Microorganisms, such as phytoplankton and bacteria, make up ≈70% of aquatic biomass and contribute 50-85% of the oxygen in Earth’s atmosphere. The microbial loop concept and the discovery of the large diversity in microbial communities acknowledge that biotic interactions between microorganisms in addition to resource competition enable the recycling of energy and nutrients in aquatic food webs. In this thesis, I have studied interactions between phytoplankton and bacteria in three brackish systems of increasing complexity. Interactions were characterized in terms of structure and function, species-specificity aspects, influence on community resilience, and the link between interactions and cycling of energy and nutrients, using a combined approach of molecular techniques, morphology and biochemical analyses, and network analysis. Species-specific core microbiomes were identified in cultures of dinoflagellate isolates with varying genotypes or phenotypes, or from locations with varying levels of anthropogenic impact. We argue that the structure of phytoplankton-bacterial communities is influenced by predictable species-specific interactions, in addition to local abiotic conditions (such as salinity). When microalgal productivity exposed to seasonal variations in light and temperature was examined in photobioreactor polycultures, the stability of microalgal biomass linked to a high bacterial response diversity, primarily seen as shifts in taxonomy. When the structural and functional response of microalgae and bacteria to temperature shifts was coupled to resilience theories (adaptive cycles, panarchy and cross-scale resilience), results suggest that resilience was enabled through internal shifts in function and diversity within and across microalgal and bacterial levels, leading to maintenance of overall community function and diversity. Further, the results suggest that phytoplankton and bacteria in a coastal eutrophied location avoid competition for both energy and nutrients by resource partitioning, indicating that phytoplankton and bacteria might coexist more frequently in dynamic shallow coastal ecosystems than previously thought.

The results from this thesis emphasize the importance of considering community interactions between phytoplankton and bacteria when studying aquatic microbial communities, both in cultures and in complex field environments.