The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.

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.

In order to identify how research contributes to the knowledge of marine litter as a pressure on beaches, we reviewed interactions of beach fauna with this pollutant. Entanglement of pinnipeds in fishing gear, negative correlations between macroinvertebrates abundance and sediment pollution, and the presence of plastic surrounding burrows were primary evidence of beach fauna interacting with stranded litter. Ingestion represents the main body of research; microplastic uptake by invertebrates has been studied by laboratory experiments and field collections to report the presence of polymers in tissues. In the natural context, the higher the urbanization surrounding beaches and sediment pollution, the higher the concentration of microplastics in organs of bivalves. This approach currently constitutes the main research direction, but ecotoxicological assays are emerging prospects to assess the effects of exposure to microplastics. Beached macroplastics entangle and entrap invertebrates and vertebrates, and studies have reported increasing negative interactions with seals and sea turtles. Changes in nesting and feeding behavior of resident and transient organisms have been shown as typical early warning indicators of marine litter impacts. The focus on fauna–litter interactions holds terrific potential for research and citizen science projects, which finally becomes a powerful driver towards environmental awareness on sandy beaches.