The combination of nanotechnology and hydroponics paves the way toward sustainable agriculture wi... more 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 μM NUF led to a 20% higher biomass and 16% higher chlorophyll content than a medium with 70 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 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.
Essential plant nutrients encapsulated or combined with nano-dimensional adsorbents define nano f... more 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. Chargebased 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. Key message Nano fertilizers enhance plant growth and stress tolerance by regulating cell division, morphogenesis, photosynthesis, nitrogen assimilation, vacuolar sequestration of excess nutrients, phytohormone and calcium signaling, and secondary metabolite biosynthesis.
We sequenced the drought-response transcriptome of the keystone tree species Prosopis cineraria f... more 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 identifed 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 232 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 identifed 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 diferent charge distributions, which might contribute diferently to their DNA search and binding. Using all-atom molecular dynamics simulations, we teased out a higher number of specifc DBD-DNA hydrogen bonds in P. cineraria, leading to a stronger DNA-binding afnity 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 efcient DNA search and binding as drought adaptation mechanisms in P. cineraria.
The book is a compilation of broad applications of Transcriptomics in the current field of scienc... more The book is a compilation of broad applications of Transcriptomics in the current field of science and technology and its impact towards the developmental aspects of crop science and clinical applications. The book focuses on the recent advancements in RNA sequencing technologies and the socio-economic impact with generations of huge transcriptome datasets aimed towards crop improvement against biotic and abiotic stress. Nevertheless, it also discusses the impact of transcriptomics in clinical studies focusing on oncology and therapeutics. The book targets mainly the young minds and provides them a basic understanding of how the omics world is contributing towards developmental aspects of science. Again, the book also discusses the various pros and cons of the myriad of datasets generated by the advanced sequencing platforms. Specifically, Chapter 1, 2, and 6 broadly explain the applications of "Transcriptomics" towards studying various abiotic and biotic stress response studies in plants. Chapter 3 focuses on the importance of the transcriptome datasets in extremophiles and studying their adaptive nature for surviving against environmental cues. Similarly, chapter 4 and 5 along with 7 and 8 emphasize on the importance and advancements in legume crops and millets, respectively, some of which are selectively known to display essential traits against various stress conditions affecting their survival. Lastly, chapters 9 and 10 are based on the promising applications of human transcriptomic studies and its profound application in science aimed towards studying various neurological disorders, diseases, and further advancement in therapeutics. Overall, the book is helpful for researchers, students and academicians for getting a better understanding on the wider-range applications of "Transcriptomic Research".
Aims: This study aimed to isolate plant growth and drought tolerance-promoting bacteria from the ... more Aims: This study aimed to isolate plant growth and drought tolerance-promoting bacteria from the nutrient-poor rhizosphere soil of Thar desert plants and unravel their molecular mechanisms of plant growth promotion. Methods and results: Among our rhizobacterial isolates, Enterobacter cloacae C1P-IITJ, Kalamiella piersonii J4-IITJ, and Peribacillus frigoritolerans T7-IITJ, significantly enhanced root and shoot growth (4–5-fold) in Arabidopsis thaliana under PEG-induced drought stress. Whole genome sequencing and biochemical analyses of the non-pathogenic bacterium T7-IITJ revealed its plant growth-promoting traits, viz., solubilization of phosphate (40−73 μg/ml), iron (24 ± 0.58 mm halo on chrome azurol S media), and nitrate (1.58 ± 0.01 μg/ml nitrite), along with production of exopolysaccharides (125 ± 20 μg/ml) and auxin-like compounds (42.6 ± 0.05 μg/ml). Transcriptome analysis of A. thaliana inoculated with T7-IITJ and exposure to drought revealed the induction of 445 plant genes (log2fold-change > 1, FDR < 0.05) for photosynthesis, auxin and jasmonate signalling, nutrient uptake, redox homeostasis, and secondary metabolite biosynthesis pathways related to beneficial bacteria-plant interaction, but repression of 503 genes (log2fold-change < −1) including many stress-responsive genes. T7-IITJ enhanced proline 2.5-fold, chlorophyll 2.5– 2.8-fold, iron 2-fold, phosphate 1.6-fold, and nitrogen 4-fold, and reduced reactive oxygen species 2–4.7-fold in plant tissues under drought. T7-IITJ also improved the germination and seedling growth of Tephrosia purpurea, Triticum aestivum, and Setaria italica under drought and inhibited the growth of two plant pathogenic fungi, Fusarium oxysporum, and Rhizoctonia solani. Conclusions: P. frigoritolerans T7-IITJ is a potent biofertilizer that regulates plant genes to promote growth and drought tolerance.
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Papers by Ayan Sadhukhan
to understand the key factors in its drought tolerance mechanism. We identifed 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 232 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
identifed 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 diferent charge distributions, which might contribute diferently to their DNA search and
binding. Using all-atom molecular dynamics simulations, we teased out a higher number of specifc DBD-DNA hydrogen
bonds in P. cineraria, leading to a stronger DNA-binding afnity 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
efcient DNA search and binding as drought adaptation mechanisms in P. cineraria.
plants and unravel their molecular mechanisms of plant growth promotion.
Methods and results: Among our rhizobacterial isolates, Enterobacter cloacae C1P-IITJ, Kalamiella piersonii J4-IITJ, and Peribacillus frigoritolerans T7-IITJ, significantly enhanced root and shoot growth (4–5-fold) in Arabidopsis thaliana under PEG-induced drought stress. Whole genome
sequencing and biochemical analyses of the non-pathogenic bacterium T7-IITJ revealed its plant growth-promoting traits, viz., solubilization of
phosphate (40−73 μg/ml), iron (24 ± 0.58 mm halo on chrome azurol S media), and nitrate (1.58 ± 0.01 μg/ml nitrite), along with production of
exopolysaccharides (125 ± 20 μg/ml) and auxin-like compounds (42.6 ± 0.05 μg/ml). Transcriptome analysis of A. thaliana inoculated with T7-IITJ
and exposure to drought revealed the induction of 445 plant genes (log2fold-change > 1, FDR < 0.05) for photosynthesis, auxin and jasmonate
signalling, nutrient uptake, redox homeostasis, and secondary metabolite biosynthesis pathways related to beneficial bacteria-plant interaction,
but repression of 503 genes (log2fold-change < −1) including many stress-responsive genes. T7-IITJ enhanced proline 2.5-fold, chlorophyll 2.5–
2.8-fold, iron 2-fold, phosphate 1.6-fold, and nitrogen 4-fold, and reduced reactive oxygen species 2–4.7-fold in plant tissues under drought. T7-IITJ
also improved the germination and seedling growth of Tephrosia purpurea, Triticum aestivum, and Setaria italica under drought and inhibited the
growth of two plant pathogenic fungi, Fusarium oxysporum, and Rhizoctonia solani.
Conclusions: P. frigoritolerans T7-IITJ is a potent biofertilizer that regulates plant genes to promote growth and drought tolerance.