Scientists have accomplished a key step in the long-term ambition to engineer nitrogen-fixation into non-legume cereal crops by demonstrating that barley can instruct soil bacteria to convert nitrogen from the air into ammonia fertiliser.

This development empowers non-legume crops to communicate directly with nitrogen-fixing bacteria and takes us a step closer to reducing our reliance on synthetic fertilisers.

The world’s human population consumes more than half their calories from three crops – rice, wheat and maize. However, these crops rely heavily on the application of synthetic fertilisers like nitrogen. The industrial production of nitrogen in the form of ammonia requires a high consumption of fossil fuels and the over-application of fertilisers can also leach into water bodies and release potent greenhouse gases into the atmosphere.

With the Earth’s atmosphere made up of 78% nitrogen, wouldn’t it be great if plants could convert the nitrogen in the air into their own fertiliser? Well they can.

Legumes produce their own nitrogen fertiliser by partnering with naturally occurring rhizobia soil bacteria. The bacteria fix nitrogen from the air into ammonia, which they exchange with plants for sugars.

Professor Giles Oldroyd, who leads research into sustainable crop nutrition at the University of Cambridge’s Crop Science Centre and Sainsbury Laboratory, is coordinating a global effort to transfer the nitrogen-fixing ability of legumes into non-legume cereals so that crops like wheat, maize and rice can, in effect, make their own fertiliser.

“Analysing the genetics of both legume and non-legume plants, we have discovered that non-legumes already have many of the genes needed to form the root nodules that house the nitrogen-fixing bacteria, Professor Oldroyd said. “There is substantial overlap in the developmental programmes plants use for lateral roots and nitrogen-fixing nodules. Studying the evolution of plant genes also indicates that many non-legumes did once form symbiotic relationships with nitrogen-fixing soil bacteria but have lost this ability over time.”

There are hundreds of processes involved in successfully establishing nitrogen-fixing symbiosis between a plant and its colonising bacteria – both from the plant and bacteria perspective – which is why it requires the collaboration of multiple teams of scientists to work on the problem. A collaboration between Professor Oldroyd’s group and the University of Oxford and Massachusetts Institute of Technology (MIT) is working on one key part – the intimate communication between the plant and bacteria.

Their latest work, published in the journal Proceedings of the National Academy of Sciences, builds on their earlier design and engineering of a unique molecular dialogue between plants and bacteria. The synthetic signalling network they developed uses rhizopine compounds as chemical signals, which act like an intimate language that is only understood by the target plant and target bacteria.

The have now shown that the non-legume crop plant, barley, can communicate directly with free-living nitrogen-fixing bacteria using rhizopine chemical signals to tell the bacteria to start fixing nitrogen from the atmosphere and to turn it into ammonia.

Dr Ponraj Paramasivan, from Professor Oldroyd's group and who contributed to the engineering of barley to synthesise and then exude rhizopine from its roots, said this was a key advantage as only the target crop would benefit. “Currently weeds also benefit from applying nitrogen fertilisers, but this tactic means that only the specific crop plant that is engineered to produce the rhizopine signal will benefit,” he said.

The research, led by Dr Timothy Haskett and Professor Philip Poole, at the Department of Plant Sciences, University of Oxford, showed that plants secreting rhizopine controlled nitrogen fixation by the bacterium on its roots. The bacteria would only fix nitrogen on the barley which released rhizopine and not on any other plant.

The next step is to ensure that the ammonia produced by the bacteria is released and provides sufficient nitrogen fertiliser to the target plant.

'Biological nitrogen fixation is one of the key processes enabling more sustainable agricultural practices and has been the subject of extensive research efforts for decades,” Professor Poole said.” This work on developing plant control of bacterial nitrogen fixation is a key part of a large effort to transfer root nodulation and nitrogen fixation to cereals. This was only made possible through a great collaborative effort bringing together the work done by multiple labs over many years.”

Professor Oldroyd said other staple crops such as maize, rice, sorghum and cassava would be included in future research for transferring nitrogen fixation into non-legumes.

Reference

Timothy L. Haskett, Ponraj Paramasivan, Marta D. Mendes, Patrick Green, Barney A. Geddes, Hayley E. Knights, Beatriz Jorrin, Min-Hyung Ryu, Paul Brett, Christopher A. Voigt, Giles E. D. Oldroyd, and Philip S. Poole. (2022) Engineered plant control of associative nitrogen fixation. PNAS

The trial will evaluate whether enhancing the natural capacity of crops to interact with common soil fungi can contribute to more sustainable, equitable food production

A field trial of genetically modified and gene edited barley is due to be planted this April. The research is evaluating whether improved crop interactions with naturally occurring soil fungi promote more sustainable food production.

Scientists are hopeful that the results from the trial will demonstrate ways to reduce the need for synthetic fertilisers, which could have significant benefits for improving soil health while contributing to more sustainable and equitable approaches to food production.

The trial is being conducted by researchers at the Crop Science Centre, an alliance between the University of Cambridge and NIAB. It will evaluate whether improving crop interactions with naturally occurring soil fungi can help them more efficiently absorb water along with nitrogen and phosphorous from the soil. Nitrogen and phosphorous are two essential nutrients critical to crop production that are often provided through synthetic fertilisers.  

While the use of synthetic fertilisers increases crop productivity, excessive applications in high and middle-income countries has caused environmental pollution that reduces biodiversity, as well as producing greenhouse gas emissions. Meanwhile, in low-income countries, fertilisers are often too expensive or unavailable to local farmers, which limits food production. That contributes to both hunger and poverty, because in regions like sub-Saharan Africa, most people depend on farming to support their families.

“Working with natural and beneficial microbial associations in plants has the potential to replace or greatly reduce the need for inorganic fertilisers, with significant benefits for improving soil health while contributing to more sustainable and equitable approaches to food production,” said Professor Giles Oldroyd, Russell R Geiger Professor of Crop Science, who is leading the work.

He added: “There is an urgent need for ecologically sound approaches to food production that can satisfy the demands of a growing global population while respecting limits on natural resources. We believe biotechnology can be a valuable tool for expanding the options available to farmers around the world.”

The trial will evaluate a barley variety that has been genetically modified to boost expression levels of the NSP2 gene. This gene is naturally present in barley and boosting its expression enhances the crop’s existing capacity to engage with mycorrhizal fungi.

In addition, the trial will test varieties of barley that have been gene edited to suppress their interaction with arbuscular mycorrhizal fungi. This will allow scientists to better quantify how the microbes support plant development by assessing the full spectrum of interactions. They will measure yield and grain nutritional content in varieties with an enhanced capacity to engage the fungi and those in which it has been suppressed--while comparing both to the performance of a typical barley plant.

Professor Oldroyd said: “Barley has properties that make it an ideal crop for studying these interactions. The ultimate goal is to understand whether this same approach can be used to enhance the capacity of other food crops to interact with soil fungi in ways that boost productivity without the need for synthetic fertilisers."

The trial will assess production under high and low phosphate conditions. It will also investigate additional potential benefits of the relationship with mycorrhizal fungi, such as protecting crops from pests and disease.

The trial will follow the regulations that govern the planting of genetically modified crops in the UK, with oversight conducted by Defra and its Advisory Committee on Releases to the Environment (ACRE.) There will also be inspections during the trial, carried out by the Genetic Modification Inspectorate, which is part of the UK’s Animal and Plant Health Agency. The inspection reports will be publicly available.

Read our FAQ's on this field trial by clicking on this link https://www.cropsciencecentre.org/news/frequently-asked-questions-about-gm-field-trials

Update: the harvest of the GM barley in the field

Talking immediately after this barley was harvested, on September 1, 2022, our field trials co-ordinator, Dr Tom Thirkell, reflected the following:

“Record-breaking warm, dry weather through July and August this year meant the crop ripened much quicker than we expected. This is mixed news; good because we don’t have to wait until later in the year when wetter weather could make the harvest tricky, but yields may be slightly reduced by the shorter growing season.

Yield data from the harvest will add to datasets collected throughout the season, including canopy height, leaf chlorophyll content, tiller number and the extent of arbuscular mycorrhizal fungal growth in the roots and soil of trial plots.

Grain from this trial is now being prepared for nutrient analysis. This will allow us to see how the beneficial symbiosis with arbuscular mycorrhizal fungi in the soil affected the uptake of phosphorus, nitrogen, and other important minerals into the grain. This trial was the first time these genotypes had been grown in the field, so every step along their growth and development was a milestone.

Despite of the unusual weather, the plants have performed well in the field, and we are excited to continue more trials in the years to come.”

Why are these field trials important?

Agricultural fertilisers contain sources of phosphorus and nitrogen that promote crop production, but their use leads to significant pollution that negatively impacts biodiversity, as well as causing greenhouse gas emissions. In low-income countries farmers often lack the financial resources to buy synthetic fertilisers and this limits their crop productivity. It is important to find alternatives to synthetic fertilisers in order to achieve sustainable crop production for all the world’s farmers.

Why are arbuscular mycorrhizal fungi important to crops?

Most plants, including cereal crops, engage in symbiotic interactions with beneficial arbuscular mycorrhizal fungi, which form highly branched structures in root cells, called arbuscules, for nutrient exchange with the plant. Arbuscular mycorrhizal fungi help plants to capture nutrients from the soil, including sources of phosphorus and nitrogen, as well as water, that are critical to support plant growth. Furthermore, these interactions increase resistance to plant diseases, as well as tolerances to many stresses, including drought and salt.

What is being tested in the field?

The barley lines in this field trial already have been studied extensively in laboratories and glasshouses. Researchers are in the process of publishing the results from these studies. They are now proposing to test the plants in the field, to find out if enhancing their capacity to engage arbuscular mycorrhizal fungi is maintained under typical farming conditions—and in ways that can reduce the need for synthetic fertilizers. Researchers will be assessing how the plants perform in terms of their yield and biomass as well as plant-susceptibility to pests and pathogens. The goal is for the genetically modified crops to contribute to efforts to sustainably boost crop productivity, helping farmers to meet rising food demands and combat hunger while also reducing agriculture’s contribution to climate change and biodiversity loss.

Why focus on barley?

Barley grows in 100 countries and is one of the most commonly used cereal grains after wheat, corn, and rice. It is a cereal that is easy to work with and in these trials the impact of overexpressing NSP2 is being assessed in barley, with the expectation that if it works in barley it can be developed in other cereal crops, if the current field trials show promising results.

Can organic farming methods alone provide the same benefits?

The impact that mycorrhizal fungi have on crop nutrition, biomass and yield is largely determined by the crop genotype, rather than levels of mycorrhizal fungi in the soil.

The principles of regenerative agriculture, or organic farming have an important role in increasing soil health by reducing soil disturbance and chemicals that reduce the abundance of mycorrhizal fungi in soils and plant roots. However, the impact of these practices will be limited unless combined with innovations in crop genetics to help crops respond more positively to mycorrhizal fungal colonisation.

What is the difference between GM and gene-editing?

Genetic modification is the process of introducing extra DNA into the plant, adding one or a small number of additional genes to a plant’s complement of several tens of thousands of genes.

Genetic editing is the technique of making small changes to a precisely targeted gene that is already present in the plant. The final gene edited plant does not carry additional genes.

Why is there a need to carry out this research in the UK?

The UK has world-class plant scientists who are at the forefront of developing scientific and technological advances that can make agriculture more sustainable. Plant biotechnology has become an established approach to improve plant breeding in many parts of the world, and genetically modified crops have been grown commercially since 1994, with large-scale cultivation of genetically modified field crops starting in 1996. It is important that the UK maintains its expertise in these technologies and explores their potential contribution to sustainable food systems.

How will the trial be regulated?

There are rigorous regulations that govern the planting of genetically modified crops in the UK, overseen by the Department for Environment, Food & Rural Affairs (Defra) and its independent Advisory Committee on Releases to the Environment (ACRE.) This includes inspections during the trial, carried out by the Genetic Modification Inspectorate, which is part of the UK’s Animal and Plant Health Agency. The ensuing inspection reports are made publicly available.

Is there a risk of cross-pollination with local wild plants or crops?

Barley is a self-pollinating crop with very low rates of cross-pollination with other barley plants. Nevertheless, the outer edge of the trial will have a 3-metre-wide strip of conventional barley to function as a buffer to reduce escape of pollen outside of the trial. In addition, no barley, other cereals, or grasses will be cultivated or allowed to grow within 20 metres of the trial.

Will the grains from the genetically modified plants be consumed?

In accordance with regulations governing the testing of genetically modified crops, the plants and seeds arising from this trial will not enter the food or feed chains.

What is the size of the trial?

The area of the proposed trial, including the barley pollen barrier, will be no more than 2100 square metres, which is around one fifth of a hectare.

What are the genes that have been modified in the barley varieties proposed for the field trial?

Scientists are seeking permission from Defra to field test a variety of barley modified to “overexpress” a naturally occurring gene native to barley called NSP2, which controls barley’s interactions with arbuscular mycorrhizal fungi. The application to Defra also requests permission to conduct a trial at a later date with a variety of barley modified with NSP2 from a common ground cover legume plant known as Medicago truncatula.

Previous research has shown that overexpression of NSP2 promotes beneficial interactions with arbuscular mycorrhizal fungi in ways that could help crops more efficiently absorb nitrogen and phosphorous from the soil without the need for fertilizers or allow farmers to greatly reduce fertilizer usage.

Scientists also want to study whether this improvement prompts the barley to engage the fungi even in soils that contain high concentrations of phosphorus, which can happen when fields are heavily fertilized. In conventional crops, heavily fertilized soils suppress or completely shut down plant interactions with arbuscular mycorrhizal fungi. But there is evidence that overexpression of NSP2 in the genetically modified barley plants could encourage interactions with the fungi in many types of field conditions. For example, in fields that have been excessively fertilized, engaging the fungi could lead to more efficient fertilizer uptake, which could reduce run-off that pollutes waterways.

Will independent experts and the public be consulted?

As part of the statutory process co-ordinated by the Department for Environment, Food & Rural Affairs (Defra), there is a period of public consultation before a decision is made on whether the field trial can go ahead. Any concerns will be considered by the independent experts of ACRE, the Advisory Committee on Releases to the Environment.

ACRE is a statutory advisory committee appointed under section 124 of the Environmental Protection Act 1990 to provide advice to government regarding the risks to human health and the environment from the release of genetically modified organisms (GMOs).

Will the knowledge gained from this trial be accessible to the public?

Yes. If approved, the results of the field trial will be published after peer review in appropriate scientific journals and using the open access model, where the papers are free for anyone to download. We will also disseminate data and new knowledge through presentations at scientific conferences.

What is the process of approval for research using genetically modified crops and microbes?

If a research project requires experimentation using genetically modified crops, approval from Defra is required. We must carry out a full risk assessment of the project, which is scrutinised by the institute’s own Biosafety Committee and other experts in-house, and then apply to Defra. In the application, we describe the nature of the experiment, the type of plant material and the specific genetic modifications we have carried out. We are also required to assess the risks to human health and the environment. The application becomes publicly available on the Defra website and the application is independently assessed by ACRE. Once the review of the risk assessment has been carried out, ACRE make their recommendation to Defra, which considers it along with any public representations that the department has received. Defra then decides whether to grant consent to conduct the field trial, and whether to impose specific conditions.

Will the consultation process for this trial be impacted by the new UK government rules on gene editing research?

On 20 January, the UK government announced new legislation will be put in place to reduce restrictions around gene-editing research. The legislation will therefore make it easier for scientists to conduct trials that seek to develop more sustainable, resilient and productive crops. Safety standards and transparency remain as before, with all scientists undertaking research of this kind obliged to notify the Department for Environment, Food and Rural Affairs (Defra) of any such trial.

The defence mechanism used by some specific resistant Heinz tomato hybrid cultivars to the destructive parasitic plant Cuscuta campestris, known as field dodders, has been discovered by Min-Yao Jhu, who is currently based at the Crop Science Centre, and her colleagues at UC Davis Sinha Lab.

 Published at the end of January in the journal Plant Physiology, this research could provide a foundation for investigating multilayer resistance against Cuscuta species. The study also has the potential for application in other essential crops attacked by parasitic plants.

 Lead author Dr. Min-Yao Jhu said “We discovered that the stem cortex in these resistant tomato cultivars responds with local lignification upon C. campestris attachment, preventing parasite entry into the host. We also identified four regulators that confer host resistance by regulating lignification.”