An overview of ecological status, vulnerability and future perspectives of European large shallow, semi-enclosed coastal systems, lagoons and transitional waters. Estuarine, Coastal and Shelf Science,

Marine environmental monitoring has tended to focus on site-specific methods of investigation. These traditional methods have low spatial and temporal resolution and are relatively labor intensive per unit area/time that they cover. To implement the Marine Strategy Framework Directive (MSFD), European Member States are required to improve marine monitoring and design monitoring networks. This can be achieved by developing and testing innovative and cost-effective monitoring systems, as well as indicators of environmental status. Here, we present several recently developed methodologies and technologies to improve marine biodiversity indicators and monitoring methods. The innovative tools are discussed concerning the technologies presently utilized as well as the advantages and disadvantages of their use in routine monitoring. In particular, the present analysis focuses on: (i) molecular approaches, including microarray, Real Time quantitative PCR (qPCR), and metagenetic (metabarcoding) tools; (ii) optical (remote) sensing and acoustic methods; and (iii) in situ monitoring instruments. We also discuss Danovaro et al. Innovative Approaches in Marine Monitoring their applications in marine monitoring within the MSFD through the analysis of case studies in order to evaluate their potential utilization in future routine marine monitoring. We show that these recently-developed technologies can present clear advantages in accuracy, efficiency and cost.

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Coastal wetlands, such as saltmarshes and mangroves that fringe transitional waters, deliver important ecosystem services that support human development. Coastal wetlands are complex social-ecological systems that occur at all latitudes, from polar regions to the tropics. This overview covers wetlands in five continents. The wetlands are of varying size, catchment size, human population and stages of economic development. Economic sectors and activities in and around the coastal wetlands and their catchments exert multiple, direct pressures. These pressures affect the state of the wetland environment, ecology and valuable ecosystem services. All the coastal wetlands were found to be affected in some ways, irrespective of the conservation status. The main economic sectors were agriculture, animal rearing including aquaculture, fisheries, tourism, urbanization, shipping, industrial development and mining. Specific human activities include land reclamation, damming, draining and water extraction, construction of ponds for aquaculture and salt extraction, construction of ports and marinas, dredging, discharge of effluents from urban and industrial areas and logging, in the case of mangroves, subsistence hunting and oil and gas extraction. The main pressures were loss of wetland habitat, changes in connectivity affecting hydrology and sedimentology, as well as contamination and pollution. These pressures lead to changes in environmental state, such as erosion, subsidence and hypoxia that threaten the sustainability of the wetlands. There are also changes in the state of the ecology, such as loss of saltmarsh plants and seagrasses, and mangrove trees, in tropical wetlands. Changes in the structure and function of the wetland ecosystems affect ecosystem

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.

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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.

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