Large amounts of natural gas hydrates have been discovered in the Qiongdongnan Basin (QDNB), South China Sea. The chemical and stable carbon isotopic composition shows that the hydrate-bound gas was a mixture of thermogenic and microbial gases. It is estimated that microbial gas accounts for 40.96% to 60.58%, showing a trend of decrease with the increase in burial depth. A significant amount of gas hydrates is thought to be stored in the mass transport deposits (MTDs), exhibiting vertical superposition characteristics. The stable carbon isotopic values of methane (δ13C1) in the MTD1, located near the seabed, are less than −55‰, while those of the methane below the bottom boundary of MTD3 are all higher than −55‰. The pure structure I (sI) and structure II (sII) gas hydrates were discovered at the depths of 8 mbsf and 145.65 mbsf, respectively, with mixed sI and sII gas hydrates occurring in the depth range 58–144 mbsf. In addition, a series of indigenous organic matters and allochthonous hydrocarbons were extracted from the hydrate-bearing sediments, which were characterized by the origin of immature terrigenous organic matter and low-moderate mature marine algal/bacterial materials, respectively. More allochthonous (migrated) hydrocarbons were also discovered in the sediments below the bottom boundary of MTD3. The gas hydrated is “wet gas” characterized by a low C1/(C2 + C3) ratio, from 2.55 to 43.33, which was mainly derived from a deeply buried source kitchen at a mature stage. There is change in the heterogeneity between the compositions of gas and biomarkers at the site GMGS5-W08 along the depth and there is generally a higher proportion of thermogenic hydrocarbons at the bottom boundary of each MTDs, which indicates a varying contribution of deeply buried thermogenic hydrocarbons. Our results indicate that the MTDs played a blocking role in regulating the vertical transportation of hydrate-related gases and affect the distribution of gas hydrate accumulation in the QDNB.
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