Human sewage is the main source of contamination of environmental waters with human enteric viruses, that can contaminate food such as shellfish. Metagenomic represents a new way of analyzing viral diversity through an a priori massive parallel sequencing approach. However, the precise identification of enteric viruses in sewage or shellfish matrices, is still challenging due to the low viral load, large diversity of viral genera and the large amounts of matrix masking viral sequences. This work compared three commercial kits using capture-based enrichment during the library preparation, for the diversity of detected enteric viruses and for the identification of viral strains in sewage and shellfish samples, focusing on four families impacting human health. Triplicate libraries were prepared for each sample and each kit. All three kits allowed the characterization of a variety of viral genera. In sewage samples, a large number of long contigs was obtained allowing a precise identification of more than 35 strains. In shellfish samples, long contigs were rarer but allowed the identification of one human astrovirus and one norovirus strains. Of the tested kits, one displayed lower variation between replicates, allowed to sequence a higher diversity of viruses from the four families of interest and yielded a higher number of nearly-whole genomes.

Since 2011, massive strandings of holopelagic Sargassum have occurred on the coasts of the Caribbean and of West Africa. Although open ocean Sargassum mats are oases of biodiversity, their stranding has a number of negative ecological, economic and health consequences. To limit these impacts, Sargassum needs to be collected as quickly as possible to avoid its decomposition, which requires accurate predictions of the date, location and abundance of the strandings. Two complementary approaches have been developed for this purpose: satellite remote sensing technique, to detect Sargassum aggregations, and modeling, to forecast Sargassum displacement and growth. The objective of this review is to provide a synthesis of the current knowledge related to Sargassum monitoring in the tropical Atlantic Ocean. To better understand the issues surrounding Sargassum and its monitoring, the first two parts are devoted to an overview of the ecology of the two most prevailing holopelagic Sargassum species, to the current issues related to their strandings, to the causes of their occurrence in the tropical Atlantic Ocean and to their seasonal and interannual variabilities. The methods used to detect Sargassum from satellite images and their limitations are examined. The transport and biogeochemical models developed for seasonal forecast and stranding predictions are described along with their limitations. As both detection and modeling rely on validation data to assess their accuracy, previous works providing in situ characterization of Sargassum are also reviewed here. The last part provides recommendations to further increase knowledge on holopelagic Sargassum and improve the predictions of their strandings.

Copper (Cu) and zinc (Zn) are common trace metal contaminants in marine environments that, despite their importance for the health of marine organisms, can be toxic. Recently, the stable isotopes of these elements have emerged as powerful tracers for studying their cycles. Thus, this review aims to connect urban and marine interfaces under a “land-sea continuum” framework to understand the complex sources, pathways, and transformations of Cu and Zn in urbanized coastal environments, a perspective currently lacking in the literature. Here, we briefly establish the sampling and analytical aspects of isotope measurement of these elements in the natural matrices of marine realms, providing a recent compilation of reference materials for analytical control. The principles of isotope fractionation are introduced and contextualized within coastal ecosystems. We summarize the isotopic signatures of major anthropogenic sources—including road-deposited sediments, non-exhaust traffic-related emissions, industrial waste, and metallurgical byproducts—and highlight the challenges of distinguishing them when isotopic ranges overlap. In parallel, natural baselines such as ores, soils, suspended particulate matter (SPM), and riverine inputs are also reviewed to contextualize environmental variability. The review examines how source isotope signatures evolve with further isotope fractionation during estuarine transport and transfer processes in the water-sediment-biota interface. Finally, this review also identifies future research directions to trace the sources, pathways, and sinks of these contaminants along the land-sea continuum, as well as the legacy and ongoing impact of urban metal pollution at catchment-to-coastal scales.

Offshore wind energy may offer many advantages: next to the aim of renewable energy production, offshore wind farms (OWFs) enable multi-purpose opportunities with nature conservation and aquaculture. OWFs may also affect the marine ecosystem. The environmental impact of OWFs is starting to be investigated regarding the effect of novel habitat introduction, underwater noise, electromagnetic fields, or exclusion of fisheries. However, the impact of chemical emissions from OWFs remains largely unknown. It is essential to account for these emissions at an early stage, to comprehensively assess the environmental impact with the objective of developing a future fit-for-purpose regulatory framework to protect the marine environment. This review compiled a literature-based list of potential OWF-related chemical emissions containing >200 organic and inorganic contaminants, including polymers. Compounds are categorised according to data source and emission type. Major gaps in assessing the impact of the compounds are identified, including challenges in environmental monitoring, numerical modelling and assessing the toxicity of individual and mixtures of chemical contaminants on marine organisms and humans consuming potential OWF aquaculture products. A risk-based prioritisation is essential to target the compounds of higher concern and overcome costs linked to assessing a wide variety of chemical contaminants. Although some countries have regulations to reduce OWF chemical emissions, standardized impact assessments or monitoring requirements for OWF-based chemical contaminants have not been established. This stresses the importance of providing more detailed information on occurrence, distribution and impact of OWF chemical emissions as an essential step towards sound ecosystem-based management of OWF installations.

The New Caledonian archipelago is an important hotspot of marine biodiversity. Due to mining activities, urbanization, and industrialization, significant amounts of contaminants are discharged into the lagoon. This study analysed the concentrations, spatial distribution, and potential drivers of 14 metallic compounds and trace elements (MTEs) and 22 persistent organic pollutants (POPs) in ~400 coral reef fish sampled from various sites around New Caledonia, across a gradient from mining centers to remote, uninhabited locations. Boosted regression trees modelling explained between 61 and 86 % of the global variation in MTEs and POPs concentration. Fish body size emerged as the most important correlate of MTEs and POPs concentrations in coral reef fish. Monthly rainfalls were the second most important variable for POPs, whereas the reef area was the second variable explaining MTE concentrations. Our modelling approach allowed us to predict and map the distribution of concentrations at the fish community level for 17 contaminants (9 MTEs and 8 POPs). Predicted concentrations ranged from ~1.5 ng.g−1 (β-endosulfan) to ~11.5 μg.g−1 (Ni), and revealed a widespread contamination throughout the lagoon, from the coast to the barrier reef. Contamination by mining-related elements (Ni, Cr…) were clearly influenced by the surface area of mining registry and to lithology to a lesser extent, whereas Hg contamination strongly depended on biological variables. Our study is the largest of its kind at the archipelago scale, combining data on 36 contaminants in ~400 fish samples with a modelling framework offering insights into underlying processes and spatial data for policy use.

Littoral environments represent the main entry point for pollutants into the sea. Microplastics (MPs) are a growing concern, especially for the Mediterranean basin characterized by densely populated coasts and a semi-enclosed morphology. This article targets MPs associated with a unique coastal habitat - the largest bioconstruction in the Mediterranean (Torre Mileto, Southern Adriatic Sea) built by the reef-building polychaete Sabellaria spinulosa (anellida). We assessed MPs abundance in samples from both bioconstruction and surrounding sediments using stereomicroscopy with UV light and micro-Raman spectroscopy. MPs distribution was analyzed according to substrate (reef vs. sediment), longshore drift (west vs. east side), and reef morphology (hummock vs. platform). Results showed a significantly higher MPs abundance in samples from the western side of the site, potentially related to a longshore drift influence on pollutant distribution. By contrast, no significant differences in MPs abundances were observed in substrates (reefs vs. surrounding sediments) and in reef morphologies (hummock vs. platform), which suggest no direct control of reef-building activity in accumulating MPs. The passive accumulation of MPs, primarily driven by wave action, is likely the main factor explaining the MPs distribution. Micro-Raman Spectroscopy analysis revealed polyethylene terephthalate as the dominant polymer, and fibers as the most abundant morphology; prevalent MPs colors were colorless and black. Data provided here indicate that polychaete reefs temporarily trap MPs, retaining such pollutant in the littoral environment. The mechanism of MPs passive accumulation observed in this study raises questions about the growing risk for this bio-engineered benthic habitats.

The French Mediterranean coast has a long history of anthropogenic metal contamination, yet current contamination levels remain largely unquantified. This study aims to provide a comprehensive overview of metal accumulation along the coastline by establishing natural background levels, identifying spatial contamination patterns, and assessing associated ecological risks. Major elements (Al, Fe) and trace metals (Mn, Pb, Zn, Cd, Cu) were measured in surface sediments from 74 sites and in three sediment cores using ICP-MS, while mercury (Hg) was analyzed using an AMA instrument. Natural background concentrations were determined based on the depth layers of three sediment cores that predate the year 1917. This timeframe has been recognized as the pre-industrial period by applying multivariate change point analysis. Approximately 60 % of sediment samples exhibited a Pollution Load Index (PLI) above 1, indicating significant anthropogenic enrichment across the coast. The Mean Effects Range Median Quotient (m-ERM-Q) exceeded 1 only at Cortiou and Toulon, suggesting a localized ecological risk. At Cortiou, Cd (2.85 mg/kg) and Cu (212.0 mg/kg) were between Effect Range-Low (ERL) and Effect Range-Median (ERM) thresholds, while Pb (264.0 mg/kg), Hg (6.73 mg/kg), and Zn (654.0 mg/kg) were above ERM, due to wastewater discharge. In Toulon Bay, Pb (79.34 mg/kg) and Cu (50,00 mg/kg) were between the ERL and ERM, while Hg (5.57 mg/kg) exceeded the ERM, linked with long-term naval and industrial activities. These findings demonstrate pervasive metal enrichment and ecological risks driven by different sources and highlight the urgent need for targeted mitigation strategies.

Coralligenous reefs are among the most diverse Mediterranean ecosystems, particularly in the circalittoral zone. Shaped by calcified red algae, sponges, cnidarians, and bryozoans, they create a complex three-dimensional structure providing shelter for diverse fauna. These reefs develop either on steep rocky walls or as bioherms when calcified algae are the dominant organisms. Their structure and composition vary with location, depth, substrate, and environmental conditions. Assessing the status of such a complex ecosystem poses significant challenges. Ecosystem-based quality indices (EBQI) have already been applied successfully to various coastal Mediterranean habitats. Using a similar methodology, a new index, the Coralligenous Ecosystem-Based Quality Index (Cor-EBQI), was developed to assess the ecological status of the coralligenous ecosystem. The index incorporates the main functional compartments of these reefs, with each compartment weighted according to its importance in ecosystem functioning. Suitable descriptors were then selected to define five status classes for each compartment. A confidence index was also created to estimate data quality based on criteria such as methodology and expert judgement. Data from 63 sites along the French Mediterranean coast, including the Gulf of Lions, Provence, the French Riviera, Corsica, and Monaco, were analyzed. The ecological status ranged from bad to high, influenced by environmental conditions, geomorphology, anthropogenic pressures, and management practices. The Cor-EBQI is designed to meet the objectives of both the Habitats and Marine Strategy Framework Directives of the European Union. As such, it offers a practical tool for future monitoring networks across the Mediterranean Sea.