This paper is the outcome of a workshop held in Rome in November 2011 on the occasion of the 25th anniversary of the POEM (Physical Oceanography of the Eastern Mediterranean) program. In the workshop discussions, a number of unresolved issues were identified for the physical and biogeochemical properties of the Mediterranean Sea as a whole, i.e., comprising the Western and Eastern sub-basins. Over the successive two years, the related ideas were discussed among the group of scientists who participated in the workshop and who have contributed to the writing of this paper. Three major topics were identified, each of them being the object of a section divided into a number of different sub-sections, each addressing a specific physical, chemical or biological issue: 1. Assessment of basin-wide physical/biochemical properties, of their variability and interactions. 2. Relative importance of external forcing functions (wind stress, heat/moisture fluxes, forcing through straits) vs. internal variability. 3. Shelf/deep sea interactions and exchanges of physical/biogeochemical properties and how they affect the sub-basin circulation and property distribution. Furthermore, a number of unresolved scientific/methodological issues were also identified and are reported in each sub-section after a short discussion of the present knowledge. They represent the collegial consensus of the scientists contributing to the paper. Naturally, the unresolved issues presented here constitute the choice of the authors and therefore they may not be exhaustive and/or complete. The overall goal is to stimulate a broader interdisciplinary discussion among the scientists of the Mediterranean oceanographic community, leading to enhanced collaborative efforts and exciting future discoveries.

The Mediterranean Sea is a semi-enclosed sea characterized by high salinities, temperatures and densities. The net evaporation exceeds the precipitation, driving an anti-estuarine circulation through the Strait of Gibraltar, contributing to very low nutrient concentrations. The Mediterranean Sea has an active overturning circulation, one shallow cell that communicates directly with the Atlantic Ocean, and two deep overturning cells, one in each of the two main basins. It is surrounded by populated areas and is thus sensitive to anthropogenic forcing. Several dramatic changes in the oceanographic and biogeochemical conditions have been observed during the past several decades, emphasizing the need to better monitor and understand the changing conditions and their drivers. During 2011 three oceanographic cruises were conducted in a coordinated fashion in order to produce baseline data of important physical and biogeochemical parameters that can be compared to historic data and be used as reference for future observational campaigns. In this article we provide information on the Mediterranean Sea oceanographic situation, and present a short review that will serve as background information for the special issue in Ocean Science on "Physical, chemical and biological oceanography of the Mediterranean Sea". An important contribution of this article is the set of figures showing the large-scale distributions of physical and chemical properties along the full length of the Mediterranean Sea.

Adriatic and Ionian seas are Mediterranean sub-basins linked through the Bimodal Oscillating System mechanism responsible for decadal reversals of the Ionian basin-wide circulation. Altimetric maps showed that the last cyclonic mode started in 2011 but unexpectedly in 2012 reversed to anticyclonic. We related this "premature" inversion to the extremely strong winter in 2012, which caused the formation of very dense Adriatic waters, flooding Ionian flanks in May and inverting the bottom pressure gradient. Using Lagrangian float measurements, the linear regression between the sea surface height and three isopycnal depths suggests that the southward deep-layer flow coincided with the surface northward geostrophic current and the anticyclonic circulation regime. Density variations at depth in the northwestern Ionian revealed the arrival of Adriatic dense waters in May and maximum density in September. Comparison between the sea level height in the northwestern Ionian and in the basin centre showed that in coincidence with the arrival of the newly formed Adriatic dense waters the sea level was lowered in the northwestern flank, inverting the surface pressure gradient. Toward the end of 2012, the density gradient between the basin flanks and its centre went to zero, coinciding with the weakening of the anticyclonic circulation and eventually with its return to the cyclonic pattern. Thus, the premature and transient reversal of Ionian surface circulation originated from the extremely harsh winter in the Adriatic, resulting in the formation and spreading of highly dense bottom waters. The present study highlights the remarkable sensitiveness of the Adriatic–Ionian BiOS to climatic forcing.

Here we report on data from an oceanographic cruise on the German research vessel Meteor covering large parts of the Mediterranean Sea during spring of 2011. The main objective of this cruise was to conduct measurements of physical, chemical and biological variables on a section across the Mediterranean Sea with the goal of producing a synoptic picture of the distribution of relevant physical and biogeochemical properties, in order to compare those to historic data sets. During the cruise, a comprehensive data set of relevant variables following the guide lines for repeat hydrography outlined by the GO-SHIP group (http://www.go-ship.org/) was collected. The measurements include salinity and temperature (CTD), an over-determined carbonate system, inorganic nutrients, oxygen, transient tracers (CFC-12, SF₆), helium isotopes and tritium, and carbon isotopes. The cruise sampled all major basins of the Mediterranean Sea following roughly an east-to-west section from the coast of Lebanon through to the Strait of Gibraltar, and to the coast of Portugal. Also a south-to-north section from the Ionian Sea to the Adriatic Sea was carried out. Additionally, sampling in the Aegean, Adriatic and Tyrrhenian Seas were carried out. The sections roughly followed lines and positions that have been sampled previously during other programs, thus providing the opportunity for comparative investigations of the temporal development of various parameters.

Temperature, salinity and oxygen data collected during April and June 2011 (M84/3 and P414 cruises respectively) are analysed to derive the oceanographic characteristics of the Eastern Mediterranean (EM) basin. These observed characteristics are compared with those from previous cruises over the period 1987–2011. As a result, the interannual and decadal variability of the EM thermohaline properties are discussed in the context of the evolution of the Eastern Mediterranean Transient (EMT) and of the general circulation of the basin. We found that the state of the EM is still far from the pre-EMT conditions, though the 2011 results possibly indicate a slow return to this status. In particular, a comparison between thermohaline property evolution deriving from interannual variability of the preconditioning and air–sea interaction (heat fluxes) in the South Adriatic and the Cretan Seas reveals aspects of the alternation of the two dense water sources (Adriatic and Aegean) during the last three decades, which have strong implications for the hydrographic characteristics of the intermediate and deep layers of the Ionian and Levantine basins.