Department of Bioscience & Bioengineering

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IIT Jodhpur

<h3>Background</h3>Plant probiotics bacteria are live microbes that promote soil health and plant growth and build the stress-tolerant capacity to the plants. They benefit the plants by increasing nutrient absorption and release of stress-related phytohormones. These plant probiotic bacteria serve a better purpose to the plant when compared to chemical fertilizers. Use of chemical fertilizers such as arsenic and cadmium can lead to soil acidification and even release of harmful gases such as methane which further pollutes the environment.<h3>Results</h3>Different bacterial species were isolated from the agricultural fields of Tattiannaram, Telangana, and identified as the efficient rhizosphere bacteria with the essential qualities of plant growth promotion by evaluating the nitrogen-fixing ability on a selective media and various other methods. Upon the molecular characterization of the isolates, they were identified as Corynebacterium spp., Bacillus spp., Lactobacillus spp., and Cytobacillus spp. The results were also examined using various bioinformatics tools for accuracy in their phylogenetic pattern.<h3>Conclusion</h3>The recognized species of plant probiotics have established roles in promoting plant growth and strengthening plant immunity. This research introduces an innovative methodology for evaluating and investigating recently identified bacterial isolates, focusing on their distinctive plant probiotic attributes. Through harnessing the potential of advantageous microorganisms and comprehending their interaction with plants and soil, our objective is to formulate inventive approaches to elevate crop productivity, enhance soil richness, and foster environmentally sustainable and robust agricultural methodologies. These characteristics exhibit promising potential for future incorporation into plant systems, fortifying growth and development, and underscoring their distinctive significance within the realm of agriculture.

World University root node

Journal of Genetic Engineering and Biotechnology

Isolation of plant growth-promoting rhizobacteria from the agricultural fields of Tattiannaram, Telangana

Extremophile land plants have evolved convergently to become tough survivors in harsh soil and climatic conditions, such as extremes of soil pH, temperature, drought, high salinity, heavy metals, high light intensity, and UV radiation. Thus, the extremophile plants hold the potential key to improving stress-resilience in crop plants in the face of global climate change and desertification. Moreover, extremophile plants also exhibit industrial importance, being the source of active pharmaceuticals, new fuels, and essential chemicals. Transcriptome analysis of extremophiles is a common approach towards discovering genes and molecular mechanisms for adaptation to stress apart from identifying the pathways responsible for the biosynthesis of commercially essential metabolites. Again, the current scenario inextremophile research ranges from the study of &nbsp;extremophile plant models, e.g., Arabidopsis lyrata, to various plants of economic and ecological significance. The genetic signatures obtained from the transcriptome libraries of these extremophiles are utilized towards their conservation by employing the genome-editing approaches apart from extending their applicability towards the introgression of abiotic tolerance traits into agronomically important crop plants. This chapter aims to summarize the recent transcriptome analyses of extremophile species from the Indian Thar desert and other extreme eco-regions of the world.

Transcriptome Analysis and Why it Matters

Chapter 3. Understanding the Facets of Extreme Land Plant Adaptation from Transcriptome Analysis

Aluminum (Al) toxicity in acid soil is one of the most severe environmental stress factors that limit world food production. Al ion (Al 3+ ) is highly reactive with negatively charged ligands of the cell and disturbs cell division and expansion at sub-micromolar levels. Since the harmful effects are caused by both cyto- and genotoxicities of Al, plant cells show various dose- and time-dependent responses. On the other hand, plants have evolved different Al tolerance strategies that protect sensitive cells from Al 3+ . These include restructuring of the cell wall to prevent deposition of Al 3+ and organic acid release by plasma membrane transporters to chelate out and exclude Al 3+ in the rhizosphere, regulated by the transcription factor STOP1 or its orthologs, and internal detoxification mechanisms including root-to-shoot translocation, antioxidant defense, and Al sequestration in vacuoles to prevent cytotoxicity. In recent years, genomics approaches, particularly genome-wide association studies and transcriptome analyses, have provided genetic evidence of well-known genes’ involvement in Al tolerance and uncovered new Al tolerance genes in plants. This chapter summarizes the findings from recent genomic studies that add to our understanding of the complex plant responses to Al toxicity.

Heavy Metal Toxicity and Tolerance in Plants: A Biological, Omics, and Genetic Engineering Approach

Aluminum Stress Tolerance in PlantsInsights from Omics Approaches

This study aimed to isolate stress-tolerant phytobeneficial bacteria as bio-inoculants for cowpea's sustainable growth under drought and nutrient deficiency conditions. However, the application successful of phytobeneficial bacteria is subject to effective in vitro screening under different physiological conditions. We isolated several Priestia species from cowpea rhizosphere that tolerates polyethylene glycol (PEG6000)-induced drought and nutrient deficiency. Of them, C8 (Priestia filamentosa; basonym: Bacillus filamentosus), followed by C29 (Priestia aryabhattai; basonym: Bacillus aryabhattai), tolerated up to 20% PEG in a low-nutrient medium. In the presence of PEG, Priestia filamentosa and Bacillus aryabhattai exhibited optimal growth in different temperatures and pH but failed to survive at extreme temperatures of 45 °C and pH 11. Priestia filamentosa preferred L-proline and L-glutamate, while L-tryptophan and L-tyrosine were the least utilized. Interestingly, Priestia filamentosa and Bacillus aryabhattai used more complex nitrogen sources, peptone, and yeast extract, than inorganic nitrogen for growth. Most importantly, under drought and nutrient deficiency, Priestia filamentosa exhibited multiple plant growth-promoting traits and more amylase and protease production than C29. Our results indicate that Priestia filamentosa is a potential bacterium to enhance the growth of cowpea plants under stressful conditions.

Current Microbiology

Isolation and Characterization of Stress-Tolerant Priestia Species from Cowpea Rhizosphere Under Drought and Nutrient Deficit Conditions

The response of a granular alignment held between fixed end walls to an impulse was introduced in the works of Nesterenko between 1983 and the years that followed. He showed analytically and experimentally that a granular chain admits a propagating solitary wave. In his analytic work, under small precompression compared to the local strain, he showed that one finds a propagating solitary wave. The solitary wave was also seen experimentally but at zero and vanishingly small precompressions. Under stronger precompression a possible Korteweg–de Vries (KdV) solitary wave was suggested though never observed. Later, others confirmed the solitary wave result at zero loading. Sen and Manciu reported seeing the solitary wave behavior in numerical simulations and in 2001 proposed an accurate solution which obtained the solitary wave at zero precompression as seen in some experiments and in numerics. Simulations showed an oscillatory tail following the solitary wave at small precompressions. In an experimental study in 1997, Costé, Falcon and Fauve and later Nesterenko et al. reported seeing propagation of a wave with an oscillatory tail. The oscillatory tail eventually consumed the solitary wave with increasing precompression. How can one reconcile Nesterenko’s solitary wave for the weakly precompressed system with Sen and Manciu’s solitary wave solution for zero precompression? Here we show that there is a separate solitary wave phase at a certain weak but finite loading regime which is distinct from Sen and Manciu’s work and this may be the reason why Nesterenko’s analytic theory seems to admit a solitary wave at finite loadings. We also offer insights into why the KdV solution is not seen. © 2023, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.

Granular Matter

Revisiting Nesterenko’s solitary wave in the precompressed granular alignment held between fixed ends

Cowpea is sensitive to drought and heat stress, particularly at the reproductive stages of development. Both stresses limit growth and yield, and their effect is more devastating when occurring concurrently. Dehydration-responsive element-binding protein 2A (DREB2A) is an important signaling hub integrating information about two different abiotic stresses, drought and heat. We identified VuDREB2A as a canonical DREB ortholog in cowpea, activating downstream stress-responsive genes by binding to DREs in their promoter. Post-translational modification of a negative regulatory domain (NRD) within the VuDREB2A protein prevents its degradation. Targeted deletion of the NRD produces a stable and constitutively active form VuDREB2A-CA. However, there is very little evidence of its practical utility under field conditions. This study overexpressed the VuDREB2A-CA in a popular cowpea variety and conducted drought- and heat-tolerance experiments across various stress regimes. Transgenic cowpea exhibited significant tolerance with consistently higher yield when exposed to over 30-d drought stress and 3-d exposure to high temperature (28&nbsp;°C˗52&nbsp;°C) without any pleiotropic alterations. The transgenic lines showed higher <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/photosynthetic-efficiency">photosynthetic efficiency</a>, <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/plant-osmotic-adjustment">osmotic adjustment</a>, antioxidant defense, <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/critical-thermal-maximum">thermotolerance</a>, and significantly higher survival and increased biomass than the wild type. Late <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/embryogenesis">embryogenesis</a> abundant 5, <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/heat-shock-protein-70">heat shock protein 70</a>, <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/dehydrin">dehydrin</a>, mitogen-activated protein kinase 2/4, <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/isoflavonoid">isoflavonoid</a> <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/reductase">reductase</a>, and myoinositol phosphate <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/synthase">synthase</a> were upregulated in transgenic lines under drought and heat stress. Through <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/gene-expression-profiling">transcriptome analysis</a> of the transgenic lines, we found significant up-regulation of various stress-responsive cowpea genes, having DRE in their promoter. Our results suggest that overexpression of VuDREB2A could improve cowpea production under drought and high temperatures.

Plant Physiology and Biochemistry

Enhanced osmotic adjustment, antioxidant defense, and photosynthesis efficiency under drought and heat stress of transgenic cowpea overexpressing an engineered DREB transcription factor

Priestia species isolated from the cowpea rhizosphere altered the transcriptome of cowpea roots by colonization and enhanced nutrient uptake, antioxidant mechanisms, and photosynthesis, protecting cowpea from drought and nutrient deficiency. Cowpea is a significant grain legume crop primarily grown in sub-Saharan Africa, Asia, and South America. Drought and nutrient deficiency affect the growth and yield of cowpea. To address this challenge, we studied the phyto-beneficial effects of stress-tolerant rhizobacteria on the biomass yield of cowpea under water- and nutrient-deficit conditions. Among the bacteria isolated, two rhizobacillus genotypes, C8 (Priestia filamentosa; basonym: Bacillus filamentosus) and C29 (Priestia aryabhattai; basonym: Bacillus aryabhattai) were evaluated for the improvement of seed germination and growth of cowpea under stress. Our study revealed that C8 protected cowpea from stress by facilitating phosphorus and potassium uptake, protecting it from oxidative damage, reducing transpiration, and enhancing CO2 assimilation. A 17% increase in root biomass upon C8 inoculation was concomitant with the induction of stress tolerance genes in cowpea roots predominantly involved in growth and metabolic processes, cell wall organization, ion homeostasis, and cellular responses to phosphate starvation. Our results indicate a metabolic alteration in cowpea root triggered by P. filamentosa, leading to efficient nutrient reallocation in the host plant. We propose inoculation with P. filamentosa as an effective strategy for improving the yield of cowpea in low-input agriculture, where chemical fertilization and irrigation are less accessible to resource-poor farmers.

Planta

Rhizosphere Priestia species altered cowpea root transcriptome and enhanced growth under drought and nutrient deficiency

A convergent, robust one-pot three-component approach for the synthesis of dihydrofuro[3,2-c]coumarins (DHFCs) was developed via the reaction of aryl/hetryl aldehydes, substituted phenacyl bromides and 4-hydroxycoumarin using N,N-diisopropyl ethyl ammonium acetate (DIPEAc) as the promoting medium. By virtue of its operational simplicity, efficiency, and wide substrate scope, the herein documented methodology constitutes a very attractive protocol addressing access to diversely substituted fused coumarin derivatives in a cost- and time-effective manner. Moreover, in silico pharmacophore modelling divulges the selective binding of the synthesized DHFC derivatives at the highly conserved active site catalytic cleft of Trichomonas vaginalis purine nucleoside phosphorylase (TvPNP), the indispensable enzyme of the protozoan purine salvage pathway and the potent anti-trichomoniasis drug target. The strong ligand binding is corroborated by excellent free energy of binding (ΔGbinding) profiles and further confirmed by all-atomistic molecular dynamics simulation analysis and deep learning based binding affinity (pKd) predictions. The docked conformations of DHFC derivatives at the active site catalytic cleft of TvPNP are structurally reminiscent of previously reported co-crystallized conformation of FormycinA (PDB ID: <a href="http://xlink.rsc.org/?pdb=1Z36">1Z36</a>), albeit the DHFC derivatives demonstrated stronger binding propensities. Detailed quantitative structure–function analysis, presented herein, may elucidate the potential role of the synthesized DHFC derivatives as future anti-trichomoniasis therapeutic leads.

New Journal of Chemistry

Convenient multicomponent synthesis of furo[3,2-c]coumarins in the promoting medium DIPEAc and assessment of their therapeutic potential through in silico pharmacophore based target screening

Recurrent spells of droughts are more common than a single drought, with intermittent moist recovery intervals. While the detrimental effects of the first drought on plant structure and physiology are unavoidable, if survived, plants can memorize the first drought to present a more robust response to the following droughts. This includes a partial stomatal opening in the watered recovery interval, higher levels of osmoprotectants and ABA, and attenuation of photosynthesis in the subsequent exposure. Short-term drought memory is regulated by ABA and other phytohormone signaling with transcriptional memory behavior in various genes. High levels of methylated histones are deposited at the drought-tolerance genes. During the recovery interval, the RNA polymerase is stalled to be activated by a pause-breaking factor in the subsequent drought. Drought leads to DNA demethylation near drought-response genes, with genetic control of the process. Progenies of the drought-exposed plants can better adapt to drought owing to the inheritance of particular methylation patterns. However, a prolonged watered recovery interval leads to loss of drought memory, mediated by certain demethylases and chromatin accessibility factors. Small RNAs act as critical regulators of drought memory by altering transcript levels of drought-responsive target genes. Further studies in the future will throw more light on the genetic control of drought memory and the interplay of genetic and epigenetic factors in its inheritance. Plants from extreme environments can give queues to understanding robust memory responses at the ecosystem level.

How do plants remember drought?

The role of commensal bacterial microbiota in the pathogenesis of human malignancies has been a research field of incomparable progress in recent years. Although breast tissue is commonly assumed to be sterile, recent studies suggest that human breast tissue may contain a bacterial microbiota. In this study, we used an immune-competent orthotopic breast cancer mouse model to explore the existence of a unique and independent bacterial microbiota in breast tumors. We observed some similarities in breast cancer microbiota with skin; however, breast tumor microbiota was mainly enriched with Gram-negative bacteria, serving as a primary source of lipopolysaccharide (LPS). In addition, dextran sulfate sodium (DSS) treatment in late-stage tumor lesions increased LPS levels in the breast tissue environment. We also discovered an increased expression of S100A7 and low level of TLR4 in late-stage tumors with or without DSS as compared to early-stage tumor lesions. The treatment of breast cancer cells with LPS increased the expression of S100A7 in breast cancer cells in vitro. Furthermore, S100A7 overexpression downregulated TLR4 and upregulated RAGE expression in breast cancer cells. Analysis of human breast cancer samples also highlighted the inverse correlation between S100A7 and TLR4 expression. Overall, these findings suggest that the commensal microbiota of breast tissue may enhance breast tumor burden through a novel LPS/S100A7/TLR4/RAGE signaling axis. © 2021 The Authors. Molecular Oncology published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.