Rhizosphere by design: breeding to select root traits that physically manipulate soil

The idea that plants have differing abilities to engineer soil to make them more stable and productive is not new. Some of the more dramatic evidence comes from environmental disasters like the Great Dust Bowl, where the transition from prairie grasses to monoculture maize led directly to devastating soil erosion. Roots act like reinforcing rods in soil and exude compounds that aggregate soils, increase water storage and help release nutrients. Roots can also have hair-like structures on their surface that increase how far they penetrate and therefore interact with soils. The ability of a plant to engineer soil therefore has significant benefits to their own productivity.
Modern plant biotechnology research has identified large variations in the hairiness and exudation of populations of crops that have nearly identical genetic makeup. For plant breeders these findings are exciting, as they suggest an ability to select crops for root traits that will have a large impact on soils. By engineering the soil at the root surface, the crop takes up more nutrients, and the transport and storage of water and gases to the crop is also enhanced. This means that crops will be able to capture and store nutrients more efficiently, as well as produce an environment more resilient to weather induced stresses, such as drought or water-logging. In the search for crops to address food security challenges, this untapped potential in improving the physical manipulation of soils by root traits offers considerable potential.
This project will explore how various root traits change the physical properties of soil to improve the efficiency with which crops can capture water and nutrients. The ultimate outputs will be data and numerical models that will help plant breeders identify optimal root traits for more sustainable agricultural production. We start by collecting root exudates from a range of crops and adding them back to different soils at specific concentrations. Physical testing of the exudates and of exudate:soil mixes will provide new information on how roots may change water dynamics and mechanical stability of soils. This information is used to adapt models from medical biology and soil mechanics to begin to describe how soils form at the interface with plant roots. Next we move to tests with plants grown in soil. We will measure how different root traits (hairiness and exudation) change water dynamics (storage, transport and hydrophobicity) using small scale probes, and extract soils to measure how its mechanical properties are affected. X-Ray imaging will measure how the soil structure changes as roots grow and soils wet and dry. Along the length of the root the effects are different due to age. Root hairs grow, die and then degrade, so we will measure changes in the mechanical and hydrological behaviour at the root-soil interface from the base of the stem to root tips to get information need to understand whole root systems. Finally we take crops to maturity in the glasshouse and field. This links into an HGCA project on soil management where we use plots that have been under different forms of soil cultivation for over 10 years. As an increasing proportion of arable farmers switch to reduced input tillage systems, the field resource lets us explore how the root traits respond under traditional conditions used for plant breeding (ploughing to 20 cm) versus much shallower cultivation. This takes our initial laboratory research into the field, allowing verification of numerical models developed in the project. We will hence explore how soils are manipulated by plants at the root-soil interface and the impact of specific root traits for improving resource capture . Plant breeders will be able to use this information to identify favourable root traits to target in the search for more sustainable crop varieties. We will also improve the understanding of the structure of soil forms and influences carbon and water dynamics.

Plant breeding can manipulate root structure, root hair length and exudation properties to physically engineer rhizosphere soil. Little quantitative understanding of the underlying processes exists, so this project will use advanced approaches from engineering science to disentangle the biophysical mechanisms that drive rhizosphere formation. The availability of near isogenic barley and maize lines with differences in root hair length and exudation provides a novel biological resource for this research. Our team is uniquely placed internationally to conduct this research. We were the first to image root hairs in intact soil, allowing modelling of their role in P acquisition. Others in our team found that root hairs aggregate soil at the interface of roots, and the impact increases in less dense soils with lower P. This could help release P and have positive impacts on rhizopshere structure that affects carbon sequestration by roots, but neither study examined the mechanisms in the soil or impacts on water dynamics.

In this project we will isolate and characterise the compounds produced by plant roots that affect surface tension and viscosity at the soil-root interface. The compounds will then be added to soil at a range of concentrations so that the impact on mechanical and hydrological properties can be measured. Using the novel maize and barley lines, we will vary root hair density, length and exudation to examine how these properties influence soil physical properties in rhizosphere samples. In addition, we will measure how the rhizosphere soil physical properties change with age and under different nutrient and physical stresses in glasshouse and field experiments. Non-invasive imaging methods will be used to validate the models and demonstrate how plants progressively change the structure of soil around their roots. The modelling and data generated on rhizosphere formation will identify root trait ideotypes for resource capture and soil sustainability.

Three strands of research, each lead by separate institutions, are brought together in this proposal: (1) root trait isolation and functioning; (2) rhizosphere biophysical formation; and (3) imaging/numerical modelling of rhizosphere formation and transport properties. By bringing together pioneering research from different areas, the project will have rapid scientific impact, with applications relevant to industry and policy. Crop mapping populations screened for root traits enable our research, which will allow future forward genetics by plant scientists to develop better varieties. Rhizosphere science has an excellent resource of microbiology studies, with our project able to access the vast amount of information already collected to achieve our ultimate goal, a numerical model that can identify ideal root trait ideotypes for sustainable agriculture. By understanding the basic processes of how the rhizosphere forms and functions, we deliver generic approaches that can be applied to investigate future crop traits that allow for decreased resource input, greater abiotic stress tolerance, better water use efficiency, more carbon capture through soil particle aggregation and the physical stabilisation/structural regeneration of soils caused by the action of crop roots. There is a dearth of process based understanding in this area, with much past research focussed on qualitative techniques. The numerical models we develop on rhizosphere formation and functioning can also be applied to understanding soil structure away from the plant, so relevant to the larger-scale functioning of terrestrial ecosystems in terms of hydrology, erosion and gas exchange.

Our non-invasive imaging research is world-leading, including recent measurements of root:root hair:soil structure interactions that enabled numerical modelling of phosphorus uptake. Thresholding and image processing algorithms that will be developed by the imaging PDRA are essential to develop this research further, and are applicable to the surge of new plant and soil science research brought about by inexpensive non-invasive imaging technologies. We involve imaging specialists in the project team to ensure the rapid and effective implementation of state-of-the-art techniques.

The plant science industry is challenged with providing farmers with more resource efficient crop varieties. At the farm gate this makes economic sense, but it is also driven by government policies such as GAEC (CAP reforms) and soil protection framework directives. Internationally we address food security, tackling the issue by understanding both plant and soil processes. Soil management practices are changing as a result of policies and socioeconomic factors on farm. By examining root trait performance under different tillage practices, we tackle the challenge of producing varieties suitable for specific environmental conditions. At present, the phenotypic plasticity of root traits is not well understood. Existing elite crop varieties have been predominantly selected in highly loosened and fertilised seedbeds that do not reflect modern on-farm conditions. Our research therefore also delivers to the agricultural engineering industry producing new forms of soil cultivation equipment, who are faced with reticence from the farming community because of perceptions about poorer crop performance. Farmers may just be selecting the wrong crop varieties.

As the rhizosphere is so important to food security and soil sustainability, it deserves greater public awareness. A starting point in this project is engagement through the Aberdeen Biodiversity Centre, who through their own Natural History Museum and links to other museums, provides the skills and contacts for public education. Our root trait lines provide a teaching resource for students to explore rhizosphere formation directly. The graphical output from our imaging research provides visual tools that will capture public interest.