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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.

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.

Ports are subject to a variety of anthropogenic impacts, and there is mounting evidence of faecal contamination through several routes. Yet, little is known about pollution in ports by faecal indicator bacteria (FIB). FIB spatio-temporal dynamics were assessed in 12 ports of the Adriatic Sea, a semi-enclosed basin under strong anthropogenic pressure, and their relationships with environmental variables were explored to gain insight into pollution sources. FIB were abundant in ports, often more so than in adjacent areas; their abundance patterns were related to salinity, oxygen, and nutrient levels. In addition, a molecular method, quantitative (q)PCR, was used to quantify FIB. qPCR enabled faster FIB determination and water quality monitoring that culture-based methods. These data provide robust baseline evidence of faecal contamination in ports and can be used to improve the management of routine port activities (dredging and ballast water exchange), having potential to spread pathogens in the sea.

The global scale of the biodiversity crisis has stimulated research into the relationship between biodiversity and ecosystem functioning (BEF). Even though the deep sea is the largest biome on Earth, BEF studies in deep-sea benthic ecosystems are scant. Moreover, the small number of recent studies, which mostly focus on meiobenthic nematodes, report conflicting results that range from a very clear positive relationship to none at all. In this BEF study, the deep-sea macrofauna were used as a model to investigate the structural and functional diversity of macrofauna assemblages at three depths (1,200, 1,900, and 3,000 m) in seven open-slope systems from the North-Eastern Atlantic Ocean to the Central-Eastern Mediterranean Sea. The presence and nature of BEF relationships were studied considering two spatial scales, the large and the basin scale, in different environmental settings. Total benthic biomass and macrofaunal predator biomass were used as proxies to assess ecosystem functioning. Ecosystem efficiency was expressed as macrofaunal biomass to biopolymeric carbon content ratio, macrofaunal biomass to prokaryotic biomass ratio, macrofaunal biomass to meiofaunal biomass ratio, and meiofaunal biomass to prokaryotic biomass ratio. On both large and basin spatial scales, some significant relationships between macrofaunal diversity and ecosystem functioning and efficiency were reported. When significant, the nature of BEF relations was positive and exponential or linear supporting the general idea that a higher diversity can enhance ecosystem functioning. Other BEF relationships were explained by the effect of environmental variables. More data from different deep-sea systems are needed, to better elucidate the consequences of biodiversity loss on the ocean floor.

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Bioindicators assess the mangroves ecological state according to the types of pressures but they differ with the ecosystem’s specificities. We investigated benthic meiofauna diversity and structure within the low human-impacted mangroves in French Guiana (South America) in response to sediment variables with various distances to the main city. Contaminant’s concentrations differed among the stations, but they remained below toxicity guidelines. Meiofauna structure (Foraminifera, Kinorhyncha, Nematoda) however varied accordingly. Nematode’s identification brought details on the sediment’s quality. The opportunistic genus Paraethmolaimus (Jensen, 1994) strongly correlated to the higher concentrations of Hg, Pb. Anoxic sediments were marked by organic enrichment in pesticides, PCB, and mangrove litter products and dominance of two tolerant genus, Terschellingia (de Man, 1888) and Spirinia (Gerlach, 1963). In each of these two stations, we found many Desmodora individuals (de Man, 1889) with the presence of epibionts highlighting the nematodes decreased fitness and defenses. Oxic sediments without contaminants were distinguished by the sensitive genera Pseudocella (Filipjev, 1927) and a higher diversity of trophic groups. Our results suggested a nematodes sensitivity to low contaminants concentrations. Further investigations at different spatio-temporal scales and levels of deterioration, would be necessary to use of this group as bioindicator of the mangroves’ ecological status.

Epibiosis is a common phenomenon in marine systems. In marine environments, ciliates are among the most common organisms adopting an epibiotic habitus and nematodes have been frequently reported as their basibionts. In the present study, we report several new records of peritrich and suctorian ciliates-nematode association worldwide: from a deep-sea pockmark field in the NW Madagascar margin (Indian Ocean), from a shallow vent area in the Gulf of Naples (Mediterranean, Tyrrhenian Sea), in a MPA area in the Gulf of Trieste (Mediterranean, Adriatic Sea), from a mangrove system in French Guiana (South America, Atlantic Ocean), and from the Maldivian Archipelago. In addition, three new species of Suctorea from the Secca delle Fumose shallow vent area (Gulf of Naples) were described: Loricophrya susannae n. sp., Thecacineta fumosae n. sp. and Acinetopsis lynni n. sp. In the light of these new records and data from the existing literature, we discuss the suctorian–nematode epibiosis relationship as a lever to biodiversity.