Gap-filling eddy covariance methane fluxes : Comparison of machine learning model predictions and uncertainties at FLUXNET-CH4 wetlands

Time series of wetland methane fluxes measured by eddy covariance require gap-filling to estimate daily, seasonal, and annual emissions. Gap-filling methane fluxes is challenging because of high variability and complex responses to multiple drivers. To date, there is no widely established gap-filling standard for wetland methane fluxes, with regards both to the best model algorithms and predictors. This study synthesizes results of different gap-filling methods systematically applied at 17 wetland sites spanning boreal to tropical regions and including all major wetland classes and two rice paddies. Procedures are proposed for: 1) creating realistic artificial gap scenarios, 2) training and evaluating gap-filling models without overstating performance, and 3) predicting halfhourly methane fluxes and annual emissions with realistic uncertainty estimates. Performance is compared between a conventional method (marginal distribution sampling) and four machine learning algorithms. The conventional method achieved similar median performance as the machine learning models but was worse than the best machine learning models and relatively insensitive to predictor choices. Of the machine learning models, decision tree algorithms performed the best in cross-validation experiments, even with a baseline predictor set, and artificial neural networks showed comparable performance when using all predictors. Soil temperature was frequently the most important predictor whilst water table depth was important at sites with substantial water table fluctuations, highlighting the value of data on wetland soil conditions. Raw gap-filling uncertainties from the machine learning models were underestimated and we propose a method to calibrate uncertainties to observations. The python code for model development, evaluation, and uncertainty estimation is publicly available. This study outlines a modular and robust machine learning workflow and makes recommendations for, and evaluates an improved baseline of, methane gap-filling models that can be implemented in multi-site syntheses or standardized products from regional and global flux networks (e.g., FLUXNET).Peer reviewe

Influence of climate variability on seasonal and interannual variations of ecosystem CO2 exchange in flooded and non-flooded rice fields in the Philippines

Seasonal rainfall in the Philippines is known to be modulated by ENSO phenomenon, with El Nino frequently contributing to reduced rainfall and drought while La Nina resulting in excessive rainfalls, floods and more intense typhoons. The alterations in rainfall patterns can have considerable feedback on solar radiation, air temperature, and soil moisture which can affect the ecosystem CO2 exchange. In this paper, we assessed the effects of the ENSO events (2008-mid 2010) on the seasonal climate conditions and determined how it affected the gross primary production (GPP), ecosystem respiration (Re), and net ecosystem production (NEP) of two contrasting rice environments: flooded and non-flooded. The 2008 dry season (DS) was under a La Nina event while the 2008 wet season (WS) was a neutral one with strong tropical cyclones associated during the wet season. The 2009DS was also La Ninna while the 2009WS was El Nino; however, the northern part of the Philippines experienced strong tropical cyclones. The 2010DS was under an El Nino event. The La Nina in 2008DS resulted in about 15% lower solar radiation (SR), 0.3 degre es Centigrade lower air temperature (Ta) and 60% higher precipitation compared to the 28-year climate normal patterns. Both flooded and non-flooded rice fields had lower NEP in 2008 DS (164 and 14 g C/m2, respectively) than in 2008 WS (295 and 82 g C/m2, respectively) because the climate anomaly resulted in SR-driven decrease in GPP. The La Nina in 2009DS even resulted in 0.2 deg C lower air temperature and 40% more precipitation than the 2008DS La Nina. This cooler temperature resulted in lower Re in flooded rice fields while the higher precipitation resulted in higher GPP in non-flooded fields since the climate was favorable for the growth of the aerobic rice, the ratoon crops and the weeds. This climate anomaly benefitted both flooded and non-flooded rice fields by increasing NEP (351 and 218 g C/m2, respectively). However, NEP decreased in 2009WS in both flooded and non-flooded rice fields (225 and 39 g C/m2, respectively) due to the devastating effects of the strong tropical cyclones that hit the northern part of the Philippines. On the other hand, the El Nino event during 2010DS resulted in about 6% higher solar radiation, 0.4 degrees Centigrade higher air temperature and 67% lower precipitation than the 28-year climate normal pattern. The NEP of flooded and non-flooded rice fields were closely similar at 187 and 174 g C/m2, respectively. This climate anomaly resulted in Ta - driven increase in Re, as well as vapor pressure deficit (VPD) - driven decrease in GPP in flooded rice fields. The GPP and Re in non-flooded rice fields were less sensitive to higher VPD and higher Ta, respectively. It appears that the net ecosystem CO2 exchange in non-flooded rice field was less sensitive to an El Nino event

Methane and nitrous oxide emissions from rice and maize production in diversified rice cropping systems

Traditional irrigated double-rice cropping systems have to cope with reduced water availability due to changes of climate and economic conditions. To quantify the shift in CH4 and N2O emissions when changing from traditional to diversified double cropping-systems, an experiment including flooded rice, non-flooded “aerobic” rice and maize was conducted during the dry season (February–June 2012) in the Philippines. Two automated static chamber–GC systems were used to continuously measure CH4 and N2O emissions in the three cropping systems of which each included three different nitrogen fertilization regimes. Turning away from flooded cropping systems leads to shifts in greenhouse gas emissions from CH4 under wet soil to N2O emissions under drier soil conditions. The global warming potential (GWP) of the non-flooded crops was lower compared to flooded rice, whereas high CH4 emissions under flooded conditions still override enhanced N2O emissions in the upland systems. The yield-scaled GWP favored maize over aerobic rice, due to lower yields of aerobic rice. However, the lower GHG emissions of upland systems are only beneficial if they are not overwhelmed by enhanced losses of soil organic carbon

Influence of climate variability on seasonal and interannual variations of ecosystem CO2 exchange in flooded and non-flooded rice fields in the Philippines

Seasonal rainfall in the Philippines is known to be modulated by ENSO phenomenon, with El Niño frequently contributing to reduced rainfall and drought while La Niña resulting in excessive rainfalls, floods and more intense typhoons. The alterations in rainfall patterns can have considerable feedback on solar radiation, air temperature, and soil moisture which can affect the ecosystem CO2 exchange. In this paper, we assessed the effects of the ENSO events (2008–mid 2010) on the seasonal climate conditions and determined how it affected the gross primary production (GPP), ecosystem respiration (Re), and net ecosystem production (NEP) of two contrasting rice environments: flooded and non-flooded. The 2008 dry season (DS) was under a La Niña event while the 2008 wet season (WS) was a neutral one with strong tropical cyclones associated during the wet season. The 2009DS was also La Niña while the 2009WS was El Niño; however, the northern part of the Philippines experienced strong tropical cyclones. The 2010DS was under an El Niño event. The La Niña in 2008DS resulted in about 15% lower solar radiation (SR), 0.3 °C lower air temperature (Ta) and 60% higher precipitation compared to the 28-year climate normal patterns. Both flooded and non-flooded rice fields had lower NEP in 2008 DS (164 and 14 g C m−2, respectively) than in 2008 WS (295 and 82 g C m−2, respectively) because the climate anomaly resulted in SR – driven decrease in GPP. The La Niña in 2009DS even resulted in 0.2 °C lower air temperature and 40% more precipitation than the 2008DS La Niña. This cooler temperature resulted in lower Re in flooded rice fields while the higher precipitation resulted in higher GPP in non-flooded fields since the climate was favorable for the growth of the aerobic rice, the ratoon crops and the weeds. This climate anomaly benefitted both flooded and non-flooded rice fields by increasing NEP (351 and 218 g C m−2, respectively). However, NEP decreased in 2009WS in both flooded and non-flooded rice fields (225 and 39 g C m−2, respectively) due to the devastating effects of the strong tropical cyclones that hit the northern part of the Philippines. On the other hand, the El Niño event during 2010DS resulted in about 6% higher solar radiation, 0.4 °C higher air temperature and 67% lower precipitation than the 28-year climate normal pattern. The NEP of flooded and non-flooded rice fields were closely similar at 187 and 174 g C m−2, respectively. This climate anomaly resulted in Ta – driven increase in Re, as well as vapor pressure deficit (VPD) – driven decrease in GPP in flooded rice fields. The GPP and Re in non-flooded rice fields were less sensitive to higher VPD and higher Ta, respectively. It appears that the net ecosystem CO2 exchange in non-flooded rice field was less sensitive to an El Niño event

Carbon uptake and water productivity for dry-seeded rice and hybrid maize grown with overhead sprinkler irrigation

A growing scarcity of irrigation water could progressively lead to changes in rice production to systems using less irrigation water for rice or more crop diversification. A shift from current production of rice on flooded soils to production of rice on non-flooded soil with water-saving irrigation or to production of more water-efficient crops will have profound effects on carbon, water, and energy exchanges. This study used the eddy covariance technique to examine C uptake and water use efficiencies for water-saving, dry-seeded rice production and production of hybrid maize under overhead sprinkler irrigation as an alternative to flooded rice during two growing seasons. Maize with its C4 physiology has greater photosynthetic capacity than rice. In 2011, maize had 1.4 times higher net C uptake than rice and twice as much grain yield as rice (10.4 vs 5.3 Mg ha−1). In 2012, lower solar radiation due to increased cloudiness and heavy rainfall during critical growth stages (late vegetative to early reproductive) decreased LAI and resulted to about 20% less net C uptake and maize yield (8.2 Mg ha−1), but the rice yield was unchanged (5.3 Mg ha−1) presumably because of improved crop management which included effective crop establishment at lower seed rate and efficient N application using fertigation. Canopy light use efficiency, crop water productivity (WPET), and photosynthetic water use efficiency were 1.8, 1.9, and 1.6 times higher for maize than rice, respectively, despite sensitivity of maize to excess water. Net C uptake, evapotranspiration, and WPET of dry-seeded rice under overhead sprinkler irrigation were comparable to those reported elsewhere for flooded rice. Average total water input (irrigation + rainfall) for rice was only 908 mm, as compared to 1300–1500 mm reported in literature for typical puddled transplanted rice

Carbon release from rice roots under paddy rice and maize-paddy rice cropping

Crop rotations encompassing flooded rice and an upland crop are commonly found in large parts of South and East Asia. However, also rice farmers in Southeast Asia increasingly switch from double-cropping paddy rice to one non-flooded crop–such as maize–in the dry season. We hypothesized that introducing maize (maize–paddy rice, M-MIX) into a double paddy rice (R-WET) cropping system will increase carbon (C) release from rice roots into the rhizosphere and the dissolved soil C pool. To test this hypothesis we assessed the kinetics of C release by the rice plants in a hydroponic greenhouse experiment, and used these data for interpreting their C release in field experiments using 13C pulse labeling of rice plants. In the greenhouse we observed that rice roots released 13C labeled dissolved organic carbon (DOC) for 21 days with a mean residence time (MRT) of 19 days after exposure to a 13CO2 pulse. The MRT of labeled dissolved inorganic carbon (DIC) released from rice roots was only 2 days. In the field 13CO2 pulse labeling increased the 13C excess of rhizosphere soil up to 0.7 ± 0.2 mg 13C kg−1 in R-WET and 0.9 ± 0.3 mg kg−1 in M-MIX. The 13C signature of bulk soil remained unaffected. DOC concentrations in R-WET were significantly higher than in M-MIX during the mature grain stage of the rice plants. Nevertheless, the 13C excess in DOC transiently increased by only 0.5 μg L−1 after labeling in 13 cm depth in one of three lysimeters previously cropped with maize (M-MIX), while no labeled DOC was detected in 13 cm depth of the R-WET lysimeters and in 60 cm depth of both treatments. In contrast, the 13C excess of DIC increased by 42.4–93.1 μg L−1 a few days after labeling with a MRT of 53–66 days in both treatments. Considering the results of the greenhouse experiment, this suggests a rapid mineralization of labeled rhizodeposits in the field and an effective transient storage of CO2 produced by respiration in soil water

Comparisons of energy balance and evapotranspiration between flooded and aerobic rice fields in the Philippines

The seasonal and annual variability of sensible heat flux (H), latent heat flux (LE), evapotranspiration (ET), crop coefficient (Kc) and crop water productivity (WPET) were investigated under two different rice environments, flooded and aerobic soil conditions, using the eddy covariance (EC) technique during 2008–2009 cropping periods. Since we had only one EC system for monitoring two rice environments, we had to move the system from one location to the other every week. In total, we had to gap-fill an average of 50–60% of the missing weekly data as well as those values rejected by the quality control tests in each rice field in all four cropping seasons. Although the EC method provides a direct measurement of LE, which is the energy used for ET, we needed to correct the values of H and LE to close the energy balance using the Bowen ratio closure method before we used LE to estimate ET. On average, the energy balance closure before correction was 0.72 ± 0.06 and it increased to 0.99 ± 0.01 after correction. The G in both flooded and aerobic fields was very low. Likewise, the energy involved in miscellaneous processes such as photosynthesis, respiration and heat storage in the rice canopy was not taken into consideration. Average for four cropping seasons, flooded rice fields had 19% more LE than aerobic fields whereas aerobic rice fields had 45% more H than flooded fields. This resulted in a lower Bowen ratio in flooded fields (0.14 ± 0.03) than in aerobic fields (0.24 ± 0.01). For our study sites, evapotranspiration was primarily controlled by net radiation. The aerobic rice fields had lower growing season ET rates (3.81 ± 0.21 mm d−1) than the flooded rice fields (4.29 ± 0.23 mm d−1), most probably due to the absence of ponded water and lower leaf area index of aerobic rice. Likewise, the crop coefficient, Kc, of aerobic rice was significantly lower than that of flooded rice. For aerobic rice, Kc values were 0.95 ± 0.01 for the vegetative stage, 1.00 ± 0.01 for the reproductive stage, 0.97 ± 0.04 for the ripening stage and 0.88 ± 0.03 for the fallow period, whereas, for flooded rice, Kc values were 1.04 ± 0.04 for the vegetative stage, 1.11 ± 0.05 for the reproductive stage, 1.04 ± 0.05 for the ripening stage and 0.93 ± 0.06 for the fallow period. The average annual ET was 1301 mm for aerobic rice and 1440 mm for flooded rice. This corresponds to about 11% lower total evapotranspiration in aerobic fields than in flooded fields. However, the crop water productivity (WPET) of aerobic rice (0.42 ± 0.03 g grain kg−1 water) was significantly lower than that of flooded rice (1.26 ± 0.26 g grain kg−1 water) because the grain yields of aerobic rice were very low since they were subjected to water stress. The results of this investigation showed significant differences in energy balance and evapotranspiration between flooded and aerobic rice ecosystems. Aerobic rice is one of the promising water-saving technologies being developed to lower the water requirements of the rice crop to address the issues of water scarcity. This information should be taken into consideration in evaluating alternative water-saving technologies for environmentally sustainable rice production systems

Comparisons of energy balance and evapotranspiration between flooded and aerobic rice fields in the Philippines

The seasonal and annual variability of sensible heat flux (H), latent heat flux (LE), evapotranspiration (ET), crop coefficient (Kc) and crop water productivity (WPET) were investigated under two different rice environments, flooded and aerobic soil conditions, using the eddy covariance (EC) technique during 2008-2009 cropping periods. Since we had only one EC system for monitoring two rice environments, we had to move the system from one location to the other every week. In total, we had to gap-fill an average of 50-60% of the missing weekly data as well as those values rejected by the quality control tests in each rice field in all four cropping seasons. Although the EC method provides a direct measurement of LE, which is the energy used for ET, we needed to correct the values of H and LE to close the energy balance using the Bowen ratio closure method before we used LE to estimate ET. On average, the energy balance closure before correction was 0.72 ± 0.06 and it increased to 0.99 ± 0.01 after correction. The G in both flooded and aerobic fields was very low. Likewise, the energy involved in miscellaneous processes such as photosynthesis, respiration and heat storage in the rice canopy was not taken into consideration. Average for four cropping seasons, flooded rice fields had 19% more LE than aerobic fields whereas aerobic rice fields had 45% more H than flooded fields. This resulted in a lower Bowen ratio in flooded fields (0.14 ± 0.03) than in aerobic fields (0.24 ± 0.01). For our study sites, evapotranspiration was primarily controlled by net radiation. The aerobic rice fields had lower growing season ET rates (3.81 ± 0.21 mm d-1) than the flooded rice fields (4.29 ± 0.23 mm d-1), most probably due to the absence of ponded water and lower leaf area index of aerobic rice. Likewise, the crop coefficient, Kc, of aerobic rice was significantly lower than that of flooded rice. For aerobic rice, Kc values were 0.95 ± 0.01 for the vegetative stage, 1.00 ± 0.01 for the reproductive stage, 0.97 ± 0.04 for the ripening stage and 0.88 ± 0.03 for the fallow period, whereas, for flooded rice, Kc values were 1.04 ± 0.04 for the vegetative stage, 1.11 ± 0.05 for the reproductive stage, 1.04 ± 0.05 for the ripening stage and 0.93 ± 0.06 for the fallow period. The average annual ET was 1301 mm for aerobic rice and 1440 mm for flooded rice. This corresponds to about 11% lower total evapotranspiration in aerobic fields than in flooded fields. However, the crop water productivity (WPET) of aerobic rice (0.42 ± 0.03 g grain kg-1 water) was significantly lower than that of flooded rice (1.26 ± 0.26 g grain kg-1 water) because the grain yields of aerobic rice were very low since they were subjected to water stress. The results of this investigation showed significant differences in energy balance and evapotranspiration between flooded and aerobic rice ecosystems. Aerobic rice is one of the promising water-saving technologies being developed to lower the water requirements of the rice crop to address the issues of water scarcity. This information should be taken into consideration in evaluating alternative water-saving technologies for environmentally sustainable rice production systems.Evapotranspiration Crop coefficient Crop water productivity Heat fluxes Flooded rice Aerobic rice

Carbon uptake and water productivity for dry-seeded rice and hybrid maize grown with overhead sprinkler irrigation

A growing scarcity of irrigation water could progressively lead to changes in rice production to systems using less irrigation water for rice or more crop diversification. A shift from current production of rice on flooded soils to production of rice on non-flooded soil with water-saving irrigation or to production of more water-efficient crops will have profound effects on carbon, water, and energy exchanges. This study used the eddy covariance technique to examine C uptake and water use efficiencies for water-saving, dry-seeded rice production and production of hybrid maize under overhead sprinkler irrigation as an alternative to flooded rice during two growing seasons. Maize with its C4 physiology has greater photosynthetic capacity than rice. In 2011, maize had 1.4 times higher net C uptake than rice and twice as much grain yield as rice (10.4 vs 5.3 Mg ha-1). In 2012, lower solar radiation due to increased cloudiness and heavy rainfall during critical growth stages (late vegetative to early reproductive) decreased LAI and resulted to about 20% less net C uptake and maize yield (8.2 Mg ha-1), but the rice yield was unchanged (5.3 Mg ha-1) presumably because of improved crop management which included effective crop establishment at lower seed rate and efficient N application using fertigation. Canopy light use efficiency, crop water productivity (WPET), and photosynthetic water use efficiency were 1.8, 1.9, and 1.6 times higher for maize than rice, respectively, despite sensitivity of maize to excess water. Net C uptake, evapotranspiration, and WPET of dry-seeded rice under overhead sprinkler irrigation were comparable to those reported elsewhere for flooded rice. Average total water input (irrigation + rainfall) for rice was only 908 mm, as compared to 1300 - 1500 mm reported in literature for typical puddled transplanted rice