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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 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.

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.

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.

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.