A Deeply Rooted Connection


Breaking down the microbiology world one bite at a time

A Deeply Rooted Connection

Each plant species is associated with a unique collection of microorganisms. The microbial communities around roots vary a little depending on soil type, but are pretty robust. We know which organisms end up in an intimate relationship, but who takes the first step? Does a plant attract bacteria it fancies, or does a bacterium hit on plants it likes? Katrin Wippel and Ke Tao (along with an international team of plant experts) decided to analyze the first spark.

The scientists studied two plant species to highlight differences in their preference for bacteria: Arabidopsis thaliana (a cousin to cabbage) and Lotus japonica (a cousin to beans). The researchers first determined which bacteria are found around the roots of both plants in their native situation using 16S-RNA sequencing. They found hundreds of bacterial species around the roots of both plants. 

Hundreds of bacterial species are hard to work with, so the researchers created a simplified microbiome for both plant species: a Synthetic Community (SynCom), see Figure 1. 16 bacterial species were chosen for A. thaliana,  and 16 for L. japonica. Wippel and Tao chose these species in such a way, that each bacterial species in one SynCom had a close relative in the other (sharing the same bacterial family). This way, the SynComs for A. thaliana and L. japonica were very similar. Could they fool A. thaliana into working with L. japonica-bacteria, or vice-versa?

Figure 1: From a large pool of root-associated bacteria, a model microbiome was chosen for A. thaliana (green) and L. japonica (red). These “synthetic communities” were chosen so that all species associated with one plant had a close relative in the other pool. From the 20 bacterial families detected, 16 families were represented in both synthetic communities. Created with BioRender.com.

To try and fool the plant species, the researchers mixed both SynComs to a total of 32 bacterial species, but still only 16 families. They then inoculated A. thaliana and L. japonica with this mix. After 5 weeks, both plants were found with only their respective set of 16 bacteria enriched on their roots! The plants could not be fooled, something in the interaction seems to be very specific indeed.

Before we continue, I need to explain a little bit of theory. In microbial communities, the order in which microbes reach a place often determines whether they will be a dominant species or live a life in the margins (the priority effect, Figure 2, left side). The first species to arrive can profit from the most food, will take most of the space and/or produce metabolites to inhibit growth of competitors. 

Figure 2: Left: the priority effect. In bare soil, the first bacteria in the soil have an advantage over latecomers regardless of the species. Right: Plant hosts create an advantage for their specific partner bacteria, allowing them to grow even as latecomers. Created with BioRender.com.

This concept of priority effect is important, because the authors showed that a plant host can selectively help its partner bacteria to overcome the priority effect (Figure 2, right side). Wippel and Tao correlated the strength of a plant-microbe interaction with the ability of the same microbe to establish itself in an already existing microbial community (Figure 3). This shows that plants might “cultivate” their preferred bacteria.

Figure 3: The strength of a plant-microbe interaction (‘Host preference index’, Y-axis) correlates with the ability of the same microbe to establish itself in an already existing microbial community (‘Invasiveness index’, X-axis). This holds true for both A. thaliana (red) and L. japonica (blue). Each marker represents one bacterial species; increasing size of the marker indicates a larger relative abundance of the species.

So what enables the plant to romance their favorite bacteria? The researchers determined which genes were active in the plant species using transcriptomics. They found that gene clusters involved in the plant immune system are selectively switched on by native partner bacteria. Also, certain genes involved in determining if a friend or foe is outside the root (with Microbe-Associated Molecular Patterns) were selectively activated. Of course, this does not yet explain exactly how the bacterium activates these genes, but it is a trove of inspiration for new research.

In sum, the interactions between plants and their bacterial babes are indeed very specific and plants work hard to get them. But whether the plant or the bacterium gives the first wink? We will have to observe another date for that!

Link to the original post: Wippel, K., Tao, K., Niu, Y. et al. Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota. Nat Microbiol 6, 1150–1162 (2021).

Featured image: https://pickupimage.com/free-photos/Garden-beds-with-seedlings-and-leafy-greens/2332866