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Key challenges to regionalization of methane fluxes in the Amazon basin are the large seasonal variation in inundated areas and habitats, the wide variety of aquatic ecosystems throughout the Amazon basin, and the variability in methane fluxes in time and space. Based on available measurements of methane emission and areal extent, seven types of aquatic systems are considered: streams and rivers, lakes, seasonally flooded forests, seasonally flooded savannas and other interfluvial wetlands, herbaceous plants on riverine floodplains, peatlands, and hydroelectric reservoirs. We evaluate the adequacy of sampling and of field methods plus atmospheric measurements, as applied to the Amazon basin, summarize published fluxes and regional estimates using bottom-up and top-down approaches, and discuss current understanding of biogeochemical and physical processes in Amazon aquatic environments and their incorporation into mechanistic and statistical models. Recommendations for further study in the Amazon basin and elsewhere include application of new remote sensing techniques, increased sampling frequency and duration, experimental studies to improve understanding of biogeochemical and physical processes, and development of models appropriate for hydrological and ecological conditions. 

Measurements of turbulence, as rate of dissipation of turbulent kinetic energy (ε), adjacent to the air-water interface are rare but essential for understanding of gas transfer velocities (k) used to compute fluxes of greenhouse gases. Variability in ε is expected over diel cycles of stratification and mixing. Monin-Obukhov similarity theory (MOST) predicts an enhancement in ε during heating (buoyancy flux, β+) relative to that for shear (u*w 3/κz where u*w is water friction velocity, κ is von Karman constant, z is depth). To verify and expand predictions, we quantified ε in the upper 0.25 m and below from profiles of temperature-gradient microstructure in combination with time series meteorology and temperature in a tropical reservoir for winds <4 m s−1. Maximum likelihood estimates of near-surface ε during heating were independent of wind speed and high, ∼5 × 10−6 m2 s−3, up to three orders of magnitude higher than predictions from u*w 3/κz, increased with heating, and were ∼10 times higher than during cooling. k, estimated using near-surface ε, was ∼10 cm hr−1, validated with k obtained from chamber measurements, and 2–5 times higher than computed from wind-based models. The flux Richardson number (Rf) varied from ∼0.4 to ∼0.001 with a median value of 0.04 in the upper 0.25 m, less than the critical value of 0.2. We extend MOST by incorporating the variability in Rf when scaling the influence of β+ relative to u*w 3/κz in estimates of ε, and by extension, k, obtained from time series meteorological and temperature data. 

Extensive floodplains and numerous lakes in the Amazon basin are well suited to examine the role of floodable lands within the context of the sources and processing of carbon within inland waters. We measured diel, seasonal and inter-annual variations of carbon dioxide concentrations and related environmental variables in open water and flooded vegetation and estimated the extension of these habitats using remote sensing in a representative central Amazon floodplain lake, Lake Janauacá. Depth-averaged values of CO2 in the open water of the lake, 157± 91 µM (mean ± SD), were less than those in an embayment near aquatic vegetation, 285±116 µM, and were variable over 24-h periods at both sites. Within floating herbaceous plant mats, mean concentration (without one outlier) was 275±77 µM and in flooded forests mean concentration was 217±78 µM. Variability in CO2 concentrations in open water resulted from changes in the extent of inundation and exchange with vegetated habitats. The best statistical model, including CO2 in aquatic plant mats, Secchi depth, rate of change in water level and chlorophyll concentrations, explained around 90% of the variability in CO2 concentration. Three-dimensional hydrodynamic modeling demonstrated that diel differences in water temperature between plant mats and open water and basin-scale motions caused lateral exchanges of CO2 linking vegetated habitats to open water. Our findings extend understanding of CO2 in tropical lakes and floodplains with measurements and models that emphasize the importance of flooded forests and aquatic herbaceous plants fringing floodplain lakes as sources of carbon dioxide to the open waters. 

Large uncertainties in estimates of methane (CH4) emissions from tropical inland waters reflect the paucity of information at appropriate temporal and spatial scales. CH4 concentrations, diffusive and ebullitive fluxes, and environmental parameters in contrasting aquatic habitats of Lake Janauaca´, an Amazon floodplain lake, measured for two years revealed patterns in temporal and spatial variability related to different aquatic habitats and environmental conditions. CH4 concentrations ranged from below detection to 96 lM, CH4 diffusive fluxes from below detection to 2342 lmol m-2 h-1, and CH4 ebullitive fluxes from 0 to 190 mmol m-2 d-1. Vegetated aquatic habitats had higher surface CH4 concentrations than open water habitats, and no significant differences in diffusive CH4 fluxes, likely due to higher k values measured in open water habitats. CH4 emissions were enhanced after a prolonged low water period, when the exposed sediments were colonized by herbaceous plants that decomposed after water levels rose, possibly fueling CH4 production. Statistical models indicated the importance of variables related to CH4 production (temperature, dissolved organic carbon) and consumption (dissolved nitrogen, oxygenated water column), as well as maximum depth.