Browsing by Author "Shiv Naresh Singh"

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Comprehensive illustration of transcriptomic and proteomic dataset for mitigation of arsenic toxicity in rice (Oryza sativa L.) by microbial consortium
(Elsevier Inc., 2022) Surabhi Awasthi; Reshu Chauhan; Yuvraj Indoliya; Abhishek Singh Chauhan; Shashank Kumar Mishra; Lalit Agrawal; Sanjay Dwivedi; Shiv Naresh Singh; Suchi Srivastava; Poonam C. Singh; Puneet Singh Chauhan; Debasis Chakrabarty; Sudhakar Srivastava; Rudra Deo Tripathi
The present article represents the data for analysis of microbial consortium (P.putida+C.vulgaris) mediated amelioration of arsenic toxicity in rice plant. In the current study the transcriptome profiling of treated rice root and shoot was performed by illumina sequencing (Platform 2000). To process the reads and to analyse differential gene expression, Fastxtoolkit, NGSQCtoolkit, Bowtie 2 (version 2.1.0), Tophat program (version 2.0.8), Cufflinks and Cuffdiff programs were used. For Proteome profiling, total soluble proteins in shoot of rice plant among different treatments were extracted and separated by 2D poly acrylamide gel electrophoresis (PAGE) and then proteins were identified with the help of MALDI-TOF/TOF. In gel based method of protein identification, the isoelectric focusing machine (IPGphor system,Bio-Rad USA), gel unit (SDS-PAGE) and MALDI-TOF/TOF (4800 proteomic analyzer Applied Biosystem, USA) were used for successful separation and positive identification of proteins. To check the differential abundance of proteins among different treatments, PDQuest software was used for data analysis. For protein identification, Mascot search engine (http://www.matrixscience.com) using NCBIprot/SwissProt databases of rice was used. The analyzed data inferred comprehensive picture of key genes and their respective proteins involved in microbial consortium mediated improved plant growth and amelioration of As induced phyto-toxicity in rice. For the more comprehensive information of data, the related full-length article entitled “Microbial consortium mediated growth promotion and Arsenic reduction in Rice: An integrated transcriptome and proteome profiling” may be accessed. © 2022
Digital hemispherical photographs and Sentinel-2 multi-spectral imagery for mapping leaf area index at regional scale over a tropical deciduous forest
(Springer, 2024) Mukunda Dev Behera; J.S.R. Krishna; Somnath Paramanik; Shubham Kumar; Soumit K. Behera; Sonik Anto; Shiv Naresh Singh; Anil Kumar Verma; Saroj K. Barik; Manas Ranjan Mohanta; Sudam Charan Sahu; Chockalingam Jeganathan; Prashant K. Srivastava; Biswajeet Pradhan
The leaf area index (LAI) provides valuable input for modeling climate and ecosystem processes. However, ground-based observations are necessitated across various phenophases from dense tropical forests for a better understanding in terms of their contribution to carbon fixation. In this study, Digital Hemispherical Photography (DHP) was used for LAI observation from Similipal Biosphere Reserve, and to predict high-resolution LAI using Random Forest Machine Learning approach. Observations were taken from ninety-three Elementary sampling units (ESUs) corresponding to the beginning and end of leaf fall seasons across moist deciduous, dry deciduous, and semi-evergreen forests. LAI demonstrated high values for dry deciduous, followed by semi-evergreen and moist deciduous forests for the start of the leaf fall season, whereas moist deciduous forests demonstrated high values during the end of the leaf fall season. Satellite-based spectral reflectance bands of Sentinel-2 and vegetation indices (VIs) were used as predictor variables, wherein the band-7, band-8, band-12, enhanced vegetation index (EVI), and Red-edge based EVI were evaluated as the most dominant responsive variables for LAI estimation. Random Forest (RF) model provided good accuracy (R2 = 0.64, RMSE = 0.62) with observed DHP-based LAI. However, a comparison of RF model-based predicted LAI with global LAI products (MOD15A2H and VNP15A2H) provided a moderate correlation. Such studies demonstrate the potential of site or region-specific case studies to evaluate coarser-resolution global LAI products for possible improvement. © International Society for Tropical Ecology 2024.
Microbial consortium mediated growth promotion and Arsenic reduction in Rice: An integrated transcriptome and proteome profiling
(Academic Press, 2021) Surabhi Awasthi; Reshu Chauhan; Yuvraj Indoliya; Abhishek Singh Chauhan; ShashankKumar Mishra; Lalit Agrawal; Sanjay Dwivedi; Shiv Naresh Singh; Suchi Srivastava; Poonam C. Singh; Puneet Singh Chauhan; Debasis Chakrabarty; Sudhakar Srivastava; Rudra Deo Tripathi
The adverse effects of arsenic (As) contamination are well known. Rice is a staple food for 50% of the world population but the accumulation of As into rice hampers the food security and safety. Thus the amelioration of As stress and reduction of As levels in rice are needed. In this study, transcriptome (Illumina sequencing) and proteome (2D gel electrophoresis) explored mechanisms of consortium (P. putida+C. vulgaris) mediated growth promotion and As amelioration in rice. The rice seedlings grown hydroponically in the Hewitt nutrient medium and after acclimatization, exposed to 50 µM As alone as well as with microbial consortium to observe the impact at morphological and molecular level. The inoculation of microbial consortium significantly ameliorated the As toxicity, improved growth of root hairs and maintained cellular integrity of the epidermis, exodermis and the stele region during As exposure. Several genes showed differential expression in As and As+P. putida. Down-regulation of As transporters (OsPIP2;2 and OsPIP2;3, OsTIP2;1) and higher expression of WRKY gene (WRKY28) during As+P. putida+C.vulgaris suggested reduction of As uptake in rice. The up-regulation of nutrient elements transporters (OsZIFL9, OsZIFL5, OsZIFL12 and OsZIP2, OsYSL15 and OsCOPT6) in the presence of consortium indicated the improved nutrient status of rice. Higher expression of regulatory elements like auxin/indole 3 acetic acid (AUX/IAA), WRKY and myeloblastosis (MYB) TFs and down-regulation of defense responsive genes such Glutathione-S-transferase, Peroxidase and Glutaredoxinduring As+P. putida+C.vulgaris exposure was also observed. Proteome profiling demonstrated differential abundance of proteins involved in photosynthesis (chlorophyll a/b binding protein, photosystem I Fe-S centre), energy metabolism (ATP synthase subunit beta) transport, signaling (tubulin 1, actin 1), defense (glutathione S-transferase, phenylalanine ammonia lyase) and amino acid metabolism (cysteine synthase, glutamine synthetase), which supported the As ameliorative and growth-promoting potential of microbial consortium during As stress in rice plants. The study gives comprehensive information about gene and protein changes in rice plants in As+consortium exposure. © 2021 The Authors
Reducing Arsenic Uptake in Cereal Crop Plants with Sugarcane Waste Application: A Comparative Study on the Effects on Physiology, Biochemistry, and Grain Nutrient Status
(Springer, 2023) Ambedkar Gautam; Nikita Basant; Navin Kumar; Kriti; Shiv Naresh Singh; Arvind Kumar Dubey; Gayatri Singh; Babita Kumari; Kavita Shah; Shekhar Mallick
C3 (Oryza sativa L.) and C4 (Zea mays L.) plants differ both in their carbon fixing mechanism, and thus, their responses toward stresses also differ. Owing to the mutually competitive nature of uptake between phosphate (iP) and arsenate (AsV) in plants, and given that the level of sucrose is also influenced by iP, interplay of their uptake mechanisms eventually results in reducing the AsV uptakes. The present study intends to comparatively assess the reduction in AsIII and AsV uptake and its toxicity between Oryza sativa L. and Zea mays L. when cultivated with sucrose-containing sugarcane wastes (SWs; bagasse, molasses, and pressmud) conducted under a simulated outdoor pot experiment. Overall improvement in growth, physiological performance, stress, and antioxidant response was exhibited in both the plants with SWs application. The SWs application also improved soil physiochemical parameters viz, pH, EC, OC, OM, and micronutrients. Application of SW also reduced the iAs accumulation in grains of both rice (50–87%) and maize (70–96%), along with enhancement in Fe (142%, and 122%, respectively), and Zn (132% and 131%, respectively). Most of the 17 grain’s amino acids (AAs) increased in maize against iAs stress, whereas Ser decreased in both, and Ile and Gly additionally in rice. Essential AAs viz. Phe, Thr, and Met are influenced negatively by iAs, whereas nonessential AAs viz. Cys, Ser, Pro, Gly in both the plant grains are positively influenced by iP and negatively by OC. Thus, the application of SWs containing residual sucrose > 9.5 µM g−1, through a fertilizer formulation or by direct soil amendments in iAs-contaminated soil can be an agronomic practice to reduce the iP fertilization and limit the iAs contamination in the food-chain. © 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.