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The El Niño-driven fire season in Indonesia in September–October 2015 produced the largest fire emissions on record since NASA's EOS satellites started making observations of tropospheric pollutants from space. In this study, measurements of carbon monoxide (CO) from the Measurement of Pollution in the Troposphere (MOPITT) on Terra and the Microwave Limb Sounder are used to characterize the anomalously high CO emitted during the 2015 Indonesian fire season transported into the wildfires was transported into the upper troposphere with time lags up to ∼2 months and continued to be tropical upper troposphere and stratosphere. The satellite measurements indicate that CO emitted from transported into the stratosphere, which resulted in higher concentrations of CO extending up to ∼20 hPa by the end of 2016. Hydrogen cyanide (HCN) measured by the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS) confirms that anomalously high HCN emitted from the same wildfires was also transported into the tropical stratosphere and persisted throughout 2017. Simulations of CO from the Community Atmosphere Model with Chemistry (CAM-chem) show a significant increase in CO concentrations in the troposphere in October 2015. However, comparisons between CAM-chem and MOPITT CO suggest that the model underestimates the amount of CO even with doubled emissions of CO in October 2015. Both the satellite measurements and the model simulations show that the pollution emitted from the wildfires over Indonesia was transported to and persisted in the tropical stratosphere much longer than the previous El-Niño driven fire events due to unprecedented amount of the fire emissions.