The WFD stresses the need to assess the ecological status of aquatic ecosystems in Europe, taking account of their structure, functions and processes, as well as their natural characteristics (physical, chemical, geographic and climatic factors) and anthropic aspects (human activities that can impact the area concerned).

Generally indicators for the ecological assessment should be easily measured, sensitive to stresses on the system, should respond to stress in a predictable manner and predict changes that can be averted by management actions. Moreover the suite of indicators should ideally represent key information about structure, function and composition of ecological system.

Traditionally, biodiversity indices, such as species richness (S),Shannon diversity (H_) and Simpson diversity (D), have been used to study the taxonomic structure of phytoplankton assembly. The advantage of these indices is that they allow direct comparison of communities that have few or no species in common. However, although some of them are able to describe the impacts of water pollution on biotic communities, these indices require a high level of expertise in taxonomic identification, because the sensitivity values are assigned at species level.

Indices based on simple community diversity indices and multi-metric indices such as the P-IBI index have been proposed for marine coastal ecosystems, lakes and rivers as well as the trophic index (TRIX) for marine coastal ecosystems.

Multi-metric indices are increasingly used to assess the ecological status of water bodies, as well as in resource and ecosystem management, because they are often more robust than their component metrics. Moreover, multimetric indices make it possible to integrate over time chemical and physical ecosystem properties that could otherwise be missed by a single sampling. They are also based on different taxonomic and functional groups within the assemblage, which respond differently to various stressors and reflect ecological status in a more comprehensive manner. The majority of these indices have been developed for assessing the ecological status of rivers and streams and are usually based on macroinvertebrates, fish, macrophytes and epilithic algae. Very little has been done so far on phytoplankton, and indeed, its taxonomic components are characterized by high spatial and temporal heterogeneity and by few quantitatively defined relationships with anthropogenic pressure, as required by the WFD indicators. As a consequence, there are very few methods compliant with the WFD that include phytoplankton taxonomical composition.

Of the non-taxonomic traits, body size has already been observed to respond to different environmental conditions in coastal marine and transitional water ecosystems with consistent patterns of variation. Indeed, various structural factors in the abiotic environment, including water dynamics, depth of photic zone, trophic state and nutrient concentration, have also been found to explain patterns of variation of phytoplankton size structure on spatial and temporal scales.

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