Genomic and transcriptomic approaches have the potential for unveiling the genome-wide response to environmental perturbations. The abundance of the catadromous European eel (Anguilla anguilla) stock has been declining since the 1980s probably due to a combination of anthropogenic and climatic factors. In this paper, we explore the transcriptomic dynamics between individuals from high (river Tiber, Italy) and low pollution (lake Bolsena, Italy) environments, which were measured for 36 PCBs, several organochlorine pesticides and brominated flame retardants and nine metals. To this end, we first (i) updated the European eel transcriptome using deep sequencing data with a total of 640,040 reads assembled into 44,896 contigs (Eeelbase release 2.0), and (ii) developed a transcriptomic platform for global gene expression profiling in the critically endangered European eel of about 15,000 annotated contigs, which was applied to detect differentially expressed genes between polluted sites. Several detoxification genes related to metabolism of pollutants were upregulated in the highly polluted site, including genes that take part in phase I of the xenobiotic metabolism (CYP3A), phase II (glutathione-S-transferase) and oxidative stress (glutathione peroxidase). In addition, key genes in the mitochondrial respiratory chain and oxidative phosphorylation were down-regulated at the Tiber site relative to the Bolsena site. Together with the induced high expression of detoxification genes, the suggested lowered expression of genes supposedly involved in metabolism suggests that pollution may also be associated with decreased respiratory and energy production.

Transitional waters are among the most productive ecosystems of the world and their biotic communities show high diversity and complex mechanisms of self-regulation that provide valuable ecosystem services and societal goods and benefits. In this work a comparison of the fish assemblages of three non-tidal Mediterranean coastal lagoons is carried out in order to evaluate the impacts of alternative management strategies. The anthropogenic pressures acting on the lagoons were quantified by means of categorical indicators, while the characteristics of the fish assemblages were summarized in multi-metric indices (MMIs). Two MMIs were developed using data collected with a beach seine net and with fyke nets, following an empirical approach that selects, from a pool of 73 metrics, the combination that maximizes the MMI/pressure relationship. The two MMIs include four metrics each, most of which are based on feeding mode functional guilds and habitat use functional guilds, and they are sensitive to anthropogenic pressures. The human activities directly or indirectly affecting water quality are the ones that most influence the fish assemblage, while the presence of artisanal fisheries, a typical and relevant resource use in these lagoons, seems to play a beneficial role. Lagoon fisheries management relies on the maintenance of infrastructures that guarantee the hydraulic functioning of the lagoon, thus ensuring exchanges with the adjacent coastal sea, and therefore indirectly contributing to the habitat quality.

The aim of this study was to evaluate the use of gonadal alterations in the thinlip grey mullet (Liza ramada) as a biological indicator in assessing aquatic ecosystems health, with particular emphasis to river ecosystems exposed to sewage discharges. For this purpose, the reproductive status and the presence of gonadal alterations were studied in 206 mullets collected from two sites on the low course of the Tiber River, downstream of a large urban sewage treatment plant and in the estuarine area, and from an uncontaminated pond considered as reference site. Intersex and irregularly shaped gonads were observed in 20.8% of the mullets from the most polluted site, and intersex gonads in 10.3% of those from the estuarine area. No alterations were detected in the fish from the reference site, which also showed distinct stages of gonadal development. Conversely, unclear stages of testicular and ovary development were observed in the fish from the two polluted river sites. The results of this study suggest that L. ramada may represent a sentinel species in environmental risk assessment and support the use of gonadal alterations of this species as a bioindicator for extensive monitoring of pollution in lower stretches of rivers and estuarine areas.

The evaluation of past and present anthropogenic impacts affecting the ecological quality status of transitional ecosystems is crucial from the perspective of protecting them from further deterioration, and to evaluate remediation and restoration measures. Contamination patterns of thick-lipped grey mullet from two Mediterranean coastal lagoons within a protected area in Italy were assessed and compared in order to evaluate their overall quality status and to collect information that can provide useful feedback on management choices aimed at enhancing environmental quality and biodiversity conservation. The quality status of the two lagoons was evaluated by an environmental assessment methodology based on indicators of direct and indirect human pressures, while a broad range of analyses were carried out to determine the presence and concentration of persistent organic pollutants (POPs) and metals in fish muscle tissue. A good quality status resulted for both lagoons, and an overall limited anthropogenic impact in the surrounding area. This could account for POPs and metal contamination levels found in mullet, although limited, and relating to their patterns. The overlap of results achieved with the two evaluation approaches can provide support for management choices in Mediterranean lagoon environments, especially for those committed to the protection and conservation of biodiversity.

Mediterranean coastal lagoons are increasingly affected by several threats, all concurrently leading to habitat degradation and loss. Methods based on fish for the assessment of the ecological status are under implementation for the Water Framework Directive requirements, to assess the overall quality of coastal lagoons. Complementary tools based on the use of single fish species as biological indicators could be useful as early detection methods of anthropogenic impacts. The analysis of skeletal anomalies in the big-scale sand smelt, Atherina boyeri, from nine Mediterranean coastal lagoons in Italy was carried out. Along with the morphological examination of fish, the environmental status of the nine lagoons was evaluated using a method based on expert judgement, by selecting and quantifying several environmental descriptors of direct and indirect human pressures acting on lagoon ecosystems. The average individual anomaly load and the frequency of individuals with severe anomalies allow to discriminate big-scale sand smelt samples on the basis of the site and of its quality status. Furthermore, a relationship between skeletal anomalies and the environmental quality of specific lagoons, driven by the anthropogenic pressures acting on them, was found. These findings support the potentiality of skeletal anomalies monitoring in big-scale sand smelt as a tool for early detection of anthropogenic impacts in coastal lagoons of the Mediterranean region.