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The main objectives of this group are six fold:
     - To understand the biophysical interactions regulating larval dispersal, recruitment pathways and connectivity of invertebrate populations in the upwelling system of the west Iberian coast. The techniques employed include multi-annual, high frequency, sampling programmes, oceanographic observations, numerical modelling and genetic markers.
     - To improve the characterisation the short-term variability of primary productivity in estuarine intertidal areas, through the use of non-destructive methodologies to quantify the photosynthetic activity of benthic microalgal films. Adaptation of optical techniques based on in vivo chlorophyll fluorescence, are applied, both in laboratory and in situ, to estimate photosynthetic carbon fixation rates by microphytobenthos.
     - To unravel invertebrate biodiversity in bathyal ecosystems from genetic to community levels, map their distribution at local to regional scales and link diversity, density and biomass patterns to the variability of natural drivers. Also, to investigate biological capacity of key species (eg. trophic ecology, symbiosis reproduction and dispersal) and understand their potential to support ecosystem functioning.
     - To develop/test methodologies for the bioassessment of coastal systems, including the performance of indicators, namely related to the implementation of the WFD, as well as remote sensing techniques, namely acoustic coupled with ground-truth sediment and biological data, to characterize and map sedimentary habitats and benthic biotopes.
     - To develop an environmental-friendly technique for disinfection of wastewater using photodynamic inactivation of microorganisms, based on porphyrine derivatives.
     - To identify the relevant pathogenic bacteria in fish farms of the Ria de Aveiro and to evaluate the impact of aquaculture systems on bacterial communities of the estuarine system Ria de Aveiro. Also, to evaluate the UVR effects on heterotrophic bacterial activity and on organic matter utilization.

Future Objectives

To attain the defined objectives, future investigation will be developed in order to:
     - Investigate the effect of weather patterns on phenology and survival of model invertebrate species. The focus will be placed on the influence of larval development environment on subsequent quality of individuals and on the response of developmental rates of egg and larvae to increases of temperature and salinity. Results will be incorporated on phenology models in order to simulate scenarios of global change. Specifically, the models will explore the effects of increasing temperature on the timing of hatching, settlement and recruitment of key crustacean species.
     - Pursue a more in-depth understanding of the ecophysiological adaptations that enable the high productivity of microphytobenthos in the stressful estuarine intertidal environment, through the study of the biochemical and behavioural mechanisms that provide photoprotection against photoinhibition due to oxidative stress. Also, the application of the knowledge gained and of the methodological tools developed in previous studies on diatom-dominated microphytobenthos to other photoautotrophs of significant ecological roles in coastal systems and of recognized biological interest, including phytoplankton and zooxanthelae (endosymbiotic associations with anthozoa), will be done.
     - Investigate more in-depth the biodiversity and functioning of deep-sea ecosystems by using experimental in situ approaches in order to gain information on reproduction, dispersal capabilities and recruitment processes of key species, and to understand their ability to recolonize after disturbance. Studies on the interconnectivity among ecosystems will be initiated. The research will contribute to the CoML syntheses on marine biodiversity and barcoding (funded by OBIS and BOLD respectively).
     - Sustain framework actions for long term ecological research and monitoring in areas of anthropogenic and natural change. Also, develop/test methodologies for the bioassessment of coastal systems and extend the study on the role and performance of indicators of change in transitional and coastal waters to disturbance sources others than organic enrichment (dredging, hypoxia, storms). Extend the AGDS approach for habitat characterisation and mapping to shallow water transition systems, as well to the whole Portuguese coastal shelf, while incorporating double-frequency surveying and specific biotope studies. In addition, develop reach out activities to promote public awareness of biodiversity and related ecological services.
     - Develop microbiological and molecular tools that can be used in the rapid detection of microbial pathogens and virulence factors in the aquatic environments and in actions of environmental bioremediation of acute chemical and biological contaminations. Samples collected in different marine environments characterized by high genetic diversity, such as estuarine water and sediments and mud volcanoes, will also be explored by metagenomic technologies directed to potential biotechnological applications.

Research Labs

The Marine and Estuarine Ecology RG has three Laboratories:
- Marine and Estuarine Ecology Lab
- Marine Primary Production Lab
- Marine Microbiology and Biotechnology Lab

The Marine and Estuarine Ecology RG also has three common infrastructures that provide support for the different Labs, for other research groups of the CESAM and the University and, in several cases, services. These infrastructures (and coordinators) are:
- Life Support Systems for Marine Organisms Lab
- Molecular Approaches in Marine Environments Lab
- Biological Research Collection

Marine and Estuarine Ecology Lab

Marine and Estuarine Ecology Lab

- Biogeochemistry of estuaries and upwelling systems: development and application of coupled oceanographic and ecological models to understand and forecast biogeochemical cycles in estuarine and upwelling systems.

- Deep-sea processes, natural resources and ecosystems: distribution and diversity of organisms and habitats in relation to natural drivers and human impact; biological capacity of key species, and their potential to support ecosystem functioning.

- Larval dispersal, recruitment and connectivity: spatial scale of metapopulational units in the marine environment, using high-frequency sampling of larval supply, genetic and geochemical markers and biophysical numerical models; large scale patterns of genetic and species diversity.

- Ecosystem health and habitat mapping: modelling and mapping of estuarine and coastal shelf benthic habitats; bio-assessment of estuarine and coastal ecosystems to natural and anthropogenic disturbance; food web ecology.

- Fisheries

- Conservation: scientific basis for the definition and management of ecologically coherent networks of marine protected areas. 

The Marine and Estuarine Ecology Lab is led by Marina CunhaVictor Quintino, and Henrique Queiroga.

Marine Primary Production Lab

Marine Primary Production Lab

Photosynthetic carbon fixation in estuarine habitats: photosynthetic responses to environmental stress in microphytobenthos and phytoplankton; photoprotection, photoinhibition and repair mechanisms; ecosystem-level primary production budgets.

Algal functional diversity and evolution: biodiversity of photoprotective processes in green algae; multi-stressor and spectral responses; evolution of functional kleptoplasty in Sacoglossa; physiological and behavioural photoprotection.

Symbiodinium diversity, eco-physiology, life history: algae-bacteria interactions; Symbiodinium as driver of microbial calcification; Eco-physiology and oxidative stress; distribution and ecology of free-living Symbiodinium in coral reef environments.

New methods for studying photosynthetic processes and primary productivity: measurement of PSII activity and improvement of primary production proxies; high-throughput approaches for photosynthetic phenotyping based on 2D imaging of chlorophyll fluorescence.

The Marine Primary Production Lab is led by João Serôdio.