Pyrosequencing and phenotypic microarray to decipher bacterial community variation in Sorghum bicolor (L.) Moench rhizosphere
- Kumar, Ashwani, Dubey, Anamika, Malla, Muneer A, Dames, Joanna F
- Authors: Kumar, Ashwani , Dubey, Anamika , Malla, Muneer A , Dames, Joanna F
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/440417 , vital:73781 , https://doi.org/10.1007/s11274-022-03288-3
- Description: Different cultivation practices and climatic conditions play an important role in governing and modulating soil microbial communities as well as soil health. This study investigated, for the first time, keystone microbial taxa inhabiting the rhizosphere of sweet sorghum (Sorghum bicolor) under extensive cultivation practices at three different field sites of South Africa (North West-South (ASHSOIL1); Mpumalanga-West – (ASHSOIL2); and Free State-North West – (ASHSOIL3)). Soil analysis of these sites revealed differences in P, K, Mg, and pH. 16S rRNA amplicon sequencing data revealed that the rhizosphere bacterial microbiome differed significantly both in the structure and composition across the samples. The sequencing data revealed that at the phylum level, the dominant group was Cyanobacteria with a relative abundance of 63.3%, 71.8%, and 81.6% from ASHSOIL1, ASHSOIL2, and ASHSOIL3, respectively. Putative metabolic requirements analyzed by METAGENassist software revealed the ASHSOIL1 sample as the prominent ammonia degrader (21.1%), followed by ASHSOIL3 (17.3%) and ASHSOIL2 (11.1%). The majority of core-microbiome taxa were found to be from Cyanobacteria, Bacteroidetes, and Proteobacteria. Functionally, community-level physiological profiling (CLPP) analysis revealed that the metabolic activity of the bacterial community in ASHSOIL3 was the highest, followed by ASHSOIL1 and ASHSOIL2. This study showed that soil pH and nutrient availability and cultivation practices played significant roles in governing the bacterial community composition in the sorghum rhizosphere across the different sites.
- Full Text:
- Date Issued: 2021
- Authors: Kumar, Ashwani , Dubey, Anamika , Malla, Muneer A , Dames, Joanna F
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/440417 , vital:73781 , https://doi.org/10.1007/s11274-022-03288-3
- Description: Different cultivation practices and climatic conditions play an important role in governing and modulating soil microbial communities as well as soil health. This study investigated, for the first time, keystone microbial taxa inhabiting the rhizosphere of sweet sorghum (Sorghum bicolor) under extensive cultivation practices at three different field sites of South Africa (North West-South (ASHSOIL1); Mpumalanga-West – (ASHSOIL2); and Free State-North West – (ASHSOIL3)). Soil analysis of these sites revealed differences in P, K, Mg, and pH. 16S rRNA amplicon sequencing data revealed that the rhizosphere bacterial microbiome differed significantly both in the structure and composition across the samples. The sequencing data revealed that at the phylum level, the dominant group was Cyanobacteria with a relative abundance of 63.3%, 71.8%, and 81.6% from ASHSOIL1, ASHSOIL2, and ASHSOIL3, respectively. Putative metabolic requirements analyzed by METAGENassist software revealed the ASHSOIL1 sample as the prominent ammonia degrader (21.1%), followed by ASHSOIL3 (17.3%) and ASHSOIL2 (11.1%). The majority of core-microbiome taxa were found to be from Cyanobacteria, Bacteroidetes, and Proteobacteria. Functionally, community-level physiological profiling (CLPP) analysis revealed that the metabolic activity of the bacterial community in ASHSOIL3 was the highest, followed by ASHSOIL1 and ASHSOIL2. This study showed that soil pH and nutrient availability and cultivation practices played significant roles in governing the bacterial community composition in the sorghum rhizosphere across the different sites.
- Full Text:
- Date Issued: 2021
Tapping the role of microbial biosurfactants in pesticide remediation: an eco-friendly approach for environmental sustainability
- Raj, Aman, Kumar, Ashwani, Dames, Joanna F
- Authors: Raj, Aman , Kumar, Ashwani , Dames, Joanna F
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/440430 , vital:73782 , https://doi.org/10.3389/fmicb.2021.791723
- Description: Pesticides are used indiscriminately all over the world to protect crops from pests and pathogens. If they are used in excess, they contaminate the soil and water bodies and negatively affect human health and the environment. However, bioremediation is the most viable option to deal with these pollutants, but it has certain limitations. Therefore, harnessing the role of microbial biosurfactants in pesticide remediation is a promising approach. Biosurfactants are the amphiphilic compounds that can help to increase the bioavailability of pesticides, and speeds up the bioremediation process. Biosurfactants lower the surface area and interfacial tension of immiscible fluids and boost the solubility and sorption of hydrophobic pesticide contaminants. They have the property of biodegradability, low toxicity, high selectivity, and broad action spectrum under extreme pH, temperature, and salinity conditions, as well as a low critical micelle concentration (CMC). All these factors can augment the process of pesticide remediation. Application of metagenomic and in-silico tools would help by rapidly characterizing pesticide degrading microorganisms at a taxonomic and functional level. A comprehensive review of the literature shows that the role of biosurfactants in the biological remediation of pesticides has received limited attention. Therefore, this article is intended to provide a detailed overview of the role of various biosurfactants in improving pesticide remediation as well as different methods used for the detection of microbial biosurfactants. Additionally, this article covers the role of advanced metagenomics tools in characterizing the biosurfactant producing pesticide degrading microbes from different environments.
- Full Text:
- Date Issued: 2021
- Authors: Raj, Aman , Kumar, Ashwani , Dames, Joanna F
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/440430 , vital:73782 , https://doi.org/10.3389/fmicb.2021.791723
- Description: Pesticides are used indiscriminately all over the world to protect crops from pests and pathogens. If they are used in excess, they contaminate the soil and water bodies and negatively affect human health and the environment. However, bioremediation is the most viable option to deal with these pollutants, but it has certain limitations. Therefore, harnessing the role of microbial biosurfactants in pesticide remediation is a promising approach. Biosurfactants are the amphiphilic compounds that can help to increase the bioavailability of pesticides, and speeds up the bioremediation process. Biosurfactants lower the surface area and interfacial tension of immiscible fluids and boost the solubility and sorption of hydrophobic pesticide contaminants. They have the property of biodegradability, low toxicity, high selectivity, and broad action spectrum under extreme pH, temperature, and salinity conditions, as well as a low critical micelle concentration (CMC). All these factors can augment the process of pesticide remediation. Application of metagenomic and in-silico tools would help by rapidly characterizing pesticide degrading microorganisms at a taxonomic and functional level. A comprehensive review of the literature shows that the role of biosurfactants in the biological remediation of pesticides has received limited attention. Therefore, this article is intended to provide a detailed overview of the role of various biosurfactants in improving pesticide remediation as well as different methods used for the detection of microbial biosurfactants. Additionally, this article covers the role of advanced metagenomics tools in characterizing the biosurfactant producing pesticide degrading microbes from different environments.
- Full Text:
- Date Issued: 2021
Current developments in arbuscular mycorrhizal fungi research and its role in salinity stress alleviation a biotechnological perspective
- Kumar, Ashwani, Dames, Joanna F, Gupta, Aditi, Sharma, Satyawati, Gilbert, Jack A, Ahmad, Parvaiz
- Authors: Kumar, Ashwani , Dames, Joanna F , Gupta, Aditi , Sharma, Satyawati , Gilbert, Jack A , Ahmad, Parvaiz
- Date: 2015
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/443998 , vital:74177 , https://doi.org/10.3109/07388551.2014.899964
- Description: Arbuscular mycorrhizal fungi (AMF) form widespread symbiotic associations with 80% of known land plants. They play a major role in plant nutrition, growth, water absorption, nutrient cycling and protection from pathogens, and as a result, contribute to ecosystem processes. Salinity stress conditions undoubtedly limit plant productivity and, therefore, the role of AMF as a biological tool for improving plant salt stress tolerance, is gaining economic importance worldwide. However, this approach requires a better understanding of how plants and AMF intimately interact with each other in saline environments and how this interaction leads to physiological changes in plants. This knowledge is important to develop sustainable strategies for successful utilization of AMF to improve plant health under a variety of stress conditions. Recent advances in the field of molecular biology, “omics” technology and advanced microscopy can provide new insight about these mechanisms of interaction between AMF and plants, as well as other microbes. This review mainly discusses the effect of salinity on AMF and plants, and role of AMF in alleviation of salinity stress including insight on methods for AMF identification. The focus remains on latest advancements in mycorrhizal research that can potentially offer an integrative understanding of the role of AMF in salinity tolerance and sustainable crop production.
- Full Text:
- Date Issued: 2015
- Authors: Kumar, Ashwani , Dames, Joanna F , Gupta, Aditi , Sharma, Satyawati , Gilbert, Jack A , Ahmad, Parvaiz
- Date: 2015
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/443998 , vital:74177 , https://doi.org/10.3109/07388551.2014.899964
- Description: Arbuscular mycorrhizal fungi (AMF) form widespread symbiotic associations with 80% of known land plants. They play a major role in plant nutrition, growth, water absorption, nutrient cycling and protection from pathogens, and as a result, contribute to ecosystem processes. Salinity stress conditions undoubtedly limit plant productivity and, therefore, the role of AMF as a biological tool for improving plant salt stress tolerance, is gaining economic importance worldwide. However, this approach requires a better understanding of how plants and AMF intimately interact with each other in saline environments and how this interaction leads to physiological changes in plants. This knowledge is important to develop sustainable strategies for successful utilization of AMF to improve plant health under a variety of stress conditions. Recent advances in the field of molecular biology, “omics” technology and advanced microscopy can provide new insight about these mechanisms of interaction between AMF and plants, as well as other microbes. This review mainly discusses the effect of salinity on AMF and plants, and role of AMF in alleviation of salinity stress including insight on methods for AMF identification. The focus remains on latest advancements in mycorrhizal research that can potentially offer an integrative understanding of the role of AMF in salinity tolerance and sustainable crop production.
- Full Text:
- Date Issued: 2015
Genetic approaches to improve salinity tolerance in plants
- Kumar, Ashwani, Gupta, Aditi, Azooz, M M, Sharma, S, Ahmad, Parvaiz, Dames, Joanna F
- Authors: Kumar, Ashwani , Gupta, Aditi , Azooz, M M , Sharma, S , Ahmad, Parvaiz , Dames, Joanna F
- Date: 2013
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/453449 , vital:75255 , ISBN , https://doi.org/10.1007/978-1-4614-6108-1_4
- Description: Abiotic stress tolerance in plants is gaining importance day by day. Different techniques are being employed to develop salt tolerant plants that directly or indirectly combat global food problems. Advanced comprehension of stress signal perception and transduction of associated molecular networks is now possible with the development in functional genomics and high throughput sequencing. In plant stress tolerance various genes, proteins, transcription factors, DNA histone-modifying enzymes, and several metabolites are playing very important role in stress tolerance. Determination of genomes of Arabidopsis, Oryza sativa spp. japonica cv. Nipponbare and integration of omics approach has augmented our knowledge pertaining to salt tolerance mechanisms of plants in natural environments. Application of transcriptomics, metabolomics, bioinformatics, and high-through-put DNA sequencing has enabled active analyses of regulatory networks that control abiotic stress responses. To unravel and exploit the function of genes is a major challenge of the post genomic era. This chapter therefore reviews the effect of salt stress on plants and the mechanism of salinity tolerance along with contributory roles of QTL, microRNA, microarray and proteomics.
- Full Text:
- Date Issued: 2013
- Authors: Kumar, Ashwani , Gupta, Aditi , Azooz, M M , Sharma, S , Ahmad, Parvaiz , Dames, Joanna F
- Date: 2013
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/453449 , vital:75255 , ISBN , https://doi.org/10.1007/978-1-4614-6108-1_4
- Description: Abiotic stress tolerance in plants is gaining importance day by day. Different techniques are being employed to develop salt tolerant plants that directly or indirectly combat global food problems. Advanced comprehension of stress signal perception and transduction of associated molecular networks is now possible with the development in functional genomics and high throughput sequencing. In plant stress tolerance various genes, proteins, transcription factors, DNA histone-modifying enzymes, and several metabolites are playing very important role in stress tolerance. Determination of genomes of Arabidopsis, Oryza sativa spp. japonica cv. Nipponbare and integration of omics approach has augmented our knowledge pertaining to salt tolerance mechanisms of plants in natural environments. Application of transcriptomics, metabolomics, bioinformatics, and high-through-put DNA sequencing has enabled active analyses of regulatory networks that control abiotic stress responses. To unravel and exploit the function of genes is a major challenge of the post genomic era. This chapter therefore reviews the effect of salt stress on plants and the mechanism of salinity tolerance along with contributory roles of QTL, microRNA, microarray and proteomics.
- Full Text:
- Date Issued: 2013
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