Author:
Navgire Gauri S.,Goel Neha,Sawhney Gifty,Sharma Mohit,Kaushik Prashant,Mohanta Yugal Kishore,Mohanta Tapan Kumar,Al-Harrasi Ahmed
Abstract
AbstractAdvances in next-generation sequencing technologies have accelerated the momentum of metagenomic studies, which is increasing yearly. The metagenomics field is one of the versatile applications in microbiology, where any interaction in the environment involving microorganisms can be the topic of study. Due to this versatility, the number of applications of this omics technology reached its horizons. Agriculture is a crucial sector involving crop plants and microorganisms interacting together. Hence, studying these interactions through the lenses of metagenomics would completely disclose a new meaning to crop health and development. The rhizosphere is an essential reservoir of the microbial community for agricultural soil. Hence, we focus on the R&D of metagenomic studies on the rhizosphere of crops such as rice, wheat, legumes, chickpea, and sorghum. These recent developments are impossible without the continuous advancement seen in the next-generation sequencing platforms; thus, a brief introduction and analysis of the available sequencing platforms are presented here to have a clear picture of the workflow. Concluding the topic is the discussion about different pipelines applied to analyze data produced by sequencing techniques and have a significant role in interpreting the outcome of a particular experiment. A plethora of different software and tools are incorporated in the automated pipelines or individually available to perform manual metagenomic analysis. Here we describe 8–10 advanced, efficient pipelines used for analysis that explain their respective workflows to simplify the whole analysis process.
Publisher
Springer Science and Business Media LLC
Subject
General Biochemistry, Genetics and Molecular Biology
Reference119 articles.
1. Council NR. The New Science of Metagenomics: Revealing the secrets of our Microbial planet. ISBN 978-0-309-10676-4, Washington, DC: The National Academies Press; 2007, 12-31. Available from: https://nap.nationalacademies.org/catalog/11902/the-new-science-of-metagenomics-revealing-the-secrets-of-our.
2. Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol. 1998;5:R245-9 https://www.sciencedirect.com/science/article/pii/S1074552198901089.
3. Laudadio I, Fulci V, Stronati L, Carissimi C. Next-generation metagenomics methodological challenges and opportunities. Omi A J Integr Biol. 2019;23:327–33. https://doi.org/10.1089/omi.2019.0073 Mary Ann Liebert Inc, publishers.
4. Acinas SG, Sánchez P, Salazar G, Cornejo-Castillo FM, Sebastián M, Logares R, et al. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Commun Biol. 2021;4:604. https://doi.org/10.1038/s42003-021-02112-2.
5. Molefe RR, Amoo AE, Babalola OO. Metagenomic insights into the bacterial community structure and functional potentials in the rhizosphere soil of maize plants. J Plant Interact 2021;16:258–69. https://doi.org/10.1080/17429145.2021.1936228 Taylor Francis.
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