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Solar radiation absorption by biomass burning aerosols has a strong warming effect over the southeast Atlantic. Interactions between the overlying smoke aerosols and low-level cloud microphysics and the subsequent albedo perturbation are, however, generally ignored in biomass burning radiative assessments. In this study, Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) are combined with Aqua satellite observations from Moderate Resolution Imaging Spectroradiometer (MODIS), Advanced Microwave Scanning Radiometer–EOS (AMSR-E), and Clouds and the Earth’s Radiant Energy System (CERES) to assess the effect of variations in the boundary layer height and the separation distance between the cloud and aerosol layers on the cloud microphysics. The merged data analyzed at a daily temporal resolution suggest that overlying smoke aerosols modify cloud properties by decreasing cloud droplet size despite an increase in the cloud liquid water as boundary layer deepens, north of 5°S. These changes are controlled by the proximity of the aerosol layer to the cloud top rather than increases in the column aerosol load. The correlations are unlikely driven by meteorological factors, as three predictors of cloud variability, lower tropospheric stability, surface winds, and mixing ratio suggest that cloud effective radius, cloud top height, and liquid water path should correlate positively. Because cloud effective radius anticorrelates with cloud liquid water over the region with large microphysical changes—north of 5°S—the overall radiative consequence at the top of the atmosphere is a strong albedo susceptibility, equivalent to a 3% albedo increase due to a 10% decrease in cloud effective radius. This albedo enhancement partially offsets the aerosol solar absorption. Our analysis emphasizes the importance of accounting for the indirect effect of smoke aerosols in the cloud microphysics when estimating the radiative impact of the biomass burning at the top of the atmosphere.