**2. Study Area**

#### *2.1. Regional Oceanographic Setting*

The Mediterranean Sea is a land-locked Sea characterized by an anti-estuarine circulation pattern which is forced by negative hydrological balance and density gradient compared to the open Atlantic Ocean [54]. Particularly, the central Mediterranean basin consists of the Adriatic and Ionian Seas (Figure 1), which are characterized by complex geomorphology and oceanography, as well as different productivity regimes. The Adriatic Sea is a small semi-enclosed shelf area connected to the eastern Mediterranean through the Otranto Strait. According to its topography, it presents strong bathymetric contrasts from north to south with its northernmost part being the shallowest (~50 m), the middle Adriatic deeper (~270 m) and the southern Adriatic the deepest (up to 1250 m) [55]. The same exists for the Ionian Sea, which constitutes distinct sub-basins with different bathymetric and hydrological characteristics. For instance, the Salerno area is characterized by a broad continental shelf with rocky bottoms, the Calabrian sector by numerous narrow submarine canyons [56], while the central Ionian by the homonymous abyssal plain. Overall, the Ionian Sea is affected by the inflow of water from the Levantine, Aegean, Adriatic and western Mediterranean basins and therefore different water masses propagate into the Ionian Sea and mixing between them can occur. The general hydrographic conditions determine substantial differences in temperature and salinity values within the study area and the large-scale circulation pattern undergoes seasonal changes resulting in diverse physical, biogeochemical, and ecological conditions [57,58].

**Figure 1.** Bathymetric map of the central Mediterranean depicting the sampling locations in the Adriatic and Ionian sub-basins along with the upper ocean current system in the study area.

#### *2.2. Water Masses and Circulation*

The Ionian Sea is affected by the inflow of diverse water masses from the Levantine, Aegean, Adriatic, and western Mediterranean. At the entrance of the Sicily Strait, inflowing surface waters occupying the upper 200 m (Modified Atlantic Water; MAW) flow eastward along the north African coast and separate into two branches: one turns northward along the Sicilian coast into a broad anticyclonic pattern, while the other continues in an easterly direction along the African coast with increasing salinity, following a large-scale counterclockwise pathway [59,60] (Figure 1). The northern branch, called the Atlantic Ionian Stream (AIS; [61]), is complicated by quasi-permanent mesoscale gyres and their spatial variable in terms of shape, position and strength lobes, meanders and transient eddies contributing to the MAW transport into the eastern Mediterranean off the southern coast of Sicily [59,62]. Such meso-scale eddies are often very efficient in transferring particles and passive tracers vertically or horizontally, contributing in this way to the propagation and mixing of water masses. The eastern-most MAW, termed Atlantic Tunisian Current (ATC; [63]), shows a marked path in winter when it cools and undergoes a severe salt enrichment forming the Levantine Intermediate Water (LIW). The LIW, enriched by Cretan intermediate water, flows westward into the Tyrrhenian Sea at 200–600 m depth as the salty outflow waters. Its role is particularly important since it is the preconditioning agent for the dense water formation of both the Adriatic Deep Water (AdDW) and Aegean Deep Water (AeDW) below 800 m [60,64–66] and their communication to the western Mediterranean basin [67].

The surface circulation of the Adriatic Sea consists of a basin-wide and seasonal variable cyclonic gyre with a northward flow along the eastern side, the Eastern Adriatic Current (EAC; [68]), and a southward return flow along the Italian coast on the western side (Western Adriatic Current; WAC; [69]) which flushes the nutrient-rich water out of the northern Adriatic [70]. During autumn and winter, a cold and relatively fresh dense water mass (AdDW) is also formed in the northern and central Adriatic Sea. Outflowing AdDW is accompanied by inflowing warmer LIW from the Ionian Sea, and this thermal circulation is driven by winter cooling of the Adriatic [71]. Overall, there are three main forcing factors affecting the circulation pattern: (a) river runoff causing heat loss and low-salinity water gain; (b) atmospheric forcing responsible for dense water formation and seasonal differences in circulation; and (c) exchange via the Strait of Otranto balancing the water budget by the intrusion of warm and salty waters from the Ionian Sea. As a result, temperature, salinity and circulation display marked spatial and temporal variations [72]. Moreover, the Adriatic Sea typically presents lower surface salinities than the rest of the central Mediterranean, mostly due to large freshwater inputs from rivers, acting as a dilution basin [73].

## *2.3. Productivity Regimes*

River runoff affects the circulation through freshwater input and impacts the marine ecosystem by introducing large amounts of organic matter, nutrients, and sediments. Particularly, Po and Apennine rivers play a major role in freshwater supply for the northern Adriatic. Beyond the seasonal character of river discharges, the long-term changes of nutrient concentrations in the northern Adriatic are also strongly influenced by atmospheric conditions and therefore connected with climatic fluctuations, which can modify the water column dynamics (e.g., vertical mixing, horizontal advection, water exchange rate between north-central Adriatic; [74]). The southern Adriatic open waters show oligotrophic characteristics comparable to the Ionian Sea, with nutrient supply to the euphotic zone strongly depending on vertical stratification and mixing processes [75]. However, higher phytoplankton densities have been observed in the surface waters along the south Italian coasts driven by intensified freshwater inputs [76,77]. Horizontal or vertical advection of nutrient-rich LIW from the Ionian Sea is also an important productivity factor [78] for specific locations within the southern Adriatic Sea where phytoplankton blooms follow deep convection events [79]. Physical and chemical parameters of these blooms [80] have

shown a switch from typical Mediterranean phosphorous- to nitrogen-limited conditions for this setting.
