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Macrophytes growing in shallow coastal zones characterised by intense metabolic activity have the capacity to modify pH within their canopy and beyond. We observed diel pH changes in shallow (5–12 m) seagrass (Posidonia oceanica) meadows spanning 0.06 pH units in September to 0.24 units in June. The carbonate system (pH, DIC, and aragonite saturation state (ΩAr)) and O2 within the meadows displayed strong diel variability driven by primary productivity, and changes in chemistry were related to structural parameters of the meadow, in particular, the leaf surface area available for photosynthesis (LAI). LAI was positively correlated to mean, max and range pHNBS and max and range ΩAr. In June, vertical mixing (as Turbulent Kinetic Energy) influenced max and min ΩAr, while in September there was no effect of hydrodynamics on the carbonate system within the canopy. Max and range ΩAr within the meadow showed a positive trend with the calcium carbonate load of the leaves, pointing to a possible link between structural parameters, ΩAr and carbonate deposition. Calcifying organisms, e.g. epiphytes with carbonate skeletons, may benefit from the modification of the carbonate system by the meadow. There is, however, concern for the ability of seagrasses to provide modifications of similar importance in the future. The predicted decline of seagrass meadows may alter the scope for alteration of pH within a seagrass meadow and in the water column above the meadow, particularly if shoot density and biomass decline, on which LAI is based. Organisms associated with seagrass communities may therefore suffer from the loss of pH buffering capacity in degraded meadows.

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 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.

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 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.

Bivalve shells can provide excellent archives of past environmental change but have not been used to interpret ocean acidification events. We investigated carbon, oxygen and trace element records from different shell layers in the mussels Mytilus galloprovincialis combined with detailed investigations of the shell ultrastructure. Mussels from the harbour of Ischia (Mediterranean, Italy) were transplanted and grown in water with mean pHT 7.3 and mean pHT 8.1 near CO2 vents on the east coast of the island. Most prominently, the shells recorded the shock of transplantation, both in their shell ultrastructure, textural and geochemical record. Shell calcite, precipitated subsequently under acidified seawater responded to the pH gradient by an in part disturbed ultrastructure. Geochemical data from all test sites show a strong metabolic effect that exceeds the influence of the low-pH environment. These field experiments showed that care is needed when interpreting potential ocean acidification signals because various parameters affect shell chemistry and ultrastructure. Besides metabolic processes, seawater pH, factors such as salinity, water temperature, food availability and population density all affect the biogenic carbonate shell archive.

Climate change and changing nutrient loadings are the two main aspects of global change that are linked to the increase in the prevalence of coastal hypoxia – the depletion of oxygen in the bottom waters of coastal areas. However, it remains uncertain how strongly these two drivers will each increase the risk of hypoxia over the next decades. Through model simulations we have investigated the relative influence of climate change and nutrient run-off on the bottom water oxygen dynamics in the Oyster Grounds, an area in the central North Sea experiencing summer stratification. Simulations were performed with a one-dimensional ecosystem model that couples hydrodynamics, pelagic biogeochemistry and sediment diagenesis. Climatological conditions for the North Sea over the next 100 yr were derived from a global-scale climate model. Our results indicate that changing climatological conditions will increase the risk of hypoxia. The bottom water oxygen concentration in late summer is predicted to decrease by 24 μM or 11.5% in the year 2100. More intense stratification is the dominant factor responsible for this decrease (58%), followed by the reduced solubility of oxygen at higher water temperature (27%), while the remaining part could be attributed to enhanced metabolic rates in warmer bottom waters (15%). Relative to these climate change effects, changes in nutrient runoff are also important and may even have a stronger impact on the bottom water oxygenation. Decreased nutrient loadings strongly decrease the probability of hypoxic events. This stresses the importance of continued eutrophication management in coastal areas, which could function as a mitigation tool to counteract the effects of rising temperatures.

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.