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Plant-Microbe Symbioses
Symbiotic associations between plants and microbes
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Mechanisms of physiological adjustment of N2 fixation in Cicer arietinum L. (chickpea) during early stages of water deficit: single or multi-factor controls

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

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Biological nitrogen fixation and plant associated microorganisms

For plant and agricultural scientists.

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Are plant–soil feedback responses explained by plant traits?

Nitrite-oxidizing bacteria are key players in the natural nitrogen cycle on Earth and in biological wastewater treatment plants. For decades, these specialist bacteria were thought to depend on nitrite as their source of energy. An international team of scientists led by Holger Daims, a microbiologist at the University of Vienna, has now shown that nitrite-oxidizing bacteria can use hydrogen as an alternative source of energy. The oxidation of hydrogen with oxygen enables their growth independent of nitrite and a lifestyle outside the nitrogen cycle. The study is published in the current issue of the journal Science.

Nitrogen, an essential chemical element for life, is transformed into its different chemical forms in numerous steps of the global nitrogen cycle. Nitrite-oxidizing bacteria are important players in nitrogen cycling since they convert the toxic nitrite to the less harmful nitrate. "Humans exploit this process in biological wastewater treatment. Moreover, the formed nitrate is a substrate for other important microbial processes and a source of nitrogen for many plants" explains Hanna Koch, first author of the study and Ph.D. student at the Department of Microbiology and Ecosystem Science of the University of Vienna. Since the description of the first nitrite-oxidizing bacteria in the 19th century, scientists have assumed that the survival of these microorganisms would depend on nitrite as their source of energy. Therefore, the presence of nitrite-oxidizing bacteria in the environment and in wastewater treatment plants has commonly been associated with the nitrogen cycle.

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Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains | Plant-Microbe Symbioses | Scoop.it

Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently~11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.


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Which is more important for classifying microbial communities: who's there or what they can do?

Which is more important for classifying microbial communities: who's there or what they can do? | Plant-Microbe Symbioses | Scoop.it
Classification is a machine-learning approach to develop predictive models that can classify samples into categories correctly. In microbial studies, these categories include disease states and habitats. An ongoing question in microbial ecology is the correct level of analysis to use in order to best discriminate biologically relevant samples. Many studies use the 16S rRNA gene as a taxonomic marker, and then ask how effectively the taxonomic profiles obtained from this marker classify or cluster different microbial communities according to their sample types. Interestingly, the answer may depend on the question being asked. For phylogenetic analysis, different levels of resolution in grouping are differentially successful at different classification tasks. These classification tasks include separating different samples by the person they came from (which depends on fine distinctions among very closely related strains or species), and separating lean from obese individuals (where very broad groups of taxa are more effective) (Knights et al., 2011b).
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Nodule carbohydrate catabolism is enhanced in the Medicago truncatula A17-Sinorhizobium medicae WSM419 symbiosis

The symbiotic association between Medicago truncatula and Sinorhizobium meliloti is a well-established model system in the legume-Rhizobium community. Despite its wide use, the symbiotic efficiency of this model has been recently questioned and an alternative microsymbiont, S. medicae, has been proposed. However, little is known about the physiological mechanisms behind the higher symbiotic efficiency of S. medicae WSM419. In the present study, we inoculated M. truncatula Jemalong A17 with either S. medicae WSM419 or S. meliloti 2011 and compared plant growth, photosynthesis, N2-fixation rates, and plant nodule carbon and nitrogen metabolic activities in the two systems. M. truncatula plants in symbiosis with S. medicae showed increased biomass and photosynthesis rates per plant. Plants grown in symbiosis with S. medicae WSM419 also showed higher N2-fixation rates, which were correlated with a larger nodule biomass, while nodule number was similar in both systems. In terms of plant nodule metabolism, M. truncatula-S. medicae WSM419 nodules showed increased sucrose-catabolic activity, mostly associated with sucrose synthase, accompanied by a reduced starch content, whereas nitrogen-assimilation activities were comparable to those measured in nodules infected with S. meliloti 2011. Taken together, these results suggest that S. medicae WSM419 is able to enhance plant carbon catabolism in M. truncatula nodules, which allows for the maintaining of high symbiotic N2-fixation rates, better growth and improved general plant performance.
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Jeffrey Ross-Ibarra on Twitter: Tell me botany doesn’t have a recruitment problem. 800 undergrad bio students say: http://t.co/aCtIslXwvo

Jeffrey Ross-Ibarra on Twitter: Tell me botany doesn’t have a recruitment problem. 800 undergrad bio students say: http://t.co/aCtIslXwvo | Plant-Microbe Symbioses | Scoop.it
Unfortunately worse for #microbiologyMT @jrossibarra: Tell me botany doesn’t have a recruitment problem: http://t.co/WJQimlhlPJ
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Good news... we are in the top 5%!
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How to Make Friends and Meet People at a Scientific Conference

How to Make Friends and Meet People at a Scientific Conference | Plant-Microbe Symbioses | Scoop.it
How to make the most of your time at a scientific conference. Tips for making friends and networking before, during, and after the conference.
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Toward a systems understanding of plant–microbe interactions

Toward a systems understanding of plant–microbe interactions | Plant-Microbe Symbioses | Scoop.it
Plants are closely associated with microorganisms including pathogens and mutualists that influence plant fitness. Molecular genetic approaches have uncovered a number of signaling components from both plants and microbes and their mode of actions. However, signaling pathways are highly interconnected and influenced by diverse sets of environmental factors. Therefore, it is important to have systems views in order to understand the true nature of plant-microbe interactions. Indeed, systems biology approaches have revealed previously overlooked or misinterpreted properties of the plant immune signaling network. Experimental reconstruction of biological networks using exhaustive combinatorial mutants is particularly powerful to elucidate network structure and properties and relationships among network components. Recent advances in metagenomics of microbial communities associated with plants further point to the importance of systems approaches and open a research area of microbial community reconstruction. In this review, we highlight the importance of a systems understanding of plant-microbe interactions, with a special emphasis on reconstruction strategies.
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APPLYING ARTIFICIAL MYCORRHIZAE IN PLANTING URBAN TREES

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"Artificial" mycorrhizae??

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Florian Klingenfuss MS thesis

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Evidence of Autoinducer-Dependent and -Independent Heterogeneous Gene Expression in Sinorhizobium fredii NGR234

Populations of genetically identical Sinorhizobium fredii NGR234 cells differ significantly in their expression profiles of autoinducer (AI)-dependent and AI-independent genes. Promoter fusions of the NGR234 AI synthase genes traI and ngrI showed high levels of phenotypic heterogeneity during growth in TY medium on a single-cell level. However, adding very high concentrations of N-(3-oxooctanoyl-)-l-homoserine lactone resulted in a more homogeneous expression profile. Similarly, the lack of internally synthesized AIs in the background of the NGR234-ΔtraI or the NGR234-ΔngrI mutant resulted in a highly homogenous expression of the corresponding promoter fusions in the population. Expression studies with reporter fusions of the promoter regions of the quorum-quenching genes dlhR and qsdR1 and the type IV pilus gene cluster located on pNGR234b suggested that factors other than AI molecules affect NGR234 phenotypic heterogeneity. Further studies with root exudates and developing Arabidopsis thaliana seedlings provide the first evidence that plant root exudates have strong effects on the heterogeneity of AI synthase and quorum-quenching genes in NGR234. Therefore, plant-released octopine appears to play a key role in modulation of heterogeneous gene expression.

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RNA Sequencing Analysis of the Broad-Host-Range Strain Sinorhizobium fredii NGR234 Identifies a Large Set of Genes Linked to Quorum Sensing-Dependent Regulation in the Background of a traI and ngrI...

The alphaproteobacterium Sinorhizobium fredii NGR234 has an exceptionally wide host range, as it forms nitrogen-fixing nodules with more legumes than any other known microsymbiont. Within its 6.9-Mbp genome, it encodes two N-acyl-homoserine-lactone synthase genes (i.e., traI and ngrI) involved in the biosynthesis of two distinct autoinducer I-type molecules. Here, we report on the construction of an NGR234-ΔtraI and an NGR234-ΔngrI mutant and their genome-wide transcriptome analysis. A high-resolution RNA sequencing (RNA-seq) analysis of early-stationary-phase cultures in the NGR234-ΔtraI background suggested that up to 316 genes were differentially expressed in the NGR234-ΔtraI mutant versus the parent strain. Similarly, in the background of NGR234-ΔngrI 466 differentially regulated genes were identified. Accordingly, a common set of 186 genes was regulated by the TraI/R and NgrI/R regulon. Coregulated genes included 42 flagellar biosynthesis genes and 22 genes linked to exopolysaccharide (EPS) biosynthesis. Among the genes and open reading frames (ORFs) that were differentially regulated in NGR234-ΔtraI were those linked to replication of the pNGR234a symbiotic plasmid and cytochrome c oxidases. Biotin and pyrroloquinoline quinone biosynthesis genes were differentially expressed in the NGR234-ΔngrI mutant as well as the entire cluster of 21 genes linked to assembly of the NGR234 type III secretion system (T3SS-II). Further, we also discovered that genes responsible for rhizopine catabolism in NGR234 were strongly repressed in the presence of high levels of N-acyl-homoserine-lactones. Together with nodulation assays, the RNA-seq-based findings suggested that quorum sensing (QS)-dependent gene regulation appears to be of higher relevance during nonsymbiotic growth rather than for life within root nodules.

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Microbes for legume improvement

Plant and agricultural crop sciences.
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Deep sequencing-based comparative transcriptional profiles of Cymbidium hybridum roots in response to mycorrhizal and non-mycorrhizal beneficial fungi

Deep sequencing-based comparative transcriptional profiles of Cymbidium hybridum roots in response to mycorrhizal and non-mycorrhizal beneficial fungi | Plant-Microbe Symbioses | Scoop.it

Background

The Orchidaceae is one of the largest families in the plant kingdom and orchid mycorrhizae (OM) are indispensable in the life cycle of all orchids under natural conditions. In spite of this, little is known concerning the mechanisms underlying orchid- mycorrhizal fungi interactions. Our previous work demonstrated that the non-mycorrhizal fungus Umbelopsis nana ZH3A-3 could improve the symbiotic effects of orchid mycorrhizal fungus Epulorhiza repens ML01 by co-cultivation with Cymbidium hybridum plantlets. Thus, we investigated the C. hybridum transcript profile associated with different beneficial fungi.

Results

More than 54,993,972 clean reads were obtained from un-normalized cDNA library prepared from fungal- and mock- treated Cymbidium roots at four time points using RNA-seq technology. These reads were assembled into 16,798 unique transcripts, with a mean length of 1127 bp. A total of 10,971 (65.31%) sequences were annotated based on BLASTX results and over ninety percent of which were assigned to plant origin. The digital gene expression profiles in Cymbidium root at 15 days post inoculation were revealed that 1674, 845 and 1743 genes were sigificantly regulated in response to ML01, ZH3A-3 and ML01+ ZH3A-3 treatments, respectively. Twenty-six genes in different regulation patterns were validated using quantitative RT-PCR. Our analysis showed that general defense responses were co- induced by three treatments, including cell wall modification, reactive oxygen species detoxification, secondary biosynthesis and hormone balanceGenes involved in phosphate transport and root morphogenesis were also detected to be up-regulated collectively. Among the OM specifically induced transcripts, genes related to signaling, protein metabolism and processing, defense, transport and auxin response were identifed. Aside from these orchid transcripts, some putative fungal genes were also identified in symbiotic roots related to plant cell wall degradation, remodeling the fungal cell wall and nutrient transport.

Conclusion

The orchid root transcriptome will facilitate our understanding of orchid - associated biological mechanism. The comparative expression profiling revealed that the transcriptional reprogramming by OM symbiosis generally overlapped that of arbuscular mycorrhizas and ectomycorrhizas. The molecular basis of OM formation and function will improve our knowledge of plant- mycorrhzial fungi interactions, and their effects on plant and fungal growth, development and differentiation.


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Hydrogen powers important nitrogen-transforming bacteria

Hydrogen powers important nitrogen-transforming bacteria | Plant-Microbe Symbioses | Scoop.it

Nitrite-oxidizing bacteria are key players in the natural nitrogen cycle on Earth and in biological wastewater treatment plants. For decades, these specialist bacteria were thought to depend on nitrite as their source of energy. An international team of scientists led by Holger Daims, a microbiologist at the University of Vienna, has now shown that nitrite-oxidizing bacteria can use hydrogen as an alternative source of energy. The oxidation of hydrogen with oxygen enables their growth independent of nitrite and a lifestyle outside the nitrogen cycle. The study is published in the current issue of the journal Science.

Nitrogen, an essential chemical element for life, is transformed into its different chemical forms in numerous steps of the global nitrogen cycle. Nitrite-oxidizing bacteria are important players in nitrogen cycling since they convert the toxic nitrite to the less harmful nitrate. "Humans exploit this process in biological wastewater treatment. Moreover, the formed nitrate is a substrate for other important microbial processes and a source of nitrogen for many plants" explains Hanna Koch, first author of the study and Ph.D. student at the Department of Microbiology and Ecosystem Science of the University of Vienna. Since the description of the first nitrite-oxidizing bacteria in the 19th century, scientists have assumed that the survival of these microorganisms would depend on nitrite as their source of energy. Therefore, the presence of nitrite-oxidizing bacteria in the environment and in wastewater treatment plants has commonly been associated with the nitrogen cycle.

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Microtubule array formation during root hair infection thread initiation and elongation in the Mesorhizobium-Lotus symbiosis

Microtubule array formation during root hair infection thread initiation and elongation in the Mesorhizobium-Lotus symbiosis | Plant-Microbe Symbioses | Scoop.it

Nuclear migration during infection thread (IT) development in root hairs is essential for legume-Rhizobium symbiosis. However, little is known about the relationships between IT formation, nuclear migration, and microtubule dynamics. To this aim, we used transgenic Lotus japonicus expressing a fusion of the green fluorescent protein and tubulin-α6 from Arabidopsis thaliana to visualize in vivo dynamics of cortical microtubules (CMT) and endoplasmic microtubules (EMTs) in root hairs in the presence or absence of Mesorhizobium loti inoculation. We also examined the effect of microtubule-depolymerizing herbicide, cremart, on IT initiation and growth, since cremart is known to inhibit nuclear migration. In live imaging studies of M. loti-treated L. japonicus root hairs, EMTs were found in deformed, curled, and infected root hairs. The continuous reorganization of the EMT array linked to the nucleus appeared to be essential for the reorientation, curling, and IT initiation and the growth of zone II root hairs which are susceptible to rhizobial infection. During IT initiation, the EMTs appeared to be linked to the root hair surface surrounding the M. loti microcolonies. During IT growth, EMTs dissociated from the curled root hair tip, remained linked to the nucleus, and appeared to surround the IT tip. Lack or disorganized EMT arrays that were no longer linked to the nucleus were observed only in infection-aborted root hairs. Cremart affected IT formation and nodulation in a concentration-dependent manner, suggesting that the microtubule (MT) organization and successive nuclear migration are essential for successful nodulation in L. japonicus by M. loti.

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Short-term impacts of energy wood harvesting on ectomycorrhizal fungal communities of Norway spruce saplings

The increased demand for harvesting energy wood raises questions about its effects on the functioning of the forest ecosystems, soil processes and biodiversity. Impacts of tree stump removal on ectomycorrhizal fungal (EMF) communities of Norway spruce saplings were studied with 454-pyrosequencing in a 3-year field experiment replicated in 3 geographical areas. This is possibly the most thorough investigation of EMF communities associated with saplings grown on sites subjected to energy wood harvesting. To separate impacts of tree stump and logging residue removal on EMF and plant variables, we used three harvesting treatments with increasing complexity from patch mounding alone (P) to patch mounding combined with logging residue removal (RP), and patch mounding combined with both logging residue and stump removal (SRP). Saplings grown in uncut forests (F) served as references for harvesting treatments. A majority of sequences (>92%) and operational taxonomic units (OTUs, 55%) were assigned as EMF. EMF OTU richness, fungal community composition or sapling growth did not differ between harvesting treatments (P, RP and SRP), while EMF OTU richness, diversity and evenness were highest and sapling growth lowest in the undisturbed reference forests (F). The short study period may partially explain the similarities in fungal and sapling variables in different harvesting treatments. In conclusion, our results indicate that neither stump removal nor logging residue removal have significant additional negative impacts on EMF communities or growth of Norway spruce saplings in the short-term compared with the impacts of more conventional harvesting methods, including clear cutting and patch mounding.

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Lipochitooligosaccharide recognition: an ancient story

  • Chitin is the second most abundant polysaccharide in nature, found in crustacean shells, insect exoskeletons and fungal cell walls. The action of chitin and chitin derivatives on plants has become a very interesting story of late. Chitin is a β1-4-linked polymer of N-acetyl-d-glucosamine (GlcNAc). In this unmodified form, chitooligosaccharides (degree of polymerization (dp) = 6–8)) are strong inducers of plant innate immunity. By contrast, when these chitooligosaccharides are acylated (so-called lipochitooligosaccharides, LCOs) and further modified, they can act as Nod factors, the key signaling molecules that play an important role in the initiation of the legume–rhizobium symbiosis. In a similar form, these molecules can also act as Myc factors, the key signaling molecules involved in the arbuscular mycorrhizal (AM) symbiosis. It has been proposed that Nod factor perception might have evolved from the more ancient AM symbiosis. Increasing evidence now suggests that LCO perception might have evolved from plant innate immunity signaling. In this review, we will discuss the evolutionary origin of symbiotic LCO recognition.
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Keystone Symposia Conference: Plant Receptor Ki...

Keystone Symposia Conference: Plant Receptor Ki... | Plant-Microbe Symbioses | Scoop.it
Keystone Symposia Conference: Plant Receptor Kinases: From Molecules to Environment, February 8—13, 2015, Taos, New Mexico on Plants and Microbes curated by Kamoun Lab @ TSL (.@KeystoneSymp Conference: Plant Receptor Kinases: From Molecules to Environment,...
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How do belowground organisms influence plant–pollinator interactions?

Aims The majority of angiosperms are pollinated by animals, and this interaction is of enormous importance in both agricultural and natural systems. Pollinator behavior is influenced by plants’ floral traits, and these traits may be modified by interactions with other community members. In recent years, knowledge of ecological linkages between above- and belowground organisms has grown tremendously. Soil communities are extremely diverse, and when their interactions with plants influence floral characteristics, they have the potential to alter pollinator attraction and visitation, but plant–pollinator interactions have been neglected in studies of the direct and indirect effects of soil organism–root interactions. Here, we review these belowground interactions, focusing on the effects of nitrogen-fixing bacteria, arbuscular mycorrhizal fungi and root-feeding herbivores, and their effects on floral traits and pollinators. Further, we identify gaps in our knowledge of these indirect effects and recommend promising directions and topics that should be addressed by future research.

Important Findings Belowground organisms can influence a wide variety of floral traits that are important mediators of pollinator attraction, including the number and size of flowers and nectar and pollen production. Other traits that are known to influence pollinators in some plant species, such as floral volatiles, color and nectar composition, have rarely or never been examined in the context of belowground plant interactions. Despite clear effects on flowers, relatively few studies have measured pollinator responses to belowground interactions. When these indirect effects have been studied, both arbuscular mycorrhizal fungi and root herbivores were found to shift pollinator visitation patterns. Depending on the interaction, these changes may either increase or decrease pollinator attraction. Finally, we discuss future directions for ecological studies that will more fully integrate belowground ecology with pollination biology. We advocate a multilevel approach to these questions to not only document indirect effect pathways between soil interactions and pollination but also identify the mechanisms driving changes in pollinator impacts and the resultant effects on plant fitness. A more thorough understanding of these indirect interactions will advance ecological theory and may inform management strategies in agriculture and conservation biology.

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There are so many interesting things we could do to explore this at the molecular level too.

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Isolation and characterization of PGPR and their effect on growth, yield and nutrient content in wheat (Triticum aestivum L.)

Isolation and characterization of PGPR and their effect on growth, yield and nutrient content in wheat (Triticum aestivum L.) | Plant-Microbe Symbioses | Scoop.it

The aims of our study were to enhance growth, yield and micronutrient status of wheat crop by various combinations of microbial strains (Bacillus megaterium,Arthrobacter chlorophenolicus and Enterobacter sp.) under pot and field experiments. Microbial strains were isolated from soils of different cropping systems and characterized by biochemical and molecular methods. Microbial strains (Bacillus megaterium BHU1 andArthrobacter chlorophenolicus BHU3) showed positive result for nitrogen fixation and phosphate solubilization, while Enterobacter sp. BHU5 gave positive result in nitrogen fixation only. However, A. chlorophenolicus and Enterobacter sp. showed HCN production while B. megaterium and Enterobacter sp. gave siderophore. Maximum N2-fixation and IAA production was observed with 15.0 mg Ng−1 carbon by A. chlorophenolicus and 26.4 µg ml−1 at tryptophan 100 µg ml−1 by Enterobacter sp, respectively. Triple combination of strains B. megaterium,A. chlorophenolicus and Enterobacter significantly increased 17.5%, 79.8%, 78.6% and 26.7% plant height, grain yield, straw yield and test weight under pot condition and also 29.4%, 27.5%, 29.5% and 17.6% under field condition. Similarly these treatment combinations showed maximum Nutrient acquisition and content of micronutrient viz. Fe, Cu, Mn and Zn in grain of wheat under both conditions. The results showed that the combined application of indigenous PGPR, B. megaterium,A. chlorophenolicus and Enterobacter can be used as efficient microbial consortium for wheat production.

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Extreme specificity of NCR gene expression in Medicago truncatula

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Interesting bioinformatic validation

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Chemically Synthesized 58-mer LysM Domain Binds Lipochitin Oligosaccharide

Chemically Synthesized 58-mer LysM Domain Binds Lipochitin Oligosaccharide | Plant-Microbe Symbioses | Scoop.it

Recognition of carbohydrates by proteins is a ubiquitous biochemical process. In legume–rhizobium symbiosis, lipochitin oligosaccharides, also referred to as nodulation (nod) factors, function as primary rhizobial signal molecules to trigger root nodule development. Perception of these signal molecules is receptor mediated, and nod factor receptor 5 (NFR5) from the model legume Lotus japonicus is predicted to contain three LysM domain binding sites. Here we studied the interactions between nod factor and each of the three NFR5 LysM domains, which were chemically synthesized. LysM domain variants (up to 58 amino acids) designed to optimize solubility were chemically assembled by solid-phase peptide synthesis (SPPS) with microwave heating. Their interaction with nod factors and chitin oligosaccharides was studied by isothermal titration calorimetry and circular dichroism (CD) spectroscopy. LysM2 showed a change in folding upon nod factor binding, thus providing direct evidence that the LysM domain of NFR5 recognizes lipochitin oligosaccharides. These results clearly show that the L. japonicus LysM2 domain binds to the nod factor from Mesorhizobium loti, thereby causing a conformational change in the LysM2 domain. The preferential affinity for nod factors over chitin oligosaccharides was demonstrated by a newly developed glycan microarray. Besides the biological implications, our approach shows that carbohydrate binding to a small protein domain can be detected by CD spectroscopy.

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Diversity of Nitrogen-Fixing Bacteria Associated with Switchgrass in the Native Tallgrass Prairie of Northern Oklahoma

witchgrass (Panicum virgatum L.) is a perennial C4 grass native to North America that is being developed as a feedstock for cellulosic ethanol production. Industrial nitrogen fertilizers enhance switchgrass biomass production but add to production and environmental costs. A potential sustainable alternative source of nitrogen is biological nitrogen fixation. As a step in this direction, we studied the diversity of nitrogen-fixing bacteria (NFB) associated with native switchgrass plants from the tallgrass prairie of northern Oklahoma (United States), using a culture-independent approach. DNA sequences from the nitrogenase structural gene, nifH, revealed over 20 putative diazotrophs from the alpha-, beta-, delta-, and gammaproteobacteria and the firmicutes associated with roots and shoots of switchgrass. Alphaproteobacteria, especially rhizobia, predominated. Sequences derived from nifH RNA indicated expression of this gene in several bacteria of the alpha-, beta-, delta-, and gammaproteobacterial groups associated with roots. Prominent among these were Rhizobium and Methylobacterium species of the alphaproteobacteria, Burkholderia and Azoarcus species of the betaproteobacteria, and Desulfuromonas and Geobacter species of the deltaproteobacteria.

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Nice work on switchgrass

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