!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
Y. (Yoan) Eynaud
Modelling the marine microbial network: the impact of physiological details
In the last ten years, some biogeochemical models have explicitly
included the microbial compartment, which contributes to the
remineralization of the organic matter among the water column in the
marine environment (e.g. Anderson and Williams, 1999). Initially, the
description of the processes describing the remineralization was
really poor. Recent work has proposed numerical studies on the impact
of more precise description of processes on the global behavior of
marine ecosystems (Fultons et al.,2004, Baklouti et al.,2006). This
works has ended up to contradictory results and it now appears
essential to focus deeper on that matter.
Also, the integration of more and more precise mechanistic details
inevitably leads to complex models production. Mathematical analysis
of such models is impossible and even numerical study and information
extraction given by simulations are hard. Recent works propose some
approaches in order to analyse such outputs (Raick et al., 2006a,
Clarck et Gelfand, 2006) or simplify it (Cox et al., 2006, Raick et
al., 2006b, Auger et al., 2008).
Meanwhile, the fundamental influence of precise choices of
mathematical formulations for processes on the dynamic of models has
been shown in simple cases (Blasius and Fussman, 2005). This work
demonstrates that different formulations describing the same process
surprisingly leads to quantitatively and qualitatively different
results. It shows that in certain case, taking account of mechanisms
is essential in the choice of the right formulation.
LMGEM is specialized in the study of biotic and abiotic
biodegradation, thus as in modeling (Tolla et al., 2006, Eichinger et
al., 2006), for instance by using the DEB theory. At the same time, we
also develop methods for simplification of in order to add mechanistic
formulation in ecosystem models (Eichinger et al., in prep). Our
original simplifying approach (Auger et al., 2008) was founded on the
hierarchical structure of ecosystem. It allows keeping relationships
between the detailed and the simplified model, including the ways
mechanisms interact. The LOPB is specialized in studying and modeling
the marine biogeochemical processes and coupling with physics.
The goals of this thesis are:
Those objectives are included in the study of the effect of the global change on ecosystem functioning. They also permit to outline the effect of those changes on the organism response (physiology, function).
- Integrate mechanistic formulations, which concern the biodegradation of organic matter by bacteria, developed in publications by
Tolla et al.(2007),
Eichinger et al. (2006)
Eichinger et al. (2009), in the ecosystem model Eco3M;
Simplify the obtained model
Study the impact of individual mechanism at the microbial community scale and on the ecosystem dynamic
Study how a global perturbation of the ecosystem impacts the individual metabolism.
More in particular I will focus on the dynamics of the microbial loop in the water column, and the interaction with phyto- and zooplankton dynamics on the context of the ECO3M model. I will focus on the processes of co-limitation, co-metabolism, competition, exudation, grazing and mineralisation.
Auger, P., Bravo de la Parra, R., Poggiale, J.-C. , Sanchez, E. and Nguyen-Huu, T. (2008) Aggregation of Variables and Applications to Population Dynamics. In: Structured Population Models in Biology and Epidemiology, Series: Lecture Notes in Mathematics, Subseries: Mathematical Biosciences Subseries , Vol. 1936 Magal, Pierre; Ruan, Shigui (Eds.), 345 p.
Baklouti, M., Faure, V., Pawlowski, L. and Sciandra, A. (2006) Investigation and sensitivity analysis of a mechanistic phytoplankton model implemented in a new modular numerical tool (Eco3M) dedicated to biogeochemical modeling, Prog. Ocean. 71, 34-58
Clark, J.,S., et Gelfand, A.E. (2006) A future for models and data in environmental science, TREE 21, 375-380
Cox, G.M., Gibbons, J.M., Wood, A.T.A., Craigon, J., Ramsden, S.J., Crout, N.M.J. (2006) Towards the systematic simplification of mechanistic models, Ecol. Model. 198, 240-246
Eichinger, M., Kooijman, S.A.L.M., Sempéré, R. and Poggiale, J.-C.} (2009) Consumption and release of dissolved organic carbon by marine bacteria in a pulsed-substrate environment: from experiments to modelling. Aquatic Microbial Ecology 56, 41-54
Eichinger, M., Poggiale, J.-C., Van Wambeke, F., Lefèvre, D., Sempéré, R. (2006) Modelling DOC assimilation and bacterial growth efficiency in biodegradation experiments: a case study in the Northeast Atlantic Ocean. Aquatic Microbial Ecology 43, 139-151
Fussmann, G.F., Blasius, B. (2005) Community response to enrichment is highly sensitive to model structure. Biology Letters 1, 9-12.
Raick, C., Beckers, J.-M., Soetaert, K., Grégoire, M. (2006a) Can principal component analysis be used to predict the dynamics of a strongly non-linear marine biogeochemical model? Ecol. Model. 196, 345-364
Raick, C., Soetaert, K., Grégoire, M. (2006b) Model complexity and performance: How far can we simplify? Prog. Ocean. 70, 27-57
Tolla, C., Kooijman, S. A. L. M., and Poggiale, J.-C. (2007) A kinetic inhibition mechanism for maintenance. Journal of Theoretical Biology, 244, 576-587
Go to projects' entry