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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 hydrodynamical model ROMS. 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 Chl a concentrations, and the rates of microbial processes (e.g. NH+4 and NO-2 oxidation, NO-3 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 importance of both steps of nitrification, ammonium oxidation to nitrate with nitrite as an explicit intermediate, is highlighted to improve the representation of microbial activity linked with OMZ. The simulated minimum oxygen concentrations are driven by the poleward meridional advection of oxygen-depleted waters offshore of 300m isobath and by the biogeochemical activity inshore of this isobath, highlighting a spatial shift of dominant processes maintaining the minimum oxygen concentrations off Namibia. [ABSTRACT FROM AUTHOR]

Abstract: Sporadic occurrences of milky turquoise waters visible in true colour satellite imagery in the Benguela upwelling system off Namibia are characterized by high reflectances due to enhanced scattering properties. Previous opinion was that the features are due to increased reflectances by elemental sulphur (S0) resulting from upwelling or eruptions of hydrogen sulphide-enriched waters. In March/April 2003, a remotely sensed offshore plume was identified as a coccolithophore bloom for the first time in this region, followed by satellite imagery and intensively investigated using ship-borne measurements. Different methods were applied such as high-performance liquid chromatography (HPLC) pigment analysis, electronic disperse X-ray analysis, scanning electronic microscopy as well as spectral particle absorption and reflectance measurements. Ocean colour satellite data of the SeaWiFS and MERIS sensors were used to investigate the blooms. The SeaWiFS coccolithophore algorithm identified the bloom in March 2003. MERIS-derived spectral reflectances which were in a good agreement with in-situ measurements were used to study the occurrence of blooms in the first half of the year 2004. The observed offshore plumes can be optically divided into two groups. Far offshore the plumes are dominated by coccolithophores Emiliania huxleyi (Type-C) increasing the reflectance by scattering. Directly outside the active upwelling area the spectral shape of reflectance is affected by absorbing phytoplankton, but the magnitude is the result of scattering by coccolithophores and possibly diatom frustules. The coccolithophore bloom water was characterized by high calcite content, the occurrence of the marker pigment 19′- hexanoyloxyfucoxanthin as well as by a double maximum in the blue spectral range of the specific absorption of phytoplankton. The coccolithophore bloom develops as a phytoplankton succession during a low wind period in a stable stratified water body with a shallow top layer under high solar radiation with the starting conditions of low silicate and high N/P ratios. In the area off Namibia the sporadic occurrence of milky turquoise water may have two different causes. The features nearshore are due to sulphur discolouration but the further offshore plumes are caused by coccolithophores. The occurrence of coccolithophores is not as sporadic as the blooms which are visible in satellite data. These results improve the interpretation of milky turquoise water identified by ocean colour satellite data in the SE Atlantic Ocean off Namibia because they verified the occurrence of coccolithophores in that region for the first time with different methods. [Copyright &y& Elsevier]

Oxygen minimum zones are major sites of fixed nitrogen loss in the ocean. Recent studies have highlighted the importance of anaerobic ammonium oxidation, anammox, in pelagic nitrogen removal. Sources of ammonium for the anammox reaction, however, remain controversial, as heterotrophic denitrification and alternative anaerobic pathways of organic matter remineralization cannot account for the ammonium requirements of reported anammox rates. Here, we explore the significance of microaerobic respiration as a source of ammonium during organic matter degradation in the oxygen-deficient waters off Namibia and Peru. Experiments with additions of double-labelled oxygen revealed high aerobic activity in the upper OMZs, likely controlled by surface organic matter export. Consistently observed oxygen consumption in samples retrieved throughout the lower OMZs hints at efficient exploitation of vertically and laterally advected, oxygenated waters in this zone by aerobic microorganisms. In accordance, metagenomic and metatranscriptomic analyses identified genes encoding for aerobic terminal oxidases and demonstrated their expression by diverse microbial communities, even in virtually anoxic waters. Our results suggest that microaerobic respiration is a major mode of organic matter remineralization and source of ammonium (~45-100%) in the upper oxygen minimum zones, and reconcile hitherto observed mismatches between ammonium producing and consuming processes therein.

Coastal waters support approximately 90 per cent of global fisheries and are therefore an important food reserve for our planet. Eutrophication of these waters, due to human activity, leads to severe oxygen depletion and the episodic occurrence of hydrogen sulphide-toxic to multi-cellular life-with disastrous consequences for coastal ecosytems. Here we show that an area of approximately 7,000 km(2) of African shelf, covered by sulphidic water, was detoxified by blooming bacteria that oxidized the biologically harmful sulphide to environmentally harmless colloidal sulphur and sulphate. Combined chemical analyses, stoichiometric modelling, isotopic incubations, comparative 16S ribosomal RNA, functional gene sequence analyses and fluorescence in situ hybridization indicate that the detoxification proceeded by chemolithotrophic oxidation of sulphide with nitrate and was mainly catalysed by two discrete populations of gamma- and epsilon-proteobacteria. Chemolithotrophic bacteria, accounting for approximately 20 per cent of the bacterioplankton in sulphidic waters, created a buffer zone between the toxic sulphidic subsurface waters and the oxic surface waters, where fish and other nekton live. This is the first time that large-scale detoxification of sulphidic waters by chemolithotrophs has been observed in an open-ocean system. The data suggest that sulphide can be completely consumed by bacteria in the subsurface waters and, thus, can be overlooked by remote sensing or monitoring of shallow coastal waters. Consequently, sulphidic bottom waters on continental shelves may be more common than previously believed, and could therefore have an important but as yet neglected effect on benthic communities.