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<article language="en">
	<journal>
		<journal_title>Ocean Science</journal_title>
		<journal_url>www.ocean-sci.net</journal_url>
		<issn>1812-0784</issn>
		<eissn>1812-0792</eissn>
		<volume_number>5</volume_number>
		<issue_number>1</issue_number>
		<publication_year>2009</publication_year>
	</journal>
	<doi>10.5194/os-5-29-2009</doi>
	<article_url>http://www.ocean-sci.net/5/29/2009/</article_url>
	<abstract_html>http://www.ocean-sci.net/5/29/2009/os-5-29-2009.html</abstract_html>
	<fulltext_pdf>http://www.ocean-sci.net/5/29/2009/os-5-29-2009.pdf</fulltext_pdf>
	<start_page>29</start_page>
	<end_page>46</end_page>
	<publication_date>2009-02-20</publication_date>
	<article_title content_type="html">Eastern Mediterranean biogeochemical flux model – Simulations of the pelagic ecosystem</article_title>
	<authors>
		<author numeration="1" affiliations="1">
			<name>G. Petihakis</name>
			<email>pet@her.hcmr.gr</email>
		</author>
		<author numeration="2" affiliations="1">
			<name>G. Triantafyllou</name>
		</author>
		<author numeration="3" affiliations="1">
			<name>K. Tsiaras</name>
		</author>
		<author numeration="4" affiliations="1">
			<name>G. Korres</name>
		</author>
		<author numeration="5" affiliations="1">
			<name>A. Pollani</name>
		</author>
		<author numeration="6" affiliations="2">
			<name>I. Hoteit</name>
		</author>
	</authors>
	<affiliations>
		<affiliation numeration="1" content_type="html">Institute of Oceanography, Hellenic Center for Marine Research, P.O. BOX 2214, Iraklion-Crete Greece, GR 71003, Greece</affiliation>
		<affiliation numeration="2" content_type="html">Scripps Institution of Oceanography, La Jolla, CA, USA</affiliation>
	</affiliations>
	<abstract content_type="html">During the second phase (2003–2006) of the Mediterranean ocean
Forecasting System Project (MFS) named Toward Environmental Predictions
(MFSTEP) one of the three major aims was the development of numerical
forecasting systems. In this context a generic Biogeochemical Flux Model
(BFM) was developed and coupled with hydrodynamic models already operating
at basin scale as well as in regional areas. In the Eastern Mediterranean
basin the BFM was coupled with the Aegean Levantine Eddy Resolving MOdel
(ALERMO). The BFM is a generic highly complex model based on ERSEM and
although a detailed description of the model and its components is beyond
the scope of this work, a short overview of the main processes, laying
emphasis on the parameter values used is presented. In addition the
performance of the model is evaluated with some preliminary results being
qualitatively compared against field observations. The model in its present
form is rather promising and reproduces all important major features
although there are some slight inefficiencies mostly related to primary and
bacterial productivity rates.</abstract>
	<references>
		<reference numeration="1" content_type="text">Abdel-Hamid, M. I., Shaaban-Dessouki, S. A. and Skulberg, O. M.: Water quality of the River Nile in Egypt. 1. Physical and chemical characteristics, Archiv. Hydrobiol., 90, 283–310, 1992. </reference>
		<reference numeration="2" content_type="text">Aksnes, D. L. and Egge, J. K.: A theoretical model for nutrient uptake in phytoplankton, Marine Ecology Progress Series, 70, 65–72, 1991. </reference>
		<reference numeration="3" content_type="text">Allen, J. I., Ekenes, M., and Evensen, G.: An Ensemble Kalman Filter with a complex marine ecosystem model: Hindcasting phytoplankton in the Cretan Sea, Ann. Geophys., 21, 399–411, 2003. </reference>
		<reference numeration="4" content_type="text">Allen, J. I., Siddorn, R. J., Blackford, C. J., and Gilbert, J. F.: Turbulence as a control on the microbial loop in a temperate seasonally stratified marine systems model, J. Sea Res., 52, 1–20, 2004. </reference>
		<reference numeration="5" content_type="text">Azam, F., Fenchel, T., Field, J. G., Gray, J. S., Meyer-Reil, L. A., and Thingstad, F.: The ecological role of water – column microbes in the sea, Mar. Ecol. Progress Ser., 10, 257–263, 1983. </reference>
		<reference numeration="6" content_type="text">Azov, Y.: Eastern Mediterranean – a marine desert? EMECS&apos;, 90(23), 225–232, 1991. </reference>
		<reference numeration="7" content_type="text">Baretta-Bekker, J. G., Baretta, J. W., and Ebenhoh, W.: Microbial dynamics in the marine ecosystem model ERSEM II with decoupled carbon assimilation and nutrient uptake, J. Sea Res., 38, 195–211, 1997. </reference>
		<reference numeration="8" content_type="text">Baretta-Bekker, J. G., Baretta, J. W., and Rasmussen, E.: The microbial foodweb in the European regional Seas Ecosystem Model, Netherlands J. Sea Res., 33, 363–379, 1995. </reference>
		<reference numeration="9" content_type="text">Baretta, J. W., Ebenhoh, W., and Ruardij, P.: The European Regional Seas Ecosystem Model, a complex marine ecosystem model, Netherlands J. Sea Res., 33, 233–246, 1995. </reference>
		<reference numeration="10" content_type="text">Blackford, C. J., Allen, J. I., and Gilbert, J. F.: Ecosystem dynamics at six contrasting sites: a generic modelling study, J. Mar. Syst., 52, 199–215, 2004. </reference>
		<reference numeration="11" content_type="text">Blumberg, A. F. and Mellor, G. L.: A Coastal Ocean Numerical Model in: Sunderman, J. and Holtz, K., Mathematical Modelling of Estuarine Physics. Proceedings of the International Symposium, Springer-Verlag Berlin, Hamburg, 203–214, 1978. </reference>
		<reference numeration="12" content_type="text">Blumberg, A. F. and Mellor, G. L.: A description of a three-dimensional coastal ocean circulation model, in: Heaps, N. S., Three-Dimensional Coastal Ocean Circulation Models, Coastal Estuarine Science, AGU, Washington, D.C., 1–16, 1987. </reference>
		<reference numeration="13" content_type="text">Bratbak, G., Heldal, M., Thingsta, T. F., Riemann, B., and Haslnund, O. H.: Incorporation of viruses into the budget of microbial C-transfer. A first approach, Mar. Ecol. Progress Ser., 83, 273–280, 1992. </reference>
		<reference numeration="14" content_type="text">Bricaud, A., Bosc, E., and Antoine, D.: Algal biomass and sea surface temperature in the Mediterranean Basin. Intercomparison of data from various satellite sensors, and implications for primary production estimates, Remote Sens. Environ., 81, 163–178, 2002. </reference>
		<reference numeration="15" content_type="text">Bryden, H. L., Candela, J., and Kinder, T. H.: Exchange through the Strait of Gibraltar, Prog. Oceanog., 33, 201–248, 1994. </reference>
		<reference numeration="16" content_type="text">Crise, A., Allen, J. ., Baretta, J., Crispi, G., Mosetti, R., and Solidoro, C.: The Mediterranean pelagic ecosystem response to physical forcing, Progress Oceanogr., 44, 219–243, 1999. </reference>
		<reference numeration="17" content_type="text">Droop, M. R.: The nutrient status of algal cells in continuous culture, J. Mar. Biol. Assoc., 54, 825–855, 1974. </reference>
		<reference numeration="18" content_type="text">Eker-Develi, E., Erkan Kideys, A., and Tugrul, S.: Role of Saharan dust on phytoplankton dynamics in the northeastern Mediterranean, Mar. Ecol. Prog. Ser., 374, 61–75, 2006. </reference>
		<reference numeration="19" content_type="text">Fuhrman, J. A.: Marine viruses and their biogeochemical and ecological effects, Nature, 399, 541–548, 1999. </reference>
		<reference numeration="20" content_type="text">Geider, R. J., Mac Intyre, H. L., and Kana, T. M.: A dynamic regulatory model of phytoplanktonic acclimation to light, nutrients and temperature, Limnol. Oceanogr., 43, 679–694, 1998. </reference>
		<reference numeration="21" content_type="text">Georgopoulos, D., Chronis, G., Zervakis, V., Lykousis, V., Poulos, S., and Iona, A.: Hydrology and circulation in the Southern Cretan Sea during the CINCS experiment (May 1994–September 1995), Progress Oceanogr., 46, 89–112, 2000. </reference>
		<reference numeration="22" content_type="text">Gill, A. E.: Atmosphere-Ocean Dynamics, Academic Press, New York, 662 pp, 1982. </reference>
		<reference numeration="23" content_type="text">Heldal, M. and Bratbak, G.: Production and decay of viruses in aquatic environments, Mar. Ecol. Progress Ser., 72, 205–212, 1991. </reference>
		<reference numeration="24" content_type="text">Hoang, H. S., De Mey, P., Tallagrand, O., and Baraille, R.: Adaptive filtering: Application to satellite data assimilation in oceanography, J. Dynam. Atmos. Ocean., 27, 257–281, 1997. </reference>
		<reference numeration="25" content_type="text">Hood, R. R., Laws, A. E., Armstrong, A. R., Bates, R. N., Brown, W. C., Carlson, A. C., Chai, F., Doney, C. S., Falkowski, G. P., Feely, A. R., Friedrichs, A. M. M., Landry, R. M., Moore, J. K., Nelson, M. D., Richardson, L. T., Salihoglu, B., Schartau, M., Toole, A. D., and Wiggert, D. J.: Pelagic functional group modeling: Progress, challenges and prospects, Deep Sea Res. II, 53, 459–512, 2006. </reference>
		<reference numeration="26" content_type="text">Hoteit, I., Pham, D. T., and Blum, J.: A semi-evolutive partially local filter for data assimilation, Mar. Pollut. Bull., 43(7–12), 164–174, 2002. </reference>
		<reference numeration="27" content_type="text">Hoteit, I., Triantafyllou, G., and Petihakis, G.: Towards a data assimilation system for the Cretan sea ecosystem using a simplified Kalman filter, J. Mar. Syst., 45, 159–171, 2004. </reference>
		<reference numeration="28" content_type="text">Hoteit, I., Triantafyllou, G., Petihakis, G., and Allen, J. I.: A singular evolutive Kalman filter to assimilate real in-situ data in a 1-D marine ecosystem model, Ann. Geophys., 21, 389–397, 2003. </reference>
		<reference numeration="29" content_type="text">Ignatiades, L., Psarra, S., Zervakis, V., Pagou, K., Souvermezoglou, E., Assimakopoulou, G., and Gotsi-Skreta, O.: Phytoplankton size-based dynamics in the Aegean Sea (Eastern Mediterranean), J. Mar. Syst., 36, 11–28, 2002. </reference>
		<reference numeration="30" content_type="text">Jaeger, L.: Monatskarten des Niederschlags fur die ganze Erde, Ber. Dtsch. Wetterdienste, 18(1839), 1–38, 1976. </reference>
		<reference numeration="31" content_type="text">Korres, G. and Lascaratos, A.: A one-way nested eddy resolving model of the Aegean and Levantine basins: Implementation and climatological runs, Analles Geophysicae, 21, 205–220, 2003. </reference>
		<reference numeration="32" content_type="text">Krom, M., Groom, S., and Zohary, T.: The Eastern Mediterranean. In: K.D. Black and G.B. Shimmield (Editors), Biogeochem. Mar. Syst., Blackwell Publishing, Oxford, 91–126, 2003. </reference>
		<reference numeration="33" content_type="text">Lykousis, V., Chronis, G., Tselepides, A., Price, N. B., Theocharis, A., Siokou-Frangou, I., Van Wambeke, F., Donavaro, R., Stavrakakis, S., Duineveld, G., Georgopoulos, D., Ignatiades, L., Souvermezoglou, E., and Voutsinou-Taliadourou, F.: Major outputs of the recent multidisciplinary biogeochemical researches undertaken in the Aegean Sea, J. Mar. Syst., 33–34, 313–334, 2002. </reference>
		<reference numeration="34" content_type="text">McGill, D.: The relative supplies of phosphate, nitrate and silicate in the Mediterranean Sea, Rapports et Proces-Verbaux des Reunions Commission Internationale pour l&apos;Exploration Scientifique de la Mer Mediterranee, 18, 734–744, 1965. </reference>
		<reference numeration="35" content_type="text">Mellor, G. L.: User&apos;s guide for a three-dimensional primitive equation, numerical ocean model (July 1998 version), Princeton University, 1998. </reference>
		<reference numeration="36" content_type="text">Mihailov, A. A.: On the phytoplankton of the Aegean Sea, Trudy Sevastopol, Biol. St., 17, 3–12, 1964. </reference>
		<reference numeration="37" content_type="text">Moutin, T. and Raimbault, P.: Primary production, carbon export and nutrients availability in western and eastern Mediterranean Sea in early summer 1996 (MINOS cruise), J. Mar. Syst., 33–34, 273–288, 2002. </reference>
		<reference numeration="38" content_type="text">Natvik, L. and Evensen, G.: Assimilation of ocean colour data into a biochemical model of the north Atlantic. Part-I. data assimilation experiments, J. Mar. Syst., 40-41, 127–153, 2003. </reference>
		<reference numeration="39" content_type="text">Parsons, T., Takahashi, M., and Hargrave, B.: Biological oceanographic processes, Pergamon Press, 330 pp., 1973. </reference>
		<reference numeration="40" content_type="text">Pinardi, N. and Masetti, E.: Variability of the large scale general circulation of the Mediterranean Sea from observations and modelling: a review, Palaeogeography, Palaeoclimatology, Palaeoecology, 158, 153–174, 2000. </reference>
		<reference numeration="41" content_type="text">Pinardi, N., Allen, I., Demirov, E., De Mey, P., Korres, G., Lascaratos, A., Le Traon, P.-Y., Maillard, C., Manzella, G., and Tziavos, C.: The Mediterranean ocean forecasting system: first phase of implementation (1998–2001), Ann. Geophys., 21, 3–20, 2003. </reference>
		<reference numeration="42" content_type="text">Polat, C. and Tugrul, S.: Chemical exchange between the Mediterranean and Black Sea via the Turkish straits, CIESM Science Series, Bull. De l&apos;Institut Oceanog, 2(17), 167–186, 1996. </reference>
		<reference numeration="43" content_type="text">Proctor, L. M. and Fuhrman, J. A.: Viral mortality of marine bacteria and cyanobacteria, Nature, 343, 60–62, 1990. </reference>
		<reference numeration="44" content_type="text">Sancak, S., Besiktepe, T. S., Yilmaz, A., Lee, M., and Frouin, R.: Evaluation of SeaWifs chlorophyll-a in the Black and Mediterranean Seas, Int. J. Remote Sens., 26(10), 2045–2060, 2005. </reference>
		<reference numeration="45" content_type="text">Siokou-Frangou, I., Bianchi, M., Christaki, U., Christou, E.D., Giannakourou, A., Gotsis, O., Ignatiades, L., Pagou, K., Pitta, P., Psarra, S., Souvermezoglou, E., Van Wambeke, F., and Zervakis, V.: Carbon flow in the planktonic food web along a gradient of oligotrophy in the Aegean Sea (Mediterranean Sea), J. Mar. Syst., 33–34, 335–353, 2002. </reference>
		<reference numeration="46" content_type="text">Skoulikidis, N. T.: Significance evaluation of factors controlling river water composition, Env. Geol., 22, 178–185, 1993. </reference>
		<reference numeration="47" content_type="text">Suttle, C. A., Chan, A. M., and Cottrell, M. T.: Infection of phytoplankton by viruses and reduction of primary production, Nature, 347, 467–469, 1990. </reference>
		<reference numeration="48" content_type="text">Theocharis, A., Balopoulos, E., Kioroglou, S., Kontoyiannis, H., and Iona, A.: A synthesis of the circulation and hydrography of the South Aegean Sea and the Straits of the Cretan Arc (March 1994–January 1995), Progress Oceanogr., 44, 469–509, 1999. </reference>
		<reference numeration="49" content_type="text">Theocharis, A., Georgopoulos, D., Lascaratos, A., and Nittis, K.: Water masses and circulation in the central region of the Eastern Mediterranean: Eastern Ionian, South Aegean and Northwest Levantine, Deep-Sea Res. II, 40(6), 1121–1142, 1993. </reference>
		<reference numeration="50" content_type="text">Triantafyllou, G., Hoteit, I., and Petihakis, G.: A singular evolutive interpolated Kalman filter for efficient data assimilation in a 3-D complex physical-biogeochemical model of the Cretan Sea, J. Marine Syst., 40–41, 213–231, 2003a. </reference>
		<reference numeration="51" content_type="text">Triantafyllou, G., Hoteit, I., and Petihakis, G.: The use of global and local EOFs for the assimilation of biochemical data into Cretan Sea ecosystem model, EGS 2003, Geophys. Res. Abstracts, 5, 10497, 2003b. </reference>
		<reference numeration="52" content_type="text">Triantafyllou, G., Hoteit, I., Petihakis, G., Allen, J. I., Pollani, A. and Dounas, C.: Efficient Reduced Kalman Filtering for Assimilating the Spatial and Temporal Variability of the Cretan Ecosystem, 33rd international Liege Colloquium on Ocean Dynamics, The use of Data Assimilation in Coupled Hydrodynamic, Ecological and Bio-Geo-Chemical Models of the Ocean, Liege, 2001. </reference>
		<reference numeration="53" content_type="text">Tselepides, A. and Polychronaki, T.: Pelagic-benthic coupling in the oligotrophic Cretan Sea (Ne Mediterranean), Final Report, IMBC, Iraklio, 1996. </reference>
		<reference numeration="54" content_type="text">Tugrul, S., Besiktepe, S. T., and Salihoglou, I.: Nutrient exchange fluxes between the Aegean and Black Seas through the Marmara Sea, Mediterranean Marine Science, 3(1), 33–42, 2002. </reference>
		<reference numeration="55" content_type="text">Vichi, M., Baretta, J., Baretta-Bekker, J., Ebenhoh, W., Kohlmeier, C., Ruardij, P., Pinardi, N., and Zavatarelli, M.: European Regional Seas Ecosystem Model III, Review of the biogeochemical equations, www.bo.ingv.it/ersem3/ERSEM_III_report.lyx,v 1.6 2004/07/28 10:44:29 mav Exp, 2004. </reference>
		<reference numeration="56" content_type="text">Vichi, M., Pinardi, N., and Masina, S.: A generalized model of pelagic biogeochemistry for the global ocean ecosystem. Part I: Theory, J. Mar. Syst., 64, 89–109, 2007. </reference>
	</references>
</article>

