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An investigation of surface phytoplankton communities was undertaken on the shelf of the northern Benguela upwelling ecosystem during austral autumn (May) and spring (September), along latitudinal transects at20º S and 23º S, from 2 to 70 nautical miles offshore, as well as on a zigzag grid located between these transects. Microscopic identification of the phytoplankton and CHEMTAX analysis of pigment biomarkers were used tocharacterise the community composition. During May 2014, warmer, more-saline water with a shallower upper mixed layer corresponding to periods of less-intense offshore Ekman transport was encountered on the shelf. Satellite imagery indicated high phytoplankton biomass extending for a considerable distance from the coast, and CHEMTAX indicated diatoms as dominant at most of the stations (52–92%), although dinoflagellates were dominant at some inshore localities (57–74%). Species of Chaetoceros, Bacteriastrum and Cylindrotheca were the most abundant, with abundance of the Pseudo-nitzschia ‘seriata-group’ being particularly high at a number of stations. In September 2014, more-intense wind-forcing resulted in a deeper upper mixed layer and stronger upwelling of colder, less-saline water. Elevated phytoplankton biomass was confined close to the coast, where diatoms accounted for most of the population (54–87%), whereas small flagellates, such as prasinophytes, haptophytes and cryptophytes, as well as the cyanobacterium Synechococcus, dominated the communities (58–90%) farther from the coast. It is hypothesised that stronger upwelling and deeper vertical mixing in September of that year were not conducive for widespread diatom growth, and that small flagellates populated the water column by being entrained from offshore onto the shelf in the upwelled water that moved in towards the coast.Keywords: Benguela upwelling ecosystem, CHEMTAX, hydrography, pigment biomarkers, SE Atlantic, species composition, surface waters

The three-component model of Brewin et al. (2010) computes fractional contributions of three phytoplankton size classes (micro- (> 20 μm), nano- (2–20 μm), picophytoplankton ( 1 mg m− 3 was limited to shelf regions along the coasts of Southern Africa and Madagascar, while values 50% of the total Chla in these regions with little change throughout the year. The AR shelf differed, with picophytoplankton dominating in summer, and micro- and nanophytoplankton the rest of the year. In the open ocean domains of the NB, SB, and AB regions, nanophytoplankton dominated for most of the year, with picophytoplankton being more prevalent during summer and autumn. In contrast, in the AR open ocean, nanophytoplankton were dominant only during winter and early spring, whereas picophytoplankton dominated throughout the year in the MC open ocean. The refined model characterised previously unknown spatial and temporal changes in size structure in various ecosystems around Southern Africa.

Hydrographic data collected in cyclonic eddies in the Mozambique Channel and Basin revealed notable differences in temperature and salinity at a depth of 100 m, the upper mixed layer, the nitracline depths, and vertical distribution of chlorophyll-a (Chl-a). Differences in temperature and salinity did not show any consistent patterns. In contrast, the differences in the upper mixed layer, nitracline depths and the vertical Chl-a profile appeared to be driven by combined effects of eddy dynamics (i.e. shoaling of isopleths) and the seasonal variation in light availability and mixing conditions in the upper layers. Cyclonic eddies studied during austral spring and summer in the Mozambique Channel exhibited shallower upper mixed layers and nitracline depths, and deeper euphotic zones. Distinct subsurface Chl-a maxima (SCM) were associated with the stratified conditions in the upper layers of these eddies. In contrast, a cyclonic eddy studied during mid-austral winter in the Mozambique Basin had a shallower e...

A comprehensive in situ dataset of chlorophyll a (Chl a; N = 18,001), net primary production (NPP; N = 165) and net community production (NCP; N = 95), were used to evaluate the performance of Moderate Resolution Imaging Spectroradiometer on Aqua (MODIS-A) algorithms for these parameters, in the South Atlantic Ocean, to facilitate the accurate generation of satellite NCP time series. For Chl a, five algorithms were tested using MODIS-A data, and OC3-CI performed best, which was subsequently used to compute NPP. Of three NPP algorithms tested, a Wavelength Resolved Model (WRM) was the most accurate, and was therefore used to estimate NCP with an empirical relationship between NCP with NPP and sea surface temperature (SST). A perturbation analysis was deployed to quantify the range of uncertainties introduced in satellite NCP from input parameters. The largest reductions in the uncertainty of satellite NCP came from MODIS-A derived NPP using the WRM (40%) and MODIS-A Chl a using OC3-CI (22%). The most accurate NCP algorithm, was used to generate a 16 year time series (2002 to 2018) from MODIS-A to assess climate and environmental drivers of NCP across the South Atlantic basin. Positive correlations between wind speed anomalies and NCP anomalies were observed in the central South Atlantic Gyre (SATL), and the Benguela Upwelling (BENG), indicating that autotrophic conditions may be fuelled by local wind-induced nutrient inputs to the mixed layer. Sea Level Height Anomalies (SLHA), used as an indicator of mesoscale eddies, were negatively correlated with NCP anomalies offshore of the BENG upwelling fronts into the SATL, suggesting autotrophic conditions are driven by mesoscale features. The Agulhas bank and Brazil-Malvinas confluence regions also had a strong negative correlation between SLHA and NCP anomalies, similarly indicating that NCP is forced by mesoscale eddy generation in this region. Positive correlations between SST anomalies and the Multivariate ENSO Index (MEI) in the SATL, indicated the influence of El Niño events on the South Atlantic Ocean, however the plankton community response was less clear. UK Natural Environment Research Council | Ref. NERC; NE / L002434 / 1 European Space Agency | Ref. AMT4SentinelFRM (ESRIN / RFQ / 3-14457 / 16 / I-BG) European Space Agency | Ref. AMT4OceanSatFlux (4000125730/18 / NL / FF / gp) NERC International Opportunity Fund Grant Satellite estimates of marine net community production in the South Atlantic from Sentinel-3 | Ref. SemSAS; NE / P00878X / 1 P&D ANP / BRASOIL | Ref. 48610.011013 / 2014-66 Oceanographic Institute of the University of São Paulo | Ref. FAPESP 2015 / 01373-0 Oceanographic Institute of the University of São Paulo | Ref. CNPq 442926 / 2015-4 Oceanographic Institute of the University of São Paulo | Ref. FAPESP 2014 / 50820-7 Oceanographic Institute of the University of São Paulo | Ref. CNPq 565060 / 2010-4 NERC | Ref. NE / R015953 / 1

Eleven incubation experiments were conducted in the South Atlantic sector of the Southern Ocean to investigate the relationship between new production (ρNO–3), regenerated production (ρNH+4), and t...

(2016). An editorial synthesis of the ACEP project: Ecosystem Processes in the KwaZulu-Natal Bight. African Journal of Marine Science: Vol. 38, No. sup1, pp. S217-S223.

Surface pigment data from a transect along the eastern boundary of the Atlantic Ocean was analysed using CHEMTAX to yield more detailed information on the composition of phytoplankton communities. Total chlorophyll a concentrations varied from 0.03 mg m?3 in a northern oligotrophic region to 30.3 mg m?3 in the Benguela ecosystem. Diatoms dominated the Benguela, while both diatoms and haptophytes were the major groups in the Canary ecosystem and the temperate NE Atlantic. Prochlorococcus was the most prominent group in the southern oligotrophic region (15.5°S-15°N) although haptophytes were also a significant component of the population. In contrast, haptophytes dominated the northern oligotrophic region (21°-40°N). Photo-pigment indices indicated that chlorophyll b was mainly associated with prasinophytes and chlorophyll c with diatoms. Elevated photosynthetic carotenoids were due to increased proportions of haptophytes, but also linked with diatoms and dinoflagellates. Photoprotective carotenoids were more prominently associated with Prochlorococcus and to a lesser extent to Synechococcus.

The Agulhas Current is a fast western boundary current flowing along the South African east coast, strongly influencing oceanographic variability on the adjacent KwaZulu-Natal shelf. Hydrographic observations in January 2010, July 2010, and July 1989 have been used to describe variations in geostrophic currents and water masses and to elucidate mechanisms of change in circulation and thermohaline structure. Differences in wind forcing, precipitation, and solar insolation caused modifications in stratification and mixing that resulted in seasonal changes in surface temperature, salinity, and mixed layer depth ZMLD between the austral summer and winter surveys. During January 2010, surface temperatures were elevated and there was a large range in salinity as the upper 10 m was influenced by river outflow and rainfall. In July 2010 and 1989, surface temperatures were lower and the salinity range was significantly less. The ZMLD in January 2010 was much shallower, varying between 5 and 40 m, while deeper ZMLD, from 9 to 107 m, was found in July 2010 and 1989. Cross-shelf, alongshore, and vertical variations in water masses during July 2010 and July 1989 were driven by deviations in the position of the inshore edge of the Agulhas Current and the influence of offshore cyclonic eddies. In January 2010, the close proximity of the current to the coast and shelf break caused increased Ekman veering in the bottom layers along the shelf edge and slope in the north and recirculation in the south.

The Agulhas Current, the largest Western Boundary Current in the Southern Hemisphere, strongly influences the oceanographic conditions of its adjacent shelf system. As a result of limited societal drivers, such as large-scale fisheries and marine mining, the South African southeast shelf, between Port Elizabeth and Port Shepstone, is one of the least studied and under-sampled shelf systems in Southern Africa. This study describes hydrographic conditions from the first two shelf-wide high-resolution surveys (January/February and July/August 2017) of this region. These data provide a baseline of environmental conditions and hydrographic processes across the shelf. The Agulhas Current, as well as cyclonic mesoscale eddies along the inshore edge of the Current, were observed to strongly drive conditions on the shelf. Substantial differences in the impacts of these cyclonic eddies were evident, with the smaller less intense January/February eddy inducing much stronger upwelling than the larger more intense July/August eddy. Indications of seasonality in temperature, salinity and chlorophyll-a were observed in the surface layers. Surface waters were 4 °C warmer in January/February than in July/August. Considerably lower salinities (33.77 g kg−1) were observed in January/February as a result of high rainfall and subsequent increased river outflow. Upwelling mechanisms such as divergence-induced upwelling, Ekman veering in the bottom boundary layer, Ekman pumping associated with cyclonic eddies, were observed to uplift colder, nutrient-rich water from deeper layers onto the mesotrophic shelf. These colder waters ultimately reached the surface as a result of wind-driven Ekman transport and vertical mixing. Tropical Surface Water, Subtropical Surface Water and South Indian Central Water were observed on the shelf. Red Sea Water as well as Antarctic Intermediate Water generally occupied the slope regions except where cyclonic eddies uplifted intermediate waters onto the shelf. The shelf-wide dissolved oxygen levels (>3 ml l−1) suggested that oxygen availability adequately facilitated the survival of the existing shelf biology.

A chemotaxonomic investigation of surface phytoplankton was undertaken on a research cruise to the Atlantic sector of the Southern Ocean during late austral summer 2009. Based on pigment signatures, several distinct regions emerged that were delineated by physical features. CHEMTAX analysis of high performance liquid chromatography (HPLC) pigment data indicated that diatoms generally dominated communities south of the Antarctic Polar Front (APF), particularly in regions of elevated biomass where chlorophyll-a (chl-a) was >1.5 µg l −1 and diatoms comprised >80% of biomass. Pigment signatures representative of haptophytes-8, indicative of Phaeocystis antarctica, were dominant near the ice shelf. Chl-a concentrations were 0.2–0.6 µg l −1 between the APF and the Subtropical Front (STF) and outputs suggested that chlorophytes, haptophytes-8 and haptophyte-6, in the form of coccolithophores, were the major constituents. Very low chl-a levels ( −1 ) were observed north of the STF and the prokaryotes Synechococcus spp. and Prochlorococcus spp. were the dominant groups in these oligotrophic waters.

A compiled set of in situ data is important to evaluate the quality of ocean-colour satellite-data records. Here we describe the data compiled for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The data were acquired from several sources (MOBY, BOUSSOLE, AERONET-OC, SeaBASS, NOMAD, MERMAID, AMT, ICES, HOT, GeP&CO), span between 1997 and 2012, and have a global distribution. Observations of the following variables were compiled: spectral remote-sensing reflectances, concentrations of chlorophyll a, spectral inherent optical properties and spectral diffuse attenuation coefficients. The data were from multi-project archives acquired via the open internet services or from individual projects, acquired directly from data providers. Methodologies were implemented for homogenisation, quality control and merging of all data. No changes were made to the original data, other than averaging of observations that were close in time and space, elimination of some points after quality control and conversion to a standard format. The final result is a merged table designed for validation of satellite-derived ocean-colour products and available in text format. Metadata of each in situ measurement (original source, cruise or experiment, principal investigator) were preserved throughout the work and made available in the final table. Using all the data in a validation exercise increases the number of matchups and enhances the representativeness of different marine regimes. By making available the metadata, it is also possible to analyse each set of data separately. The compiled data are available at doi:10.1594/PANGAEA.854832 (Valente et al., 2015).

International audience; A multidisciplinary programme, MESOBIO (Influence of mesoscale dynamics on biological productivity at multiple trophic levels in the Mozambique Channel) was undertaken in the Mozambique Channel within the framework of a scientific partnership between France and South Africa. MESOBIO focused on the signature of the highly energetic eddy dynamics in the Mozambique Channel. The Channel, which is known to be one of the most turbulent areas in the world ocean, has a great diversity of marine organisms and is the site of active pelagic fisheries. MESOBIO was mostly based on observations at sea during 12 multidisciplinary cruises between 2002 and 2010. Hydrographic measurements, sampling of biological organisms ranging from phytoplankton to top predators, and experiments on primary production and energy transfer through the food web, were conducted onboard various research vessels. The data were analysed in relation to eddy field characteristics for the periods of the cruises, including seasonal or inter-annual variability in mesoscale activity. A modelling approach was also developed within MESOBIO for both the circulation in the Channel and the biogeochemical response to eddy forcing. This paper introduces the suite of articles on the MESOBIO investigations by summarizing background knowledge for the different disciplines and the key issues that were addressed within the programme.

2004 ENVISAT Symposium, Salzburg, AUSTRIA, SEP, 2004; We measured water leaving reflectance, phytoplankton pigments, optical properties and photosynthetic parameters in the southern Benguela ecosystem in October 2002. These data were used to validate MERIS standard products: reflectance (MERIS wavelengths) and Case 1 Chlorophyll- a. In this heterogeneous area, accurate validation required sampling within a few minutes of the satellite overpass. Inter-pigment relationships e. g. Total Chlorophyll (TChla) to Total Pigment (TP) were robust (R-2 similar to 0.99) yet pigment ratios (TChla/TP) were not constant (range 0.44 to 0.62) increasing log-linearly with biomass (R-2 similar to 0.7). Photosynthetic parameters (e. g. Photosynthetic Quantum Efficiency, PQE) and optical ratios (a(676)/a(440)) also increased log-linearly with biomass (R-2 similar to 0.8). PQE, pigment and optical ratios were linearly inter-correlated (R-2 similar to 0.7 to 0.8). From these data we derived the bio-optical traits for several phytoplankton functional types (PFTs): micro-plankton (diatoms and dinoflagellates) had high biomass, pigment ratios and PQE; nano-flagellates had low to intermediate biomass, pigment ratios and PQE; prokaryotes had very low biomass, pigment ratios and PQE. We present MERIS data analysed for PFTs and new products (PQE).

The relationships between phytoplankton pigments, optical properties and photosynthetic parameters for different phytoplankton functional types (derived by diagnostic pigment indices, DPI) were determined from data acquired in the Benguela ecosystem and the offshore region in October 2002. We observed robust inter-pigment relationships: total chlorophyll-a (TChla) was highly correlated with total pigment (TP) and accessory pigment (AP). However, the regression equations for stations dominated by flagellates differed from the equations for stations dominated by diatoms and dinoflagellates. The pigment ratio TChla/TP and the optical ratio a676/a440 were not constant but increased non-linearly with increasing TChla or TP; complimentarily the AP/TP and a490/a676 ratios decreased. There were significant non linear relationships between the photosynthetic parameters Fv/Fm or σPSII measured by Fast Repetition Rate Fluorometry and TChla or TP. Pigment ratios, optical ratios, Fv/Fm and σPSII were all inter-correlated with high significance. We determined the distinctive bio-optical properties associated with dominant phytoplankton functional types (derived by DPI) that conformed to the classical partitioning: flagellates (nano-plankton, comprising several taxa) had low biomass,low TChla/TP fraction and low Fv/Fm and high σPSII; diatoms and dinoflagellates (micro-plankton) had high biomass, pigment ratios, Fv/Fm and low σPSII.

International audience; Whether for biogeochemical studies or ocean color validation activities, high-performance liquid chromatography (HPLC) is an established reference technique for the analysis of chlorophyll a and associated phytoplankton pigments. The results of an intercomparison exercise of HPLC pigment determination, performed for the first time on natural samples and involving four laboratories (each using a different HPLC procedure), are used to address three main objectives: (a) estimate (and explain) the level of agreement or discrepancy in the methods used, (b) establish whether or not the accuracy requirements for ocean color validation activities can be met, and (c) establish how higher order associations in individual pigments (i.e., sums and ratios) influence the uncertainty budget while also determining how this information can be used to minimize the variance within larger pigment databases. The round-robin test samples (11 different samples received in duplicate by each laboratory) covered a range of total chlorophyll a concentration, [TChl a], representative of open ocean conditions from 0.045 mg m(-3), typical of the highly oligotrophic surface waters of the Ionian Sea, to 2.2 mg m(-3), characteristic of the upwelling regime off Morocco. Despite the diversity in trophic conditions and HPLC methods, the agreement between laboratories, defined here as the absolute percent difference (APD), was approximately 7.0% for [TChl a], which is well within the 25% accuracy objective for remote sensing validation purposes. For other pigments (mainly chemotaxinomic carotenoids), the agreement between methods was 21.5% on average (ranging from 11.5% for fucoxanthin to 32.5% for peridinin), and inversely depended on pigment concentration (with large disagreements for pigments close to the detection limits). It is shown that better agreement between methods can be achieved if some simple procedures are employed: (a) disregarding results less than the effective limit of quantitation (LOQ, an alternative to the method detection limit, MDL), (b) standardizing the manner in which the concentration of pigment standards are determined, and (c) accurately accounting for divinyl chlorophyll a when computing [TChl a] for those methods which do not chromatographically separate it from monovinyl chlorophyll a. The use of these quality-assurance procedures improved the agreement between methods, with average APD values dropping from 7.0% to 5.5% for [TChl a] and from 21.5% to 13.9% for the principal carotenoids. Additionally, it is shown that subsequent grouping of individual pigment concentrations into sums and ratios significantly reduced the variance and, thus, improved the agreement between laboratories. This grouping, therefore, provides a simple mechanism for decreasing the variance within databases composed of merged data from different origins. Among the recommendations for improving database consistency in the future, it is suggested that submissions to a database should include the relevant information related to the limit of detection for the HPLC method. (C) 2003 Elsevier B.V. All rights reserved.