In our third installment in the series ‘Great Debates in Agronomy’, we explore the changing face of photosynthesis. New AG International’s Editor Janet Kanters spoke with Don Ort, the Robert Emerson Professor of Plant Biology and Crop Sciences at the University of Illinois, and Deputy Director of Realizing Increased Photosynthetic Efficiency (RIPE), an international research project that is engineering crops to be more productive by improving photosynthesis. His research and collaboration with researchers around the world seeks to understand and improve plant growth and photosynthetic performance in changing environmental conditions such as rising carbon dioxide levels, temperature stress and drought.
New AG International: Is there anything left to discover on photosynthesis? That is, is everything on photosynthesis known and agreed upon? Don Ort: We know a lot. I would say that photosynthesis is the best understood of all plant processes. There are about 120 reactions in photosynthesis – we know what they all are, we know all of the enzymes that are involved with them. We know a lot about where they’re located in the chloroplast in and in some cases elsewhere in the plant cell. What we know less about is the interactive regulation within photosynthesis, i.e., what are the mechanisms by which photosynthesis responds to the perturbations that occur every day. We know when light goes up and light goes down, it changes the rate of photosynthesis. But there are a lot of things that have to change in order for a new steady state to be established at the new light level. We don’t know about all the signaling within the process; this is one of the current frontiers in
photosynthesis research. And regulation is really important to understand if we’re going to engineer photosynthesis in a successful way. Yes, we can engineer things now, but more often than not we get unexpected results and I think that’s because we don’t understand these intricate regulatory processes that are going on. And they’re required to regulate on lots of levels – they’re going on at the level of gene expression, they’re going on at the level of metabolism, and they’re going on at the level of the regulation of catalysis itself.
How do environmental conditions affect photosynthesis? Environmental conditions affect photosynthesis a lot. Plants are outside and they can’t move, and so they really have to deal with what comes at them. Photosynthesis is very responsive to light intensity and
of course there is no photosynthesis at night. A lot of times during the day, a sun-exposed leaf has way too much light. Therefore, it has to dissipate that energy in order to prevent damage to the photosynthetic apparatus. There are intricate processes to do that, and if they’re not adequate then there is damage. What establishes the threshold of what is too much light versus what is not enough light varies with environmental conditions. So, if it’s freezing outside, then for most of our temperate plant species, quite low light intensity is too much light because photosynthesis can only go very slowly at those low temperatures. At more permissive temperatures, it might go a hundred or a thousand times faster. But then the temperature can get too high,
resulting in various protective processes to kick in that downregulate photosynthesis. Photosynthesis is very tightly tied to the hydraulic cycle in plants. In order for photosynthesis to occur, it has to get CO2 from the atmosphere, and the atmosphere is always much dryer than inside the leaf. Typically, in a plant, in order to get one molecule of CO2, they’ll lose ~500 molecules of water. That’s an issue for plants, that in order to get enough CO2 to do high rates of photosynthesis, they’re going to lose a lot of water. If they don’t have that water available in the soil, then they have to close down these stomatal
pores that CO2 and water exchange through; they’re not losing as much water but they’re taking in virtually no CO2 and so they can’t do as much photosynthesis. The interaction with water is one of the really key interactions of photosynthesis with the environment.
Do higher levels of CO2 in the atmosphere make a difference? Absolutely it does. That’s key to what I was just talking about; that is, as CO2 concentration goes up in the atmosphere, then the stomata will not have to be open quite as wide to take in the CO2 that’s needed, and the loss of water is less. We would measure this as water use efficiency which is the number of molecules that the plant loses for every molecule of CO2 it’s able to fix into carbohydrate. Another factor is that CO2 is the primary substrate for photosynthesis, but the level of CO2 in the atmosphere doesn’t saturate the enzyme that fixes it, and that enzyme is Rubisco. Thus, as the concentration of CO2 goes up, then the rate of that Rubisco goes faster. In addition to this improvement to water use efficiency, photosynthesis goes faster and is more efficient as CO2 concentration goes up. Do all plants react the same to elevated CO2? Elevated CO2 causes all plants to partially close their stomata and thereby improve water use efficiency. But the reaction of photosynthesis to elevated CO2 is not the same in all types of plants. There are three kinds of photosynthetic metabolism found in higher plants: there’s C3 metabolism, and that’s what most of our crop plants do; those are the ones in which the CO2 is not saturating for Rubisco.
Then there are plants that are said to have C4 metabolism, and what they do is they have two kinds of chloroplasts, and the first chloroplast fixes CO2 not with Rubisco, but with an enzyme called PEP carboxylase; rather than making a three-carbon carbohydrate, it makes a four-carbon acid. And that four-carbon acid is transported out of that mesophyll cell into a specialized bundle-sheath cell where it is decarboxylated and the CO2 is released. And the bundle-sheath cell is where Rubisco is located. This two-cell process acts as a CO2 pump – it increases the concentration of CO2 in that compartment where Rubisco is by a factor of about 10 over atmospheric. In this case, then you get very close to the substate saturation of Rubisco. Elevating the atmospheric CO2 concentration has very little impact on C4 plants. The major C4 crop plants are corn, sugarcane and sorghum. Every other crop plant you can think of is C3. The third type of photosynthetic metabolism is known as crassulacean acid metabolism which is found in plants like cactus. It, too, operates mechanism to concentrate CO2 and saturate Rubisco. And like C4, doesn’t respond to elevated CO2.
Can photosynthesis be manipulated? That is a lot of what the RIPE project is about. We are trying to manipulate it. For example, we’ve been talking about CO2. The CO2 concentration for the last 20 million years has been around 220 ppm, and so this is the time when all the ancestors to our modern crop plants evolved. For the past 10,000 years, the CO2 concentration has been about 250 ppm. Then at the beginning of the industrial revolution, it started going up, and it has actually gone up a lot – now it’s about 420 ppm. We know photosynthesis is adapted for a CO2 concentration well below that 420 ppm. This higher CO2 concentration presents advantages that we’ve already talked about, but the plants can’t take full advantage of that. Part of our engineering is trying to rebalance photosynthesis and prevent the limitations that are being caused by elevated CO2. There are other examples where evolution didn’t plan for us planting crop plants as monocultures at very high density. I mentioned earlier that
a sunlit leaf often has three or four times too much light. The paradox is that in a dense canopy like in a soybean canopy, one leaf-layer down, those leaves are light limited. We’re wasting all this light at the top of the canopy while further down in the canopy there isn’t enough light. We think the plants have really overinvested in chlorophyll. So another thing we’re engineering is light green plants. What we would like is less light absorbed at the top of the canopy so that there is more light available to transmit deeper into the canopy where it can be used more efficiently. That’s another example of trying to engineer something that evolution couldn’t anticipate because it wasn’t there, so it couldn’t select for it. The hoped-for outcome would be that as you transmit more light deeper into the canopy where it can be used, that overall photosynthesis of that canopy is going to go up. And that will support more yield.
How does photosynthesis affect nutrient uptake in plants? If we’re talking about mineral nutrients from the soil, many of those – not all of them – move by mass flow. That means that as water moves through the soil, the nutrients move with the water. At this time of year in Illinois, for example, about 80 percent of all the water that returns to the atmosphere returns through plants as transpiration. With that water stream that’s coming out of the soil into the plants and then ultimately back into the atmosphere, it’s bringing those mineral nutrients into the plant. They of course don’t evaporate out of the plant and so they’re not going into the atmosphere, they stay in the plants. They very much affect mineral uptake in that way.
The other way that’s a bit more subtle is a lot of these nutrients in the soil don’t move completely by mass flow because they’re attached to soil particles and they’re not available necessarily to move with the water as it goes through the soil. But there is a microbiome in the plant’s root zone comprised of many microorganisms that are fed by the plants. So they’re providing carbon and energy to these bacterial and fungal communities and, in turn, those fungal communities are mining things like phosphorus the plant desperately needs, and providing it to the plant. This is a synergy between the plant and the microbiome. We’re just beginning to really learn a lot about this. That’s another way in which plants are dramatically affecting nutrient uptake by supporting these soil microbial communities.
Based on photosynthesis and in light of climate change, what is the long-term outlook for plant production/nutrient uptake? Another less desirable thing that comes along with increasing CO2 in the atmosphere is greenhouse warming. I believe the biggest challenge we have going forward is warming. For many of our plants, we’re very close to what that thermal threshold is already. And it’s not necessarily an average temperature we’re concerned most about – it’s the extreme temperatures and the frequency with which we get these extreme temperatures, how long they’re present, how many heat waves and how severe they are, and how frequently they occur. One of the things we know as the atmosphere warms and there’s more energy in the atmosphere, is the frequency of these heat waves goes up, the duration of them increases and how warm it gets increases. Those I think are going to be the really dramatic factors that are the challenge for agriculture certainly, as well as for some natural ecosystems. In this case, particularly for agriculture, it’s not just photosynthesis and nutrient uptake that are going to be the only causes of yield loss. Yield loss due to warming has a lot to do with reproductive processes. Many of these are quite temperature sensitive. For instance, in corn, during silking and tasseling, just a day or a day-and-a-half where you
see 100-degree temperatures can completely prevent pollination. It’s a very fragile time during the plant’s lifecycle. The vegetative part of the plant in photosynthesis is usually OK. But it can completely abort the reproductive processes and therefore completely collapse yield.
What is the long-term outlook on photosynthesis today and in the future? It’s pretty urgent. There are a lot of projections that by the decade 2050-2060 we will need to have doubled global food production over 2005 levels. What’s called a breeding cycle, and that is from when you introduce a trait into a crop to when you get that trait into a farmer’s field, is about 12 years. We’re two to two-and-a-half breeding cycles away from a time when we need to double
productivity over what it was in 2005. We’re not on track to do that.
So how do we get there? I think research funding is part of the answer. For instance, for GMO plants, a lot of time and money is spent in regulation, in deregulating the crop. And it is necessary that genetically engineered organisms be carefully evaluated for unintended impacts. But as of now, deregulation isn’t very science based. If it were science based, there’s no doubt we would be safer, progress would go more quickly, and it wouldn’t be so enormously expensive. We do a lot of transgenic work here on campus and in my lab. We can’t afford to deregulate a crop. It’s estimated to be somewhere around USD$150 million to put a GMO trait in a farmer’s field. Only commercial agro-industry can afford to do this.
Whereas a streamlined regulatory process would allow the public sector to participate much more in this which would just create a lot more opportunity. On the positive side, another thing that’s happening is that there is a recognition now by funding agencies that there needs to be more integration. When we discover something, it’s not enough just to put it in a journal and hope somebody picks it up and takes it further. Funding agencies have never been willing to fund that research that takes a trait from the laboratory and puts it into a crop for proof of demonstration that makes it attractive to agro-industry. But now they’re starting to do that; it just takes a different kind of science. It takes science that involves several groups that are funded together to do that hand-off. ●
Don Ort, Robert Emerson Professor of Plant Biology and Crop Sciences at the University of Illinois, and Deputy Director of Realizing Increased Photosynthetic Efficiency (RIPE)
There are about 120 reactions in photosynthesis
CO2 is the primary substrate for photosynthesis
Part of our engineering is trying to rebalance photosynthesis and prevent the limitations that are being caused by elevated CO2
Light filtering through soybean canopy.
Photo: Allie Arp/RIPE project
For the first time, RIPE researchers have proven that multigene bioengineering of photosynthesis increases the yield of the major food crop soybean in field trials.
After more than a decade of working toward this goal, a collaborative team led by the University of Illinois has transgenically altered soybean plants to increase the efficiency of photosynthesis, resulting in greater yields without loss of quality.
“The number of people affected by food insufficiency continues to grow, and projections clearly show that there needs to be a change at the food supply level to change the trajectory,” said Amanda De Souza, RIPE project research scientist, and lead author. “Our research shows an effective way to contribute to food security for the people who need it most while avoiding more land being put into production. Improving photosynthesis is a major opportunity to gain the needed jump in yield potential.”
Photosynthesis is a surprisingly inefficient 100+ step process that RIPE researchers have been working to improve for more than a decade. In this first-of-its-kind work, recently published in Science, the group improved the VPZ construct within the soybean plant to improve photosynthesis and then conducted field trials to see if yield would be improved as a result.
The VPZ construct contains three genes that code for proteins of the xanthophyll cycle, which is a pigment cycle that helps in the photoprotection of the plants. Once in full sunlight, this cycle is activated in the leaves to protect them from damage, allowing leaves to dissipate the excess energy. However, when the leaves are shaded (by other leaves, clouds or the sun moving in the sky) this photoprotection needs to switch off so the leaves can continue the photosynthesis process with a reserve of sunlight. It takes several minutes for the plant to switch off the protective mechanism, costing plants valuable time that could have been used for photosynthesis.
The overexpression of the three genes from the VPZ construct accelerates the process, so every time a leaf transitions from light to shade the photoprotection switches off faster. Leaves gain extra minutes of photosynthesis which, when added up throughout the entire growing season, increases the total photosynthetic rate. This research has shown that despite achieving a more than 20 percent increase in yield, seed quality was not impacted.
“Despite higher yield, seed protein content was unchanged. This suggests some of the extra energy gained from improved photosynthesis was likely diverted to the nitrogen-fixing bacteria in the plant’s nodules,” said Stephen Long, RIPE director and Ikenberry Endowed University Chair of Crop Sciences and Plant Biology at Illinois’ Carl R. Woese Institute for Genomic Biology.
The researchers first tested their idea in tobacco plants because of the ease of transforming the crop’s genetics and the amount of seeds that can be produced from a single plant. These factors allow researchers to go from genetic transformation to a field trial within months. Once the concept was proven in tobacco, they moved into the more complicated task of putting the genetics into a food crop, soybeans.
“Having now shown very substantial yield increases in both tobacco and soybean, two very different crops, suggests this has universal applicability,” said Long. “Our study shows that realizing yield improvements is strongly affected by the environment. It is critical to determine the repeatability of this result across environments and further improvements to ensure the environmental stability of the gain.”
Additional field tests of these transgenic soybean plants are being conducted this year, with results expected in early 2023.
“The major impact of this work is to open the roads for showing that we can bioengineer photosynthesis and improve yields to increase food production in major crops,” said De Souza. “It is the beginning of the confirmation that the ideas ingrained by the RIPE project are a successful means to improve yield in major food crops.” ●
Amanda De Souza
Researchers worldwide have been working to improve water-use efficiency in crops to better cope with water-scarce conditions. In a recent study published in the Journal of Experimental Botany, a team from the University of Illinois, the Volcani Center (Agricultural Research Organization, Israel), and the University of Cambridge found that by overexpressing a sugar-sensing enzyme, called hexokinase, in field-grown tobacco plants, they could improve intrinsic water-use efficiency (iWUE) without decreasing photosynthetic rates or biomass production.
Tobacco was used as a model crop because it is relatively easy to work with within the laboratory, greenhouse and field. After showing success in the model crop, the researchers can then confidently mirror the developments in food crops, such as cassava, cowpea, rice, and soybean.
This study demonstrates the potential to generate plants with more conservative water-use throughout the growing season under field conditions and moderate water limitation, without significant yield penalty. For farmers, this could decrease soil water depletion throughout the growing season and reduce reliance on irrigation.
This work is part of Realizing Increased Photosynthetic Efficiency (RIPE), an international research project that aims to increase global food production by developing food crops that turn the sun’s energy into food more efficiently.
During photosynthesis, plants open tiny pores in their leaves, called stomata, to take in CO₂. However, when the pores are open, water is also allowed to escape through transpiration. This leaves plants with a trade-off between losing too much water for the sake of taking in CO₂.
“Stomatal pores consist of a pair of guard cells that control the opening and closure of the pores,” said Liana Acevedo-Siaca, who led this study at Illinois during her time as a postdoctoral researcher. “Previous studies have shown that genetic manipulation of signal elements that trigger stomatal movement, such as overexpressing Arabidopsis Hexokinase 1 (AtHXK1) in the guard cells, can stimulate stomatal closure and adjust that trade-off for plants.” Acevedo-Siaca now works as an associate scientist in the Global Wheat Program at the International Maize and Wheat Improvement Center (CIMMYT) in Mexico.
It was previously shown that guard-cell-targeted expression of AtHXK1 can improve WUE in crops, as well as their tolerance to drought conditions and salinity stress because hexokinase signals to the pores that there is enough sugar, eliminating the need to fix more CO₂. However, these previous studies were only evaluated in crops grown in controlled environments, such as greenhouses.
“To improve our understanding of the potential benefits of guard-cell-targeted AtHXK1, our study used two homozygous transgenic lines expressing AtHXK1 and a line that had guard-cell-targeted overexpression of AtHXK1 that were evaluated relative to wild-type field-grown tobacco to test WUE for traits related to photosynthesis and yield,” said Johannes Kromdijk, assistant professor at the University of Cambridge, who started this study in 2018. “Our results confirmed that constitutive overexpression AtHXK1 decreases productivity. We also showed that guard-cell-targeted overexpression of AtHXK1 could improve iWUE relative to wild-type without negatively impacting CO₂ assimilation. Still, this difference was strongly dependent upon leaf age, and recent rainfall could eliminate differences in performance.” ●
Nitrogen supply is frequently the second most limiting factor after water availability constraining crop growth and so there is great farmer demand for accessible sources of nitrogen, such as synthetic nitrogen in fertilizer. But there are still extensive areas in the world that cannot achieve food and nutrition security because of a lack of nitrogen.
New research co-authored by International Maize and Wheat Improvement Center (CIMMYT) scientists, published in Field Crops Research, posits that facilitating natural methods of gathering useable nitrogen in biological nitrogen fixation (BNF) can reduce the amount of synthetic nitrogen being used in global agriculture.
“This, together with increasing and changing dietary demands, shows that the future demand for nitrogen will substantially grow to meet the anticipated population of 9.7 billion people by the middle of the century,” said J.K. Ladha, adjunct professor in the department of plant sciences at University of California, Davis, and lead author of the study.
A farmer in the Ara district, in India’s Bihar state, applies NPK fertilizer.
Photo: Dakshinamurthy Vedachalam/CIMMYT
Before synthetic nitrogen, the primary source of agricultural nitrogen was gathered through BNF as bacteria living underground that convert atmospheric nitrogen into nitrogen that can be utilized by crops. Legumes are often employed as a cover crop in rotating fields to replenish nitrogen stocks; their root systems are hospitable for these nitrogen producing bacteria to thrive.
“There are ways in which BNF could be a core component of efforts to build more sustainable and regenerative agroecosystems to meet nitrogen demand with lower environmental footprints,” said Timothy Krupnik, senior system agronomist at CIMMYT in Dhaka, Bangladesh.
Plant scientists have often hypothesized that the ultimate solution for solving the ever-growing nitrogen supply challenge is to confer cereals like wheat, maize and rice with their own capacity for BNF. Recent breakthroughs in the genomics of BNF, as well as improvements in the understanding how legumes and nitrogen bacteria interact, have opened new avenues to tackle this problem much more systematically.
“Enabling cereal crops to capture their own nitrogen is a long-standing goal of plant biologists and is referred to as the holy grail of BNF research,” said P.M. Reddy, senior fellow at The Energy Research Institute, New Delhi. “The theory is that if cereal crops can assemble their own BNF system, the crop’s internal nitrogen supply and demand can be tightly regulated and synchronized.”
The study examined four methods currently being employed to establish systems within cereal crops to capture and use their own nitrogen, each with their advantages and limitations. One promising method involves identifying critical plant genes that perceive and transmit nitrogen-inducing signals in legumes. Integrating these signal genes into cereal crops might allow them to construct their own systems for BNF.
Besides the efforts to bring BNF to cereals, there are basic agronomic management tools that can shift focus from synthetic to BNF nitrogen. “Encouraging more frequent use of legumes in crop rotation will increase diversification and the flow of key ecosystem services, and would also assist the long-term sustainability of cereal-based farming system,” said Krupnik.
Growing cereal crops with less fertilizer Meanwhile, researchers at the University of California, Davis, have found a way to reduce the amount of nitrogen fertilizers needed to grow cereal crops.
The research comes out of the lab of Eduardo Blumwald, a distinguished professor of plant sciences, who has found a new pathway for cereals to capture the nitrogen they need to grow. The study was published in the journal Plant Biotechnology.
Eduardo Blumwald, right, of the UC Davis Department of Plant Sciences, with postdoctoral researcher Akhilesh Yadav, and rice they and others on the Blumwald team modified to use nitrogen more efficiently.
Photo: Trina Kleist/UC Davis
Blumwald’s research centres on increasing the conversion of nitrogen gas in the air into ammonium by soil bacteria — essentially, nitrogen fixation.
“If a plant can produce chemicals that make soil bacteria fix atmospheric nitrogen gas, we could modify the plants to produce more of these chemicals,” Blumwald said. “These chemicals will induce soil bacterial nitrogen fixation and the plants will use the ammonium formed, reducing the amount of fertilizer used.”
Blumwald’s team used chemical screening and genomics to identify compounds in rice plants that enhanced the nitrogen-fixing activity of the bacteria. Then they identified the pathways generating the chemicals and used gene editing technology to increase the production of compounds that stimulated the formation of biofilms. Those biofilms contain bacteria that enhanced nitrogen conversion. As a result, nitrogen-fixing activity of the bacteria increased, as did the amount of ammonium in the soil for the plants.
“Plants are incredible chemical factories,” he said. “What this could do is provide a sustainable alternative agricultural practice that reduces the use of excessive nitrogen fertilizers.”
The pathway could also be used by other plants. A patent application on the technique has been filed by the University of California and is pending. ●
New research from Cranfield and Nottingham Universities says that how we think about, measure and study soil must be changed to give a better understanding of how to manage this resource effectively, with academics proposing an entirely new approach for assessing soil health.
Jim Harris, professor of environmental technology at Cranfield University, led the research and said that although ‘soil health’ as a term is quite widely used now, “it is problematic as it means different things to different people, and there is no single agreed way to measure the overall health of this system. “Through this research, we want to start the conversation about how we move to a holistic picture of soil health assessment, looking at the interconnected elements of this universally important system,” he added. “Taking steps towards a bigger-picture view of soil health could help make a huge difference to some of our big challenges, not least the climate crisis.”
Current approaches measure individual soil properties and use these to try and assign a single number giving an overall soil health ‘score’, but the researchers argue this does not reflect the wider system perspective that’s needed to fully assess the condition of a soil and its health over time.
Dr. Daniel Evans, a 75th anniversary research fellow at Cranfield University who co-authored the paper commented: “Just as we don’t have a single measure or score for human health, because this can’t reflect the complexities of the whole body, we should not rely on a single score for soil health. Taking in a range of measures to look at the whole system will mean we can fully understand the direction of travel – is soil getting better, or worse?”
The researchers propose a whole system approach to assess soil health, based on a new hierarchical framework which takes in several measures, including Signs of Life (characterizing the organisms existing in soil), Signs of Function (the extent to which soils process materials), Signs of Complexity (the extent to which soil components are connected and interdependent) and Signs of Emergence (the extent to which soils respond and recover to multiple stressors).
Sacha Mooney, professor in soil physics at the University of Nottingham added, “This new approach can be applied to all soils and moves us closer to an interdisciplinary understanding of the ‘whole picture’ of the soil system, rather than separately considering the individual pieces of the jigsaw.”
Professor Harris continued: “It is hard to understate the importance of having a healthy soil system – it supports wildlife and biodiversity, reduces flood risks, stores carbon and gives us food security. Moving towards this new model of assessment is going to help land users and governments to sustainably manage our global soil resources for future generations.”
The research paper A new theory for soil health is published by the European Journal of Soil Science and was written by Professor J.A.Harris, Dr. D.L.Evans and Professor S.J.Mooney of the University of Nottingham. ●
Dr Daniel Evans
Jim Harris
The low nutrient content of martian soil and high salinity of water render them unfit for direct use for propagating food crops on Mars. But now, researchers have found that it is possible to grow food crops with alfalfa treated basaltic regolith martian soil as a substratum watered with biodesalinated water.
In the research article Farming on Mars: Treatment of basaltic regolith soil and briny water simulants sustains plant growth, published at PLOS One, researchers showed that alfalfa plants grow well in a nutrient-limited basaltic regolith simulant soil, and that the alfalfa biomass can be used as a biofertilizer to sustain growth and production of turnip, radish and lettuce in the basaltic regolith simulant soil.
Researchers also showed that marine cyanobacterium Synechococcus sp. PCC 7002 effectively desalinates the briny water simulant, and that desalination can be further enhanced by filtration through basalt-type volcanic rocks. ●
Growth of radish in alfalfa-treated (right) and untreated (left) basaltic regolith stimulant soil watered with fresh water.
A new MARPLE Diagnostics hub has been established at the Kenya Agricultural and Livestock Research Organisation (KALRO) in Njoro as part of a strategic expansion of the platform to improve global rust surveillance.
Researchers from the John Innes Centre and International Maize and Wheat Improvement Center (CIMMYT) launched the new Njoro hub by training 17 plant pathologists in the MARPLE pipeline. Participants comprised researchers from both KALRO and the PlantVillage Dream Team.
This new capability enables local researchers to identify yellow rust strains within two days of collecting samples, a process that previously took three to 12 months and was reliant on sending samples overseas. For the Njoro research station the training also represented a landmark moment, with the first ever gene sequencing taking place on site.
“Tracking the strains of rust in Kenya is incredibly important for Kenya itself but also for the wider region,” said Dave Hodson, CIMMYT rust pathologist Dave Hodson. “New dangerous rust races are arriving in East Africa and these are causing problems. Having rapid monitoring technology here in Kenya is important to get advanced early warning of new threats coming into the region so we can give timely, actionable advice to the Kenyan farmers how they can protect their crops.”
The Njoro hub marks the third of its kind globally, following the opening of the initial Ethiopian hub and a South Asian hub in Nepal during early 2022. KALRO Njoro
researchers will incorporate the platform into their ongoing rust monitoring while the Dream Team will connect the platform with their rust surveys across Kenyan farming areas.
MARPLE Diagnostics was developed by the Saunders Lab at the John Innes Centre in collaboration with CIMMYT. The project is currently funded by USAID through PlantVillage and BBSRC. ●
Researchers can identify rust strains within two days of collecting samples.
Photo: John Innes Centre
The Consortium for Precision Crop Nutrition (CPCN) has launched a global platform designed to drive international research collaboration and expand open access to crop nutrient data to farmers, their advisers and policy makers.
The online platform, powered by the Agmatix Insights solution and spearheaded by CPCN in collaboration with several leading research institutes, enables open access to essential crop nutrient concentrations data.
The platform, which comprises two active databases, serves as a critical open data resource for agricultural researchers and professionals who conduct field trials on soil fertility and crop nutrition. Enabling these users to both contribute to and benefit from the datasets, the platform has already resulted in a published paper that estimates nutrient use and storage in maize.
Developed in partnership with the International Fertilizer Association (IFA) and Wageningen University & Research (WUR), the first of the two databases looks at production and environmental factors affecting nutrient concentrations to determine the total amount of nutrients removed from the field in the harvested portion of the crop. This provides agronomists and farm advisers with the information needed to improve their plant nutrition plans, delivering key efficiencies and critical yield increases. Focused initially on nutritionally and industrially important crops, such as maize, wheat, rice and soybean, the Global Crop Nutrient Removal Database includes data on nutrient content, residues, crop yields and other associated data.
The second resource, The Nutrient Omission Trial Database, is focused on crop nutrient requirements. Created in collaboration with the IFA, the African Plant Nutrition Institute (APNI), and Innovative Solutions for Decision Agriculture, this database includes data from researchers and institutes around the globe. It aims to support site-specific recommendations on optimizing nutrient management by enabling researchers to compare crop nutrient requirements and plans.
The wide-scale provision of research data, enabled through both Global Crop Nutrient Databases, is set to advance scientific development of the sector. As well as being able to contribute data through the platform, researchers can use the datasets to perform meta-analyses, empowering deeper insights from their own data across different trial locations and fertilizer types. ●
Biologists have produced the first description of a calcium signal-controlled switch mechanism for adaptation to varying levels of salt stress
Biologists at the University of Münster (Germany) have now discovered, for the first time, that salt stress triggers calcium signals in a special group of cells in plant roots, and that these signals form a “sodium-sensing niche.” Also, the researchers identified a calcium-binding protein (CBL8) which contributes to salt tolerance specifically under severe salt stress conditions. The results of the study are published in the journal Developmental Cell.
Salt stress is caused by the accumulation of excessive salt concentrations in the soil. This inhibits plant growth and can ultimately lead to the plant dying. For this reason, plant researchers are interested in gaining a better understanding of salt stress in order to breed salt-tolerant plants.
Professor Jörg Kudla and his team at the Institute of Biology and the Biotechnology of Plants at Münster University studied the question of how plants measure the intensity of salt stress and how they react to it. The model plant they used for their tests was thale cress (Arabidopsis thaliana), which is a member of the largest group of flowering plants – the crucifers, or Brassicaceae. These include many food and forage plants such as cabbages, mustard and radishes.
Kudla said they examined Arabidopsis roots to see whether they had any type of cells that would react to salt stress, or whether the entire root would show a uniform reaction. “We also undertook investigations to see whether the intensity of the salt stress was reflected quantitively in the intensity of the calcium signal.”
The result surprised the experts: although the plant’s entire root system was exposed to stress, only a specific group of cells reacted – and only this group formed a so-called oligo-cellular calcium signal. This group of cells is located in the differentiation zone of the plant root and is formed by only a few hundred cells. Just for comparison: a root has many thousands of cells. Researchers call this area the “sodium-sensing niche.”
“This group of cells is not visible, and we can only distinguish them functionally from other cells by means of high-resolution biosensor technology,” noted Kudla. “It was a chance discovery which was extremely revealing – and significant.”
The reason is that it is in these functionally specialized cells that the primary calcium signal is formed.
In the process, the plant biologists found that the greater the level of salt stress, the stronger the calcium signal. In other words, the plant is able to provide information to the organism on the intensity of the encountered stress. This led to the question of how plant cells can distinguish between weak and strong calcium signals in order to be able to react accordingly. Generally, calcium signals are decoded by various calcium-binding proteins which act as calcium sensors.
In plants, this important task is often performed by the so-called CBL (calcineurin B-like) proteins. It has been known for some time that the CBL4 protein is important for salt tolerance, and that corresponding mutants without any functioning CBL4 protein are extremely sensitive to salt stress. In their work, the researchers discovered that mutants of a further CBL protein – CBL8 – also have reduced salt tolerance. However, cbl8 mutants – in contrast to cbl4 mutants – displayed growth inhibition only under severe salt stress. After carrying out biochemical analyses, the researchers found that a high calcium concentration activates the CBL8 protein – while the CBL4 protein is also active at lower concentrations of calcium.
“It is only under conditions of high salt stress that CBL8 helps to pump salt out of the plant,” explains Dr. Leonie Steinhorst, who was also involved in the study. “It is a kind of switch mechanism controlled by the concentration of calcium.”
One interesting aspect that the biologists discovered in this connection is the evolution of the CBL proteins. Most types of cereals – such as corn, wheat and barley – are so-called monocotyledons. They only have the CBL4 protein – in other words, they lack this switch mechanism for adapting to severe salt stress. There are also dicotyledons, such as tobacco and tomatoes, and it was possible to demonstrate in this case that gene duplication took place early in the evolutionary process and that CBL8 developed from this. As a result, these plants had a better opportunity to react to salt stress.
Looking to the future, “one interesting approach would be to introduce the CBL8 protein into monocotyledons so that they too can better adapt to salt stress,” said Kudla. “This is likely to be an increasingly important measure for plant breeders in the future in order to cope better with drought and salt stress.” ●
As an immediate reaction to elevated concentrations of salt, the concentration of calcium in the cytosol of a specific group of cells (the sodium-sensing niche) increases within one minute. Shown in false colours: red (highest concentration) > yellow > green > blue.
Photo: Jörg Kudla
The U.S.-based Soil Health Institute (SHI) recently announced its recommended measurements for assessing soil health.
These recommendations answer the No. 1 question about soil health that farmers, ranchers and their advisers have been asking since the soil health movement began.
With support from the Foundation for Food & Agriculture Research, The Samuel Roberts Noble Foundation and General Mills, the Soil Health Institute led a three-year, USD$6.5-million project to identify effective measurements for soil health across North America. SHI partnered with over 100 scientists at 124 long-term agricultural research sites in the U.S., Canada and Mexico where conventional management systems were compared with soil health-improving systems.
“This allowed us to evaluate over 30 soil health measurements at each site where they had the appropriate experimental design to allow us to come to the appropriate statistical conclusion about the effectiveness of each measurement,” said Dr. Wayne Honeycutt, president and CEO of the Soil Health Institute. “Evaluating each measurement across such a wide range of climates, soils, cropping systems and management practices also provided the scientific rigour we needed to identify which measurements could be widely used.”
The concept of soil health is basically about how well a soil is functioning. Such functions include cycling water, carbon and nutrients. Whether a heavy rain infiltrates into the soil or runs off the soil reflects how well that soil is functioning. Soil health can be improved through management, but farmers need practical, effective measurements for assessing the current status of their soil and evaluating progress at improving its health.
The Soil Health Institute found that many measurements are effective for assessing soil health from a research perspective.
“While this is good news for the science, we also wanted to identify a minimum suite of measurements that is practical and affordable for all land managers,” said Dr. Cristine Morgan, chief scientific officer of SHI, “so we also evaluated these measurements through the lens of cost, practicality, availability, redundancy and other filters.”
Based on these results, SHI recommends a minimal suite of three measurements to be widely applied across North America (and likely beyond). Those measurements include: 1) soil organic carbon concentration, 2) carbon mineralization potential, and 3) aggregate stability.
Soil organic carbon is a key component of a soil’s organic matter that influences available water holding capacity, nutrients, biodiversity, structure and other important soil properties. Carbon mineralization potential reflects the size and structure of microbial communities in soil, thereby influencing nutrient availability, soil aggregation and resilience to changing climatic conditions. Aggregate stability describes how strongly soil particles group together; this influences whether a heavy rainfall will infiltrate into a soil or run off a landscape, taking with it valuable nutrients that become detrimental to water quality. Soil aggregates also influence erosion, aeration, root growth and, therefore, nutrient uptake by plants.
While these three metrics provide a minimum suite of widely applicable measurements for assessing soil health, additional measurements may be included depending on the landowner’s or researcher’s objectives. “We have found that adding soil texture to this list of measurements allows us to calculate a soil’s available water holding capacity,” said Dr. Dianna Bagnall, research soil scientist with SHI. “We can then show a farmer how much more water they can store by increasing their organic carbon and improving soil health.” Because management does not change soil texture (sand, silt and clay), it only needs to be measured once.
Specific details on the underlying research and data analyses are described in several peer-reviewed publications and interpretive summaries. Additional manuscripts are currently in peer-review. ●
Researchers at Stanford University (U.S.) are working on ways to manipulate biological processes in plants to help them grow more efficiently and effectively in a variety of conditions.
Jennifer Brophy, an assistant professor of bioengineering, and her colleagues have designed a series of synthetic genetic circuits that allow them to control the decisions made by different types of plant cells.
In a paper published recently in Science, they used these tools to grow plants with modified root structures. Their work is the first step in designing crops that are better able to collect water and nutrients from the soil and provides a framework for designing, testing, and improving synthetic genetic circuits for other applications in plants.
“Our synthetic genetic circuits are going to allow us to build very specific root systems or very specific leaf structures to see what is optimal for the challenging environmental conditions that we know are coming,” Brophy said. “We’re making the engineering of plants much more precise.”
Current genetically modified crop varieties use relatively simple, imprecise systems that cause all of their cells to express the genes necessary to, say, resist herbicides or pests. To achieve fine-scale control over plant behaviour, Brophy and her colleagues built synthetic DNA that essentially works like a computer code with logic gates guiding the decision-making process. In this case, they used those logic gates to specify which types of cells were expressing certain genes, allowing them to adjust the number of branches in the root system without changing the rest of the plant.
The depth and shape of a plant’s root system affect how efficient it is at pulling different resources out of the soil. A shallow root system with many branches, for example, is better at absorbing phosphorus, while a deeper root system that branches at the bottom is better at collecting water and nitrogen. Using these synthetic genetic circuits, researchers could grow and test various root designs to create the most efficient crops for different circumstances. Or, in the future, they could give plants the ability to optimize themselves.
“We have modern varieties of crops that have lost their ability to respond to where soil nutrients are,” said José Dinneny, an associate professor of biology in the School of Humanities and Sciences and one of the lead authors on the paper. “The same sort of logic gates that control root branching could be used to, say, create a circuit that takes into account both the nitrogen and phosphorus concentrations in the soil, and then generates an output that is optimal for those conditions.”
Brophy designed more than 1,000 potential circuits to be able to manipulate gene expression in plants. She tested them in the leaves of tobacco plants, seeing if she could make the leaf cells create a glow-in-the-dark protein found in jellyfish. She found 188 designs that worked, which the researchers are uploading to a synthetic DNA database for other scientists to be able to use in their work.
Once they had working designs, the researchers used one of the circuits to create logic gates that would modify the expression of a specific developmental gene in a precisely defined type of root cell of Arabidopsis thaliana, a small, weedy plant that is often used as a model organism. By changing the expression level of that one gene, they were able to modify the density of branches in the root system.
Now that they’ve demonstrated that they can change the growth structure of a model organism, the researchers intend to apply these same tools to commercial crops. They’re investigating the possibility of using their genetic circuits to manipulate root structure in sorghum, a plant that can be refined into biofuel, to help it absorb water and perform photosynthesis more efficiently. ●
Synthetic genetic circuits designed to rewire gene expression in plant roots may be used to change the way they grow.
Image: Jennifer Brophy
Worms improve soil structure and help plants obtain nutrients and phosphate. But some worms do a better job than others.
Hannah Vos, with Wageningen University & Research, obtained her PhD on research on which worms are better at providing this service. And on the fly, she also discovered why this works so well in ferrous soils.
Vos focused on worms that are vital to grasslands. In an extensive field experiment, two of the five worms she studied (Aporrectodea longa and Lumbricus terrestria) appeared the most proficient in delivering the available (inanimate) phosphate to the plant. These two worms alone increased the phosphate levels in the grass by as much as 20 percent in some cases.
But the diversification in the results was considerable, noted Vos, adding this can be explained by the fact the field experiment was impacted by the dry summers of 2018 and 2019. “And, added to that, there was an ant plague. There was an ant nest in nine out of my 90 testing pots,” she said. “The ants attack the worms, which means there was quite some variation in my results.”
Phosphate in the soil can be made available to the plants through mineralization. Worms transform phosphates in organic compounds into minerals. The greater part of this inanimate phosphate is included in soil particles. Only a tiny fraction is directly available for the plants.
“In my field experiment, I used a single type of soil, which was not a type dominated by iron-oxides,” noted Vos, who discovered why worms in ferrous soils are better able to make phosphates available for the plant. The metal oxides in the soil increase to larger particles in the worm’s stomach. This reduces the total surface of metal oxides and, with it, the options to bond the
phosphate. The phosphate is thus released in suspension.
The newly discovered mechanism only works in ferrous soils. Calculations in models show the effect is considerably greater than, for example, the effect of soil acidity or the presence of organic substances in the soil and comparable to the worms’ capacity to mineralize organic phosphate.
How significant the ‘Vos-effect’ is under field conditions is yet to be determined. “In my field experiment, I used a single type of soil, which was not a type dominated by iron-oxides,” she said, adding the fact that two worm species still managed to release more phosphate is because these worms have a greater capacity to mineralize organic phosphate.
Earthworms cannot simply replace (artificial) fertilizers. “But my research shows that certain worms have potential in certain soils,” said Vos. “They are essential for the availability of phosphates, and we must take good care of these little creatures.” ●
Hannah Vos
