Browsing by Author "Poonam C. 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
Diversity analysis and risk assessment of microplastics in terrestrial soil across different landuses of northern India
(Elsevier Inc., 2025) Ekta Gupta; Shweta Yadav; Priyansha Gupta; Virendra kumar Mishra; Anju Patel; Mahua Saha; Poonam C. Singh; Pankaj Kumar Srivastava
Microplastics (MPs) are widely acknowledged as emerging pollutants in terrestrial ecosystem, yet their ecological threats in soil remain uncovered. This study presents the first comprehensive assessment of the abundance, characteristics, diversity, and ecological risks of soil-borne MPs across eight distinct landuse types in India, including industrial areas, dumping sites, municipal areas, wetlands, and various agricultural settings. Soil samples were collected and analyzed for MP abundance (MPs kg−1), morphology, polymer composition, diversity assessment and potential environmental risks. The results revealed the highest mean MP abundance in industrial areas (3710 ± 1127), followed by dumping sites (3310 ± 2195), municipal city areas (1247 ± 386), agriculture near dumping sites (546 ± 204), urban agriculture (478 ± 94), agriculture with plastic mulching (210 ± 54), peri-urban agriculture (113 ± 34), and wetlands (63 ± 21). Predominant shapes were fragments, fibers, films, and the particle sizes majorly belonged to 10–300 µm and 300–500 µm. Low-density polyethylene (LDPE), high-density polyethylene (HDPE) and polypropylene (PP) were the most abundant polymers in all the landuses. Shannon-Wiener index (SWI) and Simpson Diversity index (SDI) indicated significant variations in MPs diversity across landuses for shape, size, color, and polymer composition. Landuses were categorized as Level V (>1000) in terms of the Polymer Hazard Index (PHI), while Pollution Load Index (PLI) suggested a minor risk level. Based on the Potential Ecological Risk Index (PERI), wetlands exhibited low-risk and rest other landuses represented low to very high-risk category. The Geo-accumulation Index (Igeo) was also computed and evident as less contaminated landuse (wetland) to extremely contaminated (industrial area) landuse. This study provides baseline data on the occurrence and ecological risk of MPs in Indian soil and highlights the urgent need for targeted mitigation strategies. The findings contribute to a better understanding of MP dynamics across landuses and emphasize the necessity for policy interventions in terrestrial MPs management. © 2025 International Association for Gondwana Research
Exploring the influence of ground-dwelling ant bioturbation activity on physico-chemical, biological properties and heavy metal pollution in coal mine spoil
(Elsevier GmbH, 2024) Shbbir R. Khan; Poonam C. Singh; Martin Schmettow; Satish K. Singh; Neelkamal Rastogi
Coal mining activities increase the soil concentrations of heavy metals manifold thus impacting soil health and biodiversity. The understanding of the impact of bioturbation activities by ant colonies on soil in coal mine spoil site across different restoration ages is not studied. The study aimed to investigate the influence of bioturbation activities by two most common and distinct coal mine site inhabiting ant species (C. compressus and C. longipedem) at six different ages (2, 4, 6, 8, 10 and 12 years old) on the soil heavy metal concentrations of Fe, Zn, Mn, Cu, Ni, Pb, Cd and Cr, pH, OM, TC, TN, soil enzyme activity of DH, ACP, β-glucosidase and proteases properties of soil. Soil samples were collected from opencast coalmine spoils during October and November 2017. Reference (Ref.) soil samples (n=10 per site) were collected (from area adjacent to ant nest colony approximately 2–5 m distance) from a depth of 0–15 cm and ant nest debris soil of each ant species (n=10 per site) were collected from each site. Heavy metal pollution decreased and pH, OM, TC, TN and soil enzyme activity of DH, ACP, β-glucosidase and proteases of soil in both Ref. soil and ant nest debris soil increases with the increase of mine site restoration age. Our study revealed that different age of the mine spoil have more profound effects on the soil quality and heavy metal content. Contrary to our hypothesis, regression analysis did not support our notion that ant bioturbation activity directly accelerate heavy metal breakdown. Instead, our findings suggests that ant colonies prefer to construct their nest for the locations with lower heavy metal concentrations and higher enzyme activity and increase in soil porosity is a key factor behind the low heavy metal concentration in the nest debris soil. © 2024 Elsevier GmbH
Functional characterization of tau class glutathione-S-transferase in rice to provide tolerance against sheath blight disease
(Springer Science and Business Media Deutschland GmbH, 2020) Madhu Tiwari; Suchi Srivastava; Poonam C. Singh; Arun Kumar Mishra; Debasis Chakrabarty
Glutathione-S-transferase (GST) is an important defense gene that confers resistance against several abiotic and biotic stresses. The present study identifies a tau class GST in rice (Oryza sativa L.), OsGSTU5 (Os09g20220), which provided tolerance against sheath blight (SB) disease, caused by a necrotrophic fungus, Rhizoctonia solani (RS). Overexpression and knockdown rice transgenic lines of OsGSTU5 were generated and tested for the severity of infection during sheath blight disease. The results obtained after RS infection showed that the lesion cover area and hyphal penetration were more in knockdown line and lesser in the overexpression line. Analysis of reactive oxygen species (ROS) accumulation showed more spots of H2O2 and O2− in knockdown lines compared to overexpressed lines. Later, RS transcript level was analyzed in RS-infected transgenic lines, which manifested that the knockdown line had higher RS transcripts in comparison to the control line and least RS transcripts were observed in the overexpressed line. In conclusion, rice transgenic lines overexpressing OsGSTU5 were found to be more tolerant, while the knockdown lines were more prone to Rhizoctonia infection compared to control lines. © 2020, King Abdulaziz City for Science and Technology.
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
Transcriptome and proteome analyses reveal selenium mediated amelioration of arsenic toxicity in rice (Oryza sativa L.)
(Elsevier B.V., 2020) Reshu Chauhan; Surabhi Awasthi; Yuvraj Indoliya; Abhishek Singh Chauhan; Shashank Mishra; Lalit Agrawal; Sudhakar Srivastava; Sanjay Dwivedi; Poonam C. Singh; Shekhar Mallick; Puneet Singh Chauhan; Veena Pande; Debasis Chakrabarty; Rudra Deo Tripathi
Arsenic (As), a chronic poison and non-threshold carcinogen, is a food chain contaminant in rice, posing yield losses as well as serious health risks. Selenium (Se), a trace element, is a known antagonist of As toxicity. In present study, RNA seq. and proteome profiling, along with morphological analyses were performed to explore molecular cross-talk involved in Se mediated As stress amelioration. The repair of As induced structural deformities involving disintegration of cell wall and membranes were observed upon Se supplementation. The expression of As transporter genes viz., NIP1;1, NIP2;1, ABCG5, NRAMP1, NRAMP5, TIP2;2 as well as sulfate transporters, SULTR3;1 and SULTR3;6, were higher in As + Se compared to As alone exposure, which resulted in reduced As accumulation and toxicity. The higher expression of regulatory elements like AUX/IAA, WRKY and MYB TFs during As + Se exposure was also observed. The up-regulation of GST, PRX and GRX during As + Se exposure confirmed the amelioration of As induced oxidative stress. The abundance of proteins involved in photosynthesis, energy metabolism, transport, signaling and ROS homeostasis were found higher in As + Se than in As alone exposure. Overall, present study identified Se responsive pathways, genes and proteins involved to cope-up with As toxicity in rice. © 2020 Elsevier B.V.
Unravelling the emerging threats of microplastics to agroecosystems
(Springer Science and Business Media B.V., 2022) Shweta Yadav; Ekta Gupta; Anju Patel; Suchi Srivastava; Virendra Kumar Mishra; Poonam C. Singh; Pankaj Kumar Srivastava; Saroj Kanta Barik
In the past few decades, pollution from microplastics has emerged as an important issue on a global scale. These plastic particles are mainly the result of anthropogenic activities. Urban sprawl, industrialization, indiscriminate use and poor waste management of plastic products are the main factors responsible for the accumulation of microplastics in different ecosystems of the environment. The presence of microplastics in the soil matrix is considered an emerging threat to agroecosystems. Since most of the studies on microplastics have been done in the aquatic environment. The understanding of the ecotoxicological effects of these contaminants in terrestrial ecosystems is still limited, especially in agroecosystems. The negative effects of microplastics on the physical, chemical and biological properties of soil are now revealing. But the effects of microplastics on plant growth and yield are largely unexplored. Microplastic contamination in the soil can alter the functioning of plants by affecting the microbial community of the rhizosphere and disturbing the homeostasis of the agroecosystem. Furthermore, it may transfer into the plant system through nutrient and water absorption channels and affect plant physiology. The pervasive nature of microplastics in the soil is considered a barrier to sustainable agriculture and ecosystem functioning. The present review gives an overview of the sources, dissipation and effects of microplastics with reference to the soil–plant system, highlights the research gaps, and deciphers the possible future threats to agroecosystems. Graphical abstract: [Figure not available: see fulltext.]. © 2022, The Author(s), under exclusive licence to Springer Nature B.V.