In order to halt the loss of global biodiversity and considering the United Nations Decade for Ocean Conservation Agenda, increasing efforts to improve biomonitoring programs and assessment of ecosystem health are needed. Aquatic environments are among the most complex to monitor, requiring an array of tools to assess their status and to define conservation targets. Although several parameters need to be considered for a comprehensive ecological status assessment, it is important to identify easy-to-apply high-resolution monitoring methods. Shifts in fish composition and abundance are often good indicators of ecosystem health status in relation to anthropogenic activities. However, traditional monitoring methods are strictly related to the habitat under study and cannot be applied universally. This review summarizes the importance of ecological indicators for aquatic environments subjected to anthropogenic stressors, with a particular focus on fish communities and transitional water ecosystems. We describe the main characteristics of both traditional and novel methods for fish monitoring, highlighting their advantages and shortcomings in an attempt to identify simple and reliable ways for a correct evaluation of the dynamics of aquatic ecosystems.

The current article presents 18 new records from seven Mediterranean countries. These records include one rhodophyte, fournudibranchs, two crustaceans, one stingray and 10 bony fishes. They are grouped by country as follows: Lebanon - first record ofthe Striped bass Morone saxatilis, the stingray Himantura leoparda, the Areolate grouper Epinephelus areolatus and the Spot-finporcupinefish Diodon hystrix from various parts of the country; Turkey - first record of the invasive red alga Grateloupia turuturufrom the sea of Marmara (region of Bandırma), the sea slug Goniobranchus obsoletus and the crab Arcania brevifrons from theGulf of Antalya and the cladoceran Pleopis schmackeri from several locations along the Aegean Sea; Cyprus - first record of thealien sea slug Berthellina citrina from the region of Cape Greco and an observation of a butterflyfish Heniochus sp. from the northeasternside of the island; Greece - first record of the alien sea slug Anteaeolidiella lurana from the region of Heraklion in Creteand the record of the Atlantic spadefish Chaetodipterus faber and the Black surgeonfish Acanthurus cfr gahhm from SalaminaIsland; Slovenia - first record of the alien sea slug Thecacera pennigera from Izola; Italy - first record of the hybrid Striped bass(Morone saxatilis × Morone chrysops) from the northern Tyrrhenian Sea and a first record of the goldfish Carassius auratus fromthe region of Apulia; Libya - first record of the Red Sea goatfish Parupeneus forsskali and the African surgeonfish Acanthurusmonroviae, respectively from the eastern (Al-Tamimi area) and the western shore (Al-Khums area).

The implementation of DNA metabarcoding and environmental DNA (eDNA) to the biodiversity assessment and biomonitoring of aquatic ecosystems has great potential worldwide. However, DNA metabarcoding and eDNA are highly reliant on the coverage of the DNA barcode reference libraries that are currently hindered by the substantial lack of reference sequences. The main objective of this study was to analyze the current coverage of DNA barcode reference libraries for phytoplankton species of the aquatic Mediterranean ecoregion in the southeast of Italy (Apulia Region) in order to assess the applicability of DNA metabarcoding and eDNA in this area. To do so, we investigated three main DNA barcode reference libraries, BOLD Systems, GenBank and SILVA, for the availability of DNA barcodes of the examined phytoplankton species. The gap analysis was conducted for three molecular gene markers, 18S, 16S and COI. The results showed a considerable lack of barcodes for all three markers. However, among the three markers, 18S had a greater coverage in the reference libraries. For the 18S gene marker, the barcode coverage gap across the three types of ecosystems examined was 32.21–39.68%, 60.12–65.19% for the 16S marker gene, and 72.44–80.61 for the COI marker gene. Afterwards, the interspecific genetic distance examined on the most represented molecular marker, 18S, was able to distinguish 80% of the species mined for lakes and 70% for both marine and transitional waters. Conclusively, this work highlights the importance of filling the gaps in the reference libraries, and constitutes the basis towards the advancement of DNA metabarcoding and eDNA application for biodiversity assessment and biomonitoring.

This research investigates the occurrence of Pinna nobilis (Linnaeus, 1758) in the Mediterranean Sea, where it is an endemic and the largest bivalve species. Such a species is protected under the European Council Directive 92/43/EEC since 1992, being exposed to anthropogenic impacts. The distribution of this species has been known, in the past, only from reports in scientific literature. Presently, the concerns, threats and risks for P. nobilis are increasing and a more detailed mapping of the actual distribution from a largest to a local spatial scale is essential for the implementation of monitoring, management and conservation actions. Here we provide a systematic review on the occurrence of P. nobilis, employing and combining different sources of information, such as scientific and grey literature, NATURA 2000 geodata and citizen science records. The methodological approach is a pilot test based on a scaling down of the geographical area of study, from the whole of the Mediterranean Sea to the Italian and Apulian coastline (South-East Italy); accordingly, the above mentioned sources of data have been gradually included. The results show that the combination of multiple sources of information provide a more exact determination of the species distribution at a local scale, identifying sites where in-depth actions are required to ensure the species conservation and restoration. Also, the IUCN has recently underlined that the conservation of P. nobilis has become a difficult challenge, so that each of the spatial scales for the investigation is crucial to enable a better preservation and conservation of the species in the Mediterranean Sea.

Information on the presence of Pinnanobilis (Linnaeus, 1758) in the Mediterranean Sea is largely reported in literature because it is an endemic and, at the same time, endangered species. Besides, this record contributes to enlarge the spatial distribution of this species in the South-East Italian coastline (Adriatic Sea). P.nobilis is a protected species under the EU Habitats Directive (1992). In particular, P.nobilis has been recorded for the first time in the Aquatina Lagoon, a transitional water ecosystem included in the NATURA 2000 site “Aquatina di Frigole” (IT9150003). Therefore, this finding underlines the role of transitional water ecosystems as “nursery habitats” for P.nobilis as well as the relevance of conservation actions introduced by the EU with the NATURA 2000 network for preserving the biodiversity.

The loss of aquatic biodiversity is increasing at a rapid rate globally. There is a worldwide effort to protect, preserve and restore aquatic ecosystems. For efficient biodiversity monitoring and reliable management tools, comprehensive biodiversity data are required. The abundance and species diversity of benthic macroinvertebrates are commonly used as indicators of the aquatic ecosystem condition. Currently, macroinvertebrate species biodiversity assessment is based on morpho-taxonomy, which could be enhanced by recent advances in DNA-based tools for species identification. In particular, DNA metabarcoding has the potential to identify simultaneously many different taxa in a pool of species and to improve aquatic biomonitoring significantly, especially for indicator species. This review is focused on the current state of DNA-based aquatic biomonitoring using benthic macroinvertebrates in the Mediterranean region.