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Despite being an abundant group of significant ecological importance the phylogenetic relationships of the Octocorallia remain poorly understood and very much understudied. We used 1132 bp of two mitochondrial protein-coding genes, nad2 and mtMutS (previously referred to as msh1), to construct a phylogeny for 161 octocoral specimens from the Atlantic, including both Isididae and non-Isididae species. We found that four clades were supported using a concatenated alignment. Two of these (A and B) were in general agreement with the of Holaxonia–Alcyoniina and Anthomastus–Corallium clades identified by previous work. The third and fourth clades represent a split of the Calcaxonia–Pennatulacea clade resulting in a clade containing the Pennatulacea and a small number of Isididae specimens and a second clade containing the remaining Calcaxonia. When individual genes were considered nad2 largely agreed with previous work with MtMutS also producing a fourth clade corresponding to a split of Isididae species from the Calcaxonia–Pennatulacea clade. It is expected these difference are a consequence of the inclusion of Isisdae species that have undergone a gene inversion in the mtMutS gene causing their separation in the MtMutS only tree. The fourth clade in the concatenated tree is also suspected to be a result of this gene inversion, as there were very few Isidiae species included in previous work tree and thus this separation would not be clearly resolved. A~larger phylogeny including both Isididae and non Isididae species is required to further resolve these clades.

The present study provides new knowledge about the so far largely unexplored Coral Patch seamount which is located in the NE Atlantic Ocean half-way between the Iberian Peninsula and Madeira. For the first time a detailed hydroacoustic mapping (MBES) in conjunction with video surveys (ROV, camera sled) were performed to describe the sedimentological and biological characteristics of this sub-elliptical ENE-WSW elongated seamount. Video observations were restricted to the southwestern summit area of Coral Patch seamount (water depth: 560–760 m) and revealed that this part of the summit is dominated by exposed hard substrate, whereas soft sediment is just a minor substrate component. Although exposed hardgrounds are dominant for this summit area and, thus, offer suitable habitat for settlement by benthic organisms, the benthic megafauna shows rather scarce occurrence. In particular, scleractinian framework-building cold-water corals are apparently rare with very few isolated and small-sized live occurrences of the species Lophelia pertusa and Madrepora oculata. In contrast, dead coral framework and coral rubble are more frequent pointing to a higher abundance of cold-water corals on Coral Patch during the recent past. This is even supported by the observation of fishing lines that got entangled with rather fresh-looking coral frameworks. Overall, long lines and various species of commercially important fish were frequently observed emphasising the potential of Coral Patch as an important target for fisheries that may have impacted the entire benthic community. Hydroacoustic seabed classification covered the entire summit of Coral Patch and its northern and southern flanks (water depth: 560–2660 m) and revealed extended areas dominated by mixed and soft sediments at the northern flank and to a minor degree at its easternmost summit and southern flank. Nevertheless, these data also predict most of the summit area to be dominated by exposed bedrock which would offer suitable habitat for benthic organisms. By comparing the locally restricted video observations and the broad-scale monitoring of a much larger and deeper seafloor area as derived by hydroacoustic seabed classification, it becomes obvious that habitat information obtained by in situ sampling may provide a rather scattered pattern about the entire seamount ecosystem. Solely with a combination of both methods, a satisfactory approach to describe the diverse characteristics of a seamount ecosystem can be derived which is in turn indispensable for future scientific monitoring campaigns as well as management and conservation purposes.

Changes in marine net primary productivity (PP) and export of particulate organic carbon (EP) are projected over the 21st century with four global coupled carbon cycle-climate models. These include representations of marine ecosystems and the carbon cycle of different structure and complexity. All four models show a decrease in global mean PP and EP between 2 and 20% by 2100 relative to preindustrial conditions, for the SRES A2 emission scenario. Two different regimes for productivity changes are consistently identified in all models. The first chain of mechanisms is dominant in the low- and mid-latitude ocean and in the North Atlantic: reduced input of macro-nutrients into the euphotic zone related to enhanced stratification, reduced mixed layer depth, and slowed circulation causes a decrease in macro-nutrient concentrations and in PP and EP. The second regime is projected for parts of the Southern Ocean: an alleviation of light and/or temperature limitation leads to an increase in PP and EP as productivity is fueled by a sustained nutrient input. A region of disagreement among the models is the Arctic, where three models project an increase in PP while one model projects a decrease. Projected changes in seasonal and interannual variability are modest in most regions. Regional model skill metrics are proposed to generate multi-model mean fields that show an improved skill in representing observation-based estimates compared to a simple multi-model average. Model results are compared to recent productivity projections with three different algorithms, usually applied to infer net primary production from satellite observations.

The Black Sea northwestern shelf (NWS) is a shallow eutrophic area in which the seasonal stratification of the water column isolates the bottom waters from the atmosphere. This prevents ventilation from counterbalancing the large consumption of oxygen due to respiration in the bottom waters and in the sediments, and sets the stage for the development of seasonal hypoxia. A three-dimensional (3-D) coupled physical–biogeochemical model is used to investigate the dynamics of bottom hypoxia in the Black Sea NWS, first at seasonal and then at interannual scales (1981–2009), and to differentiate its driving factors (climatic versus eutrophication). Model skills are evaluated by a quantitative comparison of the model results to 14 123 in situ oxygen measurements available in the NOAA World Ocean and the Black Sea Commission databases, using different error metrics. This validation exercise shows that the model is able to represent the seasonal and interannual variability of the oxygen concentration and of the occurrence of hypoxia, as well as the spatial distribution of oxygen-depleted waters. During the period 1981–2009, each year exhibits seasonal bottom hypoxia at the end of summer. This phenomenon essentially covers the northern part of the NWS – which receives large inputs of nutrients from the Danube, Dniester and Dnieper rivers – and extends, during the years of severe hypoxia, towards the Romanian bay of Constanta. An index H which merges the aspects of the spatial and temporal extension of the hypoxic event is proposed to quantify, for each year, the intensity of hypoxia as an environmental stressor. In order to explain the interannual variability of H and to disentangle its drivers, we analyze the long time series of model results by means of a stepwise multiple linear regression. This statistical model gives a general relationship that links the intensity of hypoxia to eutrophication and climate-related variables. A total of 82% of the interannual variability of H is explained by the combination of four predictors: the annual riverine nitrate load (N), the sea surface temperature in the month preceding stratification (Ts), the amount of semi-labile organic matter accumulated in the sediments (C) and the sea surface temperature during late summer (Tf). Partial regression indicates that the climatic impact on hypoxia is almost as important as that of eutrophication. Accumulation of organic matter in the sediments introduces an important inertia in the recovery process after eutrophication, with a typical timescale of 9.3 yr. Seasonal fluctuations and the heterogeneous spatial distribution complicate the monitoring of bottom hypoxia, leading to contradictory conclusions when the interpretation is done from different sets of data. In particular, it appears that the recovery reported in the literature after 1995 was overestimated due to the use of observations concentrated in areas and months not typically affected by hypoxia. This stresses the urgent need for a dedicated monitoring effort in the Black Sea NWS focused on the areas and months concerned by recurrent hypoxic events.

Submarine canyons have often been identified as hotspots of secondary production with the potential to house distinct faunal assemblages and idiosyncratic ecosystems. Within these deep-sea habitats, assemblages of scavenging fauna play a vital role in reintroducing organic matter from large food falls into the wider deep-sea food chain. Free-fall baited traps were set at different depths within three submarine canyons on the Iberian Margin. Amphipods from the traps were identified to species level and counted. Scavenging amphipod assemblages were compared at different depths within each canyon and between individual canyon systems. Using data from literature, abyssal plain assemblages were compared to submarine canyon assemblages. Samples from canyons were found to contain common abyssal plain species but in greater than expected abundances. It is proposed that this is a result of the high organic carbon input into canyon systems owing to their interception of sediment from the continental shelf and input from associated estuarine systems. Community composition differed significantly between the submarine canyons and abyssal plains. The cause of this difference cannot be attributed to one environmental variable due to the numerous inherent differences between canyons and abyssal plains.

In this paper we provide an overview of new knowledge on oxygen depletion (hypoxia) and related phenomena in aquatic systems resulting from the EU-FP7 project HYPOX ("In situ monitoring of oxygen depletion in hypoxic ecosystems of coastal and open seas, and landlocked water bodies", http://www.hypox.net). In view of the anticipated oxygen loss in aquatic systems due to eutrophication and climate change, HYPOX was set up to improve capacities to monitor hypoxia as well as to understand its causes and consequences. Temporal dynamics and spatial patterns of hypoxia were analyzed in field studies in various aquatic environments, including the Baltic Sea, the Black Sea, Scottish and Scandinavian fjords, Ionian Sea lagoons and embayments, and Swiss lakes. Examples of episodic and rapid (hours) occurrences of hypoxia, as well as seasonal changes in bottom-water oxygenation in stratified systems, are discussed. Geologically driven hypoxia caused by gas seepage is demonstrated. Using novel technologies, temporal and spatial patterns of water-column oxygenation, from basin-scale seasonal patterns to meter-scale sub-micromolar oxygen distributions, were resolved. Existing multidecadal monitoring data were used to demonstrate the imprint of climate change and eutrophication on long-term oxygen distributions. Organic and inorganic proxies were used to extend investigations on past oxygen conditions to centennial and even longer timescales that cannot be resolved by monitoring. The effects of hypoxia on faunal communities and biogeochemical processes were also addressed in the project. An investigation of benthic fauna is presented as an example of hypoxia-devastated benthic communities that slowly recover upon a reduction in eutrophication in a system where naturally occurring hypoxia overlaps with anthropogenic hypoxia. Biogeochemical investigations reveal that oxygen intrusions have a strong effect on the microbially mediated redox cycling of elements. Observations and modeling studies of the sediments demonstrate the effect of seasonally changing oxygen conditions on benthic mineralization pathways and fluxes. Data quality and access are crucial in hypoxia research. Technical issues are therefore also addressed, including the availability of suitable sensor technology to resolve the gradual changes in bottom-water oxygen in marine systems that can be expected as a result of climate change. Using cabled observatories as examples, we show how the benefit of continuous oxygen monitoring can be maximized by adopting proper quality control. Finally, we discuss strategies for state-of-the-art data archiving and dissemination in compliance with global standards, and how ocean observations can contribute to global earth observation attempts.

Interest in seamount research has gathered momentum over the past five years in an effort to understand the physical, geochemical and biological characteristics as well as the interconnectedness of seamount ecosystems. The majority of biological seamount research has concentrated upon the rich and diverse suspension feeding organisms that dominate the megafauna, such as gorgonians and antipatharian corals; by comparison there have been few studies that have investigated the no less enigmatic, but possibly just as important infauna. To help fill this knowledge gap, the macrofaunal community was sampled from a total of five stations along a northerly transect (capturing water depths from ∼130 m to ∼3300 m), on Senghor Seamount (NE Atlantic). The focus of this study is on the polychaete communities. Polychaete abundance peaked at the summit and a mid-slope station (∼1500 m), a pattern mirrored by the biomass values. The polychaete community along the transect appeared to be particularly diverse, with 135 species nominally identified to putative species from a total of 954 individuals. A diversity maximum was identified on the upper slope at ∼800 m depth, with species diversity, richness and evenness also all peaking at this station. Depth is likely to be a significant factor in determining levels of similarity between stations.

Submarine canyons are sites of intense energy and material exchange between the shelf and the deep adjacent basins. To test the hypothesis that active submarine canyons represent preferential conduits of available food for the deep-sea benthos, two mooring lines were deployed at 1200 m depth from November 2008 to November 2009 inside the Blanes canyon and on the adjacent open slope (Catalan Margin, NW Mediterranean Sea). We investigated the fluxes, biochemical composition and food quality of sinking organic carbon (OC). OC fluxes in the canyon and the open slope varied among sampling periods, though not consistently in the two sites. In particular, while in the open slope the highest OC fluxes were observed in August 2009, in the canyon the highest OC fluxes occurred in April–May 2009. For almost the entire study period, the OC fluxes in the canyon were significantly higher than those in the open slope, whereas OC contents of sinking particles collected in the open slope were consistently higher than those in the canyon. This result confirms that submarine canyons are effective conveyors of OC to the deep sea. Particles transferred to the deep sea floor through the canyons are predominantly of inorganic origin, significantly higher than that reaching the open slope at a similar water depth. Using multivariate statistical tests, two major clusters of sampling periods were identified: one in the canyon that grouped trap samples collected in December 2008, concurrently with the occurrence of a major storm at the sea surface, and associated with increased fluxes of nutritionally available particles from the upper shelf. Another cluster grouped samples from both the canyon and the open slope collected in March 2009, concurrently with the occurrence of the seasonal phytoplankton bloom at the sea surface, and associated with increased fluxes of total phytopigments. Our results confirm the key ecological role of submarine canyons for the functioning of deep-sea ecosystems, and highlight the importance of canyons in linking episodic storms and primary production occurring at the sea surface to the deep sea floor.

Benthic foraminifera are an important component of the marine biota, but protocols for investigating their viability and metabolism are still extremely limited. Classical studies on benthic foraminifera have been based on direct counting under light microscopy. Typically, these organisms are stained with Rose Bengal, which binds proteins and other macromolecules, but does not allow discrimination between viable and recently dead organisms. The fluorescent in situ hybridization technique (FISH) represents a new and useful approach to identify living cells possessing an active metabolism. Our work is the first test of the suitability of the FISH technique, based on fluorescent probes targeting the 18S rRNA, to detect live benthic foraminifera. The protocol was applied on Ammonia group and Miliolids, as well as on agglutinated polythalamous (i.e., Leptohalysis scottii and Eggerella scabra) and soft-shelled monothalamous (i.e., Psammophaga sp. and saccamminid morphotypes) taxa. The results from FISH analyses were compared with those obtained, on the same specimens assayed with FISH, from microscopic analysis of the cytoplasm colour, presence of pigments and pseudopodial activity. Our results indicate that FISH targets only metabolically active foraminifera, and allows discerning from low to high cellular activity, validating the hypothesis that the intensity of the fluorescent signal emitted by the probe is dependent upon the physiological status of cells. These findings support the usefulness of this molecular approach as a key tool for obtaining information on the physiology of living foraminifera, both in field and experimental settings.

The Eastern Boundary Upwelling Systems (EBUS) contribute to one fifth of the global catches in the ocean. Often associated with Oxygen Minimum Zones (OMZs), EBUS represent key regions for the oceanic nitrogen (N) cycle. Important bioavailable N loss due to denitrification and anammox processes as well as greenhouse gas emissions (e.g, N2O) occur also in these EBUS. However, their dynamics are currently crudely represented in global models. In the climate change context, improving our capability to properly represent these areas is crucial due to anticipated changes in the winds, productivity, and oxygen content. We developed a biogeochemical model (BioEBUS) taking into account the main processes linked with EBUS and associated OMZs. We implemented this model in a 3-D realistic coupled physical/biogeochemical configuration in the Namibian upwelling system (northern Benguela) using the high-resolution hydrodynamic ROMS model. We present here a validation using in situ and satellite data as well as diagnostic metrics and sensitivity analyses of key parameters and N2O parameterizations. The impact of parameter values on the OMZ off Namibia, on N loss, and on N2O concentrations and emissions is detailed. The model realistically reproduces the vertical distribution and seasonal cycle of observed oxygen, nitrate, and chlorophyll a concentrations, and the rates of microbial processes (e.g, NH4+ and NO2− oxidation, NO3− reduction, and anammox) as well. Based on our sensitivity analyses, biogeochemical parameter values associated with organic matter decomposition, vertical sinking, and nitrification play a key role for the low-oxygen water content, N loss, and N2O concentrations in the OMZ. Moreover, the explicit parameterization of both steps of nitrification, ammonium oxidation to nitrate with nitrite as an explicit intermediate, is necessary to improve the representation of microbial activity linked with the OMZ. The simulated minimum oxygen concentrations are driven by the poleward meridional advection of oxygen-depleted waters offshore of a 300 m isobath and by the biogeochemical activity inshore of this isobath, highlighting a spatial shift of dominant processes maintaining the minimum oxygen concentrations off Namibia. In the OMZ off Namibia, the magnitude of N2O outgassing and of N loss is comparable. Anammox contributes to about 20% of total N loss, an estimate lower than currently assumed (up to 50%) for the global ocean.