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The analysis of 879 ROV dives carried out along the Italian coasts on hard substrata at mesophotic and upper bathyal depths (40-775 m) allowed us to evaluate the current basin-scale presence, relative abundance, bathymetric limits, and habitat preferences of one of the most charismatic Mediterranean habitat-former anthozoan species, Corallium rubrum (Linnaeus, 1758). The species is widespread, and its occurrence ranged from 13% of the explored sites in Ionian Calabria to a hotspot of approximately 80% in Sardinia. Population relative densities were generally low (< 10 colonies m-2), except along the Sardinian coasts and in some areas along the Apulian coast. Almost no red coral colonies were observed between 60 m and 590 m in the nine explored offshore seamounts in the Ligurian and Tyrrhenian Seas. A distinctive coastal distribution discontinuity was found in the Ionian Sea. The optimum bathymetric distribution was between 75 m and 125 m, and no colonies were found below 247 m. Red coral colonies showed a preference for biogenic habitats dominated by crustose coralline algae (CCA) and vertical substrata. The species was absent on iron wrecks. Corallium rubrum disappeared from 14% of the historical fishing banks, while it was confirmed in 86% of them, some of which have been deeply harvested in the past. In particular, the still flourishing Sardinian populations could be supported by the high reproductive potential and favourable hydrodynamic conditions in the area.

12 pages, 3 figures, supplementary information https://doi.org/10.1038/s41559-019-1091-z.-- The dataset generated and analysed during the current study is available from the corresponding author on reasonable request, The deep sea (>200 m depth) encompasses >95% of the world’s ocean volume and represents the largest and least explored biome on Earth (, This work was supported by the H2020 project MERCES (GA N. 689518) and IDEM (GA N. 11.0661/2017/750680/SUB/EN V.C2.). E.R.-L. was supported by the Norwegian project MarMine (247626), the Norwegian Institute for Water Research and the H2020 project MERCES (GA N. 689518). P.V.R.S. was supported by the NSERC Canadian Healthy Oceans Network and CFREF Ocean Frontier Institute. L.T. is supported by JPI Oceans2 and ONC. J.A. is supported by ARIM (Autonomous Robotic sea-floor Infrastructure for bentho-pelagic Monitoring; MartTERA ERA-Net Cofound). L.L. acknowledges NSF grant OCE 1634172 and the Deep-Ocean Observing Strategy subcontract from the Consortium for Ocean Leadership. H.R. was supported by the EMSO-Link project of the European Commission (Grant agreement ID: 731036), With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)

Supplementary data to this article can be found online at https://doi. org/10.1016/j.scitotenv.2021.151783, Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring., The work is the result of the DNAqua-Net workshop held in Rome, on June 10–12, 2019, organised by IRSA-CNR and supported by European Cooperation in Science and Technology (COST) grant CA15219 (DNAqua-Net). It largely benefited from the discussions with DNAqua-Net members during this event as well as other DNAqua-Net conferences.This study was carried out within the UNIVPM VIRIDE Project (n. 2017EKFA98) funded by the Ministry of University and Research of Italy (MUR) and the Italian National Project on the use of environmental DNA for the identification of marine non-indigenous species funded by the Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA). JP, TC, and LAPG were supported by the Swiss National Science Foundation (grant 31003A_179125) as well as FL with an Early Postdoc.Mobility grant (P2GEP3_171829). MS-M was supported by the Ministry of Education, Youth and Sports of the Czech Republic, European Regional Development Fund-Project CZ.02.1.01/0.0/0.0/16_019/0000845 and LTC 20063. KP was supported by the European Regional Development Fund within National Programme for Addressing Socio-Economic Challenges through R&D (L190003VLVI RITA1/02-60-05) and base financed project P190250PKKH of Estonian University of Life Sciences, IM was supported by the Slovenian Research Agency (ARRS) programme P4-0085. SD was supported by the Portuguese Foundation for Science and Technology (FCT) (CEECIND/00667/2017). LC was supported by the PON AIM 1854833 – PON Ricerca e Innovazione 2014–2020 – Azione I.2 – D.D. n. 407, 27/02/2018 – Attraction and International Mobility.VK was supported by grants PUT1389 (ETAg) and Institute of Technology, University of Tartu basic funding grant.

Effectiveness of restocking programs in Marine Fully Protected Areas' (FPAs) can be highly affected by the movement behavior of the species to protect. We analyzed the data of 744 Palinurus elephas specimens tagged, relocated inside 12 FPAs, established in the seas surrounding Sardinia (central-western Mediterranean), and then recaptured. The overall aims were to characterize the individuals' movements after the relocation and to discuss strengths and weaknesses of the current FPAs' design. Almost 80% of tagged individuals travelled progressively increasing distances, as a function of the release distance, up to a maximum value of 11,500 m. Then, for larger release distances, individuals' mobility appeared reduced and more chaotic. A similar trend was found analyzing the distances travelled with respect to the FPAs with the highest number of recaptured individuals and to the size. These results allow to establish a threshold limit of the release distance, to take into account when designing FPAs, as a useful tool to keep a portion of the individuals into FPAs' borders, in order to both preserve the species and guarantee a spillover of individuals in the commercial areas.

26 pages, 8 figures, 2 tables, supporting information https://doi.org/10.1093/zoolinnean/zlab110.-- Data availability: Sequences and data on specimens are available on GenBank and Bold databases, as specified in the main text, The current shift of fishery efforts towards the deep sea is raising concern about the vulnerability of deep-water sharks, which are often poorly studied and characterized by problematic taxonomy. For instance, in the Mediterranean Sea the taxonomy of genus Centrophorus has not been clearly unravelled yet. Since proper identification of the species is fundamental for their correct assessment and management, this study aims at clarifying the taxonomy of this genus in the Mediterranean Basin through an integrated taxonomic approach. We analysed a total of 281 gulper sharks (Centrophorus spp.) collected from various Mediterranean, Atlantic and Indian Ocean waters. Molecular data obtained from cytochrome c oxidase subunit I (COI), 16S ribosomal RNA (16S), NADH dehydrogenase subunit 2 (ND2) and a portion of a nuclear 28S ribosomal DNA gene region (28S) have highlighted the presence of a unique mitochondrial clade in the Mediterranean Sea. The morphometric results confirmed these findings, supporting the presence of a unique and distinct morphological group comprising all Mediterranean individuals. The data strongly indicate the occurrence of a single Centrophorus species in the Mediterranean, ascribable to C. cf. uyato, and suggest the need for a revision of the systematics of the genus in the area, This research was partially funded by the University of Bologna through ‘RFO’ and ‘Canziani’ grants given to FT and AC and by the European Commission Directorate – General Fisheries in the framework of the MEDITS survey. RM and LC acknowledge the support for their research grants to funds granted by the Università degli Studi di Cagliari ‘UNICA-RICCAR_2013_CAU_02’ and Ministero dell’Università e della Ricerca ‘PON AIM 1854833 - PON Ricerca e Innovazione 2014-2020 – Azione I.2 - D.D. n. 407, 27/02/2018 – Attraction and International Mobility’, respectivel, With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)

Fully Protected Areas (FPAs) represent a powerful tool for marine resources management. Among the parameters to consider for their optimal design, the movements of the species to protect are of particular importance. We examined the movement patterns of744 spiny lobsters, Palinurus elephas, tagged during a restocking program carried out in 12 Sardinian FPAs. Once the lobsters were captured, tagged, transported and released in the center of the FPA, the linear distances performed by 80% of the lobsters from the recapture (RC) to the release point (RE), (recapture distance, RC-RE) increased as a function of the point in which they were captured for the first time (release distance, C-RE), until a maximum value of about 13500 m. By a management perspective, these results highlight a behaviour, perhaps attributable to homing, representing an important starting point to take into consideration when planning FPAs. In fact, since release and recapture distances appeared related, in order to preserve a portion of the lobsters within the FPA and to guarantee a spillover of specimens in the surrounding commercial areas, the longer is the release, the bigger would be the FPA.

The precious red coral, Corallium rubrum, and the yellow gorgonian, Eunicella cavolini, have been frequently reported as co-occurring species in the deep Mediterranean Sea. However, knowledge regarding spatial distribution of the two species in the deep sea is still fragmented, as well as potential drivers of their co-occurrence. This study aims to provide data on the status of deep-dwelling red coral populations, which are now the main target of commercial harvesting, study the demography of the yellow gorgonian in the deep sea, and finally analysing their variability when co-occur. Both species exhibited the highest population density at deeper depths and the presence of an inverse relationship between population density and colony height. We found a high percentage (40% on average) of red coral harvestable colonies (> 10 mm basal diameter), as well as of living colonies (77% as average). Our study evidenced that most of co-occurring colonies were found below 130 m depth. Red coral density did not significantly vary with the presence of E. cavolini, whereas the yellow gorgonian showed significant higher density when co-occur with red coral, even if with lower height. Distance-based linear modelling (DistLM) revealed that red coral density significantly influenced the presence of the yellow gorgonian, emphasizing the need for proper conservation strategies of red coral populations in order to preserve habitat complexity and associated diversity.

Marine animal forests are important mesophotic habitats threatened by an increasing number of natural and human pressures. Although several international agreements aim to protect these vulnerable ecosystems, the Environmental Status of most of these benthic animal-structured habitats remains unknown. Based on ROV footage, we evaluated the Environmental Status of 5 black corals forests in the center of the Western Mediterranean Sea, through the Mesophotic Assemblages Conservation Status (MACS) Index. The MACS index combines two independent indices: the Index of Status of the benthic communities, analyzing conspicuous species diversity, basal layer and canopy composition; the Index of Impact, analyzing siltation level, canopy condition and marine litter occurrence. The five investigated sites are characterized by the presence of two Antipatharians, Antipathella subpinnata and Leiopathes glaberrima, dwelling in different environmental conditions. Four sites showed high and good values of the Index of Status, and only one site showed a moderate status. Regarding the Impact Index, four sites were classified with low values, except one showed a very low value. Overall, four black forests were classified in a Good and one in a Very High Environmental Status. Assessing the Environmental Status is the first step needed to monitor these essential habitats’ health over time and improve the current frameworks for their conservation and protection, such as the Marine Strategy Framework Directive

Meiofaunal abundance, assemblage structure and richness of higher taxa were investigated for the first time in two submarine canyons (Polcevera and Bisagno) of the Ligurian Sea and along the adjacent open slope, in relation with the quantity and quality of sedimentary organic matter and other environmental variables, including grain size. Meiofaunal abundance and richness of higher taxa decreased with increasing water depth (from ca. 200 down to ca. 2000-m depth) in the open slope and Polcevera canyon, whereas the highest values were observed at 500 m depth in the Bisagno canyon. The comparison between canyons and the adjacent open slope, showed the lack of significant differences in meiofaunal abundance, at the same depth except for samples collected at 200 and 2000-m depth. Overall the biodiversity was higher in canyons than in the open slope. Phytopigments, utilised as a proxy of the input of primary organic matter, were up to 3 times higher in canyon than in slope sediments and, along with grain size, explained a large portion of the variability in all meiofaunal variables. Canyon and slope showed a high beta diversity (83%), mostly due to the presence of a high portion of rare taxa in the canyons. Some taxa, such as Cladocera, Cumacea, Gastrotricha, Nemertina were exclusively encountered in canyon sediments, whereas Tardigrada were encountered only in the adjacent slope. Results reported here indicated that, differences in meiofaunal assemblages between canyons and slopes are primarily driven by quantity and quality of the available food resources and by the presence of specific topographic features.

Living (Rose-Bengal stained) benthic foraminifera were investigated in eleven stations sampled along transects following a depth gradient from Polcevera and Bisagno canyons and the adjacent open slope (Ligurian Sea), in a depth interval ranging from 200 to 2000 m. In order to understand which environmental factors influence the abundance and taxonomical composition of the foraminiferal assemblages in these two domains (canyon and open slope), qualitative and quantitative foraminiferal data were correlated to the sediment biochemical composition (in terms of phytopigments, proteins, lipids, carbohydrates and biopolymeric carbon), grain size and the main hydrological characteristics (salinity, temperature, dissolved oxygen). The Cluster Analysis and Canonical Correspondence Analysis allowed us to detect two sectors (coastal and offshore) characterized by contrasting trophic conditions. The coastal sector reflects spread meso-eutrophic conditions in both physiographic domains being possibly more impacted by the river inputs and sediment transport processes from land. In fact, the narrow continental shelf of the Ligurian Sea favors the deposition of sediment transported by riverine processes on the immediately adjacent coastal areas. As a result homogenization of sea-bottom conditions occurs, leading to an unclear differentiation between open slope and canyon foraminiferal assemblages. Conversely, the offshore sector is less affected by physical disturbance due to the sedimentary flows decreasing in relation to the larger distance from the coastline. Consequently, the lower organic matter content and lower food quality (expressed in terms of contribution of the primary material to the biopolymeric carbon pool) lead to a more oligotrophic condition, which favors the development of peculiar assemblages dominated by Glomospira charoides, Ammolagena clavata and epifaunal taxa. The first finding ever of a warm tropical species (Amphistegina lessonii) in the Ligurian Sea sediments at 500-m depth can be considered the first evidence of upward expansion of tropical species to the Northern portion of the Mediterranean Sea, which is experiencing an evident water warming linked to the ongoing global climate change.

Habitat heterogeneity is a major structuring agent of benthic assemblages promoting high turnover in species composition and ultimately contributing to overall higher diversity. Submarine canyons, a pervasive feature of the continental margins worldwide, increase habitat heterogeneity at multiple spatial scales. In the present study, we test the hypothesis that different topographic structures or/and food sources controlling the abundance, biomass and biodiversity (using meiofauna and nematodes as a model study) in canyon systems. To do so, we compared different topographic structures: canyon edge, thalweg and axis, and the upper shelf and open slope in the Gulf of Gioia (Gioia and Petrace Canyons) and in the Gulf of Naples (Dohrn Canyon) (Tyrrhenian Sea) at different depths. Our results suggest that meiofaunal abundance and biomass are generally higher in the canyon thalwegs than in the canyon edge or adjacent open slopes at regional scale. This pattern is not always confirmed for biodiversity and when thalwegs are compared to different topographic structures within the Gioia Canyon system. In our study, the role of food quantity and quality is preeminent to explain the spatial distribution of meiofaunal variables among different topographic structures at 200-m while habitat heterogeneity become relevant at 500-m and within the Dohrn Canyon. In Gioia and Petrace Canyons we observed a high food availability is associated to specific topographic structures (thalwegs) that influenced the meiofaunal abundance and diversity distribution and nematode diversity and species composition. Each topographic structure shows a high number of exclusive species that contributes to a high species turnover and high overall biodiversity in all canyon systems. Changes in nematode composition determine also differences in the functional diversity (trophic guilds composition) and life strategy of the nematode assemblages. Our findings reveal that the presence of different topographic structures influences the spatial distribution of food quality and quantity that determine the presence of exclusive taxa and species enhancing both local and regional diversity.

International audience; Skates are characterised by conservative body morphology which hampers identification and leads to frequent taxonomic confusion and market mislabelling. Accurate specimen classification is crucial for reliable stock assessments and effective conservation plans, otherwise the risk of extinction could be unnoticed. The misclassification issue is evident for the genus Dipturus, distributed worldwide, from the continental shelf and slope to the deep sea. In this study, barcode cytochrome oxidase I gene (COI) sequences were used along with species delimitation and specimen assignment methods to improve taxonomy and zoogeography of species of conservation interest inhabiting the Atlantic Ocean and Mediterranean Sea. In this study, we provided new evidence of the occurence of D. nidarosiensis in the Central-Western Mediterranean Sea and the lack of Atlantic-Mediterranean genetic divergence. The Atlantic endangered species D. laevis and D. batis clustered together under the same molecular operational taxonomic unit (MOTU) with any delimitation methods used, while the assignment approach correctly discriminated specimens into the two species. These results provided evidence that the presence of the barcode gap is not an essential predictor of identification success, but the use of different approaches is crucially needed for specimen classification, especially when threshold-or tree-based methods result less powerful. The analyses also showed how different putative, vulnerable, species dwelling across SouthWestern Atlantic and SouthEastern Pacific are frequently misidentified in public sequence repositories. Our study emphasised the limits associated to public databases, highlighting the urgency to verify and implement the information deposited therein in order to guarantee accurate species identification and thus effective conservation measures for deep-sea skates.

Summary Whole-genome sequencing data were produced from a single flathead grey mullet female and assembled into a draft genome sequence, whereas publicly available sequence data were used to obtain a male draft sequence. Two pools, each consisting of 60 unrelated individuals, respectively, of male and female fish were analyzed using Pool-Sequencing. Mapping and analysis of Pool-Seq data against the draft genome(s) revealed >30 loci potentially associated with sex, the most promising locus of which, encoding the follicle-stimulating hormone receptor (fshr) and harboring two missense variants, was genotyped on 245 fish from four Mediterranean populations. Genotype data showed that fshr represents a previously unknown sex-determining locus, although the incomplete association pattern between fshr genotype and sex-phenotype, the variability of such pattern across different populations, and the presence of other candidate loci reveal that a greater complexity underlies sex determination in the flathead grey mullet., Graphical abstract, Highlights • Three SNPs with sex-specific allele frequencies found in the grey mullet fshr gene • Two missense variants at the fshr locus are significantly associated with male sex • fshr male genotypes show divergent distribution across geographical populations • Incomplete penetrance of fshr variants suggests that additional factors exist, Genetics; Evolutionary Biology; Genomics

2 pages.-- Reply to: Ecological variables for deep-ocean monitoring must include microbiota and meiofauna for effective conservation, J. Ingels et al. Nature Ecology & Evolution 5: 27-29 (2021), doi: 10.1038/s41559-020-01335-6, Meiofauna and microbes are key components of deep-sea ecosystem assessments and were included among the list of essential variables in our recent comprehensive assessment and prioritization of a global deep-ocean monitoring and conservation strategy1. Meiofauna ranked in the top three variables, whereas microbes (bacteria, and archaea) were reported as key variables for some aspects of monitoring the deep sea. However, larger components of the deep-sea fauna (such as macro- and megafauna) received the highest priority. In their Matters Arising, Ingels and co-workers2 criticized the ranking because, in their opinion, macro- and megafaunal components cannot be considered higher-priority variables than microbes and meiofauna. They concluded that this result reflects an unequal distribution of the competence of the authors and of the respondents to the elicitation survey. However, their criticisms are unjustified for conceptual, methodological and operational reasons. On semantic and theoretical grounds, Ingels et al. confused the concept of priority with that of relevance/importance. Ingels et al. seem also to confound the concept of monitoring and protecting with the importance of research for advancing scientific knowledge; these are two partly related, but distinct, objectives. Indeed, recognizing the ecological importance of one biological component is one thing, but identifying the monitoring variables where capacity to deliver for conservation management globally is well established, is quite another. We cannot apply the same monitoring and conservation approach to all biological components because small organisms, such as prokaryotes, protists and meiofauna encompass massive numbers of undescribed species with largely unknown ecologies3,4 and shorter turnover times, which may make them more resilient to disturbance than larger biota. Even an ocean completely depleted of large fauna, for example, sharks and all predators, would remain flush with meiofauna and microbes. Yet, a deep-sea system with abundant meiofauna and prokaryotes would almost certainly function poorly without higher trophic levels. This well-known ecological principle is certainly one of the reasons there was a wide consensus among the 112 experts (including the microbiologists and meiofauna experts who participated in the expert elicitation) on censusing larger species to protect vulnerable habitats they inhabit or create. The much more limited evidence for microbial and meiofaunal endemicity, the great proportion of unidentified species and the lack of life-history information, greatly compromise any proposal to use these components as proxies for monitoring and mapping conservation areas. Thus, the results of the expert elicitation, on the one hand, reflect the maturity of the disciplines and the capability to deliver indicator information and, on the other hand, recognize the role of larger organisms in current conservation priorities, while acknowledging fundamental roles of all groups., Another important aspect overlooked by Ingels et al. is that deep-sea biodiversity was only one of the five main research areas addressed by the study. In the second research area we considered, which was dedicated to ecosystem functions, benthic faunal biomass and benthic faunal production were ranked as top variables (see table 1 in Danovaro et al.1). Because meiofauna and microbes typically dominate benthic faunal biomass at abyssal depths5,6, we took care to emphasize the functional role of microbial components: “microbes (primarily bacteria followed by archaea) largely dominate overall biomass and production. These microscopic components, essential for deep-sea ecosystem functions … we stress microbial heterotrophic and chemoautotrophic C production as two essential ecological variables needed for understanding the key processes sustaining the functioning of deep-sea food webs and biogeochemical cycles”. We also strongly disagree with the methodological criticisms of Ingels et al. As scientists, we endeavour to remove all potential sources of bias in the framework of standard good practices for data evaluation. Our study is based on expert elicitation, which is a procedure to find consensus on priorities, not an experiment with treatments and controls; thus, standard deviations cannot be treated as in ecological experimental designs. Our Perspective describes how we endeavoured to achieve an objective methodology (that is, coverage of different research fields and knowledge for each of the five main themes, scientists covered a broad range of geographic regions, different taxonomic expertise, academic qualifications and years of experience). These aspects, including statistical treatment, were discussed in detail using multiple rounds of enquiries, following rigorous procedures7, and were presented transparently in the supplementary information of our paper1. To our knowledge, the 112 scientists participating in this elicitation make this study the widest deep-sea community ever to participate in defining priorities based on standardized questions. Ingels et al. assumed that microbial and meiofaunal components were not prioritized because most of the respondents were macrofaunal or megafaunal experts. However, this is not evident in our data, because a large fraction of respondents covered multiple fields of expertise (note that the supplementary information1 reported only one main topic per scientist). Their criticism suggests that deep-sea scientists are divided into two groups: micro- meiofaunal experts competing against macro- megafaunal experts, fighting to prioritize their own work, rather than a community working together towards a common objective. Obtaining expert opinions for comprehensive deep-sea management, as we did, requires the involvement of scientists working in different sectors (such as deep-sea technologies, conservation biology, biological oceanography, biogeochemistry, policy and management), thus participants cannot simply be classified as experts by faunal size category. The fact that many scientists, in responding to the questionnaire, did not automatically prioritize their own research specialty for deep-ocean monitoring, conservation and impact assessment suggests that this is a false and non-productive dichotomy. Accordingly, we reaffirm that the expert elicitation reported in Danovaro et al.1 is robust, accurate and balanced, and simply reflects the prioritization of the groups of organisms/habitats and associated variables to monitor in light of anthropogenic impacts, conservation needs and currently available technology, feasibility and knowledge. In operational terms, environmental monitoring, especially in the deep sea, requires ready-to-use technologies and methods that are employable, which greatly influences the choice of monitoring priorities and rankings of the consulted experts. Our paper innovatively coupled this need with the readiness levels of the described technologies. We agree that the scientific community should do more to document the importance of small organisms, to establish and disseminate the best standardized practices for collecting such observations and to increase our knowledge of undescribed species and their ecological roles to use them more effectively in future monitoring plans, particularly in light of the ongoing effects of global change8,9,10. At the same time, no marine protected area (in both shallow waters and in the open ocean) or other conservation initiative anywhere targets the loss of meiofaunal or microbial diversity. The reference to the Marine Strategy Framework Directive (MSFD 2008/56/EC), designed to address the Good Environmental Status of marine ecosystems (including the deep sea), does not support the position of Ingels et al.2 as the analysis of deep-sea biodiversity in the MSFD is, at present, limited to species of commercial interest and deep-water corals. None of the European directives prioritize meiofauna or microbes. Moreover, to the best of our knowledge, there is no single ongoing, nor planned, monitoring strategy of a national agency based on or prioritizing microbial or meiofaunal diversity in their standard protocols. Given the current limitation in the use of high-throughput sequencing (for example, for the identification of meiofauna3), further efforts are thus necessary to better integrate microbes and meiofauna in future monitoring and conservation programmes. To do this, the global deep-sea community must encourage joint efforts, share common goals and use standardized tools, This work was supported by the H2020 projects MERCES (Grant agreement no. 689518), and IDEM (Grant agreement no. 11.0661/2017/750680/SUB/EN V.C2.), by the Norwegian Institute for Water Research, by the NSERC Canadian Healthy Oceans Network and CFREF Ocean Frontier Institute, by JPI Oceans2 and ONC, by ARIM (MartTERA ERA-Net Cofound), by NSF grant OCE 1634172, by DOOS from the Consortium for Ocean Leadership, by the EMSO-Link EU project (Grant agreement ID: 731036) and by the Faculty of Science RAE Improvement Fund of The University of Hong Kong, With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)

The white skate Rostroraja alba is assessed by the International Union for Conservation of Nature as Endangered globally and is now considered rare in the Mediterranean. This species has never been recorded in Sardinian seas (central western Mediterranean), but an empty eggcase was collected on a sandy bottom off the western Sardinia coasts during the MEDiterranean International Trawl Survey (MEDITS) program in 2019. A morphometric and morphological description of the Sardinian eggcase, after a comparison with measurements from other Mediterranean and Atlantic specimens, showed it to be clearly ascribable to Rostroraja alba.

The Marine Strategy Framework Directive (MSFD), introduced in June 2008, was adopted to achieve a Good Environmental Status (GES) in the EU's marine waters and to protect resources of socio-economic interest. The MSFD exerts to the marine area over which a Member State exercises jurisdictional rights in accordance with the United Nations Convention on the Law of the Sea (UNCLOS), including the deep-sea waters, seafloor and sub-seafloor of the Exclusive Economic Zones (EEZ). However, currently the MSFD focuses on coastal habitats and the shallow-water seafloor to the detriment of the deeper habitats. Despite the huge dimension of the deep sea (below 200 m of depth) covering more than 65% of the Earth's surface and including >95% of the global biosphere, the relevance of the dark portion of the seas and oceans is still almost completely neglected. Given the important bi-directional links between shallow and deep ecosystems, there is a clear need for extending the implementation of the MSFD into the deep sea, to define a sound ecosystem-based approach for the management and protection of deep-sea ecosystems and attain GES. We assembled data on drivers, anthropogenic pressures and impacts concerning the MSFD descriptors pertaining to the Mediterranean deep sea. We list deep-sea monitoring activities and the main sources providing benchmark conditions, and discuss knowledge and geographic coverage gaps. MSFD descriptors apply to the deep sea as to coastal waters, and ought to be monitored contemporaneously. We provide recommendations for guidelines for future deep-sea monitoring in the Mediterranean Sea., This study has been supported by the DG ENV project IDEM (Implementation of the MSFD to the Deep Mediterranean Sea; contract EU No 11.0661/2017/750680/SUB/EN V.C2). MC and AS-V from University of Barcelona acknowledge support from the Spanish government through Red BAMAR (ref.: CGL2016-81854-REDT), a network on marine litter, and RTD projects NUREIEV (ref. CTM2013-44598-R) and NUREIEVA (ref. CTM2016-75953-C2-1-R) on far-field and near-field impacts of the Portman Bay, SE Spain, coastal submarine mine tailings disposal site. Generalitat de Catalunya autonomous government funding to CRG Marine Geosciences (ref. 2017 SGR 315) within its support scheme to excellence research groups is equally acknowledged.

Mangroves are amongst the most productive marine ecosystems on Earth, providing a unique habitat opportunity for many species and key goods and services for human beings. Mangrove habitats are regressing at an alarming rate, due to direct anthropogenic impacts and global change. Here, in order to assess the effects of mangrove habitat degradation on benthic biodiversity and ecosystem functioning, we investigated meiofaunal biodiversity (as proxy of benthic biodiversity), benthic biomass and prokaryotic heterotrophic production (as proxies of ecosystem functioning) and trophic state in a disturbed and an undisturbed mangrove forests. We report here that disturbed mangrove area showed a loss of 20% of benthic biodiversity, with the local extinction of four Phyla (Cladocera, Kynorincha, Priapulida, Tanaidacea), a loss of 80% of microbial-mediated decomposition rates, of the benthic biomass and of the trophic resources. The results of this study strengthen the need to preserve mangrove forests and to restore those degraded to guarantee the provision of goods and services needed to support the biodiversity and functioning of wide portions of tropical ecosystems.

International audience; In a world of declining biodiversity, monitoring is becoming crucial. Molecular methods , such as metabarcoding, have the potential to rapidly expand our knowledge of biodiversity, supporting assessment, management, and conservation. In the marine environment, where hard substrata are more difficult to access than soft bottoms for quantitative ecological studies, Artificial Substrate Units (ASUs) allow for standardized sampling. We deployed ASUs within five regional seas (Baltic Sea, Northeast Atlantic Ocean, Mediterranean Sea, Black Sea, and Red Sea) for 12-26 months to measure the diversity and community composition of macroinvertebrates. We identified invertebrates using a traditional approach based on morphological characters, and by metabarcoding of the mitochondrial cytochrome oxidase I (COI) gene. We compared community composition and diversity metrics obtained using the two methods. Diversity was significantly correlated between data types. Metabarcoding of ASUs allowed for robust comparisons of community composition and diversity, but not all groups were successfully sequenced. All locations were significantly different in taxonomic composition as measured with both kinds of data. We recovered previously known regional biogeographical patterns in both datasets (e.g., low species diversity in the Black and Baltic Seas, affinity between the Bay of Biscay and the Mediterranean). We conclude that the two approaches provide complementary information and that metabarcoding shows great promise for marine monitoring. However, until its pitfalls are addressed, the use of metabarcoding in monitoring of rocky benthic assemblages should be used in addition to classical approaches rather than instead of them.

Breakwaters are man-made constructions utilized for preventing coastal erosion primarily from wave action. At the same time, defence structures, modifying currents and circulation can affect water quality and benthic assemblages. Assessing and minimizing the impact of these structures is a priority in human-modified coastal ecosystems, such as the central northern Adriatic where breakwaters extend for hundreds of kilometres. We investigated the effects of breakwater relocation on benthic features and meiofaunal diversity. To do this, we conducted a before–after comparison of (2011–2017) the relocation, which occurred in 2015. The analysis was conducted comparing a sheltered site, characterized by the presence of seagrass meadows and a wave-exposed site. Sediment features and meiofaunal variables were altered by the relocation, especially in the areas colonized by seagrass meadows. Results presented here pointed out to an enrichment in organic matter, the loss of two sensitive taxa (Cumacea and Ostracoda) and a shift in the assemblage structure with the increase of the relevance of Copepoda and Polychaeta. These results indicate that the careful management of breakwater is crucial for planning adequate conservation practices and protecting seagrass habitats and their biodiversity.

The cumulative impact of microplastic and organic enrichment is still largely unknown. Here, we investigated the microplastic contamination, the organic enrichment and their effects on meiofaunal distribution and diversity in two islands of the Maldivian archipelago: one more pristine, and another strongly anthropized. Field studies were coupled with manipulative experiments in which microplastic polymers were added to sediments from the non-anthropized island (i.e., without organic enrichment) to assess the relative effect of microplastic pollution on meiofauna assemblages. Our results reveal that the impact of microplastic contamination on meiofaunal abundance and taxa richness was more significant in the anthropized island, which was also characterized by a significant organic enrichment. Meiofauna exposed experimentally to microplastic contamination showed: i) the increased abundance of opportunistic nematodes and copepods and ii) a shift in the trophic structure, increasing relevance in epistrate-feeder nematodes. Based on all these results, we argue that the coexistence of chronic organic enrichment and microplastics can significantly increase the ecological impacts on meiofaunal assemblages. Since microplastic pollution in the oceans is predicted to increase in the next decades, its negative effects on benthic biodiversity and functioning of tropical ecosystems are expected to worsen especially when coupled with human-induced eutrophication. Urgent actions and management plans are needed to avoid the cumulative impact of microplastic and organic enrichment.

Marine litter is an ever-increasing problem that demands immediate reduction plans and mitigation actions that should act synergically to efficiently meet ambitious goals. Since the seafloor has been recognized as the major sink for marine debris, the study of litter accumulation dynamics represent a fundamental tool to evaluate possible removal actions. We analysed a 7 years (2013–2019) standardized data series collected along Sardinian fishing grounds through MEDiterranean International Trawl Survey, for which estimates of density and weight of seafloor macro-litter were calculated for over 707 hauls. Results show the absence of any temporal trend in seafloor macro-litter density and weight, but rather indicate a spatial and bathymetric segregation of different litter categories. Our data showed how different sources and physical features of macro-litter items (i.e., plastic and fishing gear, rubber, glass, metals, and cloth) led to spatially segregated accumulation hotspots. We also point out here how the identification of seafloor macro-litter hotspots using aggregated data that include plastic items could obscure the identification of other segregated but yet relevant hotspots of other macro-litter categories accumulated in the marine environment. These hotspots often occurred at shallower depths and closer to coastlines, thus representing potential spots where eventual future litter removal action could be prioritized.

Active restoration is considered a profitable strategy to return ecosystems to their predisturbance state, in a reasonable time frame. However, ecological restoration of marine ecosystems is still in its infancy if compared to the terrestrial context. A review of 498 studies published in the last 25 years was carried out within the MERCES H2020 EU project to understand the effects of marine restoration actions across coastal habitats at global scale. Here, an overview focused on the Mediterranean Sea was carried out to identify both contextual and methodological determinants of restoration success in the basin. Results show that restoration efforts across habitats are increasing, especially in seagrasses and saltmarshes, but never approached at ecosystem level. Targets, methods, response variables and standards are still very heterogeneous. Short project duration (one-two years), small restoration areas (< 1 ha), lack of controls and knowledge of baselines are still a limit for deriving generalities. Finally, restorations rarely consider future challenges linked to global change, thus impairing long- term success stories. Marine restoration is a promising approach to counteract habitat loss in coastal areas. However, restoration science needs more robust approaches leading to the development of best practices (e.g. protocols, monitoring of the effects, reasons for failure) to be applied at spatial and temporal scales so as to answer to present and future disturbance regimes.

1. Vegetated marine and freshwater habitats are being increasingly lost around the world. Habitat restoration is a critical step for conserving these valuable habitats, but new approaches are needed to increase restoration success and ensure their survival. 2. We investigated interactions between plants and bivalves through a review and analysis of 491 studies, determined the effects, mechanisms and key environmental variables involved in and driving positive and negative interactions, and produced guidelines for integrating positive interactions into restoration efforts in different habitats. 3. Fifty per cent of all interactions (both correlative and experimental studies) were positive. These were predominant between epifaunal bivalves and plants in all habitats, and between infaunal bivalves and plants in subtidal habitats. Plants primarily promoted bivalve survival and abundance by providing substrate and shelter, while bivalves promoted plant growth and survival by stabilizing and fertilizing the sediment, and reducing water turbidity. The prevalence of positive interactions increased with water temperature in subtidal habitats, but decreased with water temperature in intertidal habitats. The subset of studies conducted in a restoration context also showed mostly positive interactions. 4. Twenty‐five per cent of all interactions were negative, and these were predominant between plants and infaunal bivalves in intertidal habitats, except sulphide‐metabolizing bivalves, which facilitated plant survival. Interactions involving non‐native species were also mostly negative. 5. Synthesis and applications. Promoting facilitative interactions through plant–bivalve co‐restoration can increase restoration success. The prevalence of positive interactions depends on habitat and environmental conditions such as temperature, and was especially important in subtidal habitats (involving both infaunal and epifaunal bivalves) and in intertidal habitats (involving only epifaunal bivalves). Thus sites and species for co‐restoration must be carefully chosen to maximize the chances of success. If done properly, co‐restoration could increase initial survival, persistence and resilience of foundation species, and promote the recovery of associated biodiversity and ecosystem services.

International audience; Autonomous Reef Monitoring Structures (ARMS) have been applied worldwide to characterize the critical yet frequently overlooked biodiversity patterns of marine benthic organisms. In order to disentangle the relevance of environmental factors in benthic patterns, here, through standardized metabarcoding protocols, we analyze sessile and mobile (

Whole-genome sequence data were produced from a single flathead grey mullet female and assembled into a draft genome sequence, whereas publicly available sequence data were used to obtain a male draft sequence. Two pools, each consisting of 60 unrelated individuals respectively of male and female fish were analysed using Pool-Sequencing. Mapping and analysis of Pool-Seq data against the draft genome(s) revealed >30 loci potentially associated with sex. The most promising of these loci encoding the follicle stimulating hormone receptor (FSHR) and harbouring two missense variants, was genotyped on 245 fish from four Mediterranean populations. Genotype data showed that FSHR represents a previously unknown sex-determining locus. However, the incomplete association pattern between FSHR genotype and sex-phenotype, the variability of such pattern across different natural populations and the presence of other candidate loci suggest a greater complexity underling sex determination in the flathead grey mullet.

Seafloor macrolitter is ubiquitous in world's oceans; still, huge knowledge gaps exist on its interactions with benthic biota. We report here the colonization of plastic substrates by the Mediterranean red coral Corallium rubrum (L. 1758), occurring both in controlled conditions and in the wild at ca. 85 m depth in the Western Mediterranean Sea. Juveniles settled on seafloor macro-litter, with either arborescent or encrusting morphology, ranging from 0.6 to 3.5 mm in basal diameter and 0.2–7.1 years of age, also including a fraction (20%) of potentially sexually mature individuals. In controlled conditions, larvae settled and survived on plastic substrates for >60 days. Our insights show that marine plastic debris can provide favourable substrate for C. rubrum settlement either in controlled conditions or in the wild, suggesting their possible use in restoration activities. However, we pinpoint here that this potential benefit could result in adverse effects on population dynamics.

Carbon dioxide capture and storage (CCS), involving the injection of CO2 into the sub-seabed, is being promoted worldwide as a feasible option for reducing the anthropogenic CO2 emissions into the atmosphere. However, the effects on the marine ecosystems of potential CO2 leakages originating from these storage sites have only recently received scientific attention, and little information is available on the possible impacts of the resulting CO2-enriched seawater plumes on the surrounding benthic ecosystem. In the present study, we conducted a 20-weeks mesocosm experiment exposing coastal sediments to CO2-enriched seawater (at 5000 or 20,000 ppm), to test the effects on the microbial enzymatic activities responsible for the decomposition and turnover of the sedimentary organic matter in surface sediments down to 15 cm depth. Our results indicate that the exposure to high-CO2 concentrations reduced significantly the enzymatic activities in the top 5 cm of sediments, but had no effects on subsurface sediment horizons (from 5 to 15 cm depth). In the surface sediments, both 5000 and 20,000 ppm CO2 treatments determined a progressive decrease over time in the protein degradation (up to 80%). Conversely, the degradation rates of carbohydrates and organic phosphorous remained unaltered in the first 2 weeks, but decreased significantly (up to 50%) in the longer term when exposed at 20,000 ppm of CO2. Such effects were associated with a significant change in the composition of the biopolymeric carbon (due to the accumulation of proteins over time in sediments exposed to high-pCO2 treatments), and a significant decrease (∼20–50% at 5000 and 20,000 ppm respectively) in nitrogen regeneration. We conclude that in areas immediately surrounding an active and long-lasting leak of CO2 from CCS reservoirs, organic matter cycling would be significantly impacted in the surface sediment layers. The evidence of negligible impacts on the deeper sediments should be considered with caution and further investigated simulating the intrusion of CO2 from a subsurface source, as occurring during real CO2 leakages from CCS sites.

This paper investigated the long-term changes (from 1973 to 2013) of the seagrass meadows of Zostera marina, Zostera noltei and Cymodocea nodosa in the Adriatic Sea subjected to multiple pressures. We examined the changes of the meadows by means of field data collection, observations and analysis of aerial photography to identify the most important drivers of habitat loss. The major decline of seagrass extension observed from 1973 to 1989, was primarily driven by urban development, and by the increase of the blue tourism. From 1989 to 2007 seagrass habitats progressively recovered due to the decrease of urbanization, but from 2007 to 2013 a further significant loss of seagrass meadows was apparently driven by thermal anomalies coupled with an increasing anthropogenic pressure. Our long-term analysis provides evidence that the rates of seagrass loss are faster than the recovery rates (i.e., -4.5 loss rate vs +2.5% recovery rate per year).

International audience; We investigated the validity of Autonomous Reef Monitoring Structures (ARMS) as monitoring tools for hard bottoms across a wide geographic and environmental range. We deployed 36 ARMS in the northeast Atlantic, northwest Mediterranean, Adriatic and Red Sea at 7–17 m depth. After 12–16 months, community composition was inferred from photographs, in six plate-faces for each ARMS. Overall, we found a highly significant effect of sea region, site (within seas), and plate-face on community composition. Plate-faces thus represent distinct micro-habitats and provide pseudo-replicates, increasing statistical power. Within each sea region taken individually, there was also a highly significant effect of site and plate-face. Because strong effects were obtained despite the fusion of taxonomic categories at high taxonomic ranks (to ensure comparability among biogeographic provinces), ARMS photo-analysis appears a promising monitoring tool for each sea region. We recommend keeping three ARMS per site and analyzing more numerous sites within a sea region to investigate environmental effects.

Active restoration is considered a profitable strategy to return ecosystems to their predisturbance state, in a reasonable time frame. However, ecological restoration of marine ecosystems is still in its infancy if compared to the terrestrial context. A review of 498 studies published in the last 25 years was carried out within the MERCES H2020 EU project to understand the effects of marine restoration actions across coastal habitats at global scale. Here, an overview focused on the Mediterranean Sea was carried out to identify both contextual and methodological determinants of restoration success in the basin. Results show that restoration efforts across habitats are increasing, especially in seagrasses and saltmarshes, but never approached at ecosystem level. Targets, methods, response variables and standards are still very heterogeneous. Short project duration (one-two years), small restoration areas (< 1 ha), lack of controls and knowledge of baselines are still a limit for deriving generalities. Finally, restorations rarely consider future challenges linked to global change, thus impairing long- term success stories. Marine restoration is a promising approach to counteract habitat loss in coastal areas. However, restoration science needs more robust approaches leading to the development of best practices (e.g. protocols, monitoring of the effects, reasons for failure) to be applied at spatial and temporal scales so as to answer to present and future disturbance regimes.

Breakwaters are man-made constructions utilized for preventing coastal erosion primarily from wave action. At the same time, defence structures, modifying currents and circulation can afect water quality and benthic assemblages. Assessing and minimizing the impact of these structures is a priority in human-modifed coastal ecosystems, such as the central northern Adriatic where breakwaters extend for hundreds of kilometres. We investigated the efects of breakwater relocation on benthic features and meiofaunal diversity. To do this, we conducted a before–after comparison of (2011–2017) the relocation, which occurred in 2015. The analysis was conducted comparing a sheltered site, characterized by the presence of seagrass meadows and a wave-exposed site. Sediment features and meiofaunal variables were altered by the relocation, especially in the areas colonized by seagrass meadows. Results presented here pointed out to an enrichment in organic matter, the loss of two sensitive taxa (Cumacea and Ostracoda) and a shift in the assemblage structure with the increase of the relevance of Copepoda and Polychaeta. These results indicate that the careful management of breakwater is crucial for planning adequate conservation practices and protecting seagrass habitats and their biodiversity.

We investigated organic matter (OM) quantity, nutritional quality and degradation rates, as well as abundance and biodiversity of meiofauna and nematodes along the deep continental margin off Spitsbergen, in the Svalbard Archipelago. Sediment samples were collected in July 2010 and 2011 along a bathymetric gradient between 600 m and 2000 m depth, and total mass flux measured at the same depths from July 2010 to July 2011. In both sampling periods sedimentary OM contents and C degradation rates increased significantly with water depth, whereas OM nutritional quality was generally higher at shallower depths, with the unique exception at 600 m depth in 2010. Meiofaunal abundance and biomass (largely dominated by nematodes) showed the highest values at intermediate depths (ca 1500 m) in both sampling periods. The richness of meiofaunal higher taxa and nematode species richness did not vary significantly with water depth in both sampling periods. We suggest here that patterns in OM quantity, C degradation rates, and meiofauna community composition in 2011 were likely influenced by the intensification of the warm West Spitsbergen Current (WSC). We hypothesize that the intensity of the WSC inflow to the Arctic Ocean could have an important role on benthic biodiversity and functioning of deep-sea Arctic ecosystems.

4th World Conference on Marine Biodiversity (WCMB 2018), 13-16 May 2018, Montreal, A review of 573 studies on active restoration actions in the marine environment, published in the last 25 years, was carried out at global scale. We assessed how, where, at which spatial and temporal scales and under which socio-ecological settings restoration studies have been carried out, from very shallow to deep sea habitats. Results show that restoration efforts across habitats are increasing, especially in seagrasses and coral reefs, but never approached at ecosystem level. Targets, methods, response variables and standards are still very heterogeneous. Of the factors considered in the review, habitat, human impact intensity, realm and methods of restoration were found to be good determinant of restoration success. Short project duration (one-two years), small restoration areas (< 1 ha), lack of controls and knowledge of baselines are still a limit for deriving generalities. Finally, restorations rarely consider future challenges linked to global change this impairing long-term success stories. Restoration science needs more robust approaches leading to the development of best practices (e.g. protocols, monitoring of the effects, reasons for failure) to be applied at spatial and temporal scales so as to answer to present and future disturbance regimes. Marine restoration is a promising approach to limit habitat loss. More science is needed to increase the number of success stories

Beach nourishment is a widely utilized solution to counteract the erosion of shorelines, and there is an active discussion on its possible consequences on coastal marine assemblages. We investigated the impact caused by a small-scale beach nourishment carried out in the Western Adriatic Sea on macrofaunal recruitment and post-settlement events. Artificial substrates were deployed in proximity of nourished and non-manipulated beaches and turbidity and sedimentation rates were measured. Our results indicate that sedimentation rates in the impacted site showed a different temporal change compared to the control sites, suggesting potential modifications due to the beach nourishment. The impact site was characterized by subtle changes in terms of polychaete abundance and community structure when compared to controls, possibly due to beach nourishment, although the role of other factors cannot be ruled out. We conclude that small-scale beach nourishments appear to be an eco-sustainable approach to contrast coastal erosion.