Microorganisms (unicellular algae, bacteria) constitute fundamental compartments of aquatic ecosystems because of their high concentrations and activities. The evaluation and understanding of their behavior and role raise different problems for which traditional methodologies are often inadequate, whether they refer to global or classical microscopic analyses. Flow cytometry (FCM) has been recently used to study microorganisms in aquatic environments. Although this technology is still applied on a limited scale in our field, a large number of works has been done showing that FCM seems to be a promising tool for aquatic microbial ecology. This paper summarizes, from the literature produced during the last decade and with original data obtained in our laboratory, the main questions related to the cell identification, the evaluation of cell viability, biomasses and productions and the measurements of bacterial and phytoplanktonic activities. The representatives of sampling and observation scales is also discussed within the framework of the FCM measurements.

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International audienceTAAF ensures since 2007 the management of 5 small tropical islands lying in the southwestern Indian Ocean: the Iles Eparses. These islands share an exceptional natural heritage including many marine and terrestrial endemic species. At a regional scale the Iles Eparses are some of the most pristine ecosystems, largely preserved from anthropogenic impacts due to their geographical isolation and a historically very limited human occupation. In this context, TAAF wished that Iles Eparses become unique natural laboratories for earth scientists and environmental process observation – like climate change impacts - but also sustainable biodiversity sanctuaries for which the scientific community should provide baseline ecological data to inform on appropriate conservation tools. An inter-agency research consortium emerged in 2009 to meet this commitment for the Iles Eparses. This program was intended to set a science framework in accordance with France' objectives for Research and Conservation. It enabled between 2009 and 2014 the implementation of 18 cross-disciplinary research projects ranging from geology to ecology and represented by the variety of the proposed articles in this special issue. Altogether research projects have dramatically increased knowledge on the Iles Eparses' ecosystems and have provided the first overview of their diversity, their functions and their dynamics and its determinants. In particular applied research efforts have supplied a significant amount of ecological evidence that is now available to develop optimal conservation strategy to ensure the Iles Eparses' long-term biodiversity value. These findings point out that the continuation of research activity in the Iles Eparses should be considered a priority