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- Contribution of remote sensing products to the management of offshore aquaculture at Sagres, SW PortugalPublication . Icely, John; Moore, Gerald; Danchenko, Sergei A.; Goela, Priscila; Cristina, Sónia; Zacarias, Marielba; Newton, AliceRemote sensing can address important issues affecting offshore aquaculture such as prediction of Harmful Algal Blooms. In situ data for nutrients, chlorophyll a (Chla) and phytoplankton community from a site for long-line aquaculture for bivalves off the SW coast of Portugal has been compared during a period of upwelling with remote sensing data for Chla, sea surface temperature, salinity, direction and intensity of both currents and winds. On the 11th February the in situ nutrients levels were high and the Chla was low, but by the 12th March the converse was the situation. The evolution of this event could be followed by combining remote sensing and model data from a variety of open source web sites made available by the Earth Observation provider that demonstrated clearly the lags between the physical forcings promoting upwelling and the eventual blooms of phytoplankton.
- Assessing the effectiveness of management measures in the Ria Formosa coastal lagoon, PortugalPublication . Newton, Alice; Cañedo-Argüelles, Miguel; March, David; Goela, Priscila; Cristina, Sónia; Zacarias, Marta; Icely, JohnThe Ria Formosa is an important transitional and coastal lagoon on the south coast of Portugal that provides valuable ecosystem services. The lagoon is a protected area under national and international conventions. There is a great potential for Blue Growth sectors, such as aquaculture and coastal tourism, but these rely on good water quality. European environmental legislation, such as the Water Framework Directive, requires member states, such as Portugal to implement management measures if a surface water body is not of good ecological status. This work addresses the effectiveness of management measures, such as wastewater treatment plant implementation and dredging, on the water quality of the Ria Formosa coastal lagoon system. This is an important social-ecological issue, since management measures can be very expensive. The ecological status of Ria Formosa was evaluated, according to the physico-chemical and biological quality elements of the Water Framework Directive. The main indicators were the physico-chemical quality elements of nutrient and oxygen condition, and the biological quality element chlorophyll a, as a proxy for phytoplankton biomass, under the Water Framework Directive. The data for these quality elements from the Ria Formosa were analyzed for consistency with the classification for the Water Framework Directive water bodies. The data after the implementation of management measures was compared with historical data to evaluate if these measures had been effective. The relation between nutrient pressures, meteorological and hydrological conditions was addressed, especially rainfall and runoff. Results showed a decrease in nutrient concentration after the management interventions, despite the increase of population and intensifying agriculture in the catchment. The Ecological Status is spatially variable with an overall moderate status, indicating the need for further management measures. There is a significant reduction in nutrient pressure on the lagoon during drought years. This indicates that climate change may alter the structure and function of the lagoon in the future.
- MERIS phytoplankton time series products from the SW Iberian Peninsula (Sagres) using seasonal-trend decomposition based on loessPublication . Cristina, Sónia; Cordeiro, Clara; Lavender, Samantha; Goela, Priscila; Icely, John; Newton, AliceThe European Space Agency has acquired 10 years of data on the temporal and spatial distribution of phytoplankton biomass from the MEdium Resolution Imaging Spectrometer (MERIS) sensor for ocean color. The phytoplankton biomass was estimated with the MERIS product Algal Pigment Index 1 (API 1). Seasonal-Trend decomposition of time series based on Loess (STL) identified the temporal variability of the dynamical features in the MERIS products for water leaving reflectance ((w)()) and API 1. The advantages of STL is that it can identify seasonal components changing over time, it is responsive to nonlinear trends, and it is robust in the presence of outliers. One of the novelties in this study is the development and the implementation of an automatic procedure, stl.fit(), that searches the best data modeling by varying the values of the smoothing parameters, and by selecting the model with the lowest error measure. This procedure was applied to 10 years of monthly time series from Sagres in the Southwestern Iberian Peninsula at three Stations, 2, 10 and 18 km from the shore. Decomposing the MERIS products into seasonal, trend and irregular components with stl.fit(), the (w)() indicated dominance of the seasonal and irregular components while API 1 was mainly dominated by the seasonal component, with an increasing effect from inshore to offshore. A comparison of the seasonal components between the (w)() and the API 1 product, showed that the variations decrease along this time period due to the changes in phytoplankton functional types. Furthermore, inter-annual seasonal variation for API 1 showed the influence of upwelling events and in which month of the year these occur at each of the three Sagres stations. The stl.fit() is a good tool for any remote sensing study of time series, particularly those addressing inter-annual variations. This procedure will be made available in R software.
- Using remote sensing as a support to the implementation of the European Marine Strategy Framework Directive in SW PortugalPublication . Cristina, Sónia; Icely, John; Goela, Priscila; Angel DelValls, Tomás; Newton, AliceThe exclusive economic zones (EEZ) of coastal countries are coming under increasing pressure from various economic sectors such as fishing, aquaculture, shipping and energy production. In Europe, there is a policy to expand the maritime economic sector without damaging the environment by ensuring that these activities comply with legally binding Directives, such as the Marine Strategy Framework Directive (MSFD). However, monitoring an extensive maritime area is a logistical and economic challenge. Remote sensing is considered one of the most cost effective, methods for providing the spatial and temporal environmental data that will be necessary for the effective implementation of the MSFD. However, there is still a concern about the uncertainties associated with remote sensed products. This study has tested how a specific satellite product can contribute to the monitoring of a MSFD Descriptor for "good environmental status" (GES). The results show that the quality of the remote sensing product Algal Pigment Index 1 (API 1) from the MEdium Resolution Imaging Spectrometer (MERIS) sensor of the European Space Agency for ocean colour products can be effectively validated with in situ data from three stations off the SW Iberian Peninsula. The validation results show good agreement between the MERIS API 1 and the in situ data for the two more offshore stations, with a higher coefficient of determination (R-2) of 0.79, and with lower uncertainties for the average relative percentage difference (RPD) of 24.6% and 27.9% and a root mean square error (RMSE) of 0.40 and 0.38 for Stations B and C, respectively. Near to the coast, Station A has the lowest R-2 of 0.63 and the highest uncertainties with an RPD of 112.9% and a RMSE of 1.00. It is also the station most affected by adjacency effects from the land: when the Improved Contrast between Ocean and Land processor (ICOL) is applied the R-2 increases to 0.77 and there is a 30% reduction in the uncertainties estimated by RPD. The MERIS API 1 product decreases from inshore to offshore, with higher values occurring mainly between early spring and the end of the summer, and with lower values during winter. By using the satellite images for API 1, it is possible to detect and track the development of algal blooms in coastal and marine waters, demonstrating the usefulness of remote sensing for supporting the implementation of the MSFD with respect to Descriptor 5: Eutrophication. It is probable that remote sensing will also prove to be useful for monitoring other Descriptors of the MSFD.
- Specific absorption coefficient of phytoplankton off the Southwest coast of the Iberian Peninsula: a contribution to algorithm development for ocean colour remote sensingPublication . Goela, Priscila; Icely, John; Cristina, Sónia; Newton, Alice; Moore, Gerald; Cordeiro, ClaraThe variability in coefficients of absorption for phytoplankton was assessed for an area off the Southwest coast of Portugal. This area included three sites at 2, 10 and 18 km perpendicular to the coast, sampled at surface, mid-Secchi and Secchi depths at each site. Phytoplankton absorption coefficients were transformed into specific coefficients (a⁎ph(λ)) by normalizing them with respect to chlorophyll a (Chla) concentrations determined by High Performance Liquid Chromatography. The influence on the variability of the absorption coefficient of phytoplankton was assessed for physico-chemical and biological parameters such as nutrients or Chla levels, as well as size structure and abundance of the phytoplankton community. The results showed that the phytoplankton absorption coefficients decreased from inshore to offshore, but were relatively constant within the water column, revealing a well-mixed column. The a⁎ph(λ) varied inversely with Chla content, with minima in Autumn and Spring, matching phytoplankton blooms. The effects of the size structure of the community and pigment composition on the variability of phytoplankton absorption coefficient were studied and results showed that size structure had a greater influence on the variability of the phytoplankton absorption, although the pigment contribution was also important.
- Light absorption by particulate and dissolved organic matter in coastal and oceanic off the South west coast of Europe: a contribution to MERIS sensor validationPublication . Goela, Priscila; Cristina, Sónia; Icely, John; Newton, AliceThe two variable components of light absorption, which are important contributors to the correct adjustments of ocean colour algorithms, are considered and discussed in this study, conducted in the Southwest coast of Portugal; these are particulate absorption – separated into phytoplankton and non-algal particles absorption, and coloured dissolved organic matter absorption, expressed in terms of their coefficients – ap(), aph(), anap() and aCDOM(), respectively. This study is part of a global effort to collect data to validate marine products of MERIS, the ENVISAT ocean colour sensor, as contracted by European Space Agency (ESA). Particulate absorptions were determined with Transmittance-Reflectance approach, using NaClO bleaching to remove phytoplankton contribution to the total particulate matter absorption spectra; YSBPA absorption coefficient was assessed according to MERIS validation protocols. Phytoplankton absorption coefficients were transformed into specific coefficients – a*ph(), normalizing it with respect to chlorophyll a concentrations determined both by HPLC and spectrophotometric methods. Results show that the absorption of light by particulate matter is almost totally dependent on the phytoplankton, with no significant contribution from non-algal particles (mean contribution of 10% to total particulate absorption), both in coastal and oceanic waters, emphasising the dominance of case 1-type waters. Specific chlorophyll absorption coefficients show significant fluctuations between seasons and stations, ranging from 0.007 to 0.09 at 678 nm; however, a good correlation between ap(443) and ap at other MERIS equivalent wavelengths was found. Particulate matter has generally more weight than dissolved matter absorption in the total absorption budget. These results may contribute to improve and correct regional ocean colour algorithms.
- Using bio-optical parameters as a tool for detecting changes in the phytoplankton community (SW Portugal)Publication . Goela, Priscila; Icely, John; Cristina, Sonia; Danchenko, Sergei; Angel DelValls, T.; Newton, AliceUpwelling events off the Southwest coast of Portugal can trigger phytoplankton blooms that are important for the fisheries and aquaculture sectors in this region. However, climate change scenarios forecast fluctuations in the intensity and frequency of upwelling events, thereby potentially impacting these sectors. Shifts in the phytoplankton community were analysed from the end of 2008 until the beginning of 2012 by examining the bio-optical properties of the water column, namely the absorption coefficients for phytoplankton, non-algal particles and coloured dissolved organic matter (CDOM). The phytoplankton community was assessed by microscopy, with counts from an inverted microscope, and by chemotaxonomic methodologies, using pigment concentrations determined by High-Performance Liquid Chromatography (HPLC). Results both from microscopy and from chemotaxonomic methods showed a shift from diatom dominance related to bloom conditions matching upwelling events, to small flagellate dominance related to no-bloom conditions matching relaxation of upwelling. During bloom conditions, light absorption from phytoplankton increased markedly, while non-algal particles and CDOM absorption remained relatively constant. The dynamics of CDOM in the study area was attributed to coastal influences rather than from phytoplankton origin. Changes in phytoplankton biomass and consequent alterations in phytoplankton absorption coefficients were attributed to upwelling regimes in the area. Bio-optical parameters can contribute to environmental monitoring of coastal and oceanic waters, which in the case of the European Union, involves the implementation of the Water Framework, Marine Strategy Framework and Marine Spatial Planning Directives. (C) 2015 The Authors.Published by Elsevier Ltd.
- Assessment of the water-leaving reflectances of the oceanic and coastal waters using MERIS satellite products in Sagres off the southwest coast of PortugalPublication . Cristina, Sónia; Goela, Priscila; Icely, John; Newton, Alice; Fragoso, BrunoOptical properties of oceanic waters have provided an important tool for observing large scale fluctuations in oceanic conditions by remote sensing. However, there are still problems with calibrating the algorithms that link remote sensing data with in situ measurements, particularly, in coastal areas where there are adjacency affects from land on the reflectance data observed by the satellite sensor. As part of a contract with the European Space Agency to validate the marine products of the MERIS (Medium Resolution Imaging Spectrometer) sensor on the ENVISAT satellite, this study is taking regular measurements with a Satlantic hyperspectral radiometer ranging from inshore to offshore sites, covering both Case-1 and Case-2 waters off the south west coast of Portugal. Water-leaving reflectances (rw) were estimated from downwelling and upwelling spectral irradiances,and compared with MERIS rw for a period between September and November 2008. The results of the “matchup” analysis showed that there was reasonable agreement between the data sets over the period of study at the offshore site where the land adjacency affect on the satellite data was reduced. The greatest deviation of in situ data from satellite values was at the inshore site and at the lower wavelengths of the visible spectrum, where the rws for the blue band were most affected by atmospheric corrections. This study suggests that calibration algorithms of MERIS products with in situ data from the south west coast of Portugal could be improved by using, for example, ICOL ( Improved Contrast between Ocean and Land) processing.
- Evaluation of the MERIS marine products in coastal and oceanic waters off Cape Sagres on the south-west coast of PortugalPublication . Cristina, Sónia; Goela, Priscila; Icely, John; Moore, Gerald; Newton, AliceIn-water constituents such as chlorophyll a, total suspended matter and yellow substances, as well as radiometric data sets from field measurements with a Satlantic hyperspectral radiometer were used to evaluate the performance of Medium Resolution Imaging Spectrometer (MERIS) sensor on the ENVISAT satellite, from inshore to offshore sites on the south west coast of Portugal. It was evaluate the performance of the Regular measurements of these parameters were taken from this region between September 2008 and July 2009 covering both Case 1 and Case 2 waters. Also was evaluate the recent developments towards improving the processing protocols for MERIS data including: the ICOL (Improved Contrast between Ocean and Land) processor; the new vicarious adjustment in the near infrared; and, most recently, the implementation of the MEGS 8 processor. Eight images were obtained under cloud free conditions, without flags for high glint, ice haze and low sun during this sampling period. Water-leaving reflectances (ρw) were estimated from downwelling Es (λ) and upwelling Lu (λ) spectral irradiances, and compared with MERIS ρw. The values of ρw were processed according to the MERIS in situ measurement protocols, before they could be compared with the MERIS data. A previous study in this area (Cristina et al., 2009) shows that are still problems with the calibrating the algorithm that links remote sensing data with in situ measurements, particularly at the coastal site where there are adjacency effects from land on the reflectance data observed by the satellite sensor. In this study ICOL processor was applied to correct this problem and improve processing on the inshore station (Station A). However the improvement was not so significant for some of the “match-ups” days. The MERIS ρw and the MERIS water products processed by the MEGS 8 didn’t improve the agreement with the in situ measurements as was expected, even with the new vicarious adjustment for the infrared wavelengths. In general, these results show that some corrections most be taken under MEGS 8 processor before coming publically available.
- Standard and regional bio-optical algorithms for chlorophyll a estimates in the Atlantic off the southwestern Iberian PeninsulaPublication . Cristina, Sónia; D'Alimonte, Davide; Goela, Priscila; Kajiyama, Tamito; Icely, John; Moore, Gerald; Fragoso, Bruno; Newton, AliceThis study investigates standard and regional algal pigment index 1 (API1) estimates in the Atlantic off the southwestern Iberian Peninsula. Standard API1 data are those delivered by the Medium Resolution Imaging Spectrometer (MERIS) orbiting sensor. Equivalent quantities are computed by applying a regional inversion scheme using as input both MERIS and in situ remote sensing reflectances (R-rs). Reference data for the development of the regional algorithm and for the analysis of tested products include field measurements of total concentration of chlorophyll a (TChla) and coincident R-rs values collected at different distances from the coast. Validation results, based on matchup analysis, identifies a systematic overestimation of standard API1 versus the reference TChla values. The additional comparison of product maps in selected regions of interest confirms this tendency and demonstrates the feasibility and relevance of using regional algorithms for investigating spaceborne products. Analogous applications are hence devised for the early-stage evaluation of the forthcoming Sentinel-3/OLCI data products.