Distinct bacterial and protist plankton diversity dynamics uncovered through DNA-based monitoring in the Baltic Sea area

Planktonic microorganisms in coastal waters form the base of food web and biogeochemical cycles. The Baltic Sea area, with its pronounced environmental gradients, serves as a model coastal environment. Yet, microbial diversity assessment across these environmental gradients has so far lacked either taxonomic scope or the integration of spatial and temporal scales. Here, we analyzed protist and bacterial diversity using DNA metabarcoding across 398 samples synchronized with national monitoring of the Baltic Sea and the Kattegat-Skagerrak. We show that salinity, unlike other environmental factors, had a stronger effect on bacterial than on protist community composition. Likewise, Bayesian modeling showed that bacterial lineages were less likely than protists to occur in both lower (<9 PSU) and higher (>15 PSU) brackish salinities. Nonetheless, protist alpha diversity increased with salinity. Changes in bacterial alpha diversity were primarily seasonal and linked to influx of deepwater taxa through vertical mixing in winter. We propose that protists are ecologically less sensitive to salinity because compartmentalization allows them to disconnect basic metabolic processes from the cell membrane. Additionally, further and more frequent dispersal of bacteria might impede local adaptation. Ultimately, DNA-based environmental monitoring expands our understanding of microbial diversity patterns and the underlying factors.