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

Lead Research Organisation: University of Dundee
Department Name: Civil Engineering

Abstract

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.

Technical Summary

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.

Planned Impact

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 focused 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.

Publications

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Bengough AG (2016) Root hairs aid soil penetration by anchoring the root surface to pore walls. in Journal of experimental botany

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Cooper LJ (2017) Fluid flow in porous media using image-based modelling to parametrize Richards' equation. in Proceedings. Mathematical, physical, and engineering sciences

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Cooper LJ (2018) The effect of root exudates on rhizosphere water dynamics. in Proceedings. Mathematical, physical, and engineering sciences

 
Description Royal Society International Exchange Programme - China
Amount £24,000 (GBP)
Organisation The Royal Society 
Sector Academic/University
Country United Kingdom
Start 04/2017 
End 03/2019
 
Title Microscale mechanical and hydrological test methods to measure rhizosphere properties 
Description A small scale indenter method was developed to measure micro mechanics and the root-soil interface. This was complemented by a small-scale infiltrometer to measure hydrological properties. 
Type Of Material Biological samples 
Year Produced 2018 
Provided To Others? Yes  
Impact Capability to quantify mechanical and hydrological properties at rhizosphere scale. Will be used for research upcoming in the project. 
URL https://dl.sciencesocieties.org/publications/vzj/abstracts/17/1/170083?noSSO=1
 
Description Assessing the Performance of Grass and Soil in Resisting Erosion - Phase 1 project with CH2M and Environment Agency 
Organisation CH2M HILL
Country United States 
Sector Private 
PI Contribution We are working with CH2M (Project Partner), having been invited by them to tender as subcontractors to this Environment Agency Phase 1 project, conerning the role of grass vegetation in resisting soil erosion of flood embankments.
Collaborator Contribution Working jointly to deliver recommendations for further measurement/monitoring of grassed flood embankments, in view of literature review in progress.
Impact Collaboration has just started.
Start Year 2017
 
Description Contribution of Root Hairs, Mycorrhizae and Bacteria to Organic P Use by Crops 
Organisation China Agricultural University (CAU)
Country China 
Sector Academic/University 
PI Contribution We provide plant genetic materials and experimental know-how developed in existing projects
Collaborator Contribution The CAU partners bring expertise in stable-isotope probing methods to isolate the impact of root exudates on specific rhizosphere microbes.
Impact One paper published and several in development.
Start Year 2017
 
Description Agricultural diversification in the Highlands of Borneo 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I presented work on roots for sustainability at the workshop in Sarawak
Year(s) Of Engagement Activity 2018
 
Description Conference Talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Gave Talk ""Understanding the Rhizosheath: Opportunities for Manipulating the Soil Root Interface" at the Plant Biology Europe Conference in Copenhagen, Denmark, approximately 500 people attended the talk.
Year(s) Of Engagement Activity 2018
 
Description Ecosystems and Land Use Stakeholders Engagement Group Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Policymakers/politicians
Results and Impact A stakeholder event for Scottish Government Policy Makers was held in Edinburgh to brief on the latest advances in root biology.
Year(s) Of Engagement Activity 2017
 
Description Friends of University of Dundee Botanic Gardens talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Talk to Friends of the University of Dundee Botanic Garden, and interested members of the general public, concerning Plants and Engineering.
Title: Carbon-friendly engineering of soil with plants.
Location: University of Dundee Botanic Gardens,
Date: 7 September 2018, Dundee.
Year(s) Of Engagement Activity 2018
URL https://www.dundee.ac.uk/botanic/news/2018/article/plants-and-engineering-with-dr-neil-paterson-and-...
 
Description Genotypic variation in the formation of rhizosheath and implications for rhizosphere processes 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presented research at a workshop on Rhizosheath in Lancaster
Year(s) Of Engagement Activity 2017
 
Description Inaugural talk to public audience at University of Dundee "Discovery Days" event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Approx 200 audience (combined general public, students and academics) attended, sparking considerable discussion and interest.
Year(s) Of Engagement Activity 2018
URL https://www.dundee.ac.uk/media/dundeewebsite/revealingresearch/documents/2018-Discovery-Days-Program...
 
Description International Society of Root Research Medal Lecture 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The ISRR2017 medal lecture invites an eminent scientist who explores root-soil interactions to Dundee to present a lecture, preceded by talks and poster sessions by predominantly early career researchers. This year the invited speaker was Prof Michelle Watt from Juelich.
Year(s) Of Engagement Activity 2017
URL http://www.hutton.ac.uk/events/root-rhizosphere-workshop-and-2017-isrr-dundee-medal-lecture-root-res...
 
Description Invited participation in 25th New Phytologist Workshop (at Sommieres, France) on root traits as predictors of plant-soil functions 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Approximately 20 international scientists (mainly Europe and USA) invited to the 25th New Phytologist Workshop looking at functional interactions between root ecological traits and soil/ecosystem functions. A special topic chosen at the meeting was to focus on soil stabilisation as an important root trait function, and Alexia Stokes and helped to lead a session on this topic.
Year(s) Of Engagement Activity 2019
URL https://www.newphytologist.org/workshops/25
 
Description Invited presentation at Symposium, Juelich, 9th Nov 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Presentation entitled "Root growth and function in relation to soil strength, structure, and water".
Year(s) Of Engagement Activity 2015
 
Description NERC Planet Earth Article 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Article in the NERC Planet Earth magazine, written by journalist Julia Horton. This covered a range of projects conducted by University of Aberdeen scientists on tropical agriculture. The work draws on both our direct research in tropical countries and strategic research on plant-soil interactions, so it cuts across P. Hallett's funding portfolio.
Year(s) Of Engagement Activity 2017
URL http://www.nerc.ac.uk/planetearth/stories/1879/
 
Description NERC UnEarthed 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact NERC UnEarthed was a large event that attracted over 3000 people. There were two days dedicated to school visits and 2 days when there was free entry to the general public. During our free interactive showcase - UnEarthed - at Dynamic Earth, Edinburgh (17-19 November), families and adults could explore the tools used to make science happen and see the extraordinary work of our scientists. Our exhibit focussed on a range of research projects in tropical ecosystems, specifically on the impacts of agriculture and strategies that could be taken to minimize environmental impacts. The text we used to attract visitors was: Emerging from a Scottish forest you stumble across an orangutan in her nest, with drone footage of her natural habitat. What can this have to do with Scotland? Your food choices affect her habitat, other tropical regions, and the livelihoods of local people. A grocery basket will show you how much of what you eat is tropical. Guess the water used and greenhouse gases emitted producing this food, and then measure it yourself with a gas meter and carbon calculator.

Our research is finding solutions to make this food more sustainable and to protect the livelihoods of people living in vulnerable tropical regions. The most important tropical food is rice. You will see how rice can be selected to grow better with less water by reaching deeper soil with its roots. The other major solution is improving tropical soils. By adding carbon, we will show how they can be restored. Our man dressed as an orangutan was a highlight with kids.
Year(s) Of Engagement Activity 2017
URL http://www.nerc.ac.uk/latest/events/archive/unearthed/
 
Description New crops and cropping systems for a more sustainable future 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I presented a seminar at a workshop on New Crops for Agricultural Sustainability at Crops For the Future in Malaysia
Year(s) Of Engagement Activity 2018
 
Description One day meeting on root research, May 2015 inc. First ISRR Medal Lecture 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact One day workshop on root research, variety of poster and speaker presentations. Audience primarily Regional (Scotland), but with invited speaker from US as medal lecture recipient.
Year(s) Of Engagement Activity 2015
 
Description Platforms to test and demonstrate sustainable soil management: integration of major UK field experiments. 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact An article was written and distributed by the AHDB Newsletter and Website to highlight the impact of soil tillage on the soil physical, biological and chemical characteristics and impact on root growth.
Year(s) Of Engagement Activity 2017
 
Description Presentation for Interdisciplinary Plant Group (University of Missouri, Columbia USA) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited presentation to approx 200 participants of 34th Annual IPG meeting at University of Missouri, Columbia concerning biophysics of root-soil interactions.
Year(s) Of Engagement Activity 2017
URL https://ipg.missouri.edu/feature-stories/34thAnnu_07012017.cfm
 
Description Presentation to International Barley Hub 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Gave talk at the International Balrey Hub aways days in Birnam, UK "Rhizosphere by Design: Understanding and manipulating the barley rhizosphere"
Year(s) Of Engagement Activity 2019
 
Description Root-soil/slope Workshop and ISRR Medal Lecture in Root Research (2016) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Meeting on root-slope interactions, designed to engage with both practitioners (including members of our EPSRC Project Advisory Group), postgraduate students, and researchers.
Year(s) Of Engagement Activity 2016
URL https://roots-dundee.eventbrite.com
 
Description University of Southampton 1 day meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Spoken prsentation entitled "Understanding root growth and function in relation to predicting water uptake from field soil", at 1 day workshop hosted by Southampton University.
Year(s) Of Engagement Activity 2015
 
Description Workshop on grass reinforcement of floodbanks 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Stakeholder meeting with approx 40 attendees to discuss problems of grass erosion on floodbanks. Purpose was to refine and develop business case options for potential project with Environment Agency on improving the use of grass on floodbanks in the UK.
Year(s) Of Engagement Activity 2018
URL http://evidence.environment-agency.gov.uk/FCERM/en/Default/FCRM/Project.aspx?ProjectID=A4D87116-F4D3...