It takes three to tango: the importance of microbes, host plant, and soil management to elucidate manipulation strategies for the plant microbiome

Can J Microbiol. 2020 Jul;66(7):413-433. doi: 10.1139/cjm-2020-0085. Epub 2020 May 12.


The world's population is expected to grow to almost 10 billion by 2050, placing unprecedented demands on agriculture and natural resources. The risk in food security is also aggravated by climate change and land degradation, which compromise agricultural productivity. In recent years, our understanding of the role of microbial communities on ecosystem functioning, including plant-associated microbes, has advanced considerably. Yet, translating this knowledge into practical agricultural technologies is challenged by the intrinsic complexity of agroecosystems. Here, we review current strategies for plant microbiome manipulation, classifying them into three main pillars: (i) introducing and engineering microbiomes, (ii) breeding and engineering the host plant, and (iii) selecting agricultural practices that enhance resident soil and plant-associated microbial communities. In each of these areas, we analyze current trends in research, as well as research priorities and future perspectives.

Keywords: agroecosystems; agroécosystèmes; durabilité; endosphere; endosphère; phytobiome; rhizosphere; rhizosphère; sustainability.

Publication types

  • Review

MeSH terms

  • Agriculture / methods*
  • Agriculture / trends
  • Ecosystem
  • Microbiota* / genetics
  • Plant Development
  • Plant Roots / microbiology
  • Plants / genetics
  • Plants / microbiology*
  • Rhizosphere
  • Soil
  • Soil Microbiology*


  • Soil