Truly Predicting Root Uptake of Water: Case Study with Wheat

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

Abstract

We heavily rely on soil to support the crops on which we depend. Less obviously we also rely on soil for a host of 'free services' from which we benefit. For example, soil buffers the hydrological system greatly reducing the risk of flooding after heavy rain; soil contains very large quantities of carbon which would otherwise be released into the atmosphere where it would contribute to climate change. Given its importance it is not surprising that soil, especially its interaction with plant roots, has been extensively researched. However the complex and opaque nature of soil has always made it a difficult medium to study. Soil is complex in that it is composed of different materials (mineral particles, organic matter, water, microrganisms) of all shapes and sizes (from centimetres to microns) which aggregate together to form a complex porous material. While the function of soil is determined by the processes taking place at the micro-scale (often called pore scale), within this complex material we have traditionally only been able to measure and observe soil function at the larger, macro-scale (usually referred to as the field scale). We can manipulate soil systems at the macro-scale and empirically observe what occurs, and this empirical description is useful, but it offers no scope to truly predict how the system would respond to modification. This is important because we have the potential and most likely the future need to manipulate the underlying processes at the microscale (in both plants and soil). For example we will need to know: should our crops root deeper? Would a change in root architecture be useful? To what extent can roots adapt to stresses in the soil physical environment? What management induced changes to soil structure are desirable for future environments? Evaluating such possibilities at the field scale currently requires case by case empirical investigation with little direction offered by any underlying theory; this is a huge gap in current knowledge. Even if good theories existed to explain soil-root interactions at the micro-scale, it is not clear how this could be applied to the field scale. Understanding and manipulating the system at the scale of <1mm is all very well, but we want to make a difference at the scale of >10 kms! We need to be able to 'scale up' our micro-knowledge to a scale that is useful. Progress can be made to address the microscale understanding of soil-root interactions, however this progress will only be of real importance if we also find ways to scale up to the field situation. This is also a huge gap in knowledge. These knowledge gaps can now be addressed as a result of two recent methodological developments. Firstly new experimental techniques based on X-ray Computed Tomography (CT) are making it easier to visualise and quantify soil and root micro-structure in a non-invasive manner. Secondly, mathematical homogenisation theory offers new ways to correctly scale up micro-scale processes to macro-scale models thereby addressing the scale problem. Integrating these two new methods for the first time we will consider the specific question of water movement in soils and its uptake by wheat, an important crop for UK agriculture. We will undertake experiments to measure the micro-structure of soils and investigate how water passes through these soils to the roots of plants. Our aim will be to use this information to develop and test theoretical models of water movement and uptake and use these to evaluate the performance of different wheat root architectures. We will do this in a way that is specifically designed to enable us to 'scale up' the results so we can make predictions at the field scale, based on the observable micro-scopic characteristics of soil. Thus, because of the generic methodology produced within this project the results are not only applicable for wheat, but for wide range of agricultural crops.

Technical Summary

Recent work by our team and others has found that the multiscale nature of soils, especially soil micropores, can strongly influence how plant roots function in soil. This in turn has led us to develop dual porosity models for nutrient diffusion in the soil. In this project we will investigate how the dual porosity effects influence water movement in soil and how this in turn influences the crop, in particular wheat, water uptake. Our general approach will be to start from the simplest element in our system, a soil particle/aggregate, and work our way up in three steps by considering the single root scale and finally the soil profile/crop scale. On the smallest scale we will use X-ray CT to image the internal 3-D pore structure and water content of soil aggregates. At this scale we will import observed soil surfaces into Comsol to solve the mechanistically based Stokes equations for fluid flow enabling us to determine the Darcian permeability and soil water suction characteristic on the basis of the observed micro-structure over a range of different sizes of 'unit cell'. Through mathematical homogenization we will select the appropriate size of unit cell so that these micro-scale results can be applied in the classical macro-scale model of water flow in soil (i.e. the Richards equation). Using the imaging of a single root scale we will address issues of root-soil contact via the water film. Previously this has only been addressed theoretically with idealised soil structures. Using imaging and modeling at the single root scale we will answer questions about the functionality of different root branches for water uptake. Finally we will model and measure water uptake by the full plant root architecture allowing a comparison of the behaviour of different wheat root architectures. We will make the first simultaneous measurements of root architecture and water uptake by living plants at scales relevant to the field situation.

Planned Impact

WHO WILL BENEFIT AND HOW? A direct target group is the international agricultural research and training sector concerned with improving the well-being of farmers and consumers by enhancing the quantity and quality of food crops. A key priority is to breed crops for changing climate conditions, in particular, for conditions of severe drought (Africa, Asia etc), but also for areas of severe flooding (Asia, Europe etc). A further requirement is to substantially increase yields with some suggestions indicating by as much as 40% in the next 20 years. Our research will directly benefit crop breeders in guiding which plant root system traits are important for specific soil moisture conditions. Similarly the work will have impacts on the understanding of how soil structure interacts with crop performance which will ultimately be relevant to those involved in management/tillage of soil (i.e. farmers) and those involved in the formulation of agricultural policy and guidance. A second group of beneficiaries are agricultural and environmental policy makers concerned with the fate of pollutants and fertilizers in the environments. Flooding can cause serious eutrophication and understanding the role of plants in this process can enable us to choose crops/plants with special traits that enable the reduction of eutrophication and increase bioremediation. In the longer term our research will help refine methodologies that address persistent flooding and crop growth in extreme environments (very dry and very wet) through appropriate management of soil structure. A third group of beneficiaries are the international development community who can use the results of our research to guide the policy recommendations to areas likely to undergo significant environmental climate change, again with respect to the appropriate management of soil. COMMUNICATION AND ENGAGEMENT PLAN In addition to standard peer-reviewed publications we will also use the web and newsletters as a main means to communicate with the above stakeholders. We will produce reports designed for more general readers distributed through the partner Universities Media Relations Office, which publicizes the results of the research directly to practitioners in industry (especially the water and insurance sectors), and policymakers (especially Defra and the Environment Agency). PI Tiina Roose is a member of technology transfer committee for Environmental Knowledge Transfer Network (KTN) and thus we will disseminate the results of this research via this network to water and waste industry. Further we propose to arrange a workshop (organised by the British Soil Physics Group of which Sacha Mooney is the Chair) for scientists at the end of the project, in which we will disseminate the applications of multiscale studies of soil imaging and modelling studies and how the results would be translated into practical crop growth situation. Since the mathematical modelling and imaging techniques developed during this project are in some sense generic we will invite representatives of other science domains, such as biomedical modelling and imaging community, to attend the workshop.

Publications

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Bennett T (2018) Multiscale Models of Metallic Particles in Nematic Liquid Crystals in SIAM Journal on Applied Mathematics

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Bennett TP (2014) Multiscale models of colloidal dispersion of particles in nematic liquid crystals. in Physical review. E, Statistical, nonlinear, and soft matter physics

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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 (2014) Multiscale modelling of hydraulic conductivity in vuggy porous media. 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

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Daly KR (2016) Image-based modelling of nutrient movement in and around the rhizosphere. in Journal of experimental botany

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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

 
Description We X-ray CT scanned the soil to determine how plant roots modify the soil water content. This is so we could better predict how plants and ecosystems respond to changing climate and weather patterns.

In particular, for the first time in the world, we used soil pore scale imaging and modelling to show how to parameterise Richards' equation. Richards' equation is a classical equation describing partially saturated water flow in soil. One issue is that it is parameterised by two very time consuming equilibrium experiments: the soil water content-suction curve and partially saturated hydraulic conductivity at all levels of relative saturation. In addition to being time consuming these experiments need to be repeated separately for all soils, all soil compactions, separately for wetting and drying due to hysteresis effects, including all necessary scanning curves between wetting and drying curves. On top of these traditional struggles, for more state of the art engineering problems that involve soil microbial processes, the traditional measurements are not necessarily valid or even possible as the sample changes during the test/measurement lifetime (days, weeks and months), so that the properties measured at the start of the experiment are not the same as at the end. All this inspired us to look at the fundamentals of two-fluid (air and water) dynamics in the soil pore space and develop a new engineering workflow how to describe two-fluid movement in the soil bulk scale if the microscale pore structure is known from X-ray CT. Thus, we first set up the theoretical engineering fundamentals of how to derive Richards' equation from the known microscale and then demonstrated how to implement it on the image-based geometry. This then allowed us to investigate how the changes in soil porewater chemistry induced by plants and/or microbial activity affect the soil water movement.
Exploitation Route Policy recommendations, improved way of managing the ecosystem services. Civil engineering infrastructure design. Design and management of other self assembling organs mineral composites.
Sectors Aerospace, Defence and Marine,Agriculture, Food and Drink,Construction,Education,Environment,Manufacturing, including Industrial Biotechology

 
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 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.
First Year Of Impact 2018
Sector Agriculture, Food and Drink,Communities and Social Services/Policy,Education,Energy,Environment,Financial Services, and Management Consultancy,Transport
Impact Types Societal,Economic

 
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 ERC Consolidator Grant
Amount € 1,996,246 (EUR)
Funding ID 646809 
Organisation European Research Council (ERC) 
Sector Public
Country Belgium
Start 09/2015 
End 08/2020
 
Description IFLS Research Stimulus Fund
Amount £5,140 (GBP)
Organisation University of Southampton 
Sector Academic/University
Country United Kingdom
Start 07/2015 
End 07/2016
 
Title 3 month old wheat plant cultivar Xi19 grown in sandy loam soil at a bulk density of 1.1. g cm-3. [Pot 1] 
Description 3 month old wheat plant cultivar Xi19 grown in sandy loam soil at a bulk density of 1.1. g cm-3. Pot dimensions 1 m height and 20 cm width. Growth conditions 12 hr light 12 hr dark. Day temp 20oC, night temp 10oC. VoxelsX=3940 VoxelsY=3940 VoxelsZ=1036 VoxelSizeX=0.0579 VoxelSizeY=0.0579 VoxelSizeZ=0.0579 unit = mm datatype = Unsigned big endian bitsperelement = 16 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact High resolution images of wheat plants. 
URL http://eprints.soton.ac.uk/377866/
 
Title 3 month old wheat plant cultivar Zebedee grown in clay loam soil at a bulk density of 1.1. g cm-3 [Pot 2] 
Description 3 month old wheat plant cultivar Zebedee grown in clay loam soil at a bulk density of 1.1. g cm-3 Pot dimensions 1 m height and 20 cm width. Growth conditions 12 hr light 12 hr dark. Day temp 20oC, night temp 10oC. VoxelsX=3940 VoxelsY=3940 VoxelsZ=1200 VoxelSizeX=0.0579 VoxelSizeY=0.0579 VoxelSizeZ=0.0579 unit = mm datatype = Unsigned big endian bitsperelement = 16 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact High resolution images of wheat plants. 
URL http://eprints.soton.ac.uk/378172/
 
Title 3 month old wheat plant cultivar Zebedee grown in sandy loam soil at a bulk density of 1.1. g cm-3. [Pot 4] 
Description 3 month old wheat plant cultivar Zebedee grown in sandy loam soil at a bulk density of 1.1. g cm-3. Pot dimensions 1 m height and 20 cm width. Growth conditions 12 hr light 12 hr dark. Day temp 20oC, night temp 10oC. VoxelsX=3940 VoxelsY=3940 VoxelsZ=1036 VoxelSizeX=0.0579 VoxelSizeY=0.0579 VoxelSizeZ=0.0579 unit = mm datatype = Unsigned big endian bitsperelement = 16 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact High resolution images of wheat plants. 
 
Title 3 month old wheat plant cultivar xi19 grown in clay loam soil at a bulk density of 1.1. g cm-3. [Pot 3] 
Description 3 month old wheat plant cultivar Xi19 grown in clay loam soil at a bulk density of 1.1. g cm-3. Pot dimensions 1 m height and 20 cm width. Growth conditions 12 hr light 12 hr dark. Day temp 20oC, night temp 10oC. VoxelsX=3940 VoxelsY=3940 VoxelsZ=1200 VoxelSizeX=0.0579 VoxelSizeY=0.0579 VoxelSizeZ=0.0579 unit = mm datatype = Unsigned big endian bitsperelement = 16 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact High resolution images of wheat plants. 
URL http://eprints.soton.ac.uk/379896/
 
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 Assessing the influence of the rhizosphere on the water release characteristic using X-ray Computed Tomography 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Assessing the influence of the rhizosphere on the water release characteristic using X-ray Computed Tomography
S.R. Tracy, S. Mooney, K.R. Daly, T. Roose, N. Crout, M. Bennett, T. Pridmore, J. Foulkes
Society of Experimental Biology, Manchester, July 2014


Increase in research visibility
Year(s) Of Engagement Activity 2014
 
Description Assessing the influence of the rhizosphere on the water release charaterisitc using X-ray computed tomography 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Assessing the influence of the rhizosphere on the water release characteristic using x-ray computed tomography
SR Tracy, KR Daly, N Crout, M Bennett, T Pridmore, J Foulkes, I Sinclair, T Roose, S Mooney
EGU General Assembly, Vienna, April 2014.


increase in international visibility
Year(s) Of Engagement Activity 2014
 
Description Conference talk 
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 "Image based modelling of nutrient uptake by root hairs" K.R. Daly, S.D. Keyes, S. Masum and T. Roose sparked questions and discussions afterwards at the Rhizosphere 2015 conference in Maastricht in June 2015.

After the talk several people in the audience approach us for potential collaborations and visits to our lab.
Year(s) Of Engagement Activity 2015
 
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 Conference: Rhizo4, Maastricht 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact A large conference held every 4 years concerning all aspects of plant and soil modelling given to a wide audience. Great networking opportunity and experience of lots of other academic work in a similar field. Poster entitled "Using a whole plant crop model to assess phosphate fertiliser use in barley".
Year(s) Of Engagement Activity 2015
URL http://www.rhizo4.org
 
Description DTP/CDT Networking Event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact DTP/CDT Networking Event with Syngenta
Year(s) Of Engagement Activity 2017
 
Description EGU talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Type Of Presentation paper presentation
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk titled "Visualisation and quantification of water in bulk and rhizosphere soils using x-ray computed tomography" by S. R. Tracy, S. Mooney, K. R. Daly, N. Crout, M. Bennett, T. Pridmore, T. Roose was given at EGU annual meeting in Vienna 2015.

After the talk several international groups discussed with us potential future projects to collaborate on.
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 Image based homogenisation of water flow in soil 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Type Of Presentation poster presentation
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at the Interpore conference in Prague.

Image based homogenisation of water flow in soil
K. Daly, S. Tracy, S. Mooney, T. Roose
Interpore, Prague, May 2013.


Increased visibility and collaborations
Year(s) Of Engagement Activity 2013
 
Description Image based modelling of multi fluid flow and nutrient transport in a root-soil system 
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.D. Keyes and T. Roose. Image based modelling of multi-fluid flow and nutrient transport in a root-soil system. Gordon Research Conference 2014, 06/07/2014-11/07/2014.

increase in visibility and new collaborations
Year(s) Of Engagement Activity 2014
 
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 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 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 Multiscale image based modelling go two phase flow in soil 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Multiscale image based modelling of two phase flow in soil
KR Daly and Roose
International Conference on Scientific Computation and Differential Equations
September 16-20, 2013, Valladolid (Spain). Invited talk Daly.


further visibility of research
Year(s) Of Engagement Activity 2013
 
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 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 "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 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 Visualisation and validation of the water release curve using X-ray Computed Tomography 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Visualisation and validation of the water release curve using X-ray Computed Tomography
S.R. Tracy, S. Mooney, K.R. Daly, T. Roose, N. Crout, M. Bennett, T. Pridmore, J. Foulkes
World Congress of Soil Science, South Korea, June 2014


increase in international visibility
Year(s) Of Engagement Activity 2014
 
Description Workshop on Truly Project 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Type Of Presentation workshop facilitator
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Workshop titled "Truly predicting plant water uptake: the image based modelling approach" was attended by

The postdocs on the Truly projects gave the following two talks
1. "Truly predicting plant water uptake: the image based modelling approach" by K. R. Daly, S. R. Tracy, S. J. Mooney, T. Roose
2. "Visualisation and quantification of water in bulk and rhizosphere soils using x-ray computed tomography" by S. R. Tracy, S. Mooney, K. R. Daly and T. Roose

After the workshop several international groups (industry and academia) approached us for potential future joint projects.
Year(s) Of Engagement Activity 2015
 
Description X-ray CT imaging and image based modelling of nutrient uptake by root hairs 
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, S. Masum, T. Roose. X-ray CT imaging and image based modeling of nutrient uptake by root hairs. British Applied Mathematics Colloquium, 2014 , 29/04/2014.

Increased visibility and stimulation of the community
Year(s) Of Engagement Activity 2014