Metabarcoding the microeukaryotic community associated with roots and leaves of Zostera marina in a Danish estuary

Seagrass meadows are highly productive marine ecosystems that provide essential environmental services such as carbon sequestration and sediment stabilisation. However, their associated microbial communities, particularly microeukaryotes, remain understudied. This study presents two independent yet complementary datasets describing the microeukaryotic community associated with the leaves and roots of Zostera marina in the Limfjord, Denmark, using a DNA metabarcoding approach. Leaf-associated communities were dominated by diatoms and displayed low spatial variability. Common and dominant taxa in leaves included representatives from the genera Licmophora, Cylindrotheca, Cocconeis, Rossithidium, Tabularia, Navicula , and Berkeleya. The root-associated community was primarily dominated by ciliates, although taxa of green algae, diatoms and fungi also appeared to be important across samples. The aim of this study was to expand current knowledge of Z. marina as a model for seagrass-associated microbiome research, as well as providing a baseline for future ecological assessments and monitoring of eelgrass in Denmark.