Department of Bioscience & Bioengineering

&ldquo;IIT Jodhpur is committed to impart quality education to facilitate the creation of qualified, competent and responsible human resources to meet the emerging technological challenges of the world. It is working towards creating an equitable learning platform that is positive, accessible and effective in the face of the modern societal and scientific advancements.

Flexibility in curriculum, in all its academic programs, encompassing elements of teaching, research, creativity, innovation and entrepreneurship is the most unique feature of IIT Jodhpur. The Department of Science and Technology (DST), under the National Mission on Cyber Physical Systems, has identified IIT Jodhpur as a Technology &amp; Innovation Hub in the area of Augmented Reality and Virtual Reality. The institute has also been nominated as the coordinator for the Jodhpur City and Knowledge Cluster by the Office of Principal Scientific Adviser, Government of India.

The sprawling 852-acre IIT Jodhpur campus is a majestic tribute to the deep-rooted diverse cultural heritage of the region. The campus is an architectural masterpiece, which is slated to become an international exemplar of sustainability with net-zero energy, and advanced water and waste management strategies.&rdquo;

IIT Jodhpur

We compared the efficacy of the Indian Farmers Fertilizer Cooperative (IFFCO) liquid nano urea formulation (NUF) and conventional urea on the model plant Arabidopsis thaliana. NUF and equimolar bulk urea were applied to vermiculite-grown one-month-old plants as 0.4% foliar sprays. NUF resulted in a 0.4&nbsp;g increase in biomass, 0.5 mg g− 1 in chlorophyll, 0.17 mmol g− 1 in nitrogen, and 28.8 mg g− 1 in amino acid content of the leaves, compared to bulk urea. NUF’s zeta potential of -54.7 mV and particle size of ≃27.7&nbsp;nm, measured by dynamic light scattering and transmission electron microscopy, is suitable for stomatal uptake. A differential gene expression analysis of NUF versus urea-treated plants showed significantly higher expression levels of 211 genes (log2fold-change &gt; 0.5, FDR &lt; 0.05) involved in the biosynthesis of carbohydrates, amino acids, nucleotides, lipids, phytohormones, and secondary metabolites, cell wall biosynthesis and modification, growth and developmental processes, cell cycle, and stress response than bulk urea. On the other hand, 1,286 genes (log2fold-change &lt; -0.5) involved in cell death, abscission, senescence, nitrogen transport and metabolism, and biotic stress response showed lower expression levels upon NUF application than bulk urea. These suggest that although NUF suppresses nitrogen uptake genes, it enhances growth by higher induction of essential biomolecule synthesis and growth-promoting genes, than bulk urea. This research advances current knowledge in sustainable agriculture by elucidating the molecular mechanisms through which nano urea enhances plant productivity compared to bulk urea, potentially reducing fertilizer use.

Plant Growth Regulation

Foliar application of nano Urea enhances vegetative growth of Arabidopsis thaliana over equimolar bulk urea through higher induction of biosynthesis genes but suppression of nitrogen uptake and senescence genes.

The combination of nanotechnology and hydroponics paves the way toward sustainable agriculture with less environmental footprints. We investigated the effects of a liquid nano urea formulation (NUF) marketed by Indian Farmers Fertilizer Cooperative (IFFCO) on the model plant Arabidopsis thaliana in hydroponics, comparing it to an equimolar bulk urea. Dynamic light scattering and transmission electron microscopy confirmed NUF’s negative surface charge and sub-100-nm size, suitable for its uptake and distribution in the plant. A two-week growth in a nitrogen-free hydroponic medium with 70&nbsp;μM NUF led to a 20% higher biomass and 16% higher chlorophyll content than a medium with 70&nbsp;μM urea. Higher doses of NUF inhibited growth, whereas higher equivalent urea doses did not. Transcriptome analysis revealed that NUF led to the differential expression of more genes than urea at 12&nbsp;h to seven days of treatment. Nitrogen assimilation, growth, photosynthesis, and stress tolerance genes showed higher transcript levels in NUF than in urea. On the other hand, NUF led to greater suppression of many negative growth-regulating genes. After seven days of treatment, chlorophyll biosynthesis genes were up-regulated, while chlorophyll catabolism genes down-regulated at higher levels by NUF than by urea, correlating with the higher chlorophyll content of NUF-treated seedlings. In conclusion, NUF outperformed equimolar urea for the growth promotion of A. thaliana at a low concentration in hydroponics, leading to a greater regulation of genes for nitrogen metabolism and chlorophyll biosynthesis. Our results suggest a potential use of NUF as a nitrogen fertilizer for hydroponic agriculture.

Journal of Plant Growth Regulation

Nano urea outperforms equimolar bulk urea in the hydroponic growth of Arabidopsis thaliana by inducing higher levels of nitrogen assimilation and chlorophyll biosynthesis genes.

Essential plant nutrients encapsulated or combined with nano-dimensional adsorbents define nano fertilizers (NFs). Nanoformulation of non-essential elements enhancing plant growth and stress tolerance also comes under the umbrella of NFs. NFs have an edge over conventional chemical fertilizers, viz., higher plant biomass and yield using much lesser fertilization, thereby reducing environmental pollution. Foliar and root applications of NFs lead to their successful uptake by the plant, depending on the size, surface charge, and other physicochemical properties of NFs. Smaller NFs can pass through channels on the waxy cuticle depending on the hydrophobicity, while larger NFs pass through the stomatal conduits of leaves. Charge-based adsorption, followed by apoplastic movement and endocytosis, translocates NFs through the root, while the size of NFs influences passage into vascular tissues. Recent transcriptomic, proteomic, and metabolomic studies throw light on the molecular mechanisms of growth promotion by NFs. The expression levels of nutrient transporter genes are regulated by NFs, controlling uptake and minimizing excess nutrient toxicity. Accelerated growth by NFs is brought about by their extensive regulation of cell division, photosynthesis, carbohydrate, and nitrogen metabolism, as well as the phytohormone-dependent signaling pathways related to development, stress response, and plant defense. NFs mimic Ca,2+ eliciting second messengers and associated proteins in signaling cascades, reaching transcription factors and finally orchestrating gene expression to enhance growth and stress tolerance. Developing advanced nano fertilizers of the future must involve exploring molecular interactions with plants to reduce toxicity and improve effectiveness.

Plant Molecular Biology

Molecular mechanisms of plant productivity enhancement by nano fertilizers for sustainable agriculture

We sequenced the drought-response transcriptome of the keystone tree species Prosopis cineraria from the Indian Thar desert to understand the key factors in its drought tolerance mechanism. We identified a network of genes activated in P. cineraria involved in the biosynthesis of osmolytes, antioxidants, phytohormones, and signal transduction. Of these, up-regulation of 54 APETALA2/Ethylene-Responsive Factor (AP2/ERF) transcription factor genes, validated by real-time PCR, suggests their key role in the drought tolerance of P. cineraria. We conducted a genome-wide study of the AP2/ERF superfamily in P. cineraria, classifying its 255 proteins into 15 clades and analyzing their protein structures, gene structure, and promoter organization. The P. cineraria genome contains more copies of AP2/ERF genes than drought-sensitive plants. Further, we identified sequence polymorphisms in AP2/ERF genes between Arabian and Indian cultivars of P. cineraria. We modeled the DNA–protein complex structures of AP2/ERFs from drought-tolerant and sensitive species using AlphaFold to compare their DNA-binding ability. Though the DNA-binding domain (DBD) is relatively conserved across species, the unstructured region of these proteins possesses different charge distributions, which might contribute differently to their DNA search and binding. Using all-atom molecular dynamics simulations, we teased out a higher number of specific DBD-DNA hydrogen bonds in P. cineraria, leading to a stronger DNA-binding affinity than drought-sensitive Arabidopsis thaliana. These results directly support copy number expansion of AP2/ERF transcription factors and the evolution of their structures for more efficient DNA search and binding as drought adaptation mechanisms in P. cineraria.

World University root node

AP2/ERF Transcription Factor Orthologs of the Desert Tree Prosopis cineraria Show Higher Copy Number and DNA-Binding Affinity than Drought-Sensitive Species

This study aimed to isolate plant growth and drought tolerance-promoting bacteria from the nutrient- poor rhizosphere soil of several plant species from the Thar desert and unravel their molecular mechanisms of plant growth promotion, to develop effective biofertilizers for arid agriculture. Among our isolates of Thar desert rhizobacteria, Enterobacter cloacae C1P-IITJ, Kalamiella piersonii J4-IITJ, and Peribacillus frigoritolerans T7-IITJ, significantly enhanced root and shoot growth in the model plant Arabidopsis thaliana under PEG-induced drought stress in the lab. Whole genome sequencing and biochemical analyses of the non-pathogenic bacterium T7-IITJ revealed its plant growth-promoting traits, viz., solubilization of phosphate, iron, and nitrate and production of exopolysaccharides and auxin. Transcriptome analysis of Arabidopsis thaliana inoculated with T7-IITJ and exposure to drought revealed the induction of plant genes for photosynthesis, auxin and jasmonate signaling, nutrient mining and sequestration, redox homeostasis, and secondary metabolite biosynthesis pathways related to beneficial bacteria-plant interaction, but repression of many stress-responsive genes. Biochemical analyses indicated enhanced proline, chlorophyll, iron, phosphorous, and nitrogen content and reduced reactive oxygen species in plant tissues due to T7-IITJ inoculation. This bacterium could also improve the germination and seedling growth of Tephrosia purpurea, Triticum aestivum, and Setaria italica under drought. Additionally, T7-IITJ inhibited the growth of two plant pathogenic fungi, Rhizoctonia solani, and Fusarium oxysporum. These results suggest P. frigoritolerans T7-IITJ is a potent biofertilizer which can regulate plant genes promoting growth and drought tolerance.

Journal of Applied Microbiology

Peribacillus frigoritolerans T7-IITJ, a potential biofertilizer, induces plant growth-promoting genes of Arabidopsis thaliana

In the current study, gene network analysis revealed five novel disease-resistance proteins against bacterial leaf blight (BB) and rice blast (RB) diseases caused by Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae (M. oryzae), respectively. In silico modeling, refinement, and model quality assessment were performed to predict the best structures of these five proteins and submitted to ModelArchive for future use. An in-silico annotation indicated that the five proteins functioned in signal transduction pathways as kinases, phospholipases, transcription factors, and DNA-modifying enzymes. The proteins were localized in the nucleus and plasma membrane. Phylogenetic analysis showed the evolutionary relation of the five proteins with disease-resistance proteins (XA21, OsTRX1, PLD, and HKD-motif-containing proteins). This indicates similar disease-resistant properties between five unknown proteins and their evolutionary-related proteins. Furthermore, gene expression profiling of these proteins using public microarray data showed their differential expression under Xoo and M. oryzae infection. This study provides an&nbsp;insight into developing disease-resistant rice varieties by predicting novel candidate resistance proteins, which will assist rice breeders in improving crop yield to address future food security through molecular breeding and biotechnology.

3 Biotech

In silico characterization of five novel disease‑resistance proteins in Oryza sativa sp. japonica against bacterial leaf blight and rice blast diseases

<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.

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.