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The recent finding that microbial ammonia oxidation in the ocean is performed by archaea to a greater extent than by bacteria has drastically changed the view on oceanic nitrification. The numerical dominance of archaeal ammonia-oxidizers (AOA) over their bacterial counterparts (AOB) in large parts of the ocean leads to the hypothesis that AOA rather than AOB could be the key organisms for the oceanic production of the strong greenhouse gas nitrous oxide (N2O) that occurs as a by-product of nitrification. Very recently, enrichment cultures of marine ammonia-oxidizing archaea have been reported to produce N2O. Here, we demonstrate that archaeal ammonia monooxygenase genes (amoA) were detectable throughout the water column of the eastern tropical North Atlantic (ETNA) and eastern tropical South Pacific (ETSP) Oceans. Particularly in the ETNA, comparable patterns of abundance and expression of archaeal amoA genes and N2O co-occurred in the oxygen minimum, whereas the abundances of bacterial amoA genes were negligible. Moreover, selective inhibition of archaea in seawater incubations from the ETNA decreased the N2O production significantly. In studies with the only cultivated marine archaeal ammonia-oxidizer Nitrosopumilus maritimus SCM1, we provide the first direct evidence for N2O production in a pure culture of AOA, excluding the involvement of other microorganisms as possibly present in enrichments. N. maritimus showed high N2O production rates under low oxygen concentrations comparable to concentrations existing in the oxycline of the ETNA, whereas the N2O production from two AOB cultures was comparably low under similar conditions. Based on our findings, we hypothesize that the production of N2O in tropical ocean areas results mainly from archaeal nitrification and will be affected by the predicted decrease in dissolved oxygen in the ocean.

Mesoscale eddies seem to play an important role for both the hydrography and biogeochemistry of the eastern tropical Pacific Ocean (ETSP) off Peru. However, detailed surveys of these eddies are not available, which has so far hampered an in depth understanding of their implications for nutrient distribution and biological productivity. In this study, three eddies along a section at 16°45´ S have been surveyed intensively during R/V Meteor cruise M90 in November 2012. A coastal mode water eddy, an open ocean mode water eddy and an open ocean cyclonic eddy have been identified and sampled in order to determine both their hydrographic properties and their influence on the biogeochemical setting of the ETSP. In the thermocline the temperature of the coastal anticyclonic eddy was up to 2 °C warmer, 0.2 more saline and the swirl velocity was up to 35 cm s−1. The observed temperature and salinity anomalies, as well as swirl velocities of both types of eddies were about twice as large as had been described for the mean eddies in the ETSP. The observed heat and salt anomalies (AHA, ASA) of the anticyclonic eddy near the shelf-break of 17.7 × 1018 J and 36.6 × 1010 kg are more than twice as large as the mean AHA and ASA for the ETSP. We found that the eddies contributed to the productivity by maintaining pronounced subsurface maxima of chlorophyll of up to 6 μg L−1. Based on a comparison of the coastal (young) mode water eddy and the open ocean (old) mode water eddy we suggest that the ageing of eddies when they detach from the shelf-break and move westward to the open ocean influences the eddies' properties: chlorophyll maxima are reduced to about half (2.5–3 μg L−1) and nutrients are subducted. However, different settings at the time of formation may also contribute to the observed differences between the young and old mode water eddies. The coastal mode water eddy was found to be a site of nitrogen (N) loss in the OMZ with a maximum ΔNO3− anomaly (i.e. N loss) of about −25 μmol L−1 in 250 m water depth, whereas, the open ocean mode water and cyclonic eddies were of minor and negligible importance for the N loss, respectively. Our results show that the important role of eddies for the distribution of nutrients, as well as biogeochemical processes in the ETSP (and other OMZ/upwelling regions) can only be fully deciphered and understood through dedicated high spatial and temporal resolution oceanographic/biogeochemical surveys.

The Boknis Eck (BE) time series station, initiated in 1957, is one of the longest-operated time series stations worldwide. We present the first statistical evaluation of a data set of nine physical, chemical and biological parameters in the period of 1957–2013. In the past three to five decades, all of the measured parameters underwent significant long-term changes. Most striking is an ongoing decline in bottom water oxygen concentration, despite a significant decrease of nutrient and chlorophyll a concentrations. Temperature-enhanced oxygen consumption in the bottom water and a prolongation of the stratification period are discussed as possible reasons for the ongoing oxygen decline despite declining eutrophication. Observations at the BE station were compared with model output of the Kiel Baltic Sea Ice Ocean Model (BSIOM). Reproduced trends were in good agreement with observed trends for temperature and oxygen, but generally the oxygen concentration at the bottom has been overestimated.

Atmospheric deposition contributes potentially significant amounts of the nutrients iron, nitrogen, and phosphorus (via mineral dust and anthropogenic aerosols) to the oligotrophic tropical North Atlantic Ocean. Transport pathways, deposition processes, and source strengths contributing to this atmospheric flux are all highly variable in space and time. Atmospheric sampling was conducted during 28 research cruises through the eastern tropical North Atlantic (ETNA) over a 12-yr period, and a substantial dataset of measured concentrations of nutrients and trace metals in aerosol and rainfall over the region was acquired. This database was used to quantify (on a spatial and seasonal basis) the atmospheric input of ammonium, nitrate, soluble phosphorus, and soluble and total iron, aluminum, and manganese to the ETNA. The magnitude of atmospheric input varies strongly across the region, with high rainfall rates associated with the intertropical convergence zone contributing to high wet deposition fluxes in the south, particularly for soluble species. Dry deposition fluxes of species associated with mineral dust exhibited strong seasonality, with the highest fluxes associated with wintertime low-level transport of Saharan dust. Overall (wet plus dry) atmospheric inputs of soluble and total trace metals were used to estimate their soluble fractions. These also varied with season and were generally lower in the dry north than in the wet south. The ratio of ammonium plus nitrate to soluble iron in deposition to the ETNA was lower than the N:Fe requirement for algal growth in all cases, indicating the importance of the atmosphere as a source of excess iron.

We review here the available information on methane (CH4 ) and nitrous oxide (N2 O) from major marine, mostly coastal, oxygen (O2 )-deficient zones formed both naturally and as a result of human activities (mainly eutrophication). Concentrations of both gases in subsurface waters are affected by ambient O2 levels to varying degrees. Organic matter supply to seafloor appears to be the primary factor controlling CH4 production in sediments and its supply to (and concentration in) overlying waters, with bottom-water O2 -deficiency exerting only a modulating effect. High (micromolar level) CH4 accumulation occurs in anoxic (sulphidic) waters of silled basins, such as the Black Sea and Cariaco Basin, and over the highly productive Namibian shelf. In other regions experiencing various degrees of O2 -deficiency (hypoxia to anoxia), CH4 concentrations vary from a few to hundreds of nanomolar levels. Since coastal O2 -deficient zones are generally very productive and are sometimes located close to river mouths and submarine hydrocarbon seeps, it is difficult to differentiate any O2 -deficiency-induced enhancement from in situ production of CH4 in the water column and its inputs through freshwater runoff or seepage from sediments. While the role of bottom-water O2 -deficiency in CH4 formation appears to be secondary, even when CH4 accumulates in O2 -deficient subsurface waters, methanotrophic activity severely restricts its diffusive efflux to the atmosphere. As a result, an intensification or expansion of coastal O2 -deficient zones will probably not drastically change the present status where emission from the ocean as a whole forms an insignificant term in the atmospheric CH4 budget. The situation is different for N2 O, the production of which is greatly enhanced in low-O2 waters, and although it is lost through denitrification in most suboxic and anoxic environments, the peripheries of such environments offer most suitable conditions for its production, with the exception of enclosed anoxic basins. Most O2 -deficient systems serve as strong net sources of N2 O to the atmosphere. This is especially true for coastal upwelling regions with shallow O2 -deficient zones where a dramatic increase in N2 O production often occurs in rapidly denitrifying waters. Nitrous oxide emissions from these zones are globally significant, and so their ongoing intensification and expansion is likely to lead to a significant increase in N2 O emission from the ocean. However, a meaningful quantitative prediction of this increase is not possible at present because of continuing uncertainties concerning the formative pathways to N2 O as well as insufficient data from key coastal regions.

Ocean observations are analysed in the framework of Collaborative Research Center 754 (SFB 754) \"Climate-Biogeochemistry Interactions in the Tropical Ocean\" to study (1) the structure of tropical oxygen minimum zones (OMZs), (2) the processes that contribute to the oxygen budget, and (3) long-term changes in the oxygen distribution. The OMZ of the eastern tropical North Atlantic (ETNA), located between the well-ventilated subtropical gyre and the equatorial oxygen maximum, is composed of a deep OMZ at about 400 m in depth with its core region centred at about 20° W, 10° N and a shallow OMZ at about 100 m in depth, with the lowest oxygen concentrations in proximity to the coastal upwelling region off Mauritania and Senegal. The oxygen budget of the deep OMZ is given by oxygen consumption mainly balanced by the oxygen supply due to meridional eddy fluxes (about 60%) and vertical mixing (about 20%, locally up to 30%). Advection by zonal jets is crucial for the establishment of the equatorial oxygen maximum. In the latitude range of the deep OMZ, it dominates the oxygen supply in the upper 300 to 400 m and generates the intermediate oxygen maximum between deep and shallow OMZs. Water mass ages from transient tracers indicate substantially older water masses in the core of the deep OMZ (about 120–180 years) compared to regions north and south of it. The deoxygenation of the ETNA OMZ during recent decades suggests a substantial imbalance in the oxygen budget: about 10% of the oxygen consumption during that period was not balanced by ventilation. Long-term oxygen observations show variability on interannual, decadal and multidecadal timescales that can partly be attributed to circulation changes. In comparison to the ETNA OMZ, the eastern tropical South Pacific OMZ shows a similar structure, including an equatorial oxygen maximum driven by zonal advection but overall much lower oxygen concentrations approaching zero in extended regions. As the shape of the OMZs is set by ocean circulation, the widespread misrepresentation of the intermediate circulation in ocean circulation models substantially contributes to their oxygen bias, which might have significant impacts on predictions of future oxygen levels.

Depth profiles of nitrous oxide (N2O) were measured during six cruises to the upwelling area and oxygen minimum zone (OMZ) off Peru in 2009 and 2012/2013, covering both the coastal shelf region and the adjacent open ocean. N2O profiles displayed a strong sensitivity towards oxygen concentrations. Open ocean profiles with distances to the shelf break larger than the first baroclinic Rossby radius of deformation showed a transition from a broad maximum close to the Equator to a double-peak structure south of 5∘ S where the oxygen minimum was more pronounced. Maximum N2O concentrations in the open ocean were about 80 nM. A linear relationship between ΔN2O and apparent oxygen utilization (AOU) could be found for measurements within the upper oxycline, with a slope similar to studies in other oceanic regions. In contrast, N2O profiles close to the shelf revealed a much higher variability, and N2O concentrations higher than 100 nM were often observed. The highest N2O concentration measured at the shelf was ∼ 850 nM. Due to the extremely sharp oxygen gradients at the shelf, N2O maxima occurred in very shallow water depths of less than 50 m. In the coastal area, a linear relationship between ΔN2O and AOU could not be observed as extremely high ΔN2O values were scattered over the full range of oxygen concentrations. The data points that showed the strongest deviation from a linear ΔN2O / AOU relationship also showed signals of intense nitrogen loss. These results indicate that the coastal upwelling at the Peruvian coast and the subsequent strong remineralization in the water column causes conditions that lead to extreme N2O accumulation, most likely due to the interplay of intense mixing and high rates of remineralization which lead to a rapid switching of the OMZ waters between anoxic and oxic conditions. This, in turn, could trigger incomplete denitrification or pulses of increased nitrification with extreme N2O production.

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.

Here we present results of the first comprehensive study of sulphur compounds and methane in the oligotrophic tropical western Pacific Ocean. The concentrations of dimethylsuphide (DMS), dimethylsulphoniopropionate (DMSP), dimethylsulphoxide (DMSO), and methane (CH4), as well as various phytoplankton marker pigments in the surface ocean were measured along a north–south transit from Japan to Australia in October 2009. DMS (0.9 nmol L−1), dissolved DMSP (DMSPd, 1.6 nmol L−1) and particulate DMSP (DMSPp, 2 nmol L−1) concentrations were generally low, while dissolved DMSO (DMSOd, 4.4 nmol L−1) and particulate DMSO (DMSOp, 11.5 nmol L−1) concentrations were comparably enhanced. Positive correlations were found between DMSO and DMSP as well as DMSP and DMSO with chlorophyll a, which suggests a similar source for both compounds. Similar phytoplankton groups were identified as being important for the DMSO and DMSP pool, thus, the same algae taxa might produce both DMSP and DMSO. In contrast, phytoplankton seemed to play only a minor role for the DMS distribution in the western Pacific Ocean. The observed DMSPp : DMSOp ratios were very low and seem to be characteristic of oligotrophic tropical waters representing the extreme endpoint of the global DMSPp : DMSOp ratio vs SST relationship. It is most likely that nutrient limitation and oxidative stress in the tropical western Pacific Ocean triggered enhanced DMSO production leading to an accumulation of DMSO in the sea surface. Positive correlations between DMSPd and CH4, as well as between DMSO (particulate and total) and CH4, were found along the transit. We conclude that DMSP and DMSO and/or their degradation products might serve as potential substrates for CH4 production in the oxic surface layer of the western Pacific Ocean.

Bulk aerosol samples collected during cruise M91 of FS Meteor off the coast of Peru in December 2012 were analysed for their soluble trace metal (Fe, Al, Mn, Ti, Zn, V, Ni, Cu, Co, Cd, Pb, Th) and major ion (including NO3− and NH4+) content. These data are among the first recorded for trace metals in this relatively poorly studied region of the global marine atmosphere. To the north of  ∼  13° S, the concentrations of several elements (Fe, Ti, Zn, V, Ni, Pb) appear to be related to distance from the coast. At the south of the transect ( ∼  15–16° S), elevated concentrations of Fe, Cu, Co, and Ni were observed, and we calculated dry deposition fluxes of soluble Cu approximately an order of magnitude higher than a recent model-based estimate of total Cu deposition to the region. The model did not take account of emissions from the large smelting facilities in the south of Peru and northern Chile, and our results may indicate that these facilities constitute an important source of trace metals to the region. Calculated dry deposition fluxes (3370–17800 and 16–107 nmol m−2 d−1 for inorganic nitrogen and soluble Fe respectively) indicated that atmospheric input to the waters of the Peru upwelling system contains an excess of Fe over N, with respect to phytoplankton requirements. This may be significant as primary production in these waters has been reported to be limited by Fe availability, but atmospheric deposition is unlikely to be the dominant source of Fe to the system.