Résumé: Aquaculture is becoming a relevant and productive source of seafood, and production is expected to double in the near future. However, bivalve activities can significantly impact coastal ecosystem functioning. To study the direct and indirect impacts of oysters on the microbial food web, a OD biogeochemical modelling approach was adopted. The model was adjusted by parameter optimisation, assimilating data from several mesocosm observations of concentrations of nitrate, phosphate, silicate, dissolved organic carbon, chlorophyll, and bacterial biomass. The optimisation method provided a set of optimal parameters to fit the experimental observations of 'control' (i.e. natural water without oysters) and 'oyster' (i.e. natural water with oysters) mesocosms. The modelling results showed good accordance with the experimental observations, suggesting that the oysters directly reduced phytoplankton community biomass, thus constraining the ecosystem to a more heterotrophic state. Oysters also reduced competition between bacteria and phytoplankton for nutrient uptake, favouring higher bacterial biomass than in the control experiment. Additionally, the presence of oysters strongly increased large micro-zooplankton biomass (50-200 pm; mainly ciliates and large flagellates). This was a consequence of bacterivory by small zooplankton (5-50 mu m; mostly flagellates and small ciliates), providing a trophic link between bacteria and larger zooplankton. In conclusion, parameter optimisation showed good capacity to manage experimental data in order to build a more realistic model. Such models, in connection with future developments in aquaculture and global change scenarios, could be a promising tool for exploited ecosystem management and testing different environmental scenarios.

Résumé: Vermicompost and biochar amendments are management practices which may contribute to sustainable agroecosystems by reducing dependence on inorganic fertilizers. However, little is known about their impacts on soil microorganisms and their transfer and evolution in connected aquatic systems. The aim of this study was to determine the influence of organic manure (buffalo manure, compost or vermicompost) and biochar amendments on bacterial and viral properties in soil and water. A three year experiment was carried out with terrestrial mesocosms which were used to test the effect of organic matter amendment on maize growth. In the last year of the experiment, runoff and infiltration waters from the terrestrial mesocosms were transferred to aquatic mesocosms. Organic fertilization improved soil properties (higher C, N content and pH H 2 O ) and as a consequence increased soil bacterial and viral abundance. Bacterial diversity (Shannon ‘H’ and richness ‘S’ indices calculated from DGGE fingerprint) was also enhanced after the continuous application of organic amendments. Compared with compost, vermicompost reduced viral abundance and S but similar H and bacterial abundance were observed. The pH H 2 O , C content and bacterial and viral abundance increased in the aquatic mesocosms following organic fertilization. As a consequence, bacterial and viral diversity also increased in the water, although no differences were found between compost and vermicompost. Biochar increased soil bacterial abundance for the mineral fertilizer treatment but did not influence bacterial and viral abundance in water. However, the combination of biochar and vermicompost led to an increase of viruses in soil and a reduction of bacteria in water. Similarity dendrograms from the DGGE banding patterns showed that the structure of bacterial communities was mainly influenced by the fertilizer treatments in soil but by the presence of biochar in water. In conclusion, this study demonstrated that the nature of the organic amendment has important consequences on both soil and water microbial abundance and diversity.

Résumé: Upon phosphorus (P) deficiency, marine phytoplankton reduce their requirements for P by replacing membrane phospholipids with alternative non-phosphorus lipids. It was very recently demonstrated that a SAR11 isolate also shares this capability when phosphate starved in culture. Yet, the extent to which this process occurs in other marine heterotrophic bacteria and in the natural environment is unknown. Here, we demonstrate that the substitution of membrane phospholipids for a variety of non-phosphorus lipids is a conserved response to P deficiency among phylogenetically diverse marine heterotrophic bacteria, including members of the Alphaproteobacteria and Flavobacteria. By deletion mutagenesis and complementation in the model marine bacterium Phaeobacter sp. MED193 and heterologous expression in recombinant Escherichia coli, we confirm the roles of a phospholipase C (PlcP) and a glycosyltransferase in lipid remodelling. Analyses of the Global Ocean Sampling and Tara Oceans metagenome data sets demonstrate that PlcP is particularly abundant in areas characterized by low phosphate concentrations. Furthermore, we show that lipid remodelling occurs seasonally and responds to changing nutrient conditions in natural microbial communities from the Mediterranean Sea. Together, our results point to the key role of lipid substitution as an adaptive strategy enabling heterotrophic bacteria to thrive in the vast P-depleted areas of the ocean.