Climate change is forcing agriculture to break new ground. In future, crops must be able to cope better with drought and become more resistant to pathogens. Plant scientists at the CEPLAS Cluster of Excellence are focussing on genetic optimization. But they also show that the right fungi and bacteria are essential for plants to thrive. 

Jan Voelkel

This is quite the opposite of diversity: We get around forty per cent of our plant-based calories from just three crops. Wheat, maize and rice have become indispensable for people around the world. They are an integral part of our diet, are used to feed animals and produce energy or for medical products. That it is risky to rely so heavily on the ‘big three’ has recently become clear. The world market was significantly affected by the outbreak of war in Ukraine and the blockade of grain exports from the country. After all, Ukraine is an important player in the international wheat trade with a share of around eight per cent. Devastating periods of drought in Africa have also led to a collapse in the wheat harvest.

Globally, farm land, water and nutrients are becoming scarce and the climate is changing. At the same time, the world’s population is growing. In this situation, new strategies are needed to improve the yield and quality of crops and conserve existing resources. This is the only way to ensure a sustainable supply of plant-based food and raw materials for future generations. Understanding the basic genetic mechanisms of plants could be the way forward.

“I'm interested in understanding how plants adapt to their environment,” said Professor Dr Markus Stetter from the Institute for Plant Sciences. “When and for how long does a plant flower, or how does it cope with stress? Which genes are involved?” Stetter is a member of the CEPLAS Cluster of Excellence, in which scientists are investigating how plants adapt to changing environmental conditions, how they colonize almost every habitat on earth and how this knowledge can be used in agriculture. His main focus in on cultivated plants. “Take maize as an example: It is now available all over the world, but its wild ancestor was only found in central Mexico. Within a very short time, maize has come to adapt so that it can cope with a wide range of conditions. This allows us to see how cultivated plants have evolved in time-lapse,” said Stetter. 

Undemanding pseudocereal

This is precisely what the scientists in Stetter’s working group are interested in: tracing the change from wild to cultivated plants, how they have spread around the world and what significance these findings can have for new, more stress-tolerant breeds. In addition to maize, Stetter and his colleagues focus on one plant in particular: Amaranth, often found in puffed form as a ‘superfood’ in organic supermarkets, is a magnificent plant. It grows over a metre high and produces bright purple flowers and leaves.

Amaranth has been cultivated as a crop for around 8,000 years. It is very resistant to heat and drought, requires relatively little water and its grains contain many proteins. In addition, amaranth is not a real grain, but a so-called pseudocereal and is therefore gluten-free. It could thus play an important role in securing global food security in the future. However, amaranth has not yet undergone many of the human-made changes typical of cultivated plants. It produces relatively small seeds that fall down instead of remaining attached to the panicle. What may be advantageous for the wild plant to spread is  unfavourable for a cultivated plant that is intended to be harvested. This could be the starting point for future breeding programmes. 

Another interesting fact for the scientists is that, unlike maize, amaranth was domesticated three times independently – twice in Central America and once in South America. “This means we can look at an 8,000-year selection experiment in different regions of the world. We are investigating whether evolution is always the same or different. Ultimately, we are deciphering the genetic code and finding out how to switch genes on and off correctly so that the result is something that actually works,” said Stetter, who recently received the prestigious ERC Starting Grant from the European Research Council for his work.
Even though some amaranth plants grow and flower in the greenhouse at the Institute for Plant Sciences, Stetter’s team is mostly busy sequencing genomes on the computer. Amaranth has a relatively small genome with ‘only’ 500 million base pairs. In comparison, maize is a true genetic giant with 2.3 billion base pairs per plant. “We scan the genome of thousands of individuals of the plant ten to a hundred times,” said Stetter. From this genetic code, the scientists can decode and trace the history of populations. “The code helps us to understand how and under what conditions certain traits develop and which populations adapt well to specific locations due to certain genetic principles. In this way, our results can support targeted breeding.” 

In order to make agriculture sustainable, we need plants that deliver a good yield or a high protein content and lots of nutrients even under poor conditions. “New crops that are particularly adaptable or resilient in the face of climate change can make an important contribution to food security,” emphasized the scientist. In addition, pests and pathogens need to be better understood because they also adapt to their environment and occupy specific niches. “If we understand how pathogens work and how some plants protect themselves, this can also be useful for other plants.”

Microbes are the key factor 

Professor Dr Alga Zuccaro, one of Stetter’s colleagues at CEPLAS, pursues this line line of reseach. She aims to make plants more resistant to pathogens. However, her main focus is on the soil microbiota, i.e. the entirety of small organisms, particularly on those that interact with the plant through the roots. “In the end, we both want to understand how plants react to stress. Markus Stetter investigates this using a specific plant. My research group explores how microbes influence the immune response of various plants to biotic and abiotic stress,” explained Zuccaro.

While some microbes cause disease, others can be beneficial to the plants. They can increase plant growth in nutrient-poor environments and improve their resilience to pathogens. How exactly the interaction between the microbiota and the plant works is complex and not yet well understood. However, recent findings show that the soil microbiota is an important factor for agriculture and plant breeding. Zuccaro sees great potential here: “If we let plants grow in a nutrient-poor environment without microbes, they hardly grow at all and can even die. However, if microbes are present in the soil that interact with the plant, they survive despite the nutrient-poor environment. Our results show that microbes play a key role.”

Research into plant diseases has so far been dominated by the so-called disease triangle model. It states that the course of a disease depends on three factors: a susceptible host, contact with a potential pathogen and environmental conditions such as temperature or water availability. Depending on how these factors interact, a plant can defend itself against the pathogen and continue to grow, or it can be infected and wither away. “However, this model does not take the soil microbiota into account. All the small organisms – fungi, bacteria and other beneficial organisms – that have an influence on the plants,” said Zuccaro. 

When attacked by pathogens, plants are able to actively recruit beneficial microbes to fight them. “It’s practically a cry for help,” explained the scientist. The plant’s immune system also tries to fight the pathogens. “Our research has allowed us to extend the established disease triangle to include the influence of the soil microbiota,” said Zuccaro.

This concept also explains why the plant’s immune system has not developed elaborate protection for every pathogen: In a healthy soil environment, this is often not necessary because the pathogen has to overcome not only the immune system but also the microbiota. “This changes our understanding of evolution. We can’t just focus on pathogens and plants, we have to include the microbiota. This is what our research is all about,”explained the researcher.

The practical significance of these findings can be illustrated using a plant that plays a major role in Zuccaro’s research: barley. In Europe, around fifty per cent of the barley varieties grown are mildew-resistant thanks to mutation breeding. The resistant phenotype is the result of deactivating the MLO gene. This deactivation prevents the mildew fungus from infecting the barley leaves. “The question has always been: Why have the plants not lost this gene through evolution if it brings the great advantage of resistance? The answer is that there is a downside to it,” said Zuccaro. 

The loss of the MLO gene also means that the barley can no longer recruit helpful soil fungi as effectively, which help it to grow and absorb nutrients. In agriculture, nitrogen and phosphate are used to fertilize fields, which reduces the need for interaction with these beneficial microbes. Under these conditions, the advantage of immunity to mildew with a deactivated MLO gene predominates. However, this is not the case in the wild, without added fertilizers.

Less artificial fertilizer in agriculture 

The researchers’ aim is to disseminate this knowledge of soil microbes and use it to breed resistant plants that are nevertheless able to recruit beneficial organisms. Mildew, for example, is a pathogen of the leaf. But the beneficial interaction with the microbes takes place in the roots of the barley. “You could therefore breed plants in which the MLO gene is inactive in the leaves to achieve resistance to mildew, while it remains active in the roots to enable interaction with the microbes,” Zuccaro described the new approach. This would reduce the need for nitrogen, phosphate and pesticides. “We are trying to make breeders aware of the positive role of microbiota.” 

In industrialized world regions like Europe, such an approach may seem unnecessary because it is possible to fertilize the fields every year. However, this is not always the case in other parts of the world. Both Zuccaro and Stetter therefore agree that the findings of their plant research point the way to solutions that are important on a global scale and can also work in times of major environmental change. Another problem in many places is the over-fertilization of soils caused by industrialized agriculture. It is necessary to fully understand the various factors – the breeding, the knowledge of the importance of diverse and new crops or the interaction of all soil organisms – to achieve a more sustainable and holistic agriculture.

THE CEPLAS CLUSTER OF EXCELLENCE IN PLANT SCIENCES 
CEPLAS is a joint initiative of Heinrich Heine University Düsseldorf and the University of Cologne. The scientific goal is to research the fundamentals and interplay of complex plant traits that influence a plant’s adaptation to limited resources and yield. The results are used to develop and breed crops that can react predictably to future challenges. In addition to the Universities of Düsseldorf and Cologne, the Max Planck Institute for Plant Breeding Research and Forschungszentrum Jülich are also part of CEPLAS.