a b s t r a c t CHEMTAX was used to assess the relative contribution of the main phytoplankton classes to the total concentration of Chlorophyll a (Chl a) from the waters off SW coast of Portugal. Sampling campaigns were carried out during all seasons from 2008 to 2012, at three stations located 2, 10 and 18 km from the coast. Samples were taken from the surface, mid-Secchi and Secchi depth, for the determination of Chl a and other phytoplanktonic pigments by HPLC. Supporting data were also obtained including dissolved inorganic nutrients, salinity, transparency, temperature and upwelling indices. The CHEMTAX results were also related to microscopy counts and also spectral analysis of absorption of other samples from the same sampling campaigns. The pigment results showed that diatoms dominated from early spring to summer, coinciding with upwelling conditions, while cryptophytes, prymnesiophytes and prasinophytes dominated in autumn and winter, coinciding with seasonal stratification. Although the contribution of cyanobacteria to total Chl a was generally low, there were occasional sampling campaigns where it was exceptionally high, but these appeared not to be related to upwelling. Dinoflagellates and chrysophytes were minority groups although the pigment marker peridinin that was used to distinguish dinoflagellates was not adequate for distinguishing all the members of this group. CHEMTAX was particularly useful for discriminating between the smaller (0e20 mm) classes of the microplankton that could not be easily identified by microscopy.

Time series analysis of data for sea surface temperature and upwelling components from the southwest coast of AbstractThis study relates sea surface temperature (SST) to the upwelling conditions off the southwest coast of Portugal using statistical analyses of publically available data.Optimum Interpolation (OI) daily SST data were extracted from the United States (US) National Oceanic and Atmospheric Administration (NOAA) and data for wind speed and direction were from the US National Climatic Data Center. Time series were extracted at a daily frequency for a time horizon of 26 years. Upwelling indices were estimated using westerly (Q x ) and southerly (Q y ) Ekman transport components.In the first part of the study, time series were inspected for trend and seasonality over the whole period. The seasonally adjusted time series revealed an increasing slope for SST (0.15ºC per decade) and decreasing slopes for Q x (-84.01 m 3 .s -1 .km -1 per decade) and Q y (-25.20 m 3 .s -1 .km -1 per decade), over the time horizon. Structural breaks analysis applied to the time series showed that a statistically significant incremental increase in SST was more pronounced during the last decade. Cross-correlation between upwelling indices and SST revealed a time delay of 5 and 2 days between Q x and SST, and between Q y and SST, respectively. A spectral analysis combined with the previous analysis enabled the identification of four oceanographic seasons. Those seasons were later recognised over a restricted time period of 4 years, between 2008 and 2012; when there was an extensive sampling programme for the validation of ocean colour remote sensing imagery. The seasons were defined as: summer, with intense and regular events of upwelling; autumn, indicating relaxation of upwelling conditions; and spring and winter, showing high interannual variability in terms of number and intensity of upwelling events.

The study region in Sagres, SW Portugal, is subject to natural eutrophication of coastal waters by winddriven upwelling, which stimulates high primary productivity facilitating the recent economic expansion of bivalve aquaculture in the region. However, this economic activity is threatened by harmful algal blooms (HAB) caused by Pseudo-nitzschia spp., Dinophysis spp. and other HAB dinoflagellates, all of which can produce toxins, that can induce Amnesic Shellfish Poisoning (ASP), Diarrhetic Shellfish Poisoning (DSP) and Paralytic Shellfish Poisoning (PSP). This study couples traditional microscopy with 18S/28S rRNA microarray to improve the detection of HAB species and investigates the relation between HAB and the specific oceanographic conditions in the region. Good agreement was obtained between microscopy and microarray data for diatoms of genus Pseudo-nitzschia and dinoflagellates Dinophysis spp., Gymnodinium catenatum and raphidophyte Heterosigma akashiwo, with less effective results for Prorocentrum. Microarray provided detection of flagellates Prymnesium spp., Pseudochattonella spp., Chloromorum toxicum and the important HAB dinoflagellates of the genera Alexandrium and Azadinium, with the latter being the first recorded from the study region. Seasonality and upwelling induced by northerly winds were found to be the driving forces of HAB development, with Pseudo-nitzschia spp. causing the risk of ASP during spring and summer upwelling 2 season, and dinoflagellates causing the risk of DSP and PSP during upwelling relaxation, mainly in summer and autumn. The findings were in agreement with the results from toxicity monitoring of shellfish by the Portuguese Institute for Sea and Atmosphere (IPMA, 2014(IPMA, -2016 and confirm the suitability of the RNA microarray method for HAB detection and aquaculture management applications.