and frequent, short-distance Laccaria spore dispersal is reflected in the establishment pattern of seeds of their host, Salix reinii.

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Impact of mycorrhization on the abundance, growth and leaf nutrient status of ferns along a tropical elevational gradient

Impact of mycorrhization on the abundance, growth and leaf nutrient status of ferns along a tropical elevational gradient | Plant-Microbe Symbioses | Scoop.it

Mycorrhizal fungi are crucial for the ecological success of land plants, providing their hosts with nutrients in exchange for organic C. However, not all plants are mycorrhizal, especially ferns, of which about one-third of the species lack this symbiosis. Because the mycorrhizal status is evolutionarily ancestral, this lack of mycorrhizae must have ecological advantages, but what these advantages are and how they affect the competitive ability of non-mycorrhizal plants under natural conditions is currently unknown. To address this uncertainty, we studied terrestrial fern assemblages and species abundances as well as their mycorrhization status, leaf nutrient concentration and relative annual growth along an elevational gradient in the Ecuadorian Andes (500–4,000 m). We surveyed the mycorrhizal status of 375 root samples belonging to 85 species, and found mycorrhizae in 89 % of the samples. The degree of mycorrhization decreased with elevation but was unrelated to soil nutrients. Species with mycorrhizae were significantly more abundant than non-mycorrhizal species, but non-mycorrhizal species had significantly higher relative growth and concentrations of leaf N, P, Mg, and Ca. Our study thus shows that despite lower abundances, non-mycorrhizal fern species did not appear to be limited in their growth or nutrient supply relative to mycorrhizal ones. As a basis for future studies, we hypothesize that non-mycorrhizal fern species may be favoured in special microhabitats of the forest understory with high soil nutrient or water availability, or that the ecological benefit of mycorrhizae is not related to nutrient uptake but rather to, for example, pathogen resistance.

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Interesting

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Ectomycorrhizal Cortinarius species participate in enzymatic oxidation of humus in northern forest ecosystems

Ectomycorrhizal Cortinarius species participate in enzymatic oxidation of humus in northern forest ecosystems | Plant-Microbe Symbioses | Scoop.it

In northern forests, belowground sequestration of nitrogen (N) in complex organic pools restricts nutrient availability to plants. Oxidative extracellular enzymes produced by ectomycorrhizal fungi may aid plant N acquisition by providing access to N in macromolecular complexes. We test the hypotheses that ectomycorrhizal Cortinarius species produce Mn-dependent peroxidases, and that the activity of these enzymes declines at elevated concentrations of inorganic N.In a boreal pine forest and a sub-arctic birch forest, Cortinarius DNA was assessed by 454-sequencing of ITS amplicons and related to Mn-peroxidase activity in humus samples with- and without previous N amendment. Transcription of Cortinarius Mn-peroxidase genes was investigated in field samples. Phylogenetic analyses of Cortinarius peroxidase amplicons and genome sequences were performed.We found a significant co-localization of high peroxidase activity and DNA from Cortinarius species. Peroxidase activity was reduced by high ammonium concentrations. Amplification of mRNA sequences indicated transcription of Cortinarius Mn-peroxidase genes under field conditions. The Cortinarius glaucopus genome encodes 11 peroxidases – a number comparable to many white-rot wood decomposers.These results support the hypothesis that some ectomycorrhizal fungi – Cortinarius species in particular – may play an important role in decomposition of complex organic matter, linked to their mobilization of organically bound N.


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Microbial Growth and Carbon Use Efficiency in the Rhizosphere and Root-Free Soil

Microbial Growth and Carbon Use Efficiency in the Rhizosphere and Root-Free Soil | Plant-Microbe Symbioses | Scoop.it

Plant-microbial interactions alter C and N balance in the rhizosphere and affect the microbial carbon use efficiency (CUE)–the fundamental characteristic of microbial metabolism. Estimation of CUE in microbial hotspots with high dynamics of activity and changes of microbial physiological state from dormancy to activity is a challenge in soil microbiology. We analyzed respiratory activity, microbial DNA content and CUE by manipulation the C and nutrients availability in the soil under Beta vulgaris. All measurements were done in root-free and rhizosphere soil under steady-state conditions and during microbial growth induced by addition of glucose. Microorganisms in the rhizosphere and root-free soil differed in their CUE dynamics due to varying time delays between respiration burst and DNA increase. Constant CUE in an exponentially-growing microbial community in rhizosphere demonstrated the balanced growth. In contrast, the CUE in the root-free soil increased more than three times at the end of exponential growth and was 1.5 times higher than in the rhizosphere. Plants alter the dynamics of microbial CUE by balancing the catabolic and anabolic processes, which were decoupled in the root-free soil. The effects of N and C availability on CUE in rhizosphere and root-free soil are discussed.


Via Stéphane Hacquard
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Genome-wide Comparative Analysis of the GRAS Gene Family in Populus, Arabidopsis and Rice

GRAS genes belong to a gene family of transcription regulators that function in the regulation of plant growth and development. Our knowledge about the expansion and diversification of this gene family in flowering plants is presently limited to the herbaceous species Arabidopsis and rice. Numerous aspects, including the phylogenetic history, expansion, functional divergence and adaptive evolution await further study, especially in woody tree species. Based on the latest genome assemblies, we found 106, 34 and 60 putative GRAS genes in Populus, Arabidopsis and rice, respectively. Phylogenetic analysis revealed that GRAS proteins could be divided into at least 13 subfamilies. Tandem and segmental duplications are the most common expansion mechanisms of this gene family, and their frequent joint action may explain the rapid expansion in Populus. Site-specific shifts in evolutionary rates might be the main force driving subfamily-specific functional diversification. Adaptive evolution analysis revealed that GRAS genes have evolved mainly under purifying selection after duplication, suggesting that strong functional constraints have a bearing on the evolution of GRAS genes. Both expressed sequence tags (EST) and microarray data revealed that GRAS genes in Populus have broad expression patterns across a variety of organs/tissues. Expression divergence analyses between paralogous pairs of GRAS genes suggested that the retention of GRAS genes after duplication could be mainly attributed to substantial functional novelty such as neo-functionalization or sub-functionalization. Our study highlights the expansion and diversification of the GRAS gene family in Populus and provides the first comprehensive analysis of this gene family in the Populus genome.

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Current developments in arbuscular mycorrhizal fungi research and its role in salinity stress alleviation: a biotechnological perspective

Arbuscular mycorrhizal fungi (AMF) form widespread symbiotic associations with 80% of known land plants. They play a major role in plant nutrition, growth, water absorption, nutrient cycling and protection from pathogens, and as a result, contribute to ecosystem processes. Salinity stress conditions undoubtedly limit plant productivity and, therefore, the role of AMF as a biological tool for improving plant salt stress tolerance, is gaining economic importance worldwide. However, this approach requires a better understanding of how plants and AMF intimately interact with each other in saline environments and how this interaction leads to physiological changes in plants. This knowledge is important to develop sustainable strategies for successful utilization of AMF to improve plant health under a variety of stress conditions. Recent advances in the field of molecular biology, “omics” technology and advanced microscopy can provide new insight about these mechanisms of interaction between AMF and plants, as well as other microbes. This review mainly discusses the effect of salinity on AMF and plants, and role of AMF in alleviation of salinity stress including insight on methods for AMF identification. The focus remains on latest advancements in mycorrhizal research that can potentially offer an integrative understanding of the role of AMF in salinity tolerance and sustainable crop production.


Read More: http://informahealthcare.com/doi/abs/10.3109/07388551.2014.899964

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Scooped by Jean-Michel Ané
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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) indaphne. 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 daphnemutation 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.

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