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Sustainable agriculture: possible trajectories from mutualistic symbiosis and plant neodomestication

Sustainable agriculture: possible trajectories from mutualistic symbiosis and plant neodomestication | Plant-Microbe Symbioses | Scoop.it

Food demand will increase concomitantly with human population. Food production therefore needs to be high enough and, at the same time, minimize damage to the environment. This equation cannot be solved with current strategies. Based on recent findings, new trajectories for agriculture and plant breeding which take into account the belowground compartment and evolution of mutualistic strategy, are proposed in this opinion article. In this context, we argue that plant breeders have the opportunity to make use of native arbuscular mycorrhizal (AM) symbiosis in an innovative ecologically intensive agriculture.


Via Jean-Pierre Zryd
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Jean-Michel Ané's comment, September 25, 2013 9:15 PM
I totally agree!
Plant-Microbe Symbioses
Symbiotic associations between plants and microbes
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Impact of Fertilizer on Nodulation

Impact of Fertilizer on Nodulation | Plant-Microbe Symbioses | Scoop.it
In-furrow soybean fertilization’s impacts on nodulation and reduction in nitrogen fixation.

Because soybeans are a legume and have the ability to fix nitrogen (N), fertilization with N is not a common practice. Plants don’t begin to fix much nitrogen until after the middle of June, and wet and cool soil conditions further hamper nitrogen fixation.
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The Effects of Fungicides and Insecticides on Mycorrhiza

“Documents About the Effects of Fungicides and Insecticides on Mycorrhiza, #effects #fungicides #insecticides http://t.co/JvoNVawTbx”;


Via Daniel Wipf
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Microbe pair holds key to boosting feed crops

Microbe pair holds key to boosting feed crops | Plant-Microbe Symbioses | Scoop.it
The biotechnology research conducted at Flinders University in South Australia identified two strains of microbes that dramatically increase the ability of lucerne to fix atmospheric nitrogen, boosting the feed crop’s early growth and resilience, and ultimately its yield.
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Plant genotype, microbial recruitment and nutritional security

Agricultural food products with high nutritive value are always preferred over food products with low nutritive value. Efforts are being made to increase the nutritive value of food by incorporating dietary supplements to the food products. The same is more desirous if the nutritive value of food is increased under natural conditions in the food products especially in the agricultural produces. Fragmented researches have led to the conclusion that it is possible to increase nutritive value of the agricultural products naturally in agricultural fields. The rhizosphere is of vital importance in this regard for not only health and nutritional status of plants but also for the microorganisms colonising the rhizosphere. Remarkably robust composition of plant microbiome with respect to other soil environments clearly suggests the role of plant host in discriminating its colonisers. A large amount of biotic and abiotic factors are believed to manipulate the microbial communities in the rhizosphere. However, plant genotype has proven to be the key in giving the final shape of the rhizosphere microbiome.
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Draft Genome Sequence of Burkholderia sp. Strain PML1(12), an Ectomycorrhizosphere-Inhabiting Bacterium with Effective Mineral-Weathering Ability

We report the draft genome sequence of Burkholderia sp. PML1(12), a soil bacterium isolated from the Oak-Scleroderma citrinum ectomycorrhizosphere in the experimental forest site of Breuil-Chenue (France).
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Validation of candidate reference genes for qRT-PCR studies in symbiotic and non-symbiotic Casuarina glauca Sieb. ex Spreng. under salinity conditions

Validation of candidate reference genes for qRT-PCR studies in symbiotic and non-symbiotic Casuarina glauca Sieb. ex Spreng. under salinity conditions | Plant-Microbe Symbioses | Scoop.it
Casuarina glauca is a model actinorhizal plant species that establishes N2-fixing symbiosis with Frankia bacteria. This plant is highly resilient to extreme environments, being commonly found in saline zones. Gene expression studies by quantitative real-time polymerase chain reaction (qRT-PCR) constitute a powerful tool to analyze the mechanisms underlying plant stress-tolerance. One of the crucial steps of this technique is the selection and validation of reference genes to produce accurate data. In this work we report on the evaluation of a set of ten reference genes to be used in qRT-PCR studies in C. glauca grown under high salt concentrations, following the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines. Five independent methods (geNorm, NormFinder, BestKeeper, Coefficient of Variance, and ReFinder) were used to evaluate gene stability. According to the results, the calibration of qRT-PCR reactions with the most versus the least stable reference genes produced different expression patterns of C. glauca stress responsive genes (CgCS and CgAPX). The same was observed when data was normalized with one, two or three stable reference genes. These study constitutes a baseline for accurate qRT-PCR analysis in C. glauca exposed to high salt concentrations which should include the use of at least two stable reference genes.
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Symbiotic effectiveness and phylogeny of rhizobia isolated from faba bean (Vicia faba L.) in Sichuan hilly areas, China

A total of 54 rhizobial strains were isolated from faba bean root nodules in 21 counties of Sichuan hilly areas in China, and their symbiotic effectiveness, genetic diversity and phylogeny were assessed. Only six strains increased the shoot dry mass of the host plant significantly (P ≤ 0.05). Based on the cluster analysis of combined 16S rDNA and intergenic spacer region (IGS) PCR-RFLP, the strains were divided into 31 genotypes in eleven groups, indicating a high degree of genetic diversity among the strains. The sequence analysis of three housekeeping genes (atpD, glnII and recA) and 16S rDNA indicated that the strains represented two R. leguminosarum, two Rhizobium spp., R. mesosinicum, Agrobacterium sp. and A. tumefaciens. The strains representing four Rhizobium species were divided into two distinct nodC and nifH genotypes. However, the phylogeny of housekeeping genes and symbiotic genes was not congruent, implying that the strains had been shaped by vertical evolution of the housekeeping genes and lateral evolution of the symbiotic genes.
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Standards for plant synthetic biology: a common syntax for exchange of DNA parts

Standards for plant synthetic biology: a common syntax for exchange of DNA parts | Plant-Microbe Symbioses | Scoop.it

Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering.


Via Kamoun Lab @ TSL, Francis Martin
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Mycorrhization between Cistus ladanifer L. and Boletus edulis Bull is enhanced by the mycorrhiza helper bacteria Pseudomonas fluorescens Migula

Boletus edulis Bull. is one of the most economically and gastronomically valuable fungi worldwide. Sporocarp production normally occurs when symbiotically associated with a number of tree species in stands over 40 years old, but it has also been reported in 3-year-old Cistus ladanifer L. shrubs. Efforts toward the domestication of B. edulis have thus focused on successfully generating C. ladanifer seedlings associated with B. edulis under controlled conditions. Microorganisms have an important role mediating mycorrhizal symbiosis, such as some bacteria species which enhance mycorrhiza formation (mycorrhiza helper bacteria). Thus, in this study, we explored the effect that mycorrhiza helper bacteria have on the efficiency and intensity of the ectomycorrhizal symbiosis between C. ladanifer and B. edulis. The aim of this work was to optimize an in vitro protocol for the mycorrhizal synthesis of B. edulis with C. ladanifer by testing the effects of fungal culture time and coinoculation with the helper bacteria Pseudomonas fluorescens Migula. The results confirmed successful mycorrhizal synthesis between C. ladanifer and B. edulis. Coinoculation of B. edulis with P. fluorescens doubled within-plant mycorrhization levels although it did not result in an increased number of seedlings colonized with B. edulis mycorrhizae. B. edulis mycelium culture time also increased mycorrhization levels but not the presence of mycorrhizae. These findings bring us closer to controlled B. edulis sporocarp production in plantations.
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Why do old wines produce better wine grapes? (It's the Mycorrhiza)

“Old vines have a unique ability to access the nutrients in a vineyard's soil. Dai Crisp explains the role of mycorrhiza in a video that is for the geekiest o...”


Via Daniel Wipf
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Oxalate secretion by ectomycorrhizal Paxillus involutus is mineral-specific and controls calcium weathering from minerals

Oxalate secretion by ectomycorrhizal Paxillus involutus is mineral-specific and controls calcium weathering from minerals | Plant-Microbe Symbioses | Scoop.it

Trees and their associated rhizosphere organisms play a major role in mineral weathering driving calcium fluxes from the continents to the oceans that ultimately control long-term atmospheric CO2 and climate through the geochemical carbon cycle. Photosynthate allocation to tree roots and their mycorrhizal fungi is hypothesized to fuel the active secretion of protons and organic chelators that enhance calcium dissolution at fungal-mineral interfaces. This was tested using 14CO2 supplied to shoots of Pinus sylvestris ectomycorrhizal with the widespread fungus Paxillus involutus in monoxenic microcosms, revealing preferential allocation by the fungus of plant photoassimilate to weather grains of limestone and silicates each with a combined calcium and magnesium content of over 10 wt.%. Hyphae had acidic surfaces and linear accumulation of weathered calcium with secreted oxalate, increasing significantly in sequence: quartz, granite < basalt, olivine, limestone < gabbro. These findings confirmed the role of mineral-specific oxalate exudation in ectomycorrhizal weathering to dissolve calcium bearing minerals, thus contributing to the geochemical carbon cycle.


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High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592; a Hedysarum coronarium microsymbiont from Sassari, Italy

Rhizobium sullae strain WSM1592 is an aerobic, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen (N
2
) fixing root nodule formed on the short-lived perennial legume Hedysarum coronarium (also known as Sulla coronaria or Sulla). WSM1592 was isolated from a nodule recovered from H. coronarium roots located in Ottava, bordering Sassari, Sardinia in 1995. WSM1592 is highly effective at fixing nitrogen with H. coronarium, and is currently the commercial Sulla inoculant strain in Australia. Here we describe the features of R. sullae strain WSM1592, together with genome sequence information and its annotation. The 7,530,820 bp high-quality permanent draft genome is arranged into 118 scaffolds of 118 contigs containing 7.453 protein-coding genes and 73 RNA-only encoding genes. This rhizobial genome is sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
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Leaf metabolome in arbuscular mycorrhizal symbiosis

Leaf metabolome in arbuscular mycorrhizal symbiosis | Plant-Microbe Symbioses | Scoop.it
Most land plants are associated with arbuscular mycorrhizal fungi, which colonise the plant roots and facilitate the uptake of water and nutrients. In turn, the fungi receive plant carbohydrates. Although the fungus is morphologically restricted to the roots, the exchange of substances and involvement of phytohormone signalling has consequences on systemic shoot tissues. Recent research provides growing insight in the species-specificity of leaf metabolic responses to arbuscular mycorrhiza, revealing that various metabolites can be affected. Such mycorrhiza-mediated changes in the chemical composition of leaf tissues can confer phytoprotection against different abiotic stresses. Moreover, they have consequences on numerous biotic interactions. In this review we highlight such findings and point out fields where more research is required.
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NAU Hosting International Mycorrhiza Conference

NAU Hosting International Mycorrhiza Conference | Plant-Microbe Symbioses | Scoop.it
Northern Arizona University has been selected to host the Eighth International Conference on Mycorrhiza (ICOM8), which will take place August 3–7, 2015. The conference will bring nearly 500 people from more than 50 different countries to the High Country Conference Center.
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Bioprospecting glacial ice for plant growth promoting bacteria

Bioprospecting glacial ice for plant growth promoting bacteria | Plant-Microbe Symbioses | Scoop.it
Glaciers harbor a wide diversity of microorganisms, metabolically versatile, highly tolerant to multiple environmental stresses and potentially useful for biotechnological purposes. Among these, we hypothesized the presence of bacteria able to exhibit well-known plant growth promoting traits (PGP). These kinds of bacteria have been employed for the development of commercial biofertilizers; unfortunately, these biotechnological products have proven ineffective in colder climates, like the ones prevailing in mountainous ecosystems. In the present work, we prospected glacial ice collected from two small tropical glaciers, located above 4.900 m in the Venezuelan Andes, for cold-active PGP bacteria. The initial screening strategy allowed us to detect the best inorganic-P solubilizers at low temperatures, from a sub-sample of 50 bacterial isolates. Solubilization of tricalcium phosphate, aluminum- and iron-phosphate, occurred in liquid cultures at low temperatures and was dependent on medium acidification by gluconic acid production, when bacteria were supplied with an appropriate source of carbon. Besides, the isolates were psychrophilic and in some cases exhibited a broad range of growth-temperatures, from 4 °C to 30 °C. Additional PGP abilities, including phytohormone- and HCN production, siderophore excretion and inhibition of phytopathogens, were confirmed in vitro. Nucleotidic sequence analysis of 16S rRNA genes allowed us to place the isolates within the Pseudomonas genus. Our results support the possible use of these strains to develop cold-active biofertilizers to be used in mountainous agriculture.
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Accelerated Growth Rate and Increased Drought Stress Resilience of the Model Grass Brachypodium distachyon Colonized by Bacillus subtilis B26

Accelerated Growth Rate and Increased Drought Stress Resilience of the Model Grass  Brachypodium distachyon  Colonized by  Bacillus subtilis  B26 | Plant-Microbe Symbioses | Scoop.it
Plant growth-promoting bacteria (PGB) induce positive effects in plants, for instance, increased growth and reduced abiotic stresses susceptibility. The mechanisms by which these bacteria impact the host plant are numerous, diverse and often specific. Here, we studied the agronomical, molecular and biochemical effects of the endophytic PGB Bacillus subtilis B26 on the full life cycle of Brachypodium distachyon Bd21, an established model species for functional genomics in cereal crops and temperate grasses. Inoculation of Brachypodium with B. subtilis strain B26 increased root and shoot weights, accelerated growth rate and seed yield as compared to control plants. B. subtilis strain B26 efficiently colonized the plant and was recovered from roots, stems and blades as well as seeds of Brachypodium, indicating that the bacterium is able to migrate, spread systemically inside the plant, establish itself in the aerial plant tissues and organs, and is vertically transmitted to seeds. The presence of B. subtilis strain B26 in the seed led to systemic colonization of the next generation of Brachypodium plants. Inoculated Brachypodium seedlings and mature plants exposed to acute and chronic drought stress minimized the phenotypic effect of drought compared to plants not harbouring the bacterium. Protection from the inhibitory effects of drought by the bacterium was linked to upregulation of the drought-response genes, DREB2B-like, DHN3-like and LEA-14-A-like and modulation of the DNA methylation genes, MET1B-like, CMT3-like and DRM2-like, that regulate the process. Additionally, total soluble sugars and starch contents increased in stressed inoculated plants, a biochemical indication of drought tolerance. In conclusion, we show a single inoculation of Brachypodium with a PGB affected the whole growth cycle of the plant, accelerating its growth rates, shortening its vegetative period, and alleviating drought stress effects. These effects are relevant to grasses and cereal crops.
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The root hair 'infectome' of Medicago truncatula: secrets of hair removal

Secrets of hair removal... awesome title :-)

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The Sinorhizobium meliloti glyoxylate cycle enzyme isocitrate lyase (AceA) is required for the utilization of poly-β-hydroxybutyrate during carbon starvation

The Sinorhizobium meliloti glyoxylate cycle enzyme isocitrate lyase (AceA) is required for the utilization of poly-β-hydroxybutyrate during carbon starvation | Plant-Microbe Symbioses | Scoop.it
The glyoxylate cycle is an anaplerotic pathway of the tricarboxylic acid cycle that allows bacteria to grow using acetate, fatty acids, or poly-β-hydroxybutyrate (PHB). In Sinorhizobium meliloti, activities of the glyoxylate cycle enzymes isocitrate lyase (AceA) and malate synthase (GlcB) are present during growth on these kinds of carbon sources, but a study of the importance of these enzymes in utilizing these carbon compounds under starvation conditions has not been done. We therefore evaluated the role of AceA and GlcB in the utilization of PHB by determining the PHB degradative and growth capacities of the S. meliloti wild type and aceA and glcB mutants under carbon starvation conditions in culture. We found that only the aceA gene product was essential for bacterial growth and PHB degradation under these conditions, presumably by generating succinate from the acetyl-CoA derived from PHB catabolism, thus allowing the cells to grow in the absence of an external carbon source.
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Microbial Symbionts of Plants

Microbial Symbionts of Plants | Plant-Microbe Symbioses | Scoop.it
Plants in nature always grow with soil microorganisms, and some become intimately associated with plants to form mutualistic symbiosis. Examples of such symbiotic microorganisms include mycorrhizal fungi, cyanobacteria, and N2-fixing prokaryotes, especially rhizobia. Looser symbiotic associations involve bacteria and soil microfauna within the rhizosphere. Their metabolic activities increase nutrient availability. All of these symbioses may affect rates of growth and eventually reproduction of plants compared with growth in the absence of such associations. A symbiotic association is therefore a potential selection pressure that can influence the evolutionary success of vascular plants and hence the composition of plant communities. Application of associative bacteria for sustainable agriculture holds immense potential. These bacteria are known to enhance growth and yield of plants by fixing atmospheric nitrogen, solubilization of phosphate, production of phytohormones and siderophores, possession of antagonistic activity, as well as reducing the level of stress ethylene in host plants. This review provides examples of associations and interactions between microorganisms and plants. The cyanobacterial association with various plants such as bryophyte, pteridophyte, gymnosperm, and angiosperm was illustrated. It also describes the actinorhizae, Frankia and Rhizobium, interaction with plants and their applications.
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supn, a Novel Supernodulation Mutant in Medicago truncatula

supn, a Novel Supernodulation Mutant in Medicago truncatula | Plant-Microbe Symbioses | Scoop.it
Novel Medicago truncatula mutant line, supn, is confirmed as hyper-nodulating phenotype mutant. supn mutant is displaying short root phenotype with increasing nodule numbers approximately three folds comparing to wild type phenotype. supn is Tnt1-retrotransposon mutant, more than ~ 40 Tnt1 insertion sites wrere identified and sequenced during molecular characterization of supn. About only 10% of insertions could be accountable for super-nodulation phenotype. The predicted Medicago truncatula GSO2-like locus was isolated, cloned, and sequenced through the Tnt1-insertion screening. The putative Mt GSO2- like is 3287 bp in length with two exons and one intron, 1974 bp, 1140 bp and 173 bp lengths respectively and it is predicted to encode leucin rich-repeats receptor like protein, 999 amino acids in length. MtGS02:GFP is located at cell periphery and within the nucleus of onion epidermal cells while it is located along root cells boundaries of Medicago truncatula root. GFP localization sites within cells boundaries could be an evidence of cell to cell communication function of our predicted MtGSO2. Exogenous phytohormones were able to elucidate the differences in supn root phenotype from those of wild type and the previously characterized supernodulating, sunn mutant.
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Glutamine synthetase in Medicago truncatula, unveiling new secrets of a very old enzyme

Glutamine synthetase in Medicago truncatula, unveiling new secrets of a very old enzyme | Plant-Microbe Symbioses | Scoop.it
Glutamine synthetase (GS) catalyzes the first step at which nitrogen is brought into cellular metabolism and is also involved in the reassimilation of ammonium released by a number of metabolic pathways. Due to its unique position in plant nitrogen metabolism, GS plays essential roles in all aspects of plant development, from germination to senescence, and is a key component of nitrogen use efficiency (NUE) and plant yield. Understanding the mechanisms regulating GS activity is therefore of utmost importance and a great effort has been dedicated to understand how GS is regulated in different plant species. The present review summarizes exciting recent developments concerning the structure and regulation of GS isoenzymes, using the model legume Medicago truncatula. These include the understanding of the structural determinants of both the cytosolic and plastid located isoenzymes, the existence of a seed-specific GS gene unique to M. truncatula and closely related species and the discovery that GS isoenzymes are regulated by nitric oxide at the post-translational level. The data is discussed and integrated with the potential roles of the distinct GS isoenzymes within the whole plant context.
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Comparative Transcriptomics Reveals Distinct Hormone Action Pathways in Lateral Roots and Nodules of Soybean

Leguminous plants such as soybean produce two kinds of root lateral organs; lateral roots and nodules. Unlike shoot lateral organs that develop from the flanks of shoot apical meristem, lateral roots and nodules are formed away from the root apical meristem via dedifferentiation of preexisting cells, pericycle and cortex respectively. Commonalities in some developmental features of lateral root and nodules has led to the speculation that nodules might have adopted the developmental pathways of lateral roots. However, differences in hormonal requirement of these organs indicates that nodules might have adopted developmental pathways distinct from that of lateral roots. To understand the similarities and differences in the development of these organs we dissected lateral root and nodules at emerging and mature stages of development and determined differences in global transcriptome profiles and specifically compared the enrichment of transcription factors, and hormone biosynthesis and signaling components. Results from these analyses strengthen the conclusion that auxin and cytokinin play opposite roles in the development of nodules and lateral roots. In addition, potential orthologs of genes associated with shoot axillary meristem were enriched in nodules, but not in lateral roots. Together, these results indicate that the soybean nodule might be a modified shoot axillary organ.
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Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417

Background
Plant growth-promoting rhizobacteria (PGPR) can protect plants against pathogenic microbes through a diversity of mechanisms including competition for nutrients, production of antibiotics, and stimulation of the host immune system, a phenomenon called induced systemic resistance (ISR). In the past 30 years, the Pseudomonas spp. PGPR strains WCS358, WCS374 and WCS417 of the Willie Commelin Scholten (WCS) collection have been studied in detail in pioneering papers on the molecular basis of PGPR-mediated ISR and mechanisms of biological control of soil-borne pathogens via siderophore-mediated competition for iron.

Results
The genomes of the model WCS PGPR strains were sequenced and analyzed to unearth genetic cues related to biological questions that surfaced during the past 30 years of functional studies on these plant-beneficial microbes. Whole genome comparisons revealed important novel insights into iron acquisition strategies with consequences for both bacterial ecology and plant protection, specifics of bacterial determinants involved in plant-PGPR recognition, and diversity of protein secretion systems involved in microbe-microbe and microbe-plant communication. Furthermore, multi-locus sequence alignment and whole genome comparison revealed the taxonomic position of the WCS model strains within the Pseudomonas genus. Despite the enormous diversity of Pseudomonas spp. in soils, several plant-associated Pseudomonas spp. strains that have been isolated from different hosts at different geographic regions appear to be nearly isogenic to WCS358, WCS374, or WCS417. Interestingly, all these WCS look-a-likes have been selected because of their plant protective or plant growth-promoting properties.

Conclusions
The genome sequences of the model WCS strains revealed that they can be considered representatives of universally-present plant-beneficial Pseudomonas spp. With their well-characterized functions in the promotion of plant growth and health, the fully sequenced genomes of the WCS strains provide a genetic framework that allows for detailed analysis of the biological mechanisms of the plant-beneficial traits of these PGPR. Considering the increasing focus on the role of the root microbiome in plant health, functional genomics of the WCS strains will enhance our understanding of the diversity of functions of the root microbiome.
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Characterization of para-nitrophenol degrading bacterial communities in river water using functional markers and stable isotope probing

Microbial degradation is a major determinant of pollutant fate in the environment. Para-nitrophenol (PNP) is an EPA listed priority pollutant with wide environmental distribution but little is known about the microorganisms that degrade it in the environment. We studied the diversity of active PNP- degrading bacterial populations in river water using a novel functional marker approach coupled with [13C6]-PNP Stable Isotope Probing (SIP). Culturing together with culture independent Terminal Restriction Fragment Length Polymorphism analysis of 16S rRNA gene amplicons identified Pseudomonas syringae as the major driver of PNP degradation in river water microcosms. This was confirmed by SIP-pyrosequencing of amplified 16S rRNA. Similarly, functional gene analysisshowed that degradation followed the Gram-negative pathway involving pnpA from Pseudomonas spp. However analysis of maleylacetate reductase (mar), an enzyme common to late stages of both Gram negative and Gram positive bacterial PNP degradation pathways, identified a diverse assemblage of bacteria associated with PNP degradation, suggesting that mar had limited use as a specific marker of PNP biodegradation. Both pnpA and mar genes were detected in a PNP-degrading isolate, P. syringae AKHD2 which was isolated from river water. Our results suggest that PNP degrading cultures of Pseudomonas spp. were representative of environmental PNP degrading populations.
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Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays

Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays | Plant-Microbe Symbioses | Scoop.it
Plant genomes encode numerous small secretory peptides (SSPs) whose functions have yet to be explored. Based on structural features that characterize SSP families known to take part in postembryonic development, this comparative genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication. Because genome annotation based on short sequence homology is difficult, the criteria for the de novo identification and aggregation of conserved SSP sequences were first benchmarked across five reference plant species. The resulting gene families were then extended to 32 genome sequences, including major crops. The global phylogenetic pattern common to the functionally characterized SSP families suggests that their apparition and expansion coincide with that of the land plants. The SSP families can be searched online for members, sequences and consensus (http://bioinformatics.psb.ugent.be/webtools/PlantSSP/). Looking for putative regulators of root development, Arabidopsis thaliana SSP genes were further selected through transcriptome meta-analysis based on their expression at specific stages and in specific cell types in the course of the lateral root formation. As an additional indication that formerly uncharacterized SSPs may control development, this study showed that root growth and branching were altered by the application of synthetic peptides matching conserved SSP motifs, sometimes in very specific ways. The strategy used in the study, combining comparative genomics, transcriptome meta-analysis and peptide functional assays in planta, pinpoints factors potentially involved in non-cell-autonomous regulatory mechanisms. A similar approach can be implemented in different species for the study of a wide range of developmental programmes.
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