Is the microbial friend of my plant, my friend?

March 6, 2017 -- “Life would not long remain possible in the absence of microbes.”—Louis Pasteur (Father of Microbiology)

Is the microbial friend of my plant, my friend?

As Pasteur said, it's hard to imagine life on earth without microbes. Microbes are everywhere; from your gut to the ocean bed. Not only they are present everywhere, but they are also unimaginably diverse and numerous. If we count the cells living in and on our body, then we are more microbe than human. Despite this fact, when we think about microbes, we usually think of them as pathogens. Recent studies have shown that while some microbes are pathogens, the majority of them are beneficial and have immense roles supporting our wellbeing.

Surprisingly, not only humans, but plants also have their own galaxy of microbes. This constellation of microbes helps feed the plant with key nutrients, shields against infections, protects under heat and drought stress, and ultimately makes them healthy and happy. As in humans, not all the microbes are friends to the plant, some of them are foes as well- causing severe disease and yield loss.

The key intervention lies in selecting the good microbes while restraining the bad ones. Repackaging beneficial microbes and delivering them to plants has the potential to improve plant productivity without a need for pesticides. However, it's not always clear what and which microbes to include in this package. One approach to tackle this question will be to study healthy plots, and their microbial communities, and that's what exactly we did.

In our recent work, we used network models to map the galaxy of microbes and their potential interactions in the soil and leaves. Our model represents each type of microbe and the links between them based on whether they tend to occur together.  The we compared the networks for healthy and unhealthy plants, to see what microbes and links were associated with healthy plants and might be useful for adding to systems to make them healthier.  By also studying the microbe network associated with unhealthy plants, we can start to understand which microbes have positive and negative associations with pathogens.  We can apply the idea that "The enemy of my enemy is my friend".

This study was the most downloaded paper in the journal Phytopathology in 2016, and is available open access at


Photo Caption:

A network of interactions among microbes that influence plant health (Poudel et al. 2016)

A green node represents a host response variable (photosynthetic rate), and nodes are connected based on their type of relation with the plant or between taxa- red if negative association or blue if positive. Other nodes colored as either a shade of blue or red represent how closely the node are associated with the plant. Darker blue nodes indicate a first degree friend, medium blue have an indirect link through one other taxon as a second degree friend, and light blue have an indirect link through two other taxa as third degree friends. Similarly dark red, medium red, and light red nodes represent taxa that are negatively associated with the plant, as first, second and third degree “enemies”, respectively. Nodes colored half red and half blue have a mixed association with the host response node, either friend or foe. Management strategies to select "friend" microbes while limiting the "foe" microbes could help in designing biofertilizers and microbiome based agriculture in the future.