Sophie Rabouille

Welcome to my home page...


LOV, UMR 7093, Station Zoologique
B.P. 28 06234, Villefranche-sur-mer, France
Tel. +33 (0)4 93 76 38 32
Fax. +33 (0)4 93 76 38 34




Professional experience

Since 2007 CNRS Research Associate at the ocean observatory in Villefranche sur Mer (LOV), in the Plankton group.
2005-2007 Post doctoral fellow at the University of California at Santa Cruz (Ocean Sciences, UCSC). Supervision: C. Edwards, J.P. Zehr
2003-2005 Post doctoral fellow at the Netherlands Institute for Ecology (NIOO CEME) Supervision: K. Soetaert; collaboration with IBED-AMB


2015              Habilitation (HDR), Pierre & Marie Curie University (UPMC)
1999-2002     PhD Aquatic ecology and modelling
1999              Msc. Aquatic ecology and modelling
1994-1999     Undergraduate studies in Biology and Ecology, Paul Sabatier University, Toulouse, France


Phytoplankton ecophysiology, growth processes, nitrogen fixation, cyanobacteria, stoichiometry, modelling, aquatic ecology

I study the responses of planktonic, phototrophic organisms to their physico-chemical environment using both experimental and modeling approaches. At the university, I was trained as a biologist and ecologist; in my early career as a researcher, I was also grounded in the basics of modeling, which offered me a mechanistic understanding of biological systems. I chose to pursue this dual approach as it allows for an analysis of the relations that take place between the different components of a biological system. The exchange between theory and experience is an exciting way to test and validate hypotheses.
Complexity is one of the most intriguing and fascinating aspects of Nature; complex behaviors can emerge from the superposition of very simple independent processes. In this regard, models are fantastic investigation tools... They can for instance be used to grasp the combination of events leading to disequilibria, such as the appearance and maintenance of phytoplankton blooms. Mathematical modeling thus provides a workbench to conceptualize ideas and hypotheses about processes that may prove difficult to observe directly. Such models are, for me, a second laboratory; they complement experimental or field work.

Simulation of the successive use of different nitrogen sources in a continuous culture of Trichodesmium sp. IMS101 grown under a 12/12 light/dark regime. Concentration of combined nitrogen (DIN) in the medium, DIN uptake rate and N2 fixation rate. Horizontal black bars on the x axis show the dark period.




Light:dark regimes applied in the four experiments of the CROCOCYCLE project: 8:16 (a), 12:12 (b,d) and 16:8 (c). Light and dark phases are represented with light and blue shaded areas, respectively. The first three irradiance curves show a maximum of 130 E m-2 s-1. Both 12:12 experiments present the same daily light dose; hence, the maximum irradiance observed in the fluctuating regime is higher (328 E m-2 s-1.). In (d), the light regime from (b) is redrawn (thin line) for comparison.




Research projects






Rabouille, S., Semedo-Cabral, G. and Pedrotti M.-L. (in press). Towards a carbon budget of the diazotrophic cyanobacterium Crocosphaera: effect of irradiance. Mar. Ecol. Prog. Ser., doi: 10.3354/meps12087

Demory, D., Arsenieff, L., Simon, N., Gei, P., Rigaut-Jalabert, F., Bigeard, E., Marie, D., Six, C., Jacquet, S., Sciandra, A., Bernard, O., Rabouille, S. and Baudoux, A-C. (2017) Temperature is a key factor in Micromonas - virus interactions. ISME J 11(3), 601-612.

Rabouille, S., and Claquin, P. (2016) Photosystem-II shutdown evolved with Nitrogen fixation in UCYN-B diazotrophs. Environ Microbiol. 18: 477485. doi:10.1111/1462-2920.13157.

Combe, C., Hartmann, P., Rabouille, S., Talec, A., Bernard, O., and Sciandra, A. (2015) Long-term adaptive response to high-frequency light signals in the unicellular photosynthetic eukaryote Dunaliella salina. Biotechnol Bioeng. 112: 111-1121. DOI:10.1002/bit.25526

Grimaud, GM., Rabouille, S., Dron, A., Sciandra, A. & Bernard, O. (2014) Modelling the dynamics of carbon-nitrogen metabolism in a unicellular diazotrophic cyanobacterium, Crocosphaera watsonii WH8501, under variable light regimes. Ecol. Model. DOI:10.1016/j.ecolmodel.2014.07.016.

Chazalon, F., Rabouille, S., Hartmann, P., Sciandra, A. and Bernard, O. (2014) A dynamical model to study the response of microalgae to pulse amplitude modulated fluorometry. Proceedings of the 19th IFAC World Congress.

Hartmann, P., Demory, D., Combe, C., Hamouda, R., Bristeau, M-O., Sainte-Marie, J., Sialve, B., Steyer, J-P., Rabouille, S., Sciandra, A. &Bernard, O. (2014) Growth rate estimation of algae in raceway ponds: A novel approach. Proceedings of the 19th IFAC World Congress.

Grimaud G, Dron A, Rabouille S, Bernard O, Sciandra A (2013) Modelling light-dark regime influence on the carbon-nitrogen metabolism in a unicellular diazotrophic cyanobacterium. Proceedings of the 12th IFAC Symposium on Computer Applications in Biotechnology.

Rabouille, S., Van de Waal, D.B., Matthijs, H.C.P., and Huisman, J. (2013) Nitrogen fixation and respiratory electron transport in the cyanobacterium Cyanothece under different light/dark cycles. FEMS Microbiol Ecol: DOI: 10.1111/1574-6941.12251.

Dron, A., Rabouille, S., Claquin, P., Talec, A., Raimbault, V., and Sciandra, A. (2013) Photoperiod length paces the temporal orchestration of cell cycle and carbon-nitrogen metabolism in Crocosphaera watsonii. Environ Microbiol: doi:10.1111/1462-2920.12163.

Dron, A., Rabouille, S., Claquin, P., Chang, P., Raimbault, V., Talec, A., and Sciandra, A. (2012) Light-dark (12:12) quantification of carbohydrate fluxes in Crocosphaera watsonii. Aquat Microb Ecol 68: 43-55.

Dron, A., Rabouille, S., Claquin, P., Le Roy, B., Talec, A., and Sciandra, A. (2012) Light-Dark (12:12) cycle of carbon and nitrogen metabolism in Crocosphaera watsonii WH8501: relation to the cell cycle. Environ Microbiol 14: 967-981.

Talec A., Rabouille S., Nival P. & Sciandra A., 2010. SEMPO: a computer driven device for phytoplankton cultivation. JORD 3(4): 76.

Shi T., Ilikchyan I., Rabouille S. & Zehr J.P. 2010. Genome-wide analysis of diel gene expression in the unicellular N2-fixing cyanobacterium Crocosphaera watsonii WH 8501. Isme J 4: 621-632.

Bernard O., Sciandra A., and Rabouille S. 2009. Sensitivity of carbon fixation predictions during a bloom of Emiliania huxleyi. Biogeosciences Discuss., 6, 5339-5372.

Bernard O., Sciandra A., and Rabouille S. 2009. Predictions of carbon fixation during a bloom of Emiliania huxleyi as a function of the regulating inorganic carbon species. in Proceedings of the MATHMOD 09 conference - Full Papers CD Volume ( Vienna , Austria ), p1799-1807.

Agawin N.S.R., Rabouille S., Veldhuis M.J.W., Servatius L., Hol S., van Overzee H.M.J. and Huisman J. 2007. Competition and facilitation between unicellular nitrogen-fixing cyanobacteria and non-nitrogen-fixing phytoplankton species. Limnol. Oceanogr. 52: 2233-2248.

Rabouille S., Edwards C.A. and Zehr J.P. 2007. Modeling the vertical distribution of Prochlorococcus and Synechococcus in the North Pacific Subtropical Ocean. Environ. Microbiol. 9(10): 2588-2602.

Staal M., Rabouille S. and Stal L. 2007. On the role of oxygen for nitrogen fixation in the marine cyanobacterium Trichodesmium sp. Environ. Microbiol. 9(3): 727-736.

Rabouille S., Staal M., Stal L. and Soetaert K. 2006. Modeling the dynamic regulation of nitrogen fixation in the cyanobacterium Trichodesmium sp. Appl. Environ. Microbiol., 72(5): 3217-3227.

Rabouille S. and Salencon M.-J. 2005. Functional analysis of Microcystis vertical migration: A dynamic model as a prospecting tool -II- Influence of mixing, thermal stratification and colony diameter on the biomass production. Aquat. Microb. Ecol. 39: 281-292.

Rabouille S., Salencon M.-J. and Thebault J.-M. 2005. Functional analysis of Microcystis vertical migration: A dynamic model as a prospecting tool - I- Processes analysis. Ecol. Model. 188 (2-4): 386-403.

Rabouille, S., Thebault, J.-M., Salencon, M.-J. 2003. Simulation of carbon reserve dynamics in Microcystis and its influence on vertical migration with Yoyo model. C. R. Acad. Sci. Biologies 326(4): 349-361. Full article

Thebault, J.M., Rabouille, S. 2003. Comparison between two mathematical formulations of the phytoplankton specific growth rate as a function of light and temperature, in two simulation models (Aster and Yoyo). Ecol. Model. 163 (1-2): 145-151. Full article