Alpine wetlands sequester large amounts of soil carbon, so it is vital to gain a full understanding of their land-atmospheric CO
2 exchanges and how they contribute to regional carbon neutrality; such an understanding is currently lacking for the Qinghai—Tibet Plateau (QTP), which is undergoing unprecedented climate warming. We analyzed two-year (2018–2019) continuous CO
2 flux data, measured by eddy covariance techniques, to quantify the carbon budgets of two alpine wetlands (Luanhaizi peatland (LHZ) and Xiaobohu swamp (XBH)) on the northeastern QTP. At an 8-day scale, boosted regression tree model-based analysis showed that variations in growing season CO
2 fluxes were predominantly determined by atmospheric water vapor, having a relative contribution of more than 65%. Variations in nongrowing season CO
2 fluxes were mainly controlled by site (categorical variable) and topsoil temperature (
Ts), with cumulative relative contributions of 81.8%. At a monthly scale, structural equation models revealed that net ecosystem CO
2 exchange (NEE) at both sites was regulated more by gross primary productivity (GPP), than by ecosystem respiration (RES), which were both in turn directly controlled by atmospheric water vapor. The general linear model showed that variations in nongrowing season CO
2 fluxes were significantly (
p < 0.001) driven by the main effect of site and
Ts. Annually, LHZ acted as a net carbon source, and NEE, GPP, and RES were 41.5 ± 17.8, 631.5 ± 19.4, and 673.0 ± 37.2 g C/(m
2 year), respectively. XBH behaved as a net carbon sink, and NEE, GPP, and RES were –40.9 ± 7.5, 595.1 ± 15.4, and 554.2 ± 7.9 g C/(m
2 year), respectively. These distinctly different carbon budgets were primarily caused by the nongrowing season RES being approximately twice as large at LHZ (
p < 0.001), rather than by other equivalent growing season CO
2 fluxes (
p > 0.10). Overall, variations in growing season CO
2 fluxes were mainly controlled by atmospheric water vapor, while those of the nongrowing season were jointly determined by site attributes and soil temperatures. Our results highlight the different carbon functions of alpine peatland and alpine swampland, and show that nongrowing season CO
2 emissions should be taken into full consideration when upscaling regional carbon budgets. Current and predicted marked winter warming will directly stimulate increased CO
2 emissions from alpine wetlands, which will positively feedback to climate change.
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