Forecasting changes in microclimate and microbial diversity within plant canopies (MicroMic) | 2017-2019

Screen Shot 2017-09-21 at 8.07.07 PMMicro-organisms living within tree canopies experience microclimates that are highly variable in both space and time. Leaf surface temperature can differ by several degrees between the canopies of two adjacent trees, between sun and shade leaves of the same tree, and even between the edge and the center of the same leaf. Foliar microbial communities can also influence tree health (e.g. by fighting pathogens) and contribute to major ecosystem functions such as carbon and nitrogen uptake (e.g. by modulating stomatal closure) and influencing senescence and nutrient cycling (e.g. via litter decomposition). The aim of this project is to understand better how microclimatic heterogeneity and microbial diversity are linked within tree canopies and how this can affect leaf function. Metagenomics and state-of-the-art techniques in microclimate and automated phenological measurements will be compared to microclimate simulations from the canopy SVAT model MuSICA and used to explore how microbial and plant function varies spatially within the canopy and over the growing season. This study is a collaboration between ECOFUN and the INRA UMR BIOGECO.

Project organisationScreen Shot 2019-02-07 at 4.37.20 PM

To acheive the overall goal the project is organised into 3 main goals:

WP1: determining within-canopy variation in microclimate and leaf functional traits under current and future climate
WP2: modelling within-canopy variation in the structure and function of phyllosphere microbial communities under current and future climates
WP3:consequences of climate-driven changes in phyllosphere microbial communities on nutrient cyclng and coupling of terrestrial and aquatic ecosystems
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The MicroMic team


From left to right: Laura Clave, Joelle Berthier, Lisa Wingate, Adria Barbeta, Regis Burlett, Tania Fort, Charlie Pauvert, Yannick Mellerin (Corinne Vacher behind the camera!)

The Labex MicroMic team has brought together a group of talented young researchers and engineers from across the world:


Koen and Lisa participate in the SOERE phenology network workshop on leaf senescence measurement at the Observatoire de Haute Provence

Project partners

The Labex MicroMic team also benefits from working closely and continuously with researchers and engineers working in Bordeaux and on the Labex Project HYDROBEECH :

The project also works closely with the INRA  platform based in Pierroton, Cestas.

Publications and Communications

Peer-reviewed articles

Barbeta, A., Jones, S., Clavé, L., Wingate, L., Gimeno, T.E., Fréjaville, B., Wohl, S. & Ogée, J. (submitted) Hydrogen isotopic fractionation affects the identification and quantification of tree water sources in a temperate deciduous forest. HESS Discussions

Hufkens, K., Basler, D., Milliman, T., Melaas, E.K., Richardson, A. (2018) An integrated phenology modelling framework in R. Methods in Ecology and Evolution, logo_openaccesslogo_link

Hufkens, K., Filippa, G., Cremonese, E., Migliavacca, M., Brown, T., D’Odorico, P., Peichl, M., Gielen, B., Hortnagl, L., Soudani, K., Papale, D., Rebmann, C., Brown, T. & Wingate, L. (2018) Assimilating phenology datasets automatically across ICOS ecosystem stations. International Agrophysics, 32, 439-455 doi:10.1515/intag-2017-0039 logo_openaccesslogo_link

Klosterman, S., Hufkens, K. & Richardson, A.D. (2018). Later springs green-up faster: the relation between onset and completion of green-up in deciduous forests of North America. International Journal of Biometerorology

Richardson, A., Hufkens, K., Milliman, T., Frolking, S. (2018) Intercomparison of phenological transition dates derived from the PhenoCam Dataset V1.0 and MODIS satellite remote sensing. Scientific Reports, 8, 5679 doi:10.1038/s41598-018-23804-6 logo_openaccesslogo_link

Communications at international conferences and laboratories
  • Hufkens, K. & Richardson, A.D. The Phenor R package for vegetation phenology modelling: an open source toolkit to facilitate model-data integration and promote scientific reproducability. Geophysical Research Abstracts, Vol. 20, EGU2018-8110, Vienna, France, 9-13th April 2018
  • Hufkens, K. & Richardson, A.D. PhenoCam network update: public release of a processed dataset, and potential applications. Geophysical Research Abstracts, Vol. 20, EGU2018-8009, Vienna, France, 9-13th April 2018

    The MicroMic project has received funding from the French National Reserach Agncy (ANR) in the frame of the Investments for the future programme, within the Cluster of Excellence COTE (ANR-10_LABX-45).