The Mar Piccolo of Taranto, classified as a 'Site of National Interest' (SIN), is a semi-enclosed basin divided into two inlets with lagoon features and sea influences, seriously affected by anthropic activities. In the framework of the RITMARE project, a study has been carried out to evaluate the functionality of this ecosystem. As part of this work, measurements of the water abiotic parameters were performed in order to assess the physical-chemical features of this area after the activation, in the last decade, of treatment plants for various urban and industrial dumping. Seawater intrusions and continental inputs, as well as several submarine freshwater springs, clearly affect physical-chemical characteristics of the water column in the two inlets. This finding suggests that small-scale patterns in water circulation have the potential to influence the chemical properties of the seawater. The comparison with a 20-year dataset reveals a drastic decrease in nutrient concentrations after the year 2000, validating the functionality of the treatment plants. The reduction of nutrient inputs into the basin (up to -90 % in the first inlet characterized by lower hydraulic residence time) has changed the biogeochemical characteristics of the Mar Piccolo from being relatively eutrophic to moderately oligotrophic.

The benthic ecosystem functioning is a rarely applied holistic approach that integrates the main chemical and biological features of the benthic domain with the key processes responsible for the flux of energy and C through the system. For the first time, such conceptual model, with an emphasis on the heterotrophic pathways, has been applied to the sediments at four stations within one of the most polluted coastal areas in Italy: the Mar Piccolo of Taranto. The functioning of the benthic ecosystem was different according to the investigated site. Nearby the military arsenal, i.e., the main source of organic contaminants and heavy metals, the system seemed inhibited at all the investigated structural and functional levels. Slow microbial processes of C reworking together with very limited densities of benthic fauna suggested a modest transfer of C both into a solid microbial loop and to the higher trophic levels. On the other hand, the ingression of marine water through the "Navigabile" channel seemed to stimulate the organic matter degradation and, consequently, the proliferation of meiofauna and macrofauna. In the innermost part of the basin, the system functioning, to some extent, is less impacted by contaminants and more influenced by mussel farms. The organic matter produced by these bivalves fueled faster C reworking by benthic prokaryotes and enhanced the proliferation of filter feeders.

The intense shipping traffic characterising the Adriatic Sea favours the spread of marine organisms. Yet, a study of 12 Adriatic ports (4 on the western side and 8 on the eastern side of the basin) found that non-indigenous species (NIS) accounted for only 4% of the benthic communities settled on hard substrates. The cirripeds Amphibalanus amphitrite and Balanus trigonus, found in 8 harbours, were the most common invaders followed by Amphibalanus eburneus, the ascidian Styela plicata, and the bivalve Magallana gigas. The highest percentage of NIS was recorded in Venice and Ploče, the harbours with the least rich native communities; the lowest percentage was retrieved in Trieste, Koper, Pula, and Rijeka, the harbours hosting the highest species diversity. In contrast, the ports of Bari and Ancona showed both high NIS percentages and highly diversified communities.

The response of phytoplankton assemblages to the closure of urban sewage outfalls (USOs) was examined for the Mar Piccolo of Taranto (Mediterranean Sea), a productive semi-enclosed coastal marine ecosystem devoted to shellfish farming. Phytoplankton dynamics were investigated in relation to environmental variables, with a particular emphasis on harmful algal blooms (HABs). Recent analyses evidenced a general reduction of the inorganic nutrient loads, except for nitrates and silicates. Also phytoplankton biomass (chlorophyll a) and abundances were characterized by a decrease of the values, except for the inner area of the basin (second inlet). The phytoplankton composition changed, with nano-sized species, indicators of oligotrophic conditions, becoming dominant over micro-sized species. If the closure of the USOs affected phytoplankton dynamics, however, it did not preserve the Mar Piccolo from HABs and anoxia crises. About 25 harmful species have been detected throughout the years, such as the potentially domoic acid producers Pseudo-nitzschia cf. galaxiae and P seudo-nitzschia cf. multistriata, identified for the first time in these waters. The presence of HABs represents a threat for human health and aquaculture. Urgent initiatives are needed to improve the communication with authorities responsible for environmental protection, economic development, and public health for a sustainable mussel culture in the Mar Piccolo.

The Mar Piccolo is a semi-enclosed basin subject to different natural and anthropogenic stressors. In order to better understand plankton dynamics and preferential carbon pathways within the planktonic trophic web, an integrated approach was adopted for the first time by examining all trophic levels (virioplankton, the heterotrophic and phototrophic fractions of pico-, nano- and microplankton, as well as mesozooplankton). Plankton abundance and biomass were investigated during four surveys in the period 2013-2014. Beside unveiling the dynamics of different plankton groups in the Mar Piccolo, the study revealed that high portion of the plankton carbon (C) pool was constituted by small-sized (<2 μm) planktonic fractions. The prevalence of small-sized species within micro- and mesozooplankton communities was observed as well. The succession of planktonic communities was clearly driven by the seasonality, i.e. by the nutrient availability and physical features of the water column. Our hypothesis is that beside the 'bottom-up' control and the grazing pressure, inferred from the C pools of different plankton groups, the presence of mussel farms in the Mar Piccolo exerts a profound impact on plankton communities, not only due to the important sequestration of the plankton biomass but also by strongly influencing its structure.