Spotlight on research: the root microbiome and the “soil-borne legacy”

Welcome to Spotlight on Research! Every year, researchers publish thousands of studies and in hundreds of journals – and most aren’t really accessible to the general public. In the interest of increasing the accessibility of some cool research, in each episode, I’m going to summarize a recent study that I find interesting and potentially relevant to horticultural crop production in our region.

Today’s episode focuses on a commentary recently published in the journal Cell (Bakker et al., 2018). It is one of several papers from a team of researchers from the Netherlands who have written several papers on the topic of the rhizosphere microbiome. This is not a description of a specific study, but more a description of the current state of knowledge in this field.

You can read on, or, if you’d rather listen to or watch this presentation – check out this 8-minute video clip.

First, it’s important to define a few terms. The rhizosphere is the interface between the plant and root. As plant roots grow, they slough off dead root cells, and roots exude stuff, including amino acids, sugars and other compounds, into the soil around them. Researchers have estimated that up to 10-40% of the photosynthates that plants produce are secreted into the rhizosphere. These exudates and dead root cells are delicious sources of nutrients if you are a microbe – and as such, the rhizosphere contains much higher microbial population densities than the surrounding soil.

A microbiome refers to the community of microorganisms (including bacteria, fungi and viruses) that inhabit a particular environment. Increasingly, we talk about the importance of the human microbiome in human health. In agricultural or natural environments, we can talk about the microbiome in the air, on the leaves, within the plant, in the soil, or specifically within the rhizosphere.

It’s specifically the new information that we are learning about the rhizosphere microbiome that is the subject of today’s paper. This sentence from the paper summarizes it well: “It appears that plants evolved adaptive strategies by which they utilize root-associated microbiota to optimize both nutrient acquisition and immunity”.

Let’s talk first about immunity, or resistance to pathogens. From a series of studies with Arabidopsis, a plant in the brassica family, we know that when plants are infected with the pathogen that causes downy mildew, there are measurable changes in the rhizosphere microbes: some organisms become more or less prevalent. When a mixture of the microbes that increase in prevalence are added to the soil with other plants growing in them, this induces systemic resistance in those plants – meaning those plants become less susceptible to the downy mildew pathogen. The same thing happens when the soil is “pre-conditioned” by adding downy-mildew infected plants to it. This is called the “cry for help” hypothesis, in which plants directly alter their root microbiome when they are under attack, which selectively enriches microbes in the soil that protect plants. This protective effect persists and can benefit future plant generations.

This is sometimes called “suppressive soil memory”, because under certain circumstances, soils can accumulate microbes that protect plants against a pathogen that has been prevalent in that soil. While the example we just talked about was using a non-crop plant, this phenomenon has also been shown for crop plants and their pathogens: for example, to Rhizoctonia solani in sugarbeet and to Fusarium oxysporum in common bean.

So, how does this happen?  It appears that plant defense signalling and the root microbiome are interconnected. When plants are infected by pathogens, this triggers defense responses that are systemic, or that move throughout the plant. Two compounds in particular play key roles in this process: salicylic acid (SA) and jasmonic acid (JA). Researchers have shown that plants that don’t produce SA or JA normally due to mutations produce different types of root exudates and have different root microbiomes compared with plants that do produce SA and JA normally. Again, this suggests that plant’s defense signalling strategies directly influence the root microbiomes.

In addition to defense, it also appears that the rhizosphere microbiome affects how plants acquire nutrients. For example, when plants are starved of phosphorus (P), genes involved in the P starvation response are turned on. This causes plant roots to excrete organic acids that directly increase P availablility. At the same time, plant roots excrete other compounds that cause changes in the root microbiome. In turn, some of the microbes that become more prevalent increase the availability of P indirectly. Researchers have also learned recently that the P-starvation response genes turn off the plant defense genes, resulting in less SA and JA production. The net result of this is that the root microbiome shifts to prioritize nutrient stress rather than plant defense. Interestingly, when the root-derived bacterial community from P-starved plants is provided to other plants, their P starvation response genes are turned on – so the microbiome also appears to communicate to other plants that P-starvation may be a threat.

Putting it all together: We know that plants respond to stresses (pathogens, drought, nutrient deficiency) by either stimulating or selecting against certain microbes – thus changing the rhizosphere microbiome. We know that these effects vary with type of plant, and even between varieties for a given type of plant. We are learning that the rhizosphere microbiome performs important functions for the plant: helping take up nutrients or water, protecting against invaders, and signaling the presence of stresses to other plants. And lastly, it seems that this complicated network of responses is somehow coordinated in the plant, such that microbiome functions that are most beneficial to the plant at any given time are prioritized. While there is certainly the potential to use this information to possibly change the microbiome to maximize crop growth, the thing that I found most compelling in these articles was that we’re beginning to piece together a very complex story about co-evolution between plants, their environment, and their microbial neighbors. There is still a lot to learn –what we know so far is just the tip of the proverbial iceberg.

Do you have questions about this topic, or suggestions for other topics to explore in Spotlight on Research? If so, please reach out and let me know. Thanks for reading, and stay tuned for the next edition.  



Berendsen RL, CMG Pieterse, and PAHM Bakker (2012) The rhizosphere microbiome and plant health. Trends in Plant Science 17(8)

Pieterse CMJ, R de Jonge, and RL Berendsen (2016) The Soil-Borne Supremacy. Trends in Plant Science 21(3)

Bakker PAHM, CMK Pieterse, R de Jonge and RL Berendsen (2018) The Soil-Borne Legacy.  Cell 172