The brackish Baltic Sea hosts species of various origins and environmental tolerances. These immigrated to the sea 10,000 to 15,000 years ago or have been introduced to the area over the relatively recent history of the system. The Baltic Sea has only one known endemic species. While information on some abiotic parameters extends back as long as five centuries and first quantitative snapshot data on biota (on exploited fish populations) originate generally from the same time, international coordination of research began in the early twentieth century. Continuous, annual Baltic Sea-wide long-term datasets on several organism groups (plankton, benthos, fish) are generally available since the mid-1950s. Based on a variety of available data sources (published papers, reports, grey literature, unpublished data), the Baltic Sea, incl. Kattegat, hosts altogether at least 6,065 species, including at least 1,700 phytoplankton, 442 phytobenthos, at least 1,199 zooplankton, at least 569 meiozoobenthos, 1,476 macrozoobenthos, at least 380 vertebrate parasites, about 200 fish, 3 seal, and 83 bird species. In general, but not in all organism groups, high sub-regional total species richness is associated with elevated salinity. Although in comparison with fully marine areas the Baltic Sea supports fewer species, several facets of the system's diversity remain underexplored to this day, such as micro-organisms, foraminiferans, meiobenthos and parasites. In the future, climate change and its interactions with multiple anthropogenic forcings are likely to have major impacts on the Baltic biodiversity.

Assessments of the environmental status of the Baltic Sea as called for by the Marine Strategy Framework Directive (MSFD) must be based on a set of indicators. A pre-core indicator is the diatom/dinoflagellate index (Dia/Dino index), which reflects the dominance of diatoms or dinoflagellates during the phytoplankton spring bloom. Here we explain the principles of the Dia/Dino index and the conditions for its calculation using examples from two very different water bodies, the Eastern Gotland Basin and Kiel Bay. The index is based on seasonal mean diatom and dinoflagellate biomass values. A precondition for its applicability is the coverage of the bloom. As a criterion, the maximum value of diatom or dinoflagellate biomass has to exceed a predefined threshold, e.g., 1000 µg/L in the investigated areas. If this condition is not fulfilled, an alternative Dia/Dino index can be calculated based on silicate consumption data. Changes in the dominance of these two phytoplankton classes impact the food web because both their quality as a food source for grazers and their periods of occurrence differ. If diatoms are dominant, their rapid sinking reduces the food stock for zooplankton but delivers plenty of food to the zoobenthos. Consequently, the Dia/Dino index can be used to follow the food pathway (Descriptor 4 of MSFD: "food web"). Moreover, a low Dia/Dino index may indicate silicate limitation caused by eutrophication (Descriptor 5 of MSFD: "eutrophication"). The Dia/Dino index was able to identify the regime shift that occurred at the end of the 1980s in the Baltic Proper. Diatom dominance, and thus a high Dia/Dino index, are typical in historical data and are therefore assumed to reflect good environmental status (GES). In assessments of the environmental status of the Eastern Gotland Basin and Kiel Bay, Dia/Dino index GES thresholds of 0.5 and 0.75, respectively, are suggested. The GES thresholds as calculated by the alternative Dia/Dino index are 0.84 and 0.94, respectively.

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During the latest years medium-sized (15-30 lm), single-celled dinoflagellates have been reported to form blooms in the northern Baltic Proper and the Gulf of Finland in winter and spring. Recent studies (Kremp et al., 2003. Proceedings of the 7th International conference of Modern and Fossil Dinoflagellates, September 21-25, Nagasaki, Japan, 66 pp.) indicate that those blooms are caused by two isomorphic species -Scrippsiella hangoei (Schiller) Larsen, and a new species, tentatively belonging to the genus Woloszynskia. Until now there has been no report on how widely distributed these phytoplankton species are in the Baltic Sea. In this study, the occurrence of Scrippsiella/Woloszynskia complex in the entire Baltic Sea was investigated, by using monitoring data from 1997 to 2003. The species occurred in a salinity range from 2 to 8 PSU. Highest concentrations were observed at salinity 4.5-6.5 PSU. Maximum cell densities of Scrippsiella/Woloszynskia complex in the water column were mainly obtained in April or in the beginning of May by the water temperature <3°C prior to stratification was formed. In the central Gulf of Finland, the second maximum was found in 1999 and 2002 by the temperature >6°C. Bloom formations in the Baltic Proper and in the Gulf of Finland may not only be explained by optimum temperature and salinity, but also with other factors e.g. high nutrient concentrations and good seeding conditions from the sediments.

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There are very few time series documenting clear trends of change in the biomass of total phytoplankton or single taxa that coincide with trends of increasing nutrient concentrations. Weekly or biweekly monitoring since 1997 on a cross section of the central Gulf of Finland (NE Baltic Sea) with similar climatic and hydrographic conditions, but different nutrient levels, provided a uniform dataset. In order to evaluate seasonal (June-September) patterns of phytoplankton succession, more than 1,200 samples were statistically analyzed by selecting 12 dominant taxa using wet weight biomass values. In addition, the continuously measured hydrographic parameters on board the ships of opportunity, and simultaneous nutrient analyses gave high frequency information on the water masses. The objective of this study was to identify the taxa that may prove indicative in the assessment of eutrophication in the appropriate monitoring time periods. None of the most common bloomforming species (Aphanizomenon sp., Nodularia spumigena, and Heterocapsa triquetra) showed reliable correlations with enhanced nutrient concentrations. The species we suggest as reliable eutrophication indicators-oscillatorialean cyanobacteria and the diatoms Cyclotella choctawhatcheeana and Cylindrotheca closterium-showed the best relationships with total phosphorus concentrations. Their maxima appear toward the end of July or in August-September when phytoplankton community structure is more stable, and less frequent observations may give adequate results. Another diatom, Skeletonema costatum, exhibited stronger correlations with dissolved inorganic and total nitrogen in June, during the period of the summer phytoplankton minimum.

Abstract. Egg production of Acartia clausi and Centropages hamatus was measured along 6 transects in the Skagerrak every third day from 26 May to 20 June 1990. Egg production was highest in the shallow waters north of Denmark, with occasional peaks in frontal regions along the Swedish and the Danish west coasts. Linear regression analysis showed that the egg production was significantly (p < 0.05) related to chlorophyll a measured either as average surface concentration or integrated over the whole water column. When analysing each transect or each time period separately, the surface chlorophyll generally was a better predictor of egg production than the depth-integrated chlorophyll. Regressions improved when analysing the whole area for a short period of time rather than analysing a single transect for a month. The data suggest that the Skagerrak planktonic system functions more similarly over the whole area in a short period of time than over a month in a restricted area. Mixing within the system in frontal regions or in connection with eddies is more important for the secondary production than transport to it by the Baltic Current or the Jutland Current.