Search

Genome sequence-driven molecular typing tools have the potential to uncover the population biology and genetic diversity of rapidly evolving plant pathogens like Magnaporthe oryzae. Here, we report a new molecular typing technique -a digitally portable tool for population genetic analysis of M. oryzae to decipher the genetic diversity. Our genotyping tool exploiting allelic variations in housekeeping and virulence genes coupled with pathotyping revealed a prevalence of genetically homogenous populations within a single-field and plant niches such as leaf and panicle. The M. oryzae inciting leaf-blast and panicle-blast were confirmed to be genetically identical with no or minor nucleotide polymorphism in 17 genomic loci analyzed. Genetic loci such as Mlc1, Mpg1, Mps1, Slp1, Cal, Ef-Tu, Pfk, and Pgk were highly polymorphic as indicated by the haplotype-diversity, the number of polymorphic sites, and the number of mutations. The genetically homogenous single field population showed high virulence variability or diversity on monogenic rice differentials. The study indicated that the genetic similarity displayed by the isolates collected from a particular geographical location had no consequence on their virulence pattern on rice differentials carrying single/multiple resistance genes. The data on virulence diversity showed by the identical Sequence Types (STs) is indicative of no congruence between polymorphic virulence genes-based pathotyping and conserved housekeeping genes-based genotyping.

Background The fundamental role and contributions of phyllosphere habitat in shaping plant functional ecology are poorly investigated, and often underestimated. Phyllosphere -the harsh and dynamic foliar-photosynthetic-habitat is continuously exposed to vagaries of changing weather events during the entire plant life. With its adapted microbiota, the phyllosphere-niche brings microbial diversity to the plant-holobiont pool and potentially modulates a multitude of plant and agronomic traits. The phyllomicrobiome structure and the consequent ecological functions are vulnerable to a host of biotic (Genotypes) and abiotic-factors (Environment) which is further compounded by agronomic-transactions on domesticated agricultural crops. However, the ecological forces driving the phyllomicrobiome assemblage and functions are among the most under-studied aspects of plant biology. Despite the reports on the occurrence of diverse prokaryotic phyla such as Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria on phyllosphere habitat, the functional characterization leading to their utilization for agricultural sustainability is not yet adequately explored.Currently, the metagenomic-Next-Generation-Sequencing (mNGS) technique scanning the conserved V3-V4 region of ribosomal RNA gene is a widely adopted strategy for microbiome-investigations. However, the structural and functional validation of mNGS annotations by microbiological methods is not integrated into the microbiome exploration-programs. In the present study, we combined the high throughput mNGS approach with conventional microbiological methods to decipher the core-functional-phyllomicrobiome of contrasting rice genotypes varying in their response to blast disease grown in contrasting agroclimatic zones in India. We, further, scanned the rice phyllosphere by electron microscopy to show the microbial communities on leaf. Magnaporthe oryzae -the phyllosphere pathogen inciting necrotic lesion on cereal crops is managed by the deployment of ‘non-durable’ blast resistance genes and ‘toxic’ fungicidal molecules. Nowadays, there is a growing consensus for devising an alternative strategy for mitigating blast owing to a recent ban on the use of most commonly used fungicidal molecule, tricyclazole. In the present work, we further identified phyllosphere- core-functional microbial groups leading to the proposal of phyllomicrobiome assisted rice blast management strategy. Multi-pronged activities of phyllomicrobiome against Magnaporthe oryzae (antifungal activity), rice innate immunity (defense elicitation), and rice blast disease (disease suppression) have been elaborated for effective management of blast by phyllomicrobiome re-engineering. ResultsRice phyllomicrobiome of tropical “Island-Zone” displayed marginally more bacterial community diversity than that of temperate ‘Mountain-Zone’. Principal coordinate analysis based on Bray Curtis and ANoSIM method indicated nearly converging-phyllomicrobiome profiles on two contrasting rice genotypes grown in the same agroclimatic zone. However, the rice genotype grown in the contrasting Mountain-zone and Island-zone displayed diverse-phyllomicrobiome profiles indicating a strong influence of environmental factors rather than the genotype on phyllomicrobiome structure and assembly. The predominance of Phyla such as Proteobacteria, Actinobacteria, and Firmicutes was observed on the rice phyllosphere irrespective of the genotypes and environmental conditions. The core-microbiome analysis showed multi-microbiota-core consisting of Acidovorax, Arthrobacter, Bacillus, Clavibacter, Clostridium, Cronobacter, Curtobacterium, Deinococcus, Erwinia, Exiguobacterium, Hymenobacter, Kineococcus, Klebsiella, Methylobacterium, Methylocella, Microbacterium, Nocardioides, Pantoea, Pedobacter, Pseudomonas, Salmonella, Serratia, Sphingomonas and Streptomyces on phyllosphere of rice genotypes grown in contrasting agroclimatic zones. The linear discriminant analysis (LDA) effect size (LEfSe) method revealed ten and two distinct bacterial genera in blast-resistant and -susceptible genotypes, respectively. The analysis further indicated 15 and 16 climate-zone specific bacterial genera for Mountain and Island zone, respectively. SparCC based network analysis of phyllomicrobiome showed hundreds of complex intra-microbial cooperative or competitive interactions on the rice genotypes and agroclimatic zones. Our microbiological validation of mNGS data further confirmed the presence of resident Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas on the rice phyllosphere. Strikingly, the two contrasting agroclimatic zones displayed genetically identical bacterial isolates on the phyllosphere that could be attributed to the spatio-temporal transmission of core-phyllomicrobiome, perhaps, aided by rice seeds. A total of 59 distinct bacterial isolates were obtained, identified, and evaluated for their functional attributes on Magnaporthe oryzae and rice plant. The phyllomicrobiome associated core-bacterial communities showed secreted-metabolite and volatile-compound mediated antifungal activity on M. oryzae. Upon phyllobacterization (a term coined for spraying of bacterial cells on the phyllosphere), the core bacterial species such as Acinetobacter baumannii, Aureimonas sp., Pantoea ananatis, P. eucrina, and Pseudomonas putida elicited plant defense and contributed significantly to blast disease suppression. Transcriptional analysis by qPCR indicated induction of rice innate immunity associated genes such as OsPR1.1, OsNPR1, OsPDF2.2, OsFMO, OsPAD4, OsCEBiP, and OsCERK1 in phyllobacterized rice seedlings. ConclusionsThe rice genotypes growing in a particular agroclimatic zone showed a convergent phyllomicrobiome assemblage and composition. Conversely, diverging phyllomicrobiome assembly was observed on rice genotype cultivated in the contrasting agroclimatic zones. Agroclimatic zones and the associated climatic-factors rather than plant-genotypes per se appeared to drive phyllomicrobiome structure and composition on the rice genotypes. Our integrated mNGS method and microbiological validation divulged Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas as core phyllomicrobiome of rice. Genetically identical bacterial communities belonging to Pantoea intercepted on the phyllosphere of rice grown in the two contrasting agroclimatic zones are suggestive of spatio-temporal transmission of phyllomicrobiome aided by seed. The core-microbiome mediated phyllobacterization showed potential for blast disease suppression by direct-antibiosis and defense elicitation. The identification of phyllosphere adapted functional core-bacterial communities in our study and their co-occurrence dynamics presents an opportunity to devise novel strategies for rice blast management through phyllomicrobiome reengineering in the future.

Permanent wilting point (PWP) is generally used to ascertain plant resistance against abiotic drought stress and designated as the soil water content (θ) corresponding to soil suction (ψ) at 1500 kPa obtained from the soil water retention curve. Determination of PWP based on only pre-assumed ψ may not represent true wilting condition for soils with contrasting water retention abilities. In addition to ψ, there is a need to explore significance of additional plant parameters (i.e., stomatal conductance and photosynthetic status) in determining PWP. This study introduces a new framework for determining PWP by integrating plant leaf response and ψ during drought. Axonopus compressus were grown in two distinct textured soils (clayey loam and silty sand), after which drought was initiated till wilting. Thereafter, ψ and θ within the root zone were measured along with corresponding leaf stomatal conductance and photosynthetic status. It was found that coarse textured silty sand causes wilting at much lower ψ (≈ 300 kPa) than clayey loam (≈ 1600 kPa). Plant response to drought was dependent on the relative porosity and mineralogy of the soil, which governs the ease at which roots can grow, assimilate soil O2, and uptake water. For clay loam, the held water within the soil matrix does not facilitate easy root water uptake by relatively coarse root morphology. Contrastingly, fine root hair formation in silty sand facilitated higher plant water uptake and doubled the plant survival time.

Sustainable biomaterials such as natural fibers and biochars have been increasingly used in green infrastructures such as landfill covers for its dual-advantages of climate change mitigation and waste management. The existing studies did not systematically discuss the comparison on how biochar (stable carbon) and fiber (likely degradable), influence plant growth and water retention abilities in unsaturated soils. Also, the effect of photochemistry in the amended soils has rarely been investigated. This study addresses the limitations of previous investigations by exploring plant parameters such as photochemical yield, stomatal conductance, root area index, and unsaturated soil hydraulic parameters, including soil water retention curves (SWRC) of amended soils. Pot experiments were conducted in an environmentally controlled greenhouse. Two biochars from different plant-based feedstocks (Eichhornia crassipes, Prosopis juliflora) and one natural fiber (coir pith fiber) were mixed with soil at 5% and 10% application rate (by weight). Grass species of Axonopus compressus was planted to study the effects of different amendment materials and its corresponding plant responses during an applied drought period. The test results show that biochar amended soils increased the shoot growth by up to 100−200%. The stomatal conductance of the grass leaves increased by 54%−101% during the drought period for both biochars and coir amended soil. Furthermore, at low suction, the coir had a high water retention capacity than the biochars, explaining the observed higher stomatal conductance values. Importantly, it was discovered that the plant photochemical quantum yield responses associated with plant wilting was found to vary between 1500 and 1800 kPa for all the soil treatments. The study concludes with a newly developed mathematical expression based on the measurements of plant parameters and soil suction. The new equation could be used to optimize the irrigation frequency in order to apply any informed measures to maintain green infrastructures.

Weeds, pests, and pathogens are among the pre-harvest constraints in rice farming across rice-growing countries. For weed management, manual weeding and herbicides are widely practiced. Among the herbicides, glyphosate [N-(phosphonomethyl) glycine] is a broad-spectrum systemic chemical extensively used in agriculture. Being a competitive structural analog to phosphoenolpyruvate, it selectively inhibits the conserved 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) enzyme required for the biosynthesis of aromatic amino acids and essential metabolites in eukaryotes and prokaryotes. In the present study, we investigated the antifungal and defense elicitor activity of glyphosate against Magnaporthe oryzae on transgenic-rice overexpressing a glyphosate-resistance OsEPSPS gene (T173I + P177S; TIPS OsmEPSPS) for blast disease management. The glyphosate foliar spray on OsmEPSPS transgenic rice lines showed both prophylactic and curative suppression of blast disease comparable to a blasticide, tricyclazole. The glyphosate displayed direct antifungal activity on Magnaporthe oryzae as well as enhanced the levels of antioxidant enzymes and photosynthetic pigments in rice. However, the genes associated with phytohormones-mediated defense (OsPAD4, OsNPR1.3, and OsFMO) and innate immunity pathway (OsCEBiP and OsCERK1) were found repressed upon glyphosate spray. Altogether, the current study is the first report highlighting the overexpression of a crop-specific TIPS mutation in conjugation with glyphosate application showing potential for blast disease management in rice cultivation.

Aims We investigated and compared the variability in biomechanical properties of Chrysopogon zizanioides L. (vetiver grass), including tensile strength, Young's modulus, and breakage strain, which have direct implication to root reinforcement to slope. Methods We tested the effects of growth condition (pots versus field), root water content (hydrated versus oven dried), and loading speed (16 mm/min versus 200 mm/min) on the biomechanical properties of vetiver roots (n = 344) via a series of uniaxial tensile tests. We also measured the root biomechanical traits such as diameter, density, degree of saturation, and relative root dry weight. Results Although the strength and modulus followed a negative power law relationship with root diameter (R2 up to 0.69), the strain–diameter relationship was linear (R2 = 0.20). Growth condition and loading speed did not have significant effects on the root biomechanical properties, whereas root water content showed significant effects on these properties, particularly in fine roots ( Conclusion A major source of the variability in strength, modulus, and strain of vetiver roots was root water content, which occurred primarily in fine roots (

Blast disease caused by Magnaporthe oryzae is an important production constraint in rice farming worldwide. Novel strategies are needed to combat blast disease as the current options like host resistance and fungicides are either unstable or not-acceptable. Black pepper associated Pseudomonas putida BP25 endogenously colonized rice -a monocot, in a density-dependent manner with altered root growth and defense activation, also showed biocontrol activity against blast caused by M. oryzae. Fluorescence imaging of P. putida BP25 primed seedlings revealed extensive bacterial colonization in roots that was further confirmed in plate assay and qPCR. Although initial counts could be correlated with bacterial dose used for priming, the bacterial population stabilized 14-days post priming suggesting internal regulation of endophyte colonization. Endophytic colonization of rice triggered alteration in root morphology, possibly, due trade-off between growth and defense. P. putida BP25 significantly inhibited the mycelium of M. oryzae by both volatile and non-volatile metabolites and also seed priming protected the rice from blast. Activities of defense related peroxidase and phenols were found increased in primed plants. qPCR assay of rice defense and developmental genes indicated increased expression of Systemic Acquired Resistance (SAR) related OsPR1-1 (Pathogenesis Related protein 1-1) and down-regulation of OsPR3. In addition, rice seedlings emerged from endophyte priming showed down-regulation of stress responsive OsACO4 and OsACS6 involved in inter-nodal elongation which plays an important role in growth and development.