A comprehensive dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea

Abstract

The Baltic Sea is one of the largest brackish water environments on earth and is characterised by pronounced physicochemical gradients and seasonal dynamics. Although the Baltic Sea has a long history of microscopy-based plankton monitoring, DNA-based metabarcoding has so far mainly been limited to individual transect cruises or time-series of single stations. Here we report a dataset covering spatiotemporal variation in prokaryotic and eukaryotic microbial communities and physicochemical parameters. Within 13-months between January 2019 and February 2020, 341 water samples were collected at 22 stations during monthly cruises along the salinity gradient. Both salinity and seasonality are strongly reflected in the data. Since the dataset was generated with both metabarcoding and microscopy-based methods, it provides unique opportunities for both technical and ecological analyses, and is a valuable biodiversity reference for future studies, in the prospect of climate change.

Fig. 1

Overview of water analyses conducted, and parameters observed.

Fig. 2

Overview of the sampled stations in the Baltic Sea, the Kattegat and the Skagerrak and general data structure based on 18S and 16S rRNA metabarcoding data. (A) Map of the Baltic Sea with its salinity gradient (redrawn from) and the 22 sampled stations. Three of the stations (indicated with grey circles in the map) had less than five samples and were not included in the analyses presented in panels B and C. (B) Seasonal variation in relative abundance of prokaryotic (16S) and eukaryotic (18S) microbial plankton on class level at the individual stations. Mean salinity level (PSU) measured and number of samples taken (n) at each station are depicted. (C) NMDS plots of β-diversity measured by Bray-Curtis distance of 16S and 18S sequencing data; of all stations and three individual stations at the extremes and the middle of the salinity gradient. For plots of individual stations, data points are not sized by salinity.

Fig. 3

Evaluation of water sample volumes required for metabarcoding. Samples from three sampling occasions (circle colour) and taken in different sample volumes of 10–500 ml (circle size in panel D) were taken in five replicates. (A) α-diversity measured by Shannon index, (B) α-diversity as richness measured by number of unique ASVs, (C) violin plots of β-diversity between replicates and (D) NMDS plots of β-diversity between all samples. β-diversity was measured with Bray-Curtis distance.