A data assimilation tool for the Pagasitikos Gulf ecosystem dynamics: Methods and benefits G. Korres a, ⁎, G. Triantafyllou a , G. Petihakis a , D.E. Raitsos a , I. Hoteit b , A. Pollani a , S. Colella c , K. Tsiaras a a Hellenic Centre for Marine Research, P.O. Box 712, 19013, Anavyssos, Greece b King Abdullah University of Science and Technology, Thuwai 23955-6900, Saudi Arabia c Istituto di Scienze dell'Atmosfera e del Clima, CNR, Italy abstract article info Available online 10 November 2011 Keywords: High-resolution data assimilation SEEK filter SEIK filter Ocean color Ecosystem modelling Within the framework of the European INSEA project, an advanced assimilation system has been implemen- ted for the Pagasitikos Gulf ecosystem. The system is based on a multivariate sequential data assimilation scheme that combines satellite ocean sea color (chlorophyll-a) data with the predictions of a three- dimensional coupled physical–biochemical model of the Pagasitikos Gulf ecosystem presented in a compan- ion paper. The hydrodynamics are solved with a very high resolution (1/100°) implementation of the Prince- ton Ocean Model (POM). This model is nested within a coarser resolution model of the Aegean Sea which is part of the Greek POSEIDON forecasting system. The forecast of the Aegean Sea model, itself nested and ini- tialized from a Mediterranean implementation of POM, is also used to periodically re-initalize the Pagatisikos hydrodynamics model using variational initialization techniques. The ecosystem dynamics of Pagasitikos are tackled with a stand-alone implementation of the European Seas Ecosystem Model (ERSEM). The assimila- tion scheme is based on the Singular Evolutive Extended Kalman (SEEK) filter, in which the error statistics are parameterized by means of a suitable set of Empirical Orthogonal Functions (EOFs). The assimilation experiments were performed for year 2003 and additionally for a 9-month period over 2006 during which the physical model was forced with the POSEIDON-ETA 6-hour atmospheric fields. The assim- ilation system is validated by assessing the relevance of the system in fitting the data, the impact of the as- similation on non-observed biochemical processes and the overall quality of the forecasts. Assimilation of either GlobColour in 2003 or SeaWiFS in 2006 chlorophyll-a data enhances the identification of the ecological state of the Pagasitikos Gulf. Results, however, suggest that subsurface ecological observations are needed to improve the controllability of the ecosystem in the deep layers. © 2011 Elsevier B.V. All rights reserved. 1. Introduction Pagasitikos is a semi-enclosed gulf situated on the western part of Aegean Sea north of the island of Evia connected at the south with the Aegean Sea through the 5.5 km wide, narrow channel of Trikeri. The predominant weak winds of the area result in small to moderate water currents while renewal occurs mainly through the deep- water layer of the Trikeri channel. During winter months the water mass of Pagasitikos is fairly mixed, forming a two-layer thermocline which remains for the rest of the year, with the exception of August that three layers are observed. Inflow of fresh waters in the areas of Volos and Almyros observed during winter and spring adds to the complexity of the system. The basin is highly influenced both by an- thropogenic activities (inflow of nutrients at the north and west parts) as well as by water exchange through the Trikeri channel resulting in the development of functional sub-areas within the gulf. Thus the inner part is characterized by eutrophic conditions with spo- radic formation of harmful algal blooms while the central part acts as a buffer with mesotrophic characteristics influenced by the oligotro- phic outer area. Pagasitikos is a rather sensitive ecosystem due to its semi-enclosed nature and the shallow depths. The human activity in the coastal areas is not significant with agricultural farming being the major occupation. However during the last years there has been a shift towards intensive production of cereal and cotton with the use of large quantities of fertilizers rich in nitrogen, phosphate and sulfur. A significant proportion of these chemicals find its way into the marine ecosystem carried by rain waters through a network of periodic small torrents. The only major city is Volos at the north part of the gulf with a population of 120,000 inhabitants and a well- developed industrial sector. It was during 60s when the first heavy in- dustries were built attracting workers from the surrounding areas and leading into a population explosion. The fast growth of the area and the absence of the necessary infrastructure caused serious threats to the Pagasitikos Gulf ecosystem, as it became the recipient for major quantities of rural and industrial effluents. Journal of Marine Systems 94 (2012) S102–S117 ⁎ Corresponding author at: Hellenic Centre for Marine Research, P.O. Box 712, 19013, Anavyssos, Greece. Tel.: + 30 22910 76402. E-mail address: gkorres@ath.hcmr.gr (G. Korres). 0924-7963/$ – see front matter © 2011 Elsevier B.V. All rights reserved. doi:10.1016/j.jmarsys.2011.11.004 Contents lists available at SciVerse ScienceDirect Journal of Marine Systems journal homepage: www.elsevier.com/locate/jmarsys