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Plastic debris in aquatic environments is colonized by microbes, yet factors influencing biofilm development and composition on plastics remain poorly understood. Here, we explored the microbial assemblages associated with different types of plastic debris collected from two coastal sites in the Mediterranean Sea. All plastic samples were heavily colonized by prokaryotes, with abundances up to 1.9×107 cells/cm2. Microbial assemblages on plastics significantly differed between the two geographic areas but not between polymer types, suggesting a major role of the environment as source for the plastisphere composition. Nevertheless, plastic communities differed from those in the surrounding seawater and sediments, indicating a further selection of microbial taxa on the plastic substrates. The presence of potential pathogens on the plastic surface reflected the levels of microbial pollution in the surrounding environment, regardless of the polymer type, and confirmed the role of plastics as carriers for potentially pathogenic microorganisms across the coastal ocean, deserving further investigations.

The large-scale deep-sea biodiversity distribution of the benthic fauna was explored in the Mediterranean Sea, which can be seen as a miniature model of the oceans of the world. Within the framework of the BIOFUN project (\"Biodiversity and Ecosystem Functioning in Contrasting Southern European Deep-sea Environments: from viruses to megafauna\"), we investigated the large spatial scale variability (over >1,000 km) of the bathyal macrofauna communities that inhabit the Mediterranean basin, and their relationships with the environmental variables. The macrofauna abundance, biomass, community structure and functional diversity were analysed and the α-diversity and β-diversity were estimated across six selected slope areas at different longitudes and along three main depths. The macrobenthic standing stock and α-diversity were lower in the deep-sea sediments of the eastern Mediterranean basin, compared to the western and central basins. The macrofaunal standing stock and diversity decreased significantly from the upper bathyal to the lower bathyal slope stations. The major changes in the community composition of the higher taxa and in the trophic (functional) structure occurred at different longitudes, rather than at increasing water depth. For the β-diversity, very high dissimilarities emerged at all levels: (i) between basins; (ii) between slopes within the same basin; and (iii) between stations at different depths; this therefore demonstrates the high macrofaunal diversity of the Mediterranean basins at large spatial scales. Overall, the food sources (i.e., quantity and quality) that characterised the west, central and eastern Mediterranean basins, as well as sediment grain size, appear to influence the macrobenthic standing stock and the biodiversity along the different slope areas.

Krill species are key organisms in the Antarctic food web. Biochemical composition in terms of lipids, proteins, carbohydrates, and fatty acids and its implications for spatial distribution were investigated in specimens of Euphausia superba and Euphausia crystallorophias collected in the Ross Sea and the adjacent Pacific region during an acoustic survey carried out within the framework of the 19th Italian National Program for Research in Antarctica (PNRA) Expedition, to gain insights into their trophic relationships and bioenergetic strategies. In both species, the body biochemical composition (wet) showed a predominance of proteins (62–86%), followed by lipids and carbohydrates, and, among identified lipid classes, the two species did not seem to differ much in fatty acid composition. Results showed the highest dissimilarity in biochemical composition between species relative to differences in latitude (24%) and to inshore/offshore haul (22%). Fatty acid analysis, and particularly PUFA/SFA and 18PUFA/16PUFA ratios, allowed identification of a more pronounced omnivorous kind of diet in E. crystallorophias relative to E. superba.

More than 80% of wastewaters are discharged into rivers or seas, with a negative impact on water quality along the coast due to the presence of potential pathogens of faecal origin. Escherichia coli and enterococci are important indicators to assess, monitor, and predict microbial water quality in natural ecosystems. During rainfall events, the amount of wastewater delivered to rivers and coastal systems is increased dramatically. This study implements measures capable of monitoring the pathways of wastewater discharge to rivers and the transport of faecal bacteria to the coastal area during and following extreme rainfall events. Spatio-temporal variability of faecal microorganisms and their relationship with environmental variables and sewage outflow in an area located in the western Adriatic coast (Fano, Italy) was monitored. The daily monitoring during the rainy events was carried out for two summer seasons, for a total of five sampling periods. These results highlight that faecal microbial contaminations were related to rainy events with a high flow of wastewater, with recovery times for the microbiological indicators varying between 24 and 72 h and influenced by a dynamic dispersion. The positive correlation between ammonium and faecal bacteria at the Arzilla River and the consequences in seawater can provide a theoretical basis for controlling ammonium levels in rivers as a proxy to monitor the potential risk of bathing waters pathogen pollution.

Harbors are hubs of human activity and are subject to the continuous discharge and release of industrial, agricultural, and municipal waste and contaminants. Benthic organisms are largely known to reflect environmental conditions they live in. Despite meio- and macrofauna interacting within the benthic system, they are ecologically distinct components of the benthos and as such may not necessarily respond to environmental conditions and/or disturbances in the same way. However, in a few field studies the spatial patterns of meio- and macrofauna have been simultaneously compared. In the present study, we assess the response and patterns in the abundance, diversity, and distribution of the two benthic size classes to the different environmental conditions they live in ( i.e ., sediment concentrations of selected trace metals and polycyclic aromatic hydrocarbons (PAHs); organic matter contents and grain size) characterizing the Ancona Harbor (Adriatic Sea). Meio- and macrofauna provided partially similar types of information depending on the indices used (univariate measures or community structure/species composition) and the different ‘response-to-stress’. The community structure ( i.e ., taxa composition) of both benthic size components clearly showed differences among sampling stations located from inside to outside the harbor, reflecting the marked environmental heterogeneity and disturbance typically characterizing these systems. Notwithstanding, the univariate measures ( i.e ., meio- and macrofauna total abundance, diversity indices and equitability) didn’t show similar spatial patterns. Meiofauna were likely to be more sensitive to the effects of environmental features and contaminants than macrofauna. Overall, trace metals and PAHs affected the community composition of the two benthic components, but only the meiofauna abundance and diversity were related to the environmental variables considered ( i.e ., quantity and quality of organic matter). Our results pinpoint the importance of studying both meio- and macrofauna communities, which could provide greater insight into the processes affecting the investigated area and reveal different aspects of the benthic ecosystems in response to harbor conditions.

The marine fish farming industry is growing at a significant rate, yet a number of concerns still remain with regards to environmental impacts on the surrounding coastal sea and its biota. Here, we assessed the impact of intensive farming on benthic prokaryotic communities at a Mediterranean sea bass and sea bream intensive aquaculture site over a period of 10 months, in relation to the increase in fish biomass within the cage together with the organic matter enrichment in the sediments. We report positive relationships between prokaryotic abundance and both organic matter and fish biomass, and a contextual decrease in prokaryotic diversity below the cages. A significant shift in microbial community composition occurred in fish farm sediments (FF) over time, indicating a likely impact of ongoing aquaculture activity on prokaryotic communities. Among the dominant taxa at the impacted site, we found Epsilonproteobacteria and Bacteroidetes, which showed a general increase with fish biomass. Analyses on specialist taxa underlined significant contributions of Clostridiales and Bacteroidales in the farmed sediments. Finally, sea bream and sea bass gut microbiome-related taxa were detected during the sampling period. Our results indicate that prokaryotic community composition underneath the cages is related to fish biomass and organic enrichment over the course of production, and confirms that the study of benthic microbial communities at aquaculture sites represents a useful tool to assess the impact of intensive mariculture on the surrounding environment.

Combined sewer overflows (CSOs) close to water bodies are a cause of grave environmental concern. In the past few decades, major storm events have become increasingly common in some regions, and the meteorological scenarios predict a further increase in their frequency. Consequently, CSO control and treatment according to best practices, the adoption of innovative treatment solutions and careful sewer system management are urgently needed. A growing number of publications has been addressing the quality, quantity and types of available water management and treatment options. In this study, we describe the construction of an innovative detention reservoir along the Arzilla River (Fano, Italy) whose function is to store diluted CSO wastewater exceeding the capacity of a combined drain system. River water sampling and testing for microbial contamination downstream of the tank after a heavy rain event found a considerable reduction of fecal coliform concentrations, which would have compounded the impact of stormwater on the bathing site. These preliminary results suggest that the detention tank exerted beneficial environmental effects on bathing water by lowering the microbial load.

The deep-sea represents a substantial portion of the biosphere and has a major influence on carbon cycling and global biogeochemistry. Benthic deep-sea prokaryotes have crucial roles in this ecosystem, with their recycling of organic matter from the photic zone. Despite this, little is known about the large-scale distribution of prokaryotes in the surface deep-sea sediments. To assess the influence of environmental and trophic variables on the large-scale distribution of prokaryotes, we investigated the prokaryotic assemblage composition (Bacteria to Archaea and Euryarchaeota to Crenarchaeota ratio) and activity in the surface deep-sea sediments of the Mediterranean Sea and the adjacent North Atlantic Ocean. Prokaryotic abundance and biomass did not vary significantly across the Mediterranean Sea; however, there were depth-related trends in all areas. The abundance of prokaryotes was positively correlated with the sedimentary concentration of protein, an indicator of the quality and bioavailability of organic matter. Moving eastwards, the Bacteria contribution to the total prokaryotes decreased, which appears to be linked to the more oligotrophic conditions of the Eastern Mediterranean basins. Despite the increased importance of Archaea, the contributions of Crenarchaeota Marine Group I to the total pool was relatively constant across the investigated stations, with the exception of Matapan-Vavilov Deep, in which Euryarchaeota Marine Group II dominated. Overall, our data suggest that deeper areas of the Mediterranean Sea share more similar communities with each other than with shallower sites. Freshness and quality of sedimentary organic matter were identified through Generalized Additive Model analysis as the major factors for describing the variation in the prokaryotic community structure and activity in the surface deep-sea sediments. Longitude was also important in explaining the observed variability, which suggests that the overlying water masses might have a critical role in shaping the benthic communities.

The enumeration of Archaea in deep-sea sediment samples is still limited, although different methodological procedures have been applied. Among these, catalysed reporter deposition-fluorescence in situ hybridisation (CARD-FISH) technique is a promising tool for estimation of archaeal abundance in deep-sea sediment samples. Comparing different permeabilisation treatments, the best results obtained both on archaeal pure cultures and on natural assemblages were with hydrochloric acid (0.1 M) and proteinase K (0.004 U/ml) treatments. The application of CARD-FISH on deep-sea sediments revealed that Archaea reach up to 41% of total prokaryotic cells. Specific probes for planktonic Archaea showed that marine Crenarchaea dominated archaeal seafloor communities. No clear bathymetric trends were observed for archaeal abundances and the morphology of continental margin (slope vs. canyon) seems not to have a direct influence on archaeal relative abundances. The site-specific sediment habitat—both abiotic environmental setting and sedimentary organic matter quality—explain up to 65% of variance of archaeal, crenarchaeal and euryarchaeal relative abundance, suggesting a wide ecophysiological adaptation to deep-sea benthic ecosystems. The findings demonstrate that Archaea are an important component of benthic microbial assemblages so far neglected, and hence they lay the groundwork for more focused research on their ecological importance in the functioning of deep-sea benthic ecosystems.

Microbiota plays an essential role in fish growth and health and may be influenced by the changing environmental conditions. Here, we explored the microbiota of wild common sole, one of the most important fishery resources in the Mediterranean Sea, collected from different areas in the North Adriatic Sea. Our results show that the sole microbiota differs from that of the surrounding environment and among the different body sites (gill, skin and gut). Gut microbiota composition showed to be strongly related to fish age, rather than maturity, sex or sampling site. Age-related shifts in gut microbial communities were identified, with increased abundances of Bacteroidia and Desulfobacteria, unveiling potential microbial proxies for age estimation crucial for fisheries management. Our results expand the limited knowledge of the wild common sole microbiota, also in the light of the potential usefulness of the fish microbiota as a tool for future stock identification and connectivity studies.