Western Tropical North Atlantic Research Articles

Coccolith-calcite Sr/Ca as a proxy for transient export production related to Saharan dust deposition in the tropical North Atlantic

Atmospheric dust deposition can modulate the earth’s climate and atmospheric CO2 through fertilising the ocean (nutrient source) and by accelerating the biological carbon pump through fuelling the ballasting process. To distinguish the biogeochemical effects of Saharan dust with respect to fertilization and ballasting, and to gain a broader perspective on the coccolith calcite Sr/Ca in relation to the drivers of coccolith export production, we determined the coccolith-Sr/Ca from a one-year (2012–2013) time-series sediment trap record in the western tropical North Atlantic (M4—49°N/12°W). High Sr/Ca were linked to enhanced export production in the upper part of the photic zone, most notably under windier, dry, and dustier conditions during spring. Attenuated Sr/Ca in the autumn probably reflect a combination of lower Sr-incorporation by dominant but small-size placolith-bearing species and the presence of “aged” coccoliths rapidly scavenged during a highly productive and usually fast export event, likely added by (wet) dust ballasting. Higher Sr/Ca observed in the large coccolith size fractions support the existing notion that larger-sized coccolithophores incorporate more Sr during calcification under the same environmental conditions. The presence of the abnormally Sr-rich species Scyphosphaera apsteinii is also shown in the separated large fraction of our Sr/Ca seasonal data.

Seasonal variation of the sea surface salinity in the western tropical North Atlantic on two contrasting years of precipitation in the Amazon Basin

Seasonal variation of the sea surface salinity in the western tropical North Atlantic on two contrasting years of precipitation in the Amazon Basin

Planktonic habitats in the Amazon Plume region of the Western Tropical North Atlantic

Planktonic habitats in the Amazon Plume region of the Western Tropical North Atlantic

Multi‐Year Predictability of Global Sea Surface Temperature Using Model‐Analogs

AbstractThe multi‐year predictability of global sea surface temperature (SST) is examined by applying a model‐analog method to four control simulations to make forecasts at leads of 1–36 months over 1961–2015. The forecasts are found to have skill for annual mean SST at Year 2 (i.e., leads of 13–24 months) or even Year 3 (i.e., leads of 25–36 months) in the tropical Pacific, the North and South Pacific, the southwest Indian Ocean, and the northwestern tropical Atlantic. The seasonality in forecast skill suggests that July is the best time to initialize multi‐year forecasts. The evolution of forecast skill for tropical Pacific SSTs indicates that the predictability of some El Niño Southern Oscillation events is nearly the same at leads of 6 and 18 or 24 months. Further, these El Niño and La Niña events can be predicted at leads of up to 24 and 30 months, respectively.

Methylphosphonate-driven methane formation and its link to primary production in the oligotrophic North Atlantic

Methylphosphonate is an organic phosphorus compound used by microorganisms when phosphate, a key nutrient limiting growth in most marine surface waters, becomes unavailable. Microbial methylphosphonate use can result in the formation of methane, a potent greenhouse gas, in oxic waters where methane production is traditionally unexpected. The extent and controlling factors of such aerobic methane formation remain underexplored. Here, we show high potential net rates of methylphosphonate-driven methane formation (median 0.4 nmol methane L−1 d−1) in the upper water column of the western tropical North Atlantic. The rates are repressed but still quantifiable in the presence of in-situ or added phosphate, suggesting that some methylphosphonate-driven methane formation persists in phosphate-replete waters. The genetic potential for methylphosphonate utilisation is present in and transcribed by key photo- and heterotrophic microbial taxa, such as Pelagibacterales, SAR116, and Trichodesmium. While the large cyanobacterial nitrogen-fixers dominate in the surface layer, phosphonate utilisation by Alphaproteobacteria appears to become more important in deeper depths. We estimate that at our study site, a substantial part (median 11%) of the measured surface carbon fixation can be sustained by phosphorus liberated from phosphonate utilisation, highlighting the ecological importance of phosphonates in the carbon cycle of the oligotrophic ocean.

Deglacial Temperature and Carbonate Saturation State Variability in the Tropical Atlantic at Antarctic Intermediate Water Depths

AbstractVariations in the Atlantic Meridional Overturning Circulation (AMOC) redistribute heat and nutrients, causing pronounced anomalies of temperature and nutrient concentrations in the subsurface ocean. However, exactly how millennial‐scale deglacial AMOC variability influenced the subsurface is debated, and the role of other deglacial forcings of subsurface temperature change is unclear. Here, we present a new deglacial temperature reconstruction, which, with published records, helps assess competing hypotheses for deglacial warming in the upper tropical North Atlantic. Our record provides new evidence of regional subsurface warming in the western tropical North Atlantic within the core of modern Antarctic Intermediate Water (AAIW) during Heinrich Stadial 1 (HS1), an early deglacial interval of iceberg discharge into the North Atlantic. Our results are consistent with model simulations that suggest subsurface heat accumulates in the northern high‐latitude convection regions and along the upper AMOC return path when the AMOC weakens, and with warming due to rising greenhouse gases. Warming of AAIW may have also contributed to warming in the tropics at modern AAIW depths during late HS1. Nutrient and reconstructions from the same site suggest a link between AMOC intensity and the northward extent of AAIW in the northern tropics across the deglaciation and on millennial time scales. However, the timing of the initial deglacial increase in AAIW to the northern tropics is ambiguous. Deglacial trends and variability of in the upper North Atlantic have likely biased temperature reconstructions based on the elemental composition of calcitic benthic foraminifera.

Heterologous expression of genes from a cyanobacterial endosymbiont highlights substrate exchanges with its diatom host.

A few genera of diatoms are widespread and thrive in low-nutrient waters of the open ocean due to their close association with N2-fixing, filamentous heterocyst-forming cyanobacteria. In one of these symbioses, the symbiont, Richelia euintracellularis, has penetrated the cell envelope of the host, Hemiaulus hauckii, and lives inside the host cytoplasm. How the partners interact, including how the symbiont sustains high rates of N2 fixation, is unstudied. Since R. euintracellularis has evaded isolation, heterologous expression of genes in model laboratory organisms was performed to identify the function of proteins from the endosymbiont. Gene complementation of a cyanobacterial invertase mutant and expression of the protein in Escherichia coli showed that R. euintracellularis HH01 possesses a neutral invertase that splits sucrose producing glucose and fructose. Several solute-binding proteins (SBPs) of ABC transporters encoded in the genome of R. euintracellularis HH01 were expressed in E. coli, and their substrates were characterized. The selected SBPs directly linked the host as the source of several substrates, e.g. sugars (sucrose and galactose), amino acids (glutamate and phenylalanine), and a polyamine (spermidine), to support the cyanobacterial symbiont. Finally, transcripts of genes encoding the invertase and SBPs were consistently detected in wild populations of H. hauckii collected from multiple stations and depths in the western tropical North Atlantic. Our results support the idea that the diatom host provides the endosymbiotic cyanobacterium with organic carbon to fuel N2 fixation. This knowledge is key to understanding the physiology of the globally significant H. hauckii-R. euintracellularis symbiosis.

Considerations for hypothetical carbon dioxide removal via alkalinity addition in the Amazon River watershed

Abstract. The Amazon River plume plays a critical role in shaping the carbonate chemistry over a vast area in the western tropical North Atlantic. We conduct a sensitivity analysis of hypothetical ocean alkalinity enhancement (OAE) via quicklime addition in the Amazon River watershed, examining the response of carbonate chemistry and air–sea carbon dioxide flux to the alkalinity addition. Through a series of sensitivity tests, we show that the detectability of the OAE-induced alkalinity increment depends on the perturbation strength (or size of the alkalinity addition, ΔTA) and the number of samples: there is a 90 % chance to meet a minimum detectability requirement with ΔTA>15 µmol kg−1 and sample size >40, given background variability of 15–30 µmol kg−1. OAE-induced pCO2 reduction at the Amazon plume surface would range between 0–25 µatm when ΔTA=20 µmol kg−1, decreasing with increasing salinity (S). Adding 20 µmol kg−1 of alkalinity at the river mouth could elevate the total carbon uptake in the Amazon River plume (15<S<35) by at least 0.07–0.1 Mt CO2 per month, and a major portion of the uptake would occur in the saltiest region (S>32) due to its large size, comprising approximately 80 % of the S>15 plume area. However, the lowest-salinity region (S<15) has a greater drop in surface ocean partial pressure of CO2 (pCO2sw) due to its low buffer capacity, potentially allowing for observational detectability of pCO2sw reduction in this region. Reduced outgassing in this part of the plume, while more uncertain, may also be important for total additional CO2 uptake. Such sensitivity tests are useful in designing minimalistic field trials and setting achievable goals for monitoring, reporting, and verification purposes.

Idealized hydrodynamical numerical model dataset with no-river runoff at the western tropical North Atlantic.

The western tropical North Atlantic (WTNA) is a very complex region, with the influence of intense western boundary currents in connection with equatorial zonal currents, important atmospheric forcings (e.g Intertropical Convergence Zone), mesoscale activities (e.g NBC rings), and the world's largest river discharge as the Amazon River runoff. The volume discharge is equivalent to more than one-third of the Atlantic river freshwater input, with a plume that spreads over the region reaching the northwestward Caribbean Sea and eastward longitudes of 30°W, andinfluencing from physical to biological structures. Therefore, in order to enable and encourage more understanding of the region, here we present a dataset based on an idealized scenario of no river runoff of the Amazon River and Par ´a River in the WTNA. The numerical simulations were conducted with a regional oceanicmodeling system (ROMS) model and three pairs of files were generated with themodel outputs: (i) ROMS-files, with the parameters of the ROMS-outputs raw data in a NetCDF format and monthly and weekly frequencies; (ii) MATLAB-files, which contain oceanographic parameters also in monthly and weekly frequencies; and (iii) NetCDF-files, with oceanographic parameters again in monthly and weekly frequencies. For each file, we present the coordinates and variable names, descriptions, and correspondent units. The dataset is available in the Science Data Bank repository (doi: https://doi.org/10.57760/sciencedb.02145).

The Dynamical Tropopause Location as a Potential Predictor for North Atlantic Tropical Cyclone Activity

Abstract Tropical cyclones are among the most devastating natural phenomena that can cause severe damage when undergoing landfall. In the wake of the poorly forecast 2013 North Atlantic hurricane season, Rossby wave breaking on the 350-K isentropic surface has been linked to tropical cyclone activity measured by the accumulated cyclone energy (ACE). Here, ERA5 data and HURDAT2 tropical cyclone data are used to argue that the latitude of the 2 potential vorticity unit (PVU; 1 PVU = 10−6 K kg−1 m2 s−1) contour on the 360-K isentropic surface in the western North Atlantic is linked to changes in vertical wind shear and relative humidity during the month of September. A more equatorward position of the 2-PVU contour is shown to be linked to an increase in vertical wind shear and a reduction in relative humidity, as manifested in an increased ventilation index, in the tropical western North Atlantic during September. The more equatorward position is further linked to a reduction in the number of named storms, storm and hurricane days, hurricane lifetime, and number of tropical cyclones making landfall. Changes in genesis location are shown to be of importance for the changes in landfall frequency and hurricane lifetime. In summary, the 2-PVU contour latitude in the western North Atlantic can, therefore, potentially be used as a predictor in seasonal and subseasonal forecasting. Significance Statement Forecasts for the North Atlantic hurricane season are operationally produced. Their aim is to predict the number of tropical cyclones and their total energy throughout the season. This study proposes to include the tropopause latitude in these forecasts, as it is shown to be linked to vertical wind shear and midtropospheric relative humidity in the western tropical North Atlantic. The tropopause latitude is thereby linked to the number of tropical cyclones, their lifetime, and the total energy throughout the season. This link is particularly strong during September.

Seasonal Eddy Variability in the Northwestern Tropical Atlantic Ocean

Abstract Eddies in the northwestern tropical Atlantic Ocean play a crucial role in transporting the South Atlantic Upper Ocean Water to the North Atlantic and connect the Atlantic and the Caribbean Sea. Although surface characteristics of those eddies have been well studied, their vertical structures and governing mechanisms are much less known. Here, using a time-dependent energetics framework based on the multiscale window transform, we examine the seasonal variability of the eddy kinetic energy (EKE) in the northwestern tropical Atlantic. Both altimeter-based data and ocean reanalyses show a substantial EKE seasonal cycle in the North Brazil Current Retroflection (NBCR) region that is mostly trapped in the upper 200 m. In the most energetic NBCR region, the EKE reaches its minimum in April–June and maximum in July–September. By analyzing six ocean reanalysis products, we find that barotropic instability is the controlling mechanism for the seasonal eddy variability in the NBCR region. Nonlocal processes, including advection and pressure work, play opposite roles in the EKE seasonal cycle. In the eastern part of the NBCR region, the EKE seasonal evolution is similar to the NBCR region. However, it is the nonlocal processes that control the EKE seasonality. In the western part of the NBCR region, the EKE magnitude is one order of magnitude smaller than in the NBCR region and shows a different seasonal cycle, which peaks in March and reaches its minimum in October–November. Our results highlight the complex mechanisms governing eddy variability in the northwestern tropical Atlantic and provide insights into their potential changes with changing background conditions.

Influence of the ITCZ and OMZ on the isotopic composition of suspended particulate matter in the western tropical North Atlantic

The tropical North Atlantic Ocean is a complex region where the intertropical convergence zone (ITCZ) and the oxygen minimum zone (OMZ) play important roles in the control of the physical and biogeochemical processes and affect the efficiency of the carbon pump. Changes in the composition of the particulate organic matter (POM) have been extensively studied in the eastern tropical North Atlantic and recent findings suggested less effective remineralization in the OMZ by comparison with well‑oxygenated waters. However, dynamics of the POM in the western tropical North Atlantic, including the effect of the hypoxic condition on the isotopic signature of the POM, has been poorly understood. This study uses data collected in October 2018 during the PIRATA XVIII cruise (38°W) to describe the biogeochemical variability and isotopic composition of suspended POM in the water column, with emphasis on the effect of the ITCZ and the OMZ on the POM. The ITCZ, located between 5°N and 10°N, was responsible for the low sea surface salinity and local upwelling, thus favoring the high biological productivity found in this band. Although a clear relation between δ13CPOC values and the ITCZ position was not found, low δ15NTPN values (∼2‰) and high silicate concentration observed on the surface between 4°N-6°N suggested that dust deposition and its associated enhancement of the diazotrophic activity may be important in the southernmost part of the ITCZ. Preferential remineralization of fractions rich in 13C (proteins, carbohydrates) and nitrogen compounds resulted in low δ13CPOC and high C:N values observed at depth. However, these alterations were attenuated in the OMZ, suggesting that reduced remineralization expected in waters with low oxygen concentrations may also affect the isotopic POM signature. Additionally, the minimum δ15NTPN value (∼1‰) observed in the core of the OMZ confirms that, although microbial activity may be important in this region, nitrogen-loss processes are not predominant in the western tropical Atlantic.

Mercury methylation linked to nitrification in the tropical North Atlantic Ocean

Methylmercury (MeHg) is a toxin that poses health risks to humans and wildlife, primarily through consumption of seafood (Sunderland and Mason, 2007). Most MeHg bioaccumulation by marine fish likely occurs in the upper 200 m of the ocean, which is mostly oxygenated (Mason et al., 2012). However, mechanisms of Hg methylation in oxic seawater remain unknown, since the hgcAB gene cluster, which encodes proteins for MeHg production, had been found exclusively in anaerobic microbes (Gilmour et al., 2013; Parks et al., 2013). Recent work, however, has shown that hgc genes are widespread in oxic seawater, including in the microaerophilic nitrifier, Nitrospina (Tada et al., 2020; Tada et al., 2021; Gionfriddo et al., 2016; Bowman et al., 2020). Here, we show that potential MeHg production rates in Western Tropical North Atlantic Ocean surface waters, within and near the Amazon River plume, were correlated positively and strongly to nitrification rates and Nitrospina-specific 16S gene expression. Potential Hg methylation and nitrification rates were highest at the most saline and least turbid stations, indicating that sediment particles and nutrient-rich, riverine discharges were not the primary factors promoting either process. These novel results in oxic seawater provide further evidence that Hg methylation is linked to abundant, nitrifying microbes and may help explain marine MeHg distributions.

Complementary description and record of Peltidium perturbatum Geddes, 1968 (Copepoda, Harpacticoida, Peltidiidae) from the Northwestern Tropical Atlantic

Abstract During a survey of the zooplankton community of a protected coastal system on the Caribbean coast of Mexico, several adult females and immature individuals of the usually benthic or epiphytic harpacticoid copepod genus Peltidium, were recovered; they were identified as the Bahamian species P. perturbatum Geddes, 1968. This species has not been recorded from other areas of the Northwestern Tropical Atlantic (NWTA) region after its original description. Based on the examination of the Mexican Caribbean material, a complementary description of this species is presented including new details of antennules, caudal rami, leg 1, and cuticular ornamentation by using SEM analysis. Its finding in the Mexican Caribbean represents the southernmost record of the genus in the Americas and the first record for the Mexican copepod fauna. A key to the known species of the genus in the NWTA is also provided.

Impact of Saharan dust on landfalling North Atlantic tropical cyclones over North America in September

Using reanalysis data and model simulations, this study reveals an increase in September landfalling North Atlantic tropical cyclones (TCs) during years that have a strengthened Saharan dust plume, and the related physical processes are investigated by analyzing the relationship of dust aerosol optical depth with TC track, intensity, and the related meteorological environment. Suppression of the sea surface temperature (SST) by the Saharan dust plume can hinder TC tracks over the central tropical North Atlantic, inducing westward development of TC tracks to the western tropical North Atlantic with higher SST, which is more conducive to TCs forming major hurricanes. This physical process increases TC landfalls in North America, especially major hurricane landfalls in the continental United States, leading to greater potential destructiveness.摘要本项研究利用再分析数据和模式模拟数据分析了沙尘的气溶胶光学厚度与台风的登陆, 轨迹, 强度及相关气象环境参数的关系, 揭示了9月北大西洋台风的登陆次数会在撒哈拉沙尘较强的年份中增加, 以及这一现象的物理机制. 撒哈拉沙尘对热带北大西洋中部海表温度具有抑制作用, 会阻碍该地区的台风活动, 因此台风只能向西移动进入海表温度较高的热带北大西洋西部, 从而更易于形成强台风. 这一物理过程将导致台风登陆北美大陆的频次增加, 特别是强台风登陆美国的可能性增强, 产生更大的潜在破坏性.

Global-Scale Environmental Niche and Habitat of Blue Shark (Prionace glauca) by Size and Sex: A Pivotal Step to Improving Stock Management

Blue shark (Prionace glauca) is amongst the most abundant shark species in international trade, however this highly migratory species has little effective management and the need for spatio-temporal strategies increases, possibly involving the most vulnerable stage or sex classes. We combined 265,595 blue shark observations (capture or satellite tag) with environmental data to present the first global-scale analysis of species’ habitat preferences for five size and sex classes (small juveniles, large juvenile males and females, adult males and females). We leveraged the understanding of blue shark biotic environmental associations to develop two indicators of foraging location: productivity fronts in mesotrophic areas and mesopelagic micronekton in oligotrophic environments. Temperature (at surface and mixed layer depth plus 100 m) and sea surface height anomaly were used to exclude unsuitable abiotic environments. To capture the horizontal and vertical extent of thermal habitat for the blue shark, we defined the temperature niche relative to both sea surface temperature (SST) and the temperature 100 m below the mixed layer depth (Tmld+100). We show that the lifetime foraging niche incorporates highly diverse biotic and abiotic conditions: the blue shark tends to shift from mesotrophic and temperate surface waters during juvenile stages to more oligotrophic and warm surface waters for adults. However, low productivity limits all classes of blue shark habitat in the tropical western North Atlantic, and both low productivity and warm temperatures limit habitat in most of the equatorial Indian Ocean (except for the adult males) and tropical eastern Pacific. Large females tend to have greater habitat overlap with small juveniles than large males, more defined by temperature than productivity preferences. In particular, large juvenile females tend to extend their range into higher latitudes than large males, likely due to greater tolerance to relatively cold waters. Large juvenile and adult females also seem to avoid areas with intermediate SST (~21.7-24.0°C), resulting in separation from large males mostly in the tropical and temperate latitudes in the cold and warm seasons, respectively. The habitat requirements of sensitive size- and sex-specific stages to blue shark population dynamics are essential in management to improve conservation of this near-threatened species.

Increased Interannual Variability in the Dipole Mode of Extreme High-Temperature Events over East China during Summer after the Early 1990s and Associated Mechanisms

Abstract The dominant mode of the interannual variability in the frequency of extreme high-temperature events (FEHE) during summer over eastern China showed a dipole mode with reversed anomalies of FEHE over northeastern and southern China. This study found that the interannual variability of this dipole mode underwent an interdecadal increase after the early 1990s. The anomalous atmospheric circulation responsible for the FEHE dipole mode was associated with the air–sea interaction over the western tropical Pacific and North Atlantic. Due to the weakened correlation between the SST in the tropical Pacific and in the Indian Ocean after the early 1990s, a meridional atmospheric wave train induced by the anomalous SST around the Maritime Continent (MCSST) was intensified during 1994–2013, which was also contributed by the increased interannual variability of MCSST. However, under the influence of the anomalous SST in the Indian Ocean concurrent with the anomalous MCSST, the meridional wave train was weakened and contributed less to the dipole mode during 1972–93. In addition, the dipole mode was associated with the atmospheric wave trains at middle to high latitudes, which were different during the two periods and related to different air–sea interaction in the North Atlantic. The interannual variability of the dipole mode induced by the associated SST anomalies in the North Atlantic during 1994–2013 was significantly larger than that during 1972–93. Therefore, the interannual variability of the dipole mode was increased after the early 1990s.

A new species of Esola Edwards, 1891 (Crustacea, Copepoda, Harpacticoida, Laophontidae) from the Caribbean coast of Colombia.

A new species of the harpacticoid copepod genus Esola is described from specimens collected in Rodadero Beach, on Gaira Bay, on the Caribbean coast of Colombia. The species, E.wellsisp. nov., is described, illustrated, and com­pared with its congeners. Esolawellsisp. nov. differs from its known congeners in details of the armature of legs 1–4. It most closely resembles E.bulbifera (Norman, 1911) in the armature formula of P1–P5 but differs from the latter in several respects, including the female antennule segmentation (7-segmented in E.bulbifera but distinctly 6-segmented in E.wellsisp. nov.) and in the shape and size of the male P3ENP2 apophysis, among other characters. This is the second species of the genus known from the Caribbean and the second record of Esola in the Northwestern Tropical Atlantic. The genus now contains eight species. A key to the known species of the genus is also included.

Pacific and Atlantic Multidecadal Variability Relations with the Choco and Caribbean Low-Level Jets during the 1900–2015 Period

This study analyzes the variability of the Choco jet (CJ) and Caribbean low-level jet (CLLJ) with consideration of the simultaneous Pacific interdecadal oscillation (PDO) and Atlantic multidecadal oscillation (AMO) low-frequency mean states and their effects on the atmospheric circulation and rainfall in northwestern South America and Central America for the 1900–2015 period, during the seasons with the highest intensities of the CJ (September–November (SON)) and the CLLJ (June–August). Variations in the sea surface temperature (SST) anomaly positioning in the eastern Pacific, tropical North Atlantic (TNA)/Caribbean Sea during different mean states restrict the anomalous circulation, and, consequently, the intensity of the CJ and CLLJ. During the warm AMO (WAMO)/cold PDO (CPDO), the SST gradient from the tropical Pacific into the TNA, accompanied by a cyclonic circulation near the east coast of the Americas, intensifies the west–east circulation in the region, strengthening the CJ and weakening the CLLJ during SON such that rainfall increases over Colombia, Central America and in adjacent oceans. During the cold AMO (CAMO)/warm PDO (WPDO) phase, a relative east/west SST gradient occurs in TNA, consistent with a cyclonic circulation in western TNA, establishing an anomalous southwest–northwestward circulation from the eastern Pacific into the Caribbean basin, forming a well-configured CJ, increasing precipitation over Central America and its adjacent oceans. For the CLLJ, during CAMO phases, the anticyclonic circulations extended over most of the TNA favor its intensification from 30° W to the Caribbean Sea. In contrast, during WAMO, the cyclonic circulation near the east coast of the United States restricts its intensification to the Caribbean Sea region. To the best of our knowledge, the results presented here are new and might be useful in atmospheric modeling and extreme event studies.

Small pigmented eukaryote assemblages of the western tropical North Atlantic around the Amazon River plume during spring discharge

Small pigmented eukaryotes (⩽ 5 µm) are an important, but overlooked component of global marine phytoplankton. The Amazon River plume delivers nutrients into the oligotrophic western tropical North Atlantic, shades the deeper waters, and drives the structure of microphytoplankton (> 20 µm) communities. For small pigmented eukaryotes, however, diversity and distribution in the region remain unknown, despite their significant contribution to open ocean primary production and other biogeochemical processes. To investigate how habitats created by the Amazon river plume shape small pigmented eukaryote communities, we used high-throughput sequencing of the 18S ribosomal RNA genes from up to five distinct small pigmented eukaryote cell populations, identified and sorted by flow cytometry. Small pigmented eukaryotes dominated small phytoplankton biomass across all habitat types, but the population abundances varied among stations resulting in a random distribution. Small pigmented eukaryote communities were consistently dominated by Chloropicophyceae (0.8–2 µm) and Bacillariophyceae (0.8–3.5 µm), accompanied by MOCH-5 at the surface or by Dinophyceae at the chlorophyll maximum. Taxonomic composition only displayed differences in the old plume core and at one of the plume margin stations. Such results reflect the dynamic interactions of the plume and offshore oceanic waters and suggest that the resident small pigmented eukaryote diversity was not strongly affected by habitat types at this time of the year.