Eddy-covariance observations. We used eddy-covariance observations of carbon fluxes between ecosystems and the atmosphere from FLUXNET 2015 dataset63 (Tier 1; https://fluxnet.org/data/download-data/). The data used half-hourly and hourly carbon fluxes and their concurrent meteorological observations from 197 sites around the world (Fig. S8), including net ecosystem exchange (NEE_VUT_USTAR50), ecosystem respiration (RECO_DT_VUT_USTAR50 estimated from a daytime partitioning method21 (DT) and RECO_NT_VUT_USTAR50 estimated from a nighttime partitioning method22 (NT), air temperature (TA_F), solar radiation (SW_IN_F), and vapour pressure deficit (VPD_F) and relative humidity (RH). For the missing RH value, we applied random forest (RF) method to fill the gap using TA_F and VPD_F as drivers20. We also used a modified method20 to estimate ecosystem respiration from NEE_VUT_USTAR50, that is RECO_DT-RH.
Modified partitioning method (DT-RH). The DT-RH partitioning method has been successfully applied and demonstrated at three sites20. Here we briefly recapitulate our method. DT-RH modeling strategy is based on the following assumptions: (1) temperature sensitivity of ER was different between daytime and nighttime; (2) the effect of moister conditions on ER might vary from negative in wet ecosystems to positive in dry ones. This method was modified from the study of ref.21 by adding a relative humidity (RH) term as follows:

where α (µmol C J− 1) is the canopy-scale quantum yield, which represents the initial slope of the light-response curve; β (µmol C m− 2 s− 1) is the maximum CO2 uptake rate of the canopy at light saturation, which in turn is regulated by VPD. The threshold of VPD (VPD0) is set to 10 hPa. k is a coefficient to quantify the response of the maximum CO2 uptake to VPD, and Q is the global radiation (W m− 2). Rref (µmol C m− 2 s− 1) is the base respiration rate at the reference temperature (Tref = 15℃). E0 (℃) is the temperature sensitivity of ER and Tair (℃) is the air temperature. \(\stackrel{-}{RH}\) is the mean value of RH at a certain data window and ε is a fitted site-specific parameter, which indicates the positive and negative relationship between \(\stackrel{-}{RH}\) and the standardized respiration rate64 (i.e., the ratio of daytime ER (DER) and Rref, day, DER/Rref, day, referred to as site characteristics) across different sites. The standardized respiration rate (DER/Rref, day) was first calculated from the DT-E0 method20. The parameter \(\epsilon\)was set to -1 if a negative correlation existed between DER/Rref, day and \(\stackrel{-}{RH}\); otherwise, it was set to 1. The other parameters (α, β0, k, daytime Rref (Rref, day) and E0 (E0, day)) were estimated by fitting the entire model to the daytime data, whereas nighttime Rref (Rref, night) and E0 (E0, night) were estimated using nighttime data. We then applied Rref, day and E0, day to estimate daytime ER, and used Rref, night and E0, night to estimate nighttime ER.
Global forcing data. To compute the global flux products at monthly resolution via upscaling, we collected the global meteorological data and Normalized Difference Vegetation Index (NDVI). We extracted gridded monthly diurnal temperature range (DTR), daily mean temperature (Tair), monthly average daily minimum (Tmin) and maximum temperature (Tmax), frost day frequency (Frs), precipitation (Pre), vapour pressure (Vap), wet day frequency (Wet) and potential evapotranspiration (PET) time series data at 0.5° spatial resolution which were obtained from Climate Research Unit (CRU TS v. 4.04, https://crudata.uea.ac.uk/cru/data/hrg/). We also used monthly surface solar radiation (Rg), air relative humidity (RH) and surface volumetric soil moisture (0-7cm, SWC) data from the fifth-generation ECMWF atmospheric reanalysis of the global climate (ERA5) at 0.1°, 0.25° and 0.25° spatial resolution separately. In parallel, we collected global standardized precipitation-ET index (SPEI) data with 0.5° spatial resolution and a monthly time resolution as a measure of drought intensity (https://spei.csic.es/database.html). We obtained the biweekly Global Inventory Modeling and Mapping Studies third-generation (GIMMS-3g) NDVI dataset (https://ecocast.arc.nasa.gov/data/pub/gimms/3g.v1/) with a spatial resolution of 1/12° (~ 8km). Here, we composited the biweekly GIMMS-NDVI3g data to monthly temporal resolution by selecting the higher of the two composites in the same month and then aggregated to 0.5° × 0.5° to match the resolution of meteorological data. To analyze the effects of elevated atmospheric CO2 concentrations on long-term changes of ER, we used global atmospheric CO2 concentration averages from the National Oceanic and Atmospheric Administration (NOAA, https://gml.noaa.gov/ccgg/trends/gl_data.html) from 1989 to 2018.
Global ecosystem respiration estimation. A machine learning method (i.e., random forest65) was applied to estimate global terrestrial ecosystem respiration (ER) from 1989 to 2018. Firstly, we estimated ER based on half-hourly (or hourly) eddy covariance data from 197 globally distributed flux towers using DT-RH method20, which modified daytime flux partitioning method to estimate ER by integrating the different daytime and nighttime temperature sensitivities of respiration along with relative humidity. Secondly, we convert half-hourly (or hourly) scale ER data to a monthly scale at each site, and yield a global dataset composed of monthly estimates of local respiration and forcing data (i.e., DTR, Tair, Tmin, Tmax, Frs, Vap, PET, RH, Wet, Rg, SPEI, SWC) from each tower. Thirdly. we used these global dataset to train the random forest model (RF) and then created maps of gridded monthly ER at 0.5° resolution covering the whole period 1989–2018, namely DT-RH products. In addition, in order to consider the impact of land cover change on ER estimates, we also added NDVI into the global training dataset in steps two and three. The other steps remained consistent, and this ER product named DT-RH_NDVI. Since the results were highly consistent between DT-RH and DT-RH_NDVI (Table S1 and Fig. S4), we only used ER dataset from DT-RH for the following analyses. RF model was created by using h2o package (https://github.com/h2oai/h2o-3) in R. To evaluate the performance of our approach, we firstly evaluated the accuracy of training data by comparing with available measured monthly night-time ecosystem respiration at site scale (Fig. S9) using R2 (coefficient of determination). Mean monthly estimates across global sites showed considerably higher accuracy in DT-RH method than DT and NT methods (RMSEDT−RH = 4.37 ± 0.24, RMSEDT = 11.83 ± 0.67, and RMSENT = 6.0 ± 0.46 g C m− 2 month− 1, respectively; Fig. S1). Then, the validity of our data-driven ER product was supported by internal cross-validation at FLUXNET sites (R2 = 0.715, RMSE = 26.322 g C m− 2 month− 1; Table S1), which was better performance than the standard methods18 (i.e., R2DT = 0.64, RMSEDT = 34.2 g C m− 2 month− 1; R2NT = 0.64, RMSENT = 34.5 g C m− 2 month− 1).
For this study, we also used ER data from FLUXCOM (version RS + METEO)18,66 and the Coupled Model Intercomparison Project Phase 6 (CMIP6) models24–29. The FLUXCOM ER product is based on machine learning methods that upscale FLUXNET67 observations of carbon fluxes, which estimate from two flux partitioning approaches21,22. We collected FLUXCOM-ER product generated by random forest (RF) method at 0.5° spatial resolution and monthly time scale over the period 1989–2018. The six of model simulations from CMIP6 were considered in our analysis, including BCC-CSM2-MR, BCC-ESM1, CESM2, CMCC-CM2-SR5, CMCC-ESM2, MPI-ESM1-2-LR. From these model outputs, we extracted years 1989 to 2014 for comparison with our inferred estimates of ER.
Statistical analyses. All statistical analyses were carried out in R version 4.0.568. We used the piecewise linear regression method to determine the turning point of ER during 1989–2018. The temporal trends of ER were calculated by combining the results of a Theil-Sen median trend analysis and a Mann-Kendall test with R package “trend”. Before conducting the variable importance and partial correlation analysis, we first detrended all time series data to avoid auto-correlation and to make the time series stationary. We used random forest models69 to identify those statistically significant factors contributing to ER, including MAT, SWC, SPEI, MAP, Rg. Variable importance was determined by the increase in node purity (IncNodePurity) which was measured as the decrease in the residual sum of squares if the variable was excluded70,71. Greater values of IncNodePurity indicated a greater importance of variables. Random forest analyses were implemented in “rfPermute” package, and variable importance was tested for significance by 1000 permutations. The direct response of ER to temperature and soil moisture was further examined using the partial correlation analysis. To compare with other studies on global and regional TER estimates, we defined three regions10,11 based on annual air temperature (MAT): tropical (MAT > 17 ℃), temperate (2 ℃ ≤ MAT ≤ 17 ℃), and boreal (MAT < 2 ℃). ALL these analyses were performed at the pixel, regional, and global scales.