At the mouth of the Amazon River, a widespread carbonate ecosystem exists below the river plume, generating a hard-bottom reef (∼9500 km2) that includes mainly large sponges but also rhodolith beds. The mesozooplankton associated with the pelagic realm over the reef formation was characterized, considering the estuarine plume and oceanic influence. Vertical hauls were carried out using a standard plankton net with 200 μm mesh size during September 2014. An indicator index was applied to express species importance as ecological indicators in community. Information on functional traits was gathered for the most abundant copepod species. Overall, 179 zooplankton taxa were recorded. Copepods were the richest (92 species), most diverse and most abundant group, whereas meroplankton were rare and less abundant. Species diversity (>3.0 bits.ind-1) and evenness (>0.6) were high, indicating a complex community. Small holoplanktonic species dominated the zooplankton, and the total density varied from 107.98 ind. m-3 over the reef area to 2,609.24 ind. m-3 in the estuarine plume, with a significant difference between coastal and oceanic areas. The most abundant copepods were the coastal species ithona plumifera and Clausocalanus furcatus and early stages copepodites of Paracalanidae. The holoplanktonic Oikopleura, an important producer of mucous houses, was very abundant on the reefs. The indicator species index revealed three groups: (1) indicative of coastal waters under the influence of the estuarine plume [Euterpina acutifrons, Parvocalanus crassirostris, Oikopleura (Vexillaria) dioica and Hydromedusae]; (2) characterized coastal and oceanic conditions (Clausocalanus); (3) characterized the reef system (O. plumifera). Two major copepods functional groups were identified and sorted according to their trophic strategy and coastal-oceanic distribution. The species that dominated the coastal area and the area over the rhodolith beds are indicators of the estuarine plume and are mixed with species of the North Brazil Current. These species practically disappear offshore, where occur oceanic species commonly found in other oligotrophic tropical areas. This ecosystem shows a mixture of estuarine, coastal and oceanic communities coexisting in the waters over the Amazon reefs, with no significant differences among these areas. However, the MDS clearly separated the communities along the salinity gradient in the plume.

Oceanographic features influence the early stages of fish to a high degree. We investigated the influence of continental shelf-slope gradient on the ichthyoplankton composition and distribution off Northeastern Brazil. Two oceanographic campaigns were performed during July-August 2010 and 2012. The samplings were performed along three transects composed by three stations, covering the continental shelf and slope areas. Abiotic data were obtained by an ADCP and a CTD. The ichthyoplankton was sampled through diurnal and nocturnal hauls using a 500-µm bongo net from 200 m to the surface. A total of 1634 larvae and 4023 eggs, representing 91 genera and 76 species, were collected. Higher concentrations of fish eggs were found on the continental shelf, probably because of the North Brazil Undercurrent flux. Higher concentrations of larvae were found at night and could be associated with net avoidance or natural variation. Neritic, oceanic and transition groups of species association were determined. Larvae of neritic, demersal and pelagic fishes prevailed on the continental shelf, while larvae of oceanic, mesopelagic and bathypelagic fishes on the continental slope. Melanostomiidae, Scorpaena sp., Lestidium atlanticum, Lampadena sp. and Diaphus sp. were identified as indicators of the continental slope.

Connectivity Between Coastal-Oceanic Zooplankton the reproduction and the trophic strategies were the main factors in structuring the community. We found a pelagic gradient for the zooplankton community varying from a low diverse eutrophic coastal area to a high diverse oligotrophic oceanic area, located over a varied, high biomass benthic habitat, which is mostly covered by calcareous algae functioning on the shallow shelf as a large reef system.

In the area around the archipelago of São Pedro e São Paulo (ASPSP), a set of small rocky islands in the Equatorial Atlantic, the thermocline begins at a more superficial depth than in the surrounding waters. This raises the question if there is any change in heterotrophic microplanktonic protists assemblages occurring in the surface mixed layer and in the subsurface layer. To answer this question, we sampled seawater in seven depths (between 1-100 m) with a 10L Niskin bottle and obtained temperature and salinity profiles with a CTD at eight sites around the ASPSP. The depth of the surface mixed layer varied between 18-63 meters. Dinoflagellates dominated in terms of abundance representing over 80% and 65% of the individuals found in the surface and subsurface layers, respectively. A PERMANOVA test revealed significant differences (p < 0.001) among the dinoflagellate and tintinnid assemblages occurring in both layers, but no evidence for difference in the radiolarian assemblage was detected. Good ecological indicators were found mainly within the dinoflagellate assemblage. The thermocline induced stratification allowed the development of different microplanktonic protists assemblages above and under the depth of the surface mixed layer in the upper 100 m of the water column.

The plankton trophic structure of a hypereutrophic tropical estuarine system was evaluated in the dry and wet seasons, as well as during the dry–wet transition period, over 1 year. Correlations between micro- and mesozooplankton abundance and composition and both size-fractioned phytoplankton biomass and abiotic variables were investigated in order to understand seasonal variations in plankton interactions and provide a conceptual trophic model for the plankton community. Rainfall is the main environmental forcing factor for this system, and the plankton community responded accordingly, with different structures during each season sampled. The resulting trophic model shows a multivorous food web, where both longer microbial and shorter herbivore food webs occur simultaneously. Microzooplankton play a crucial role in this ecosystem, linking both small and large phytoplankton to the mesozooplankton. These results have important implications for estuarine management practices, particularly under highly eutrophic conditions.