Browsing by Author "Fragoso, Bruno"
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- 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.
- Avaliação da acumulação de organismos (biofouling) em painéis de recrutamento de PVC e eficiência de materiais não tóxicos em redes numa aquacultura de ostras (Sagres)Publication . Fragoso, Bruno; Icely, John; Serrão, EsterA acumulação indesejada de organismos em estruturas colocadas pelo homem no ambiente aquático, provoca problemas técnicos e económicos, especialmente na indústria da aquacultura. A acumulação de organismos na aquacultura de ostras em Sagres, foi avaliada através de duas experiências baseadas no Projecto CRAB, financiado pela EU. Parâmetros ambientais, como a temperatura, salinidade, profundidade de Secchi e clorofila-a, foram registados. O recrutamento mensal foi avaliado através da colocação mensal de painéis de PVC. O desenvolvimento da sucessão foi observado mensalmente sobre painéis, ao longo de 2 anos de imersão. Mensalmente os painéis foram fotografados, o peso e a espessura registados. Amostras de 5cm2 da superfície dos painéis foram recolhidas, para identificação dos organismos no final da imersão, para o recrutamento mensal e para a sucessão. A temperatura foi geralmente mais baixa durante períodos de vento Norte e mais quente com ventos oriundos de Sul. Concentrações de clorofila-a mais elevadas ocorreram durante períodos de temperaturas baixas e profundidades de Secchi reduzidas, indicando a ocorrência de afloramento costeiro. No recrutamento mensal, o peso e a espessura, registaram os valores mais elevados entre Maio e Agosto de 2005. Para a sucessão, o peso e a espessura registaram os valores mais elevados entre Junho e Outubro 2005. Os organismos identificados foram algas castanhas da família Ectocarpaceae, algas verdes (Ulva), algas vermelhas (Ceramium), hidrozoários, briozoários, cirrípedes (Balanus perforatus) e serpulídeos (Pomatoceros triqueter). Coberturas não tóxicas de silicone e microfibras em redes, foram usadas para redução da acumulação de organismos. Após o período de imersão na aquacultura, mediram-se as áreas da malha das redes, através de fotografias digitais. A cobertura de silicone mostrou uma menor colmatação das malhas, comparativamente aos controlos, o efeito da rede com microfibras foi menos significativo. Este estudo foi incluído no manual “ European Best Practice in Aquaculture Biofouling, 2007” do projecto CRAB.
- 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.
- 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.
- 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.
- Technical note: Algal Pigment Index 2 in the Atlantic off the southwest Iberian Peninsula: standard and regional algorithmsPublication . Goela, Priscila; Cristina, Sónia; Kajiyama, Tamito; Icely, John; Moore, Gerald; Fragoso, Bruno; Newton, AliceIn this study, Algal Pigment Index 2 (API2) is investigated in Sagres, an area located in the Atlantic off the southwestern Iberian Peninsula. Standard results provided by the MEdium Resolution Image Spectrometer (MERIS) ocean colour sensor were compared with alternative data products, determined through a regional inversion scheme, using both MERIS and in situ remote sensing reflectances (R-rs) as input data. The reference quantity for performance assessment is in situ total chlorophyll a (TChl a) concentration estimated through a phytoplankton absorption coefficient (i.e. equivalent to API2). Additional comparison of data products has also been addressed for TChl a concentration determined by high-performance liquid chromatography. The MERIS matchup analysis revealed a systematic underestimation of TChl a, which was confirmed with an independent comparison of product map analysis. The study demonstrates the importance of regional algorithms for the study area that could complement upcoming standard results of the current Sentinel-3/OLCI space mission.
- Water framework directive implementation: intercalibration exercise for biological quality elements: a case study for the south coast of PortugalPublication . Goela, Priscila; Newton, Alice; Cristina, Sónia; Fragoso, BrunoThis work summarises the Intercalibration Exercise (IE) required for the Common Implementation Strategy of the Water Framework Directive (WFD; 2000/60/EC) that was carried out in Portugal, and applied to a coastal region. The WFD aims to achieve good ec ological status for all waters in the European Community by 2015. The Ecological Status of a water body is determined us ing a range of Hydromorphological and Physico-Chemical Quality Elements as well Biological Quality Elements (BQE ). In coastal waters, the Biological Elements include Phytoplankton, Other Aquatic Flora and Benthic Inverteb rate Fauna. Good cooperation with the other Member States allowed the IE to proceed without a complete da ta set, and Portugal was ab le to intercalibrate and harmonise methods within the North Ea st Atlantic Geographica l Intercalibration Group for most of the BQE. The appropriate metrics and corre sponding methods were agreed under the framework of the RECITAL (Reference Conditions and Intercalibra tion) project, funded by the Port uguese Water Institu te, INAG. Some preliminary sampling was undertaken, but not su fficient to establish the Reference Conditions. The study area was a coastal lagoon in the southern part of Portugal. The focus was on the Phytoplankton Quality Element, but other BQE were also taken into account. Two sampli ng stations in Ria Formosa coastal lagoon were considered in this exercise: Ramalhete a nd Ponte. The metrics adopted by the Intercalibration Exercise groups were applied enabli ng the classification for the two sta tions of Good/High Status for the majority of the BQE parameters.