CE04 - Innovations scientifiques et technologiques pour accompagner la transition écologique

A unique MR imager outside the laboratory: new horizons in agro-ecosystems – OutLabMRI

In situ MRI determination of water quantity and fluxes to better characterize carbon sequestration in agroecosystems

To better understand carbon sequestration in terrestrial agroecosystems, it is critical to locally measure both upward (xylem) and downward (phloem) sap flow rates in plants. In this context, MRI is a unique and powerful analytical tool if it can be moved outside of the laboratory. This project aims to develop such a sensor to measure both water content and sap flow rates in plants, locally and non-invasively, in their natural environments (in situ).

How can we measure water content and sap flow rates in situ both locally and non-invasively?

Grasslands and forests are the two main terrestrial ecosystems limiting global warming due to their high capability to store carbon. Sap flows play a critical role by absorbing water and mineral salts used for transpiration and photosynthesis (xylem) and transporting the photosynthate carbons (phloem) to the carbon sinks (e.g., wood, roots, soil). In the context of global warming, a fine understanding of these transport mechanisms is necessary. However, a sensor able to measure each flow directly in the plant and in situ does not exist yet.<br />To measure water quantity and flow rates non-invasively, and in a given spatial volume (i.e., localized), MRI is the analytical tool of choice. However, such instruments typically cannot be moved and only laboratory experiments can be performed. Recently, portable MRI has been developed. To be able to move the MRI device, its magnetic field intensity (and so its sensitivity) must be significantly decreased. In addition to being low-field, we are also able to record the NMR signal in a thin slice due to the magnet being equipped with a high precision lift, making it possible to obtain 1D images (or profiles).<br />The project objective is to develop an MRI sensor to measure water quantity and flow in plants in their natural environments. To obtain spatial information, the sensor will use the technological developments described above. The sensibility of this MRI device will be evaluated in different environmental conditions, particularly under drought stress, and on different plants.

The versatility of this MRI sensor will be demonstrated by designing experiments on the two main terrestrial ecosystems: grasslands and forests. Concerning forests, we will focus our study on the aerial parts of the plants, while for grasslands, we will study the root systems in rhizotrons, i.e. in a model system.
First, we will compare the MRI results with the reference methods for each of the ecosystems. Nowadays, measuring xylem flow rates in trees in situ can be easily done and it will be possible to compare our results to these gold standard methods (heat dissipation, heat pulse). Regarding the phloem, no in situ method is currently available. Low-field MRI results will be validated in comparison to flow measurements obtained from a dedicated high field MRI device. To validate measurements on root systems, several analytical methods will be merged (flow micro sensors, hydric potential, 2D light imaging) and combined thanks to mathematical modeling.
To study ecosystems in a context of global warming, it is critical to know the sensor detection limit. This is the aim of the second task. Each biological system will undergo drought stress during MRI measurements. The results will demonstrate whether or not this sensor can give more information than the current reference methods.

The initial work focused on sensor developments. Indeed, the measurement depth is dependent on the magnet temperature. As this instrument will be used outside, the magnet temperature will change according to daily temperature fluctuations. We simultaneously worked on two complementary solutions. The first one dealt with the thermic insulation of the system to limit the temperature variations. The second consisted in measuring the magnet temperature and correcting the magnet position, in real-time, to keep the same measurement zone.
We observed on model root systems a circadian variation of the MRI signal intensity in well hydrated conditions. The use of water by the plant to perform photosynthesis explains these signal modulations. MRI observations are consistent with classical ecophysiological measurements (e.g. leaf water potential, soil water content). In drought conditions, and thus in the absence of photosynthesis, the MRI signal no longer varied between days and nights. We also demonstrated that the signal was proportional to the root water content, regardless of the grassland species. Portable MRI gives complementary information to the current analytical methods used to study root systems.
We demonstrated that water content could be measured by our sensor on branches. After performing measurements in the laboratory to find the relationship between the sensor signal and the water content, we showed that measurements on intact trees followed the same relationship. This relationship was independent of the tree species and functional type. Before performing flow measurements in the aboveground parts of trees (trunk and branches), it is critical to localize the flow measurement position from the 1D MRI profiles. Our results show that heartwood (dead wood without flow) and sapwood (containing xylem) can be differentiated based on their MRI signal. Furthermore, by using xylem and phloem magnetic properties (i.e., transverse relaxation time T2), it is possible to highlight the spatial position of each flow.

The full characterization of this MRI sensor will give the scientific community a new instrument with which to characterize agroecosystems. This sensor may lead to unique knowledge linked to the carbon storage processes.
These in situ experiments open up new avenues for MRI applications outside of the laboratory. Indeed, the difficulty in using such instruments outside of standard laboratory conditions will have been tackled. It will then be possible to use such devices in other fields. For example, it could be used to characterize raw materials/food during industrial processes. This sensor could also join the industrial and scientific revolution in the microfluidic area. Indeed, this field is inspired by liquid flows and their exchange in living science, a characterization done in our project.

Results obtained on the root systems were published in Plants (doi: 10.3390/plants10040782). Several communications were performed on either the sensor developments or results obtained on grassland model ecosystems. The details of the communications are available on the HAL-ANR webpage, accessible through the link present in the useful links section.

Forest and grassland are the two main terrestrial ecosystems able to mitigate global warming thanks to their high capability to store carbon. Ascendant (xylem) and descendant (phloem) sap flows play a key role in this storage by routing the water necessary for the oxygenic photosynthesis and then transporting the assimilated carbon into the carbon sinks, e.g. wood, roots or soil. In the current context of global warming, a better understanding of these transport mechanisms is key to ensure these ecosystems can continue to play their carbon sink role. Unfortunately, no sensor allowing studying these mechanisms directly in the plant and in its natural ecosystem exists yet.

In this project, we will set and validate a new versatile MRI instrument to measure locally and non-invasively water content and flow rate outside the laboratory (in situ). This approach allows exploiting the unique and advantageous features of MRI: it is non-invasive, can measure water quantities and flow rates and is spatially selective, i.e. measurements can be performed in well-defined plant areas. The aim of this project will be to validate this instrument as a new tool to study both forest and grassland agro-ecosystems. For each of them, we will demonstrate the advantages of this new sensor relatively to the in-situ reference methods (such as lysimeters, sap flow sensors, gravimetric methods …). This instrument will be evaluated in regards of its capabilities to:
(1) give localized information (specificity), especially to measure both xylem and phloem sap flows as they do not go through the same cells in plants and, to discriminate the root heterogeneity directly in the soil;
(2) perform measurements under several environmental conditions (sensibility). We will focus on the hydric stress in order to detect cavitation in trees and recovery of grasses
(3) evaluate the carbon storage by the ecosystems thanks to sugar concentration measurements by the in-situ MRI instrument.

To maximize the success rate of this project, a multi-disciplinary team has been gathered. The skills of the scientists involved are going from vegetal physiology to applied mathematics through ecosystem modelling. Furthermore, Carel Windt, an internationally renowned scientist for his skill to develop in-situ MRI sensor, will follow the project and bring his expertise to the scientific discussions and choices.

At the end of this project, the interest of this new sensor will have been demonstrated and its deployment at larger scale, to have a better understanding of the carbon storage mechanisms, will be possible. The following step would be to create a network of in-situ MRI instruments. Thus, measurements at the individual level would bring more knowledge on the plant itself while exploiting the network data would lead to a better understanding of the whole plant community as an ecosystem. Furthermore, new applications could be tested, especially in microfluidic sciences or in bio-based industries, two fields having currently a high gross rate. To disseminate as widely as possible our results, we will communicate to several scientific communities which could be interested by our results (MRI, functional ecology), to the public thanks to vulgarization (scientific days, articles in scientific magazine). Furthermore, we will make available the instrument to the scientific community through dedicated networks like AnaEE.

Project coordination

Guilhem Pages (Qualité des Produits Animaux)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.


EMMAH Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes
UREP Unité Mixte de Recherche sur l'Ecosystème Prairial
QuaPA Qualité des Produits Animaux
PIAF Physique et Physiologie Intégratives de l'Arbre en environnement fluctuant

Help of the ANR 487,527 euros
Beginning and duration of the scientific project: December 2019 - 48 Months

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