Zooplankton is a key group of organisms in aquatic ecosystems that regulate element cycling, transport carbon and energy between trophic levels, and stabilize aquatic community structure. Their ecological importance is further emphasized by the fact that zooplankton are also microbial hotspots for diverse prokaryotic and eukaryotic microbes. The association between zooplankton and the microbes ranges from beneficial symbiotic to harmful parasitic interactions. Symbiotic associations contribute to multiple ecological functions, such as enhanced nutrient recycling, adaptation to unfavourable conditions and combating stresses, while parasitic interactions reduce species fecundity and increase mortality. Hence, the association between zooplankton and their microbes contributes to the structure and functioning of aquatic ecosystems. However, the dynamics of zooplankton-associated prokaryotic and eukaryotic organisms is largely unknown. 

In this study, the diversity, dynamics and drivers of the zooplankton symbiotic and parasitic communities were studied across the Baltic Sea environmental gradients to increase understanding about their ecological roles in aquatic ecosystems. The zooplankton associated microbial community composition was revealed by DNA metabarcoding, statistical modelling and machine learning. The communities were examined from different angles: taxonomic composition, functional clustering and phylogenetic structure. In Chapters I and IV of this thesis, the dynamics of zooplankton-associated symbiotic prokaryotes and parasitic eukaryotes were elucidated from the perspective of taxonomic composition, which were observed to fluctuate with environmental gradients and showed some host-specificity. Diet diversity and composition, and the ecological niche of the host contributed to the dynamics of zooplankton-associated microbial communities. In Chapter II, by focusing on bacterial communities associated with zooplankton, functional grouping of different bacterial taxa increased the explained variance of the symbiotic community structure. The mismatch between the bacterial functionality grouping and host or environmental gradients emphasized the general influence of environmental parameters, such as temperature and phosphorus, and more specific effects of host diet composition on gut bacterial communities. Chapter III investigated dynamic patterns of zooplankton microbiome identified by phylogenetic structure, in addition to the observed taxonomic and functional variation. The distribution of phylogenetically clustered and divergent communities was highly location-specific, implying the importance of background bacteria to symbiotic communities. Besides the abundant bacteria, the contribution of less abundant bacteria to the structure of the communities was significant, suggesting that the entire bacterial community needs to be considered to understand the dynamics and functions of the microbiome. 

This thesis reveals that zooplankton-associated microbial communities are subject to both environmental factors and host feeding behaviour, and that the gut bacterial functionality contributes to the zooplanktons’ adaptation capacity to different environmental conditions.  Focusing on the symbionts’ functionality and phylogeny, rather than taxonomic composition, improves our understanding of the microbiome dynamics. This thesis provides inspiration to further map symbiotic communities at large ecological scales and advances our understanding of the species diversity and potential functionality hidden inside organisms.