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

Lead Research Organisation: University of Southampton
Department Name: Faculty of Engineering & the Environment

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 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.

Publications

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

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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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Daly K (2017) Modelling water dynamics in the rhizosphere in Rhizosphere

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Daly KR (2018) Determination of macro-scale soil properties from pore scale structures: image-based modelling of poroelastic structures. in Proceedings. Mathematical, physical, and engineering sciences

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Daly KR (2018) Determination of macro-scale soil properties from pore-scale structures: model derivation. in Proceedings. Mathematical, physical, and engineering sciences

 
Description We learned that the plant exuded mucilage acts as a solute in the soil changing soil water properties. This can be used to breed plants for better plant-soil interaction.
As a result of this award we can now make recommendations on how to better manage soils in various settings.

The summary of applicability of our findings is below.
Knowledge: development of new knowledge and technology to deal with image based prediction of plant behaviour of partially saturated soil provides impetus and guidance to apply these methodologies to other porous media and granular flow systems such as powder storage and manipulation, mesoporous semiconductor device manufacture etc.

Economy/industry: clear beneficiaries/impacts are geotechnical engineering consultancies (Arup, MottMacDonald, Atkins,Ramboll), agronomy consultancies (Adas, Agrii), and agencies involved in managing and maintaining large UK infrastructures (Highways Agency, Network Rail), Environment Agency, Defra.

Society: 10% of world energy is spent on managing soil and other granular materials (UN, IPCC). Efficiencies in this will be crucial for mitigating climate change. UK infrastructure renewals, enhancements and maintenance is estimated to cost ~£13B pa.

Education/academia: the new technology highlights to researchers in mathematical sciences where new fundamental research endeavours are needed and enables researches in civil engineering, biological/agri sciences, natural environment conservation sciences to apply these new tools developed to wide variety of problems they have not been able to address until now.

Public: will clearly benefit and be impacted by better environment and infrastructure management. In addition, the grass roots outreach activities are hopefully on the longer term resulting in the larger numbers of school children being hopefully inspired to become engineers and increase the prosperity of the UK. I also want to highlight the issue of neurodiverse people being able to be top level engineers.
Exploitation Route Plant breeding and changes in soil/crop management practises.See above.
Sectors Aerospace, Defence and Marine,Agriculture, Food and Drink,Construction,Education,Energy,Environment,Financial Services, and Management Consultancy,Transport

 
Description Direct industrial impact via engagement with Bayer and Syngenta and policy impact via The Parliamentary and Scientific Committee meeting. The narrative impact summary is below: Knowledge: development of new knowledge and technology to deal with image based prediction of behaviour of partially saturated soil that interacts dynamically with plants provides impetus and guidance to apply this agriscience methodology to other porous media and granular flow systems such as powder storage and manipulation, mesoporous semiconductor device manufacture etc. Economy/industry: clear beneficiaries/impacts are geotechnical engineering consultancies (Arup, MottMacDonald, Atkins,Ramboll), agronomy consultancies (Adas, Agrii), and agencies involved in managing and maintaining large UK infrastructures (Highways Agency, Network Rail), Environment Agency, Defra. Society: 10% of world energy is spent on managing soil and other granular materials (UN, IPCC). Efficiencies in this will be crucial for mitigating climate change. UK infrastructure renewals, enhancements and maintenance is estimated to cost ~£13B pa. Education/academia: the new technology highlights to researchers in mathematical sciences where new fundamental research endeavours are needed and enables researches in civil engineering, biological/agri sciences, natural environment conservation sciences to apply these new tools developed to wide variety of problems they have not been able to address until now. Public: will clearly benefit and be impacted by better environment and infrastructure management. In addition, the grass roots outreach activities are hopefully on the longer term resulting in the larger numbers of school children being hopefully inspired to become engineers and increase the prosperity of the UK. I also want to highlight the issue of neurodiverse people being able to be top level engineers.
Sector Agriculture, Food and Drink,Chemicals,Construction,Digital/Communication/Information Technologies (including Software),Education,Environment
Impact Types Societal,Economic,Policy & public services

 
Description The Parliamentary and Scientific Committee Discussion meeting on "Are we looking after our soils?" organised by Stephen Metcalfe MP
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
Impact This meeting on Nov 3rd 2015 was to discuss the importance of soils on the UK plc. One of the recommendations was to look into introducing "caring for soils" into farmer tenancy agreements as part of the revised bill dealing with short term tenants. Ie similar to housing tenants who are required to take care of the house they are renting and hand it back in a good conditions, it was suggested that the farmers should also take care of the soil and hand it back in equally good or improved conditions at the end of their term.
 
Description 2015 Kirkham Conference Travel Grant
Amount $500 (USD)
Organisation Soil Science Society of America 
Sector Learned Society
Country United States
Start 04/2016 
End 04/2016
 
Description Kirkham Conference Travel Grant
Amount $500 (USD)
Organisation Soil Science Society of America 
Sector Learned Society
Country United States
Start 04/2016 
End 04/2016
 
Description Nature's amazing biopolymer: basic mechanical and hydrological properties of soil affected by plant exudates 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Talk at EGU General Assembly 2016
Vol. 18, EGU2016-17476-1, 2016
Year(s) Of Engagement Activity 2016
 
Description Aladdin and the mystery of the flying carpet 
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 Aladdin and the mystery of the flying carpet
University of Southampton Science and Engineering day, 18th March
Year(s) Of Engagement Activity 2017
 
Description An invited talk at Bayer CropScience's Workshop titled "Soil and Root Health" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Feb 2016: Bayer CropScience's - Soil and Root Health Symposium. This event will take place on February 16-17, 2016 at the headquarter campus of Bayer CropScience at Monheim, Germany.
Year(s) Of Engagement Activity 2016
 
Description Conference talk at Rhizosphere 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Talk titled "Fusing synchrotron imaging, spectroscopy and computational modelling for enhanced understanding of nutrient dynamics" by S.D. Keyes, K. R. Daly and T. Roose at Rhizosphere 2015 conference in Maastricht sparked questions and discussion.

after the talk several international people approached us for potential future collaborations and lab visits.
Year(s) Of Engagement Activity 2015
 
Description Feb 14-17 2018 Phenome 2018 Tuscon Arizona US. Keynote speaker for the theme "Algorithms and Data Management for Phenotype Quantification and Analysis". 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Feb 14-17 2018 Phenome 2018 Tuscon Arizona US. Keynote speaker for the theme "Algorithms and Data Management for Phenotype Quantification and Analysis".
Year(s) Of Engagement Activity 2018
 
Description Fluid Flow Under Your Skin and Beneath Your Feet 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Abstract of the talkc. The behaviour of fluids flowing though porous media has important implications for our understanding of biological processes and civil engineering applications. By combining mathematical modelling with the latest high-resolution imaging techniques and high performance computing it is now possible to investigate fluid flow in porous media that can be difficult to achieve experimentally. In this talk I will present applications of these techniques for modelling fluid flow through lymph nodes and soil.
The lymphatic system returns fluid to the bloodstream from the tissues to maintain tissue fluid homeostasis. Lymph nodes distributed throughout the system filter the lymphatic fluid. The afferent and efferent lymph flow conditions of lymph nodes can be measured in experiments; however, it is difficult to measure the flow within the nodes. The movement of water through soil is important for food security and the stability of embankments. The equations to model the processes in soil are parameterised using indirect measurements and empirical fitting. Image-based modelling is used to investigate the relationship between the pore structure and the modelling parameters of these two systems.
Year(s) Of Engagement Activity 2018
 
Description Imaging Solute Movement through Ridged and Flat Planting Systems 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at the conference Rhizosphere in Saskatoon, Canada in July 2019 and at ToScA conference in the UK in Sept 2019.
Talk title: Imaging Solute Movement through Ridged and Flat Planting Systems
Authors: Callum Scotson, Simon Duncan, Tiina Roose
Year(s) Of Engagement Activity 2019
 
Description July 2018 Plenary speaker at Society of Mathematical Biology conference in Sydney. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact July 2018 Plenary speaker at Society of Mathematical Biology conference in Sydney.
Year(s) Of Engagement Activity 2018
 
Description K.R. Daly, S. Keyes, T. Roose, Modelling root-soil interactions, International exploratory workshop on "Quantifying the role of biophysical processes in soil structure dynamics", 14-15 April 2016, Zurich (Invited talk) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact K.R. Daly, S. Keyes, T. Roose, Modelling root-soil interactions, International exploratory workshop
on "Quantifying the role of biophysical processes in soil structure dynamics", 14-15 April 2016,
Zurich (Invited talk)
Year(s) Of Engagement Activity 2016
 
Description K.R. Daly, S.D. Keyes and T. Roose, Image based modelling of plant scale soil properties, BSSS/SSP conference 7th-8th September 2016 (poster) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster at the British Soil Science Society Conference:
K.R. Daly, S.D. Keyes and T. Roose, Image based modelling of plant scale soil properties, BSSS/SSP
conference 7th-8th September 2016 (poster)
Year(s) Of Engagement Activity 2016
 
Description Keynote talk at Keystone 2016 "Microphytobiomes". Title of the talk "Multiscale Modelling of Plant-Soil Interaction" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Nov 2016: Keystone Symposia on Molecular and Cellular Science. Invited to give a Keynote address by Drs. Jan E. Leach, Kellye A. Eversole, Jonathan A. Eisen, Gwyn Beattie and Marcos A. Machado, we are Keystone Symposia on Phytobiomes: From Microbes to Plant Ecosystems, held in Santa Fe.
Year(s) Of Engagement Activity 2016
URL https://www.keystonesymposia.org/17S2
 
Description Keynote talk at Kirkham Conference 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact April 2016: Kirkham conference invited speaker; talk titled "Multiscale mathematical modelling of plant-soil interaction"
Year(s) Of Engagement Activity 2016
URL https://www.soils.org/membership/divisions/soil-physics-and-hydrology/kirkham-conferences
 
Description Mechanical and biophysical constraints affecting soil bioturbation by earthworms and plant roots. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Ruiz, S., 2018., July. Mechanical and biophysical constraints affecting soil bioturbation by earthworms and plant roots. In 11th European Conference on Mathematical and Theoretical Biology (ECMTB).
Location: Lisbon, Portugal
Dates: 23/07/2018-27/07/2018
Number of people: 10-20
Demographic: Scientists, Professors
Year(s) Of Engagement Activity 2018
 
Description Meet the scientist, Sherborne House School 11th March 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Primary school outreach event during the Science week:
Meet the scientist, Sherborne House School 11th March 2016
Year(s) Of Engagement Activity 2016
 
Description Minisymposia at BAMC titled "Multi scale analysis of porous media" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Porous materials are a fundamental building block of many terrestrialmaterials, eco-systems, biological tissues, and manmade engineering materials. There are numerous examples of porous materials for which enhanced modelling and optimisation techniques will offer significant gains in efficiency and productivity. In agriculture, 30% of UK wheat currently needs to be grown on drought-prone land, where yields are limited by the scarcity of water in the soil. In the construction industry, the reuse of pulverised fuel ash as a low porosity material for flood embankments is limited by the potential leaching of heavy metals into the surrounding environment. To overcome these, and many other problems there is a clear need to go beyond idealised models and develop a more detailed understanding of flow and transport phenomena in such systems.
The mathematics of multiscale modelling in porous media is a rapidly growing field with wide ranging applications and collaborative opportunities. In this mini symposium we will discuss the mathematics of porous media. We will focus on pore scale and continuous descriptions of transport, fluid dynamics and structural mechanics. In addition talks will focus on how asymptotic techniques can be used to exploit the large variations in scales within these materials to link properties on the pore scale to macro-scale observations.
Whilst the main focus of the session is on the mathematical developments occurring in different areas of porous media, we will also focus on application and how mathematical techniques can be integrated with Computed Tomography and continuum scale measurements to inform industry practise, answer fundamental questions, and optimise porous materials across a range of different applications
Speakers
The session will include talks from five speakers working in different areas of porous media at different scales.
Dr Keith Daly - University of Southampton
Combining homogenisation theory and image based modelling to predict the poro-elastic properties of multi-constituent soils
Dr Laura Cooper - University of Warwick
Macroscopic effects of microscale interfaces
Dr Rebecca Shipley - University College London
Porous medium models to predict spatial heterogeneity in anti-cancer therapy efficacy
Mr Simon Duncan - University of Southampton
Solute movement and uptake in dynamic poroelastic materials
Dr Matteo Icardi - University of Nottingham
Upscaling reactive and electrochemical transport in porous media
Year(s) Of Engagement Activity 2018
 
Description Modeling the Comparative Impact of Root Hairs on Phosphorus Uptake Under Different Field Conditions 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Ruiz, S., Koebernick, N., Duncan, S., McKay Fletcher, D.M., Scotson, C., Boghi, A., Marin, M., Bengough, A.G., George, T.S., Brown, L.K., Hallett, P.D., and Roose, T., 2019. Modeling the Comparative Impact of Root Hairs on Phosphorus Uptake Under Different Field Conditions. In Rhizosphere 5.
Location: Saskatoon, Saskatchewan, Canada
Dates: 07/07/2019-11/07/2019
Format: talk
Year(s) Of Engagement Activity 2019
 
Description Monitoring phosphorus mobility in soil relevant for root uptake using microdialysis and X-ray computed tomography 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at Rhizosphere conference
Title: Monitoring phosphorus mobility in soil relevant for root uptake using microdialysis and X-ray computed tomography
Co-authors: Chiara Petroselli, Katherine Williams, Callum Scotson, Daniel McKay Fletcher, Siul Ruiz, Tiina Roose
Audience: International scientific conference
Year(s) Of Engagement Activity 2019
 
Description Multimodal Imaging of Plant-Soil Interaction for Better and More Predictive Modelling of Rhizosphere Processes 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Roose, T., Petroselli, C., Williams, K., Dias, T., Scotson, C., McKay Fletcher, D.M., Ruiz, S. and Van Veelen, A., 2019, December. Invited Paper 487194: Multimodal Imaging of Plant-Soil Interaction for Better and More Predictive Modelling of Rhizosphere Processes. In AGU Fall Meeting 2019. AGU.
Location: San Francisco, CA, USA
Dates: 09/12/2019-13/12/2019
Demographic: Scientists, Professors, Students
Year(s) Of Engagement Activity 2019
 
Description On the Need to Establish an International Soil Modelling Consortium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Type Of Presentation keynote/invited speaker
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference presentation preparation for Complex Soil Systems Conference in Berkeley Sept 3-5 2014.
Full list of authors of this presentation is:
Vereecken H., Vanderborght J., Schnepf A., Brüggemann N., Amelung W., Herbst M., Javaux M., Van der Zee S.E.A.T.M., Or D., ┼áimunek J., van Genuchten M. Th., Vrugt J.A., Hopmans J.W., Young M.H., Baveye P., Pachepsky Y., Vanclooster M., Hallett P.D., Tiktak A., Jacques D., Vogel T., Jarvis N., Finke P., Jiménez J.J., Garnier P., Li C., Ogee J, Mollier A., Lafolie F., Cousin I., Pot V., Maron P.A., Roose T., Wall D.H., Schwen, A., Doussan C., Vogel H.J., Govers G., Durner W., Priesack E., Roth K., Horn R., Kollet S., Rinaldo A., Whitmore A., Goulding K., Parton, W.J.

Establishment of the world wide soil modelling consortium.
Year(s) Of Engagement Activity 2014
 
Description On the need to establish an international soil modelling consortium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Type Of Presentation keynote/invited speaker
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This was a presentation at the Soil Science Society of America Meeting in Longreach CA Nov 2-5 2014
Full author list of the presentation is:
Vereecken H., Vanderborght J., Schnepf A., Brüggemann N., Amelung W., Herbst M., Javaux M., Van der Zee S.E.A.T.M., Or D., ┼áimunek J., van Genuchten M. Th., Vrugt J.A., Hopmans J.W., Young M.H., Baveye P., Pachepsky Y., Vanclooster M., Hallett P.D., Tiktak A., Jacques D., Vogel T., Jarvis N., Finke P., Jiménez J.J., Garnier P., Li C., Ogee J, Mollier A., Lafolie F., Cousin I., Pot V., Maron P.A., Roose T., Wall D.H., Schwen, A., Doussan C., Vogel H.J., Govers G., Durner W., Priesack E., Roth K., Horn R., Kollet S., Rinaldo A., Whitmore A., Goulding K., Parton, W.J.

Formation of the international soil modelling consortium
Year(s) Of Engagement Activity 2014
 
Description Poster presentation: Rhizosphere by Design: Parameterising Richards' Equations Using Image Based Modelling 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Root Rhizosphere Workshop with ISRR Dundee Medal Lecture, 24th May 2017, James Hutton Institute, Dundee
Year(s) Of Engagement Activity 2017
 
Description Poster presentation: Image Based Modelling of Two Fluid Flow in Soil 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Poster presentation at Kirkham conference 2016 "The Root Zone - Soil Physics and Beyond", Ben Gurion University of the Negev, Sede Boqer, Israel, leading to discussions about fluid flow in soil and relevance of upscaling.
Year(s) Of Engagement Activity 2016
 
Description Poster presentation: RHIZOSPHERE BY DESIGN: PARAMETERISATION OF RICHARDS' EQUATION USING IMAGE BASED MODELLING 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Poster presentation Soil security programme and British Society of Soil Science annual conference
Year(s) Of Engagement Activity 2016
 
Description Presentation at Soil security programme spring meeting: Rhizosphere by Design - Project Update 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Presentation to update other members of the Soil Security Programme on the progress of the Rhizosphere by Design project and encourage collaboration.
Year(s) Of Engagement Activity 2016
 
Description Presented problem at Multiscale modelling workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Presented problem on root segmentation at Multiscale modelling workshop to encourage collaboration and solve an image processing problem.
Year(s) Of Engagement Activity 2016
 
Description Rhizosphere by Design: Root hair impact on soil structure formation in the rhizosphere 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Poster presentation at Soil security programme / BSSS annual conference, University of Reading
Poster was well received and sparked discussions with peers
Full author list:
N. Koebernick, S. D. Keyes, L. J. Cooper, M. Naveed, L.K. Brown, T. S. George, A. G. Bengough, I. Sinclair, P. D. Hallett, and T. Roose
Year(s) Of Engagement Activity 2016
 
Description Rhizosphere by design - In situ imaging of rhizosphere structure formation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Talk at spring meeting of Soil Security Programme 2016, which sparked questions and debate,
Full author list: N. Koebernick, S. D. Keyes, L. J. Cooper, M. Naveed, L.K. Brown, T. S. George, A. G. Bengough, I. Sinclair, P. D. Hallett, and T. Roose
Year(s) Of Engagement Activity 2016
 
Description Root hair impact on soil structure formation in the rhizosphere 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation and pitch talk at the Kirkham Conference 2016 - "The Root Zone - Soil Physics and Beyond", Ben Gurion University of the Negev, Sede Boqer, Israel
The poster was well received and sparked dicussions with other visitors
Full author list: N. Koebernick, S. D. Keyes, L. J. Cooper, M. Naveed, L.K. Brown, T. S. George, A. G. Bengough, I. Sinclair, P. D. Hallett, and T. Roose
Year(s) Of Engagement Activity 2016
 
Description Root induced compaction alleviation by root hairs -visualization with synchrotron imaging 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at the European Geophysical Union conference in Vienna Spring 2018.
Year(s) Of Engagement Activity 2018
 
Description Scaling the impact of rhizosphere processes - from imaged pore scale nutrient uptake to full field continuum models. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Ruiz, S., et al., 2018., December. Scaling the impact of rhizosphere processes - from imaged pore scale nutrient uptake to full field continuum models. In AGU Fall Meeting Abstracts.
Location: Washington D.C., USA
Dates: 10/12/2018-14/12/2018
Number of people: 10-20
Demographic: Scientists, Professors, Students
Year(s) Of Engagement Activity 2018
 
Description Soil, Climatic and Biophysical Constraints Determine Global Distribution and Activity Windows of Earthworms 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Ruiz, S., Bickel, S., Lehmann, P. and Or, D., 2019, December. Soil, Climatic and Biophysical Constraints Determine Global Distribution and Activity Windows of Earthworms. In AGU Fall Meeting 2019. AGU.
Location: San Francisco, CA, USA
Dates: 09/12/2019-13/12/2019
Conference number: 5 BILLION
Number of people: 10-20
Demographic: Scientists, Professors, Students
Year(s) Of Engagement Activity 2019
 
Description Talk at TOSCA conference titled "Optimisation of gold nanoparticles as a novel contrast medium for plant root and soil X-ray CT imaging" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact a. Optimisation of gold nanoparticles as a novel contrast medium for plant root and soil X-ray CT imaging

b. Callum Scotson, Arjen van Veelen, Simon Duncan, Maria Munoz-Hernando, Iain Dunlop, Samuel Keyes, Tiina Roose

c. Better understanding of plant root systems and their interactions with soil is vital to our future food security. The use of X-ray CT imaging to study soil and root systems is now widespread, but the poor contrast inherent to such systems currently limits the scope of these investigations. In biomedical imaging, contrast media have come to play a fundamental role in enabling fine structures and dynamic processes to be imaged. However, the use of contrast media in plant and soil imaging has until now been little-explored. Gold nanoparticles are a highly promising candidate for these applications, since they exhibit low toxicity and can be functionalised to target specific tissues or sites of biophysicochemical interest. However, the characteristics of their transport and stability in the challenging environments of soils and plants are largely unknown. Since nanoparticle stability is compromised by salinity, acidity and strong surface charges, a major hurdle to their use in environmental applications is the development of suitable coatings to mitigate the effect of these influences. We have undertaken a suite of experiments to quantify the stability of coated and uncoated gold nanoparticles in a range of soils, soil solutions and soil analogues, using complementary 4D X-ray CT, UV-Vis, ICP-MS, SEM and Zeta particle size analyses. We show how coating strategies were developed using these screening tools, producing suspensions with suitable stability for use in real soil environments. We then show how 4D imaging of nanoparticle transport in soils and soil analogues allows the dynamics of flow and surface interactions in these media to be quantified. Using these data, we will discuss the optimisation of nanoparticle coatings and X-ray imaging protocols for soil and plant applications, and discuss the possibilities for using functionalised gold nanoparticles to probe nutrient and water dynamics in these systems using multi-scale X-ray CT.
Year(s) Of Engagement Activity 2017
 
Description Talk at AGU Fall meeting 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Type Of Presentation keynote/invited speaker
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk titled "Current advancements and challenges in soil-root interactions modelling" by A. Schnepf, K. Huber, B. Abesha, F. Meaner, D. Leitner, T. Roose, M. Javaux, J. Vanderbroght, H. Vereecken was given at AGU Fall meeting 15-19 Dec 2014 in San Francisco.

Collaborations discussed
Year(s) Of Engagement Activity 2014
 
Description Talk titled "High resolution synchrotron imaging of rhizosphere structure " at the EGU 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact High resolution synchrotron imaging of rhizosphere structure ; European Geophysical Union 2018 meeting

Nicolai Koebernick1, Keith R. Daly1, Samuel D. Keyes1, Timothy S. George2, Lawrie K. Brown2, Annette Raffan3, Laura J. Cooper1, Muhammad Naveed3, Anthony G. Bengough2,4, Ian Sinclair1, Paul D. Hallett3 and Tiina Roose1,$
1 Bioengineering Sciences Research Group, Engineering Sciences Academic Unit, Faculty of Engineering and the Environment, University of Southampton, Southampton SO17 1BJ, United Kingdom
2 Ecological Sciences Group, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
3 Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen AB24 3UU , United Kingdom
4 School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom
$ corresponding author
Email corresponding author: t.roose@soton.ac.uk
Keywords: non-invasive imaging, rhizosphere, root hairs, soil structure, root exudates

Plant roots induce hydromechanical stresses and release organic compounds into soil, which are major drivers of soil structure formation. Whilst it is well known that roots impact the structure and physico-chemical properties of the rhizosphere, the underlying processes and their impact on resource flows to plants require greater investigation. We are exploring how different root traits physically manipulate soils, drawing on near isogenic barley lines that differ in root hairs, architecture and exudation, as well as new imaging approaches to quantify rhizosphere impacts.
A barley wildtype and its mutant with greatly reduced root hair growth were grown in specially designed assays that enabled high-resolution synchrotron imaging of rhizosphere structure with resolutions sufficient to detect root hairs. A sandy loam textured soil (Dystric Cambisol, sieved to < 1 mm) was used as a growth medium. The results showed that root hairs may play an important role in rhizosphere structure formation by alleviating the compression that is induced by growing roots. Root induced compression was evidenced by decreased air-filled pore space between 0.1 and 0.8 mm from the root surface. However, at the root-soil interface, the pore space increased for the root hair bearing barley genotype, but not for the barley mutants with no root hairs.
In a similar experiment, conducted with a remoulded soil (Dystric Cambisol, sieved to <250 um), both genotypes showed increased porosity at the root soil interface with no significant differences between the genotypes. Pore size distribution was narrower at the root-soil interface and became wider with distance from the root due to the decreased volume of large pores near the root surface.
Increased porosity near the root is discussed as an effect of the geometry of soil particles at the root surface. A model is proposed that describes the variation in porosity around roots, taking into account both root induced compression and the simplified geometry of solid mineral particles at the root surface.
Year(s) Of Engagement Activity 2018
 
Description Talk titled "Imaging and modelling of rhizosphere processes" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Geophysical Research Abstracts
Vol. 20, EGU2018-18157, 2018
EGU General Assembly 2018
© Author(s) 2018. CC Attribution 4.0 license.
Imaging and modelling of rhizosphere processes
Arjen van Veelen, Nico Koebernick, Dan McKay Fletcher, Callum Scotson, Keith Daly, Robbie Mayone, Simon Duncan, and Tiina Roose
University of Southampton, Faculty of Engineering and the Environment, United Kingdom (a.van-veelen@soton.ac.uk)
Most human food relies on the production of crops. Crops get their nutrients and water from the soil. In addition, soil has many other important functions, including the buffering of hydrological systems to prevent flooding and the provision of a carbon sink, lowering atmospheric carbon. Although bulk soil chemical processes are relatively well understood, there is a critical lack of studies characterising the dynamics of physico-chemical properties in the rhi- zosphere, such as nutrient cycles and release of plant exudates. These changes to the soil can drastically change the soil's hydraulic, nutrient and carbon functionality. This emphasises the importance to visualise physico-chemical information, in order to understand key processes of plant-soil interactions. In our interdisciplinary project, Data Intensive Modelling of the Rhizosphere Processes (DIMR), we aim to characterise and visualise these dynamics. The aim of the programme is to visualise pore geometry in soils using X-ray Computed Tomography (CT), com- bined with Nuclear Magnetic Resonance Imaging (NMRI) to visualize plant exudates and water distribution. In addition, we use synchrotron X-ray Fluorescence (XRF) and X-ray Absorption Spectroscopy (XAS) to understand both soil chemistry and speciation at the root-soil interface, all leading to a better understanding of rhizosphere processes. These methods can be combined with predictive models of soil-root processes to understand rhizosphere functionality. We will discuss how chemical data obtained from both NMR and XRF and XAS spectroscopy can enable a step change in multiscale modelling of rhizosphere processes.
Year(s) Of Engagement Activity 2018
 
Description Talk titled "Rhizosphere by Design" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Soil Security Programme Meeting, 28-29th March 2017, Leeds University
Year(s) Of Engagement Activity 2017
 
Description Talk titled "Rhizosphere soil aggregation: disentangling the mechanisms and impacts through a combination of imaging, physical testing and numerical modelling " 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Title
Rhizosphere soil aggregation: disentangling the mechanisms and impacts through a combination of imaging, physical testing and numerical modelling

Coauthors

Nicolai Koebernick1, Keith R. Daly1, Samuel D. Keyes1, Timothy S. George2, Lawrie K. Brown2, Annette Raffan3, Laura J. Cooper1, Muhammad Naveed3, Anthony G. Bengough2,4, Ian Sinclair1, Paul D. Hallett3 and Tiina
Roose1,$

1 Bioengineering Sciences Research Group, Engineering Sciences Academic Unit, Faculty of Engineering and the Environment, University of Southampton, Southampton SO17 1BJ, United Kingdom
2 Ecological Sciences Group, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
3 Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen AB24 3UU , United Kingdom
4 School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom
$ corresponding author

Abstract

Plant roots induce hydromechanical stresses and release organic compounds into soil, which are major drivers of soil aggregation. Whilst it is well known that roots stabilise and aggregate soil, the underlying processes and their impact on resource flows to plants requires greater investigation. We are exploring how different root traits physically manipulate soils, drawing on near isogenic crop lines that differ in root hairs, architecture and exudation, as well as new physical approaches to quantify rhizosphere impacts. These approaches include hydromechanical tests that bridge soil physics, soil biology and materials science, small-scale measurements and non-invasive imaging to measure the rhizosphere directly. We use these data in image-based models to describe retention and transport of water and nutrients in the rhizosphere.
Micromechanics tests have found that barley root exudates initially disperse soil, followed by gelling after microbial decomposition of these exudates. Maize exudates on the other hand, caused gelling of the soil, whereas this impact decreased with microbial decomposition. From our data on exudate viscosity, contact angle and surface tension, we have modelled the direct impact on water retention and transport in the rhizosphere, using 3D imaging with Synchrotron X-Ray CT with sufficient resolution to detect root hairs. Root growth compression by barley decreased pore-space between 0.8 mm and 0.1 mm from the root surface. However, at the root-soil interface, this compression was alleviated by root hair bearing barley genotypes, but not for barley mutants with no root hairs. From root hairs to exudates, plant roots have many traits that drive soil aggregation.

Conference meeting details
MadSoil Workshop "Formation, Properties and Function of Soil Microaggregates"
10-12 October 2017
Munich, Germany

Number of people in audience
100
International
Year(s) Of Engagement Activity 2017
 
Description Understanding the Fundamental Properties of Root Exudates Under Drying 
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 Poster presentation at Rhizosphere 2019 in Saskatoon Canada
Title: Understanding the Fundamental Properties of Root Exudates Under Drying
Authors: K. A. Williams, S. A . Ruiz, T. Roose
Poster, Rhizosphere 5, Saskatoon, Canada. (International conference on soil science)
Year(s) Of Engagement Activity 2019
 
Description X-ray Insider: X-ray CT blog for KS2 pupils 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Blog written for key stage 2 pupils to demonstrate how experiments are carried our and to encourage an interest in science.
Year(s) Of Engagement Activity 2015,2016
URL http://xrayinsider.blogspot.co.uk/