Exploring the rhizosphere:

Imaging root-soil interactions using X-ray Computed

Tomography

Dr. Saoirse Tracy

School of Agriculture & Food Science University College Dublin

Saoirse.tracy@ucd.ie@SaoirseT

The hidden half of plants - The Rhizosphere

non adapted genotype

Target Traits1. root hair length/density2. longer seminal roots 3. more lateral roots 4. greater biomass5. steeper root angles

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Root exudates as food source

GLUE CO2

Enmeshment by fungal hyphae

The hidden half

The rhizosphere

Key root traits

The Rhizosphere

Rhizosphere

Roots

Microbes

Water + Nutrients

Soil

The Rhizosphere: My research sphere

PhD - University of Nottingham, 2008 –2012: The response of root system architecture to soil compaction

Post-doc project –University of Nottingham - 2012 –2015: Predicting wheat root water uptake

Assistant Professor -University College Dublin. Since 2015 –Setting up own lab researching soil health, rhizosphere processes and root interactions

Better visualisationIf soil is a black box how do we visualise it?

The Soil Health Concept

- What makes a soil healthy?

Image taken from Ritz and Rickson, 2017.

- 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

Agriculture

Soil Health

Soil structure

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

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

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 2030

• 2050 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

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.

Roots are key to the second green revolution

Sir Paul Nurse, President of theRoyal Society highlighted that agreater understanding of plantbiology and soil interactions iskey to tackling the foodchallenges of the 21st Century

Are roots key to the second green revolution?

Methods used to investigate root growth

Drilling soil cores Column experiments

Root scanningRoot washing Agar plating

Tracking individual /groups of cells

Roots play a vital role in plant growth and development,therefore understanding how they interact with theirsurroundings 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

Limitations of rhizosphere studies

X-ray gunDetector Manipulator

What is X-ray Computed Tomography?

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

Soil

Root material

Pore space

Maize in loamy sand, resolution 44µm

Soil

Roots Pore space

Mooney, Pridmore & Bennett (2012) Marschner Review, Plant & Soil

Root system development of a tomato seedling grown in soil

Tracy et al. (2012) Annals of Botany

The next stage – interacting root systems

Mairhofer et al. 2012, Plant Physiology.

3 x wheat plants with interacting roots

Assessing the influence of the rhizosphere on the water release characteristic using X-ray Computed

Tomography

Postdoctoral Research

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

The aim of this research was to develop models ofwater movement and uptake accounting for themicro-scale structure of soils and roots and applythese models to evaluate differing root systemarchitectures

Research to understand soil water dynamics

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

Measuring individual air filled pores

3D pore thickness heat maps for a representative clay loam (a-c) and loamy sand (e-f) sample.

- Pore characteristic measurements (volume, surface area, thickness) were collected for water and air filled pores in 3D

Tracy et al., 2015, Water Resources Research

Modelling hydraulic conductivity in the rhizosphere

Daly et al, 2015, JXB

- 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

Tracy et al., 2015, Journal of Experimental Botany

Microbes as habitat engineers?

Root exudates as food source

GLUECO

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Enmeshment by fungal hyphae

The influence of microbes on pore connectivity

Helliwell et al., 2014, Soil Biology & Biochemistry

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

The influence of microbes on pore formation

The UCD X-ray CT Facility

GE Vtomex M March 2017Max sample diameter = 30 cm Min resolution = 2 micron

GE Nanotom M March 2018Max sample diameter = 25 cm Min resolution = 0.3 micron

PhD students

- David Hobson – Cultivation practices and root:soilinteractions of winter wheat.

- Conor Bracken – Impact of multispecies pastures on

N2O emissions.

- 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.

My team

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

Prof. Sacha Mooney Dr. Craig Sturrock Prof. Malcolm BennettProf. Jeremy RobertsProf. Tony PridmoreDr. Jon Helliwell Dr. Stefan Mairhofer Prof. Tiina RooseDr. Keith DalyDr. John FoulkesProf. Debbie SparkesDr. Ann McNeillProf. Mark TesterDr. Ian DoddDr. Paul Sweeney

Acknowledgements