Marine soft sediments form the second largest habitat on the planet. Organisms residing in this environment represent a vast reservoir of biodiversity, and play key roles in ecosystem processes. Most benthic organisms depend on organic matter (OM) inputs from phytoplankton in the overlying water column as food supply, but human impacts such as eutrophication and climate change are profoundly altering natural ecosystem dynamics. The consequences of changes in benthic-pelagic coupling for the biodiversity and functioning of soft-sediment communities have yet to be resolved. 

The aim of this thesis is to assess the role of OM settling on soft-sediments microeukaryotic (small organisms < 1 mm) and bacterial communities. The intents are two-fold, to investigate impacts on (1) community structure and diversity (chapters I, II and IV); and (2) ecosystem functioning, notably in relation to nitrogen (N) cycling (chapters I and III). 

Our results show that settling OM quantity and quality both had a significant impact on microeukaryotic alpha-diversity. We observed a decrease in alpha-diversity following settling of diatom-derived spring bloom OM, possibly as a result of competitive exclusion, while cyanobacteria-derived summer bloom OM did not affect alpha-diversity (chapters I and IV). We also found that high biomass of diatoms and others fast sinking phytoplankton groups in the water column led to lower microeukaryotic alpha diversity after this material settled on the seafloor (chapter IV). Presumably, following this large sedimentation event, sediment oxygen (O₂) demand was strongly stimulated, excluding O₂-sensitive taxa. Overall, we propose that the assembly of microeukaryotic communities was primarily mediated by OM settling quantity (chapter IV), while differences in OM quality led to significant but more subtle changes, occurring at fine taxonomic level (chapter I). The response of bacterial communities to OM settling was less pronounced, and probably restricted to the uppermost sediment layer (chapters I and IV). We did, however, observe a significant effect of OM quality on bacterial communities assembly at the sediment-water interface, with taxa favored either by diatom- or by cyanobacteria-derived OM (chapter II). This study also showed that feedback mechanisms from nutrient recycling in the sediment could play a role in this response. Finally, our results indicated a substantial influence of OM quality on N cycling at the sediment-water interface. We found that settling of fresh OM (i.e. low C:N ratio) stimulated denitrification activity (chapters I and III), while simultaneously promoting more N recycling to the water column than settling of degraded OM (i.e. high C:N ratio) did (chapter III).  

Altogether, our results indicate that current changes in OM settling dynamics in marine systems will likely impact microeukaryotic and, to some extent, bacterial biodiversity in soft sediments. Alterations in settling OM quality, in particular, may also affect crucial microbial processes involved in N cycling. This thesis highlights the importance of considering benthic-pelagic coupling mechanisms to better understand likely future changes in marine ecosystems.