Root Rumble: Exploring the Competitive World of Plant Microbiomes

Stéphane Haquard’s research team aims to unravel the complex composition of the plant microbiome and to understand the factors that regulate its unique makeup - promoting the growth of plants and protecting them from diseases.

When we talk about the microbiome, we usually think of the human microbiome - the microbiome of the gut or skin. Plants also don't live alone; they have their own community of microorganisms called microbiome. These tiny organisms colonize the roots and other parts of the plant in a vast array. The plant and these microbes, consisting of bacteria, archaea, and fungi, create a complex relationship.

While the microbes may be invisible to the naked eye, the significance of these small inhabitants cannot be overlooked. They play a crucial role in plant nutrition, impact plant health, enhance resilience to stress like drought, and aid in defending against pathogens.

The way billions of microbes interact with each other is very complex. Additionally, the type of plants, the condition of the soil, and the climate also affect which microbes live in a plant's environment.

Bacteria produce small molecules for competition

In the past the scientists have identified signals from plants and the environment that influence the formation of the microbiota at the roots. They could also show that plants rely on the presence of bacteria for healthy growth.

But what is the exact role of microbial interactions and their competing activity in this process?

The discovery of penicillin showed us that microorganisms are capable of producing substances that have a targeted effect against other microorganisms. This discovery marked a revolution in 20th century medicine. In 1928, Sir Alexander Fleming discovered that molds of the genus Penicillium can kill bacteria. Since then, many other antibacterial substances have been discovered and developed.

Most of the time we think about the clinical applications, while the ecological functions of these substances is often overlooked. These molecules are produced to help microorganisms compete better, usually for food. Microbes want to make sure they have access to resources without others getting in their way. Making these molecules that keep competitors away, is essential for these microorganisms to thrive. 

Finding a needle in the haystack

There is a huge diversity of these antimicrobial molecules because all the time microbes produce antimicrobial substances, other microbes may evolve resistance mechanisms.

The scientists discovered a bacterium called Pseudomonas brassicacearum, which showed a remarkably strong inhibitory effect on numerous other bacteria in the root microbiota. This bacterium produces two molecules which work together to control the other microbes. The first molecule is a substance called 2,4-diacetylphloroglucinol, which works against microbes. The second molecule intercepts the important nutrient iron and steals it away from the bacterial competitors.

The team then designed versions of the bacterium Pseudomonas brassicacearum which are unable to produce the two specific molecules to see what the influence of these molecules to the plant root community is. They found that the two natural chemicals, produced by a single bacterium, not only change the types of bacteria in the root but also gives the bacterium P. brassicacearum an advantage in colonization and dominance on the root.

Competition is good for business

Like in many communities, competition among the different parties involved can foster diversity and ultimately lead to stronger and more resilient systems. The same applies to the plant microbiome. The more competition, the more diversity occurs and the less chance is there that one strain takes over und unbalances the system.

The challenge is now to understand which antimicrobials are produced by which microbe, in order to understand how the network of antimicrobials are shaping the microbial communities.

Stéphane accepts this challenge and not only wants to find antibacterial molecules but also molecules produced by bacteria which act against fungi within the microbiome.

Learning more about the tiny world of microorganisms and their living with plants will help towards finding better ways to keep plants healthy and to develop more sustainable crop protection technologies.



Getzke, F., Hassani, M. A., Crüsemann, M., Malisic, M., Zhang, P., Ishigaki, Y., Böhringer, N., Jiménez Fernández, A., Wang, L., Ordon, J., Ma, K.-W., Thiergart, T., Harbort, C. J., Wesseler, H., Miyauchi, S., Garrido-Oter, R., Shirasu, K., Schäberle, T. F., Hacquard, S., & Schulze-Lefert, P. Co-functioning of bacterial exometabolites drives root microbiota establishment. PNAS 2023.

Go to Editor View