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The assessment of the ecological status, as required by the Water Framework Directive (WFD), plays an important role in coastal zone management, but only a small number of ecological indices are applicable on rocky bottoms. In this study, we apply a previously defined ecological quality index based on the cartography of littoral and upper-sublittoral rocky-shore communities (CARLIT), based on the sensitivity of algae dominated communities to anthropogenic impacts along a moderate urban gradient. We also apply this index in four Marine Protected Areas (MPAs), proposed as reference sites at a regional scale. After comparing the outputs with water variables and other quality indices, we can affirm that (1) the CARLIT index is suitable to detect different kinds of anthropogenic pressures, that (2) the choice of proper reference sites is a focal point in the fulfilment of the WFD (Water Framework Directive) and that (3) historical data are important to define reference conditions and the degradation of ecological status.

Abstract: The variations in the expression of two hydrolytic ectoenzymes (leucine aminopeptidase – LA – and β glucosidase — BG) were studied in the southern Tyrrhenian Sea during spring 2004. This area is characterised by a complex morphology and hydrodynamism, which generate significant differences between different sectors, particularly in the 0–100 m layer. However, the area generally exhibits oligotrophic features such as low autotrophic pigment and organic matter concentrations and a higher bacterial biomass than the phytoplanktonic one. Despite this general bottom-up pressure, adaptations by the microbial consumers were indicated by the ectoenzymatic activities and by the relationships between the enzymes, their organic substrates and their producers (namely the bacteria). In particular, bacteria were able to exploit the inorganic N supply (nitrite+nitrate provided by irregular intrusions of intermediate waters) to escape the bottom-up limitation and produce enzymes such as BG devoted to the degradation of cellulose remnants and, therefore, also able to take advantage on this refractory organic matter. In the 200–800 m layer, where trophic limitation was strong due to the low values of potentially-labile organic matter (namely proteins), the peculiar hydrodynamism led to the formation of nepheloid layers rich in organic matter, which provided the bacteria with substrates and allowed the development of a significant correlation between LA activity and its own organic substrate. Furthermore, a reduction of the bottom-up pressure was also indicated by a higher mean bacteria cell size in the entire water column of the central and eastern sectors, and a significantly increased expression of BG related to the increase in the cell size. The ectoenzymatic activities, therefore, suggested that the southern Tyrrhenian Sea should be considered as a mosaic of subsystems, where the peculiar hydrological features stimulate bacterial adaptations and enhance the channelling of energy embedded in refractory materials into the food web. [Copyright &y& Elsevier]