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Amazon floodplain ecosystems include open water and intermittent flood forest and agricultural systems with different water types. They are a significant natural source of methane (CH4) in the tropics. When soils are flooded and become anoxic, CH4 is produced by methanogenesis, while microbially mediated aerobic and anaerobic oxidation of CH4 serves as the primary biological sink of this greenhouse gas. Measurements of rates and controls on CH4 production and emission in the Amazon basin mainly come from studies on individual wetlands and floodplain lakes. Similarly, microbial communities in those Amazon floodplain habitats have been studied on individual lakes based on sequence-specific DNA analysis. Existing biogeochemical ecosystem models of CH4 from the Amazon floodplains focus on soil properties or involve factors such as pH, redox potentials, or substrates. None of these models incorporate appropriate seasonal inundation; neither the microbiota does it as a component. In this sense, our chapter will highlight how the important efforts already contributed to understand the CH4 emission and its connections with abiotic and biotic factors in Amazon floodplains, as well as emphasize the need of encouraging cooperation and exchange of experience between research teams by using different approaches and scientific methods."