Amazonian floodplains exhibit complex hydrological patterns, with flood pulses causing large seasonal fluctuations in water level and hydrodynamics. Research on flooding dynamics in tropical floodplains has revealed a substantial impact on plankton community structure. Our field study focused on the Curuai floodplain, a tropical system within the Amazon Basin in northern Brazil. We conducted parallel transects sampling across seven lakes of the floodplain during both rising and falling water periods. The objective is to quantify carbon biomass partition among bacterioplankton, phytoplankton, and zooplankton and to understand how hydrological changes influence plankton communities and their interactions. Phytoplankton accounted for the largest fraction of the plankton carbon (> 70%), followed by zooplankton (≈16%), with bacteria contributing the least to the total carbon pool (< 10%). Hydrological variations significantly altered the structure and interactions of plankton communities. During the rising water period, increased water transparency led to higher amounts of bacteria, cryptophytes, and a greater contribution of cladocerans to the zooplankton carbon stock. The greater crustacean zooplankton biomass during the flood coincided with a lower phytoplankton biomass, including cyanobacteria. Bacterial production seemed to sustain a microbial loop that was relatively independent from the classical food web, and microorganisms were likely a carbon sink during the rising water. The falling water period was marked by a more productive environment, characterized by higher nutrient levels (total nitrogen: 240.0–700.0 µg L−1), organic carbon (0.7–12.0 mg L−1), and temperatures (29.9–34.9 °C), which influenced community structure and plankton interactions. Rotifers experienced a significant biomass increase, ranging from 103.4 µg C L−1 during the rising water period to 290.0 µg C L−1 during the falling water period, and the biomass ratio between rotifers and bacteria rose from 0.5 to 5.4, on average. Copepods also exerted a greater impact on bacterioplankton during this period. Cyanobacteria’s relative contribution doubled during the falling water period, constituting, on average, 42% of the phytoplankton carbon biomass and predominantly consisting of potentially toxic species. This likely disrupted the phytoplankton–zooplankton relationships, and the high primary productivity most likely flowed mainly through microbial pathways in the studied Amazonian floodplain system.
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