Understanding and shaping the root habitat

Fertile soils are the most important prerequisite for the sustainable production of plant biomass and therefore form the basis of many bioeconomic value chains. You can find detailed information on the structure and functions of soil and the sustainable use of this indispensable resource in our topic dossier Soil – the basis for sustainable economic activity (only available in German).

Rhizosphere – hotspot of biological activity and metabolic activity

The most biologically active part of the soil is the rhizosphere. At the intersection between soil, plants and soil organisms, processes take place that influence growth, nutrient uptake and the tolerance of plants to biotic and abiotic stress. Understanding and even controlling these processes harbours enormous potential for sustainable agriculture.

Roots release metabolic products

In addition to anchoring the plant in the soil, the main tasks of the root are to absorb and transport water and mineral salts. They also serve the plant as a reservoir and enable it to make contact with living organisms in the soil. Various plant metabolic products are excreted via the roots. The release of organic compounds into the soil is known as exudation.

Root exudates include sugars, amino acids, organic acids, phytohormones and enzymes. Plants release these compounds to influence the physical, chemical and biological properties of the rhizosphere in their favour. Organic acids, for example, change the pH value of the soil and play an important role in making minerals such as phosphorus available.

Root exudates and soil organisms

The many organic compounds that plants supply to the soil make the rhizosphere a hotspot for the activity of soil organisms – the edaphon. The most important soil inhabitants include microorganisms such as bacteria, archaea, fungi and invertebrates such as worms and insects. They are involved in the decomposition and conversion of organic matter in the soil and contribute to long-term soil fertility with their metabolic activity.

Root exudates play an important role in the dialogue between roots and soil organisms. Plants use exudates to attract beneficial microorganisms or stimulate their activity. Exudates also serve as a defence against harmful microorganisms, parasitic plants or invertebrate herbivores. Certain microorganisms, in turn, can stimulate root exudation through their own excretions.

Root symbioses

Root exudates also initiate the symbiotic relationships of plants with certain soil organisms. These fungi and bacteria bind nutrients that are essential for plant growth, such as nitrogen, phosphorus and potassium. They make them available to the plant and exchange them for carbohydrates produced by photosynthesis. The best-studied root symbioses are those between plants and arbuscular mycorrhizal fungi, as well as between legumes and certain soil bacteria – the rhizobia, or nodule bacteria.

Rhizobia penetrate plants such as legumes via the root hairs and small nodules form on the roots. They are colonised by the bacteria and create a favourable environment for bacterial nitrogen fixation. The bacteria bind elementary nitrogen from the air and reduce it to ammonia or ammonium. Plants require nitrogen to grow; the bacteria make it available to them. This is why legumes are generally independent of nitrogen fertilisers. The plants themselves are even used as so-called ‘green fertilisers’ to enrich soils with bound nitrogen.

Around 80 % of land plants live in interdependence with arbuscular mycorrhizal fungi. This makes arbuscular mycorrhiza the most widespread symbiosis in the plant kingdom. The mycorrhizal fungi colonise the plant roots and form a hyphal network in the soil. They use this to collect water and mineral nutrients such as phosphorus and nitrogen from the soil and transport them to the plant roots.
In return, they obtain sugar and lipids from photosynthesis. The arbuscular mycorrhiza helps crops to produce better yields, makes them more resistant to drought and, for reasons that are as of yet unexplained, also more resistant to disease.

In addition to nodule bacteria, there are other bacteria in the rhizosphere that promote plant growth and plant health. They also belong to the group of plant growth-promoting rhizobacteria (PGPR). For example, some produce phytohormones that stimulate plant development or enzymes that break down fungal cell walls and thus protect against harmful pathogens.

Fertile soils are an increasingly scarce resource. Due to increasing drought, large parts of southern Europe are already threatened by desertification. The growth of cities is also leading to ever greater soil sealing. In the past, the primary goal of agriculture was to increase yields. This contributed above all to food security, but led to misguided developments in agricultural practice, the consequences of which are becoming increasingly apparent today.

One example is the excessive use of mineral fertilisers: these can contribute to soil acidification and affect the composition and function of the soil microbiome. This also disrupts the formation of root symbioses. Without the protective microorganisms, plants become more susceptible to disease and more sensitive to environmental stress. Over-fertilisation can also reduce root growth because plants put more energy into the above-ground parts of the plant. Some pesticides used to control fungi also have a negative effect on root symbioses. They have been shown to reduce the occurrence and diversity of arbuscular mycorrhizal fungi.

Complex habitat – complex research

Over the past two decades, researchers have increasingly worked on developing innovative approaches to tackle these problems and sustainably increase or maintain yields in the face of increasing climate extremes. One important research goal is to reduce the use of synthetic fertilisers and pesticides. For example, by specifically inoculating soils or seeds with beneficial bacteria or symbiotic mycorrhizal fungi, or by cultivating legumes as catch crops. Scientists are therefore studying the triangular relationship between soil, roots and microorganisms in order to be able to influence them in a targeted manner.

However, due to the chemical and biological complexity of the soil, this research is a difficult endeavour. Often, for example, the complex conditions in nature have to be analysed in extensive field trials.

Reshaping the rhizosphere

The targeted modification of the interaction between plants and soil organisms is known as ecological engineering, or in the case of roots, rhizosphere engineering . To increase plant productivity, all three components of the rhizosphere - plant, soil and microbes - can be modified. For example, soil quality can be improved through targeted soil management. Another area of research is whether the cultivation of plants with longer roots helps to tap deeper water resources and better withstand periods of drought. But above all, influencing the soil microbiome is seen as the key to sustainable intensification of agriculture.

BonaRes and Rhizo4Bio: BMBF-funded soil and rhizosphere research

Under the umbrella of the funding initiative BonaRes - ‘Soil as a sustainable resource for the bioeconomy ’, the BMBF has been supporting ten research networks and the BonaRes Centre since 2015. The aim of the initiative is to promote the sustainable use and protection of soils. Since 2018, six project networks of the BMBF funding programme Rhizo4Bio - ‘Plant roots and soil ecosystems: Importance of the rhizosphere for the bioeconomy ‘ have been complementing BonaRes research. The projects are particularly focused on the interaction of plant roots with the surrounding soil space and the organisms living there. Some promising research approaches are presented below as examples. Special emphasis is placed on the Rhizo4Bio projects.

Droughts are becoming more frequent and the lack of water is increasingly becoming a problem for European agriculture. In order to make crops more resistant to drought, researchers are starting at the root. They are looking for plant varieties whose root systems are better suited to absorbing water due to their architecture, for example because they are more branched, longer or thicker. They are also researching cultivation practices for more efficient water utilisation and are initiating the breeding of plants with advantageous root architecture.

Identifying drought-resistant cereal varieties

In the DROOGHT project funded by the European Research Council, Guillaume Lobet and his team from the Jülich Institute of Agrosphere are investigating whether there is a correlation between root diameter and the ability of plants to absorb water. If the plant scientist's assumption is confirmed, cereal plants with a root system optimised for water uptake could be identified in the future based on the root diameter.

The Rhizo4Bio project Rhizotraits, in which researchers led by the University of Bayreuth want to find out which properties of roots and the neighbouring rhizosphere make plants more resistant to climate change, is pursuing a similar approach. Old grain varieties are the researchers' hope. Project coordinator Johanna Pausch assumes that these varieties still contain properties that could be an important key to the drought resistance of plants. Among other things, the team is investigating drought resistance, exudates, the microorganism communities in the rhizosphere and the length, density and branching of the roots of 48 maize and wheat genotypes.

Deep-rooted plants tap into water reserves in the subsoil

In order to reach deeper sources of water and nutrients, some plants have developed long roots. Some are so long that they reach into the subsoil – an area of the soil that is only slightly rooted and revitalised. Researchers are trialling the cultivation of deep-rooted plants as a strategy for developing more resilient agricultural systems.

In the Rhizo4Bio project CROP, a team led by Guillaume Lobet from the Jülich Research Centre in cooperation with the University of Hohenheim is investigating whether the combined cultivation of wheat plants with deep and shallow root systems has a positive effect on their resistance to drought stress or nutrient deficiency. The different root architectures should ensure that nutrients and water are absorbed along the entire soil profile and distributed evenly in the soil. Root exudates are also distributed more evenly in the soil, which has a positive effect on the microorganisms that promote the plants' resistance to stress.

Deep-rooted catch crop mixtures are at the centre of the Rhizo4Bio project RootWayS. A team led by Iris Zimmermann and Sandra Spielvogel from the Institute of Plant Nutrition and Soil Science at Kiel University is researching the cultivation of catch crop mixtures in conventional arable farming. With their long roots, catch crops build roads into the subsoil. Maize plants, which are cultivated as a subsequent crop, can then utilise the existing root channels and access water and nutrients in the subsoil more quickly.

Agroforestry systems

The deep-reaching roots of shrubs and trees could also help to supply fields and pastures with additional nutrients and water. Agroforestry systems are already being trialled in the BonaRes project SIGNAL. The project is being led by Göttingen soil researchers working with Edzo Veldkamp.

Adapted root architecture through genetic engineering and breeding

Researchers are also looking for ways to influence root architecture through molecular biology and breeding so that plants become more resistant to drought stress or better able to access nutrients. However, this research is still at the basic stage, as the underlying genes have yet to be identified. At the Centre National de la recherche scientifique (CNRS) in France, researchers are investigating which genes can improve the root hydraulics of maize plants as part of the HyArchi project funded by the European Research Council ERC.

More root hairs - less drought stress

Another way of changing root architecture is being trialled in the European cooperation project ‘RootsPlus’. Here, an international team of researchers is investigating whether the soil bacterium Rhizobium rhizogenes can make native crops more drought-tolerant. The bacterium stimulates the formation of new roots with a remarkably large number of root hairs. These so-called ‘hairy roots’ could help plants to absorb water more efficiently and quickly after short periods of rainfall.

Microorganisms associated with plants influence the health and growth of plants. In agricultural practice, the targeted application of microorganisms has so far only made up a small part. Some important current research approaches and objectives for understanding and optimising the soil microbiome for agriculture are summarised below.

Microbial cocktails against yield depression and soil fatigue

Monocultures reduce the diversity of the soil microbiome, making it easier for harmful microorganisms to thrive. For instance, it has been observed that wheat yields fall when the grain is repeatedly cultivated on the same area. In the Rhizo4Bio project RhizoWheat - ‘Rhizosphere processes and yield depression in wheat crop rotations’, researchers led by Henning Kage and Nora Honsdorf from Kiel University are investigating this phenomenon. Among other things, they are studying how the inoculation of soils with selected microorganisms affects the yield reduction syndrome.

It has also been observed in fruit growing that the growth of young fruit trees is restricted if they are repeatedly cultivated in the same field. This is referred to as post-planting disease or soil fatigue. In the BonaRes project ORDIAmur - ‘Overcoming regrowth disease using an integrated approach’, researchers led by Traud Winkelmann from the University of Hanover are investigating the causes of this problem. They have found initial indications of the pathogens causing the disease and will test whether inoculating the soil with microorganisms can immunise the plants.

Soil bacteria and mycorrhizal fungi help to save fertiliser

Modern agriculture can no longer do without mineral fertilisers. To save on or even replace synthetic fertilisers, scientists see great potential in the targeted use of soil microorganisms because they make it easier for plants to access elements such as nitrogen or phosphorus. Researchers around the world are working to better understand the interaction between microbes and plants.

In the Rhizo4Bio project Bread and Beer - ‘Production of wheat and barley with reduced input in organic farming’, a team led by Sylvia Schnell from Justus Liebig University Giessen is investigating whether the inoculation of cereal seeds with the soil bacterium Harmannibacter diazotrophicus improves growth and grain quality when the plants receive little nitrogen fertiliser.

In industry, a similar approach is being pursued by the companies Bayer and Ginko Bioworks. Their aim is to enable plants to cover their own nitrogen requirements by coating the seed with nitrogen-fixing bacteria.

Symbiotic mycorrhizal fungi

Mycorrhizal fungi are already used in organic farming systems for soil inoculation in order to save fertiliser and promote the stress resistance of plants. However, there is still a need for research in this area, as it is not yet possible to predict which plant will harmonise best with which fungus. One of the research goals of Caroline Gutjahr and her team at the Max Planck Institute of Molecular Plant Physiology in Potsdam is therefore to enable predictions to be made about which plant-fungus pairs work best together in which location. Her research is supported by the European Research Council ERC, among others.

Self-fertilising cereals

A very long-term and ambitious research goal is to develop cereal plants that fertilise themselves. This is exactly what an international research team wants to achieve in the ENSA project - ‘Enabling Nutrient Symbioses in Agriculture’. Under the leadership of Giles Oldroyd, Director of the University of Cambridge Crop Science Centre in the UK, the symbiosis experts are looking for ways to transfer the root nodule symbiosis of legume plants to cereal plants. Cereal plants already form symbioses with mycorrhizal fungi, but not with nitrogen-fixing rhizobia.

The researchers therefore want to reconnect basic plant signalling pathways of mycorrhizal symbiosis in order to enable symbiosis between cereal plants and rhizobia. A team from the University of Freiburg is also part of this international research network, which has the vision of replacing synthetic nitrogen fertilisers with the use of beneficial microorganisms.

With their project, the researchers initially want to support small farmers in sub-Saharan Africa and open up new opportunities for sustainable, safe and affordable food.