A methodology to estimate the residence time of estuaries

The residence time has long been used as a classification parameter for estuaries and other semi- enclosed water bodies. It aims to quantify the time water remains inside the estuary, being used as an indicator both for pollution assessment and for ecological processes. Estuaries with a short residence time will export nutrients from upstream sources more rapidly then estuaries with longer residence time. On the other hand the residence time determines if micro-algae can stay long enough to generate a bloom. As a consequence, estuaries with very short residence time are expected to have much lower algae blooms, then estuaries with longer residence time. In addition, estuaries with residence times shorter than the doubling time of algae cells will inhibit formation of algae blooms (EPA, 2001). The residence time is also an important issue for processes taking place in the sediment. The fluxes of particulate matter and associated adsorbed species from the water column to the sediment depends of the particle’s vertical velocity, water depth and residence time. This is particularly important for the fine fractions with lower sinking velocities. The question is how to compute the residence time and how does it depend on the computation method adopted.

Sardine (Sardina pilchardus) delayed mortality associated with purse seine slipping: contributing stressors and responses

Tese dout., Ciências e Tecnologias das Pescas, Universidade do Algarve, 2009

Electrochemical methodology to study labile trace metal/natural organic matter complexation at low concentration levels in natural waters

A new electrochemical methodology to study labile trace metal/natural organic matter complexation at low concentration levels in natural waters is presented. This methodology consists of three steps: (i) an estimation of the complex diffusion coefficient (DML), (ii) determination at low pH of the total metal concentration initially present in the sample, (iii) a metal titration at the desired pH. The free and bound metal concentrations are determined for each point of the titration and modeled with the non-ideal competitive adsorption (NICA-Donnan) model in order to obtain the binding parameters. In this methodology, it is recommended to determine the hydrodynamic transport parameter, α, for each set of hydrodynamic conditions used in the voltammetric measurements. The methodology was tested using two fractions of natural organic matter (NOM) isolated from the Loire river, namely the hydrophobic organic matter (HPO) and the transphilic organic matter (TPI), and a well characterized fulvic acid (Laurentian fulvic acid, LFA). The complex diffusion coefficients obtained at pH 5 were 0.4 ± 0.2 for Pb and Cu/HPO, 1.8 ± 0.2 for Pb/TPI and (0.612 ± 0.009) × 10−10 m2 s−1 for Pb/LFA. NICA-Donnan parameters for lead binding were obtained for the HPO and TPI fractions. The new lead/LFA results were successfully predicted using parameters derived in our previous work.

An integrated and comparative approach to genetic selection of the aquaculture species Dicentrarchus labrax

The European sea bass, Dicentrarchus labrax, is one of the most important marine species cultivated in Southern Europe and has not benefited from selective breeding. One of the major goals in the sea bass (D. labrax) aquaculture industry is to understand and control the complexity of growth associated traits. The aim of the methodology developed for the studies reported in the thesis was not only to establish genetic and genomic resources for sea bass, but to also develop a conceptual strategy to efficiently create knowledge in a research environment that can easily be transferred to the aquaculture industry. The strategy involved; i) establishing an annotated sea bass transcriptome and then using it to, ii) identify new genetic markers for target QTL regions so that, iii) new QTL analysis could be performed and marker based resolution of the DNA regions of interest increased, and then iv) to merge the linkage map and the physical map in order to map the QTL confidence intervals to the sea bass genome and identify genes underlying the targeted traits. Finally to test if genes in the QTL regions that are candidates for divergent growth phenotypes have modified patterns of transcription that reflects the modified whole organism physiology SuperSAGE-SOLiD4 gene expression was used with sea bass with high growth heterogeneity. The SuperSAGE contributed to significantly increase the transcriptome information for sea bass muscle, brain and liver and also led to the identification of putative candidate genes lying in the genomic region of growth related QTL. Lastly all differentially expressed transcripts in brain, liver and muscle of the European sea bass with divergent specific growth rates were mapped to gene pathways and networks and the regulatory pathways most affected identified and established the tissue specific changes underlying the divergent SGR. Owing to the importance of European sea bass to Mediterranean aquaculture and the developed genomics resources from the present thesis and from other studies it should be possible to implement genetic selection programs using marker assisted selection.