Coastal fish indicate human-induced changes in the Mediterranean littoral

Beyond taxonomy: A functional approach reveals patterns of reef fish response to wastewater pollution

Coral reefs face severe threats from climate change and local stressors like wastewater pollution, which significantly impact reef ecosystems but remain underexplored. Reef fish are essential for supporting human livelihoods through fisheries and maintaining ecosystem functions such as nutrient cycling and algae control. While most research focuses on wastewater's effects on benthic communities, its impact on reef fish physiology, behavior, and community structure is poorly understood. Few studies apply trait-based approaches to evaluate wastewater's influence on fish's ecological roles. This study systematically reviews 52 papers and conducts a meta-analysis of eight control-impact studies to assess wastewater effects on reef fish taxonomic and functional structure. Taxonomy-based metrics revealed mixed responses, with studies reporting declines, increases, or no changes in abundance, richness, and biomass in polluted sites. Functional analysis provided clearer patterns: polluted sites were dominated by smaller, high-resilience species at mid-trophic levels, while control sites supported larger, low-resilience species at diverse depths and trophic levels. Functional richness was generally higher in control sites. Pollutant-specific effects varied: sediments impaired feeding efficiency and growth, while nutrient enrichment shifted species composition by favoring lower trophic levels. These findings demonstrate the limitations of taxonomy-based metrics and highlight the value of functional approaches for detecting early ecosystem degradation. Integrating functional ecology with wastewater characterization enhances predictions of ecological responses and supports targeted management strategies. This research emphasizes the urgency of addressing wastewater pollution to safeguard reef biodiversity and ecosystem services critical to human well-being.

Prospecting microbiota of Adriatic fish: Bacillus velezensis as a potential probiotic candidate

BACKGROUND

Aquaculture is one of the fastest growing sectors of food production and covers more than half of the market demand for fish and fishery products. However, aquaculture itself faces numerous challenges, such as infectious disease outbreaks, which are one of the limiting factors for the growth and environmental sustainability of modern aquaculture. Understanding the composition and diversity of the gut microbiota of fish is important to elucidate its role in host health and aquaculture management. In addition, the gut microbiota represents a valuable source of bacteria with probiotic potential for farmed fish.

RESULTS

In this study, we analysed the intestinal microbiota of two economically important fish species, the European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata), using 16S rRNA gene amplicon sequencing. The taxonomic analysis identified 462 amplicon sequence variants at a similarity level of 99 and showed similar alpha diversity indices between seabass and gilthead seabream. Beta diversity analysis showed no significant differentiation in gut microbiota between fish species or aquaculture sites. Among the culturable isolates, a high proportion of Photobacterium damselae and Bacillus spp. was detected. We selected a single Bacillus velezensis isolate and further characterised its biosynthetic potential by performing whole genome sequencing. Its genome contains biosynthetic gene clusters for most of the common secondary metabolites typical of B. velezensis. Antibiotic susceptibility testing showed the sensitivity of the selected isolates to several antibiotics according to EFSA recommendations. Furthermore, stimulation of peripheral blood leukocytes (PBL) with B. velezensis resulted in a strong pro-inflammatory response, with a pronounced upregulation of cytokines il1b, il6, tnfa and il10 observed over time.

CONCLUSIONS

Overall, this study provides an insight into the composition of the intestinal microbiota and the diversity of culturable intestinal bacteria of two economically most important fish species from Adriatic cage culture and sheds light on the autochthonous intestinal B. velezensis as a promising probiotic candidate for Mediterranean aquaculture.

Vibriosis Outbreaks in Aquaculture: Addressing Environmental and Public Health Concerns and Preventive Therapies Using Gilthead Seabream Farming as a Model System

Bacterial and viral diseases in aquaculture result in severe production and economic losses. Among pathogenic bacteria, species belonging to the Vibrio genus are one of the most common and widespread disease-causing agents. Vibrio infections play a leading role in constraining the sustainable growth of the aquaculture sector worldwide and, consequently, are the target of manifold disease prevention strategies. During the early, larval stages of development, Vibrio species are a common cause of high mortality rates in reared fish and shellfish, circumstances under which the host organisms might be highly susceptible to disease preventive or treatment strategies such as vaccines and antibiotics use, respectively. Regardless of host developmental stage, Vibrio infections may occur suddenly and can lead to the loss of the entire population reared in a given aquaculture system. Furthermore, the frequency of Vibrio-associated diseases in humans is increasing globally and has been linked to anthropic activities, in particular human-driven climate change and intensive livestock production. In this context, here we cover the current knowledge of Vibrio infections in fish aquaculture, with a focus on the model species gilthead seabream (Sparus aurata), a highly valuable reared fish in the Mediterranean climatic zone. Molecular methods currently used for fast detection and identification of Vibrio pathogens and their antibiotic resistance profiles are addressed. Targeted therapeutic approaches are critically examined. They include vaccination, phage therapy and probiotics supplementation, which bear promise in supressing vibriosis in land-based fish rearing and in mitigating possible threats to human health and the environment. This literature review suggests that antibiotic resistance is increasing among Vibrio species, with the use of probiotics constituting a promising, sustainable approach to prevent Vibrio infections in aquaculture.

An Analysis of Adriatic Ichthyofauna—Ecology, Zoogeography, and Conservation Status

The paper presents an analysis of biogeographic and habitat distribution patterns, and the conservation status data of Adriatic fishes, based on the last published checklist and evidence-based critical analyses of species presence. The total number of species recorded in the Adriatic is 449. The Adriatic has 58.8% of Mediterranean species richness, 76.1% of its families, and 87.8% of its orders. Among species discovered in the Adriatic after 2010, twelve species were attributed to biological invasion, mostly Atlantic immigrants or alien species, and ten species were attributed to improved research on the native ichthyofauna of the Adriatic area. About 58% of species are native species of Atlanto-Mediterranean origin, 21% are native species of wider global occurrence, 15% are Mediterranean or Mediterranean and Black Sea endemics and 5% originated outside Mediterranean Sea. The majority of species inhabit the benthic environment (71.9%), while others occur in the pelagic environment (20.7%) or are euryhaline (7.3%). The benthic littoral species are the most numerous Adriatic fishes, representing 40% of all species richness, whereas pelagic fishes are mainly eurybathic or epipelagic; only 3.6% of species are deep pelagic species. A Red Book of marine fishes of the Adriatic Sea is urgently needed to assess their conservation status, covering the entire Adriatic Sea and reviewing all fish species to assess their conservation status.

Early evidence of a shift in juvenile fish communities in response to conditions in nursery areas

A multivariate analysis of juvenile fish community data, sampled at two nursery sites at an interval of 17 years (2000-early, and 2017-late), was conducted to elucidate the trends of change in littoral juvenile fish communities along the eastern Adriatic coast. Fishing, trophic and taxonomic composition to the community data were analysed for possible causality. The ichthyofaunal composition differed significantly for Site, Period and all interactions. According to the mMDS ordination plot, four groups of communities were defined, with clear cyclicity. No patterns were found in species composition between sites in the early period, while the observed community changes were governed by the same pattern at both sites in the late period. The species that contributed most to the observed changes were non-commercial, small, benthic resident fishes, such as gobiids and blennids, or those associated with canopy alga for shelter and feeding. The analysis correctly allocated samples based on community information to Sites and Periods. The data obtained provided an invaluable opportunity to test for the generality of potential patterns of change in littoral fish communities, suggesting that significantly modified juvenile fish communities may be the result of constant human embankment and marine infrastructure construction along the coast in recent decades, rather than climate change or fishing pressure, as generally considered.

The date mussel Lithophaga lithophaga: Biology, ecology and the multiple impacts of its illegal fishery

The date mussel Lithophaga lithophaga is an edible endolithic bivalve, protected by the EU Habitats Directive and other international agreements, living inside carbonate rocks. Its illegal harvesting is carried by breaking the rocks where the bivalve grows. The impact has cascade consequences as it causes permanent changes in the substrate characteristics, the removal of benthic species, a shift from highly complex to structurally simplified habitats. As a result, the rich biodiversity of rocky reefs turns into a biological desert, named "barren". Along with the over exploitation of fish, this practice leads to the increase of sea urchin density and grazing pressure on habitats, hampering the resilience of the associated biodiversity and functions. This paper summarizes the information on date mussel biology, ecology, ecotoxicology, fishery and the legal framework regulating its protection. Evidence indicates that illegal harvesting is still operated and widespread along the Mediterranean and has huge costs in terms of loss of natural capital and ecosystem services, and in terms of active ecological restoration. Two case study areas (the Sorrento and Salento peninsulas) were selected to assess the economic costs of this practice. Tangible economic costs in terms of ecosystems services' loss are huge (from ca. 35,000 to more than 400,000 euros/year in 6.6 km of Sorrento and ca. 1.8 million euros/year along the 69 km of Salento). These costs are, on average, ca. 30 times lower than those of ecosystem restoration. Data mining from websites indicates that date mussels are presently commercialized in hundreds of restaurants in Greece, Balkan countries, Spain and Italy, favoured also by the lack of appropriate consumer information. This practice should be controlled and contrasted at local scale, enforced by national legislations, and implemented by transnational initiatives. Social campaigns are needed to increase public awareness of the serious consequences of date-mussel fishery and consumption.

Two - stages bloom of Margalefidinium cf. polykrikoides in a Mediterranean shallow bay (Ionian Sea, Italy)

The emergence of a red tide resulting in yellow-brownish discoloration of waters in Porto Cesareo bay (Italy) during July-August 2018 is reported. The species responsible for the bloom was the dinoflagellate Margalefidinium cf. polykrikoides. Cell densities reached 9.1 × 10⁶ cells L^-1 during the initial outbreak. A second peak was observed about three weeks later reaching 6.7 × 10⁵ cells L^-1. Study of live specimens showed great variation in cell size and shape. Different cyst morphotypes were found in the water samples and in the sediment. For the first time, we followed several stages of the life cycle of M. cf. polykrikoides in natural samples. Fish die-offs in the bay were not observed, however this high-density bloom may have caused consequences on the ecosystem (amount of mucilage on the beach) and in turn, on tourism that is the main activity in the area during the summer season.

Increasing habitat complexity on seawalls: Investigating large- and small-scale effects on fish assemblages

The construction of artificial structures in the marine environment is increasing globally. Eco-engineering aims to mitigate the negative ecological impacts of built infrastructure through designing structures to be multifunctional, benefiting both humans and nature. To date, the focus of eco-engineering has largely been on benefits for benthic invertebrates and algae. Here, the potential effect of eco-engineered habitats designed for benthic species on fish was investigated. Eco-engineered habitats ("flowerpots") were added to an intertidal seawall in Sydney Harbour, Australia. Responses of fish assemblages to the added habitats were quantified at two spatial scales; large (among seawalls) and small (within a seawall). Data were collected during high tide using cameras attached to the seawall to observe pelagic and benthic fish. At the larger spatial scale, herbivores, planktivores, and invertebrate predators were generally more abundant at the seawall with the added flowerpots, although results were temporally variable. At the smaller spatial scale, certain benthic species were more abundant around flowerpots than at the adjacent control areas of seawall, although there was no general pattern of differences in species density and trophic group abundance of pelagic fish between areas of the seawall with or without added habitats. Although we did not find consistent, statistically significant findings throughout our study, the field of research to improve fish habitat within human-use constraints is promising and important, although it is in its early stages (it is experimental and requires a lot of trial and error). To advance this field, it is important to document when effects were detected, and when they were not, so that others can refine the designs or scale of habitat enhancements or their study approaches (e.g., sampling protocols).

The development of a preliminary rock reef fish multimetric index for assessing thermal and urban impacts in a tropical bay

We developed a multimetric index for assessing ecological conditions in rocky reefs areas to evaluate thermal and urban influences on fish community. Eight metrics were selected to assess thermal influence: (1) total number of species; (2) number of water column species; (3) number of transient species; (4) density of individuals with low resilience; (5) density of omnivores; (6) density of carnivores; (7) number of cryptic species; (8) density of herbivores. For urban influence, six metrics were selected: (1) total density; (2) ratio between the number of rare species and the total number of species; (3) density of individuals with heavy fishing pressure; (4) number of resident species; (5) number of cryptic species; (6) density of herbivores. This preliminary index succeed in discriminating control/impacted sites and proved to be an important tool to assess impacts that alter fish community and have potential to be used in tropical rock reef coastal areas.

Response of a seagrass fish assemblage to improved wastewater treatment

We compared the structure of a seagrass fish assemblage near a sewage outlet before and after improvements to wastewater treatment. To determine whether responses by the fish assemblage were due to changes in water quality or to other factors, comparisons were made with the structure of a fish assemblage from a nearby site unaffected by sewage effluent. Total species richness, density and biomass of fish, decreased at both sites over the 30-year period. An increase in mean trophic level near the sewage outlet following improvements in water quality indicated that wastewater treatment had another important effect. This result is consistent with the reductions in food webs supporting pelagic and benthic fishes that typically accompany decreases in nutrient inputs. Although improvements to wastewater treatment explained much of the variation in the structure of the fish assemblage at PC, our results also suggest that fishing and climate change, at both sites.

Sewage pollution impact on Mediterranean rocky-reef fish assemblages

The effects of sewage outfalls on subtidal fish assemblages were studied along the NW coasts of Malta (Sicily channel, Mediterranean Sea) by means of underwater visual census. The presence of two spatially distinct outfalls discharging untreated wastewaters allowed to use a balanced symmetrical after control/impact (ACI) design that consisted of two putatively impacted locations and two controls, with four sites nested in each location. Surveys were performed in 2006 at two random dates. The study highlighted significant changes at both assemblage and individual species levels. Fish assemblages structures were different between controls and sewages, where total abundance of fish were higher. The responses of individual species to sewage pollution were mostly related to an anomalous increase of two small opportunistic species i.e. Gobius bucchichii and Parablennius rouxi and to a decrease of species of the genus Symphodus, particularly S. roissali and S. ocellatus. Moreover in correspondence of the outfalls, significant changes of the fish size distribution were detected for several species. These results support the use of fish assemblages as biological indicators for marine coastal waters and demonstrated the possibility to obtain sharp signals of environmental impact from some individual fish species.

Development of a fish-based multimetric index to assess the ecological quality of marine habitats: the Marine Fish Community Index

In this paper the Marine Fish Community Index (MFCI) for the assessment of ecological status of marine environment is proposed. The MFCI was divided into 4 typologies: Rocky subtidal; shallow, intermediate and deep soft-bottoms. Based on the typical community associated to each typology and the DPSIR analysis performed, a set of metrics were selected and tested through a multiple correlation matrix (Pearson's coefficient) and the core ones included in the index. The MFCI was applied in all typologies and the scores obtained with each metric were analyzed. In order to test the robustness of the MFCI the final ecological value of each zone was recalculated by removing successively one metric at a time. The MFCI showed a sensitive and robust response in the ecological status assessment. Since it incorporates both functional and structural community information, the MFCI can be useful in the context of the Marine Strategy Framework Directive as well as in other contexts of conservation and sustainable management of the marine environment.

Trace metal concentrations in Posidonia oceanica of North Corsica (northwestern Mediterranean Sea): use as a biological monitor?

Background

Within semi-closed areas like the Mediterranean Sea, anthropic wastes tend to concentrate in the environment. Metals, in particular, are known to persist in the environment and can affect human health due to accumulation in the food chain. The seagrass Posidonia oceanica, widely found in Mediterranean coastal waters, has been chosen as a "sentinel" to quantify the distribution of such pollutants within the marine environment. Using a technique similar to dendrochronology in trees, it can act as an indicator of pollutant levels over a timeframe of several months to years. In the present study, we measured and compared the levels of eight trace metals (Cr, Ni, Cu, Zn, As, Se, Cd, and Pb) in sheaths dated by lepidochronology and in leaves of shoots sampled from P. oceanica meadows collected from six offshore sites in northern Corsica between 1988 and 2004; in the aim to determine 1) the spatial and 2) temporal variations of these metals in these areas and 3) to compared these two types of tissues.

Results

We found low trace metal concentrations with no increase over the last decade, confirming the potential use of Corsican seagrass beds as reference sites for the Mediterranean Sea. Temporal trends of trace metal concentrations in sheaths were not significant for Cr, Ni, Cu, As or Se, but Zn, Cd, and Pb levels decreased, probably due to the reduced anthropic use of these metals. Similar temporal trends between Cu levels in leaves (living tissue) and in sheaths (dead tissue) demonstrated that lepidochronology linked with Cu monitoring is effective for surveying the temporal variability of this metal.

Conclusion

Leaves of P. oceanica can give an indication of the metal concentration in the environment over a short time period (months) with good accuracy. On the contrary, sheaths, which gave an indication of changes over long time periods (decades), seem to be less sensitive to variations in the metal concentration in the environment. Changes in human consumption of metals (e.g., the reduction of Pb in fuel) are clearly reflected in both organs. These results confirm that P. oceanica is a good bioindicator of metals and a good biomonitor species for assessing Cu in the environment.

Desertification of Mediterranean rocky reefs caused by date-mussel, Lithophaga lithophaga (Mollusca: Bivalvia), fishery: effects on adult and juvenile abundance of a temperate fish

Macroalgal beds in temperate rocky habitats provide shelter and food for many adult reef fishes and their juvenile stages. In the Mediterranean Sea, the fishery of the endolithic date-mussel Lithophaga lithophaga (which involves dismantling of rocky substrates inhabited by these bivalves) may cause formation of barrens in shallow rocky reefs. Preliminary data collected in SW Apulia (SE Italy) show that rocky reefs impacted by this destructive fishery display different distribution patterns of adult Coris julis (a common labrid fish in the Mediterranean basin), and lower abundance of juveniles. The ecological implications of date-mussel fishery for dynamics of fish populations and rocky-reef ecosystem functioning (e.g., nursery role) are discussed.

The effects of sewage discharge on shallow hard substrate sessile assemblages

On rocky shores, sewage discharges can modify natural distribution patterns of sessile organisms. The impact of sewage on shallow hard substrate assemblages has been assessed along SW Apulian coast (Ionian Sea, Italy), providing a framework to evaluate the benefits of future sewage displacement to deeper waters. Four locations (three controls and one putatively impacted) were selected and three sites were chosen at each location. Each site was sampled by 10 replicate photographic records. Univariate analyses revealed that the outfall did not affect the spatial distribution of number of taxa, total cover and abundance of some dominant taxa (mostly algae, sponges and bryozoans). The outfall negatively influenced the natural distribution pattern of filamentous green algae, whilst some algae (i.e. Gelidiales and Colpomenia sinuosa) were exclusively present at the impacted location. Multivariate analyses revealed that the outfall heavily modified the natural pattern of variability in the structure of the assemblage.