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

Planktonic microorganisms in coastal waters form the foundation of food webs and biogeochemical cycles while exposed to pronounced environmental gradients, especially brackish salinities. Yet, commonplace ecological assessment overlooks most of their diversity. Here, we analyzed the protist and bacterial diversity from new and publicly available DNA metabarcoding data collected alongside the Swedish marine monitoring program. We show that salinity, unlike other environmental factors, had a stronger effect on bacterial than protist community composition. The seasonality of protist but not bacterial families showed high geographic variation. Bacterial alpha diversity increased with dissolved inorganic nitrogen, while protist alpha diversity was highest in near-marine salinities. Microbial community composition patterns displayed interannual stability despite technical differences affecting the detection of rare taxa. Co-occurrence analysis identified clusters of potentially interdependent microorganisms. Bayesian modeling showed that the same bacterial lineages were less likely than protists to occur in both lower (<9 PSU) and higher (>15 PSU) brackish salinities. We propose that protists are less ecologically sensitive to salinity due to the disconnection of basic metabolic processes from the cell membrane through compartmentalization. Ultimately, incorporating DNA metabarcoding into an environmental monitoring program allowed us to connect ecological and biogeographic processes with understudied taxa and biodiversity dynamics.