The Rhizosphere
Imagine soil as the open ocean; lots of space, but very little food. Bulk soil is what we call the soil that is not being influenced by a root. The nutrients that used to be there have already been used up or are tightly locked away, and the organisms that still live there are just waiting to get lucky. They probably haven’t seen the sun in thousands of years. The oxygen might be limiting, depending on how deep, waterlogged, or how tightly packed the particles are. It is likely that this soil is rather static, with not much going on chemically or biologically. Then a young little root starts pushing its way through the soil, and along with changing the physical properties of the soil around it, it starts changing the chemical ones too. It is covered in a thick gooey mucilage, which is made of water and sugars, so that it can lubricate its path through the rough soil. The mucilage also plays an important part in keeping the soil immediately around the root moist, and preventing it from total desiccation if the soil gets too dry. Suddenly, the soil doesn’t have the same characteristics it used to have; it has ceased being what we call bulk soil, and has become the rhizosphere.
The rhizosphere is the layer of soil, and all its inhabitants, that are being changed by the activity of this living root. Scientists often define it as the soil that sticks to the root when you pull out a plant from the soil and shake it up (Figure 1). Its size and distribution will change depending on what you are measuring- the effects of oxygen diffusion, for instance, might be a lot more limited than those of water availability, caused by the same root. But the important thing to note is that this region will behave in a very different way to the bulk soil. By some estimates, this is the most active and complex interface on Earth (Philippot et al. 2013).
The root tip also has a thick layer of cells that will be sloughed off as it grows. These cells have full metabolic capacities even when they are no longer in contact with the root, which makes us think that they are involved in important functions like nutrient acquisition or protection against pathogens (Zhao et al. 2000).
As the root gets older, it will start to release a very significant proportion of its carbon the plant fixes through photosynthesis; some say it’s a mere 0.4% (Rovira 1969) others go as high as 40% (Hogberg et al. 2001), and yet others believe it is more likely around 20%. The consensus, however, is that the amount is significant enough to have an effect on the plant’s ability to produce healthy seeds (what biologists call fitness). Furthermore, these carbon compounds, called root exudates or rhizodeposition, come in very different forms, and we don’t yet understand the full diversity of compound types, how they change during the plant’s life, or the reasons why the plant would invest so much into an apparently bottomless pit.
As far as the exudates go, the limitations to studying them kept us in the dark for a long time. This isn’t meant to suggest that now those limitations have been overcome; studying soil and the processes that happen therein is still a very complex job because of, well, the soil. It is dark, so light-based experiments which work so nicely in water aren’t useful. It is very complex, both in structure and composition, so as soon as you insert a shovel or pull a root out, you’ve changed it. It’s sticky and dirty, so chemicals within it are hard to quantify and even identify. For these and many more reasons, researchers choose to focus on the aboveground section of the plants and the processes of interest. But over many years we have learned a few things about exudation:
- Not all exudates are easy to decompose, or meant to feed the microbes.
- Different plant species will produce different cocktails of exudates.
- Some compounds are meant to attract certain types of microbes, while others are meant to repel them.
- Some exudates are for the plant’s own use in making nutrients such as iron more soluble and thus available for the roots to uptake.
- Biotic stress (pathogens) and abiotic stress (drought) will cause the plants to change the exudates they are releasing, which suggests that they have a function in how the roots deal with their environment.
Root or rhizosphere priming
What happens if you have a bunch of hungry people, and suddenly you open up a grocery store near them? We have probably all been there- you go shopping before dinner and you end up buying so much more than you need. Priming is based on microbes suddenly being released from their carbon starvation by the root exudates, so they have energy to make new enzymes and divide into more cells. It will result in increased respiration in the soil as the microbes eat up all the harder-to-chew organic matter because of the root-driven increase in available energy. For a long time, researchers focused on this observation to formulate their hypotheses: if the respiration was increasing, it meant that all the compounds being released were being consumed, and over time this would lead to less carbon stored in the soil. This ties in with the debate on the origin and fate of soil organic matter (SOM), which is another fascinating can of worms.
In our lab, we have focused on understanding how different the root exudates of common tree species are, and what those differences could mean for the microbes that grow in the soil. In a recent publication (Zwetsloot et al. 2018), we show that the whole root exudate cocktail is pretty unique for each tree species. We also found that not all exudates have the same effects on the soil- if you give the microbes a less common plant molecule like catechol, they won’t eat it and the soil won’t release much CO2. We don’t know why but it could be that these compounds are even toxic to the microbes lowering their activity even further. If you give them simple glucose, they will readily gobble it up and release a lot of gas. Once they ran out of glucose, they may chew away on SOM as well.
Root exudates and soil carbon storage
Climate change models are constantly modifying the values for sinks and sources of atmospheric carbon dioxide, but one of the recurring trouble ones is soil. Whether soil is a sink or a source of CO2 will depend on plant cover, water fluctuations, assumed microbial activity, agricultural management practices, and the list goes on and on. Understanding what role root exudates play on microbial activity, and ultimately what controls them, is key to better inform these models and thus enable better predictions of climate change. It is well known that agriculture can be a source of atmospheric carbon, but it also has huge potential to be a net sink.
Although we still don’t know what the balance here is, recent evidence suggests that root exudates do more good for carbon storage in the soil than bad. In fact, there are many reasons to believe that most of the soil carbon is originally plant-made, exuded, and then modified by the microbes before it becomes stable and gets to be old. For a long time researchers thought it was just the leftovers of decaying leaves and bits of stem that the microbes couldn’t eat. They used to think of soil carbon as going down a pipe, from CO2 in the air to plant tissue, to humus in the soil. So the thought of the soil microbes eating it up meant that it would go back to CO2 in the air and contribute to climate change. But we now know that there is a lot more dimensions to it than just a pipe with one direction, and root exudates are a huge part of that cycle.
Investing in root exudates
Let’s think a little more about the question posed in the introduction: Why would plants invest in root exudates? Don’t plants have roots for the purpose of taking up resources from the soil, like minerals and water? A root that is leaking carbon sounds like the opposite scenario and is totally counterintuitive- unless there is a benefit. In fact, roots release many different chemicals into the soil, including delicious sugars, amino acids and organic acids, but also more complex molecules like phenolic compounds. All these chemicals are produced by the plant and carry a cost with them. Just as you wouldn’t give away your hard-earned savings to charity, but rather put them to work by giving them to someone you trust, we assume the plant is investing in its rhizosphere microbes, as opposed to just being generous.
If you look at the plant from an economic perspective, you could view the carbon that plants acquire through photosynthesis as a currency. Once the carbon dioxide from the atmosphere has been made into sugars or other organic compounds (equivalent to a long day of work), a decision needs to be made about how this carbon is spent. Do we want to invest it into growing taller, into defense against insects that want to chew on the leaves, or into developing beautiful flowers to produce seeds and reproduce? Or, most importantly for this story, shall we invest our carbon into root exudates? For the plant the answer to this question is going to be the same as for any investor: “it depends on the situation”. Keep in mind that the ultimate goal for this plant is to survive, grow and reproduce (increase its fitness!!). Then imagine the situation where a plant is under attack by a root-chewing insect: here it is easy to decide where the carbon currency is going to go. We are having enormous problems belowground and we need to defend ourselves. A plant can do this in different ways. One strategy would be to produce toxins (these could be exudates or part of the root tissue itself). Another approach would be to produce more roots. Of course, the plant will always have different needs to take into consideration. Moreover, there are “maintenance costs” that will always require some carbon. Yet, the basic principle stays the same even in these more complex scenarios: a plant will invest in processes that are essential and beneficial to its survival given a certain set of circumstances. Just like a successful family business, the plants that invest wisely in strategies that pay off will do better than their neighbors (higher fitness), thus making more seeds that will grow up and invest like their parents. Over time, these traits become the norm as the successful investors reproduce and outcompete the plants that don’t invest wisely.
Root exudates and plant nutrition
Now let’s take this principle and look at some different examples of how root exudates can be beneficial to plant growth and health. One of the most shocking examples involves plant phosphorus nutrition (Hinsinger 2001). Plants can only take up phosphorus in the form of phosphates – one phosphorus atom with a few oxygens and sometimes hydrogens bound to it. Moreover, these phosphates need to be in solution because roots take up nutrients from the water, not from a solid piece of soil. The unfortunate thing about this is that phosphates love hanging out with soil minerals. The soil and phosphate molecules chemically interact and can form bonds that prevent the phosphate from floating around in the water. Even though there is phosphorus in the soil, it is locked away from the plants. Depending on the minerals present and how much phosphorus we can find in a particular soil, this may be more or less of a problem. Researchers were interested in seeing whether the amount and type of root exudates are different between plants that are grown in a low-phosphorus vs. high-phosphorus soil. They found that certain plant species (not all!) will produce organic acids when they are grown in a soil with very low phosphate content, but they won’t do this when there is an excess of phosphate in the soil (Neumann & Römheld 1999). They then tested what the effect of these organic acids was on soil chemistry. It turns out that the organic acids can free up the phosphates that are locked away by the soil minerals. Now you can imagine how beneficial these root exudates can be to the plant. To further test this, the researchers compared plants that could produce a lot of organic acids to plants that released very few organic acids into the soil. When the soil received phosphorus fertilization, there was no difference. However, when phosphorus was the limiting nutrient, plants that could exude organic acids performed a lot better and had a higher concentration of phosphorus in their leaves and fruit, than those that could not release acids. In this case, while releasing root exudates into the soil results in a loss of carbon currency for the plant, it is worth the investment because the overall health of the plant increased. You can compare it to the situation where you are very hungry. All of a sudden, you don’t mind spending some money on buying a sandwich. If you had just eaten, it is likely you would save your money for something else.
Exudates as a signal
Another very common role of root exudates is to act as a signal to other organisms that live in the soil (Tawaraya et al. 1998). Because phosphorus can be a tricky nutrient for plants to take up from the soil, this next example is going to be about phosphorus too. However, in this scenario, root exudates are not functioning as a magic potion suddenly freeing up phosphates from their soil mineral prison. Instead, the plant is exuding specific chemicals to attract mycorrhizal fungi. These micro-organisms grow partly inside or around plant roots while also casting a wide net of hyphae far into the bulk soil (Figure 2). These tiny hair-like structures function similarly to roots and can absorb nutrients too far away for the plant to reach. Because hyphae are very thin, they can also cover a greater soil surface than plant roots could by themselves, and reach into tiny soil pores that roots would have not penetrated. Mycorrhizal fungi can pass on these nutrients to the plant, but not without a reward. While mycorrhizal fungi are excellent scavengers for soil nutrients like phosphorus, they have a harder time with finding enough carbon to survive. Unlike the plant, they cannot fix carbon dioxide from the atmosphere through photosynthesis. So it only seems a fair exchange that the plants provide the fungi with carbon-rich compounds like sugars in return. For this relationship to take place, the first step is that the plant and fungi find each other. That’s where the root exudates play an important role. They carry the message to the fungi saying: “Here I am! Your plant buddy with juicy roots and lots of sugars. I need more phosphorus nutrition. Can you help me? You will be rewarded.”
Because not all interactions are positive… root exudates as a weapon
While they exude a significant amount of nutritious, easy to digest carbon, plants will also invest in compounds that repel harmful organisms like pests and herbivores. In this example (by Dong et al. 2001), tobacco plants can secrete an enzyme that will disrupt bacterial compounds used in communication (called quorum-sensing molecules) and thus avoid an infection. Another group (Brigham et al. 1999) found that the individual root cells of purple gromwell (Lithospermum erythrorhizon) produced and released a strong antimicrobial compound that could inhibit bacterial and fungal growth in soil. This compound, called naphthoquinone, was only produced after the cells were attacked by a pathogen, which suggests that the plant can control it and use it for its own defense.
The soil is a competitive place, like any environment in which resources are limited and many organisms want access to them. Plants need to be very selective on who they recruit to their rhizospheres, and who they keep out. It is important to note that competition in the rhizosphere includes other plants who might want to get into the same resource pools, just as they would compete for light aboveground. It isn’t surprising, under that scenario, that a lot of invasive plants will produce root exudates that inhibit other plants. A common example, and a favorite among researchers, in spotted knapweed (Centaurea maculosa) which has been studied extensively. Many researchers have found that native plant species are especially susceptible to catechin, a compound released by knapweed roots (Bais et al. 2003, He et al. 2009, Pollock et al . 2009) and argued that this compound might be the reason for the success of spotted knapweed as an invasive species.
Farmers may be familiar with the inhibiting effects that certain brassica species have on other crops. Members of this family are known to inhibit the association of other plants with mycorrhizal fungi, thus limiting their ability to extract phosphorous and other nutrients from the soil. Although the full extent of this competition strategy isn’t fully understood, it does seem that invasive weeds like garlic mustard, Alliaria petiolata, can selectively inhibit other plants’ friendly fungi by releasing chemicals into the soil and ruining the communication (Burke 2008).
Here we described some of the different functions that root exudates can have in soils, but there are many more. To complicate things even further, the same compounds can have multiple functions. For example, the same chemical can repel one species of insect but attract another one. Or a root exudate can function as a phosphorus-releaser but simultaneously be toxic to other microbes in the rhizosphere. So far researchers have mainly focused on studying one individual function of one specific chemical. Yet, the rhizosphere is exposed to many root chemicals at the same time. We are only at the beginning of understanding of these complex interactions that root exudates can cause in the soil.
This is beyond the scope of our article, but sometimes these signals get co-opted by parasites and pathogens. There is an absolutely beautiful example of how root exudates and above-ground secondary metabolites (basically any compound that a plant produces for other purposes than staying alive) can create the worst agricultural nightmare or the perfectly sustainable solution. The same compounds that many plants use to signal their mycorrhizal friends is intercepted by seeds of the malicious striga, or witchweed, that parasitizes corn plants and sucks all their resources away. At the same time, stem boring insects devastate the transport between leaves and roots. And all this happens in corn fields already severely limited by poor soils. Check out this source for details on the push-pull system for corn in Kenya.
Ok, so how can we use exudates?
In light of the recent debates around farming and conventional practices, people on many different levels are searching for new options and alternatives that avoid controversy (like genetic engineering technology) and increase sustainability (mainly by decreasing inputs). We are convinced that root exudates will play a huge role in making agriculture more efficient.
One very promising area of research is the study of rhizosphere microbiomes. The US government secured over $120 million in funding to study microbiomes, which are the collection of microbial genes found in a bigger organism [You can read more about this initiative and why it matters here]. Just like human gut microbiomes are now being correlated with obesity, autism, and even depression, plant microbiomes are being studied to see if they can increase nutrient use efficiency and drought tolerance. Did you ever think that you are made up of more microbial genes than human genes? We know, it’s terrifying. Anyway, just like humans, plants are very dependent on their microbial partners for a lot of nutrient acquisition, and we think that those processes are mediated by root exudates. In our lab, we are investigating the connections between root exudates and microbial composition in the rhizosphere by looking at a biofuel crop with a lot of potential- shrub willows.
While the technology to manipulate and exploit root exudates might still be far off, there are some examples of agricultural applications of these principals. As mentioned before, the Kenyan push-pull system is dependent on the push plant (a legume intercropped with the corn) liberating root exudates that inhibit the weed’s germination and repel the insect pest. Phytoremediation and phytoextraction are both technologies that rely indirectly on root exudation. In the former, the passive release of simple carbon sources can stimulate the microbes to start working on the more complicated carbon molecules like petroleum. In the latter, acids may be releasing heavy metals form soil particles, allowing the roots to uptake them and store them in the plant tissues. This the allows for the contaminants to be concentrated in the plants and removed from the environment.
Conclusion
Humans have been taking advantage of root exudates since we started growing crops, without even knowing it, and are just starting to understand how important they are. The more attention we pay to them, the easier it will become to selectively breed crops that produce more of this or that, to achieve yield gains or tolerance, or even more nutritious food. Add to that the microbiome and all the potential that microbial genes hold, and we could be revolutionizing agriculture in a very natural way- no more moving soil or nutrients around the globe, no more synthetic inputs and polluting waterways, and maybe even enough food for 9 billion humans. Maybe wishful thinking, but there’s only one way to find out!
References
Bais, H.P., Walker, T.S., Kennan, A.J., Stermitz, F.R. and Vivanco, J.M., 2003. Structure-dependent phytotoxicity of catechins and other flavonoids: flavonoid conversions by cell-free protein extracts of Centaurea maculosa (spotted knapweed) roots. Journal of agricultural and food chemistry, 51(4), pp.897-901.
Yi-Hu Dong., Lian-Hui, W., Jin-Ling, X., Hai-Bao, Z., & al, e. (2001). Quenching quorum-sensing-dependent bacterial infection by an N-acyl homoserine lactonase. Nature, 411(6839), pp. 813-7.
He, W.M., Feng, Y., Ridenour, W.M., Thelen, G.C., Pollock, J.L., Diaconu, A. and Callaway, R.M., 2009. Novel weapons and invasion: biogeographic differences in the competitive effects of Centaurea maculosa and its root exudate (±)-catechin. Oecologia, 159(4), pp.803-815.
Hinsinger P., 2001. Bioavailability of soil inorganic P in the rhizosphere as affected by root-induced chemical changes: a review. Plant and Soil, 237(2), pp. 173-195.
Pollock, J.L., Callaway, R.M., Thelen, G.C. and Holben, W.E., 2009. Catechin–metal interactions as a mechanism for conditional allelopathy by the invasive plant Centaurea maculosa. Journal of Ecology, 97(6), pp.1234-1242.
Neumann, G. and Römheld, V., 1999. Root excretion of carboxylic acids and protons in phosphorus-deficient plants. Plant and Soil 211(1), pp. 121-130.
Tawaraya, K., Hashimoto K., and Wagatsuma, T., 1998. Effect of root exudate fractions from P-deficient and P-sufficient onion plants on root colonization by arbuscular mycorrhizal fungus Gigaspora margarita. Mycorrhiza, 8, pp. 67-70.