Loading...
52 results
Search Results
Now showing 1 - 10 of 52
- 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.
- 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.
- Temporal and spatial variation of phytopigments in the Western part of the Ria Formosa lagoon, Southern PortugalPublication . Pereira, M.; Icely, John; Mudge, S.; Newton, Alice; Rubina, R.The spatial and temporal variation of phytoplankton pigments in the western part of Ria Formosa, Portugal, was investigated between September 2000 and July 2002. Sampling stations included the ocean boundary (Anc˜ao inlet) and two different landward boundary situations: 1) the shallow westernmost “blind end” of the lagoon (Ponte) and 2) near a main sewage outlet (Ramalhete). Nutrient concentrations were higher during the first year of sampling but were lower than those recorded in previous studies. This decrease in the concentration of nutrients was possibly the result of the 1997 relocation of the Anc˜ao inlet, which allowed better water circulation in the lagoon. Throughout this study, concentrations of chlorophyll a determined by high-performance liquid chromatography were consistently low. Inter-annual variability in the pattern of chlorophyll a concentration was observed in the form of a bimodal peak (spring/summer and autumn) between September 2000 and June 2001 and more uniformconcentrations from September 2001 until July 2002. Principal component analysis of the concentrations of all pigments did not indicate any spatial- or tidal-related variations but did show that pigment concentrations varied over time. Partial least squares analysis corroborated this temporal shift of the phytoplankton pigment abundance and composition and showed that these shifts could be linked to certain environmental variables. Fucoxanthin was the dominant accessory pigment and was strongly correlated with chlorophyll a. Other marker pigments present in lower concentrations included chlorophyll b, 19′-hexanoyloxyfucoxanthin, neoxanthin, alloxanthin, diadinoxanthin, lutein, zeaxanthin, and beta-carotene. PLS analysis was used to infer the dominant phytoplanktonic groups in the lagoon. This analysis established that diatoms and other algal groups with a similar pigment profile dominated the phytoplankton community throughout the year. Cryptophytes were the second most abundant group in the lagoon. The remaining groups, including dinoflagellates, cyanophytes, and chlorophytes, contributed much less to the total algal biomass (generally <10%).
- 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.
- Evaluation of eutrophication in the Ria Formosa coastal lagoon, PortugalPublication . Newton, Alice; Icely, John; Falcão, Manuela; Nobre, A.; Nunes, J.; Ferreira, J.; Vale, C.The Ria Formosa is a shallow mesotidal lagoon on the south coast of Portugal, with natural biogeochemical cycles essentially regulated by tidal exchanges at the seawater boundaries and at the sediment interface. Existing data on nutrients in the water column and the sediment, together with chlorophyll a and oxygen saturation in the water column,compared using different models for assessing eutrophication. The European Environmental Agency criteria are based on the comparison of nutrient concentrations which indicate that the situation in the Ria Formosa is ‘‘poor’’ to ‘‘bad’’. In contrast, the United States Estuarine Eutrophication Assessment is based on symptoms, including high chlorophyll a and low oxygen saturation, which indicate that the Ria Formosa is near pristine. Despite these contradictions, a preliminary assessment by Driving forces, Pressures, State, Impact, Reponses(DPSIR) of eutrophication demonstrate the potential for episodic eutrophic conditions from treated and untreated domestic effluent as well as from non-point source agricultural run off. Sediments are also an important source of nutrients in the lagoon, but their contribution to potential eutrophic conditions is unknown.
- 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.
- Forecasting closures on shellfish farms using machine learningPublication . O’Donncha, Fearghal; Akhriev, Albert; Fragoso, Bruno; Icely, JohnBiotoxins and harmful algal blooms (HABs) are damaging to aquaculture operations. Occurrences lead to disrupted operations, fish kills, and significant risks to human health. The conditions leading to blooms are driven by known, but complex processes. Heuristics exist about the drivers but the nonlinearity and opaqueness of relationships make it difficult to resolve using traditional rule-based mathematical models. An alternative approach leverages machine learning to uncover the conditions that lead to the closure of farms. This paper presents a comprehensive framework that combines semi-automated machine learning with ensemble classification approaches to predict site closures. Performance is evaluated on 7 years of site closure data from a shellfish farm in Southwest Portugal, together with publicly available environmental data. The model reports an accuracy of 83% across a challenging forecasting task. The proposed framework provides a pragmatic, scalable, site-specific decision tool to help aquaculture stakeholders mitigate the impacts of HABs.
- 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.