The effects of replacing over-mature forest with secondary forests and plantations are significant for terrestrial ecosystem carbon (C) dynamics. However, the carbon balance and recovery time of this replacement process remain unclear. This study measured the fluxes of CH
4 and CO
2 in soils and the annual net C sequestration (ANCS) from seven ecosystems with different vegetation types (over-mature forest (OMF), Korean pine plantation (KPP), hardwood forest (HWF),
Betula platyphylla forest (BPF),
Populous davidiana forest (PDF), mixed deciduous forest (MDF), and Mongolian oak forest (MOF)) using the static chamber-gas chromatography method and the relative growth equation method. We examined the effects of environmental factors (e.g., air and soil temperature, soil volumetric water content (SVWC), soil pH, nitrate nitrogen (NO
3−-N), ammonium nitrogen (NH
4+-N), and soil organic carbon (SOC)) on CH
4 and CO
2 fluxes at the Maoershan Ecosystem Research Station in Northeast China. The carbon source or sink of OMF, KPP, and five secondary forests (HWF, BPF, PDF, MDF, and MOF) were then evaluated based on net ecosystem C balance. The results revealed that the mean annual CH
4 fluxes varied between −0.046 and −0.077 mg m
−2 h
−1. The mean annual absorption of CH
4 in the secondary forests and OMF were respectively 1.09–1.67 times and 1.11 times higher than that of KPP (0.046 mg m
−2 h
−1,
p < 0.05). The mean annual CO
2 fluxes varied between 140.425 and 250.023 mg m
−2 h
−1. The CO
2 fluxes in the secondary forests and KPP soils were respectively 1.33–1.78 times and 1.16 times higher than that of OMF (140.425 mg m
−2 h
−1,
p < 0.05). The CH
4 and CO
2 fluxes were mainly influenced by air and soil temperature, SVWC, soil pH, NO
3−-N, NH
4+-N, and SOC in Northeast China. The ANCS of vegetation (3.41 ± 0.27 − 6.26 ± 0.75 t C ha
−1 y
−1) varied widely among different forest types: KPP had the largest ANCS (6.26 ± 0.75 t C ha
−1 y
−1, which was higher than secondary forests and OMF by 1.20–1.84 times and 1.46 times, respectively,
p > 0.05). Carbon sources and sinks were significantly different among the seven types of vegetation: OMF and KPP were observed to be the greatest C sinks, and secondary forests were shown to be the weakest carbon sinks or net C sources in the study region.
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