Tag Archives: #plants

Researchers Are First in the World to Watch Plants ‘Drink’ Water in Real-time (Botany)

Scientists at the University of Nottingham have become the first in the world to find a way to observe how plant roots take in and circulate water at the cellular level, which could help to identify future drought- and flood-resistant crops.

The inability to monitor water uptake inside roots—without damaging the specimen—has been a key stumbling block for researchers seeking to understand the motion of fluids in living plant cells and tissues.

Study lead, Dr. Kevin Webb from the Optics and Photonics Research Group, explains, “To observe water uptake in living plants without damaging them, we have applied a sensitive, laser-based, optical microscopy technique to see water movement inside living roots non-invasively, which has never been done before.

“Fundamentally, the process by which plants are able to thrive and become productive crops is based on how well it can take up water and how well it can manage that process. Water plays an essential role as a solvent for nutrients, minerals and other biomolecules in plant tissues. We’ve developed a way to allow ourselves to watch that process at the level of single cells. We can not only see the water going up inside the root, but also where and how it travels around.

“Feeding the world’s growing population is already a problem. Climate change is causing huge shifts in the pattern and density of waterfall on the planet which leads to problems growing crops in regions hit by floods or droughts. By selecting plants that are better at coping with stress, the goal is to increase global food productivity by understanding and using plant varieties with the best chances of survival that can be most productive in any given environment, no matter how dry or wet.”

How it works

For the study, water transport measurements were performed on the roots of Arabidopsis thaliana, which is a ‘model plant’ for scientists since they can be easily genetically-engineered to interfere with basic processes like water uptake.

The conversion of high-intensity green light into bio-friendly red wavelengths, within the Titanium:Sapphire laser used in the study. Credit: University of Nottingham

Using a gentle laser, the new imaging technique—based on the Nobel Prize-winning Raman scattering technique—allowed researchers to measure water traveling up through the root system of Arabidopsis at the cellular level, and to run a mathematical model to explain and quantify this.

The researchers used ‘heavy’ water (deuterium oxide, or D2O), which contains an extra neutron in the nucleus of each hydrogen atom. By scanning a laser in a line across the root while the plant drank, it was possible to see the ‘heavy’ water moving past via the root tip.

In Arabidopsis that had been genetically-altered to compromise its water uptake, these measurements—combined with the mathematical model—revealed an important water barrier within the root. This confirmed for the first time that water uptake is restricted within the central tissues of the root, inside of which the water vessels are located.

Co-lead, Malcolm Bennett, Professor of Plant Sciences at the University, said, “This innovative technique is a real game-changer in plant science—enabling researchers to visualize water movement at a cell and second scale within living plant tissues for the very first time. This promises to help us address important questions such as—how do plants ‘sense’ water availability? Answers to this question are vital for designing future crops better adapted to the challenges we face with climate change and altered weather patterns.”

The findings of this Leverhulme Trust-funded study, are published in the journal Nature Communications in a paper titled: “Non-invasive hydrodynamic imaging in plant roots at cellular resolution.”

Future applications

While developing the method, the research initially focused on plant cells, which are about 10 times the size of human cells and therefore more easily observed. The research team is currently porting these same methods to human cells to understand exactly the same kinds of processes at an even smaller scale.

Just as with plants, there are tissues in the human body responsible for handling water, which is crucial to function. Transparent tissues of the eye, for example, can suffer from diseases of fluid handling which include ocular lens cataracts; macular degeneration and glaucoma. In future, the new Raman imaging technique could become a valuable healthcare monitoring and detection tool.

Next steps

The researchers are working towards a commercial path for their hydrodynamic Raman imaging technique, and have just applied for funding with four UK and EU agriculture companies to look at tracers that move from plant leaves to roots to understand both directions of water transport. In parallel, the team is working on portable versions of the technology to allow water transport measurements to be taken into the field by farmers and scientists to monitor water handling in crops growing in challenging local environments.

The research team is currently bidding for a European Research Council Synergy Grant with partners in the EU and UK to take the study of water uptake and drought resistance towards being a new tool to help choose and understand how particular crops can be matched to particular local growth conditions.

Featured image: The conversion of high-intensity green light into bio-friendly red wavelengths, within the Titanium:Sapphire laser used in the study. Credit: University of Nottingham

Reference: Flavius C. Pascut et al, Non-invasive hydrodynamic imaging in plant roots at cellular resolution, Nature Communications (2021). DOI: 10.1038/s41467-021-24913-z

Provided by University of Nottingham

This Plant Derivative Inhibit SARS-CoV-2 Entry (Botany)

Using a bioactivity-guided chromatographic approach, in addition to mass-spectrometry (MS), Guillermo H. Jimenez-Aleman and colleagues identified the antiviral metabolite as Pheophorbide a (PheoA), a porphyrin chlorophyll derivative very similar to animal antiviral metabolite Protoporphyrin IX, in the bryophyte Marchantia polymorpha. Their study recently appeared in BioRxiv.

To confirm the antiviral potential of PheoA, a commercially available PheoA stock solution was serially diluted and mixed with a virus stock to inoculate Vero E6 and Huh7-ACE2 cells (human hepatoma cells expressing ACE2). They found that PheoA has an extraordinary antiviral activity against SARS-CoV-2 preventing infection of cultured monkey and human cells, without noticeable citotoxicity. Additionally, it has been shown that, PheoA prevents coronavirus entry into the cells by directly targeting the viral particle.

Antiviral spectrum of PheoA against different RNA viruses © Guillermo H. Jimenez-Aleman et al.

They also determined the antiviral spectrum of PheoA on different enveloped and non-enveloped viruses. They showed that, besides SARS-CoV-2, PheoA also displayed a broad-spectrum antiviral activity against enveloped (+)strand RNA viral pathogens such as HCV, West Nile, and other coronaviruses, but not against (-)strand RNA viruses, such as VSV.

Finally, they determined whether the addition of PheoA to remdesivir treatment could result in a synergistic effect on viral infection. They showed that increasing concentrations of PheoA (upto 40nM) improved remdesivir efficacy and viceversa.

“Our results indicate that PheoA displays a remarkable potency and a satisfactory therapeutic index, and suggest that it may be considered as a potential candidate for antiviral therapy against SARS-CoV-2.”

— they concluded.

Featured image: Scheme of Pheophobide a preparation from plant material. KG, Silica gel 60. AcOEt, ethyl acetate. MeOH, methanol. © Guillermo H. Jimenez-Aleman et al.

Reference: Guillermo H Jimenez-Aleman, Victoria Castro, Addis Longdaitsbehere, Marta Gutierrez-Rodriguez, Urtzi Garaigorta, Pablo Gastaminza, Roberto Solano, “SARS-CoV-2 fears green: the chlorophyll catabolite Pheophorbide a is a potent antiviral”, bioRxiv 2021.07.31.454592; doi: https://doi.org/10.1101/2021.07.31.454592

Note for editors of other websites: To reuse this article fully or partially kindly give credit either to our author/editor S. Aman or provide a link of our article

Blushing Plants Reveal When Fungi Are Growing in Their Roots (Botany)

Scientists have created plants whose cells and tissues ‘blush’ with beetroot pigments when they are colonised by fungi that help them take up nutrients from the soil.

We can now follow how the relationship between the fungi and plant root develops, in real-time, from the moment they come into contact.

— Sebastian Schornack

This is the first time this vital, 400 million year old process has been visualised in real time in full root systems of living plants. Understanding the dynamics of plant colonisation by fungi could help to make food production more sustainable in the future.

Almost all crop plants form associations with a particular type of fungi – called arbuscular mycorrhiza fungi – in the soil, which greatly expand their root surface area. This mutually beneficial interaction boosts the plant’s ability to take up nutrients that are vital for growth. 

The more nutrients plants obtain naturally, the less artificial fertilisers are needed. Understanding this natural process, as the first step towards potentially enhancing it, is an ongoing research challenge. Progress is likely to pay huge dividends for agricultural productivity.

In a study published in the journal PLOS Biology, researchers used the bright red pigments of beetroot – called betalains – to visually track soil fungi as they colonised plant roots in a living plant. 

“We can now follow how the relationship between the fungi and plant root develops, in real-time, from the moment they come into contact. We previously had no idea about what happened because there was no way to visualise it in a living plant without the use of elaborate microscopy,” said Dr Sebastian Schornack, a researcher at the University of Cambridge’s Sainsbury Laboratory and joint senior author of the paper. 

To achieve their results, the researchers engineered two model plant species – a legume and a tobacco plant – so that they would produce the highly visible betalain pigments when arbuscular mycorrhiza fungi were present in their roots. This involved combining the control regions of two genes activated by mycorrhizal fungi with genes that synthesise red-coloured betalain pigments.

The plants were then grown in a transparent structure so that the root system was visible, and images of the roots could be taken with a flatbed scanner without disturbing the plants.

Using their technique, the researchers could select red pigmented parts of the root system to observe the fungus more closely as it entered individual plant cells and formed elaborate tree-like structures – called arbuscules – which grow inside the plant’s roots. Arbuscules take up nutrients from the soil that would otherwise be beyond the reach of the plant. 

Other methods exist to visualise this process, but these involve digging up and killing the plant and the use of chemicals or expensive microscopy. This work makes it possible for the first time to watch by eye and with simple imaging how symbiotic fungi start colonising living plant roots, and inhabit parts of the plant root system over time.

“This is an exciting new tool to visualise this, and other, important plant processes. Beetroot pigments are a distinctive colour, so they’re very easy to see. They also have the advantage of being natural plant pigments, so they are well tolerated by plants,” said Dr Sam Brockington, a researcher in the University of Cambridge’s Department of Plant Sciences, and joint senior author of the paper.

Mycorrhiza fungi are attracting growing interest in agriculture. This new technique provides the ability to ‘track and trace’ the presence of symbiotic fungi in soils from different sources and locations. The researchers say this will enable the selection of fungi that colonise plants fastest and provide the biggest benefits in agricultural scenarios.

Understanding and exploiting the dynamics of plant root system colonisation by fungi has potential to enhance future crop production in an environmentally sustainable way. If plants can take up more nutrients naturally, this will reduce the need for artificial fertilisers – saving money and reducing associated water pollution. 

This research was funded by the Biotechnology and Biological Sciences Research Council, Gatsby Charitable Foundation, Royal Society, and Natural Environment Research Council.

Featured image: Cells of roots colonised by fungi turn red © University of Cambridge

Timoneda, A. & Yunusov, T. et al: ‘MycoRed: Betalain pigments enable in vivo real-time visualisation of arbuscular mycorrhizal colonisation.’ PLOS Biology, July 2021. DOI: 10.1371/journal.pbio.3001326

Provided by University of Cambridge

Tomato Fruits Send Electrical Warnings to the Rest of the Plant When Attacked by Insects (Botany)

A recent study in Frontiers in Sustainable Food Systems shows that the fruits of a type of tomato plant send electrical signals to the rest of the plant when they are infested by caterpillars. Plants have a multitude of chemical and hormonal signaling pathways, which are generally transmitted through the sap (the nutrient-rich water that moves through the plant). In the case of fruits, nutrients flow exclusively to the fruit and there has been little research into whether there is any communication in the opposite direction–i.e. from fruit to plant.

“We usually forget that a plant’s fruits are living and semiautonomous parts of their mother-plants, far more complex than we currently think. Since fruits are part of the plant, made of the same tissues of the leaves and stems, why couldn’t they communicate with the plant, informing it about what they are experiencing, just like regular leaves do?” says first author Dr Gabriela Niemeyer Reissig, of the Federal University of Pelotas, Brazil. “What we found is that fruits can share important information such as caterpillar attacks–which is a serious issue for a plant–with the rest of the plant, and that can probably prepare other parts of the plant for the same attack.”

A tomato’s defense

To test the hypothesis that fruits communicate by electrical signals, Niemeyer Reissig and her collaborators placed tomato plants in a Faraday’s cage with electrodes at the ends of the branches connecting the fruits to the plant. They then measured the electrical responses before, during and after the fruits had been attacked by Helicoverpa armigera caterpillars for 24 hours. The team also used machine learning to identify patterns in the signals.

The results showed a clear difference between the signals before and after attack. In addition, the authors measured the biochemical responses, such as defensive chemicals like hydrogen peroxide, across other parts of the plant. This showed that these defenses were triggered even in parts of the plant that were far away from the damage caused by the caterpillars.

The authors emphasize that these are still early results. Their measurements provide a “big picture” view of all of the electrical signals, rather than distinguishing individual signals more precisely. It will also be interesting to see whether this phenomenon holds true for other plant species, as well as different types of threats.

That said, this novel use of machine learning appears to have very high potential for answering these and other future questions. The technique may also provide new–and possibly more environmentally friendly–approaches for insect control in agriculture.

“If studies like ours continue to advance and the techniques for measuring electrical signals in open environments continue to improve, it will be possible to detect infestation of agricultural pests quite early, allowing for less aggressive control measures and more accurate insect management,” explains Niemeyer Reissig. “Understanding how the plant interacts with its fruits, and the fruits among themselves, may bring insights about how to ‘manipulate’ this communication for enhancing fruit quality, resistance to pests and shelf life after harvest.”

Reference: Gabriela Niemeyer Reissig et al., “Fruit Herbivory Alters Plant Electrome: Evidence for Fruit-Shoot Long-Distance Electrical Signaling in Tomato Plants”, Front. Sustain. Food Syst., 20 July 2021 | https://doi.org/10.3389/fsufs.2021.657401

Provided by Frontiers

Arrival of Land Plants Changed Earth’s Climate Control System (Botany)

The arrival of plants on land about 400 million years ago may have changed the way the Earth naturally regulates its own climate, according to a new study led by researchers at UCL and Yale.

The carbon cycle, the process through which carbon moves between rocks, oceans, living organisms and the atmosphere, acts as Earth’s natural thermostat, regulating its temperature over long time periods.

In a new study, published in the journal Nature, researchers looked at samples from rocks spanning the last three billion years and found evidence of a dramatic change in how this cycle functioned about 400 million years ago, when plants started to colonise land.

Specifically, the researchers noted a change in the chemistry of seawater recorded in the rock that indicates a major shift in the global formation of clay – the “clay mineral factory” – from the oceans to the land.

Since clay forming in the ocean (reverse weathering) leads to carbon dioxide being released into the atmosphere, while clay on land is a byproduct of chemical weathering that removes carbon dioxide from the air, this reduced the amount of carbon in the atmosphere, leading to a cooler planet and a seesawing climate, with alternating ice ages and warmer periods.

The researchers suggested the switch was caused by the spread of land plants keeping soils and clays on land, stopping carbon from being washed into the ocean, and by the growth in marine life using silicon for their skeletons and cell walls, such as sponges, single-celled algae and radiolarians (a group of protozoa), leading to a drop in silicon in the seawater required for clay formation.

Senior author Dr Philip Pogge von Strandmann (UCL Earth Sciences) said: “Our study suggests that the carbon cycle operated in a fundamentally different way for most of Earth’s history compared to the present day.

“The shift, which occurred gradually between 400 to 500 million years ago, appears to be linked to two major biological innovations at the time: the spread of plants on land and the growth of marine organisms that extract silicon from water to create their skeletons and cells walls.

“Before this change, atmospheric carbon dioxide remained high, leading to a stable, greenhouse climate. Since then, our climate has bounced back and forth between ice ages and warmer periods. This kind of change promotes evolution and during this period the evolution of complex life accelerated, with land-based animals forming for the first time.

“A less carbon-rich atmosphere is also more sensitive to change, allowing humans to influence the climate more easily through the burning of fossil fuels.”

First author Boriana Kalderon-Asael, a PhD student at Yale University, said: “By measuring lithium isotopes in rocks spanning most of Earth’s history, we aimed to investigate if anything had changed in the functioning of the carbon cycle over a large time scale. We found that it had, and this change appears to be linked to the growth of plant life on land and silicon-using animal life in the sea.”

first author looks for sediment samples

In the study, researchers measured lithium isotopes in 600 samples of rock taken from many different locations around the world. Lithium has two naturally occurring stable isotopes – one with three protons and three neutrons, and one with three protons and four neutrons.

When clay forms slowly on land, it strongly favours lithium-6, leaving surrounding water enriched with the other, heavier isotope, lithium-7. Analysing their samples using mass spectrometry, the researchers found a rise in the levels of lithium isotope-7 in seawater recorded in the rock occurring between 400 and 500 million years ago, suggesting a major shift in Earth’s clay production coinciding with the spread of plants on land and emergence of silicon-using marine life.

Clay forms on land as a residue of chemical weathering, the primary long-term process through which carbon dioxide is removed from the atmosphere. This occurs when atmospheric carbon combines with water to form a weak acid, carbonic acid, which falls to the ground as rain and dissolves rocks, releasing ions including calcium ions that flow into the ocean. Eventually, the carbon is locked up in rocks on the ocean floor. In contrast, carbon drawdown by plant photosynthesis is negated once the plants decay, and rarely affects carbon dioxide levels on timescales longer than a few hundred years.

When clay forms in the ocean, carbon stays in the water and is eventually released into the air as part of the continual exchange of carbon that occurs when air meets water.

The study received support from the European Research Council and NASA.


Kalderon-Asael, B., Katchinoff, J.A.R., Planavsky, N.J. et al. A lithium-isotope perspective on the evolution of carbon and silicon cycles. Nature 595, 394–398 (2021). https://doi.org/10.1038/s41586-021-03612-1


  • Top: Moss. Credit: iStock. Middle: Sampling of Ordovician (450 million year old) sediments by first author Boriana Kalderon-Asael. Credit: Ashleigh Hood.

Provided by UCL

Stanford Ecologists Develop A Theory About How Plants ‘Pay’ Their Microbes (Ecology)

Combining economics, psychology and studies of fertilizer application, researchers find that plants nearly follow an “equal pay for equal work” rule when giving resources to partner microbes – except when those microbes underperform.

“Equal pay for equal work,” a motto touted by many people, turns out to be relevant to the plant world as well. According to new research by Stanford University ecologists, plants allocate resources to their microbial partners in proportion to how much they benefit from that partnership.

“The vast majority of plants rely on microbes to provide them with the nutrients they need to grow and reproduce,” explained Brian Steidinger, a former postdoctoral researcher in the lab of Stanford ecologist, Kabir Peay. “The problem is that these microbes differ in how well they do the job. We wanted to see how the plants reward their microbial employees.”

In a new study, published July 6 in the journal American Naturalist, the researchers investigated this question by analyzing data from several studies that detail how different plants “pay” their symbionts with carbon relative to the “work” those symbionts perform for the plants – in the form of supplying nutrients, like phosphorus and nitrogen. What they found was that plants don’t quite achieve “equal pay” because they tend not to penalize low-performing microbes as much as would be expected in a truly equal system. The researchers were able to come up with a simple mathematical equation to represent most of the plant-microbe exchanges they observed.

“It’s a square root relationship,” said Peay, who is an associate professor of biology in the School of Humanities and Sciences. “Meaning, if microbe B does one-quarter as much work as microbe A, it still gets 50 percent as many resources – the square root of one-quarter.”

When the researchers tested their equation against 13 measurements of plant resource exchange with microbe partners, they were able to explain around 66 percent of the variability in the ratio of plant payments to two different microbes.

“The biggest surprise was the simplicity of the model,” said Steidinger. “You don’t get a lot of short equations in ecology. Or anywhere else.”

The fruit of frustration

When asked about the motivation for developing this equation, Steidinger summed it up with one word: frustration.

“There is a lot of really interesting literature in a field called ‘biological market theory’ that deals with how plants should preferentially allocate resources. But for the folks who actually run experiments, it is difficult to translate these models into clean predictions,” said Steidinger. “We wanted to make that clean prediction.”

An informal survey of the Peay lab members encouraged the researchers to start with the assumption of equal pay because most people agreed it was reasonable to guess that plants treat all microbes the same. To reach their final equation, Steidinger and Peay then factored in the diminishing returns seen in the fertilizer models and assessed them through the lens of biological market theory literature – which uses human markets as a mathematical analogy for exchanges of services in the natural world.

“It turns out if the plant is flush with resources – in this case, the sugars it feeds to its microbes – and if the nutrients are valuable enough, the plant pays its microbes according to a square-root law,” said Peay.

The square-root model is a strong start to addressing Steidinger’s original frustration but it is not quite at the level of realism he wants to eventually achieve.

“For instance, our model allows a useless microbe to be fired without the plant losing resources,” said Steidinger. “But, just as in the human world, it takes an investment to hire a microbe and that initial investment is a gamble that microbial layabouts can consume at their leisure.”

Weber’s Law

In an attempt to explain why plants follow the square-root model, the researchers turned to a law in psychology. Weber’s Law addresses how humans perceive differences in stimuli, such as noise, light or the size of different objects. It explains that, the stronger the stimuli, the worse we are at identifying when it changes. This law has been shown to hold for many non-human animals as well – describing, for example, how birds and bats forage for food and how fish school. Now the researchers suggest it’s a good analogy for their plant payment scheme too.

“Our model says that plant should go easy on low-performing microbes, seemingly overpaying the 25-percent-as-good microbe with 50 percent as much resources,” said Peay. “Well, it’s long been known that humans and non-human animals sense differences in quantity in a way that might bias them towards similar leniency.”

In other words, the researchers suggest that, like a human trying to detect the volumes of specific noises in a loud room, a plant making optimal payment decisions may be relatively insensitive to differences in the quality of its microbial employees. And the researchers argue that this insensitivity may be for the best, as it encourages plants to maintain a certain level of microbial diversity, which can help give the plant options for dealing with environmental changes it encounters throughout its lifetime.

“I think what we’re seeing is plants behave like animals not because they have the same perceptional limitations – and certainly not because they think like animals – but because we face similar challenges in making the best choices when there are diminishing returns on investment,” says Steidinger.

This research was funded by the U.S. Department of Energy Office of Science, Office of Biological & Environmental Research, Early Career Research Program; the National Science Foundation Division of Environmental Biology; and an Alexander von Humboldt Postdoctoral Research Fellowship.

Featured image: Plants and microbes exchange resources in symbiotic relationships – but Stanford ecologists suggest that plants don’t quite compensate all their microbes equally. (Image credit: Getty Images)

Provided by Stanford University

Acid Sensor Discovered in Plants (Botany)

If plants are flooded, they lack oxygen and their cells over-acidify. A sensor protein detects this and triggers a stress response. Researchers have now presented details about this topic in the journal Current Biology.

Climate change is causing increased flooding and prolonged waterlogging in northern Europe, but also in many other parts of the world. This can damage meadow grasses, field crops or other plants – their leaves die, the roots rot.

The damage is caused by a lack of oxygen and the accumulation of acids. How do plants perceive this over-acidification, how do they react to it? This is what researchers from Würzburg, Jena (Germany) and Talca (Chile) describe in the journal Current Biology.

Biophysicists Dr. Tobias Maierhofer and Professor Rainer Hedrich from the Chair of Molecular Plant Physiology and Biophysics at Julius-Maximilians-Universität (JMU) Würzburg in Bavaria, Germany, were in charge of the study.

Anion channel recognises acidification

Everyone is probably familiar with the effect of over-acidification from their own experience: When exercising too hard, muscles are undersupplied with oxygen and acidosis occurs. Muscle pain and poor performance are the consequences.

“In plants, a lack of oxygen also causes acidification of the cells,” says Tobias Maierhofer. The team led by the JMU researcher has now discovered the sensor in the model plant Arabidopsis thaliana (thale cress) that perceives the acidification and translates it into an electrical signal. It is a protein in the cell membrane, the anion channel SLAH3.

Super-resolution microscopy clarifies structure

Professor Markus Sauer of the JMU Chair of Biotechnology and Biophysics has developed a microscopy method that can be used to look at proteins in high resolution. With the help of his methodology, the team was able to clarify how the anion channel SLAH3 reacts during acidification.

In the non-active state, the channel is present as a complex of two subunits in the cell membrane. With a lack of oxygen, the acidity and thus the proton content in the cell increases, and protons bind to two specific amino acids of the channel.

“This protonation changes the structure of SLAH3 and the channel breaks down into its two subunits,” explains Maierhofer, who is an expert on anion channels. As single copies, the two units now become conductive for anions, which leads to electrical excitation of the cell membrane.

Mutants react weaker to flooding

The electrical signal in turn triggers further reactions in the plant. Among other things, photosynthesis is reduced. “We assume that this is an adaptation to the flooding stress: the plants switch to a kind of resting state,” says Maierhofer.

The JMU researchers also investigated how Arabidopsis mutants lacking SLAH3 react to flooding. These plants did not try to reduce their photosynthetic output – even though photosynthesis is not possible at all in the muddy, murky flood water where too little light reaches the leaves.

Investigating genetic control during flooding

The anion channel SLAH3 can thus convert an acidification of the cell interior directly into an electrical signal. In this way, it functions like a pH sensor.

Next, the researchers want to investigate how the electrical signal is transported in the plant and translated into a stress-avoiding response. The necessary tools for this, such as pH-insensitive mutants, are available. This makes it possible to study in detail the genetic rerouting of the physiology of plants during flooding.

The results of this basic research could prove significant for agricultural practice: “With the knowledge we are gaining, we can take a targeted approach to breed crops that are more tolerant to waterlogging,” says JMU researcher Maierhofer.

Featured image: When plants are flooded for a long time, they suffer damage. Würzburg researchers are investigating what happens in plant cells during flooding. (Image: Dorothea Graus / Universität Würzburg)


Acidosis-induced activation of anion channel SLAH3 in the flooding-related stress response of Arabidopsis, Julian Lehmann, Morten E. Jorgensen, Stefanie Fratz, Heike M. Müller, Jana Kusch, Sönke Scherzer, Carlos Navarro-Retamal, Dominik Mayer, Jennifer Böhm, Kai R. Konrad, Ulrich Terpitz, Ingo Dreyer, Thomas D. Mueller, Markus Sauer, Rainer Hedrich, Dietmar Geiger and Tobias Maierhofer, Current Biology, 2021, doi: 10.1016/j.cub.2021.06.018

Provided by University of Wurzburg

How Information Beyond the Genetic Sequence Is Encoded In The Plant Sperm? (Botany)

Hereditary information is passed from parent to offspring in the genetic code, DNA, and epigenetically through chemically induced modifications around the DNA.

New research from the John Innes Centre has uncovered a mechanism which adjusts these modifications, altering the way information beyond the genetic code is passed down the generations.

DNA methylation, one example of these epigenetic modifications, happens when a methyl group or chemical cap is added to the DNA, switching a gene, or genes, on or off.

As germline (eggs and sperm) cells develop some of the methyl markers are reset, affecting the information passed onto the next generation.

How this process worked during plant reproduction has until now, been unclear.

The exciting research, published in Science, reveals the molecular mechanism of DNA methylation reprogramming in the male germline of plants.

Inside the plant’s male reproductive parts (the anthers), cells that will divide to produce the sperm (meiocytes) are surrounded by cells that nourish them. These nurse cells are called tapetal cells.

The John Innes Centre team discovered that tapetal cells produce an abundance of small RNA molecules and observed that this is caused by a protein called CLSY3, found specifically within tapetal cells in the anther. These small RNAs were shown to move from the tapetal cells into the meiocytes. Here they add new methyl marks to transposons (unstable genetic elements) with the same DNA code.

“This discovery changes the way we think about epigenetic inheritance across generations in plants by showing that small RNAs produced by germline nurse cells can determine the DNA methylome in the sperm. The key role played by these small RNAs in determining the inherited DNA methylome indicates convergent functional evolution between plant and animal reproduction,” says corresponding author Dr Xiaoqi Feng, Group Leader at the John Innes Centre.

This reprogramming stops the transposons from jumping around in the germ cells, and this protects the integrity of the genome between generations.

Gypsy1 transposon is active (shown by yellow fluorescence) in the microspores (progenitors of sperm cells) when tapetal small RNAs are absent. © John Innes Centre

In the meiocytes, these small RNAs also target genes with similar DNA sequences as the source transposons, helping to control gene expression and facilitate meiosis, a type of cell division that leads to the production of sperm.

The findings have wide application across plant and animal kingdoms and provide a vital new clue for the world-wide community of researchers studying epigenetics.

Previous work has shown that cereal crops, like maize and rice, have similar tapetal small RNAs, however, it was unclear why these small RNAs are important for fertility and yield. The mechanistic insight generated by this study points to new directions of investigations and may help develop biotechnology to target DNA methylation in commercial crops.

Joint first author Dr Jincheng Long said: “Our study could open a new avenue of crop biotechnology. For example, through the manipulation of small RNA directed DNA methylation of the cells that directly contribute to seed formation and the breeding process.”

The study is also important in fundamental biological terms, joint first author Dr James Walker explains, “Our work demonstrates that paternal epigenetic inheritance is determined by tapetal cells, which drive reprogramming at a scale unprecedented in plants.

“The molecular mechanism our work revealed pushes our understanding of de novo DNA methylation to the next level, showing how new methyl marks are established at specific sites in specific cells.”

Featured image: CLSY3 (fused with a yellow fluorescent protein) is specifically expressed in the tapetal cells surrounding the germ cells. © John Innes Centre

Provided by John Innes Center

How Plants Become Good Neighbors in Times of Stress? (Botany)

Scientists have discovered how plants manage to live alongside each other in places that are dark and shady.

Moderate shade or even the threat of shade – detected by phytochrome photoreceptors – causes plants to elongate to try to outgrow the competition.

But in the deep gloom of a dense forest or a cramped crop canopy where resources and photosynthesis are limited, this strategy doesn’t work. In these conditions it would be a waste of energy and detrimental to survival to elongate stems because seedlings would never be able to over-grow larger neighbours.

So how do plants prevent elongated growth under deep shade conditions? The secret lies in their internal clocks, says the research collaboration from the John Innes Centre and the University of Bristol.

They have discovered that when plants detect deep shade, this changes the expression of genes in certain parts of the circadian clock – the internal daily timer found in plants and other organisms. These clock components perform an additional role in suppressing stem elongation, blocking the over-topping of neighbours that would normally happen in moderate shade.

The work identifies a previously unknown role for the circadian clock in regulating plant development, and the findings have implications for both natural plant populations and crops, say the researchers.

The study is relevant to natural plant populations because the researchers identify a new process that controls the development of plants growing under conditions such as those found in temperate woodlands in summer and tropical rainforests.

Crops are often grown in dense stands which means that the plants shade each other; so the findings identify processes that might be manipulated to allow crops to be grown more densely or to control their height.

Professor Antony Dodd of the John Innes Centre said, “The biological clock of plants is a key regulator of their development and fitness. This work sheds new light on a new role for circadian rhythms in adapting plants to competition with other plants in their environments.”

Professor Kerry Franklin of the University of Bristol said, “The majority of plant shade avoidance research focuses on early neighbour detection and moderate shading. This work reveals new insights into how plants adapt to very deep shade, where resources are severely limited.”

The study provides evidence for the robustness and stability of the circadian clock in stressful environments, information that may be useful in developing new generations of crops in a challenging climate.

Featured image: How do plants prevent elongated growth under deep shade conditions? The secret lies in their internal clocks. © Pexels

Reference: Donald Fraser et al., “Phytochrome A elevates plant circadian-clock components to suppress shade avoidance in deep-canopy shade”, PNAS July 6, 2021 118 (27) e2108176118; https://doi.org/10.1073/pnas.2108176118

Provided by John Innes Center