Biology subjects

SADHUKHAN, A.

Publications and source records attributed to SADHUKHAN, A..

8 recordsLinked to original sources

bioRxiv2026

Agroforestry reshapes soil bacterial communities to enhance Ricinus communis oil quality and bioactivity over monocropping: comparative metagenomics and culture-dependent insights

An agroforestry (AF) system improves crop quality, ecosystem services, and microbial resilience, but its effects on oilseed bioactivity and soil microbiomes are still underexplored. This study compared AF and monocropping systems for castor (Ricinus communis L.) grown in Rajasthan, India, to evaluate plant productivity, seed oil composition, antimicrobial properties, and soil bacterial communities. AF enhanced seed morphology and germination. Castor oil from agroforestry had a 2.4-fold higher phenolic content, 2% more ricinoleic acid, and lower levels of oleic and linoleic acids compared to monocropping, confirmed by infrared spectroscopy and gas chromatography, along with increased expression of the RcDGAT2 gene involved in fatty acid biosynthesis. This led to improved antimicrobial activity against Bacillus mobilis and Pseudomonas fluorescens. Full-length 16S rRNA gene sequencing on the Nanopore platform identified 17 bacterial phyla in soil microbiomes, with Proteobacteria and Firmicutes as the dominant phyla. While alpha diversity was similar, AF soils showed distinct taxonomic shifts, enriching bacteria such as Alkalimonas, Aureimonas, Blastopirellula, Glutamicibacter, Rhizobium, Rhizomicrobium, and Rhodovulum, linked to nutrient cycling and plant growth promotion. Isolated rhizospheric/root endophytic Bacillus safensis and Enterobacter cloacae from AF castor exhibited plant growth-promoting traits via biochemical tests and whole-genome sequencing; their oil biosynthesis genes likely contribute to host oil quality by enhancing precursor supply and phenolic pathways. These isolates enhanced the growth of the model plant Arabidopsis thaliana. In summary, AF enhances the bioactivity of castor oil and microbial functions by modulating plant-soil-microbe interactions, thereby supporting sustainable crop quality and soil health.

microbiology↗

bioRxiv2026

Genome-wide association study and transcriptomics reveal the genetic architecture of alkalinity tolerance in Arabidopsis thaliana

Alkalinity stress significantly restricts global plant productivity, yet the genetic basis for plant tolerance remains largely uncharacterized. In this study, a genome-wide association study was performed using 218 diverse natural Arabidopsis thaliana ecotypes to identify the top 73 SNPs associated with alkalinity tolerance, measured by relative root length in hydroponic growth media containing NaHCO3 at pH 8.0. Prominent association peaks were localized near genes involved in lipid metabolism (GGL20), protein degradation (AT3G17570), and vesicle-mediated protein sorting (VPS13B and AT5G57210). Expression level and protein polymorphisms in these genes were associated with alkalinity tolerance. T-DNA mutants of GGL20, AT3G17570, and the chromatin-modifying gene AFR1 showed alkaline hypersensitivity, reduced root length, iron content, and rosette size, and elevated hydrogen peroxide. Conversely, mutants of the DNA repair gene ETG1 exhibited greater tolerance than wild type in hydroponics, solid media, and soil assays, confirming their role in alkalinity tolerance. Transcriptome and network analyses revealed that alkalinity responses significantly overlap with iron deficiency pathways, identifying hub genes involved in ribosome assembly and translation control. These findings provide a comprehensive map of the genetic and transcriptional landscape of alkalinity adaptation and offer promising candidate genes for engineering crops resilient to alkaline soil conditions.

plant biology↗

bioRxiv2026

Expression genome-wide association study and differential methylome profiling reveal upstream regulators of drought memory genes in Arabidopsis thaliana

Plants adapt to recurrent drought through transcriptional memory, yet the upstream regulators remain largely unknown. This study integrated expression genome-wide association study (eGWAS) across 115 Arabidopsis thaliana ecotypes with differential methylome profiling to identify these regulators. Focusing on the memory genes LKR, HIS1-3, and DREB1A, eGWAS identified signaling and epigenetic loci involved in ABA/JA responses and DNA methylation. Methylome profiling by whole-genome bisulfite sequencing of ecotypes contrasting in drought tolerance, as well as in superinduction of memory genes, revealed significantly greater methylation variation during the second drought (D2) than during the first (D1), highlighting the role of epigenetic reprogramming in memory maintenance. Functional validation using T-DNA mutants demonstrated specific modulation of the D2/D1 induction ratio without affecting initial drought responses. Mutants of LKR eGWAS-delineated genes AT1G56660, AT2G19120, AT4G16490, and DEG3, those of HIS1-3 eGWAS genes AT1G14220, AT2G24960, AT3G10845, AT3G19340, CNGC10, EMB2770, GRF7, and RPP2A, and DREB1A eGWAS genes AT1G67000, AT3G61610, AT5G62110, HK2, JMJ12, and LUP5 abolished respective memory gene induction. The eGWAS and methylome approaches converged on DNA repair, chromatin modification, vesicular transport, and proteostasis as core memory hubs. These findings reveal a genetic-epigenetic interplay that coordinates transcriptional memory, priming plants for rapid reactivation of stress pathways during recurrent drought.

plant biology↗

bioRxiv2025

Genome-wide association study, network analysis, and reverse genetics pinpoint novel genes associated with seedling root growth variation of Arabidopsis thaliana under drought

Development of drought-resilient crops requires a precise understanding of molecular signaling in the root, the primary organ encountering drought. This study unraveled novel genetic loci contributing to drought tolerance by exploiting the natural variation in seedling root growth of Arabidopsis thaliana under PEG-induced drought stress. Through a genome-wide association study (GWAS) of 207 worldwide Arabidopsis thaliana ecotypes from regions with varied rainfall, 68 protein-coding genes were identified, associated with the top 50 single-nucleotide polymorphisms (P < 10- 3), explaining 63% of the observed variation in root length. Subsequent network and functional enrichment analyses of the GWAS-delineated genes demarcated key biological processes crucial for maintaining root growth under drought, including DNA repair, tRNA editing, protein folding and quality control, cell cycle regulation, stress granule assembly, and the pyridoxal 5'-phosphate (PLP) salvage pathway regulating oxidative stress in roots. Expression level polymorphisms, promoter cis-element variations, and amino acid substitutions affecting predicted protein dynamics, with phenotype and climate associations, were identified. Finally, reverse genetic evaluation using T-DNA insertion knockout/knockdown mutants confirmed a direct association of the identified candidate genes, AT1G06690 (PLP pathway), AT4G26990 and RBP45C (stress granule assembly), ACD55.5 (protein folding), PCMP-A4 (RNA modification), SKS6 and ANAC094 (cell wall remodeling), and INCENP (cell cycle regulation), with seedling drought tolerance. Furthermore, the knockdown of AT1G06690 led to higher accumulation of hydrogen peroxide in root tissues, inhibiting growth. Future translation of the current findings into crops will provide new tools for the improvement of drought tolerance by modulating root traits through biotechnology and breeding.

genetics↗

bioRxiv2025

A desert endophyte, Priestia megaterium SI1-IITJ, improves fluoride stress tolerance by reducing fluoride content of plant tissues and perturbing salt tolerance and defense genes of Arabidopsis thaliana

We isolated a fluoride (F-)-resistant bacterium, Priestia megaterium SI1-IITJ, from thse internal root tissues of several Thar Desert plants, Aerva javanica, Cyperus conglomeratus, Senna tora, and Tephrosia purpurea, tolerating up to 100 mM NaF. The root endophytic behavior of the isolate was confirmed by scanning electron microscopy. SI1-IITJ possesses plant growth-promoting properties, including auxin production (19.8 g mL-1), phosphate solubilization (index 3.64), ACC deaminase (0.54 mmol -ketobutyrate mL-1) and nitrate reductase (0.65 mol mL-1 nitrite) activities, revealed by biochemical tests and whole genome sequencing. SI1-IITJ extrudes F- from the cell, possibly through an F- efflux transporter, CrcB, identified in its genome. Significant growth improvements were observed in Arabidopsis thaliana under F- stress in hydroponics and soil culture upon coculture with SI1-IITJ, which improved the chlorophyll content by 1.6%, total nitrogen by 30.4%, and reduced reactive oxygen species by 48.9% and F- content by 63.9% in plant tissues. A differential gene expression analysis of A. thaliana by transcriptome sequencing indicated an unperturbed F- exporter, AtFEX1, but up-regulation of 55 genes regulating root meristem growth, cell wall modification, chlorophyll biosynthesis, Fe homeostasis, and high salt- and abiotic stress-responsive genes. On the other hand, 103 genes were down-regulated, suppressing systemic acquired resistance, plant defense, and H2O2 production. In conclusion, our results provide genomic insights into the mechanisms of F- toxicity alleviation and plant growth enhancement by a desert PGPR, highlighting Priestia megaterium SI1-IITJ as a potential biofertilizer for mitigating F- stress in plants.

plant biology↗

bioRxiv2024

Foliar application of nano urea results in higher biomass, chlorophyll, and nitrogen content than equimolar bulk urea through differential gene regulation in Arabidopsis thaliana

Indian Farmers Fertilizer Cooperative (IFFCO)s liquid nano urea formulation (NUF) was applied to one-month-old Arabidopsis thaliana plants grown in vermiculite as a 0.4% foliar spray twice at an interval of 10 days and compared with sprays of equimolar bulk urea. NUF resulted in a 51 {+/-} 14.9% increase in biomass, 29.5 {+/-} 9.1% in chlorophyll, 8.4 {+/-} 3.1% in nitrogen, and 4.5 {+/-} 0.3% in amino acid content of the leaves, compared to bulk urea. NUFs zeta potential of -54.7 mV and particle size of [~=]27.7 nm, measured by dynamic light scattering and transmission electron microscopy, make it suitable for stomatal uptake. We conducted a differential gene expression analysis by mRNA sequencing to understand the molecular basis of the phenotypic gains under NUF rather than urea. NUF resulted in significantly higher expression levels of 211 genes (log2fold-change > 0.5, FDR < 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 < -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. Our results suggest that although NUF foliar spray suppresses nitrogen uptake genes, possibly due to nitrogen excess, it enhances growth by up-regulating the synthesis of essential biomolecules and growth-promoting genes, compared to bulk urea.

plant biology↗

bioRxiv2024

Effects of nano urea on growth and gene expression of Arabidopsis thaliana in hydroponics

IntroductionHydroponics enables precise control over nutrient delivery, optimized water requirements and growing conditions. The combination of nanotechnology and hydroponics paves the way towards sustainable agriculture with less environmental footprints. We investigated the effects of nano urea on the model plant Arabidopsis thaliana in hydroponics. MethodsA growth experiment in a nitrogen-free hydroponic medium compared the effects of a liquid nano urea formulation (NUF) marketed by Indian Farmers Fertilizer Cooperative (IFFCO) to an equimolar bulk urea. Transcriptome analysis identified the molecular mechanisms of growth enhancement. Dynamic light scattering and transmission electron microscopy confirmed NUFs negative surface charge and sub-100 nm size, correlating its uptake and distribution in the plant. Results and discussionA two-week growth in the hydroponic medium with 70 M NUF led to a 20% higher biomass and 16% higher chlorophyll content than a medium with 70 M urea. Higher doses of NUF inhibited growth, whereas higher equivalent urea doses did not. 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 got up-regulated, while chlorophyll catabolism genes got 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.

plant biology↗

bioRxiv2023

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

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.

plant biology↗