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The mean share of heterocystous cyanobacteria in total chlorophyll-a production in coastal waters, based on cyanobacterial marker carotenoid and chloropigments preserved in recent sediments (0-5 cm, ca 30 years), has been studied in the Gulf of Gdańsk (southern Baltic) and for comparison in the Oslofjord/Drammensfjord (southern Norway). First of all, Baltic cyanobacteria, both from laboratory cultures and field samples, were analysed to select marker heterocysteous cyanobacteria carotenoids for sediments. The pigment relation to diatom percentages of different salinity preferences has been tested, to confirm origin of cyanobacteria. The results indicate that canthaxanthin is the best marker of heterocystous cyanobacteria in the southern Baltic Sea. These filamentous cyanobacteria inflow to the Gulf of Gdańsk from the open sea and their abundance has increased in the last thirty years, in comparison with previous time. In that period they made up ca 4.6% of the total chlorophyll-a production in the Gulf of Gdańsk. The estimate for Oslofjord, at the same assumptions, suggests that heterocystous cyanobacteria occurred there also (up to 5.8% of the total chlorophyll-a production), were of marine origin, but their abundance has decreased during the last thirty years. Such an estimate may be used in environmental modelling and can be applied to other coastal areas, once the marker pigments of the main cyanobacteria species have been identified, and the percentage of total chlorophyll-a produced in a basin, preserved in sediments, has been determined for such area.
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