Interactions between prokaryotes and eukaryotes in a coastal late summer Baltic Sea community.

Interactions between eukaryotes and bacterioplankton are at the core of the microbial loop and have been studied in various aquatic systems to understand ecosystem function and energy transfer. Shallow eutrophic waters, overgrown by vegetation, are a common habitat type in the Baltic proper but have been less studied compared to off-shore pelagic systems. A high-resolution characterization of the bacterial and eukaryotic communities in a coastal Baltic Sea habitat was performed to reveal interactions and community composition shifts. Sampling was done at two time points during a declining late summer temperature peak (22.5°C to 18.7°C) in the Åland archipelago. 16S and 18S rRNA gene amplicon sequencing was performed, followed by co-occurrence analyses based on count data and taxonomic annotations. The community compositions at the two time points were significantly different from each other. The changes in the eukaryotic populations were characterized by a shift in genus within the frequently occurring heterotrophic ciliates, from Strombidium (Oligotrichia) to Cryptocaryon (Prostomatea). Phototrophic dinoflagellates (Gonyaulacales) were in part replaced by heterotrophic Peridinales and a relative increase of heterotrophic nanoflagellates was also observed, contributing to a transition from a partly phototrophic to a more heterotrophic community. Due to this transition, a decrease in primary production and an increase in the predation pressure on the bacterial community would be expected. Within the heterotrophic bacterial community, these shifts were apparent within the actinobacterial phyla, with a decline of the relative abundances of Micrococcales and an increase of Frankiales and Acidiomicrobia, between the first and second time point. These results show that co-occurrence patterns between eukaryotes and prokaryotes in a shallow eutrophic aquatic location are affected by temperature and interactions that together have the potential to affect both production and transfer of energy.