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.

Colossoma macropomum is the second largest scaled fish of the Amazon. It is economically important for commercial fisheries and for aquaculture, but few studies have examined the diversity and genetic structure of natural populations of this species. The aim of this study was to investigate the levels of genetic variability and connectivity that exist between three natural populations of C. macropomum from the Amazon basin. In total, 247 samples were collected from the municipalities of Tefé, Manaus, and Santarém. The populations were genotyped using a panel of 12 multiplex microsatellite markers. The genetic diversity found in these populations was high and similar to other populations described in the literature. These populations showed a pattern of high gene flow associated with the lack of a genetic structure pattern, indicating that the number of migrants per generation and recent migration rates are high. The values of the F_ST, R_ST, and exact test of differentiation were not significant for pairwise comparisons between populations. The Bayesian population clustering analysis indicated a single population. Thus, the data provide evidence for high genetic diversity and high gene flow among C. macropomum populations in the investigated region of the Amazon basin. This information is important for programs aiming at the conservation of natural populations.