Peatland degradation is expected to increase the rate of aerobic decomposition in surface soil (0–30 cm). Carbon stored in both the subsurface (30–60 cm) and deeper layers (>60 cm) of peatlands is also expected to be metabolized after degradation. However, little is known about how methane were emissions from subsurface and the deeper layers of peatlands during degradation. Three peatland degradation stages: S1, intact fen with high water table; S2, lightly degraded fen with a fluctuating water table; S3, heavily degraded fen with a lower water table were chosen to quantify the differences in CH4 emissions at different peatland degradation stages. CH4 emissions and methanogens of subsurface and deep soil were also measured to reveal the contribution rates of subsurface methane emission in this study. After four-years experiment, we found that the abundance of methanogens and methane emissions decreased as peatlands were more heavily degraded. We also found that the contribution rate of methane emission decreased from peat surface to subsurface and deep layer, and this trend varied with peatland degradation. A higher contribution rate was found in the subsurface methane emissions from S1 (32.63%) and S2 (19.94%). Importantly, when peatlands were heavily degraded, the subsurface changed from a CH4 source to a sink. Decreased methane emissions of the degraded peatlands was also associated with a high abundance of methanogens (R2 = 0.75, p < 0.05). Thus, we conclude that peatland degradation reduces methanogens and methane emissions from both surface and deep soils. Peatland degradation induced aerobic condition and substrate limitation are the main reasons for the reduced methane emission from Zoige peatland.
