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APLIM: Advanced Plant Life Imaging and Metrology

Advanced imaging and metrology of plant life.

Interview with Jean-Luc Verdeil, researcher at the AGAP (Genetic Improvement of Mediterranean and Tropical Plants) joint research unit, Cirad, and Christophe Goze-Bac, Director of the BioNanoNMRI platform, CNRS.

1. Could you briefly present your project?

The APLIM project aims to develop MRI (Magnetic Resonance Imaging) and NMR (Nuclear Magnetic Resonance) methodologies for the study of plants under stress. Our initial observation was that in Montpellier there were many teams working on the response of plants to water stress in the context of climate change, but none of them had access to methods for water visualization and the dynamic monitoring of its transport. This is precisely what MRI technologies allow, paving the way for in vivo visualization of water in plants. Faced with the difficulties for plant physiologists to better comprehend and master this technique, we wanted to develop it and make it accessible to them.
This very ambitious project analysed several types of stress: hydric, saline and biotic stresses. Christophe Goze-Bac’s team, in collaboration with plant biologists developed tailor-made tools adapted to plants, as the existing tools were exclusively intended for animal health and biology: horizontal MRI, with very large antennas (adapted to humans (medical MRI) or mice (animal MRI)). The plants studied are vertical, and very small. Antennas of a few millimetres have been developed for Arabidopsis, a few centimetres for sorghum. Clip-on antennas have been developed to reach the different parts of the plant. This is a technological achievement that allows to adapt to the geometry of the plant and thus can be installed around the stems, leaves or roots. A portable NMR was also developed from the beginning of the project to be used in the field (thesis co-financed by the NUMEV Labex, Cirad and APLIM). This equipment gives access to water contents and allow measurement of water fluxes in plants in greenhouses and fields, in a non-invasive way.
Another important issue was the maintenance of plants in good environmental conditions inside the NMR/MRI equipment. To do this, Agap research unit’s teams and Jean-Luc Verdeil developed mini greenhouses with adapted lighting systems.
The collaboration between plant specialists and the Physics laboratory of the University of Montpellier on this subject was totally new. Researchers who did not usually collaborate were thus brought to work together. In order to facilitate this collaboration between very distant disciplines, researchers from each domain were associated to the project from the beginning, and for each action and work plan, a plant biologist and a physics specialist were associated. Hiring doctoral students was also a determining factor in establishing the link between laboratories. A total of five theses have been produced during the project, with constant back and forth between physics and plant sciences. This required a great open-mindedness and the ability to combine disciplines. The students really played the game and adapted to the complementary discipline in a remarkable way.

2. What are the main achievements of your project?

The project is a good example of consultation and multidisciplinarity. Initially, we had difficulties working together across very different disciplines. Simple things like terminology were obstacles. The word "field" does not have the same meaning for an agronomist as it does for a physicist... The organization of training courses was essential: plants, plant physiology for physicists and MRI, basic principles for plant researchers. Very quickly, we were able to overcome our differences to co-construct around biological questions.
Two patents were filed (antennae / homogeneous development of the magnetic field; 3D printing, magnetic field-compatible).
In terms of applications, the most important results were obtained on sorghum, tomato, grapevine and rice. The project has led to important advances in understanding the role of tissues in water management. In sorghum, for example, we have been able to demonstrate a direct relationship between the two types of parenchyma (a trait for which there is great diversity) and the capacity of cells to store water in the stem and to remobilize it in the event of water deficit. The possibility of measuring water fluxes in each conductive vascular bundle has highlighted the complexity of this plant vascular system. This means reviewing the relationship between sorghum vascular system architecture and its functioning, and raises many questions. Jeanne Simon, one of our PhD students from Inrae Avignon, received the prize for the best oral presentation at the 11th ISH symposium organized in Finland, with her thesis on "A combined modelling and MRI approach for the study of water and carbon fluxes in tomatoes in response to hydric and thermal stress". MRI images of sodium obtained by developing adapted sodium antennas could be obtained for the first time in plants (rice and date palm). MRI to visualize the water fluxes is a good tool to study the dynamics of desalination processes in situ.
A whole part of the project focused on the chemistry of nanoparticles (partnership with the Yannick Guari laboratory (Institut Carnot Chimie Balard Cirimat), to trace water fluxes in the plant. A post-doc worked on this topic (on Arabidopsis) with the BPMP research unit. A Thai student did a thesis on the design of nanoprobes that can incorporate molecules to serve as cargo in coffee plants.

3. How has your project and the Foundation’s support to your project had a structuring effect on the Agro community?

The funding we received allowed us to work together in totally innovative fields. It also led us to seek co-financing (only 50% of the necessary funding was provided by Agropolis Fondation), skills that enabled us to think about the sustainability of the project from the beginning.
In concrete terms, the project will continue, with the creation of a platform open to plant researchers at the Charles Coulomb laboratory. We have communicated at the regional level (research on cabbage with teams from Toulouse), and with the South. The work on portable NMR will be continued via a new thesis funded by IRD and Montpellier University to work on Millet and Sorghum directly in the field with our partners in Senegal.
We have also contacted private companies, more specifically a local SME that wanted to produce climatic chambers. While this project was unsuccessful, one with another local private company is currently being completed: a collaboration contract has been signed with the university to develop the instrumentation (vertical MRI dedicated to plants) and make the functional portable system more reliable.
Finally, as for the project continuation, great efforts have been made on the MRI image processing of plants (within the framework of the APLIM project and one of its satellite projects, VITIMAGE). At the end of the project, we will have a user-friendly open source image processing tool to exploit MRI imagery in plants (APLIMtoolset). This tool, still in the test phase, should be ready by the end of 2020-early 2021. With this tool, we will be able to reach an even larger community at the international level.

Link to project description