Seeking the root causes

31 May 2019 - By: Jonathan Smith

Seeking the root causes

By Jonathan Smith

Plant roots are anything but the passive piping systems that they might appear to be. A group of researchers at the 2018 SEB Annual Meeting chatted about how roots can be shaped by the environment, and how they help plants adapt to increasing pressures brought on by climate change.

With the frequency of stressful events, such as droughts and floods, increasing with climate change, knowing how plants can adapt to these events could help efforts to conserve biodiversity and improve food security around the world.

One hugely important tool that plants use to handle stress is the roots. In addition to providing a physical anchor into the earth, roots make up a complex piping structure, drawing water and nutrients into the plant’s vascular system. This piping system has enormous potential, able to sustain even the tallest plants in the world, the Redwoods,1 which can reach over 100 m in height.

The root system is far from a passive set of pipes, however. Roots are dynamic, and come in a variety of shapes and architectures. Their architecture is shaped by the plant’s environment and, yet, the plant doesn’t even have a brain or nervous system! The features and mechanisms of this amazing plasticity were discussed in the Shaping Root Architecture session in the SEB’s annual meeting in Florence last year.

In this article, I chat with some of the researchers from this session, getting a peek at some of their latest research on plasticity in root architecture.
microCT imaging
microCT imaging reveals the root architecture, and yellow probes reveal the nutrient levels near to the roots Photo: Amanda Rasmussen


Reducing the use of artificial fertilisers in agriculture could help cut costs, water pollution, and greenhouse gas emissions.2 One way to help with this task is to improve how a plant’s roots suck up nutrients like fertiliser from the soil. This kind of challenge requires extensive knowledge about the root architecture and physiology, and how they interact to produce a phenotype.

“Architecture is just one aspect of roots that we need to understand as the output of a series of physiology processes,” Dr Amanda Rasmussen (University of Nottingham, UK) told me. Her group, therefore, developed a procedure that measures both root physiology and architecture. The group grew maize in special columns and imaged the root structure and location using micro-computed tomography (micro-CT), just like an X-ray scanner images our bones.

The group then inserted probes into the soil near the roots and used a second technique, microdialysis, to measure how the roots absorb nutrients over time. They then reimaged the setup with micro-CT to check how far the probes lay from the roots.

“This was the first time the two techniques (micro-CT and microdialysis) had been combined,” said Amanda. “Since we are interested in root physiology—not just architecture and not just soil nutrient content—we realised we could gain a lot more information by combining the two techniques and determine how the roots change their own nutrient environment.”

Her group’s results were surprising. Whilst the nutrient ammonium was depleted just outside of the roots over time, the concentrations of another nutrient, nitrate, were actually high at the same location. Amanda likened the latter process to a flock of sheep attempting to pass through a small gate into a field.

“The sheep are like nitrate ions and the gate a nitrate transporter—as they get closer to the gate they bunch up, waiting to get through, which increases the concentration of sheep/nitrate next to the gate.”

Amanda’s group now hopes to use this technique to see how the roots change their uptake in different soil and atmospheric conditions. Furthermore, Amanda aims to work with crop breeders to see how the most efficient breeds perform in this assay, which could reveal key information about how to optimise the use of artificial fertilisers in the field.

“This means breeders, molecular biologists, and physiologists need each other to unravel the exciting mysteries that plants are hiding!” Rasmussen enthused.


Being literally rooted to the spot, plants are under a lot of pressure to adapt to the environment around them. This pressure has crafted incredibly complex plasticity mechanisms for detecting and responding to new stimuli, without even needing a nervous system.

Dr Kirsten Ten Tusscher (Utrecht University, the Netherlands) told me that studying plant molecular plasticity systems could give us clues on how to improve crop security against stressful events, such as flooding and fluctuations in salt levels in the soil. Events like these are becoming more frequent as climate change takes hold.

“In my opinion a lot is already known about plant plasticity, but not much is yet fully understood to the extent that we can easily manipulate it, or know what the trade-offs are,” she said.

Kirsten’s team of computational biologists are interested in many areas of plant plasticity, but one big area is how roots can grow to avoid high salt in soil. “The root’s cells are somehow able to communicate with one another and figure out at which side of the root the salt levels are highest and hence where the root should bend away from,” she told me.

The researchers came up with computational models of this process. The models are designed to explain the root’s behaviour by predicting the action of the hormone auxin, which is a key molecule in cell division and the growth of a plant’s shoots and roots.3

Auxin is involved in the directional growth of roots by moving from one side of the root to the other. The side with the most auxin, in this case, the side with the most salt, grows the most, steering the root away from the salt source. This redistribution of auxin happens thanks to transporter proteins (e.g. PIN1 and PIN2) moving the hormone in and out of cells.

Kirsten’s models suggested that the key auxin transporters involved in the process were PIN2 and AUX1. However, these molecules weren’t changing their expression fast enough to steer the root away from the salt in time. The models instead identified rapid changes in PIN1 that helped to avoid the salt.

Kirsten hopes to find out more about this process, such as how it interacts with gravity sensing in the roots, and how changes in transporter protein production are triggered by salt stimuli.
Tiny pots produce fewer shoots, whereas larger pots result in more shoots Photo: Tom Bennet


Plants seem to ‘know’ how big their pot is. This is especially evident with bonsai trees, which stay tiny because they are kept in very tiny plant pots. But even so, why would they need this behaviour in the wild?

“This is an important question, since—fairly obviously—plants don’t grow in pots in their natural environment!” explained Dr Tom Bennett (University of Leeds, UK). “We believe that many plants growing in natural conditions exist in a restricted volume of soil, whether that is due to physical constraints, such as soil depth, or biological constraints, such as the presence of other plants.”

In fact, understanding how plants know their spatial growth limit could have big implications for agriculture. As a farmer, you would prefer not to buy unneeded fertiliser if you knew that your crops are restricted by shallow soil, for example.

Despite the potential applications of this area, it’s still a mystery how plants do it. “It’s not clear, for instance, what the roots actually detect; whether it is a mechanical stimulus, or whether it’s connected to the chemistry of the soil,” Tom remarked. “Our work at least suggests that it is not simply a read-out of the amount of nutrients present in the soil.”

To help shed light on this question, Tom’s group tested plants, including oilseed rape, barley, and wheat, and measured how the pot size impacted the plant’s shoot size. They also added fertiliser to see if this would affect the crowded plants. However, it seemed that plants just became insensitive to nutrients when they reached their limit, be it the edge of the pot or the presence of a neighbouring plant.

“Fundamentally, I think this reflects the amazing ability of plants to make complex, pro-active decisions about their growth,” said Tom. “Rather than waiting to run out of resources, plants make early developmental choices that allow them to avoid resource limitation later in their life.”

Tom’s group also found that the plant’s growth decision could be mediated by alterations in the activity of a plant growth hormone called cytokinin. Building on these results, Tom’s group is aiming to find out the exact mechanisms by which the plant detects its limits, how the roots ‘tell’ the shoot how much it can grow, and how much they can apply this to agriculture. “The soil at our own Leeds University farm is quite shallow, so that gives us a good opportunity to test some of these ideas!” he commented.


Imagine that you are playing tennis with a particular strategy, and you’re winning. Chances are that you would prefer your strategy to stay the same, because changing it could risk losing you the game. However, if you’re losing, you have less to lose by changing strategies, even though it’s still a risk. This illustrates a concept called Risk Sensitivity Theory, that is, that you are more likely to embrace risks when you have fewer advantages.

Whilst this theory has been investigated in many fields, including economics, psychology, and animal behaviour, Hagai Shemesh (Tel-Hai College, Israel) studies this theory in plant roots.

“With animals, we are aware of the fact that they have a brain and that we have a brain—we assume that we both use it when we are solving problems,” Hagai explained to me. “I think the fact plants don’t have a brain, and still solve complex problems, makes plant research more interesting and intriguing.”

To help him see if plants show risk sensitivity, Hagai’s group used the roots of the pea plant (Pisum sativum) as the model. This is because the environment of the roots is more stable than the that of the shoots, and pea plant roots are thick and easy to work with. The group measured the mass of the roots to see which would risk growing in which situations.

Each plant was then given choices.4 Some plants could ‘choose’ to grow their roots in pots with constant amounts of plentiful fertiliser, or into pots with fluctuating levels of fertiliser. The behaviour of these plants corresponded to the winning tennis player scenario, and they didn’t want to grow their roots into the pot with fluctuating levels.

Other plants had the choice of a pot with a constant level of low fertiliser, or a pot with fluctuating levels. The behaviour of these plants corresponded to the losing tennis player scenario, and they were much more keen on growing into the pot with the fluctuating levels.

“The most interesting thing about these findings is that they tell us something about animals and humans,” Hagai commented. “If plants can solve this dilemma without a brain, maybe when we’re dealing with such problems, we’re not necessarily using our brain, unlike what we always assume.”

It is too early to tell exactly what molecular mechanisms plants use to solve these more complex problems without a brain, but this behaviour could have applications in agriculture, or conservation in climate change. However, Hagai is hoping to build on this work by teaming up with an economist to study some cognitive paradoxes in plants.

In the meantime, change is coming for the plant behaviour field as a whole. “It’s early, but there’s big progress in accepting the fact that plants are more complex than we thought,” Hagai enthused.


One vital way to understand how stressful stimuli affect roots is to image their visible characteristics. However, this is not as simple as it seems.

As any muddied gardener will tell you, plant roots only grow in opaque soil, which makes it hard to image them in the laboratory. In fact, the most common, and very laborious, way to study the root architecture of a plant is using ‘shovelomics’, that is, digging up the plant, washing the roots, and imaging them afterwards.5

One way to get around the opacity of the plant growth medium is to grow plants in transparent mineral solutions, known as hydroponics. Whilst this allows for easy root imaging, hydroponics don’t closely resemble the natural environment of most plant models, potentially altering the physiological processes involved in root growth from those that occur in plants grown in soil.

Ludovico Cademartiri (Iowa State University, USA) has a solution; he essentially grows plants in a transparent soil-like medium. “For us, it was an interesting engineering challenge,” he said. Part of this challenge is that the material needs to have enough pores to let the nutrients pass to the roots, but pores actually make materials more opaque because light gets refracted and diverted as it passes the pores.

To solve the problem, Ludovico’s team developed a porous soil-like medium containing a special hydrogel along with air, water, and nutrients. However, unlike soil, this medium can become transparent by adding water. “By temporarily saturating the pores with nutrient solution, the medium becomes transparent enough to characterise the root system by photography and microscopy,” Ludovico told me.

Unlike hydroponics, the group’s new medium showed few detriments for root growth compared with normal soil. When analysed in the special medium, the roots of the soybean Glycine max resembled the roots of those in regular soil in the field. In addition, the transparent medium seems to encourage more ‘natural’ physiological processes than do hydroponics, given that genes associated with the stress from lack of oxygen showed normal expression in plants grown in this medium, whereas they had increased expression in plants grown in hydroponic solutions.

Importantly for studies in stress-related root plasticity, this transparent medium can be tailored to contain specific toxins, nutrients, and sensing molecules, making it a flexible tool. “I think this is a new platform that will enable a reductionist approach to the study of root phenotypes and root development,” said Ludovico.

Excited by the potential of this new medium for more easily imaging roots, the group is collaborating with partners in academia, industry, and even education. Ludovico told me that his group is most excited about using this material to study how plant roots can grow towards chemical and mechanical stimuli.


The common theme of this session was that the roots make up a highly reactive part of the plant, dynamically changing their course and growth in response to the environment. They can even make complex calculations on growth without the need for a brain.

The session also demonstrated the pace of change in the field, with new techniques being developed that could change the way we study roots and their architecture. It may not be long, therefore, before we can unravel more about how plants adapt to stressful circumstances, and perhaps use this knowledge to improve conservation and food security in the face of increasingly extreme events in climate change.


1. Accessed 19 January 2019.

2 Shcherbak I, Millar N, Robertson GP. 2014. Global metaanalysis of the nonlinear response of soil nitrous oxide (N2O) emissions to fertilizer nitrogen. PNAS, 111, 9199–9204.

3. Julkowska MM, Testerink C. 2015. Tuning plant signaling and growth to survive salt. Trends Plant Sci, 20(9), 586–594.

4. Dener E, Kacelnik A, Shemesh H. 2016. Pea plants show risk sensitivity. Curr Biol, 26(13), 1763–1767.

5. Accessed 20 January 2019.


Category: Features
Jonathan Smith

Jonathan Smith

Jonathan Smith is a Science Journalist at Labbiotech EU. He completed his PhD at University of Leicester on behaviour and neurobiology in desert locusts and is a keen science writer and communicator. You can follow Jonathan here (Twitter @j-ivories).