Exploring the Plant Microbiome Through Multi-omics Approaches

  • Rubén López-Mondéjar
  • Martin Kostovčík
  • Salvador Lladó
  • Lorena Carro
  • Paula García-FraileEmail author


Like many other high organisms, plants harbour a microbiome. The plant microbiome can be defined as the communities of microbial symbionts (microbiota) plus their collective genetic material, which determines the properties of the interactions between the microbes themselves and with their host.

The plant microbiome is crucial in plant health and crop yields. The understanding and management of the plant microbiome have the potential to decrease plant diseases and increase agricultural production; this can allow a reduction in the use of chemical fertilisers and pesticides in fields, thereby increasing the production of food to sustain the human population while simultaneously protecting the environment and human health. Consequently, many scientific studies in recent years have focused on unravelling the secrets of the plant microbiome, and the development of several omics techniques has greatly contributed to this aim.

In this chapter, we will review the methodologies of the application of high-throughput sequencing techniques in performing metagenomics studies focused on the microbiota as a part of the plant microbiome, we will provide an overview of the most recent research on this topic, and we will review other omics approaches important in deciphering and understanding the plant microbiome in full, presenting some of the main goals addressed to date.



The Czech Science Foundation (GAČR) under the grant number 16-15293Y and BIOCEV, the Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University provided funding to Rubén López-Mondejar, Martin Kostovčík and Paula García-Fraile, and Salvador Lladó was funded by the Czech Science Foundation (GAČR) under grant number 14-09040P. Lorena Carro thanks the School of Biology (Newcastle University) for a postdoctoral contract.


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Copyright information

© Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  • Rubén López-Mondéjar
    • 1
  • Martin Kostovčík
    • 1
  • Salvador Lladó
    • 2
  • Lorena Carro
    • 3
  • Paula García-Fraile
    • 1
    Email author
  1. 1.Institute of Microbiology of the CAS, v. v. i.VestecCzech Republic
  2. 2.Institute of Microbiology of the CAS, v. v. i.Prague 4Czech Republic
  3. 3.School of Biology, Newcastle UniversityNewcastle upon TyneUK

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