Micro-eukaryotic plankton diversity in an intensive aquaculture system for production of Scophthalmus maximus and Solea senegalensis

Microbial communities are key players in the process of nutrient cycling and maintenance of fish health in aquaculture systems. The role and importance of bacteria in these systems has been widely studied. However, very little is known about micro-eukaryotic plankton composition and function in aquaculture systems. Here we used denaturing gradient gel electrophoresis (DGGE) and Illumina 18S rRNA gene deep sequencing analysis to study the structure and diversity of micro-eukaryotic communities of Scophthalmus maximus (turbot) and Solea senegalensis (sole) recirculating aquaculture systems (RAS) with shallow raceway systems (SRS). Although there were pronounced differences between turbot and sole RAS micro-eukaryotic communities, both systems were dominated by thraustochytrids and bacterial grazers belonging to nematodes, ciliates and choanoflagellates and a large fraction of unknown organisms (unassigned at higher taxonomic levels). The dominance of bacterial grazers may have a significant effect on the composition of bacterioplankton communities in RAS with potential consequences on the biogeochemical processes, water quality and fish health. This study provides novel insights into the composition and putative function of micro-eukaryotic communities in turbot and sole RAS and underlines the need of a better understanding of their role in aquaculture systems.