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Distribution of cyanobacteria cannot be evaluated using chlorophyll a (Chl a ) in vivo fluorescence, as most of their Chl a is located in non-fluorescing photosystem I. Phycobilin fluorescence, in turn, is noted as a useful tool in the detection of cyanobacterial blooms. We applied phycocyanin (PC) fluorometer in the monitoring of the filamentous cyanobacterial bloom in the Baltic Sea. For the bloom forming filamentous cyanobacteria Aphanizomenon flos-aquae and Nodularia spumigena , PC fluorescence maximum was identified using the excitation–emission fluorescence matrix. Consequently, the optical setup of our instrument was noted to be appropriate for the detection of PC, and with minor or no interference from Chl a and phycoerythrin fluorescence, respectively. During summer 2005, the instrument was installed on a ferryboat commuting between Helsinki (Finland) and Travemunde (Germany), and data were collected during 32 transects providing altogether 200 000 fluorescence records. PC in vivo fluorescence was compared with Chl a in vivo fluorescence and turbidity measured simultaneously, and with Chl a concentration and biomass of the bloom forming filamentous cyanobacteria determined from discrete water samples. PC fluorescence showed a linear relation to the biomass of the bloom forming filamentous cyanobacteria, and the other sources of PC fluorescence are considered minor in the open Baltic Sea. Estimated by PC fluorescence, cyanobacterial bloom initiated late June at the Northern Baltic Proper, rapidly extended to the central Baltic Proper and the Gulf of Finland, and peaked in the mid-July with values up to 10 mg l −1 (fresh weight). In late July, bloom vanished in most areas. During single transects, or for the whole summer, the variability in Chl a concentrations was explained more by PC fluorescence than by Chl a fluorescence. Thus, filamentous cyanobacteria dominated the overall variability in phytoplankton biomass. Consequently, we show that during the cyanobacterial blooms, the estimation of Chl a concentration using only Chl a in vivo fluorescence is not applicable, but PC in vivo fluorescence is required as a predictor as well.

Finnish Institute of Marine Research (FIMR) as a founding member of Alg@line consortium has been a forerunner in the field of monitoring research using commercial ferries. In 1992 FIMR started continuous measurements on board the ferry Finnjet, crossing the Baltic Sea Proper, using unattended recording and sampling system. During the spring of 2007 the ferrybox monitoring system was reinstalled in a new ferry Finnmaid providing real time observed data transmission with satellite connection. Chlorophyll-a (Chla) still remains the principal monitoring parameter. However, the distribution of cyanobacteria cannot be evaluated using Chla in vivo fluorescence, as most of their Chla is located in the poorly-fluorescing photosystem I. Instead, phycocyanin (PC) fluorescence is used in the detection of cyanobacterial blooms in 2005-07. PC fluorescence shows a linear relation to the biomass of the bloom forming filamentous cyanobacteria. During blooms of filamentous cyanobacteria the variability in Chla concentrations is better explained by PC fluorescence than by Chla fluorescence. Additionally, Chla records have been applied in validation of MODIS satellite monitoring for the water quality.

The Baltic Sea is a unique continental brackish water sea. Today the Baltic Sea is eutro- phied and the blooms of harmful planktonic algae are annual phenomena. The blooms are harmful to the marine ecosystem as well as to the recreational and economic use of marine resources. High-quality research gives reliable information on the state of the ecosystem and its changes. Adequate monitoring information is a prerequisite for sound protection measures and only research is able to reliably show the effects of the protection investments. Because the phytoplankton blooms are extremely patchy and temporally rapidly changing, they often remain unobserved when using traditional sampling methods.