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SCENARIO - Understanding Acute Oak Decline using X-ray micro-tomography and leaf reflectance: linking reduced tree water transport capacity to changes in xylem and leaf cellular structure.

Project Description

First recorded in the UK in the early 1900’s, Acute Oak Decline (AOD) is widely recognised as a threat to native English oaks. Outbreaks of disease have gone through several historic and distinct episodes with the current, ongoing spread having started around 2002. The disease, however, is poorly understood and described as multi-causal, probably involving both biotic and abiotic drivers. Trees with AOD show symptoms like reduced foliage and lesions on the trunks. A likely cause of stress in the symptomatic trees is lack of water in the canopy leaves due to blockages of the trachea in the xylem tissue of trunk and branch, and this may, in turn, cause a change in leaf intracellular structure.

In preliminary field work we have been able to identify differences in canopy leaf near-infrared reflectance between trees with and without lesions. The data also suggests that this difference may be driven by changes in leaf intercellular structure (described as the ‘N’ parameter in the widely used PROSPECT leaf reflectance model).

X-ray micro-tomography of leaves can reveal their internal structure, similar to histology but for a full 3-dimensional volume, instead of a single slice. X-ray micro-tomography of xylem can reveal the network of tracheary elements (i.e. water transport) and its connectivity. When using a synchrotron light source, scan times are in the range of a few minutes, allowing for the scanning of a statistically significant numbers of samples in a matter of hours or days. In addition, the resolution and signal-to-noise ratio can be improved significantly in comparison to laboratory machines.

We propose to investigate the cellular structure of leaves and xylem tissue from trunk and branches to establish whether trees affected by AOD show a change in leaf and xylem cell structure that can be linked to a change in the tree’s water transport capacity.

Proposal outline:
1. Analysis of X-ray tomography data of leaves to quantify leaf intracellular structure and attribute the observed difference in leaf near-infrared reflectance to changes in intracellular structure. An initial experiment at the Diamond light source has produced scan data for leaves samples from 8 pairs of symptomatic and asymptomatic trees. After tomographic reconstruction, these will be analysed to determine, among others, mean leaf density, leaf density profile, mean number of intracellular and cellular layers, to find correlations with the leaf reflectance parameter N.
2. Analysis of X-ray tomography data of trunk and branch xylem tissue and of leaves to attribute the changes in leaf intracellular structure to water stress caused by blockages of trachea cells. A new set of trunk, branch and leaf samples will be collected from trees showing a gradient of AOD symptoms (from mild to severe) and prepared for X-ray micro-tomography at the Diamond light source. After scanning and tomographic reconstruction, these samples will be analysed to determine and link intracellular and cellular changes of the xylem and leaf samples.
3. Through field based tree water transport observations, establish a link between AOD, a reduction in tree water transport capacity, and cellular changes.

Training opportunities:
The student will be trained in laboratory skills required to develop optimal ways of preparing the leaf and xylem tissue samples for X-ray micro-tomography scanning and will receive specialist training to use the X-ray micro-tomography beam at the Diamond Light Source in Harwell. There will be training in effective experimentation design, with a view on sound statistical principles together with efficient data collection and management.

Student profile:
Applicants should hold or expect to gain a minimum of a 2:1 Bachelor Degree, Masters Degree with Merit, or equivalent in (ideally) ecology or biology with a strong and passionate enthusiasm for scientific research, involving field, lab and computer based work. They must have good interpersonal skills for working within an interdisciplinary team environment. They must also be able to work responsibly on their own initiative in the field. Ideally, the candidate will have strong numerical literacy and have an aptitude for programming (in R). Desirable attributes would be skills in forest/tree science, general botany, plant physiology or image analysis. We would also hope the candidate has good writing and oral presentation skills.

To apply, please follow the instructions at

Funding Notes

This project is potentially funded by the Scenario NERC Doctoral Training Partnership, subject to a competition to identify the strongest applicants.

This project has CASE funding from Bartletts Tree Experts.

Due to restrictions on the funding this studentship is open to UK students and EU students who have lived in the UK for the past three years. The DTP can only fund a very limited number of international students, so only applications from international students with an outstanding academic background placing them in the top 10% of their cohort will be considered.


Hendry et al. (2005) Information Note FCIN 73* Forestry Commission, Edinburgh; Denman & Webber, (2010) Plant Pathology 57, 368; Denman et al. (2014) Forestry 87, 535-51;
Jacquemoud & Baret (1990) Remote Sens. Environ. 34(2), 75-91.

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