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Ye R, Tomo C, Chan N, Wolfe BE. Penicillium molds impact the transcriptome and evolution of the cheese bacterium Staphylococcus equorum. mSphere 2023; 8:e0004723. [PMID: 37219436 PMCID: PMC10449494 DOI: 10.1128/msphere.00047-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
The observation that Penicillium molds can inhibit the growth of Staphylococcus was a catalyst for the antibiotic revolution. Considerable attention has been paid to purified Penicillium metabolites that inhibit bacteria, but little is known about how Penicillium species impact the ecology and evolution of bacteria in multispecies microbial communities. Here, we investigated how four different species of Penicillium can impact global transcription and evolution of a widespread Staphylococcus species (S. equorum) using the cheese rind model microbiome. Through RNA sequencing, we identified a core transcriptional response of S. equorum against all five tested Penicillium strains, including upregulation of thiamine biosynthesis, fatty acid degradation, and amino acid metabolism as well as downregulation of genes involved in the transport of siderophores. In a 12-week evolution experiment where we co-cultured S. equorum with the same Penicillium strains, we observed surprisingly few non-synonymous mutations across S. equorum populations evolved with the Penicillium species. A mutation in a putative DHH family phosphoesterase gene only occurred in populations evolved without Penicillium and decreased the fitness of S. equorum when co-cultured with an antagonistic Penicillium strain. Our results highlight the potential for conserved mechanisms of Staphylococcus-Penicillium interactions and demonstrate how fungal biotic environments may constrain the evolution of bacterial species.IMPORTANCEFungi and bacteria are commonly found co-occurring both in natural and synthetic microbiomes, but our understanding of fungal-bacterial interactions is limited to a handful of species. Conserved mechanisms of interactions and evolutionary consequences of fungal-bacterial interactions are largely unknown. Our RNA sequencing and experimental evolution data with Penicillium species and the bacterium S. equorum demonstrate that divergent fungal species can elicit conserved transcriptional and genomic responses in co-occurring bacteria. Penicillium molds are integral to the discovery of novel antibiotics and production of certain foods. By understanding how Penicillium species affect bacteria, our work can further efforts to design and manage Penicillium-dominated microbial communities in industry and food production.
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Affiliation(s)
- Ruby Ye
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Christopher Tomo
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Neal Chan
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Benjamin E. Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, USA
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2
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Tannous J, Cosetta CM, Drott MT, Rush TA, Abraham PE, Giannone RJ, Keller NP, Wolfe BE. LaeA-Regulated Fungal Traits Mediate Bacterial Community Assembly. mBio 2023:e0076923. [PMID: 37162223 DOI: 10.1128/mbio.00769-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Potent antimicrobial metabolites are produced by filamentous fungi in pure culture, but their ecological functions in nature are often unknown. Using an antibacterial Penicillium isolate and a cheese rind microbial community, we demonstrate that a fungal specialized metabolite can regulate the diversity of bacterial communities. Inactivation of the global regulator, LaeA, resulted in the loss of antibacterial activity in the Penicillium isolate. Cheese rind bacterial communities assembled with the laeA deletion strain had significantly higher bacterial abundances than the wild-type strain. RNA-sequencing and metabolite profiling demonstrated a striking reduction in the expression and production of the natural product pseurotin in the laeA deletion strain. Inactivation of a core gene in the pseurotin biosynthetic cluster restored bacterial community composition, confirming the role of pseurotins in mediating bacterial community assembly. Our discovery demonstrates how global regulators of fungal transcription can control the assembly of bacterial communities and highlights an ecological role for a widespread class of fungal specialized metabolites. IMPORTANCE Cheese rinds are economically important microbial communities where fungi can impact food quality and aesthetics. The specific mechanisms by which fungi can regulate bacterial community assembly in cheeses, other fermented foods, and microbiomes in general are largely unknown. Our study highlights how specialized metabolites secreted by a Penicillium species can mediate cheese rind development via differential inhibition of bacterial community members. Because LaeA regulates specialized metabolites and other ecologically relevant traits in a wide range of filamentous fungi, this global regulator may have similar impacts in other fungus-dominated microbiomes.
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Affiliation(s)
- Joanna Tannous
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Casey M Cosetta
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Milton T Drott
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, USA
| | - Tomás A Rush
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Richard J Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, USA
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3
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El-Sayed ESR, Zaki AG. Unlocking the biosynthetic potential of Penicillium roqueforti for hyperproduction of the immunosuppressant mycophenolic acid: Gamma radiation mutagenesis and response surface optimization of fermentation medium. Biotechnol Appl Biochem 2023; 70:306-317. [PMID: 35481612 DOI: 10.1002/bab.2353] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/10/2022] [Indexed: 11/09/2022]
Abstract
Based on the broad clinical utility of the immunosuppressant mycophenolic acid (MPA), this article aims to intensify the biosynthetic potential of Penicillium roqueforti for more effective hyperproduction of the drug. Several mutants were generated from irradiation mutagenesis and screened. Two strains (GM1013 and GM1093) presented an elevated MPA productivity with significant yield constancy over 10 subsequent generations. By investigating the effect of some phosphorous sources and mineral salts on MPA production by the two mutants, KH2 PO4 and FeSO4 ·7H2 O were most preferred by the two mutants for higher MPA production rates. Statistics-dependent experimental designs were also employed for optimizing medium components for maximum MPA production. Medium components were primarily screened using the Plackett-Burman model to demonstrate the most important components that most significantly affect MPA production. The concentrations of these significant components were then optimized through a central composite rotatable model. In conclusion, gamma-radiation mutation and response surface optimization resulted in a promising MPA productivity by P. roqueforti GM1013. To our knowledge, the MPA-yield achieved in this study (2933.32 mg L-1 ) is the highest reported by academic laboratories from P. roqueforti cultures, which could be of economic value for a prospective large industrialized application.
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Affiliation(s)
- El-Sayed R El-Sayed
- Plant Research Department, Nuclear Research Center, Egyptian Atomic Energy Authority, Cairo, Egypt
| | - Amira G Zaki
- Plant Research Department, Nuclear Research Center, Egyptian Atomic Energy Authority, Cairo, Egypt
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Caron T, Piver ML, Péron AC, Lieben P, Lavigne R, Brunel S, Roueyre D, Place M, Bonnarme P, Giraud T, Branca A, Landaud S, Chassard C. Strong effect of Penicillium roqueforti populations on volatile and metabolic compounds responsible for aromas, flavor and texture in blue cheeses. Int J Food Microbiol 2021; 354:109174. [PMID: 34103155 DOI: 10.1016/j.ijfoodmicro.2021.109174] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 01/25/2023]
Abstract
Studies of food microorganism domestication can provide important insight into adaptation mechanisms and lead to commercial applications. Penicillium roqueforti is a fungus with four genetically differentiated populations, two of which were independently domesticated for blue cheese-making, with the other two populations thriving in other environments. Most blue cheeses are made with strains from a single P. roqueforti population, whereas Roquefort cheeses are inoculated with strains from a second population. We made blue cheeses in accordance with the production specifications for Roquefort-type cheeses, inoculating each cheese with a single P. roqueforti strain, using a total of three strains from each of the four populations. We investigated differences between the cheeses made with the strains from the four P. roqueforti populations, in terms of the induced flora, the proportion of blue color, water activity and the identity and abundance of aqueous and organic metabolites as proxies for proteolysis and lipolysis as well as volatile compounds responsible for flavor and aroma. We found that the population-of-origin of the P. roqueforti strains used for inoculation had a minor impact on bacterial diversity and no effect on the abundance of the main microorganism. The cheeses produced with P. roqueforti strains from cheese populations had a higher percentage of blue area and a higher abundance of the volatile compounds typical of blue cheeses, such as methyl ketones and secondary alcohols. In particular, the Roquefort strains produced higher amounts of these aromatic compounds, partly due to more efficient proteolysis and lipolysis. The Roquefort strains also led to cheeses with a lower water availability, an important feature for preventing spoilage in blue cheeses, which is subject to controls for the sale of Roquefort cheese. The typical appearance and flavors of blue cheeses thus result from human selection on P. roqueforti, leading to the acquisition of specific features by the two cheese populations. These findings have important implications for our understanding of adaptation and domestication, and for cheese improvement.
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Affiliation(s)
- Thibault Caron
- Ecologie Systematique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, 91400 Orsay, France; Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France.
| | - Mélanie Le Piver
- Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France
| | - Anne-Claire Péron
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - Pascale Lieben
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - René Lavigne
- Université Clermont Auvergne, INRAE, Vetagro Sup, UMRF, 20 Côte de Reyne, 15000 Aurillac, France
| | - Sammy Brunel
- Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France
| | - Daniel Roueyre
- Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France
| | - Michel Place
- Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France
| | - Pascal Bonnarme
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - Tatiana Giraud
- Ecologie Systematique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, 91400 Orsay, France
| | - Antoine Branca
- Ecologie Systematique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, 91400 Orsay, France
| | - Sophie Landaud
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - Christophe Chassard
- Université Clermont Auvergne, INRAE, Vetagro Sup, UMRF, 20 Côte de Reyne, 15000 Aurillac, France
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Voidarou C, Antoniadou M, Rozos G, Tzora A, Skoufos I, Varzakas T, Lagiou A, Bezirtzoglou E. Fermentative Foods: Microbiology, Biochemistry, Potential Human Health Benefits and Public Health Issues. Foods 2020; 10:E69. [PMID: 33396397 PMCID: PMC7823516 DOI: 10.3390/foods10010069] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 12/26/2020] [Accepted: 12/27/2020] [Indexed: 02/06/2023] Open
Abstract
Fermented foods identify cultures and civilizations. History, climate and the particulars of local production of raw materials have urged humanity to exploit various pathways of fermentation to produce a wide variety of traditional edible products which represent adaptations to specific conditions. Nowadays, industrial-scale production has flooded the markets with ferments. According to recent estimates, the current size of the global market of fermented foods is in the vicinity of USD 30 billion, with increasing trends. Modern challenges include tailor-made fermented foods for people with special dietary needs, such as patients suffering from Crohn's disease or other ailments. Another major challenge concerns the safety of artisan fermented products, an issue that could be tackled with the aid of molecular biology and concerns not only the presence of pathogens but also the foodborne microbial resistance. The basis of all these is, of course, the microbiome, an aggregation of different species of bacteria and yeasts that thrives on the carbohydrates of the raw materials. In this review, the microbiology of fermented foods is discussed with a special reference to groups of products and to specific products indicative of the diversity that a fermentation process can take. Their impact is also discussed with emphasis on health and oral health status. From Hippocrates until modern approaches to disease therapy, diet was thought to be of the most important factors for health stability of the human natural microbiome. After all, to quote Pasteur, "Gentlemen, the microbes will have the last word for human health." In that sense, it is the microbiomes of fermented foods that will acquire a leading role in future nutrition and therapeutics.
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Affiliation(s)
- Chrysa Voidarou
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, School of Agriculture, University of Ioannina, 47132 Arta, Greece; (C.V.); (A.T.); (I.S.)
| | - Maria Antoniadou
- School of Dentistry, National and Kapodistrian University of Athens, 11521 Athens, Greece;
| | - Georgios Rozos
- Laboratory of Microbiology, Biotechnology & Hygiene, Department of Agricultural Development, Democritus University of Thrace, 68200 Orestiada, Greece;
| | - Athina Tzora
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, School of Agriculture, University of Ioannina, 47132 Arta, Greece; (C.V.); (A.T.); (I.S.)
| | - Ioannis Skoufos
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, School of Agriculture, University of Ioannina, 47132 Arta, Greece; (C.V.); (A.T.); (I.S.)
| | - Theodoros Varzakas
- Department of Food Science and Technology, University of the Peloponnese, 24100 Kalamata, Greece
| | - Areti Lagiou
- Department of Public and Community Health, University of West Attika, 11521 Athens, Greece;
| | - Eugenia Bezirtzoglou
- Laboratory of Hygiene and Environmental Protection, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
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Sun X, Lyu G, Luan Y, Yang H, Zhao Z. Metabolomic study of the soybean pastes fermented by the single species Penicillium glabrum GQ1-3 and Aspergillus oryzae HGPA20. Food Chem 2019; 295:622-629. [PMID: 31174804 DOI: 10.1016/j.foodchem.2019.05.162] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 05/16/2019] [Accepted: 05/23/2019] [Indexed: 01/22/2023]
Abstract
Penicillium glabrum GQ1-3 and Aspergillus oryzae HGPA20 isolated from home-made soybean pastes were separately inoculated into soybean paste subjected to brine fermentation for 90 days. The amino acid nitrogen contents of the two fermentation systems were detected every 10 days, and both reached the maximum level at 40 days. The samples fermented for 40 days were analyzed via gas chromatography-time of flight mass spectrometry. Using univariate, multivariate and KEGG analyses, 72 differential metabolites were obtained, and 7 metabolic pathways closely related to fermentation were screened. The relative contents of 2-oxoglutarate, ornithine, glutamine, and citrulline were higher in GQ1-3, whereas those of l-homoserine, aspartic acid, and asparagine were higher in HGPA20. These findings indicate that α-ketoglutaric acid-derived amino acid synthesis is preponderant in GQ1-3, whereas oxaloacetate-derived type is predominant in HGPA20. The different pathways of amino acid synthesis lead to the distinct nutrients and umami substances in the fermented soybean pastes.
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Affiliation(s)
- Xiaodong Sun
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China; College of Environment and Resources, Dalian Minzu University, Dalian 116600, China.
| | - Guozhong Lyu
- College of Environment and Resources, Dalian Minzu University, Dalian 116600, China.
| | - Yushi Luan
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China.
| | - Hong Yang
- College of Environment and Resources, Dalian Minzu University, Dalian 116600, China.
| | - Zhihui Zhao
- College of Environment and Resources, Dalian Minzu University, Dalian 116600, China.
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Costanzo N, Rodolfi M, Musarella R, Ceniti C, Santoro A, Britti D, Casalinuovo F. Microbial quality evaluation of grated cheese samples collected at retail level in Calabria (Italy). J Food Saf 2018. [DOI: 10.1111/jfs.12530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicola Costanzo
- Department of Health SciencesUniversity of Catanzaro Magna Græcia, Viale Europa, 88100 Catanzaro Cz Italy
| | - Marinella Rodolfi
- Department of Earth and Environmental SciencesUniversity of Pavia, Via Volta n. 4, 56100 Pisa Italy
| | - Rosanna Musarella
- Experimental Zooprophylactic Institute of Southern Viale Crotone, 88100 Catanzaro CZ Italy
| | - Carlotta Ceniti
- Department of Health SciencesUniversity of Catanzaro Magna Græcia, Viale Europa, 88100 Catanzaro Cz Italy
| | - Adriano Santoro
- Department of Veterinary Medicine and Animal ProductionUniversity of Naples Federico II Via Federico Delpino, 1, 80137 Napoli NA
| | - Domenico Britti
- Department of Health SciencesUniversity of Catanzaro Magna Græcia, Viale Europa, 88100 Catanzaro Cz Italy
| | - Francesco Casalinuovo
- Experimental Zooprophylactic Institute of Southern Viale Crotone, 88100 Catanzaro CZ Italy
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Dubey MK, Aamir M, Kaushik MS, Khare S, Meena M, Singh S, Upadhyay RS. PR Toxin - Biosynthesis, Genetic Regulation, Toxicological Potential, Prevention and Control Measures: Overview and Challenges. Front Pharmacol 2018; 9:288. [PMID: 29651243 PMCID: PMC5885497 DOI: 10.3389/fphar.2018.00288] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 03/13/2018] [Indexed: 01/28/2023] Open
Abstract
Out of the various mycotoxigenic food and feed contaminant, the fungal species belonging to Penicillium genera, particularly Penicillium roqueforti is of great economic importance, and well known for its crucial role in the manufacturing of Roquefort and Gorgonzola cheese. The mycotoxicosis effect of this mold is due to secretion of several metabolites, of which PR toxin is of considerable importance, with regard to food quality and safety challenges issues. The food products and silages enriched with PR toxin could lead into damage to vital internal organs, gastrointestinal perturbations, carcinogenicity, immunotoxicity, necrosis, and enzyme inhibition. Moreover, it also has the significant mutagenic potential to disrupt/alter the crucial processes like DNA replication, transcription, and translation at the molecular level. The high genetic diversities in between the various strains of P. roqueforti persuaded their nominations with Protected Geographical Indication (PGI), accordingly to the cheese type, they have been employed. Recently, the biosynthetic mechanism and toxicogenetic studies unraveled the role of ari1 and prx gene clusters that cross-talk with the synthesis of other metabolites or involve other cross-regulatory pathways to negatively regulate/inhibit the other biosynthetic route targeted for production of a strain-specific metabolites. Interestingly, the chemical conversion that imparts toxic properties to PR toxin is the substitution/oxidation of functional hydroxyl group (-OH) to aldehyde group (-CHO). The rapid conversion of PR toxin to the other derivatives such as PR imine, PR amide, and PR acid, based on conditions available reflects their unstability and degradative aspects. Since the PR toxin-induced toxicity could not be eliminated safely, the assessment of dose-response and other pharmacological aspects for its safe consumption is indispensable. The present review describes the natural occurrences, diversity, biosynthesis, genetics, toxicological aspects, control and prevention strategies, and other management aspects of PR toxin with paying special attention on economic impacts with intended legislations for avoiding PR toxin contamination with respect to food security and other biosafety purposes.
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Affiliation(s)
- Manish K. Dubey
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Mohd Aamir
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Manish S. Kaushik
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Saumya Khare
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Mukesh Meena
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
- Centre for Transgenic Plant Development, Department of Biotechnology, Faculty of Science, Hamdard University, New Delhi, India
| | - Surendra Singh
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Ram S. Upadhyay
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
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