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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.
- 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.
- Harmful phytoplankton diversity and dynamics in an upwelling region (Sagres, SW Portugal) revealed by ribosomal RNA microarray combined with microscopyPublication . Danchenko, Sergei; Fragoso, Bruno; Guillebault, Delphine; Icely, John; Berzano, Marco; Newton, AliceThe study region in Sagres, SW Portugal, is subject to natural eutrophication of coastal waters by wind-driven 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 the diatoms 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 catenation 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 Alexandrum and Azadinium, with the latter being one of the first records from the study region. Seasonality and upwelling induced by northerly winds were found to be the driving forces of HAB development, with Pseudonitzschia spp. causing the risk of ASP during spring and summer upwelling 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 and confirm the suitability of the RNA microarray method for HABs detection and aquaculture management applications.
- 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.
- Phytoplankton allelochemical interactions change microbial food web dynamicsPublication . Weissbach, Astrid; Rudstrom, Maria; Olofsson, Martin; Béchemin, Christian; Icely, John; Newton, Alice; Tillmann, Urban; Legrand, CatherineThis study investigates the effect of filtrates from an allelopathic dinoflagellate, Alexandrium tamarense, on four microbial food webs that have been manipulated experimentally from natural seawater by modifying the availability of resources in the form of dissolved organic carbon with additions of peptone, and by altering the grazing pressure with size fractionation. Bacterial production was generally not affected by allelochemicals, but bacteria showed higher net growth in all food webs when allelochemicals were added, whereas heterotrophic nanoflagellates . 7 mm and ciliates were constrained in all food webs. Allelochemicals had the largest negative effects on microbial communities with low grazing pressure. In food webs with high grazing pressure and additional resources, phytoplankton and small nanoflagellates were positively affected by the addition of allelochemicals, suggesting that those were interfering with trophic interactions in the microbial communities. By the lysis of organisms sensitive towards allelochemicals, resources are made available and grazing pressure on certain microorganisms is reduced. However, the intensity of these interactions is modulated by both the availability of resources and the biomass of grazers in the initial food web.
- The yield of microphytobenthic chlorophyll from nutrients: enriched experiments in microcosmsPublication . Brito, Ana; Newton, Alice; Tett, Paul; Icely, John; Fernandes, TeresaThe yield of phytoplankton chlorophyll from nitrogen is a useful parameter in the study of eutrophication of coastal waters, providing the link between chlorophyll formation and nutrient consumption. This parameter has been estimated for microphytobenthos from Ria Formosa lagoon on the south coast of Portugal with a series of three experiments conducted in May and September 2007. Six sediment cores were collected from Ria Formosa in acrylic cylinders and cork stoppers were placed in the bottom. Water samples were collected in large containers and prepared (filtered and enriched) to be pumped to the top of the sediment inside the acrylic cylinders, which are the microcosms of the experiments. Microcosms were isolated to avoid water exchanges and placed in large tanks full of water to maintain temperature stability. Experiments were run for 5 to 9 days in a continuous diluted nutrient enriched system. One of the experiments was carried out with half the microcosms in the dark to evaluate the nutrient fluxes between the sediment and the water column, when no algal growth is expected. Nutrient fluxes of muddy sediments, during the two last days of the experiment in the dark were estimated to be 0.1015 μmol cm−2d−1 for nitrogen, −0.0015 μmol cm−2d−1 for phosphorus, and 0.1395 μmol cm−2d−1 for silicon. The yield of chlorophyll was determined to be between 3.65 and 4.11 μg chl (μmol N)−1 from nitrogen and between 4.03 and 4.77 μg chl (μmol Si)−1 for silicon in muddy sediments. It was not possible to determine the yield from phosphorus. These values are higher than for phytoplankton which may be due to physiological reasons, or due to the presence of a smaller fraction of microheterotrophs, which would divert nutrients. For sand, smaller yields were obtained but it is likely that this was mainly due to the fact that the values of the sediment fluxes used were the ones obtained for mud, which are higher than they should be for sand. This extra input of nutrients is considered to be taken up by algae, thereby decreasing the value of the yield. Therefore, reliable chlorophyll yield estimates for sand could not be obtained.
- 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.
- The coastal syndromes and hotspots on the coastPublication . Newton, Alice; Carruthers, Tim; Icely, JohnHuman intervention has resulted in a number of global and riverriver-mouth syndromes that are mirrored by coastal syndromes caused by erosion, subsidence, salinization of aquifers, urbanization, eutrophication, invasive species and over exploitation of natural resources. These problems are now global, with few coastal zones remaining unaffected and pristine. However, the problems are particularly severe at “hotspots” in the coastal zone. These include river-mouth systems where fluxes of water, sediment, fertilizers and contaminants are focused; urbanized coasts and megacities where vulnerable populations are concentrated; Arctic coasts where the effects of climate change are accelerating a fundamental state change; and, at low lying coasts that are at risk of flooding, storm surges, sea-level rise and subsidence such as Micronesian island states where managed realignment and setback is not an option. A range of societal responses and appropriate governance frameworks will be necessary to treat the coastal syndromes.
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