Sustainable Agriculture: Role of Metagenomics and Metabolomics in Exploring the Soil Microbiota

Gupta, Neeraj; Vats, Siddharth; Bhargava, Prachi

doi:10.1007/978-981-13-0347-0_11

Cited by 24 publications

(11 citation statements)

References 64 publications

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“…These studies and evidence reflect the importance of metagenomics application as a tool in unlocking the knowledge of biota that are influenced by abiotic factors in sustainable agriculture. Major challenges currently faced in agriculture in maintaining a balance between sustainability and increasing fiscal growth rate are the environmental threats, social threats, economic threats, and other factors like global warming, urbanization, and pollution ( Gupta et al, 2018 ; Figure 4 ).…”

Section: Metagenomics and Sustainable Agriculturementioning

confidence: 99%

Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review

et al. 2022

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Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.

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Section: Metagenomics and Sustainable Agriculturementioning

confidence: 99%

Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review

et al. 2022

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“…Metagenomics is the direct analysis of genome (Zolfo et al, 2018). The microbial DNA is extracted directly from the soil sample (Gupta et al, 2018; Jeffries et al, 2018). This repute of metagenomics is the major advantage enabling the DNA analysis of non-culturable microbes present in the sample, i.e., culture independent approach (Perito and Cavalieri, 2018).…”

Section: Keys Of Systems Biologymentioning

confidence: 99%

Gene Editing and Systems Biology Tools for Pesticide Bioremediation: A Review

2019

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Bioremediation is the degradation potential of microorganisms to dissimilate the complex chemical compounds from the surrounding environment. The genetics and biochemistry of biodegradation processes in datasets opened the way of systems biology. Systemic biology aid the study of interacting parts involved in the system. The significant keys of system biology are biodegradation network, computational biology, and omics approaches. Biodegradation network consists of all the databases and datasets which aid in assisting the degradation and deterioration potential of microorganisms for bioremediation processes. This review deciphers the bio-degradation network, i.e., the databases and datasets (UM-BBD, PAN, PTID, etc.) aiding in assisting the degradation and deterioration potential of microorganisms for bioremediation processes, computational biology and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation experiments. Besides, the present review also describes the gene editing tools like CRISPR Cas, TALEN, and ZFNs which can possibly make design microbe with functional gene of interest for degradation of particular recalcitrant for improved bioremediation.

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“…In recent years, steady‐state metabolomic found its application in multiple disciplines. Given the close relationship between physiological and/or pharmacological external cues and the impact on the systemic metabolic profile, this experimental approach has been extensively used in nutrition, 72,73 agricultural, 74,75 dairy, 76,77 toxicology, 78,79 preclinical, and clinical studies. In life sciences, targeted metabolomics has been mainly employed for the characterization of known metabolites and pathways (i.e., amino acids, glycolysis, Krebs cycle, and pentose phosphate pathway) in in vitro, ex vivo, and in vivo experimental settings 6,80–90 .…”

Section: Main Applications Of Steady‐state Metabolomicsmentioning

confidence: 99%

Investigating metabolism by mass spectrometry: From steady state to dynamic view

et al. 2020

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Metabolism is the set of life‐sustaining reactions in organisms. These biochemical reactions are organized in metabolic pathways, in which one metabolite is converted through a series of steps catalyzed by enzymes in another chemical compound. Metabolic reactions are categorized as catabolic, the breaking down of metabolites to produce energy, and/or anabolic, the synthesis of compounds that consume energy. The balance between catabolism of the preferential fuel substrate and anabolism defines the overall metabolism of a cell or tissue. Metabolomics is a powerful tool to gain new insights contributing to the identification of complex molecular mechanisms in the field of biomedical research, both basic and translational. The enormous potential of this kind of analyses consists of two key aspects: (i) the possibility of performing so‐called targeted and untargeted experiments through which it is feasible to verify or formulate a hypothesis, respectively, and (ii) the opportunity to run either steady‐state analyses to have snapshots of the metabolome at a given time under different experimental conditions or dynamic analyses through the use of labeled tracers. In this review, we will highlight the most important practical (e.g., different sample extraction approaches) and conceptual steps to consider for metabolomic analysis, describing also the main application contexts in which it is used. In addition, we will provide some insights into the most innovative approaches and progress in the field of data analysis and processing, highlighting how this part is essential for the proper extrapolation and interpretation of data.

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Sustainable Agriculture: Role of Metagenomics and Metabolomics in Exploring the Soil Microbiota

Cited by 24 publications

References 64 publications

Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review

Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review

Gene Editing and Systems Biology Tools for Pesticide Bioremediation: A Review

Investigating metabolism by mass spectrometry: From steady state to dynamic view

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