Paddy soils make up the largest anthropogenic wetlands on earth, and are characterized by a prominent potential for organic carbon (C) sequestration. By quantifying the plant‐ and microbial‐derived C in soils across four climate zones, we identified that organic C accrual is achieved via contrasting pathways in paddy and upland soils. Paddies are 39%–127% more efficient in soil organic C (SOC) sequestration than their adjacent upland counterparts, with greater differences in warmer than cooler climates. Upland soils are more replenished by microbial‐derived C, whereas paddy soils are enriched with a greater proportion of plant‐derived C, because of the retarded microbial decomposition under anaerobic conditions induced by the flooding of paddies. Under both land‐use types, the maximal contribution of plant residues to SOC is at intermediate mean annual temperature (15–20°C), neutral soil (pH~7.3), and low clay/sand ratio. By contrast, high temperature (~24°C), low soil pH (~5), and large clay/sand ratio are favorable for strengthening the contribution of microbial necromass. The greater contribution of microbial necromass to SOC in waterlogged paddies in warmer climates is likely due to the fast anabolism from bacteria, whereas fungi are unlikely to be involved as they are aerobic. In the scenario of land‐use conversion from paddy to upland, a total of 504 Tg C may be lost as CO₂ from paddy soils (0–15 cm) solely in eastern China, with 90% released from the less protected plant‐derived C. Hence, preserving paddy systems and other anthropogenic wetlands and increasing their C storage through sustainable management are critical for maintaining global soil C stock and mitigating climate change.

Rice paddies account for ~9% or the world’s cropland area and are characterized by environmental conditions promoting soil organic carbon storage, methane emissions and to a lesser extent nitrous oxide emissions. Here, we synthesize data from 612 sites across 51 countries to estimate global carbon stocks in paddy soils and determine the main factors affecting paddy soil carbon storage. Paddy soils (0–100 cm) contain 18 Pg carbon worldwide. Paddy soil carbon stocks decrease with increasing mean annual temperature and soil pH, whereas mean annual precipitation and clay content had minor impacts. Meta-analysis shows that paddy soil carbon stocks can be increased through several management practices. However, greenhouse gas mitigation through paddy soil carbon storage is generally outweighed by increases in methane and nitrous oxide emissions. Our results emphasize the key role of paddies in the global carbon cycle, and the importance of paddy management in minimizing anthropogenic greenhouse gas emissions.

Soils were incubated for 80 days in a continuously labeled ¹⁴ CO ₂ atmosphere to measure the amount of labeled C incorporated into the microbial biomass. Microbial assimilation of ¹⁴ C differed between soils and accounted for 0.12% to 0.59% of soil organic carbon (SOC). Assuming a terrestrial area of 1.4 × 10 ⁸ km ² , this represents a potential global sequestration of 0.6 to 4.9 Pg C year ⁻¹ . Estimated global C sequestration rates suggest a “missing sink” for carbon of between 2 and 3 Pg C year ⁻¹ . To determine whether ¹⁴ CO ₂ incorporation was mediated by autotrophic microorganisms, the diversity and abundance of CO ₂ -fixing bacteria and algae were investigated using clone library sequencing, terminal restriction fragment length polymorphism (T-RFLP), and quantitative PCR (qPCR) of the ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) gene ( cbbL ). Phylogenetic analysis showed that the dominant cbbL -containing bacteria were Azospirillum lipoferum , Rhodopseudomonas palustris , Bradyrhizobium japonicum , Ralstonia eutropha , and cbbL -containing chromophytic algae of the genera Xanthophyta and Bacillariophyta . Multivariate analyses of T-RFLP profiles revealed significant differences in cbbL -containing microbial communities between soils. Differences in cbbL gene diversity were shown to be correlated with differences in SOC content. Bacterial and algal cbbL gene abundances were between 10 ⁶ and 10 ⁸ and 10 ³ to 10 ⁵ copies g ⁻¹ soil, respectively. Bacterial cbbL abundance was shown to be positively correlated with RubisCO activity ( r = 0.853; P < 0.05), and both cbbL abundance and RubisCO activity were significantly related to the synthesis rates of [ ¹⁴ C]SOC ( r = 0.967 and 0.946, respectively; P < 0.01). These data offer new insights into the importance of microbial autotrophy in terrestrial C cycling.