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Frontiers in Plant Proteomics: Leveraging Proteomics to Understand Plant–Microbe Interactions (2012)

Frontiers in Plant Proteomics: Leveraging Proteomics to Understand Plant–Microbe Interactions (2012) | Plant-Microbe Symbioses | Scoop.it

Understanding the interactions of plants with beneficial and pathogenic microbes is a promising avenue to improve crop productivity and agriculture sustainability. Proteomic techniques provide a unique angle to describe these intricate interactions and test hypotheses. The various approaches for proteomic analysis generally include protein/peptide separation and identification, but can also provide quantification and the characterization of post-translational modifications. In this review, we discuss how these techniques have been applied to the study of plant-microbe interactions. We also present some areas where this field of study would benefit from the utilization of newly developed methods that overcome previous limitations. Finally, we reinforce the need for expanding, integrating, and curating protein databases, as well as the benefits of combining protein-level datasets with those from genetic analyses and other high-throughput large-scale approaches for a systems-level view of plant-microbe interactions.

 

Dhileepkumar Jayaraman, Kari L. Forshey, Paul A. Grimsrud and Jean-Michel Ané


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Plant-Microbe Symbioses
Symbiotic associations between plants and microbes
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Significant nonsymbiotic nitrogen fixation in Patagonian ombrotrophic bogs

Significant nonsymbiotic nitrogen fixation in Patagonian ombrotrophic bogs | Plant-Microbe Symbioses | Scoop.it
Nitrogen (N) nutrition in pristine peatlands relies on the natural input of inorganic N through atmospheric deposition or biological dinitrogen (N2) fixation. However, N2 fixation and its significance for N cycling, plant productivity, and peat buildup are mostly associated with the presence of Sphagnum mosses. Here, we report high nonsymbiotic N2-fixation rates in two pristine Patagonian bogs with diversified vegetation and natural N deposition. Nonsymbiotic N2 fixation was measured in samples from 0 to 10, 10 to 20, and 40 to 50 cm depth using the 15N2 assay as well as the acetylene reduction assay (ARA). The ARA considerably underestimated N2 fixation and can thus not be recommended for peatland studies. Based on the 15N2 assay, high nonsymbiotic N2-fixation rates of 0.3–1.4 μmol N2 g−1 day−1 were found down to 50 cm under micro-oxic conditions (2 vol.%) in samples from plots covered by Sphagnum magellanicum or by vascular cushion plants, latter characterized by dense and deep aerenchyma roots. Peat N concentrations point to greater potential of nonsymbiotic N2 fixation under cushion plants, likely because of the availability of easily decomposable organic compounds and oxic conditions in the rhizosphere. In the Sphagnum plots, high N2 fixation below 10 cm depth rather reflects the potential during dry periods or low water level when oxygen penetrates the top peat layer and triggers peat mineralization. Natural abundance of the 15N isotope of live Sphagnum (5.6 δ‰) from 0 to 10 cm points to solely N uptake from atmospheric deposition and nonsymbiotic N2 fixation. A mean 15N signature of −0.7 δ‰ of peat from the cushion plant plots indicates additional N supply from N mineralization. Our findings suggest that nonsymbiotic N2 fixation overcomes N deficiency in different vegetation communities and has great significance for N cycling and peat accumulation in pristine peatlands.
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Very interesting

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Leaf bacteria fertilize trees, researchers claim

Leaf bacteria fertilize trees, researchers claim | Plant-Microbe Symbioses | Scoop.it
One of the fastest growing trees, poplars, may rely on tiny microbes in their leaves to fuel their growth. For more than a decade, a lone researcher has been building a case for nitrogen fixation by bacteria living in poplar leaves. There have been many claims of nitrogen fixation in plants outside nodules where it was known to occur for more than a century. Newly reported experiments involving rice grown on nitrogen-poor soil and poplar cuttings put in air with heavy nitrogen should help convince the skeptics. In addition, another researcher finds evidence of nitrogen fixation in the needles of limber pine and Englemann spruce. If these bacteria prove to be widespread, they could be used to boost crop production on marginal soils.
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An Autophosphorylation Site Database for Leucine-Rich Repeat Receptor-Like Kinases in Arabidopsis thaliana

An Autophosphorylation Site Database for Leucine-Rich Repeat Receptor-Like Kinases in Arabidopsis thaliana | Plant-Microbe Symbioses | Scoop.it
Leucine-rich repeat receptor-like kinases (LRR RLKs) form a large family of plant signaling proteins consisting of an extracellular domain connected by a single-pass transmembrane sequence to a cytoplasmic kinase domain. Autophosphorylation on specific Ser and/or Thr residues in the cytoplasmic domain is often critical for the activation of several LRR RLK family members with proven functional roles in plant growth regulation, morphogenesis, disease resistance, and stress responses. While identification and functional characterization of in vivo phosphorylation sites is ultimately required for full understanding of LRR RLK biology and function, bacterial expression of recombinant LRR RLK cytoplasmic catalytic domains for identification of in vitro autophosphorylation sites provides a useful resource for further targeted identification and functional analysis of in vivo sites. In this study we employed high-throughput cloning and a variety of mass spectrometry approaches to generate an autophosphorylation site database representative of more than 30% of the approximately 223 LRR RLKs in Arabidopsis thaliana. His-tagged constructs of complete cytoplasmic domains were used to identify a total of 591 phosphorylation events across 73 LRR RLKs, with 496 sites uniquely assigned to specific Ser (268 sites) or Thr (228 sites) residues in 68 LRR RLKs. Multiple autophosphorylation sites per LRR RLK were the norm, with an average of seven sites per cytoplasmic domain, while some proteins showed more than 20 unique autophosphorylation sites. The database was used to analyze trends in the localization of phosphorylation sites across cytoplasmic kinase subdomains, and to derive a statistically significant sequence motif for phosphoSer autophosphorylation.
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That should be super useful but... where is this database??

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The reallocation of carbon in P deficient lupins affects biological nitrogen fixation

The reallocation of carbon in P deficient lupins affects biological nitrogen fixation | Plant-Microbe Symbioses | Scoop.it
It is not known how phosphate (P) deficiency affects the allocation of carbon (C) to biological nitrogen fixation (BNF) in legumes. The alteration of the respiratory and photosynthetic C costs of BNF was investigated under P deficiency. Although BNF can impose considerable sink stimulation on host respiratory and photosynthetic C, it is not known how the change in the C and energy allocation during P deficiency may affect BNF. Nodulated Lupinus luteus plants were grown in sand culture, using a modified Long Ashton nutrient solution containing no nitrogen (N) for ca. four weeks, after which one set was exposed to a P-deficient nutrient medium, while the other set continued growing on a P-sufficient nutrient medium. Phosphorus stress was measured at 20 days after onset of P-starvation. During P stress the decline in nodular P levels was associated with lower BNF and nodule growth. There was also a shift in the balance of photosynthetic and respiratory C toward a loss of C during P stress. Below-ground respiration declined under limiting P conditions. However, during this decline there was also a shift in the proportion of respiratory energy from maintenance toward growth respiration. Under P stress, there was an increased allocation of C toward root growth, thereby decreasing the amount of C available for maintenance respiration. It is therefore possible that the decline in BNF under P deficiency may be due to this change in resource allocation away from respiration associated with direct nutrient uptake, but rather toward a long term nutrient acquisition strategy of increased root growth.
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Milestones of Plant Evolution

Milestones of Plant Evolution | Plant-Microbe Symbioses | Scoop.it
Nearly all life and our human culture depend on plants. We consume plants and plant-derived material every day in large amounts as food, raw material for clothes, construction etc. However, most of us might not be aware of that plants (defined in a broad sense as oxygen-producing photosynthesizing organisms, as in this book) did so much more for us over the past 3.8 billion years. Without the great oxygenation event no complex animal life (as we know it) would have been possible on earth. Plants produced the fossil energy resources which enabled the industrial revolution and which we still depend on.
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Enzymes of importance to rhizosphere processes

Enzymes of importance to rhizosphere processes | Plant-Microbe Symbioses | Scoop.it
All processes and functions taking place in the rhizosphere are dominated by the activities of plant roots, rhizosphere microorganisms and root-microorganism interactions, and enzymes are recognized as main actors of all activities occurring in rhizosphere environments. Rhizosphere enzymes have, in general, a higher activity than those operating in bulk soil, asthe rhizosphere soil is richer in organic C substrates. Enzymes, produced and released by both roots and microorganisms concur to altering the availability of nutrients in the rhizosphere, being implied in the hydrolysis of C-substrates and organic forms of nutrients such as N, P and S.

The production and activity of rhizosphere enzymes is controlled by several factors, in turn depending on soil-plant-microorganism interactions. In general, higher activity of rhizosphere enzymes can be interpreted as a greater functional diversity of the microbial community. An interesting aspect is their in volvement in the possible removal of both inorganic and organic pollutants from the terrestrial food chain.

The lack of satisfying methodologies for measuring the location and activity of rhizosphere enzymes has often hampered a clear knowledge of their properties and functions. Sophisticated technologies, now available, will be helpful to reveal the origins, locations and activities of enzymes in rhizosphere.

The main scope of the present paper is to cover briefly general and specific concepts about rhizosphere enzymes and their role in soil processes. Examples chosen among those published recently, supporting and confirming properties, features, and functions of rhizosphere enzymes will be illustrated.
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Photosynthesis is induced in rice plants that associate with arbuscular mycorrhizal fungi and are grown under arsenate and arsenite stress

Photosynthesis is induced in rice plants that associate with arbuscular mycorrhizal fungi and are grown under arsenate and arsenite stress | Plant-Microbe Symbioses | Scoop.it
The metalloid arsenic (As) increases in agricultural soils because of anthropogenic activities and may have phytotoxic effects depending on the available concentrations. Plant performance can be improved by arbuscular mycorrhiza (AM) association under challenging conditions, such as those caused by excessive soil As levels. In this study, the influence of AM on CO2 assimilation, chlorophyll a fluorescence, SPAD-chlorophyll contents and plant growth was investigated in rice plants exposed to arsenate (AsV) or arsenite (AsIII) and inoculated or not with Rhizophagus irregularis. Under AsV and AsIII exposure, AM rice plants had greater biomass accumulation and relative chlorophyll content, increased water-use efficiency, higher carbon assimilation rate and higher stomatal conductance and transpiration rates than non-AM rice plants did. Chlorophyll a fluorescence analysis revealed significant differences in the response of AM-associated and -non-associated plants to As. Mycorrhization increased the maximum and actual quantum yields of photosystem II and the electron transport rate, maintaining higher values even under As exposure. Apart from the negative effects of AsV and AsIII on the photosynthetic rates and PSII efficiency in rice leaves, taken together, these results indicate that AM is able to sustain higher rice photosynthesis efficiency even under elevated As concentrations, especially when As is present as AsV.
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Supplementation with solutions of lipo-chitooligosacharide Nod Bj V (C18:1, MeFuc) and thuricin 17 regulates leaf arrangement, biomass, and root development of canola ( Brassica napus [L.])

Recent work has shown that plant-to-microbe signals can enhance the growth of a wide range of crops. Nevertheless, canola (Brassica napus L.), which forms neither arbuscular mycorrhizal nor nitrogen-fixing symbioses, has not been rigorously evaluated for its capacity to perceive and respond to microbe-to-plant signals. It was shown previously that the Bradyrhizobium japonicum lipo-chitooligosaccharide (LCO) and Bacillus thuringiensis bacteriocin thuricin 17 enhance the germination and growth of other crop species. To evaluate canola’s response, B. napus plants were grown in controlled environment chambers, in either peat pellets or large plant culture vessels. In the peat pellet system, plants that were irrigated with 10−6 M LCO, and grown at 30 °C, produced one more leaf than water- or signal-treated plants that were grown at 25/20 °C. The numbers of cotyledons (seed leaves) produced by thuricin 17-treated plants was greater than LCO treated plants and the control treatment. Among the plants grown in vessels, those grown with 0.2 M NaCl and 10−9 M thuricin 17 were taller than either treated or untreated plants that were grown with 10−5 M NaCl. Under 10/4 °C and 4 × 10−5 M NaCl conditions, only seeds treated with thuricin 17 produced roots. Among the plants grown in vessels at 30/30 °C, those treated with 10−11 M thuricin 17 resulted in approximately one more leaf per plant than nM. Root lengths were shortened with 10−5 M NaCl and 10−9 M thuricin 17, compared to lower salinities. At 30/30 °C, plants grown with 10−5 M NaCl and 10−9 M thuricin 17 were heavier than plants grown in nonsaline media without thuricin 17. Where LCO supplementation may stimulate a competitive form, thuricin 17 supplementation triggers a reduction in the plant’s surface area, which may reduce the plant’s vulnerability to prohibitive salinity levels.
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10-6 M LCOs... That's  very concentrated.

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Response of soil, leaf endosphere and phyllosphere bacterial communities to elevated CO 2 and soil temperature in a rice paddy

Aims
The objective of this study was to elucidate the composition of bacterial communities from the soil, and endosphere and phyllosphere of upper and lower leaves and clarify the responses to elevated CO2 and/or soil temperature.
Methods
Using 454 pyrosequencing, the 16S rRNA gene was analyzed from various bacterial communities in a rice paddy that was exposed to different atmospheric CO2 concentrations (ambient, +200 μmol.mol−1) and soil temperatures (ambient, +2 °C).
Results
The treatments of elevated temperature and elevated CO2 plus temperature exerted significant influence on the structure of bacterial communities from the lower leaf endosphere. A significant influence of elevated CO2 plus temperature on the community structure was also observed in the upper leaf phyllosphere. The richness and diversity of bacterial communities from the lower leaf phyllosphere, upper leaf endosphere, and upper leaf phyllosphere were significantly affected by elevated CO2 plus temperature. However, we did not observe any significant influence of all climate change treatments (elevated CO2, elevated temperature, and their combination) on the richness, diversity, and structure of soil bacterial communities. We also did not observe any significant effect of the single factor, elevated CO2, on the structure of the leaf endosphere and phyllosphere bacterial communities. Enterobacteriaceae and Xanthomonadaceae were the most shifted phylotypes in response to elevated temperature and elevated CO2 plus temperature.
Conclusions
Soil bacterial communities were more resistant to the tested climate change factors compare with foliar bacterial communities. Temperature was a more important factor in shaping the structure of foliar bacterial communities compared with CO2. The response of leaf-associated bacterial communities could be influenced by the leaf location (upper leaf or lower leaf) within the rice plants and by the habitats (leaf endosphere or phyllosphere).
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Fundamental shift in vitamin B12 eco-physiology of a model alga demonstrated by experimental evolution

A widespread and complex distribution of vitamin requirements exists over the entire tree of life, with many species having evolved vitamin dependence, both within and between different lineages. Vitamin availability has been proposed to drive selection for vitamin dependence, in a process that links an organism’s metabolism to the environment, but this has never been demonstrated directly. Moreover, understanding the physiological processes and evolutionary dynamics that influence metabolic demand for these important micronutrients has significant implications in terms of nutrient acquisition and, in microbial organisms, can affect community composition and metabolic exchange between coexisting species. Here we investigate the origins of vitamin dependence, using an experimental evolution approach with the vitamin B12-independent model green alga Chlamydomonas reinhardtii. In fewer than 500 generations of growth in the presence of vitamin B12, we observe the evolution of a B12-dependent clone that rapidly displaces its ancestor. Genetic characterization of this line reveals a type-II Gulliver-related transposable element integrated into the B12-independent methionine synthase gene (METE), knocking out gene function and fundamentally altering the physiology of the alga.
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Nice!

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Mycorrhiza Fungi May Mitigate Future 'Phosphate Crisis' - Oryza (blog)

Mycorrhiza Fungi May Mitigate Future 'Phosphate Crisis' - Oryza (blog) | Plant-Microbe Symbioses | Scoop.it

“For over 500 million years mycorrhiza fungi have been involved in a symbiotic relationship with plants, providing a secondary root system more extensive and efficient than plants own root system for sustainable nutrition supply.”


Via Daniel Wipf
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Truffle hunting in Provence

Truffle hunting in Provence | Plant-Microbe Symbioses | Scoop.it
Nelly Pellegrin is always accompanied by Flair when she goes truffle-hunting. The Brittany dog may be only three years old, but he is already expert at finding "black diamonds".

The dog's pointer-like behaviour directs his mistress to these underground sac fungi in her truffle garden near Cabrieres-d'Aigues in south-eastern France's Vaucluse department.

A brief and slippery ascent leads to a stand of holm oaks where the roots of the trees have been inoculated with the slow-growing truffle mycorrhiza - truffle cultivation reaches back to the early 19th century.

"Cherche les truffes," Pellegrin commands, and Flair immediately begins sniffing for the scent he has been trained to find.
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Arbuscular mycorrhizal fungal diversity associated with Eleocharis obtusa and Panicum capillare growing in an extreme petroleum hydrocarbon-polluted sedimentation basin

Arbuscular mycorrhizal fungi (AMF) have been extensively studied in natural and agricultural ecosystems, but little is known about their diversity and community structure in highly petroleum-polluted soils. In this study we described an unexpected diversity of AMF in a sedimentation basin of a former petro-chemical plant, in which petroleum hydrocarbon (PH) wastes were dumped for many decades. We used high-throughput PCR, cloning and sequencing on 18S rDNA to assess the molecular diversity of AMF associated with Eleocharis obtusa and Panicum capillare spontaneously inhabiting extremely PH-contaminated sediments. The analyses of rhizosphere and root samples over two years showed a remarkable AMF richness comparable with that found in temperate natural ecosystems. Twenty-one taxa, encompassing the major families within Glomeromycota, were detected. The most abundant OTUs belong to genera Claroideoglomus, Diversispora, Rhizophagus and Paraglomus. Both plants had very similar overall community structures and OTU abundances, however AMF community structure differed when comparing the overall OTU distribution across the two years of sampling. This could be likely explained by variations in precipitations between 2011 and 2012. Our study provides the first view of AMF molecular diversity in soils extremely polluted by PH, and demonstrated the ability of AMF to colonize and establish in harsh environments.
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MuTAnT: a family of Mutator-like transposable elements targeting TA microsatellites in Medicago truncatula

Transposable elements (TEs) are mobile DNA segments, abundant and dynamic in plant genomes. Because their mobility can be potentially deleterious to the host, a variety of mechanisms evolved limiting that negative impact, one of them being preference for a specific target insertion site. Here, we describe a family of Mutator-like DNA transposons in Medicago truncatula targeting TA microsatellites. We identified 218 copies of MuTAnTs and an element carrying a complete ORF encoding a mudrA-like transposase. Most insertion sites are flanked by a variable number of TA tandem repeats, indicating that MuTAnTs are specifically targeting TA microsatellites. Other TE families flanked by TA repeats (e.g. TAFT elements in maize) were described previously, however we identified the first putative autonomous element sharing that characteristics with a related group of short non-autonomous transposons.
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Tall fescue cultivar and fungal endophyte combinations influence plant growth and root exudate composition

Tall fescue cultivar and fungal endophyte combinations influence plant growth and root exudate composition | Plant-Microbe Symbioses | Scoop.it
Tall fescue [Lolium arundinaceum (Schreb.)] is a cool-season perennial grass used in pastures throughout the Southeastern United States. The grass can harbor a shoot-specific fungal endophyte (Epichloë coenophiala) thought to provide the plant with enhanced resistance to biotic and abiotic stresses. Because alkaloids produced by the common variety of the endophyte cause severe animal health issues, focus has been on replacing the common-toxic strain with novel varieties that do not produce the mammal-toxic alkaloids but maintain abiotic and biotic stress tolerance benefits. Little attention has been given to the influence of the plant-fungal symbiosis on rhizosphere processes. Therefore, our objective was to study the influence of this relationship on plant biomass production and root exudate composition in tall fescue cultivars PDF and 97TF1, which were either not infected with the endophyte (E-), infected with the common toxic endophyte (CTE+) strain or with one of two novel endophytes (AR542E+, AR584E+). Plants were grown sterile for 3 weeks after which plant biomass, total organic carbon, total phenolic content and detailed chemical composition of root exudates were determined. Plant biomass production and exudate phenolic and organic carbon content were influenced by endophyte status, tall fescue cultivar, and their interaction. GC-TOF MS identified 132 compounds, including lipids, carbohydrates and carboxylic acids. Cluster analysis showed that the interaction between endophyte and cultivar resulted in unique exudate profiles. This is the first detailed study to assess how endophyte infection, notably with novel endophytes, and tall fescue cultivar interact to influence root exudate composition. Our results illustrate that tall fescue cultivar and endophyte status can influence plant growth and root exudate composition, which may help explain the observed influence of this symbiosis on rhizosphere biogeochemical processes.
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Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi | Plant-Microbe Symbioses | Scoop.it
Rapid development of high-throughput (HTS) molecular identification methods has revolutionized our knowledge about taxonomic diversity and ecology of fungi. However, PCR-based methods exhibit multiple technical shortcomings that may bias our understanding of the fungal kingdom. This study was initiated to quantify potential biases in fungal community ecology by comparing the relative performance of amplicon-free shotgun metagenomics and amplicons of nine primer pairs over seven nuclear ribosomal DNA (rDNA) regions often used in metabarcoding analyses. The internal transcribed spacer (ITS) barcodes ITS1 and ITS2 provided greater taxonomic and functional resolution and richness of operational taxonomic units (OTUs) at the 97% similarity threshold compared to barcodes located within the ribosomal small subunit (SSU) and large subunit (LSU) genes. All barcode-primer pair combinations provided consistent results in ranking taxonomic richness and recovering the importance of floristic variables in driving fungal community composition in soils of Papua New Guinea. The choice of forward primer explained up to 2.0% of the variation in OTU-level analysis of the ITS1 and ITS2 barcode data sets. Across the whole data set, barcode-primer pair combination explained 37.6–38.1% of the variation, which surpassed any environmental signal. Overall, the metagenomics data set recovered a similar taxonomic overview, but resulted in much lower fungal rDNA sequencing depth, inability to infer OTUs, and high uncertainty in identification. We recommend the use of ITS2 or the whole ITS region for metabarcoding and we advocate careful choice of primer pairs in consideration of the relative proportion of fungal DNA and expected dominant groups.
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Cell Cycle Control by the Master Regulator CtrA in Sinorhizobium meliloti

Cell Cycle Control by the Master Regulator CtrA in  Sinorhizobium meliloti | Plant-Microbe Symbioses | Scoop.it
In all domains of life, proper regulation of the cell cycle is critical to coordinate genome replication, segregation and cell division. In some groups of bacteria, e.g. Alphaproteobacteria, tight regulation of the cell cycle is also necessary for the morphological and functional differentiation of cells. Sinorhizobium meliloti is an alphaproteobacterium that forms an economically and ecologically important nitrogen-fixing symbiosis with specific legume hosts. During this symbiosis S. meliloti undergoes an elaborate cellular differentiation within host root cells. The differentiation of S. meliloti results in massive amplification of the genome, cell branching and/or elongation, and loss of reproductive capacity. In Caulobacter crescentus, cellular differentiation is tightly linked to the cell cycle via the activity of the master regulator CtrA, and recent research in S. meliloti suggests that CtrA might also be key to cellular differentiation during symbiosis. However, the regulatory circuit driving cell cycle progression in S. meliloti is not well characterized in both the free-living and symbiotic state. Here, we investigated the regulation and function of CtrA in S. meliloti. We demonstrated that depletion of CtrA cause cell elongation, branching and genome amplification, similar to that observed in nitrogen-fixing bacteroids. We also showed that the cell cycle regulated proteolytic degradation of CtrA is essential in S. meliloti, suggesting a possible mechanism of CtrA depletion in differentiated bacteroids. Using a combination of ChIP-Seq and gene expression microarray analysis we found that although S. meliloti CtrA regulates similar processes as C. crescentus CtrA, it does so through different target genes. For example, our data suggest that CtrA does not control the expression of the Fts complex to control the timing of cell division during the cell cycle, but instead it negatively regulates the septum-inhibiting Min system. Our findings provide valuable insight into how highly conserved genetic networks can evolve, possibly to fit the diverse lifestyles of different bacteria.
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Root-inhabiting fungi in alien plant species in relation to invasion status and soil chemical properties

Root-inhabiting fungi in alien plant species in relation to invasion status and soil chemical properties | Plant-Microbe Symbioses | Scoop.it
In order to recognize interactions between alien vascular plants and soil microorganisms and thus better understand the mechanisms of plant invasions, we examined the mycorrhizal status, arbuscular mycorrhizal fungi (AMF) colonization rate, arbuscular mycorrhiza (AM) morphology and presence of fungal root endophytes in 37 non-native species in Central Europe. We also studied the AMF diversity and chemical properties of soils from under these species. The plant and soil materials were collected in southern Poland. We found that 35 of the species formed AM and their mycorrhizal status depended on species identity. Thirty-three taxa had AM of Arum-type alone. Lycopersicon esculentum showed intermediate AM morphology and Eragrostis albensis developed both Arum and Paris. The mycelia of dark septate endophytes (DSE) were observed in 32 of the species, while sporangia of Olpidium spp. were found in the roots of 10. Thirteen common and worldwide occurring AMF species as well as three unidentified spore morphotypes were isolated from trap cultures established with the soils from under the plant species. Claroideoglomus claroideum, Funneliformis mosseae and Septoglomus constrictum were found the most frequently. The presence of root-inhabiting fungi and the intensity of their colonization were not correlated with soil chemical properties, plant invasion status, their local abundance and habitat type. No relationships were also found between the presence of AMF, DSE and Olpidium spp. These suggest that other edaphic conditions, plant and fungal species identity or the abundance of these fungi in soils might have an impact on the occurrence and intensity of fungal root colonization in the plants under study.
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Future challenges and perspectives for applying microbial biotechnology in sustainable agriculture based on a better understanding of plant-microbiome interactions

Future challenges and perspectives for applying microbial biotechnology in sustainable agriculture based on a better understanding of plant-microbiome interactions | Plant-Microbe Symbioses | Scoop.it
An intensive agricultural production is necessary to satisfy food requirements for the growing world population. However, its realization is associated with the mass consumption of non-renewable natural resources and with the emission of greenhouse gases causing climate changes. The research challenge is to meet sustainable environmental and economical issues without compromising yields. In this context, exploiting the agro-ecosystem services ofsoil microbial communities appears as a promising effective approach. This chapter reviews the research efforts aimed atimproving a sustainable and healthy agricultural production through the appropriate management of soil microorganisms.First, the plant-associated microbiome is briefly described. Then, the current research technologies for formulation and application of inocula based on specific beneficial plant-associated microbesare summarized. Finally, the perspectives and opportunities to manage naturally existing microbial populations, including those non-culturable, are analyzed. This analysis concerns: (i) a description of the already available, culture-independent, molecular techniques addressed at increasing our understanding of root-microbiome interactions; (ii) how to improve the ability of soil microbes for alleviating the negative impacts of stress factors on crop productivity; and (iii) whether plants can structure their root-associated microbial communities and, leading on from this, whether the rhizosphere can be engineered (biased) to encourage beneficial organisms, while prevent presence of pathogens.
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Growing rice in controlled environments

Growing rice in controlled environments | Plant-Microbe Symbioses | Scoop.it
Rice (Oryza sativa) is less frequently used in basic research than Arabidopsis, although rice is a valuable model system for many monocot crops and possesses a high genetic variability in physiologically as well as agriculturally relevant features such as abiotic stress tolerance, nutrient efficiency and flower time control. A reason is the seemingly difficult cultivation of rice outside the rice production area. This review aims to assist newcomers to the field to develop cultivation protocols for their local controlled environment. The main challenges are high light demands, photoperiodicity and low micronutrient efficiency. The nutrient efficiency problem can be overcome by adding micronutrient fertiliser to potting substrates and keeping the soil waterlogged to increase micronutrient availability and mobility. Cultivation of rice on adjusted hydroponic solutions with high iron concentration provides the basis for successful heavy isotope labelling. Many rice cultivars need high light intensities in combination with short-day conditions to complete their life cycle. However, some photoperiod-insensitive cultivars will flower even under relatively low light intensities. In highly photoperiod-sensitive cultivars, like Nipponbare, flowering can be induced by a limited period of short-day treatment in the sensitive period, after which the cultivation can be continued in long-day conditions. The life cycle of many cultivars is completed in 90 to 120 days, its length being thus comparable to Arabidopsis and shorter than in other cereals. In conclusion, with the right cultivation technique, rice is an amiable model species for researchers beyond the rice area too.
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Quantitative time-course proteome analysis of Mesorhizobium loti during nodule maturation

Quantitative time-course proteome analysis of Mesorhizobium loti during nodule maturation | Plant-Microbe Symbioses | Scoop.it
Rhizobia are nitrogen-fixing bacteria that establish a symbiotic relationship with leguminous plants. To understand the mechanism by which rhizobia alter their metabolism to establish successful nitrogen-fixing symbiotic relationship with hosts, Lotus japonicus were inoculated with Mesorhizobium loti. Bacteroids were isolated from nodules harvested at 2 weeks (the early stage of nodule development), and at 3 and 4 weeks (the intermediate stage of nodule development) post-inoculation. Using a quantitative time-course proteome analysis, we quantified the variations in the expression of 537 proteins in M. loti bacteroids during the course of nodule maturation. The results revealed significant changes in the carbon and amino acid metabolisms by M. loti upon differentiating into bacteroids. Furthermore, our findings suggested that M. loti enters a nitrogen-deficient condition during the early stages of nodule development, and then a nitrogen-rich condition during the intermediate stages of nodule development. In addition, our data indicated that M. loti assimilated ammonia during the intermediate stages of nodule development. Our results provide new insights into the course of physiological transitions undergone by M. loti during nodule maturation.
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Molecular mechanisms underlying the close association between soil Burkholderia and fungi

Bacterial species belonging to the genus Burkholderia have been repeatedly reported to be associated with fungi but the extent and specificity of these associations in soils remain undetermined. To assess whether associations between Burkholderia and fungi are widespread in soils, we performed a co-occurrence analysis in an intercontinental soil sample collection. This revealed that Burkholderia significantly co-occurred with a wide range of fungi. To analyse the molecular basis of the interaction, we selected two model fungi frequently co-occurring with Burkholderia, Alternaria alternata and Fusarium solani, and analysed the proteome changes caused by cultivation with either fungus in the widespread soil inhabitant B. glathei, whose genome we sequenced. Co-cultivation with both fungi led to very similar changes in the B. glathei proteome. Our results indicate that B. glathei significantly benefits from the interaction, which is exemplified by a lower abundance of several starvation factors that were highly expressed in pure culture. However, co-cultivation also gave rise to stress factors, as indicated by the increased expression of multidrug efflux pumps and proteins involved in oxidative stress response. Our data suggest that the ability of Burkholderia to establish a close association with fungi mainly lies in the capacities to utilize fungal-secreted metabolites and to overcome fungal defense mechanisms. This work indicates that beneficial interactions with fungi might contribute to the survival strategy of Burkholderia species in environments with sub-optimal conditions, including acidic soils.
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Does plant immunity have a central role in the legume rhizobium symbiosis?

Plants are exposed to many different microbes in their habitat. These microbes may be benign or pathogenic, but in some cases they are beneficial. The rhizosphere provides an especially rich palette for colonization by beneficial (associative and symbiotic) microorganisms, which raises the question as to how roots can distinguish such ‘friends’ from possible ‘foes’ (i.e., pathogens). Plants possess an innate immunity system that can recognize pathogens, through an arsenal of protein receptors. These receptors include receptor-like kinases (RLK) and receptor-like proteins (RLP) located at the plasma membrane, as well as intracellular receptors (so called NBS-LRR proteins or R proteins) that recognize molecules released by microbes into the plant cell. The key rhizobial, symbiotic signaling molecule (called Nod factor) is perceived by the host legume plant using LysM-domain containing RLKs. Perception of the symbiotic Nod factor triggers signaling cascades leading to bacterial infection and accommodation of the symbiont in a newly formed root organ, the nodule, resulting in a nitrogen-fixing root nodule symbiosis (RNS). The net result of this symbiosis is the intracellular colonization of the plant with thousands of bacteria; a process that seems to occur in spite of the immune ability of plants to prevent pathogen infection. In this review, we discuss the potential of the invading rhizobial symbiont to actively avoid this innate immunity response, as well as specific examples of where the plant immune response may modulate rhizobial infection and host range.
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Rhizobia and Soybeans: A Beneficial Relationship

Rhizobia and Soybeans: A Beneficial Relationship | Plant-Microbe Symbioses | Scoop.it
Remember that soybeans are legumes and fix nitrogen, but they might need a little assistance to make sure the environment is right for bacteria to flourish and maximize nitrogen fixation.

Soybeans are invaded by three distinct types of rhizobia bacteria: rhizobium fredii, bradyrhizobium japonicum and bradyrhizobium elkanii. When soybean seeds germinate, the bacteria invade the root hairs of the seedlings and begin to multiply. These soil-dwelling bacteria have the ability to penetrate soybean roots, which respond by building nodules to house them. The bacteria fix nitrogen in symbiosis with the soybean roots, which provide other nutrients and sugar.
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