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Phytoplankton play a central role in the planetary cycling of important elements and compounds. Understanding how phytoplankton are responding to climate change is consequently a major question in Earth Sciences. Monitoring phytoplankton is key to answering this question. Satellite remote sensing of ocean colour is our only means of monitoring phytoplankton in the entire surface ocean at high temporal and large spatial scales, and the continuous ocean-colour data record is now approaching a length suitable for addressing questions around climate change, at least in some regions. Yet, developing ocean-colour algorithms for climate change studies requires addressing issues of ambiguity in the ocean-colour signal. For example, for the same chlorophyll-a concentration (Chl-a) of phytoplankton, the colour of the ocean can be different depending on the type of phytoplankton present. One route to tackle the issue of ambiguity is by enriching the ocean-colour data with information on sea surface temperature (SST), a good proxy of changes in three phytoplankton size classes (PSCs) independent of changes in total Chl-a, a measure of phytoplankton biomass. Using a global surface in-situ dataset of HPLC (high performance liquid chromatography) pigments, size-fractionated filtration data, and concurrent satellite SST spanning from 1991 to 2021, we re-tuned, validated and advanced an SST-dependent three-component model that quantifies the relationship between total Chl-a and Chl-a associated with the three PSCs (pico-, nano- and microplankton). Similar to previous studies, striking dependencies between model parameters and SST were captured, which were found to improve model performance significantly. These relationships were applied to 40 years of monthly composites of satellite SST, and significant trends in model parameters were observed globally, in response to climate warming. Changes in these parameters highlight issues in estimating long-term trends in phytoplankton biomass (Chl-a) from ocean colour using standard empirical algorithms, which implicitly assume a fixed relationship between total Chl-a and Chl-a of the three size classes. The proposed ecological model will be at the centre of a new ocean-colour modelling framework, designed for investigating the response of phytoplankton to climate change, described in subsequent parts of this series of papers., This work is supported primarily by a UKRI Future Leader Fellowship (MR/V022792/1). Additional supports from the UK National Centre for Earth Observation (NCEO), the Simons Foundation Project Collaboration on Computational Biogeochemical Modeling of Marine Ecosystems (CBIOMES, 549947, Shubha Sathyendranath), and Royal Society International Exchanges 2021 Cost Share (NSFC) grant (IEC NSFC 211058) are acknowledged. Astrid Bracher and Vanda Brotas are funded by the European Union’s Horizon 2020 Research and Innovation Programme (N810139): Project Portugal Twinning for Innovation and Excellence in Marine Science and Earth Observation (PORTWIMS). Astrid Bracher is also funded by the ESA 656 S5P+Innovation Theme 7 Ocean Colour (S5POC) project (No. 4000127533/19/I-NS). The AWI in-situ data are supported by the Helmholtz Infrastructure Initiative FRAM. Tarron Lamont and Ray Barlow acknowledge funding, logistical, and administrative support from the South African National Department of Forestry, Fisheries and the Environment (DFFE), Bayworld Centre for Research and Education (BCRE), and the South African National Research Foundation (NRF grants: 129229 and 132073). Fang Shen is funded by National Natural Science Foundation of China (No. 42076187 and No. 41771378) for the sampling of in-situ data in eastern China seas. The Atlantic Meridional Transect (AMT) is funded by the UK Natural Environment Research Council (NERC) through its National Capability Long-term Single Centre Science Programme, Climate Linked Atlantic Sector Science (grant number NE/R015953/1) to Plymouth Marine Laboratory. This work contributes to the international IMBeR project and is contribution number 386 of the AMT programme. The authors would like to acknowledge all the contributors who have shared in-situ data to the public domains, including the Western Channel Observatory, TARA Ocean, Rothera Research Station, NASA SeaBASS, ADON, Government of Canada, DATAONE, BCODMO, EDI Data Portal, PANGAEA, and BODC, and all the scientists and crew who were involved in the collection of in-situ data are sincerely appreciated. We thank NOAA for providing daily and monthly OISST (version 2) SST data; ESA for providing monthly SST-CCI (version 2.1) SST data; ESA for providing monthly OC-CCI (version 5.0) Chl-a climatology data; GEBCO for providing bathymetric data (GEBCO2021 Grid). The authors also thank Hongyan Xi for providing comments and suggestions on the early version of the manuscript.

A global in-situ data set for validation of ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI) is presented. This version of the compilation, starting in 1997, now extends to 2021, which is important for the validation of the most recent satellite optical sensors such as Sentinel 3B OLCI and NOAA-20 VIIRS. The data set comprises in-situ observations of the following variables: spectral remote-sensing reflectance, concentration of chlorophyll-a, spectral inherent optical properties, spectral diffuse attenuation coefficient and total suspended matter. Data were obtained from multi-project archives acquired via open internet services, or from individual projects, acquired directly from data providers. Methodologies were implemented for homogenisation, quality control and merging of all data. Minimal changes were made on the original data, other than conversion to a standard format, elimination of some points after quality control and averaging of observations that were close in time and space. The result is a merged table available in text format. Overall, the size of the data set grew with 151,673 rows, with each row representing a unique station in space and time (cf 136,250 rows in previous version; Valente et al., 2019). Observations of remote-sensing reflectance increased to 68,641 (cf 59,781 in previous version; Valente et al., 2019). There was also a near tenfold increase in chlorophyll data since 2016. Metadata of each in situ measurement (original source, cruise or experiment, principal investigator) are included in the final table. By making the metadata available, provenance is better documented, and it is also possible to analyse each set of data separately. The compiled data are available at https://doi.pangaea.de/10.1594/PANGAEA.941318 (Valente et al., 2022)., SI

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 is a major Western Boundary Current that flows along the southeast slope of southern Africa and has an influence on the biogeochemistry of adjacent ecosystems through localised upwelling of cool, nutrient-rich water up the slope and onto the shelf. Variability in pigments and absorption were therefore examined to determine the adaptation of phytoplankton communities to changing nutrient and irradiance conditions during mid-summer. Chlorophyll a concentrations varied from 0.1 mg m−3 offshore to 7.3 mg m−3 inshore in response to the nutrient enrichment. CHEMTAX analysis revealed that diatoms were the dominant group at most of the inshore stations, mixed populations of diatoms, haptophytes and prasinophytes characterised the shelf edge populations, while haptophytes and Prochlorococcus dominated the offshore stations over the slope. Diatom populations were associated with cool, lower salinity water and prokaryotes with warm, higher salinity water, while flagellates occurred in both water types. Nutrient relationships deviated from Redfield ratios and there appeared to be a greater uptake of silicate at elevated nutrient levels where diatoms were dominant, but nitrate was preferably utilized at low concentrations when flagellates and prokaryotes comprised the communities. Populations acclimated to changing irradiance by adjustments in their absorption and proportion of accessory pigments. Prokaryote dominated communities had high chlorophyll-specific absorption coefficients and a high proportion of chlorophyll a and photoprotective carotenoids. Diatoms had low chlorophyll-specific absorption and elevated proportions of photosynthetic carotenoids and chlorophyll a. Flagellate dominated communities had intermediate chlorophyll-specific absorption and had elevated absorption by chlorophyll a, chlorophyll b and photosynthetic carotenoids. Ratios of UV absorption at 330 nm to chlorophyll a absorption at 676 nm displayed an increasing trend with increased irradiance near the surface, particularly for prokaryotes. Overall, nutrients and irradiance were the main drivers influencing phytoplankton adaptation and acclimation.

Phytoplankton community structure was elucidated during summer and winter in the KwaZulu-Natal Bight using pigment and CHEMTAX analyses. The surface pattern in January 2010 indicated that diatoms, haptophytes and prasinophytes tended to be the most prominent groups inshore and in the southern sector of the bight, whereas Prochlorococcus and Synechococcus were more dominant in the north and towards the offshore region. At the deep chlorophyll maximum (DCM), diatoms were dominant in the inner bight and in the south, with prasinophytes being the prominent flagellates, but this changed to Prochlorococcus and pelagophytes being the important groups in the northern sector and outer part of the bight. A different pattern was observed at the surface in July 2010, where diatoms, haptophytes, prasinophytes and cryptophytes in varying proportions comprised most of the community in the inner half of the bight, whereas Synechococcus and haptophytes were the main groups in the outer sector. A similar pattern occurred a...

During February 2010, studies of primary production (PP) and physiology were conducted at five selected sites in the KwaZulu-Natal (KZN) Bight of the Agulhas ecosystem as part of a programme to elucidate the influence of major physical driving forces and nutrient inputs on the structure and functioning of biological communities. These sites were located in the vicinity of the Durban lee eddy, in the midshelf region of the central part of the bight, off the Thukela Mouth, and to the north and south of Richards Bay. At four of the sites, chlorophyll a ranged from 0.10 to 1.44 mg m–3 and integrated PP ranged between 0.35 and 2.58 g C m–2 d–1. The highest biomass and PP, which were comparable to those observed in a wind-driven upwelling system, were associated with a diatom community observed at the midshelf site, and varied between 0.26 and 4.27 mg m–3 and 7.22 and 9.89 g C m–2 d–1, respectively. Environmental conditions at each of the sites differed substantially and appeared to be influential in initiating...

Phytoplankton size structure is an important indicator of the state of the pelagic ecosystem. Stimulated by the paucity of in situ observations on size structure, and by the sampling advantages of autonomous remote platforms, new efforts are being made to infer the size-structure of the phytoplankton from oceanographic variables that may be measured at high temporal and spatial resolution, such as total chlorophyll concentration. Large-scale analysis of in situ data has revealed coherent relationships between size-fractionated chlorophyll and total chlorophyll that can be quantified using the three-component model of Brewin et al. (2010). However, there are variations surrounding these general relationships. In this paper, we first revise the three-component model using a global dataset of surface phytoplankton pigment measurements. Then, using estimates of the average irradiance in the mixed-layer, we investigate the influence of ambient light on the parameters of the three-component model. We observe significant relationships between model parameters and the average irradiance in the mixed-layer, consistent with ecological knowledge. These relationships are incorporated explicitly into the three-component model to illustrate variations in the relationship between size-structure and total chlorophyll, ensuing from variations in light availability. The new model may be used as a tool to investigate modifications in size-structure in the context of a changing climate.

Cross-shelf distributions of temperature, salinity, water masses, and dissolved oxygen in St. Helena Bay revealed substantial vertical and seasonal variations. In the surface layers, nearshore and offshore temperature and salinity patterns differed, with bay-scale variability linked to upwelling dynamics and coastal processes, while the offshore region was influenced by solar insolation. Spectral analysis revealed that an annual signal prevailed at most stations, and corroborated contrasting patterns between the offshore and nearshore regions, with phase differences suggesting shoreward propagation of the offshore temperature signal. The shelf was dominated by Modified Upwelled Water (MUW) and Subantarctic Mode Water (SAMW), which comprised the primary source of upwelled water. Clear zonation of MUW was evident across the shelf, resulting from seasonal variations in locations of the oceanic and bifurcated shelf-break fronts. Dynamics within St. Helena Bay consistently differed from those further offshore, due to the influences of the shelf-break front, Cape Columbine upwelling plume, and cyclonic recirculation, which appeared to be associated with an intraannual signal with a periodicity of 3–4 months. Persistent hypoxia in the bottom waters suggested the occurrence of a permanent reservoir of Low Oxygen Water (LOW). Seasonal shoreward and offshore expansion of LOW occurred throughout the upwelling season, with maximum extent reached during summer and autumn, due to the coupled effects of advection and local phytoplankton decay. While wind mixing ventilated the water column at nearshore stations in winter, and the onset of upwelling during spring introduced oxygen-richer water from further offshore, hypoxia persisted in the center of the Bay.

Investigations of primary production (PP) were undertaken in the southern Benguela ecosystem during two research surveys in October 2006 and May 2007. Significant differences in environmental conditions, as well as biomass and PP, were observed between October and May. During October, integrated biomass and PP were significantly higher, ranging from 20.43 to 355.01 mg m −2 , and 0.71 to 6.98 g C m −2 d −1 , respectively, than in May, where the range was 47.92–141.79 mg m −2 , and 0.70–3.35 g C m −2 d −1 , respectively. Distribution patterns indicated low biomass and PP in newly upwelled water along the coast, higher biomass and PP in the mid-shelf region, while lower values were observed at and beyond the shelf edge. Latitudinal variations showed consistently higher biomass and PP in the St. Helena Bay region compared to biomass and PP south of Cape Town. During both surveys, phytoplankton communities were comprised primarily of diatoms and small flagellates, with no significant differences. Phytoplankton adaptation to environmental variability was characterised by increased P m B and E k under elevated temperatures and irradiance, while no clear relationships were evident for α B . Generalised Additive Models (GAMs) showed that photosynthetic parameters were all significant predictors of photosynthesis rates ( P z ), with P m B being the most important, accounting for 36.97% of the deviance in P z . However, biomass levels and environmental conditions exerted a much greater influence on P z , with irradiance explaining the largest proportion (68.24%) of the deviance. Multiple predictor GAMs revealed that 96.26% of the deviance in P z could be explained by a model which included nitrate, chlorophyll a , and irradiance.

Variability of hydrographic characteristics and phytoplankton distribution associated with mesoscale eddies in the Mozambique Channel was investigated during four cruises in September 2007, December 2008, November 2009, and April/May 2010. Satellite altimetry was used to map the location of mesoscale features, and together with ETOPO1 bathymetry, was used in a Discriminant Function Analysis to classify in situ sampling stations into five categories, namely cyclonic (C), anti-cyclonic (A), frontal (F), divergence (D), and shelf (S). Fluorescence profiles were integrated through four depth ranges in the upper 200 m and used to determine the depth of the maximum chlorophyll a concentration and to model the euphotic zone depth. At a depth of 100 m, distinctly different hydrographic characteristics were observed between mesoscale features with cyclonic eddies consisting of Subtropical Surface Water and anti-cyclonic eddies containing Tropical Surface Water from the Indian Ocean. Hydrographic properties at divergence and frontal stations reflected a mixture of these water masses, while shelf stations showed considerable variability as a result of the interaction of eddies with the continental slope. Chlorophyll a concentrations in the surface waters were found to be low, with subsurface levels being significantly greater. Phytoplankton biomass in cyclonic and anti-cyclonic eddies was relatively low and not significantly different. The interaction of mesoscale eddies with the continental slope on the western side of the Channel caused upwelling of cooler, nutrient-rich water, which resulted in elevated phytoplankton biomass in the shelf regions. Strong currents at the perimeters of these eddies produced offshore advection of the high biomass into the frontal regions.

The MESOBIO programme investigated mesoscale dynamics using an integrated ecosystem approach, linking physical and biogeochemical processes with different trophic levels. Observation and modeling were used in combination to explain the main processes occurring in the mesoscale eddy field. The particular shape of the Mozambique Channel, composed of two basins interconnected through a narrow zone, favours the generation of mesoscale eddies and increases the opportunity for eddy-shelf interactions. Phytoplankton abundance peaked in areas of nutrient enrichment that are often found in the core of cyclonic eddies, as well as on the continental shelf. Grazers in zooplankton communities exhibited high biovolume in cyclonic eddies, but their abundance was lower in fronts and divergence zones, with lowest biovolume in anticyclones. Biovolume was highest at shelf stations, but very variable and similar to phytoplankton. Age of eddies, their subsequent maturation stage and the dynamics of the eddy field played a major role effecting zooplankton abundance. Micronekton presented abundance patterns coherent with zooplankton distribution, however this was only demonstrated by acoustic methods, whereas mid-water trawl collection and predators stomach contents (predators being used as biological samplers) did not reveal significant relationships with mesoscale features. For upper trophic levels, the average density of foraging seabirds was lowest in anticyclones, highest in cyclones and at intermediate levels in divergence, shelf and frontal zones. However, multifaceted behavioral responses were observed in such a highly variable environment. Swordfish was clearly associated with divergence zones, and to a lesser extent with fronts, suggesting that the higher density in divergences was related to the presence of its main prey, essentially large squids. Although tunas tended to be more abundant in areas with weak geostrophic currents, their relationship to mesoscale features was not straightforward as adult tunas caught by longline have the ability to explore different foraging habitats over a broad range of depths. Several suggestions for advancing eddy-related research from the current state of knowledge are proposed in the second part of the paper.

An investigation of phytoplankton pigment and absorption characteristics was undertaken during three research cruises in the Mozambique Channel to elucidate community structure and examine the adaptation of populations to mesoscale features at the surface and the deep chlorophyll maximum (DCM). Total chlorophyll a concentration (TChla) at the surface was determined to be greater in cyclonic eddies than in anticyclones, while TChla in divergence and shelf zones were similar to cyclones, with frontal zones being slightly lower. TChla at the DCM was similar for all categories, although there was a tendency for anticyclones to have lower TChla. Prokaryotes were the most significant phytoplankton group at the surface, with small flagellates also being of secondary importance, while flagellates dominated at the DCM. A few shelf stations, and frontal and shelf stations close to the shelf, displayed high TChla and diatom domination, particularly at the DCM. Absorption properties and photopigment indices revealed that prokaryote dominated communities had high chlorophyll-specific absorption coefficients, a large range in the proportion of TChla within the total pigment pool and a high proportion of photoprotective carotenoids. Diatoms had low chlorophyll-specific absorption, a relatively high proportion of TChla, and elevated proportions of photosynthetic carotenoids and chlorophyll c. Flagellate dominated communities had intermediate chlorophyll-specific absorption, a lower proportion of TChla, elevated photosynthetic carotenoids and intermediate chlorophyll c.

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.

Phytoplankton absorption, pigments and active fluorescence were investigated at five focus sites in a shelf region during summer and winter to elucidate the adaptation of communities to changing environmental conditions. We determined that the availability of nutrients and changing irradiance were the key drivers of phytoplankton growth and photoacclimation in an ecosystem influenced by a warm western boundary current. Diatoms dominated the communities in the winter, while mixed diatom-flagellate populations generally prevailed in summer. Prokaryotes were dominant in the surface layer at one site where warm water flowed onto the shelf. Diatom and flagellate communities were associated with cooler, lower salinity water and prokaryotes with warm, higher salinity water. Populations appeared not be nutrient stressed and actively drew down silicates and nitrates, with nitrates being rapidly utilized resulting in low ambient nitrate levels in the upper water column. The phytoplankton acclimated to changing irradiance conditions by increasing the quantum yield of photochemistry with decreasing irradiance and adjusting the absorption of light by accessory pigments. Prokaryote dominated communities had high chlorophyll-specific absorption coefficients, and a high proportion of spectral absorption by chlorophyll a and photoprotective carotenoids. Diatoms had low chlorophyll-specific absorption and elevated absorption by photosynthetic carotenoids and chlorophyll c. Although flagellate-dominated communities had intermediate chlorophyll-specific absorption, their proportion of absorption by photosynthetic carotenoids and chlorophyll c was similar to the diatoms.

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.

Using a decade of satellite ocean-colour observations and a model that links chlorophyll-a to the size of the phytoplankton cells, parameterised using pigment data from the Indian Ocean, we examine the implications of the Indian Ocean Dipole (IOD) for phytoplankton size structure. The inferred interannual anomalies in phytoplankton size structure are related to those in sea-surface temperature (SST) and sea-surface height (SSH), derived using satellite radiometry and altimetry, and stratification, derived using the Simple Ocean Data Assimilation (SODA) database. In regions influenced by the Indian Ocean Dipole, we observe a tight correlation between phytoplankton size structure and the physical variables, such that interannual variations in the physical variables accounts for up to 70% of the total variance in phytoplankton size structure. For much of the Indian Ocean, low temperature, low SSH and low stratification (indicative of a turbulent environment) are correlated with larger size classes, consistent with theories on coupling between physical–chemical processes and ecosystem structure. To the extent that phytoplankton function is related to its size structure, changes in physical forcing are likely to influence biogeochemical cycles in the region and the pelagic food web. The limitations of our approach are discussed and we highlight future challenges in satellite ocean-colour monitoring, should climate change lead to any modification in our marine ecosystem.

Phytoplankton absorption and pigment characteristics of a red tide were investigated in coastal waters of the southern Benguela. Diagnostic indices indicated that dinoflagellates were the dominant phytoplankton group, with diatoms and small flagellates being of secondary importance. Very high biomass was observed close to the coast where chlorophyll a concentrations of up to 117 mg m–3 were measured. Both measured (aph) and reconstructed pigment absorption (apig) displayed an increasing trend with chlorophyll a, while the package effect index (Qa*) decreased, indicating increased packaging with an increase in biomass. Proportioning of the total pigment absorption between 400 and 700 nm revealed that chlorophyll a accounted for 39–65% of the absorption, while photosynthetic carotenoids (15–30%) and chlorophyll cs (15–30%) were also prominent in absorbing light for photosynthesis.Keywords: absorption, phytoplankton, pigments, red tideAfrican Journal of Marine Science 2012, 34(2): 241–248

Two distinct morphotypes of the coccolithophore Emiliania huxleyi were observed as part of the phytoplankton succession offshore of Namibia, where coastal upwelling created strong gradients in sea ...

Summary The increase in the areal extent of the subtropical gyres over the past decade has been attributed to a global tendency towards increased water-column stratification. Here, we examine how vertical stratifi- cation governs the community structure of the pico- phytoplankton that dominate these vast marine ecosystems. We analysed phytoplankton community composition in the three Southern Subtropical basins of the Pacific, Indian and Atlantic Oceans using a variety of methods and show that the distributions of picocyanobacteria and photosynthetic picoeukary- otes (PPEs) are strongly correlated with depth and strength of vertical mixing: the changes in community structure occur at various taxonomic levels. In well-mixed waters, PPEs, in particular haptophytes, dominate, whereas in strongly stratified waters, pico- cyanobacteria of the genus Prochlorococcus are prevalent, regardless of whether the relative contribu- tions to total biomass are assessed in terms of pigment or of carbon. This ecological diochotomy within the picophytoplankton supports the hypoth- esis that genomic streamlining provides a selective advantage for Prochlorococcus in highly stable, olig- otrophic systems, but may restrict their ability to dominate in regions subject to dynamic mixing.

Error-quantified, synoptic-scale relationships between chlorophyll-a (Chl-a) and phytoplankton pigment groups at the sea surface are presented. A total of ten pigment groups were considered to represent three Phytoplankton Size Classes (PSCs, micro-, nano- and picoplankton) and seven Phytoplankton Functional Types (PFTs, i.e. diatoms, dinoflagellates, green algae, prymnesiophytes (haptophytes), pico-eukaryotes, prokaryotes and Prochlorococcus sp.). The observed relationships between Chl-a and PSCs/PFTs were well-defined at the global scale to show that a community shift of phytoplankton at the basin and global scales is reflected by a change in Chl-a of the total community. Thus, Chl-a of the total community can be used as an index of not only phytoplankton biomass but also of their community structure. Within these relationships, we also found non-monotonic variations with Chl-a for certain pico-sized phytoplankton (pico-eukaryotes, Prokaryotes and Prochlorococcus sp.) and nano-sized phytoplankton (Green algae, prymnesiophytes). The relationships were quantified with a least-square fitting approach in order to enable an estimation of the PFTs from Chl-a where PFTs are expressed as a percentage of the total Chl-a. The estimated uncertainty of the relationships depends on both PFT and Chl-a concentration. Maximum uncertainty of 31.8% was found for diatoms at Chl-a = 0.49 mg m−3. However, the mean uncertainty of the relationships over all PFTs was 5.9% over the entire Chl-a range observed in situ (0.02 < Chl-a < 4.26 mg m−3). The relationships were applied to SeaWiFS satellite Chl-a data from 1998 to 2009 to show the global climatological fields of the surface distribution of PFTs. Results show that microplankton are present in the mid and high latitudes, constituting only ~10.9% of the entire phytoplankton community in the mean field for 1998–2009, in which diatoms explain ~7.5%. Nanoplankton are ubiquitous throughout the global surface oceans, except the subtropical gyres, constituting ~45.5%, of which prymnesiophytes (haptophytes) are the major group explaining ~31.7% while green algae contribute ~13.9%. Picoplankton are dominant in the subtropical gyres, but constitute ~43.6% globally, of which prokaryotes are the major group explaining ~26.5% (Prochlorococcus sp. explaining 22.8%), while pico-eukaryotes explain ~17.2% and are relatively abundant in the South Pacific. These results may be of use to evaluate global marine ecosystem models.

An investigation of the circulation patterns and thermohaline structures in the Delagoa Bight, Mozambique, was undertaken during May 2004, August 2004, April 2005, and April 2006, using hydrographic surveys, surface drifters and satellite imagery. Hydrographic and satellite data during May 2004 illustrated a cyclonic eddy centred at 26° S, 34.25° E in the Bight. A surface drifter remained trapped in this eddy for six weeks between 8 May and 20 June 2004 before moving southward in the Agulhas Current. During August 2004, the core of a cyclonic eddy was located south of the Bight, while no cyclonic eddy was observed during April 2005 or in April 2006. The Delagoa Bight eddy appeared to be more transient than previously thought. Important observations were the recurrent northward current (25–30 cm s–1) occurring subsurface on the shelf, and the prominence of cooler upwelled water at various locations due to the interaction of passing eddies with the bottom topography of the Bight.Keywords: coastal countercurrent, cyclonic lee eddy, Delagoa Bight, upwellingAfrican Journal of Marine Science 2010, 32(3): 553–562

An investigation of phytoplankton production and physiology was undertaken during two research cruises on the southeastern shelf of southern Africa. The data set included photosynthesis-irradiance and active fluorescence parameters, phytoplankton absorption coefficients and HPLC pigment concentrations. Primary production was estimated to vary over a similar range for both cruises within 0.27–3.69 g C m−2 d−1. Pigment indices indicated that diatoms were dominant on the first cruise and the communities were subject to conditions where the mixed layer was deeper than the euphotic zone and they optimized their photosynthesis to very low light intensities at the bottom and below the euphotic zone. Mixed diatom-flagellate populations were observed during the second cruise where the euphotic zone was deeper than the mixed layer and the populations adapted to irradiances higher in the euphotic zone. In response to a mean lower water column PAR, it was found that these mixed communities increased the proportion of chlorophyll a in the pigment pool and had a higher quantum yield of photochemistry and higher light-limited photosynthetic efficiency.

The Benguela system is one of the four major eastern boundary upwelling systems of the world. It is unusual as there are two stratified subtropical or warm temperate boundary regions, on either side of the major wind-driven upwelling region(19–34°S), which itself is subdivided at 26°S by the powerful Luderitz upwelling cell. Important biological components cross the boundary areas at different stages to complete the life-history cycle. While the “Bakun triad” of factors responsible for the development of large pelagic fish populations (enrichment, concentration and retention) provide an important unifying principle for understanding the compromise implicit in adaptation to upwelling systems, the role of predation has been neglected, as has the fish yield relative to photosynthesis. The role global climate change will have in the Benguela in terms of shifting boundaries or weakening or intensifying gradients is being explored. The interannual and decadal signals are so strong in the region that long term trends are difficult to distinguish. Intensive resource utilisation and the collapse of several fish stocks occurred in the Benguela region during the 1960s and 1970s, with different recovery trajectories in the north and the south. The Angolan subsystem can be described as a subtropical transition zone between the wind-driven upwelling system and the Equatorial Atlantic, with gentle upwelling-favourable winds, well-defined seasons, intermediate productivity and moderate, declining fisheries. It is separated from the Namibian subsystem by the Angola-Benguela front.The northern Benguela shelf is a typical coastal upwelling system with equatorward winds, cool water, high plankton biomass and moderate to high fish biomass, which is currently in a depleted state. A shift from sardines to horse mackerel occurred during the period 1970–1990, while hake have never fully recovered from intensive fishing pressure up to 1990. Widespread oxygen-depleted waters and sulphur eruptions result from local and remote forcing, restricting the habitat available for pelagic and demersal fish species.The Luderitz–Orange River Cone is an intensive perennial upwelling cell where strong winds, high turbulence and strong offshore transport constitute a partial barrier to epipelagic fish species. Upwelling source water alters in salinity and oxygen, across this boundary zone. A decline in upwelling-favourable winds occurred between 1990 and 2005.The southern Benguela region is characterised by a pulsed, seasonal, wind-driven upwelling at discrete centres and warm Agulhas water offshore. High primary productivity forms a belt of enrichment along the coast, constrained by a front. Low-oxygen water, which only occurs close inshore, may adversely affect some resources. The west coast is primarily a nursery ground for several fish species which spawn on the Agulhas Bank and are transported by alongshore jet currents to the west coast.The Agulhas Bank forms the southern boundary of the Benguela system and it displays characteristics of both an upwelling and a temperate shallow shelf system, with seasonal stratification and mixing, coastal, shelf-edge and dynamic upwelling, moderate productivity and a well oxygenated shelf. A large biomass of fish occupies the Bank during the summer season, with some evidence for tight coupling between trophic levels. A cool ridge of upwelled water, with links to coastal upwelling and to the Agulhas Current, appears to play an important but poorly understood role affecting the distribution and productivity of pelagic fish. A boom in sardine and anchovy populations was accompanied by an eastward shift, followed by 5 years of poor recruitment by sardine but successful recruitment of anchovy, indicating changes in the early life-history patterns of these two species.

We derived size-specific photosynthetic rates for eastern boundary upwelling regions using satellite ocean colour, by a simple approach that links photosynthetic rate to phytoplankton size classes with the optical absorption of phytoplankton. Comparisons with a conventional chlorophyll-based photosynthetic algorithm and with in situ measurements showed good agreement with our approach ( r 2 = 0.728, p

The phytoplankton pigment composition (chlorophylls and carotenoids) from 17 Atlantic Meridional Transect (AMT) cruises over the period 1995–2005 was analysed to determine the distributions of pigments and plankton in the Atlantic Ocean between 50°N and 50°S. Data were quality assured by statistical methods, including regression of total chlorophyll a (TChla) versus accessory pigments (AP) and comparison of the AMT-TChla with contemporary SeaWiFS-TChla (cruises AMT-05 to -17). Comparisons of province-mean TChla (±SD) for in situ and satellite data showed good agreement for each cruise. ‘Taxa-specific’ pigments were used to define phytoplankton functional types (PFTs) for each of the biogeochemical provinces along the AMT. Pigment ratios (e.g. TChla/AP) were analysed for each cruise and for each province as indices (characteristic properties) of particular PFTs. Mostly robust positive correlations were observed between TChla and pigment ratios for different PFTs, for some provinces and most cruises. These were consistent with previous observations. Generally there were no significant trends of mean TChla or pigment ratios within provinces over the period 1995–2005, although the previously reported perturbation due to the 1997–1998 ENSO was evident.

Phytoplankton production was investigated throughout the whole Benguela ecosystem in winter 1999 and in summer 2002 during two four-week research cruises from Cape Town, South Africa, through Namibian waters to Namibe in southern Angola. Primary production ranged from 0.14–2.26 g C m−2 d−1 during June–July 1999 and from 0.39–8.83 g C m−2 d−1 during February–March 2002. Mean productivity values indicated that the Benguela ecosystem was twice as productive in summer than in winter. In 1999, most of the productivity occurred within a temperature range of 13.5–18 °C, whereas in 2002 elevated production was associated with temperatures of 14–22 °C. The relationship between primary production and chlorophyll a was good for winter 1999 but poor for summer 2002, suggesting that predicting primary production from chlorophyll a is not straightforward for the Benguela ecosystem.

An investigation of pigments, phytoplankton types and absorption characteristics was conducted in the Delagoa and Natal Bights during late winter and spring in the southwest Indian Ocean. The study demonstrated that small flagellates dominated the phytoplankton communities in both bights and were ubiquitous across a temperature range of 18–24 °C. Diatoms were dominant in patches of cool water ( 22 °C. Absorption coefficients varied closely with variations in chlorophyll a and specific coefficients were lower for diatoms compared to flagellates. Chlorophyll-specific coefficients also provided useful information on the level of pigment packaging and were related to the proportion of chlorophylls and carotenoids in the pigment pool.

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).

We review the concept of phytoplankton functional types (PFTs) in marine ecosystems as a means of advancing bio-mechanistic models that can be coupled to the global carbon cycle and the Earth's climate system. Conventional classification of phytoplankton by size may seem arbitrary, but there appears clear links between size and environmental characteristics (availability of essential nutrients and light) that regulate photosynthesis, phytoplankton selection and succession. Taking a minimalist approach, small phytoplankton (picoplankton) survive in permanently stratified systems with low nutrients, high surface light and low light in deep clines, whereas large phytoplankton (microplankton) thrive in high nutrient, turbulent, high light, near surface systems. Nutrient-light environmental conditions are characteristic properties of globally, latitudinal-dispersed biogeochemical provinces. These contrasting nutrient-light regimes define the extreme ends of the bio-energetic scale of photosynthesis and set the end points of the primary range of phytoplankton functional processes. To determine PFTs from remotely sensed ocean colour data, there must be a specific bio-optical trait (BOT) that can be associated with the phytoplankton species or taxa. We investigate the connection of the bio-energetic scale to phytoplankton types and their BOTs, which is the first, but crucial step for classifying PFTs on the basis of functional processes, from which refinements and further partitioning can be developed.

Pigment indices were used to characterise the seasonal succession of phytoplankton, and associated changes in chlorophyll a and accessory pigments, in subtropical waters of the three ocean basins in the southern hemisphere. Diagnostic indices revealed the dominance of small flagellates and elevated biomass during winter–spring in the Pacific, mixed flagellate–prokaryote communities and intermediate biomass during early summer in the Atlantic, and prokaryote dominance with low biomass in mid-summer in the Indian Ocean. Photo-pigment indices indicated only a small variation in the chlorophyll a proportion of total pigments across the ocean basins, but the accessory pigments varied considerably. Under low temperature and irradiance conditions, the photosynthetic carotenoids were prominent, but as temperatures and irradiance increased and nutrients declined, there was a significant increase in the proportion of photoprotective carotenoids. At high temperatures and irradiances, the photoprotective carotenoids were the largest component of the pigment pool, exceeding the proportion of chlorophyll a . These variations in phytoplankton composition, and their photoacclimation status, could be explained according to environmental changes and have implications for satellite estimations of biomass and primary production.

A non-linear model that uses satellite-derived chlorophyll to estimate water-column primary production was developed and tested using data from the Delagoa Bight, where the model results compared well with local estimates. The data were also used to assess variations in phytoplankton biomass and daily water-column primary production (PZT ;m g Cm � 2 day � 1 ), in relation to physico-chemical variables. The distribution of phytoplankton biomass and primary production was partly influenced by gyre circulation and other water flow in the Bight, such as eddies, eastern Madagascar current and the Agulhas current. The locally-developed model could be applied throughout the region to estimate primary production. For low biomass (

By using data collected during a continuous circumnavigation of the Southern Hemisphere, we observed clear patterns in the population-genetic structure of Prochlorococcus , the most abundant photosynthetic organism on Earth, between and within the three Southern Subtropical Gyres. The same mechanisms that were previously invoked to account for the vertical distribution of ecotypes at local scales accounted for the global (horizontal) patterns we observed. Basin-scale and seasonal variations in the structure and strength of vertical stratification provide a basis for understanding large-scale horizontal distribution in genetic and physiological traits of Prochlorococcus , and perhaps of marine microbial communities in general.

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.

The distributions of monomethylamine (MMA), dimethylamine (DMA), trimethylamine (TMA) and ammonium (NH+4) were investigated in the Arabian Sea. The data set presented is the first to describe the distribution of MAs on an oceanic scale. Throughout the region concentrations of NH+4 were up to two orders of magnitude greater than those of the MAs. MMA (0–66 nM) was generally the most abundant MA, whilst TMA was only found at concentrations

The increase in the areal extent of the subtropical gyres over the past decade has been attributed to a global tendency towards increased water-column stratification. Here, we examine how vertical stratification governs the community structure of the picophytoplankton that dominate these vast marine ecosystems. We analysed phytoplankton community composition in the three Southern Subtropical basins of the Pacific, Indian and Atlantic Oceans using a variety of methods and show that the distributions of picocyanobacteria and photosynthetic picoeukaryotes (PPEs) are strongly correlated with depth and strength of vertical mixing: the changes in community structure occur at various taxonomic levels. In well-mixed waters, PPEs, in particular haptophytes, dominate, whereas in strongly stratified waters, picocyanobacteria of the genus Prochlorococcus are prevalent, regardless of whether the relative contributions to total biomass are assessed in terms of pigment or of carbon. This ecological diochotomy within the picophytoplankton supports the hypothesis that genomic streamlining provides a selective advantage for Prochlorococcus in highly stable, oligotrophic systems, but may restrict their ability to dominate in regions subject to dynamic mixing.

Phytoplankton production and physiology were investigated at six selected locations during a research cruise in early October 2007 in Tanzanian coastal waters. The dataset included photosynthesis–irradiance and active fluorescence parameters, phytoplankton absorption coefficients, and pigment concentrations. Primary production was estimated to vary over the range 0.79–1.89 g C m–2 d–1. Diagnostic pigments indicated that micro–nanophytoplankton comprised the communities at three stations and nano–picoplankton at the other three stations. At all stations, the populations maximised their photosynthesis in the upper water column under elevated irradiance and low nutrient conditions. Significant photosynthetic activity was also observed at depth under very low light where the communities increased their quantum yield of photochemistry and the proportion of accessory chlorophylls b and c and photosynthetic carotenoids.Keywords: physiological adaptation, primary production, Tanzania coastal watersAfrican Journal of Marine Science 2011, 33(2): 283–295

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.