The relative importance of the benthic microbial food web and the effects of wind-induced sediment resuspension on the benthic and pelagic microbial food web of two stations in the southern coastal Baltic were studied in the field, during resuspension experiments with natural sediment cores and during plankton wheel experiments with an artificially assembled model benthic microbial food web.

Benthic and planktonic heterotrophic protists contributed approximately the same biomass per unit area in the field. The heterotrophic flagellate communities in the sediment and in the water column showed a considerable taxonomic overlap, while the ciliate communities in both habitats were usually comprised of different taxa. Rhizopods contributed 30% to benthic heterotrophic protistan biomass on average, but they were of minor importance within the protozooplankton. Their taxonomic composition and seasonal dynamics were studied in more detail at a third station, revealing a high species richness and a summer abundance maximum. Protistan abundances in the sediment and in the water column of the more shallow station were positively correlated, but taxonomic data indicate that the direct exchange between benthic and planktonic communites was only partly responsible.

Experimental resuspension acted as a passive transport mechanism on benthic heterotrophic protists, diatoms, pico- and nanoautotrophs into the water column. In addition, it fostered growth of resuspended diatoms, other autotrophs and heterotrophic nanoplankton, most likely due to released nutrient and food limitation. In contrast, benthic rhizopod community structure responded only marginally to disturbance by resuspension.

During a series of plankton wheel experiments, resuspended benthic ciliate and rhizopod populations grew quicker than sedimented populations provided food supply was sufficient. The trophic link between ciliates and heterotrophic flagellates, and presumably also other trophic links in the model benthic microbial food web, became closer in suspension.

These results show that resuspension may strongly affect the structure of the heterotrophic protistan community and the functioning of the microbial food web in shallow coastal waters.