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Rhizosphere Metagenomics: Methods and Challenges

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Omics Science for Rhizosphere Biology

Part of the book series: Rhizosphere Biology ((RHBIO))

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Abstract

“Rhizosphere” is a narrow region associated with plant roots, acting as a residing place for millions of microorganisms. The rhizosphere-associated microbes are collectively called as root microbiome or rhizobiome. These microbiomes play a vital role in plant health by manipulating their growth and development. Rhizobiomes include both beneficial communities which enhance plant growth and improve plant defense mechanisms and pathogens which are harmful to plants. Nevertheless, the beneficial communities compete with the pathogens and colonize the roots. Though the significance of rhizosphere microbial community is well acknowledged, characterization of a plenty of microbes colonizing the rhizosphere is not done. Studying the rhizobiome of a crop species is an essential factor of crop improvement. “Metagenomics” is a frontier science that deals with study of metagenomes found in an environment such as rhizosphere. In this chapter, we have reviewed the most important metagenomic approaches and attributes to study the microbial diversity in the rhizosphere. We have discussed about the methods and software programs available for metagenome assembly, binning strategies, taxonomic classification, and functional annotation of metagenomics datasets. In addition, we have briefly pointed out the bottlenecks of the metagenomics approaches in studying the rhizobiomes.

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Acknowledgments

The authors are thankful to the reviewer for his/her cautious evaluation of our manuscript and his/her valuable comments and suggestions. A special thanks to Dr. Ashok Kumar M, Senior Research Fellow, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, for his assistance in drawing the figures for the manuscript.

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  1. Department of Genetic Engineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Kanchipuram, Chennai, TamilNadu, India

    Abiramavalli Moorthy & Usha Balasundaram

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  1. Abiramavalli Moorthy
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  2. Usha Balasundaram
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Editors and Affiliations

  1. Amity Institute of Nanotechnology, Amity University Uttar Pradesh, Noida, Uttar Pradesh, India

    Ramesh Namdeo Pudake

  2. Department of Life Sciences, National Institute of Technology, Rourkela, Odisha, India

    Binod Bihari Sahu

  3. Directorate of Life Sciences, Defence Research and Development Organisation, New Delhi, Delhi, India

    Maya Kumari

  4. Department of Biological Sciences, C.B.S.H., G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India

    Anil K. Sharma

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Moorthy, A., Balasundaram, U. (2021). Rhizosphere Metagenomics: Methods and Challenges. In: Pudake, R.N., Sahu, B.B., Kumari, M., Sharma, A.K. (eds) Omics Science for Rhizosphere Biology. Rhizosphere Biology. Springer, Singapore. https://doi.org/10.1007/978-981-16-0889-6_1

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