Exploring the rhizosphere: Imaging root-soil interactions using X-ray Computed Tomography

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1 Exploring the rhizosphere: Imaging root-soil interactions using X-ray Computed Tomography Dr. Saoirse Tracy School of Agriculture & Food Science University College

2 nitrate/water phosphate/micronutrients The Rhizosphere The hidden half of plants - The Rhizosphere The hidden half Target Traits 1. root hair length/density 2. longer seminal roots 3. more lateral roots 4. greater biomass 5. steeper root angles 5 1 non adapted genotype adapted genotype Key root traits The rhizosphere Enmeshment by fungal hyphae GLUE CO 2 Root exudates as food source

3 The Rhizosphere: My research sphere PhD - University of Nottingham, : The response of root system architecture to soil compaction Soil Post-doc project University of Nottingham : Predicting wheat root water uptake Roots Rhizosphere Water + Nutrients Microbes Assistant Professor - University College Dublin. Since 2015 Setting up own lab researching soil health, rhizosphere processes and root interactions

4 If soil Better is a black visualisation box how do we visualise it?

5 The Soil Health Concept - What makes a soil healthy? - A balance between soil physical, chemical and biological properties will enhance soil quality and enable all soil functions to be carried out. - A greater understanding of soil physical, chemical and biological properties and crucial and how they interact is key Image taken from Ritz and Rickson, 2017.

6 Is soil structure at the basis of agriculture? - We no longer view soil as an inert material but a living organism with complex processes occurring at several scales simultaneously Agriculture Soil Health Soil structure

7 Soil management to restore and improve our soils Aim = To maintain a fertile seedbed and root zone, whilst retaining maximum resistance to soil degradation 1. Enhance Productivity 2. Control soil degradation 3. Concept of sustainable intensification Prof. Jane Rickson, Cranfield University

8 Food Security The world must grow more crops on the currently available land to meet the increasing demand for food, feed and fuel We need 50% more production on less land with less water using less energy fertiliser and pesticide whilst not increasing GHG emissions by Challenge - double food production Climate Change Sustainability Technology will be critical 4 Technologies have raised yields since the 1950 s Mechanisation, Fertilisers, Crop Protection Chemicals Better crop varieties Food security considerations

9 Are roots key to the second green revolution? Roots are key to the second green revolution Prof. J Lynch said the second Green Revolution can t depend on irrigation or fertiliser. He states that to grow more food under tough conditions affordably, we re going to have to breed plants with improved roots. Sir Paul Nurse, President of the Royal Society highlighted that a greater understanding of plant biology and soil interactions is key to tackling the food challenges of the 21 st Century

10 Methods used to investigate root growth Drilling soil cores Column experiments Tracking individual /groups of cells Root washing Root scanning Agar plating

11 Limitations of rhizosphere studies Roots play a vital role in plant growth and development, therefore understanding how they interact with their surroundings is important however: Study is limited by the opacity of soil Traditional methods disturb the soil The 3-D heterogeneous nature of soil is dynamic in space and time

12 Detector Manipulator X-ray gun What is X-ray Computed Tomography?

13 The Root Imaging Challenge Similar attenuation of roots, water and pore spaces has led many researchers to work with sandy soils, with low moisture content & with thick rooting plants Roots Pore space Pore space Root material Soil Soil Maize in loamy sand, resolution 44µm Mooney, Pridmore & Bennett (2012) Marschner Review, Plant & Soil

14 Root system development of a tomato seedling grown in soil Tracy et al. (2012) Annals of Botany

15 Mairhofer et al. 2012, Plant Physiology. The next stage interacting root systems 3 x wheat plants with interacting roots

16 Postdoctoral Research Assessing the influence of the rhizosphere on the water release characteristic using X-ray Computed Tomography

17 Soil physics: Our knowledge gaps In the field: - Visual observations In the lab: - Destruction of structure - Our knowledge of soil water interactions at the field and column scale is much better than at the individual pore scale - This is because it has only recently been possible to observe this scale meaningfully

18 Research to understand soil water dynamics The aim of this research was to develop models of water movement and uptake accounting for the micro-scale structure of soils and roots and apply these models to evaluate differing root system architectures This research has two key aims: 1. Using X-ray CT to visualise the precise water distribution in soil in 3D 2. Derive calculated water release curves by feeding image data directly into models

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20 Measuring individual air filled pores - Pore characteristic measurements (volume, surface area, thickness) were collected for water and air filled pores in 3D 3D pore thickness heat maps for a representative clay loam (a-c) and loamy sand (e-f) sample. Tracy et al., 2015, Water Resources Research

21 Modelling hydraulic conductivity in the rhizosphere - 3D imaging data was combined with numerical modelling - During rhizosphere formation hydraulic conductivity decreases as water content reduces due to smaller pores - Significant difference between bulk and rhizosphere soils in the clay Daly et al, 2015, JXB Tracy et al., 2015, Journal of Experimental Botany

22 Microbes as habitat engineers? GLUE CO 2 Enmeshment by fungal hyphae Root exudates as food source

23 The influence of microbes on pore connectivity Helliwell et al., 2014, Soil Biology & Biochemistry

24 The influence of microbes on pore formation Fig. 3. An isolated pore from the centre of a representative clay loam sample, showing changes to pore morphology with time after: a) 0 weeks; b) 2 weeks; c) 4 weeks; d) 8 weeks; e) 24 weeks of incubation. Helliwell et al., 2014, Soil Biology & Biochemistry

25 The UCD X-ray CT Facility GE Vtomex M March 2017 Max sample diameter = 30 cm Min resolution = 2 micron GE Nanotom M March 2018 Max sample diameter = 25 cm Min resolution = 0.3 micron

26 PhD students - David Hobson Cultivation practices and root:soil interactions of winter wheat. - Conor Bracken Impact of multispecies pastures on N 2 O emissions. My team - Shane Brett - Cultivation practices and root:soil interactions of field beans. - Micheal Byrne Impact of soil biostimulants on root system architecture. - Stephen Kehoe Root phenotyping to improve Irish cereal crops to abiotic stresses. Msc students - Asaf Shnel Impact of rooting characteristics on soil physical parameters in multi-species pastures.

27 Summary X-ray CT can be utilised to give us new insights into soil processes and root interactions over time The rhizosphere is the key interface for plant resource acquisition A greater understanding of root system architecture and crop productivity is required Ensuring good soil health will allow normal soil functioning

28 Acknowledgements Prof. Sacha Mooney Dr. Craig Sturrock Prof. Malcolm Bennett Prof. Jeremy Roberts Prof. Tony Pridmore Dr. Jon Helliwell Dr. Stefan Mairhofer Prof. Tiina Roose Dr. Keith Daly Dr. John Foulkes Prof. Debbie Sparkes Dr. Ann McNeill Prof. Mark Tester Dr. Ian Dodd Dr. Paul Sweeney