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The characteristics, formation mechanisms, and influences on physical properties of carbonate minerals in shale reservoirs of Wufeng-Longmaxi formations in Sichuan Basin are systematically investigated by utilizing electron probe microscope with spectrometer and energy spectrometer, combined with physical properties and whole rock X-diffraction and organic carbon data. The research yielded the findings that follow: First, the main carbonate minerals are calcite, dolomite, and ferriferous dolomite. Calcite is a single mineral that fills the siliceous shell cavity of radiolarians and exists between mineral particles. Ferriferous dolomite always rings dolomite, which is a single mineral that is present among mineral particles and aggregates. Second, calcite is produced by microorganisms that secrete calcium carbonate in the surface of seawater. The siliceous skeleton cavity of radiolarian and seawater both precipitate calcite, which partially dissolves while settling in seawater before depositing on the seabed and being preserved by burial. Thirdly, the dolomite is a diagenetic mineral formed on the water-sediment interface with physiological activities of sulfate bacteria, and the ferriferous dolomite is produced by methanogenic metabolism during the initial burial of muddy sediments. Fourthly, organic carbon, pyrite, quartz, and clay minerals are closely related to reservoir physical properties, while carbonate has no effect on porosity and permeability as a whole. Future research on shale reservoir diagenesis should make use of the in-situ detection and element area scanning, in particular with the spectrogram from electron probe microscope technology, which provides typical petrological evidences for the study of characteristics, formation mechanism, and influence on physical properties of carbonate minerals in shale reservoirs. [ABSTRACT FROM AUTHOR]