DNA metabarcoding in the Baltic Sea area, 2015-2017

16S (V3-V4) and 18S (V4) metabarcoding results from the following sampling efforts: 1. Bi-weekly sampling along the Swedish marine monitoring program across twelve locations in Baltic Proper, Kattegat, and Skagerrak. For all the locations, sampling was performed between February 2016 and March 2017. Additionally, one station (Släggö, Skagerrak) was sampled from August 2015. 2. Weekly sampling at multiple depths (5, 10, and 15 meters in most cases) at Tångesund, Sweden (Skagerrak), performed in 2016 between August 22nd and October 10th. 3. Three longitudinal transects in Skagerrak, performed in 2016 on August 18th, 4. Replicate samples collected at Släggö marine station (Skagerrak) on the same date (August 20th 2019) and stored as filters before DNA extraction for 1 week, 1 month, 3 months, or 6 months, in either -20°C or -80°C. The extracted DNA was stored at -20°C until mid-2023 when the amplicon sequencing was performed. All the contextual data has been obtained from the SharkWeb portal maintained by the Swedish Meteorological and Hydrological Institute. Note 1: For many samples, 18S metabarcoding library preparation was performed twice. First (run A), 20 amplification cycles were used. Since that was insufficient, the library preparation was repeated with 24 amplification cycles (run B). The number of amplification cycles has been given in the column nr_pcr_cycles, and the amplification run (A or B) has been explicitly stated in the sample alias. In downstream analyses, after denoising, we summed the ASV counts for both runs when applicable. Note 2: These samples are preprocessed with a modified version of the cutadapt-based amplicon-mulit-cutudapt pipeline originally developed for the Insect Biome Atlas project. The original read files contained mixed 16S and 18S sequences, which have been separated by detecting the primer sequences.