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Ecosystem modeling predicts the structure and functioning of ecosystems from initial conditions and knowledge of ecological processes. The compromise between the number of state variables and accuracy of predictions is the key issue for reliability of this technique. Although many ecosystem models are only focused on eutrophication and water quality, new technologies have increased the data acquisition rate for a larger number of state variables,which allows the complexity of simulations to increase. A comprehensive description of the main phytoplankton ecological processes included in most models relating hydrodynamics with eutrophication is developed in this section by considering the size of the cells as a variable from which many other state variables can be mirrored.

In this chapter possible changes thatwould occur in the ecosystem of a lagoon in response to a terrorist attack will be identified and discussed. A very brief revision will be done on ecosystem organization, succession, effects of pollutants and biomagnification, and lagoon water renewal characteristics in order to draw possible scenarios under a terrorist attack. Simple Stella models will be used to simulate a lagoon ecosystem and demonstrate the possible consequences of an attack.

The term food web or trophic network defines a set of interconnected food chains by which energy and materials circulate within an ecosystem. The classical food web could be divided into two broad categories: the grazing web, which typically begins with green plants, algae, or photosynthesizing plankton, and the detrital web, which begins with organic debris. In a grazing web, materials typically pass from plants to herbivores to flesh eaters. In a detrital web, materials pass from plant and animal matter to decomposers as fungi and bacteria, then to detritivores, and then to their predators. In water ecosystems, the classical food web is represented by the planktonic and benthic food webs, which are interconnected. Additionally, the “microbial loop” represents an alternative pathway of carbon flowthat leads from bacteria to protozoa to metazoa, with dissolved organic matter (DOM) being utilized as substrate by the bacteria, which include nanoplankton (2–20 μm in size) and picoplankton (0.2–2 μm in size).

A terrorist attack involving a toxic chemical added to a water resource could have multiple effects on the aquatic ecosystem of that resource. This is particularly significant for systems such as lakes and reservoirs,where the residence time of water is long and there is more opportunity for organisms to be exposed to the chemical. Atoxic chemical release in a lake ecosystem may cause bioaccumulation in fish tissues for a period of time after an attack. Bioaccumulation occurs due to direct uptake through the gill, aswell as dietary uptake, and is important because the health of humans and wildlife may be affected through the consumption of contaminated fish (Mackay and Fraser, 2000). A toxic chemical may also affect fish biomass either through direct mortality, the reduction of growth and reproduction, or alteration of the food chain, where food items may also experience reduced biomass (Pastorok et al., 2001). The maintenance of fish biomass in a system can be important for a recreational, commercial, or subsistence fishery, as well as for the support of surrounding wildlife.

Chemical weapons (CW) use toxic properties of chemical substances to kill, injure or incapacitate an enemy during warfare. Chemical weapons are classi- fied by the United Nations (together with nuclear and bacteriological weapon) as weapons of mass destruction.

The trend of monitoring natural water ecosystems is increasing the quantity of identified components and thus improving the methods of determination and identification. This is very important for long-term monitoring, however, another system must be used when dealing with ecosystems after a terrorist attack. In these situations, the aim is to verify surface water pollution and, if confirmed, identify the specific type of pollution, and all this should be done as quickly as possible.

During the first two weeks of December of 2005, NATO sponsored an Advanced Study Institute (ASI) In Istanbul, Turkey. Part of this ASI involved a case study of a terrorist attack, where a chemical was assumed to be dumped into Sulunger Lake in Turkey. This chapter documents the response developed by the ASI participants to this scenario, in terms of hydrodynamic transport, ecosystem effects, and decision making.