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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.

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 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.

Confocal Raman microscopy (CRM) mapping was used to investigate the microstructural arrangement and organic matrix distribution within the skeleton of the coral Porites lutea. Relative changes in the crystallographic orientation of crystals within the fibrous fan-system could be mapped, without the need to prepare thin sections, as required if this information is obtained by polarized light microscopy. Simultaneously, incremental growth lines can be visualized without the necessity of etching and hence alteration of sample surface. Using these methods two types of growth lines could be identified: one corresponds to the well-known incremental growth layers, whereas the second type of growth lines resemble denticle finger-like structures (most likely traces of former spines or skeletal surfaces). We hypothesize that these lines represent the outer skeletal surface before another growth cycle of elongation, infilling and thickening of skeletal areas continues. We show that CRM mapping with high spatial resolution can significantly improve our understanding of the micro-structural arrangement and growth patterns in coral skeletons.

Shelf-to-basin sediment transport during storms was studied at the southwestern end of the Gulf of Lions from November 2003 to March 2004. Waves, near-bottom currents, temperature and sediment fluxes were measured on the inner shelf at 28-m depth, in the Cap de Creus submarine canyon head at 300-m depth and in the northwestern Mediterranean basin at 2350-m depth. This paper is a synthesis of results published separately in different papers; it includes some new data and focusses on the subject of storms. It is the first paper in which simultaneous data about the effect of storms on the shelf, the slope and in the basin are shown together. During the winter studied, there were two severe E-SE storms with significant wave heights ≥ 7 m: one in December 2003 and one in February 2004. During these storms, coastal water was exported off-shelf producing strong near-bottom currents (up to 82 cm s−1) at the canyon head that resuspended sediment and increased the downcanyon sediment fluxes by several orders of magnitude. The suspended sediment flux increase in the canyon head was much larger during the February storm than during the December storm. At the deep basin site, particle fluxes also increased drastically (1–2 orders of magnitude) immediately after the February storm but not after the December storm. The reason was that the February storm was reinforced by dense shelf water cascading and was long enough (43 h) to transfer large amounts of resuspended sediment from shallow shelf areas to the canyon head and from there to the northwestern Mediterranean basin. Thus, in the western Gulf of Lions, severe winter E-SE storms occurring during the dense shelf water cascading period can significantly increase the transfer to deep-sea (> 2000 m) environments of shelf and slope resuspended material, including anthropogenic contaminants and organic matter.

This work aims at characterising the seamount physiography and biology in the OSPAR Convention limits (north-east Atlantic Ocean) and Mediterranean Sea. We first inferred potential abundance, location and morphological characteristics of seamounts, and secondly, summarized the existing biological, geological and oceanographic in situ research, identifying examples of well-studied seamounts. Our study showed that the seamount population in the OSPAR area (north-east Atlantic) and in the Mediterranean Sea is large with around 557 and 101 seamount-like features, respectively. Similarly, seamounts occupy large areas of about 616 000 km2 in the OSPAR region and of about 89 500 km2 in the Mediterranean Sea. The presence of seamounts in the north-east Atlantic has been known since the late 19th century, but overall knowledge regarding seamount ecology and geology is still relatively poor. Only 37 seamounts in the OSPAR area (3.5% of all seamounts in the region), 22 in the Mediterranean Sea (9.2% of all seamounts in the region) and 25 in the north-east Atlantic south of the OSPAR area have in situ information. Seamounts mapped in both areas are in general very heterogeneous, showing diverse geophysical characteristics. These differences will likely affect the biological diversity and production of resident and associated organisms.

The growing field of ocean acidification research is concerned with the investigation of organism responses to increasing pCO2 values. One important approach in this context is culture work using seawater with adjusted CO2 levels. As aqueous pCO2 is difficult to measure directly in small-scale experiments, it is generally calculated from two other measured parameters of the carbonate system (often AT, CT or pH). Unfortunately, the overall uncertainties of measured and subsequently calculated values are often unknown. Especially under high pCO2, this can become a severe problem with respect to the interpretation of physiological and ecological data. In the few datasets from ocean acidification research where all three of these parameters were measured, pCO2 values calculated from AT and CT are typically about 30% lower (i.e. ~300 μatm at a target pCO2 of 1000 μatm) than those calculated from AT and pH or CT and pH. This study presents and discusses these discrepancies as well as likely consequences for the ocean acidification community. Until this problem is solved, one has to consider that calculated parameters of the carbonate system (e.g. pCO2, calcite saturation state) may not be comparable between studies, and that this may have important implications for the interpretation of CO2 perturbation experiments.

Coastal time series of ocean carbonate chemistry are critical for understanding how global anthropogenic change manifests in near-shore ecosystems. Yet, they are few and have low temporal resolution. At the time series station Point B in the northwestern Mediterranean Sea, seawater was sampled weekly from 2007 through 2015, at 1 and 50 m, and analyzed for total dissolved inorganic carbon (CT) and total alkalinity (AT). Parameters of the carbonate system such as pH (pHT, total hydrogen ion scale) were calculated and a deconvolution analysis was performed to identify drivers of change. The rate of surface ocean acidification was −0.0028 ± 0.0003 units pHT yr−1. This rate is larger than previously identified open-ocean trends due to rapid warming that occurred over the study period (0.072 ± 0.022 °C yr−1). The total pHT change over the study period was of similar magnitude as the diel pHT variability at this site. The acidification trend can be attributed to atmospheric carbon dioxide (CO2) forcing (59 %, 2.08 ± 0.01 ppm CO2 yr−1) and warming (41 %). Similar trends were observed at 50 m but rates were generally slower. At 1 m depth, the increase in atmospheric CO2 accounted for approximately 40 % of the observed increase in CT (2.97 ± 0.20 µmol kg−1 yr−1). The remaining increase in CT may have been driven by the same unidentified process that caused an increase in AT (2.08 ± 0.19 µmol kg−1 yr−1). Based on the analysis of monthly trends, synchronous increases in CT and AT were fastest in the spring–summer transition. The driving process of the interannual increase in AT has a seasonal and shallow component, which may indicate riverine or groundwater influence. This study exemplifies the importance of understanding changes in coastal carbonate chemistry through the lens of biogeochemical cycling at the land–sea interface. This is the first coastal acidification time series providing multiyear data at high temporal resolution. The data confirm rapid warming in the Mediterranean Sea and demonstrate coastal acidification with a synchronous increase in total alkalinity.

This note describes a profiling mooring with an interdisciplinary suite of sensors taking profiles between 180 and 30 m depth. It consists of an underwater winch, moored below 180 m depth, and a profiling instrumentation platform. In its described setup it can take about 200 profiles at pre-programmed times or intervals with one set of batteries. This allows for studies over an extended period of time (e.g. two daily profiles over a time of 3 months). The Gotland Deep Environmental Sampling Station (GODESS) in the Eastern Gotland Basin of the Baltic Sea is aimed at investigations of redoxcline dynamics. The described system can be readily adapted to other research foci by changing the profiling instrumentation platform and its payload.

In June 2009, 22 spectrometers from 14 institutes measured tropospheric and stratospheric NO2 from the ground for more than 11 days during the Cabauw Intercomparison Campaign of Nitrogen Dioxide measuring Instruments (CINDI), at Cabauw, NL (51.97° N, 4.93° E). All visible instruments used a common wavelength range and set of cross sections for the spectral analysis. Most of the instruments were of the multi-axis design with analysis by differential spectroscopy software (MAX-DOAS), whose non-zenith slant columns were compared by examining slopes of their least-squares straight line fits to mean values of a selection of instruments, after taking 30-min averages. Zenith slant columns near twilight were compared by fits to interpolated values of a reference instrument, then normalised by the mean of the slopes of the best instruments. For visible MAX-DOAS instruments, the means of the fitted slopes for NO2 and O4 of all except one instrument were within 10% of unity at almost all non-zenith elevations, and most were within 5%. Values for UV MAX-DOAS instruments were almost as good, being 12% and 7%, respectively. For visible instruments at zenith near twilight, the means of the fitted slopes of all instruments were within 5% of unity. This level of agreement is as good as that of previous intercomparisons, despite the site not being ideal for zenith twilight measurements. It bodes well for the future of measurements of tropospheric NO2, as previous intercomparisons were only for zenith instruments focussing on stratospheric NO2, with their longer heritage.