Transcriptome Analysis of Wheat-Tilletia indica Interaction Provides Defense and Pathogenesis-Related Genes.

Karnal bunt (Tilletia indica Mitra) is an internationally quarantined disease of wheat. Until now, very little information has been available on the molecular basis of resistance and pathogenicity of T. indica. To investigate the molecular basis of host−pathogen interaction, the transcriptome of T. indica inoculated resistant (HD29) and susceptible (WH542) genotypes of wheat were analyzed. Approximately 58 million reads were generated using RNA sequencing by the Illumina NextSeq500 platform. These sequence reads were aligned to a reference genome of wheat to compare the expression level of genes in resistant and susceptible genotypes. The high-quality reads were deposited in the NCBI SRA database (SRP159223). More than 80,000 genes were expressed in both the resistant and susceptible wheat genotypes. Of these, 76,088 were commonly expressed genes, including 3184 significantly upregulated and 1778 downregulated genes. Four thousand one hundred thirteen and 5604 genes were exclusively expressed in susceptible and resistant genotypes, respectively. Based on the significance, 503 genes were upregulated and 387 genes were downregulated. Using gene ontology, the majority of coding sequences were associated with response to stimuli, stress, carbohydrate metabolism, developmental process, and catalytic activity. Highly differentially expressed genes (integral component of membrane, exonuclease activity, nucleic acid binding, DNA binding, metal ion binding) were validated in resistant and susceptible genotypes using qPCR analysis and similar expression levels were found in RNA-Seq. Apart from the wheat, the mapping of T. indica was 7.07% and 7.63% of resistant and susceptible hosts, respectively, upon infection, which revealed significant pathogenesis-related genes. This first study provided in-depth information and new insights into wheat−T. indica interaction for managing Karnal bunt disease of wheat.

Multilocus Sequence Typing and Single Nucleotide Polymorphism Analysis in Tilletia indica Isolates Inciting Karnal Bunt of Wheat.

Karnal bunt of wheat is an internationally quarantined disease affecting trade, quality, and production of wheat. During 2015-2016, a severe outbreak of Karnal bunt disease occurred in north-western plain zone of India. The present study was undertaken to decipher genetic variations in Indian isolates of Tilletia indica collected from different locations. Seven multilocus sequence fragments were selected to differentiate and characterize these T. indica isolates. A phylogenetic tree constructed based on pooled sequences of actin-related protein 2 (ARP2), ß-tubulin (TUB), eukaryotic translation initiation factor 3 subunit A (EIF3A), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone 2B (H2B), phosphoglycerate kinase (PGK), and serine/threonine-protein kinase (STPK) showed that isolate KB-11 (Kaithal, Haryana) was highly conserved as it was located in cluster 1 and has the maximum sequence similarity with the reference strain. Other isolates in cluster 1 included KB-16 and KB-17, both from Uttar Pradesh, and KB-19 from Haryana. Isolates KB-07 (Jind, Haryana) and KB-18 (Mujaffar Nagar, Uttar Pradesh) were the most diverse and grouped in a subgroup of cluster 2. Maximum numbers of single nucleotide polymorphisms (SNPs) (675) were in the PGK gene across the T. indica isolates. The minimum numbers of SNPs (67) were in KB-11 (Kaithal, Haryana), while the maximum number of SNPs (165) was identified in KB-18, followed by 164 SNPs in KB-14. KB-18 isolate was found to be the most diverse amongst all T. indica isolates. This first study on multilocus sequence typing (MLST) revealed that the population of T. indica was highly diverse.

PGPR-mediated expression of salt tolerance gene in soybean through volatiles under sodium nitroprusside.

Increasing evidence shows that nitric oxide (NO), a typical signaling molecule plays important role in development of plant and in bacteria-plant interaction. In the present study, we tested the effect of sodium nitroprusside (SNP)-a nitric oxide donor, on bacterial metabolism and its role in establishment of PGPR-plant interaction under salinity condition. In the present study, we adopted methods namely, biofilm formation assay, GC-MS analysis of bacterial volatiles, chemotaxis assay of root exudates (REs), measurement of electrolyte leakage and lipid peroxidation, and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) for gene expression. GC-MS analysis revealed that three new volatile organic compounds (VOCs) were expressed after treatment with SNP. Two VOCs namely, 4-nitroguaiacol and quinoline were found to promote soybean seed germination under 100 mM NaCl stress. Chemotaxis assay revealed that SNP treatment, altered root exudates profiling (SS-RE), found more attracted to Pseudomonas simiae bacterial cells as compared to non-treated root exudates (S-RE) under salt stress. Expression of Peroxidase (POX), catalase (CAT), vegetative storage protein (VSP), and nitrite reductase (NR) genes were up-regulated in T6 treatment seedlings, whereas, high affinity K+ transporter (HKT1), lipoxygenase (LOX), polyphenol oxidase (PPO), and pyrroline-5-carboxylate synthase (P5CS) genes were down-regulated under salt stress. The findings suggest that NO improves the efficiency and establishment of PGPR strain in the plant environment during salt condition. This strategy may be applied on soybean plants to increase their growth during salinity stress.

Induced drought tolerance through wild and mutant bacterial strain Pseudomonas simiae in mung bean (Vigna radiata L.).

The present study focused on the overproducing mutant of a plant growth promoting rhizobacterium (PGPR) Pseudomonas simiae strain AU (MTCC-12057) for significant drought tolerance in mung bean plants. Five mutants namely AU-M1, AU-M2, AU-M3, AU-M4 and AU-M5 were made after treatment of wild type strain with N-methyl-N-nitro-N-nitrosoguanidine. Mutant strain AU-M4 was recorded for enhanced ACC deaminase (ACC-D) activity, indole acetic acid (IAA) production and inorganic phosphate (Pi) solubilization compared to wild strain and other four mutant strains under drought condition. AU-M4 showed higher phosphate solubilization index (8.17) together with higher ACC-D activity (98 nmol/mg/h) and IAA concentration (69.35 µg/ml) compared with the wild type P. simiae strain AU ACC-D activity (79 nmol/mg/h) and IAA concentration (38.98 µg/ml) respectively. In this report, we investigated the effect of both wild and mutant type bacterial strain on mung bean plants under drought stress. Results showed that mutant AU-M4 and wild type strain AU inoculated plants exhibited superior tolerance against drought stress, as shown by their enhanced plant biomass (fresh weight), higher water content, higher proline accumulation and lower osmotic stress injury. Mutant AU-M4 and wild strain AU inoculated plants reduced the ethylene level by 59 and 45% respectively, compared to the control under stress condition. Furthermore, bacterial inoculated plants showed enhanced induced systemic drought tolerance by reducing stomata size and net photosynthesis resulting higher water content in mung bean plants that may help in survival of plants during drought condition. To mitigate the effects of drought stress, use of PGPR will be needed to ensure sufficient production of food from crop plants. Taking current leads available, concerted future research is needed in this area, particularly on field evaluation with application of potential microorganisms.

Induced defense-related proteins in soybean (Glycine max L. Merrill) plants by Carnobacterium sp. SJ-5 upon challenge inoculation of Fusarium oxysporum.

The aim of the present study was to analyze induced expression of defense-related proteins in the soybean plants by rhizobacterial stain Carnobacterium sp. SJ-5 upon challenge inoculation with Fusarium oxysporum. Determination of the enzymatic activity of the different defense-related enzymes, phenylalanine ammonia lyase (PAL), lipoxygenase (LOX), peroxidase (POD) and polyphenol oxidase (PPO) was performed in the major parts of Glycine max L. Merrill using spectrophotometric method. Native-polyacrylamide gel electrophoresis analysis of the POD and PPO was employed followed by activity staining to find out the isoforms of respective enzymes. Activities of the PAL, LOX, POD and PPO were found to be highest in the bacterized root tissue of the soybean plants challenged with F. oxysporum. Isoform analysis revealed that PPO1, PPO4 and POD2 isoforms were expressed at higher levels in bacterized soybean root tissues challenge inoculated with the pathogen. Conclusively it was found that bacterial strain Carnobacterium sp. SJ-5 protect soybean plants from wilt disease caused by F. oxysporum by elicitation of the defense-related enzymes.

Rhizobacterium-mediated growth promotion and expression of stress enzymes in Glycine max L. Merrill against Fusarium wilt upon challenge inoculation.

Wilt disease of soybean caused by a very common soil-borne fungus, Fusarium oxysporum is one of the most destructive diseases of the crop. The aim of the present study was to characterize plant growth-promotion activities and induced resistance of a rhizobacterial strain for the soybean plant against F. oxysporum. Rhizobacterium strain SJ-5 exhibited plant growth-promotion characteristics and antagonistic activity against the test pathogen on dual plate assay. It was identified as a Carnobacterium sp. A 950 bp PCR product was amplified from Carnobacterium sp. strain SJ-5, using zwittermicin A self-resistance gene-specific primers (zmaR). The strain produced indole 3-acetic acid (19 µg/ml) in the presence of salt stress and exhibited growth in Dworkin and Foster salt medium amended with 1-aminocyclopropane-1-carboxylate (ACC) through ACC deaminase activity (277 nmol/mg/h) as compared to the control. Strain seeds treated with the strain significantly enhanced the quorum of healthy plants after challenge inoculation at 14 days after seeding. An increase in the activity of stress enzymes after challenge inoculation with the test pathogen is reported. Treatment with the bacterium resulted in an increase in the chlorophyll content in the leaves in comparison with challenge-inoculated plants.

Effect of nitric oxide signaling in bacterial-treated soybean plant under salt stress.

To understand protective roles of nitric oxide against salt stress, the effects of exogenous sodium nitroprusside on activities of lipoxygenase, peroxidase, phenylalanine ammonialyase, catalase, superoxide dismutase enzymes, proline accumulation, and distribution of sodium in soybean plants under salt were determined. Application of sodium nitroprusside + bacterium enhanced plant growth-promotion characteristics, activities of different enzymes, and proline accumulation in the presence of sodium nitroprusside under salt stress. Treatment with NaCl at 200 mM and sodium nitroprusside (0.1 mM) reduced Na⁺ levels but increased K⁺ levels in leaves in comparison with the NaCl-treated plants. Correspondingly, the plants treated with exogenous sodium nitroprusside and NaCl maintained a lower ratio of [Na⁺]/[K⁺] in NaCl-stressed plants.

Method of moments for computational microemulsion analysis and prediction in tertiary oil recovery.

We discuss the application of Helfrich's surface torque density concept to microemulsion design and analysis from three different angles: (i) from the point of view of coarse-grained molecular simulations, using Dissipative Particle Dynamics, including charge interactions and added salt, (ii) using an approximate double-film model for the surface, and (iii) comparison with formulation approaches. The simulations use that the surface torque can be calculated unambiguously from the stress profile, provided the surface is tensionless. Very good agreement is found on predicting optimal salinity (or the absence of that) for a range of surfactants: dioctyl sodium sulfosuccinate, various twin-tailed sulfonates and sodium dodecyl sulfate. The simulations are very fast, on par with times for experiments, thus they could lead to a practical tool for discovery of more efficient surfactants, although much remains to be done with respect to other important variables: oil composition, surfactant mixtures, aggregation in solution, and so on. The microscopic model (second approach) is highly approximate: it is essentially based on two opposing swelling tendencies, that are both of osmotic nature. In accordance with the model, the tails are swollen by the oil and the charged head groups are confined in a salty layer in Donnan equilibrium with the salt solution. In this way, the surface interactions are purely entropic. The comparison of the film model with existing formulation approaches (third approach) covers the interfacial tension minimum, Winsor R theory, quantitative structure property relations (QSPR), hydrophilic-lipophilic deviation (HLD), HLD-net average curvature, and temperature coefficients. Using the surface torque analysis, we succeed in deriving in an ab initio way QSPR empirical coefficients that have been known for decades, but until now, have been obscure in origin.

Soybean growth-promotion by Pseudomonas sp. strain VS1 under salt stress.

In the present study, we employ Pseudomonas sp. strain VS1 showed in vitro plant growth-promotion characteristics and promoted soybean seed emergence under salt stress. Strain produced indole 3-acetic acid in the presence of salt stresses that exhibited high numbers of lateral root as compared to control. Bacterial strain exhibited growth in DF salt medium amended with 1-aminocyclopropane-1-carboxylate through ACC deaminase activity. Bacterial-treated soybean seeds were subjected to salt stress and significantly enhanced emergence at 7 days after seeding. Strain untreated soybean plants had a 33% seed germination when 200 mM NaCl was applied at 0 DAS and the root length was significantly decreased compared to the strain treated plants (LSD0.05 = 0.21). Most importantly, the application of 200 mM NaCl at 0 DAS resulted in only a 9% of lateral root in untreated plants as compared to strain treated plants.

Modeling polymer-induced interactions between two grafted surfaces: comparison between interfacial statistical associating fluid theory and self-consistent field theory.

The interaction between two polymer grafted surfaces is important in many applications, such as nanocomposites, colloid stabilization, and polymer alloys. In our previous work [Jain et al., J. Chem. Phys. 128, 154910 (2008)], we showed that interfacial statistical associating fluid density theory (iSAFT) successfully calculates the structure of grafted polymer chains in the absence/presence of a free polymer. In the current work, we have applied this density functional theory to calculate the force of interaction between two such grafted monolayers in implicit good solvent conditions. In particular, we have considered the case where the segment sizes of the free (sigma(f)) and grafted (sigma(g)) polymers are different. The interactions between the two monolayers in the absence of the free polymer are always repulsive. However, in the presence of the free polymer, the force either can be purely repulsive or can have an attractive minimum depending upon the relative chain lengths of the free (N(f)) and grafted polymers (N(g)). The attractive minimum is observed only when the ratio alpha = N(f)/N(g) is greater than a critical value. We find that these critical values of alpha satisfy the following scaling relation: rho(g) square root(N(g)) beta(3) proportional to alpha(-lambda), where beta = sigma(f)/sigma(g) and lambda is the scaling exponent. For beta = 1 or the same segment sizes of the free and grafted polymers, this scaling relation is in agreement with those from previous theoretical studies using self-consistent field theory (SCFT). Detailed comparisons between iSAFT and SCFT are made for the structures of the monolayers and their forces of interaction. These comparisons lead to interesting implications for the modeling of nanocomposite thermodynamics.

Microstructure and depletion forces in polymer-colloid mixtures from an interfacial statistical associating fluid theory.

By using a classical density functional theory (interfacial statistical associating fluid theory), we investigate the structure and effective forces in nonadsorbing polymer-colloid mixtures. The theory is tested under a wide range of conditions and performs very well in comparison to simulation data. A comprehensive study is conducted characterizing the role of polymer concentration, particle/polymer-segment size ratio, and polymer chain length on the structure, polymer induced depletion forces, and the colloid-colloid osmotic second virial coefficient. The theory correctly captures a depletion layer on two different length scales, one on the order of the segment diameter (semidilute regime) and the other on the order of the polymer radius of gyration (dilute regime). The particle/polymer-segment size ratio is demonstrated to play a significant role on the polymer structure near the particle surface at low polymer concentrations, but this effect diminishes at higher polymer concentrations. Results for the polymer-mediated mean force between colloidal particles show that increasing the concentration of the polymer solution encourages particle-particle attraction, while decreasing the range of depletion attraction. At intermediate to high concentrations, depletion attraction can be coupled to a midrange repulsion, especially for colloids in solutions of short chains. Colloid-colloid second virial coefficient calculations indicate that the net repulsion between colloids at low polymer densities gives way to net attraction at higher densities, in agreement with available simulation data. Furthermore, the results indicate a higher tendency toward colloidal aggregation for larger colloids in solutions of longer chains.

Modified interfacial statistical associating fluid theory: application to tethered polymer chains.

Modified interfacial statistical associating fluid theory density functional theory is extended to tethered polymer chains in the absence or presence of free polymer chains. The structures of the "dry" and "wet" polymer brushes have been calculated and compared with simulation results available in the literature. The comparisons show that the theory accurately predicts the structure of the tethered polymer brush. The average brush heights calculated from the theory agree with well-established scaling theories for tethered polymers. However, these scaling theories cannot predict the detailed structure, accurately. The effects of the segment-segment interactions of the tethered polymer and the free polymer have been effectively captured by the theory.

Modified interfacial statistical associating fluid theory: a perturbation density functional theory for inhomogeneous complex fluids.

A density functional theory based on Wertheim's first order perturbation theory is developed for inhomogeneous complex fluids. The theory is derived along similar lines as interfacial statistical associating fluid theory [S. Tripathi and W. G. Chapman, J. Chem. Phys. 122, 094506 (2005)]. However, the derivation is more general and applies broadly to a range of systems, retaining the simplicity of a segment density based theory. Furthermore, the theory gives the exact density profile for ideal chains in an external field. The general avail of the theory has been demonstrated by applying the theory to lipids near surfaces, lipid bilayers, and copolymer thin films. The theoretical results show excellent agreement with the results from molecular simulations.