AQUA-USERS Newsletter 2, March 2016
AQUAculture USEr driven  
operational Remote Sensing information services

Dear reader,

Welcome to the second issue of the AQUA-USERS newsletter! It has been a busy and exciting period for the AQUA-USERS team as we have been working on method development and improvements to make Earth observation data usable for the aquaculture industry, on technical implementation of our methods and on our first case study on site selection and characterisation. In the final year of the project, we are now working on bringing all the pieces together in the final near-real time case study on daily aquaculture management.

In this issue of our newsletter, we introduce you to the project consortium, present some of the exciting outcomes of AQUA-USERS, namely the improved method for detection of harmful algae blooms and an example of site selection case study for Denmark. You will also meet our user Finisterra, a mussel producer from the beautiful Algarve coast. In the next issue we will focus on the tools we have developed to make our results available to the user community.
If you would like more regular updates on what is going on within AQUA-USERS, please follow @AQUA-USERS on Twitter and visit our website. If this newsletter is not displayed correctly, please view the web version.
We hope that you'll enjoy our updates!

Marnix Laanen, Water Insight, coordinator, and the AQUA-USERS team
The AQUA-USERS consortium
Our consortium consists of nine partners from five countries. Two partners are universities: the Free University of Amsterdam, (VU) and the University of Lisbon (FFCUL), three partners are small companies: Water Insight (WI), DHI-GRAS (GRAS) and Sagremarisco (SGM), and four partners are large national or independent research organisations: Plymouth Marine Laboratory (PML), the Norwegian Institute for Water Research (NIVA), DHI and Deltares. The collective expertise of the consortium covers a wide range of fields relevant for aquaculture, bringing together these competences of the partners for the benefit of the aquaculture industry: Remote sensing of water quality (WI, VU, PML, NIVA, FFCUL, GRAS, SGM, Deltares), in-situ optical observation techniques (WI, NIVA, PML, SGM), lab techniques for growing algae cultures and measuring optical properties (PML, FFCUL), environmental modelling (DHI), web GIS development (PML), database design (WI), spatial analysis (WI, PML, DHI, GRAS), knowledge on aquaculture production systems and environmental interactions (NIVA, DHI, SGM), socio-economic expertise (Deltares) and commercialisation (WI).
Project news
User meeting in Venice
The second user meeting of AQUA-USERS took place in June 2015 in Venice in conjunction with the project mid-term . Seven users from five countries representing different finfish and shellfish farming systems attended the meeting and provided very valuable feedback on the developments within the project so far and guidance for further activities. Most of our users are innovative aquaculture companies who wish to improve their production by incorporating cutting edge technology. They are excited about access to near-real time data on different aspect of the ecosystem surrounding their production sites. Also, aquaculture producer organisations are represented on our user board who show particular interest in the site selection and characterisation as a tool for guidance in future development of the regional aquaculture sectors.

Improved detection of harmful algae blooms

Harmful algal blooms (HABs) are considered a major environmental problem and threat to the aquaculture industry in many European countries. Harmful algal species produce toxins that can be concentrated by filter-feeding shellfish and cause amnesia or paralysis when ingested. In high concentration HAB species may cause massive fin-fish suffocation and mortality through clogging the gill tissues. Harmful blooms result in economic losses through closure of shellfish grounds and direct damage of fish farms. A recent major bloom along the coast of Chile illustrates the devastating effect that toxic micro algae can have: almost 25 million salmon were killed within a few days, causing losses of around $800m. Early warning of HABs allows t
he aquaculture industry to take mitigation measures to minimise stock losses and reduce economical loses. Therefore, one of the research objectives of AQUA-USERS is improving the detection of harmful algae species from space.

If the bloom is high in biomass, harmful algae can be observed from space using satellite sensors. Within AQUA-USERS, an existing method for HAB detection from space using ocean colour data has been improved and extended. The species considered within the project include Karenia mikimotoi, Pseudo-nitzschia spp., Phaeocystis globosa, Lingulodinium polyedrum and Pseudochattonella sp.. The detection and classification algorithms are ‘trained’ using the full spectrum of water-leaving radiances, absorption and backscattering; while false alarms are minimised by labelling as ‘unknown’ any data that cannot be reliably classified. For some species, the detection accuracy could further be improved by incorporating measurements of optical properties obtained from algae cultured in the lab. By comparison with in-situ measurements the method has been validated for high-biomass bloom-forming species that cause a characteristic colouring of the water. These techniques are more beneficial for HAB warning than previous satellite-based systems based only elevated chlorophyll concentration.

More details can be found in two project deliverables: the method description and a report on its implementation.

Site selection
The Danish site selection case study takes a look at suitability of areas for rainbow trout production on a national level. The expected growth of the trout farming industry is accompanied by public and regulatory concerns over the environmental and health risks of sea cage fish farming. Hence the selection of new sites for trout farming is increasingly challenging.

To identify potential areas for future trout farms, an analytical framework was defined that includes key aspects of spatial suitability, namely spatial restrictions, optimal production conditions and environmental impacts. Spatial restrictions refer to areas already occupied by or reserved to other activities such as shipping routes, cables, nature protected areas or military zones. Production conditions influencing the well-being of the fish or the site infrastructure that are considered include temperature, salinity, nutrients, water depth, wave height and current speed. Environmental impacts refer to environmental conditions that do not support production of finfish because the aquaculture production can impact the environmental status negatively. Data on physico-chemical and environmental conditions was extracted from coupled 3-dimensional hydrodynamic-ecosystem models covering the Baltic Sea and Inner Danish waters.

For each of these key characteristics, a suitability function was defined to indicate how this parameter influences suitability for rainbow trout production. The spatial distribution of these suitability indices was mapped, and they were integrated using GIS by multiplying the normalized scores (each ranging between 0 and 1). A total of 15 GIS layers were used resulting in a map indicating areas suitable for rainbow trout production in Denmark. The goal beyond AQUA-USERS is to embed such suitability models in a generic site selection tool that the users can feed with data relevant for their specific site selection.

The full report on this case study can be downloaded here.

New satellites launched

With the launch of the first Sentinel satellites, Copernicus, the European Earth observation programme, has heralded a new era in Earth observation. The programme shifts its focus from demonstration and research to operational missions set to support users for decades to come. Last month saw the successful launch of Sentinel-3a, the first of a group of medium-resolution satellites that will systematically cover the Earth's surface every two days delivering near-real time data for observation of oceans, land and atmosphere. The spectral bands of the OLCI instrument onboard Sentinel-3 are specifically designed to detect and quantify water constituents and will allow for unprecedented monitoring capabilities at 300m spatial resolution. A sneak peek into what we can expect from Sentinel-3 can be seen on the right (© ESA). The satellite is currently in its commissioning phase and is expected to be operational in about 4 months. Unfortunately, this will be too late to be included in the AQUA-USERS case studies, but the team will certainly take up the data to improve and further develop the services set up within the project!
User in the spotlight: Finisterra
Finisterra is a small company producing mussels on longlines off the Algarve coast in southern Portugal. The energetic owner, Lourenço Pinto Ribeiro, is one of the pioneers of the modern shellfish production sector in Portugal. In the clear waters near Sagres, his mussels feed off the algae that grow when cold nutrient-rich waters well up from the deep. However, some of the algae pose a threat to his production: frequently blooms of species occur that do not harm the mussels themselves, but contain toxins that can harm humans. In these cases, the site is closed so that the mussels cannot be harvested and sold. Such closures can last up to several weeks posing great challenges to the producers.

From AQUA-USERS Lourenço hopes to receive early warning of oncoming blooms and to develop a better overall understanding of the ecosystem dynamics that directly influence the growth and well-being of his mussels. At one of the project meeting in Portugal, the consortium got a taste of his mussels and we can confirm that his product is excellent!
Upcoming events
AQUA-USERS will be presented at a number of upcoming conferences:
  • 9-13/5/2016 ESA Living Planet Symposium (Prague, Czech Republic): Poster "Characterisation of Danish waters with EO and modelling for aquaculture site selection" by DHI-GRAS, poster "Ocean colour products from remote sensing related to in situ data for supporting management of offshore aquaculture" by SGM and WI, poster "Ocean Colour contribution to aquaculture management: bloom phenology, climatologies and thresholds. A case study under the AQUA-USERS project" by FCUL and a general presentation on the AQUA-USERS project by the coordinator on behalf of the entire consortium. 
  • 20-23/9/2016 Aquaculture Europe 2016 (Edinburgh, UK): AQUA-USERS will be present with a booth and several contributions to the conference programme. Details will follow later edition of this newsletter.
We are looking forward to meeting and discussing with interested parties. If you are attending these events, stop by and say hello!
New Publications
In the last few months, the members of AQUA-USERS consortium have (co-)authored a number of scientific publications relating to monitoring water quality and algal blooms:

Brito, A.C., Sá, C., Brotas, V., Brewin, R.J.W., Silva, T., Vitorinod, J., Platt, T. & Sathyendranath, S. (2015) Effect of phytoplankton size classes on bio-optical properties of phytoplankton in the Western Iberian coast: Application of models. Remote Sensing of Environment, 156: 537–550.

Brito, A.C., Sá, C., Mendes, C.R., Brand, T., Dias, A.M., Brotas, V. & Davidson, K. (2015) Structure of late summer phytoplankton community in the Firth of Lorn (Scotland) using microscopy and HPLC-CHEMTAX. Estuarine, Coastal and Shelf Science, 167: 86–101.
Brouwer, R., Brouwer, S., Eleveld, M.A., Verbraak, M., Wagtendonk, A. & van der Woerd, H.J. (2016) Public willingness to pay for alternative management regimes of remote marine protected areas in the North Sea. Marine Policy, 68: 195-204. 

Cristina, S., Icely, J., Goela, P.C., DelValls, T.A. & Newton, A. (2015) Using remote sensing as a support to the implementation of the European Marine Strategy Framework Directive in SW Portugal. Continental Shelf Research, 108: 169–177.
Goela, P.C., Danchenko, S., Icely, J.D., Lubian, L.M., Cristina, S. & Newton, A. (2014) Using CHEMTAX to evaluate seasonal and interannual dynamics of the phytoplankton community off the South-west coast of Portugal. Estuarine, Coastal and Shelf Science, 151: 112-123.
Goela, P.C., Icely, J., Cristina, S., Danchenko, S., DelValls T.A. & Newton, A. (2015) Using bio-optical parameters as a tool for detecting changes in the phytoplankton community (SW Portugal). Estuarine, Coastal and Shelf Science, 167: 125–137.
Groetsch, P.M.M., Simis, S.G.H., Eleveld, M.A. & Peters, S.W.M. (2016) Spring Blooms in the Baltic Sea have weakened but lengthened from 2000 to 2014. Biogeosciences (forthcoming).

Miller, P.I., Xu, W., Carruthers, M. (2015) Seasonal shelf-sea front mapping using satellite ocean colour and temperature to support development of a marine protected area network. Deep Sea Research Part II: Topical Studies in Oceanography, 119: 3-19.

Sá, C., D'Alimonte, D., Brito, A.C.,  Kajiyamad, T., Mendes, C.R., Vitorino, J., Oliveira, P.B., da Silva, J.C.B. & Brotas, V. (2015) Validation of standard and alternative satellite ocean-color chlorophyll products off Western Iberia. Remote Sensing of Environment, 168: 403–419.
Shutler, J.D., Warren, M.A, Miller, P.I., Barciela, R., Mahdon, R., Land, P.E., Edwards, K., Wither, A., Jonas, P., Murdoch, N., Roast, S.D., Clements, O., Kurekin, A. (2015). Operational monitoring and forecasting of bathing water quality through exploiting satellite Earth observation and models: The AlgaRisk demonstration service. Computers & Geosciences, 77: 87–96.

AQUA-USERS is funded under the European Community’s 7th Framework Program (Theme SPA.2013.1.1-06 2013.1.1-06: Stimulating development of downstream services and service evolution, Grant Agreement No 607325)