Description: Water sampling was carried out weekly between April and October 2016. Water samples were taken from two shallow sites (less than 5 km apart) in the Orkneys. Sampling was done using a bucket at both sampling locations. Water for filtration was transported to the Orkney Lobster Hatchery where 500–1000 mL of water was filtered over 0.4 µm polycarbonate (PC) filter (Whatman, 47mm). Filters were stored at -20 °C until DNA isolation in the laboratory. The samples were processed at the AWI to produce a metabarcoding data set with the goal of analysing the general diversity at the two sites but also to investigate the dynamics of harmful algal bloom species (HABs). As the data also contained a wealth of information on protistan parasites they were used to produce an additional manuscript on oomycete infections in the planktonic foodweb at the two sites. The bioinformatic processing of the raw sequence files was conducted as follows. The low-quality 3'-ends of the reads were trimmed by Trimmomatic (version 0.38) and the paired-ends were merged by VSEARCH (version 2.3.0). Cutadapt (version 1.19, was used to adjust the sequence orientation and to remove the forward and reverse primer matching sequence segments. Sequences were only kept in the sequence pool if both primer matching segments could be detected. To ensure a high sequence quality the remaining sequences were filtered by VSEARCH and only kept if the expected base error (sum of all base error probabilities) of a sequence was above 0.25. Chimeric sequences were predicted sample-wise by VSEARCH in de novo mode with default settings and removed from the sequence pool as well. Only samples which consisted of at least 10000 sequences after filtering were considered for further analyses. The remaining sequences were clustered into OTUs by the tool swarm (version 2.2.2) with default settings. For each OTU the most abundant amplicon was selected as representative and taxonomically annotated with the default classifier implemented in mothur (version 1.38.1). As reference the Protist Ribosomal Reference database (PR2), version 4.10 was chosen and the minimum confidence cut-off for annotation was set to a value of 80. Further details of the pipeline are provided in (Sprong, et al. 2020; doi:10.1016/j.seares.2020.101914).

Description: Water samples were collected from the long-term ecological research (LTER) site at Helgoland and the eukaryotic microbial community was assessed. 18S V4 region was amplified using the primer set 528iF /964iR and amplicon sequencing was performed on an Illumina MiSeq™ sequencer in a 2 × 300 bp paired-end run. Sequence data have been deposited in the European Nucleotide Archive (ENA) at the European Bioinformatics Institute (EMBL-EBI) under accession number PRJEB37135 using the data brokerage service of the German Federation for Biological Data (GFBio). 21 million sequences remained after bioinformatic processing and were clustered into Operational Taxonomic Units (OTUs). The Protist Ribosomal Reference database (PR2), version 4.11.1 was used as reference database.