Figure showing the connection between plants, soil, and the microbiome for phytostimulation, nutrient acquisition, disease suppression, herbivore resistance, and abiotic stress tolerance

Micaela Tosi, Eduardo Kovalski Mitter, Jonathan Gaiero, and Kari Dunfield. 2020. It takes three to tango: the importance of microbes, host plant and soil management to elucidate manipulation strategies for the plant microbiome. Canadian Journal of Microbiology. doi:10.1139/cjm-2020-0085.
Research summary by Micaela Tosi, Eduardo Kovalski Mitter, and Cameron Ogilvie

Key messages

  • Plants live and interact with microbes that regulate their growth.
  • Plant microbiomes can be manipulated in three ways: manipulating the plant, modifying the soil, and manipulating the microbiome directly
  • Microbial processes can reduce dependence on chemical inputs like fertilizers and pesticides

Plants interact with a large number of microorganisms (bacteria, fungi, protozoa, archaea, and viruses). And because plants and microbes are so interconnected, researchers have started to think about plants, microbes, and their environment as a distinct entity called the “plant microbiome.”

Plants rely on microbes for many functions such as nutrition, tolerance to drought or heat stress, and protection against pathogens. If microbes are indeed allies in plant growth, is it possible to manipulate them to enhance crop production? To address this, the authors dug into the literature to understand the ways plant-associated microbes affect plant growth, how they can be manipulated, and if these manipulations are feasible in agricultural systems.

What they found?

There are three possible ways to manipulate the plant microbiome to improve crop growth. The first is to modify the microbiome directly by adding beneficial microbes to the plant or the soil. The most basic example of this is adding a single microbe species. But because microbiomes are complex, adding a single species has produced inconsistent results in previous experiments. New technology allows scientists to create and introduce complex microbial mixtures called “consortia” into crop fields, or even to transplant “whole” microbiomes from other fields. These, together with improved application methods, may get better results in field applications.

The second way to modify the plant microbiome is manipulating the plant. Over the years, crops have been bred under optimal conditions with the help of fertilizers, irrigation, and pesticides. Because of this, plants became less dependent on their microbial partners and more dependent on these external inputs. To recover the plant’s natural partners, new cultivars can be developed that have stronger associations with the microbiome.

Finally, the plant microbiome can be manipulated in favour of crop growth by modifying the soil environment. Many of the microbes colonizing plants come from the surrounding soil and, therefore, they could be modified using common agricultural practices such as diverse crop rotations and reducing nutrient/pesticide inputs. This could be the most accessible and cost-effective approach, but more research is needed to understand the impacts of these practices on the plant microbiome.  

Why it matters?

Manipulating microorganisms that live closely with plants may improve the sustainability of modern agriculture, especially in the context of climate change. By modifying the soil environment, manipulating plants, and manipulating the plant microbiome  directly, it is possible to improve crop production while reducing agriculture’s impact on the environment. This is a challenging goal however, and our current understanding is not enough to recommend practical application guidelines. In the meantime, the authors have summarized and discussed the current understanding and knowledge gaps for future research.  

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