DHEMISA aims to investigate the dynamics of aquatic heterotrophic microorganisms, from heterotrophic prokaryotes to microzooplankton, with a new automated flow cytometer (Cytopro) specially designed for this purpose by both an EU SME (Cytobuoy bv, NL) and the AMU host team belonging to the Mediterranean Institute of Oceanography (MIO). DHEMISA is a joint project between MIO and IRSTEA, both members of the OT-Med consortium. The PostDoc who joined the MIO team will validate the Cytopro automated cytometer and develop its application to study the dynamics of heterotrophic microorganisms in a laboratory and in situ, (1) in the Berre Lagoon and in a (2) Mediterranean lake (monitored by the pôle ONEMA- IRSTEA), where food web structure will be related to the ecosystem functioning characteristics, namely organic matter degradation and ecosystem metabolism. In terms of microbial ecology, this new tool will address simultaneously mineralisers and grazers and consequently will have a considerable impact on the assessment of the quantification of organic matter mineralisation and its transfer to higher trophic levels. As demonstrated for phytoplankton, in situ high frequency observation of heterotrophic microorganisms at the single cell level is a prerequisite to achieve a better characterisation and quantification of the dynamics of both their biological activity and their interaction with the autotrophic compartment. The ultimate stage of DHEMISA project will be coupling of Cytosense and Cytopro instruments to address simultaneously the short term variations of both compartments (phytoplankton and heterotrophic microorganisms). This will provide a more detailed information of their dynamics allowing a real breakthrough in the field of microbial ecology.