The use of molecular tools (DNA barcoding and metabarcoding) for the identification of species and ecosystem biomonitoring is a promising innovative approach. The effectiveness of these tools is, however, highly dependent on the reliability and coverage of the DNA sequence reference libraries and it also depends on the identification of primer sets that work on the broadest range of taxa. In this study, a gap analysis of available DNA barcodes in the international libraries was conducted using the aquatic macroinvertebrate species checklist of the Apulia region in the southeast of Italy. Our analyses show that 42% of the 1546 examined species do not have representative DNA barcodes in the reference libraries, indicating the importance of working toward their completeness and addressing this effort toward specific taxonomic groups. We also analyzed the DNA barcode reference libraries for the primer set used to barcode species. Only for 52% of the examined barcoded species were the primers reported, indicating the importance of uploading this information in the databases for a more effective DNA barcode implementation effort and extensive use of the metabarcoding method. In this paper, a new combination of primers has revealed its experimental effectiveness at least on the species belonging to the three most represented taxa in the aquatic ecosystems of the Apulia region, highlighting the opportunity to develop combinations of primers useful at the regional level and the importance of studying DNA barcode gaps at the local/regional level. The DNA barcode coverage also varies among different taxonomic groups and aquatic ecosystem types in which a large number of species are rare. We tested the application of the DNA barcoding single species to a lagoon ecosystem (the lagoon named “Acquatina di Frigole” in the Apulia region) and we sampled two macroinvertebrate species lacking DNA barcodes from “Aquatina di Frigole” NATURA 2000 Site IT9150003, Fabulina fabula and Tritia nitida, generated two new CO1 barcodes and added them to a DNA barcode reference library.

Salento Peninsula (Apulia, southern Italy) is characterised by many active sinkholes, which represent the main geological hazard. The stretch of coastline between the village of Casalabate and Le Cesine wildlife reserve is highly affected, with a system of dunes separating the low beach from extensive wetlands, which were subject to uncontrolled urban development after reclamation. The overall morphology is characterized by flat topography, whilst from a hydrogeological standpoint, the mixing of inland freshwater with advancing brackish water favours the higher aggressivity with respect to soluble rocks, and the development of enhanced dissolution (hyperkarst). The relict landscapes within the protected areas still allow for the recognition of actively occurring sinkholes, which cause damage to houses, the road network and infrastructures. In this article the case of Aquatina di Frigole is described, where in the last 15 years numerous sinkholes have formed, with the processes still in rapid evolution. Detailed surveys allow for to identification of the mechanisms of sinkhole formation (suffusion sinkholes), the deriving cluster, and the main hydrogeological links among the different water bodies in the area. Acquatina di Frigole provides an excellent natural laboratory to observe development and evolution of sinkholes, and their relationships with the stratigraphic and hydrogeological elements.

The dispersion of commercial plastics in the marine environments is a major threat to biodiversity and ecosystem services of the last decades. The lower density of the plastics with respect to marine water density determines their floating, transferring, and accumulation in sandy beaches. Sandy beaches represent a natural sink ecosystem for marine plastics, where the latter are fragmented and photo-degraded in relation to the kind of polymer. Here, we propose an accurate and cost-effective method, the differential scanning calorimetry (DSC), to identify different polymers from plastic samples collected on the Aquatina di Frigole beach (Apulia Region, Southeast of Italy), included in the NATURA 2000 Site coded as IT9150003. Our results reveal the exclusive presence of thermoplastic polymers in the beach plastic samples, mostly belonging to the polyolefin family. They appear to be remnants of larger plastic fragments, which could impact biodiversity and ecosystem services such as beach recreation activities and tourism.

The ecological assessment of European aquatic ecosystems is regulated under the framework directives on strategy for water and marine environments. Benthic macroinvertebrates are the most used biological quality element for ecological assessment of rivers, coastal-marines, and transitional waters. The morphological identification of benthic macroinvertebrates is the current tool for their assessment. Recently, DNA-based tools have been proposed as effective alternatives. The main current limits of DNA-based applications include the incompleteness of species recorded in the DNA barcode reference libraries and the primers bias. Here, we analysed the influence of the incompleteness of DNA barcode databases on species diversity indices, ecological indicators, and ecological assessment in transitional waters of the southeast Mediterranean, taking into account the availability of commonly sequenced and deposited genomic regions for listed species. The ecological quality status assigned through the potential application of both approaches to the analysed transitional water ecosystems was different in 27% of sites. We also analysed the inter-specific genetic distances to evaluate the potential application of the DNA metabarcoding method. Overall, this work highlights the importance to expand the barcode databases and to analyse, at the regional level, the gaps in the DNA barcodes.

Body size is a key trait of species, populations, and organisms; it relates to abundance, home range, metabolic rates, and stressors. As reported by Damuth’s law, the relationship between body size and abundance is negative with a slope value of −0.75. In aquatic ecosystems, particularly for benthic macroinvertebrates, the slope value deviates from the expected value of −0.75. This variation may depend on abiotic and biotic factors as well as methods that are used to sample benthic macroinvertebrates. “Leaf-bags” and “Surber-net” are the most used methods and they provide different data about the body size structures and abundance of the sampled benthic macroinvertebrates. Here, we used the slope of the body size–abundance relationships to compare the benthic macroinvertebrate assemblages sampled with two sampling methods (Leaf-bags and Surber-net). We found that Leaf-bags sampled a greater number of smaller taxa than Surber-net, which collected individuals of larger sizes. In our study, differences in the benthic macroinvertebrate body size structures collected with these two sampling methods were evident even if the experiment was performed at a limited spatio–temporal scale. Therefore, Leaf-bags and Surber-net should be used as complementary rather than alternative techniques since they sample integrated information from the benthic macroinvertebrate communities.