Free-living nematodes were investigated in the Mar Piccolo of Taranto (Ionian Sea), a semi-enclosed basin of strategic importance for its complex productive infrastructure but in need of remediation due to the alarming amounts of heavy metals and synthetic organic contaminants in the sediments. Abundance, genera composition, biodiversity and trophic traits of nematodes were related to the gradual transition from marine to more brackish conditions and to the varying levels of contaminants in different sub-areas of the basin. Nematodes were more abundant and diverse at the most marine site while low numbers and diversity characterized the most contaminated station. Going towards the innermost part of the basin, gradually increasing values of abundance and biodiversity were observed although the assemblage was susceptible to the organic enrichment caused by mussel farms. The use of nematodes as ecological indicators mirrored the response of the assemblage to the main patterns acting in the basin (High/Good scores at the most marine site and Poor/Bad scores at the most contaminated station), giving a clear indication of environmental quality to stakeholders/authority that can contribute to address remediation actions in contaminated sediments.

The soft-bottom zoobenthic community structure of Izmir Bay was examined seasonally at eight stations (depth-range: 19–67 m) in 2009. A total of 427 species were found. Polychaeta had the highest number of species (50% of total species) and individuals (75%), whereas Echinodermata possessed the highest biomass (47%). The number of species varied from 3 to 79 (0.1 m−2), the density from 60 to 5360 ind.m−2, and the biomass from 1 to 530 g.m−2. The most numerically dominant species were the polychaetes Aricidea claudiae, Streblospio gynobranchiata, Levinsenia demiri and Sternaspis scutata. The distribution of zoobenthos was strongly related to spatial differences in total organic carbon, sediment texture and depth among different regions of the bay rather than temporal differences among seasons. However, significant seasonal variability in community structure (mainly differences in the relative abundance of species) was present. The inner region of the bay can be classified as ‘poor’ or ‘bad’ based on the results of biotic indices (H′, AMBI, m-AMBI and BENTIX). Among biotic indices, only H′ and m-AMBI appeared to be capable of explaining the bay's benthic quality status. Thirteen alien species were also found. Streblospio gynobranchiata, Prionospio pulchra, Pseudopolydora paucibranchiata and Polydora cornuta formed dense populations in the inner most polluted part of the bay and are considered to be new pollution indicator species in the eastern Mediterranean Sea.