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- EcoDynamo - Ecological Dynamics Model ApplicationPublication . Pereira, António; Duarte, Pedro
- ECODOURO - Modelling the effect of freshwater reduction and pulse discharge on the water dynamics and processes of the Crestuma ReservoirPublication . Bordalo, Adriano; Duarte, Pedro; Wiebe, WilliamThis report deals with the activities carried out during the project 72 months, from March 15, 2003 to September 15, 2006 under the framework of the ECODOURO - Modelling the effect of freshwater reduction and pulse discharge on the water dynamics and processes of the Crestuma Reservoir (POCTI/MGS/45533/2002). The report includes the fieldwork, data interpretation and mathematical modeling according to the seven working packages presented in the original proposal. Data is available to the public at http://ecodouro.icbas.up.pt. The main objectives of this goal oriented research project implemented on the Crestuma Reservoir (Douro River) are: i. To evaluate the long-term effects of flow reduction on key environmental variables and processes that occur in the Crestuma Reservoir; and ii. To evaluate the effect of high frequency oscillations (freshwater pulse discharges) on the ecosystem dynamics in terms of water column stratification, water temperature and turbidity, oxygen, nutrient availability, phytoplankton biomass and primary productivity. The original requested budget was reduced by 19%, and the evaluation commission recommended the non-acquisition of a second multiprobe CTD. Thus, the entire field survey program was changed accordingly. The seasonal sampling was conducted at two anchor stations located about 500 m and 2,500 m from the Crestuma dam crest. Surveys were performed on December 2003 (Fall), February 2004 (Winter), May 2004 (Spring) and August 2004 (Summer). An un-scheduled survey was carried out at the onset of the program (May 2003), in order to gather basic data since no departure data (short term series) were available contrarily to what was though. This approach proved to be very useful and the obtained results were applied in the following surveys. Moreover, since no workable bathymetrics were available to the research team (only depth contours in chart format restricted to the navigational channel) several dedicated surveys were organized in order to generate bottom contour maps for the last 10 km of the reservoir, covering the two-field stations location. As a result, a costume-made GIS was created and data used to run the model. All technical details of both the employed models (2D-vertically resolved model and the coupled biogeochemical model), including the complete mathematical formulae, are 2 presented in Annexes I and II. The rationale for selection of the modeled parameters are presented; the field data obtained from the 4+1 surveys were used to initialize the models. It was found that the different flow time-scales might influence water dynamics, biogeochemistry and primary productivity. For example, during the day, longitudinal flows results from upstream forcing, with river water entering into the reservoir. A clear longitudinal flow profile emergeed, disturbed in some points by depth changes that forces upwelling of bottom water. During the night, in the absence of river flow, at it happens frequently in Spring through Fall, convective flow dominated, with surface cooled water sinking to the bottom and forcing the ascent of bottom water. Vertical flows may be larger than horizontal ones. On the other hand, the highest phytoplankton production was observed in May and September, when microalgae were using more efficiently the available light. Furthermore, phytoplankton efficiency decreased from morning to dawn. Considering the objectives of this project, several model simulations were carried out to analyze the effects of flow variability on water column stratification and quality (cf. – Annexe III). These simulations were carried out with the same average flow magnitude and forcing conditions, in terms of water temperature, nutrients and chlorophyll concentrations, but different flow frequencies and amplitudes. Results obtained suggest that flow variability may not have a large effect on water temperature, nutrient and chlorophyll concentration and net primary production at annual time scales. However, when the time scale under analysis is reduced to seasonal and monthly, effects of flow variability become apparent, especially during the summer period and when flow is hold constant. Constant flow implies that extreme low and high values do not occur. Under this situation of “extreme” flow regulation, it appears that the synergies between river forcing and reservoir processes tend to reduce phytoplankton biomass. Therefore, from a management point of view, it is apparent that stabilizing the flow may prevent the development of phytoplankton blooms. On the other hand, results presented and discussed in Annex IV suggest that the Crestuma reservoir has undergone some important changes over the period 1999-2005, with significant increases in nitrogen and phosphorus and a decrease in the nitrogen: phosphorus ratio i.e. the Redfield ratio. One possible change, arising from the shifts in the nitrogen: phosphorus ratio, is the apparent autumn shift towards nitrate-nitrogen limitation of phytoplankton. Apart from increasing nutrient runoff within the watershed, the 3 noticeable nutrient increase trend found in the Crestuma resevoir may also be explained by the reduction of chlorophyll as a result of the massive development of the invasive clam Corbicula sp. Thus, the Crestuma reservoir is now a predominantly heterotrophic ecosystem that is the source of water to 20% of the Portuguese population and feeds the Douro estuary with most of the water that reaches the Atlantic Ocean. As a result of this project, a full functional calibrated with dedicated data model is available. During the 72 mo of the project, three young researchers were able to work and get training in the different areas covered by the program. Due to the enormous amount of data gathered, only two research papers were published. Thus, in the near future, two papers will be submitted (as a result of Annex III and Annex IV), and two additional papers are under preparation. Part of the obtained data has being used for teaching purposes at undergraduate and Master/PhD levels by the PI and the Cemas team.
- DSS Application (Ria Formosa Lagoon)Publication . Pereira, António; Duarte, PedroThis report presents the Decision Support System (DSS) applied to the Ria Formosa lagoon using an agent-based simulation approach. The idea is to include the interests of the decision-makers and stakeholders in the ecological system simulation; these entities are modelled as intelligent agents that communicate with the simulation tool (EcoDynamo) building one multi-agent community system. The intelligent agents, each one with some goals about the simulation results of the simulated system, have perception of their environment, reason, using their knowledge and are able to change the simulated environment by using a given set of configurable actions. Two intelligent agents are being developed at the moment: one calibration agent and one aquaculture/farming agent. The former intends to optimise the fit between observed and simulated results, and the latter looks for production optimisation. The agent used to generate this report is a development tool that includes actions from both agents. This report also introduces ECOLANG, a communication language developed during the DITTY project, with the main purpose of interchanging information between the simulation application of aquatic ecosystems - EcoDynamo - and external agents. Finally, the report focuses on the integration of the Analytical Hierarchy Process (AHP), developed by the University of Siena, in the aquaculture/farming agent decision process (Siena 2005 and Siena 2006)
- Fecundity, spore recruitment and size in Gelidium sesquipedale (Gelidiales,Rhodophyta)Publication . Santos, R.; Duarte, PedroGelidium sesquipedale fecundity was quantified by counting tetrasporangial sori and cystocarps per meter squared and by estimating the number of spores contained inside them . These were obtained by regression on a size metric of reproductive structures . Tetrasporangial sori length and cystocarp thickness were the best estimators of spore number. To assess spore recruitment, 12 pottery tiles were fixed to the bottom, and the appearance of small fronds was monitored. No clear seasonal pattern of reproduction was found . Tetraspore production peaked in March 1990 with 10.4 x 106 spores m-2, whereas the carpospore peak was lower, 4.9 x 10 5 spores m-2 in July 1989. Recruitment followed tetraspore peaks . The probability of a G. sesquipedale tetraspore making the transition to a recruit was 4.7 x 10-5. Frond length was significantly related to tetrasporangial sori number, while cystocarp number was only related to frond branching order. Minimum size for reproduction was 6.9 cm for gametophytes and 5.4 cm for tetrasporophytes; very rarely were cystocarpic fronds smaller than 9 cm, while tetrasporic fronds were often longer than 15 cm . Cystocarpic fronds were significantly shorter and had more branches than tetrasporic fronds .
- Impact of Oporto Metropolitan Area carbon dioxide emissions over the adjacent coastal zonePublication . Carvalho, Rogério; Barros, Nelson; Duarte, PedroConcerns about global warming over the last years have stimulated a large number of studies regarding atmospheric and oceanic carbon dioxide (CO2) concentration and its consequences. In spite of the available data on global atmospheric CO2, there is only limited knowledge on CO2 variability at regional scales. Moreover, there is an important gap in our understanding of the contribution of high CO2 emission regions, such as metropolitan areas, to CO2 concentrations over nearby coastal areas–considered by several authors as an important CO2 sink. A possible working hypothesis is that, large littoral metropolitan areas may have a significant influence on CO2 atmospheric concentrations over those areas and exert an important influence on sea-air CO2 exchanges. Therefore, the main objective of this study is to estimate CO2 concentration at a regional scale, under the influence of Oporto Metropolitan Area (OMA) emissions as a first test of this hypothesis. To fulfil this objective, an emission database was built and used to force, together with meteorological synoptic data, a mesoscale atmospheric dispersion model. The model was used to simulate several weather scenarios and estimate CO2 concentrations along a ca. 90 km stretch of the Portuguese northern shore. The results obtained suggest that emissions from OMA have an important influence on CO2 atmospheric concentrations up to 6–12 km offshore, particularly in autumn and winter. However, this CO2 increase does not seem to have the potential to significantly affect sea-air CO2 exchanges, although this is just a preliminary conclusion that has to be tested by field work.
- The relationship between phytoplankton diversity and community function in a coastal lagoonPublication . Duarte, Pedro; Macedo, M.F.; Cancela da Fonseca, LuísThe decrease of biodiversity related to the phenomena of global climate change is stimulating the scientific community towards a better understanding of the relationships between biodiversity and ecosystem functioning. In ecosystems where marked biodiversity changes occur at seasonal time scales, it is easier to relate them with ecosystem functioning. The objective of this work is to analyse the relationship between phytoplankton diversity and primary production in St. André coastal lagoon – SW Portugal. This lagoon is artificially opened to the sea every year in early spring, exhibiting a shift from a marine dominated to a low salinity ecosystem in winter. Data on salinity, temperature, nutrients, phytoplankton species composition, chlorophyll a (Chl a) concentration and primary production were analysed over a year. Modelling studies based on production-irradiance curves were also conducted. A total of 19 taxa were identified among diatoms, dinoflagellates and euglenophyceans, the less abundant group. Lowest diversities (Shannon– Wiener index) were observed just before the opening to the sea. Results show a negative correlation (p<0.05) between diversity and chlorophyll a (Chl a) concentration (0.2–40.3 mg Chl a m-3). Higher Chl a values corresponded to periods when the community was dominated by the dinoflagellate Prorocentrum minimum (>90% of cell abundance) and production was maximal (up to 234.8 mg C m-3 h-1). Maximal photosynthetic rates (Pmax) (2.0–22.5 mg C mg Chl a-1 h-1) were higher under lower Chl a concentrations. The results of this work suggest that decreases in diversity are associated with increases in biomass and production, whereas increases correspond to opposite trends. It is suggested that these trends, contrary to those observed in terrestrial and in some benthic ecosystems, may be a result of low habitat diversity in the water column and resulting competitive pressure. The occurrence of the highest photosynthetic rates when Chl a is low, under some of the highest diversities, suggests a more efficient use of irradiance under low biomass–high diversity conditions. Results suggest that this increased efficiency is not explained by potential reductions in nutrient limitation and intraspecific competition under lower biomasses and may be a result of niche complementarity.
- Um algoritmo para dimensionamento de ciclonesPublication . Maurício, Pedro; Silva, Pedro; Fonseca, Ana; Duarte, PedroOs ciclones são instrumentos de separação gás-sólido, largamente utilizados na indústria. O seu dimensionamento resulta da conjugação de diversas variáveis que afectam a performance deste equipamento, muitas vezes através de um processo iterativo baseado na experiência do executante, com alguma subjectividade associada. Neste estudo desenvolveu-se um algoritmo de dimensionamento automático de ciclones que permite obter resultados fiáveis, optimizando as dimensões e o número de ciclones e respectivas dimensões a partir de duas restrições – eficiência mínima de captura das partículas e perda de carga máxima do gás. Cyclones are gas-solid separation devices, largely used in industry. The cyclone design process is based on the combination of several variables that influence its performance. This is an iterative process dependent, most of the times, on individual experience. In this study, an algorithm was developed for automatic cyclone designing, which has produced reproducible results, optimizing the dimensions and the number of cyclones given two limiting conditions – minimum particle capture efficiency and maximum head loss.
- Pelagic metabolism of the Douro estuary (Portugal) - Factors controlling primary productionPublication . Azevedo, Isabel C.; Duarte, Pedro; Bordalo, AdrianoThe pelagic metabolism of the Douro estuary (Portugal) and the factors influencing primary production (PP) and community respiration (CR) in this system were studied during an annual cycle (December 2002 - December 2003). Sampling surveys were conducted twice a month during ebb and flood spring tides and water samples were collected for PP and CR assessments at three stations along the estuary (lower, middle and upper stretches). During the study period, PP values were in the range of 4.7-1878.5 mg C m-2 d-1 (average, 319.9 mg C m-2 d-1). River discharge controlled phytoplankton biomass inputs into the estuary as well as residence time. A decreasing trend in water column PP from the upper to the lower estuary related to higher nitrogen concentrations and phytoplankton biomass from riverine origin was observed. An inverse trend was found for CR, i.e., higher values were found in the lower, more urbanized stretch. During the study period, averaged CR values reached 1154 mg C m-2 d-1. In general, heterotrophy dominated the entire estuary, except in the upper stretch from May through July, when increased PP, but also lower CR values were recorded. A positive correlation between chlorophyll a and Pmax was found which is unusual in coastal ecosystems, where a decreasing trend of the P/B ratio as a function of net primary production is generally observed. This could be explained by the relatively low phytoplankton biomass, preventing intraspecific competition from lowering photosynthetic capacity, on one hand, and the physiology of phytoplankton related to their origin in a semi-lotic (reservoir) ecosystem. No significant differences between tides were observed for all variables, except for the water light extinction coefficient (k) values, reflecting higher turbidity during the ebb.
- Mathematical modelling to assess the carrying capacity for multi-species culture within coastal watersPublication . Duarte, Pedro; Meneses, R.; Hawkins, A.J.S.; Zhu, M.; Fang, J. G.; Grant, J.In the context of aquaculture, carrying capacity is generally understood as the standing stock of a particular species at which production is maximised without negatively affecting growth rates. The estimation of carrying capacity for aquaculture is a complex issue. That complexity stems from the many interactions between and among cultivated and non-cultivated species, as well as between those species and their physical and chemical environments. Mathematical models may help to resolve these interactions, by analysing them in a dynamic manner. Previous carrying capacity models have considered the biogeochemical processes that influence growth of cultivated species in great detail. However, physical processes tend to have been addressed very simplistically. Further, most modelling has been for monocultures, despite the increasing importance of multi-species (=polyculture) systems. We present here a two-dimensional coupled physical–biogeochemical model implemented for Sungo Bay, Shandong Province, People’s Republic of China. Sungo Bay is used for extensive polyculture, where bivalve shellfish and kelp are the most important cultivated species. Data collected over 13 years (1983–2000)was available for modelling. Our main objectives were to implement the model, achieving reasonable calibration and validation with independent data sets, for use in estimating the environmental carrying capacity for polyculture of scallops and oysters. Findings indicate that the model successfully reproduces some of the main features of the simulated system. Although requiring some further work to improve predictive capability in parts, predictions clearly indicate that Sungo Bay is being exploited close to the environmental carrying capacity for suspension-feeding shellfish. Comparison of different culture scenarios also indicates that any significant increase in yield will depend largely on a more optimal spatial distribution of the different cultivated species.
- Different modelling tools of aquatic ecosystems: A proposal for a unified approachPublication . Pereira, António; Duarte, Pedro; Norro, A.Over the last few decades, several modelling tools have been developed for the simulation of hydrodynamic and biogeochemical processes in aquatic ecosystems. Until late 70's, coupling hydrodynamic models to biogeochemical models was not common and today, problems linked to the different scales of interest remain. The time scale of hydrodynamic phenomena in coastal zone (minutes to hours) is much lower than that of biogeochemistry (few days). Over the last years, there has been an increasing tendency to couple hydrodynamic and biogeochemical models in a clear recognition of the importance of incorporating in one model the feedbacks between physical, chemical and biological processes. However, different modelling teams tend to adopt different modelling tools, with the result that benchmarking exercises are sometimes difficult to achieve in projects involving several institutions. Therefore, the objectives of this paper are to provide a quick overview of available modelling approaches for hydrodynamic and biogeochemical modelling, to help people choose among the diversity of available models, as a function of their particular needs, and to propose a unified approach to allow modellers to share software code, based on the object oriented programming potentiality. This approach is based on having object dynamic link libraries that may be linked to different model shells. Each object represents different processes and respective variables, e.g. hydrodynamic, phytoplankton and zooplankton objects. Some simple rules are proposed to link available objects to programs written in different source codes.