Tag Archives: root

Timelapse reveals the hidden dance of roots — and how mutant plants do it differently

A group of Stanford researchers has an unusual pastime: they watch plants grow. Not in real-time, mind you: they speed it up, compressing 100 hours of growth in less than a minute. With this approach and a special robot, they’ve uncovered some surprising things about how roots grow.

Wiggling roots find their way through rough soils.

Compared to the other parts of plants, we know surprisingly little about roots. The reason is simple, but hard to overcome: they grow underground, as opposed to above it. To overcome this obstacle, several research groups have grown plants in clear gel that allows plant observations.

The Stanford group in biologist Philip Benfey’s lab set up a system where they took a picture every 15 minutes for several days after the plant had germinated, obtaining a time-lapse video of roots growing.

A lot of the time, roots grew in winding, corkscrew-ike movements. This phenomenon reportedly “fascinated Charles Darwin”, says Benfey, and it’s not really clear why it happens.

In the case of shoots, it’s clear why: twining and circling make it easier to latch onto things. But for roots, it’s not clear why it happens. Maybe it makes it easier to burrow into the ground or figure out where “down” is, but there’s still a lot of mystery surrounding this phenomenon. The new study helps shed a bit more light on it.

For starters, researchers found that some plants don’t do the corkscrew movements. When they investigated the cause, they found it in a mutation of a gene called HK1. Plants with a mutant HK1 grow straight down instead of meandering. They also grow down twice as deep, which raises even more questions about roots’ normal winding growth — what do they have to gain in such an inefficient pattern?

New time-lapse videos capture something that’s too slow for our eyes to see: the growing tips of rice roots make corkscrew-like motions, waggling and winding in a helical path as they burrow into the soil. Footage courtesy of Benfey/Goldman labs. Produced by Veronique Koch.

The answer could come from Daniel Goldman’s lab at Georgia Tech. Goldman and colleagues carried observations of mutant rice roots that grew over a perforated plastic plate, finding that spiraling roots were three times more likely to find a hole and grow through the other side. So if plant roots encounter an obstacle in their natural environment, straight-line growth would make it much harder to grow through.

The idea was further explored through a soft-pliable robot. The robot unfurls from its tip like a root and served as a root model. Researchers set it loose in an obstacle course with unevenly spaced pegs, without any sensors or any way to sense the pegs.

All the robot had were two inflatable plastic tubes nested inside each other. The inside tube would grow and push from the inside out, making the root elongate from the top, while a pair of contracting “muscles” also made the robot bend from side to side as it grew. With this alone, the robot was able to make its way around the pegs as it grew. But when the bending movement was stopped, it would quickly get stuck in the pegs.

The idea was further tested in a dirt mix used for baseball fields, to mimic obstacles the root would encounter in soil. It confirmed their idea: mutant seeds struggled growing adequately, while the normal seeds had no real trouble. While questions still remain about this process, the theory seems to add up: roots grow in a corkscrew movement because it helps them establish a foothold in unpleasant soils.

Journal References: Isaiah Taylor et al, Mechanism and function of root circumnutation, Proceedings of the National Academy of Sciences (2021). DOI: 10.1073/pnas.2018940118


Researchers identify gene that makes plants and fungi play nice — we’ll use it to make better crops

Researchers at the Department of Energy’s Oak Ridge National Laboratory (ORNL) are hacking the plant-fungi relationship to help us grow better, more productive, more resilient crops.


Image credits Gustavo Torres.

The team has identified a specific gene that controls the symbiotic relationship between plants and fungi in the soil and used it to facilitate symbiosis in a plant species that typically resists such fungi. The research paves the way towards the development of food and bioenergy crops that can withstand harsh growing conditions, resist pathogens and pests, require less chemical fertilizer, and produce more plentiful per acre.

Magic ‘shrooms

“If we can understand the molecular mechanism that controls the relationship between plants and beneficial fungi, then we can start using this symbiosis to acquire specific conditions in plants such as resistance to drought, pathogens, improving nitrogen and nutrition uptake and more,” said ORNL molecular geneticist Jessy Labbe, the paper’s first author.

“The resulting plants would grow larger and need less water and fertilizer, for instance.”

The fungi Labbe refers to are known as mycorrhizal fungi (a mycorrhiza is a symbiotic association between a fungus and a plant), and they form a sheath around plant roots that benefits both participants. An estimated 80% of plant species have mycorrhizal fungi associated with their roots.

The plant receives water and raw minerals, particularly phosphorus, and ‘trades’ carbon-rich compounds in return. The fungal structure extends much farther than the plant host’s roots, allowing it to tap into a larger volume of soils. There is also some evidence suggesting these fungi also communicate with neighboring plants to limit the spread of pathogens and pests.Their relationship is so close that these fungal helpers may have been what allowed the ancient colonization of land by plants.

Given the importance of this partnership, biologists have been really eager to find the genetic mechanisms which underpin it. The current discovery is the culmination of 10 years of research at the ORNL and partner institutions that focused on producing better bioenergy feedstock crops such as the poplar tree (Populus).

Together with improvements in genomic sequencing, quantitative genetics, and high-performance computing over the last decades, the team drew on the ORNL data to narrow down the search to a particular receptor protein, PtLecRLK1. Once they had identified the likely candidate gene, the researchers took to the lab to validate their findings. Lab testing later confirmed that they were onto the right gene.

The researchers chose Arabidopsis, a plant known to treat the mycorrhizal fungus L. bicolor as a threat for the experiments. They engineered a version of this plant to expresses the PtLecRLK1 protein and then inoculated the plants with L. bicolor. The fungus completely enveloped the plant’s root tips, they report, forming a fungal sheath indicative of symbiote formation.

“We showed that we can convert a non-host into a host of this symbiont,” said ORNL quantitative geneticist Wellington Muchero, a co-author of the paper. “If we can make Arabidopsis interact with this fungus, then we believe we can make other biofuel crops like switchgrass, or food crops like corn also interact and confer the exact same benefits. It opens up all sorts of opportunities in diverse plant systems. Surprisingly, one gene is all you need.”

Jerry Tuskan, the director of the DOE’s Center for Bioenergy Innovation (CBI), which supported this research, calls the results “remarkable”, saying it paves the way towards new bioenergy crops that can thrive “on marginal, non-agricultural lands.”

“We could target as much as 20-40 million acres of marginal land with hardy bioenergy crops that need less water, boosting the prospects for successful rural, biobased economies supplying sustainable alternatives for gasoline and industrial feedstocks,” he concludes.

The paper “Mediation of plant–mycorrhizal interaction by a lectin receptor-like kinase” has been published in the journal Nature Plants.


Research is getting to the root of climate change with bigger, deeper plant roots

New research is trying to give plants stronger, deeper roots to make them scrub more CO2 out of the atmosphere.


Image via Pixabay.

Researchers at the Salk Institute are investigating the molecular mechanisms that govern root growth pattern in plants. Their research aims to patch a big hole in our knowledge — while we understand how plant roots develop, we still have no idea which biochemical mechanisms guide the process and how. The team, however, reports to finding a gene that determines whether roots grow deep or shallow in the soil and plans to use it to mitigate climate warming.

Deep roots are not reached by the scorch

“We are incredibly excited about this first discovery on the road to realizing the goals of the Harnessing Plants Initiative,” says Associate Professor Wolfgang Busch, senior author on the paper and a member of Salk’s Plant Molecular and Cellular Biology Laboratory and its Integrative Biology Laboratory.

“Reducing atmospheric CO2 levels is one of the great challenges of our time, and it is personally very meaningful to me to be working toward a solution.”

The study came about as part of Salk’s Harnessing Plants Initiative, which aims to grow plants with deeper and more robust roots. These roots, they hope, will store increased amounts of carbon underground for longer periods of time while helping to meaningfully reduce CO2 in the atmosphere.

The researchers used thale cress (Arabidopsis thaliana) as a model plant, working to identify the genes (and gene variants) that regulate auxin. Auxin is a key plant hormone that has been linked to nearly every aspect of plant growth, but its exact effect on the growth patterns of root systems remained unclear. That’s exactly what the team wanted to find out.

“In order to better view the root growth, I developed and optimized a novel method for studying plant root systems in soil,” says first author Takehiko Ogura, a postdoctoral fellow in the Busch lab. “The roots of A. thaliana are incredibly small so they are not easily visible, but by slicing the plant in half we could better observe and measure the root distributions in the soil.”

One gene called EXOCYST70A3, the team reports, seems to be directly responsible for the development of root system architecture. EXOCYST70A3, they explain, controls the plant’s auxin pathways but doesn’t interfere with other pathways because it acts on a protein PIN4, which mediates the transport of auxin. When the team chemically altered the EXOCYST70A3 gene, the plant’s root system shifted orientation and grew deeper into the soil.

“Biological systems are incredibly complex, so it can be difficult to connect plants’ molecular mechanisms to an environmental response,” says Ogura. “By linking how this gene influences root behavior, we have revealed an important step in how plants adapt to changing environments through the auxin pathway.”

“We hope to use this knowledge of the auxin pathway as a way to uncover more components that are related to these genes and their effect on root system architecture,” adds Busch. “This will help us create better, more adaptable crop plants, such as soybean and corn, that farmers can grow to produce more food for a growing world population.”

In addition to helping plants scrub CO2 out of the atmosphere, the team hopes that these findings can help other researchers understand how plants adapt to differences between seasons, such as various levels of rainfall. This could also point to new ways to tailor plants to better suit today’s warming, changing climate.

The paper “Root System Depth in Arabidopsis Is Shaped by EXOCYST70A3 via the Dynamic Modulation of Auxin Transport” has been published in the journal Cell.

Plant roots may hold the key to the next generation drought-resistant crops

If we want to feed the world, we’d better pay attention to root architecture, not just the upper half of the plant, researchers warn.

A freesia’s root architecture helps the plant store food to survive seasonal weather conditions. Image credits: Brian Atkinson.

In the past decades, the developed world has been spoiled: not only do we have access to an essentially unlimited supply of food, but the variety and year-round diversity are also unprecedented. There’s also more food overall — the world produces 17% more food per person today than 30 years ago, even considering a significant population growth. But as the population continues to grow and climate change continues to take its toll, feeding the world might become more problematic.

Naturally, scientists are working on ways to improve crops and plant varieties, by tweaking their genes, the pesticide use, and even improving the surrounding soil. But if you ask a group of Nottingham researchers, they’ll likely tell you that the solution lies beneath the ground — in the plants’ roots.

‘You could argue that for the last 10,000 years, we have selected crop varieties on the basis of the upper half, and not focused on this hidden part of crops,’ said Malcolm Bennett, professor of plant science at the University of Nottingham, UK. ‘If we could select new crop varieties based on root architecture, we could significantly improve their ability to forage for water.’

The most visible effects of drought are seen in the overground components, particularly in leaves, but the hidden half is just as important — if not even more so. Roots provide anchorage to all plants, absorb water and nutrients from the soil and store food for the plant. When there’s not much water around, roots can grow deeper to suck water from further underground. If nutrients are sufficient towards the surface, shallow roots grow denser.

It’s easy to understand why roots are relatively understudied: they’re beneath ground, which makes them much more difficult to study. In order to overcome that, Bennett and colleagues used an X-ray micro-computed tomography (micro CT). It’s a technique commonly used in human medicine, but Bennett’s machine is a colossus — 3-4 times larger than a typical medical scanner, allowing them to image living roots in great detail.

Maize develops from a single kernel from which both the stem and earliest roots grow. The root system grows around a primary root supported by smaller lateral roots. As the plants grow older, aboveground brace roots sprout and become the main source of nutrients and water. Image credits: Brian Atkinson.

Because plants can withstand more X-ray radiation than humans, the resolution is also improved, allowing researchers to image even the thinnest of roots. Furthermore, scanning can be done repeatedly to monitor changes. In total, over 8,000 X-ray snaps were taken, with computer algorithms stitching them together to develop an incredibly detailed 3D image.

Among many other plants, the team used this approach to scan hundreds of varieties of wheat to see how they respond to stress. The results were surprising.

‘We noted something fascinating. Plants that were most efficient at using water changed the angle of their roots when you applied drought stress,’ said Prof. Bennett. ‘Steeper rooting angles allowed them to forage for deeper sources of water.’

Prof. Bennett also said that recently, they identified master genes that control root angle in maize and rice. This root angle is extremely important in water absorption, which in turn affects how plants manage dry spells.

‘To maintain wheat yields here (in the UK), we need to have new varieties with roots that grow an extra half metre at least,’ Prof. Bennett explained. Other parts of Europe are similarly concerned about water shortages and its effect on crops.

‘We could optimise crop root systems to take up nutrients more efficiently, such as selecting deeper rooting varieties to capture nitrogen as it moves deeper into soil,’ said Prof Bennett. ‘The idea of selecting new varieties based on root architecture is gaining support amongst breeding companies and researchers.’

Sugar beet grows around a main tap root which stores the sucrose harvested for sugar. The cells dyed green, as viewed under a microscope, form the cortex of the plant, where nutrients and sucrose are stored. Image credits: Brian Atkinson.

Dr. Christophe Maurel, plant scientist at the National Center for Scientific Research (CNRS), says that these findings could also be useful in the case of another very important crop: maize. Maize can be susceptible to drought in Europe because it flowers in summer, unlike wheat, which flowers earlier.

But there’s also a downside to having roots that suck up more water.

‘The more vessels at the root tips, the more susceptible they were to invasion by soil bacteria,’ Dr. Maurel said, meaning there is a trade-off between a better ability to withstand drought and vulnerability to infection.

Maurel also highlights that in a way, scientists are almost in an arms race with global warming — drawing conclusions is not something that can be done immediately, and it will be a while before results go from the lab and onto agricultural fields — but in the meantime, temperatures continue to rise.

 ‘We might help breeders not in five years, but maybe 10 to 20 years,’ he said. ‘Anyway, in 10 to 20 years we will be facing even stronger challenges with drought and climate change.’

Roots evolved at least twice — independently

A new study found that modern roots evolved at least twice, slowly taking the familiar shapes of today.

Convergent evolution

Despite popular belief, evolution doesn’t cherry pick the best traits to develop. It’s more of a random development taking place, and if the change is good, then the individual has more chances to pass its genes on — and it starts to become the norm. Sometimes, a trait is so useful that different species in different times or places develop it independently. This is called convergent evolution.

A classic example of convergent evolution is flight. Birds and bats are completely unrelated, yet they’ve both developed flight, a trait that defines both groups (even though they do it differently). Now, researchers have found another example of convergent evolution: roots.

It’s hard to imagine a world without plants, but they weren’t always around (at least, as we know them today). Land plants evolved from a group of green algae, perhaps as early as 850 years ago, but roots developed much later. The earliest root impressions date from the Late Silurian, some 420 million years ago (after sharks had developed as a group, for context). The evolution of roots came with dramatic global consequences. They disturbed the soil and absorbed nutrients such as nitrate and phosphate, promoting soil acidification. This, in turn, enabled the weathering of deeper rocks, injecting carbon compounds deeper into the soils — which changed the Earth’s climate. It’s believed that this change might have even led to a mass extinction.

But for plants, there’s no denying it: roots were an amazing thing.

Old Roots

Sandy Hetherington and Liam Dolan, the authors of a new study, studied the so-called Rhynie chert — a 407 million-year-old sedimentary deposit that contains exceptionally well-preserved remains of the oldest known terrestrial ecosystem. Located in Aberdeenshire, Scotland, this chert formation holds various remarkable plant fossils including lichen and roots.

Examining chert samples under the microscope, the two have found pieces of a tissue called meristem, belonging to a plant called Asteroxylon mackiei — an extinct vascular plant, related to today’s club mosses.

The meristem is the defining feature of modern-day plant roots — a self-renewing structure comprising of undifferentiated cells capable of growing into a variety of different tissues, depending on the plant’s needs.

But here’s the thing: the meristem in Asteroxylon mackiei appears to be a transitional stage towards the more modern type of meristem. But since a relative of Asteroxylon mackiei had already developed modern meristem, it seems that the feature had developed independently before.

The study has been published in Nature.