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
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
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.
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.
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.
People |
ORCID iD |
Tiina Roose (Principal Investigator) | |
Ian Sinclair (Co-Investigator) |
Publications
Cooper LJ
(2017)
Fluid flow in porous media using image-based modelling to parametrize Richards' equation.
in Proceedings. Mathematical, physical, and engineering sciences
Cooper LJ
(2018)
The effect of root exudates on rhizosphere water dynamics.
in Proceedings. Mathematical, physical, and engineering sciences
Daly K
(2017)
Modelling water dynamics in the rhizosphere
in Rhizosphere
Daly KR
(2018)
Determination of macro-scale soil properties from pore-scale structures: model derivation.
in Proceedings. Mathematical, physical, and engineering sciences
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
Duncan S
(2017)
Mathematical modelling of water and solute movement in ridge plant systems with dynamic ponding
in European Journal of Soil Science
Duncan S
(2018)
Mathematical modelling of water and solute movement in ridged versus flat planting systems
in European Journal of Soil Science
Duncan SJ
(2019)
Multiple Scale Homogenisation of Nutrient Movement and Crop Growth in Partially Saturated Soil.
in Bulletin of mathematical biology
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 | 2015 Kirkham Conference Travel Grant |
Amount | $500 (USD) |
Organisation | Soil Science Society of America |
Sector | Learned Society |
Country | United States |
Start | 03/2016 |
End | 04/2016 |
Description | Kirkham Conference Travel Grant |
Amount | $500 (USD) |
Organisation | Soil Science Society of America |
Sector | Learned Society |
Country | United States |
Start | 03/2016 |
End | 04/2016 |
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 | 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 | 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., Šimunek 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., Šimunek 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/ |