New cold‐water coral (CWC) sites were recorded along the Apulian margin (Central Mediterranean). The species composition and depth distribution of CWCs were updated. A distribution of the CWC sites coincident with the course of the dense‐water masses that flow between the Southern Adriatic and Northern Ionian was confirmed. The faunal assemblages of five of these CWC sites were investigated and compared using experimental longlines during the spring–summer and autumn–winter seasons, between 2010 and 2014. Differences in ecological variables amongst the sites in each season were evaluated by means of a set of univariate and multivariate methods (analysis of variance, permutational multivariate analysis of variance, non‐metric multidimensional scaling). Although some differences were detected in relation to the different depths examined during spring–summer, the CWC sites showed similar features in terms of species richness and diversity as well as in the abundance of the same fish species (Galeus melastomus, Conger conger, Helicolenus dactylopterus, Merluccius merluccius, Phycis blennoides and Pagellus bogaraveo) most probably because of the distribution of adult specimens in structurally complex and heterogeneous habitats, which act as a potential ‘refuge network’ with respect to commercial fishing. The presence of maturing and mature individuals as well as post‐reproductive females indicates that these CWC sites also act as spawning areas, representing a potential ‘renewal network’ for the fish populations. The term ‘network’ used here refers to several similar subsystems (CWC sites) that play the same ecological role in a wider system (Apulian margin). These CWC communities need coherent conservation measures and management strategies according to the Ecosystem Approach to Fisheries.

An exploration of the structure of demersal and benthopelagic assemblages in the northwestern Ionian Sea was carried out by means of a set of statistical analyses. Self-organising map (SOM) and clustering methods applied to 183 taxa and their biomass (kg km −2) provided the classification of 1288 experimental hauls exploring the bathymetric range 10−800 m from 1995 to 2012. Six clusters were identified according to their similarities in species abundances (biomass), confirming the depth gradient as the main structuring agent. In order to identify key representative species in each cluster, the taxa were ranked by means of an indicator value index (IndVal) and the contribution of species to beta diversity (BD). Furthermore, the clusters were described by means of environmental and fishing characteristics. Particular habitat type, distance to canyon and fishing effort segregated the assemblages on the coastal shelf and slope. Temporal differences were detected in 2 bathyal groups, which were most likely affected by the 1990s environmental change in the deepwater circulation known as the Eastern Mediterranean Transient. The overall total BD in the study area was calculated as 0.79, with a temporal decrease observed at a rate of 0.7% yr −1. The approaches used are useful to identify and characterize the species aggregations inside complex faunal assemblages, without a priori assumptions about data distribution. These results can be a starting point for defining functional groups for Mediterranean food web modelling approaches, as well as for identifying indicator species to assess the environmental status in the context of the Marine Strategy Framework Directive.

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The exploitation of fishery resources acts as a driving force on cetaceans both directly, by determining their fishing mortality or injury as by-catch species, and indirectly, through the lowering the availability of their prey. This competitive overlap between fishing and cetaceans often results in inadequate solutions so that in some cases there have been cases of intentional cetacean culling to maximize fishing production. A modelling approach applied to investigate the ecological roles of cetaceans in the food web could prove more effective to integrate ecological and fishing aspects and to provide suggestions for management. The comparative analysis carried out in the Gulf of Taranto (Northern Ionian Sea, Central Mediterranean Sea) showed that fishing exploitation provides impacts on the investigated food web greater than those due to cetacean predation. Trawling was estimated to be the most negatively impacting fishing gear considering the mortality rates and consumption flows. On the other hand, the striped dolphin was the main impact on the food web due to its highest consumption flows. Analysis showed a negative and non-selective impact on the exploited species due to the fishing gears, while the odontocetes proved to select their prey species and provide a positive impact in the assemblage. In particular, while the fishing gears are primarily size selective, targeting mostly large and economically valuable fish, the odontocetes seem to follow a co-evolution process with their prey, developing a specialization in their resources, providing control of the meso-consumers and ensuring a trophic stability in the ecosystem.