Formation of carbonate laminae in shale and their impact on organic matter in Dongying depression

Abstract

Carbonates, the main components of oil shale that influence oil and gas accumulation, are becoming increasingly significant in oil shale studies. This paper aims to examine the formation mechanisms of various carbonate minerals in shale and their impact on oil enrichment. In the Dongying Depression, two predominant types of carbonate minerals have been identified: micritic carbonate and grain carbonate. Micritic carbonate primarily forms through biogenic processes, where alternating carbonate and clay mineral laminae result from the periodic stratification of lacustrine water bodies. These layers are relatively thin. Micritic carbonate rocks contain low organic matter and predominantly feature narrow slit-like pores, leading to a tight pore structure that hinders oil shale accumulation. In contrast, grain carbonate formation is governed by diagenetic processes. Influenced by deep fluids, these carbonate laminae are mainly composed of lens-shaped, coarsely crystalline calcite and exhibit significant thickness. Grain carbonate rocks have a relatively high organic matter content, with pore spaces primarily consisting of bottleneck- and slit-shaped throats. This configuration enhances reservoir capacity and creates favorable conditions for oil shale accumulation.

Introduction

Shale oil, a key unconventional oil and gas resource in the global energy transition, has garnered significant attention from the international academic and industrial communities for its exploration and development potential. Currently, global research on shale oil primarily focuses on marine sedimentary systems, such as the Barnett, Bakken, and Eagle Ford shales in North America, as well as marine shale formations in southern China^1,2,3,4.

In recent years, advancements in exploration technology have highlighted the growing importance of continental shale oil resources. Industrially valuable shale oil reservoirs have been discovered in continental sedimentary basins such as the Uinta Basin in the United States, the Sumatra Basin in Indonesia, and the Bohai Bay Basin in China^5,6,7,8,9. Compared to marine sedimentary systems, lacustrine shale oil reservoirs exhibit distinct characteristics: they form in highly dynamic lake environments, feature complex mineral compositions, and generally contain higher carbonate content, often displaying a mix of multiple rock types^8,9,10,11,12. Notably, the abundance of layered carbonates in lacustrine shales correlates significantly with recoverable resource volume, making this relationship a crucial topic in foundational shale oil research.

Lacustrine carbonate sedimentation is driven by interconnected processes involving periodic paleoclimate fluctuations, hydrodynamic gradients, and evolving water chemistry. Contemporary sedimentological studies indicate that deep fluid processes (e.g., volcanism, hydrothermal activity) exert dual influences on basin evolution: (1) altering aqueous geochemistry through the transport of dissolved components and (2) regulating biological communities and sedimentation dynamics via thermal effects^{13,14,15,16,17,18}. Notably, carbonate-clay laminae exhibit strong spatial correlation with organic matter enrichment across diverse depositional settings. Some researchers have proposed a microbial-induced carbonate precipitation mechanism, suggesting that biological activity (such as algae metabolism and organic matter degradation) modulates the carbonate solubility balance^19,20,21,22. However, other studies have found that certain high total organic carbon (TOC) intervals do not coincide with carbonate enrichment, suggesting that this relationship may be highly environment-dependent^{23,24,25,26,27}. This ongoing theoretical debate underscores the need for further investigation into the formation mechanisms of carbonate rocks and their synergistic enrichment with organic matter.

A fundamental paradox arises from traditional sedimentological theory, which predicts that carbonate precipitation thrives in high-energy shallow waters, whereas organic preservation requires low-energy conditions. This contradicts empirical observations in lacustrine shales, where carbonate layer-TOC correlations are consistently positive. The "high-carbonate/high-TOC" paradox suggests that deep fluid-mediated processes may modify sedimentary systems. Therefore, understanding how deep fluids influence carbonate layer formation and organic matter coupling is critical for advancing continental shale oil accumulation theory.

This study investigates organic-rich shale from the lower sub-section of the third member and the upper sub-section of the fourth member of the Paleogene Shahejie Formation in the Dongying Sag of the Bohai Bay Basin. An integrated approach was applied, incorporating (1) systematic core analysis, (2) quantitative mineralogy, (3) elemental geochemistry, and (4) reservoir characterization. This study aims to resolve the genetic classification criteria for carbonate rocks, the influence of deep fluids on carbonate layer formation, and the coupling mechanisms between carbonate genesis, organic enrichment, and reservoir quality. These findings establish a novel theoretical framework for predicting terrestrial shale oil sweet spots.

Geological setting

The Bohai Bay Basin is a major oil- and gas-bearing basin in eastern China, covering approximately 200,000 km². The Dongying Depression, located in the basin’s eastern region, spans an area of 5,700 km²²⁸ (Fig. 1A). It is a faulted and subsided basin that developed on the Paleozoic basement’s paleo-topographic framework. The Dongying Depression is divided into three zones: the northern steep slope zone, the southern gentle slope zone, and the central anticline zone. The segmentation of the central anticline zone has led to the formation of four depressions as follows: Niu Zhuang, Li Jin, Min Feng, and Bo Xing^29,30 (Fig. 1B).

Fig. 1

(A): Location and distribution of igneous rocks in the Dongying Depression²⁹. (B): Geological cross-section of the Dongying Depression along section A-A'³⁰. (C): Stratigraphic column diagram.

The Dongying Depression has undergone evolutionary processes from the Paleozoic to the Cenozoic era, with the Paleogene and Neogene representing the thickest and most significant sedimentary formations in the basin. The Paleogene primarily consists of three stratigraphic units: the Kongdian Formation, the Dongying Formation, and the Shahejie Formation^{30,31,32,33,34} (Fig. 1C).

The Shahejie Formation is subdivided into four sections, from top to bottom: the first member (Es1), the second member (Es2), the third member (Es3), and the fourth member (Es4) (Fig. 1C). The Es3 and Es4 sections mainly consist of thick-bedded mudstone and calcareous mudstone^30,35,36,37. The Es4 section is further divided into the Lower Subsection (Es4-2) and Upper Subsection (Es4-1), while the Es3 section is subdivided into the Lower Subsection (Es3-3), Middle Subsection (Es3-2), and Upper Subsection (Es3-1)^38,39,40,41.

The Es3-3 and Es4-1 sections serve as the primary reservoirs for oil shale, characterized by organic-rich mud shale and abundant laminated carbonate rocks^40,41,42,43 (Fig. 1C). Additionally, extensive igneous rocks are present in the Binnan Uplift, located in the western part of the Dongying Depression, as well as in the Boxing Sag in the southern region. These igneous rocks, predominantly composed of intermediate basalt and gabbro, are primarily concentrated in the Es3-3 and Es4-1 sections^34,35 (Fig. 1A).

Samples and methods

The wells Fy1, Ny1, Ly1, and Fyp1 were selected for core observation in this study due to their complete core recovery and the presence of abundant carbonate rocks and tuffaceous interlayers within the Es3-Es4 interval. Core observations were conducted at the Sinopec Shengli Oilfield core repository. Based on these observations, a total of 40 core samples from the Es3-3 and Es4-1 sections were systematically analyzed.

The samples were prepared by wire-cutting them into rectangular prisms measuring 4 cm × 3 cm × 1 cm. Each prism was then enlarged tenfold, and a RELION micro-drill (1 mm diameter) was used to collect samples from the carbonate and organic matter layers (Fig. 2). Using a polarized light microscope, fluorescence microscope, scanning electron microscope (SEM), and cathodoluminescence microscope, four sections of each sample were simultaneously prepared for observation as follows: 1) Polarized Light Microscopy: Conducted using a ZEISS Axioskop 40 polarizing microscope to analyze mineral composition, content, and structural characteristics at room temperature (23 °C). 2) SEM Microscopy: Samples were mounted on trays and coated with conductive adhesive. A freshly fractured surface was gold-sputtered to enhance conductivity before observation using a JSM-6510LV SEM with an acceleration voltage of 50 kV. 3) Cathodoluminescence Microscopy: The Energy-dispersive X-ray (EDX) spectroscopy system was used to analyze mineral types, pore structures, and various mineral morphologies. Observations were conducted with a Leica CL8200 cathodoluminescence microscope, and results were captured using a digital camera attached to the microscope. All observations were performed at the National Key Laboratory of Oil and Gas Resources and Engineering, China University of Petroleum (Beijing).

Fig. 2

Locations of micro-drilling and thin section sampling. (A): Well FYP1, 3457.5 m, Es4-1, grain carbonate rock; (B): Well FY1, 3458.57 m, Es4-1, grain carbonate rock; (C): Well LY1, 3631.3 m, Es4-1, grain carbonate rock; (D): Well FY1, 3243.4 m, Es3-3, micritic carbonate rock; (E): Well FY1, 3128.6 m, Es3-3, micritic carbonate rock; (F): Well NY1, 3294.3 m, Es3-3, micritic carbonate rock. The yellow arrows indicate the locations of carbonate rocks, while the red arrows denote the locations of clay laminae.

After magnifying the prisms tenfold, samples from carbonate and organic matter laminations were collected from various locations of the same specimen using a RELION micro-drill (1 mm diameter). These samples were ground to 200 mesh for thermal decomposition, TOC analysis, trace element analysis, rare earth element analysis, and carbon–oxygen and strontium isotope analysis. Detailed descriptions of the experimental methods and relevant standards can be found in the referenced literature^4,10,31. Micro-area sampling was performed at the Beijing Institute of Nuclear Geology, while subsequent analysis and testing were conducted at the Research Institute of Petroleum Exploration and Development of China.

Various types of carbonate rock samples underwent N₂ adsorption testing to compare their reservoir characteristics. This testing was performed using an ASAP 2460 surface area and porosity analyzer with MicroActive software at the Research Institute of Petroleum Exploration and Development in China. Additionally, data on total organic carbon content, clay mineral XRD, and other drilling analyses from the four sampled wells were provided by Sinopec Shengli Oilfield Branch.

Results

Lithological features

The Es3-3 and Es4-1 intervals in the Fy1, Ly1, Ny1, and Fyp1 wells exhibit significant vertical lithological variations. The Es3-3 interval is predominantly composed of thick-bedded calcareous mudstone and laminated shale, with minor interbedded micritic limestone. In contrast, the Es4-1 interval mainly consists of blocky shale, laminated shale, and mudstone, with laminated shale containing interbedded tuffaceous layers. Carbonate minerals within the core primarily occur in laminated and granular forms, embedded within the clay mineral interlayers of mudstone and shale (Fig. 3).

Fig. 3

Core description and comprehensive testing analysis of the core section in the Fy1 Well.

Mudstone

The core exhibits gray-brown and dark gray hues, with poorly developed laminations and faintly visible bedding (Fig. 4A). Microscopic observations reveal that the laminae are underdeveloped, with clay, feldspar, quartz, and carbonate occurring as a disordered mixed deposit (Fig. 4B). The dominant clay mineral is sheet-like illite. Due to the high clay content, thin sections display deep yellow or brown hues, while feldspar and quartz are primarily dispersed and suspended within the matrix (Fig. 4C–D).

Fig. 4

Petrological and mineralogical characteristics of mudstone and shale. (A): Well FY1, gray-brown mudstone, dense blocky texture, 3173.5 m (core photograph). (B): Well FY1, gray-brown mudstone, 3173.5 m (cross-polarized light); the yellow arrow indicates detrital feldspar, while the clay minerals appear darker. (C): Well FY1, gray-brown mudstone, 3173.5 m (cathodoluminescence); the red arrow indicates carbonate minerals (orange-red), and the blue arrow indicates feldspar (blue). (D): Well FY1, gray-brown mudstone, 3173.5 m (scanning electron microscopy); platy illite (I) and quartz (Q) occupy the pores. (E): Well FYP1, shale, 3456.19 m (core photograph); well-developed laminations are observed. (F): Well LY1, shale, 3692.3 m (cross-polarized light); the yellow arrow indicates carbonate laminations, the red arrow indicates clay minerals, and the blue arrow indicates organic matter laminations. (G): Well FYP1, shale, 3456.19 m (cross-polarized light); the yellow arrow indicates detrital feldspar. (H): Well FYP1, shale, 3456.19 m (cathodoluminescence); the red arrow indicates carbonate minerals (orange-red), and the blue arrow indicates feldspar (blue). (I): Well FYP1, shale, 3456.19 m (scanning electron microscopy); the platy illite–smectite (I/S) interlayer is filled with spheroidal pyrite (Pr).

X-ray diffraction (XRD) analysis indicates that this rock type contains 6% carbonate, with quartz and feldspar contents of 27% and 7%, respectively. The clay content is 5%, while pyrite accounts for 2%. Additionally, the organic carbon content is notably high, ranging from 2 to 5% (Fig. 5).

Fig. 5

XRD composition analysis diagram of the rock.

Shale

The core exhibits a dark gray color with faintly visible laminations (Fig. 4E). Microscopic observations reveal well-developed laminations composed primarily of clay layers, organic matter layers, and mixed layers containing clay, feldspar, quartz, and carbonate (Fig. 4F). The clay layers are relatively thin, typically less than 0.1 mm thick, and consist of fine particles with a dark brown coloration. Coarse-grained quartz and feldspar particles are frequently observed within the laminations (Fig. 4G, H), along with well-developed pyrite (Fig. 4I).

XRD analysis indicates that this rock type contains 9% carbonate, 26% quartz, and 3% feldspar. The clay content is 58%, while pyrite accounts for 4%. Additionally, the organic carbon content is relatively high, generally ranging from 3 to 5%, with some samples exceeding 10% (Fig. 5).

Grain carbonates rock

The core appears dark gray and exhibits strong effervescence when treated with hydrochloric acid, indicating the presence of carbonate minerals. It displays a laminated structure with well-defined boundaries between layers. The core is primarily composed of carbonate and clay laminations, which are rich in feldspar (Fig. 2A–C). The laminations are relatively thin, typically ranging from 0.1 mm to 0.3 mm in thickness. The carbonate laminations often display continuous, lens-shaped or wavy patterns. Cracks within the carbonate crystals are filled with brown asphaltite (Fig. 6A, B).

Fig. 6

Microscopic characteristics of carbonate rocks. In this figure, yellow arrows indicate microcracks, while red arrows denote dissolution pores. (A): Well FY1, 3458.57 m, grain carbonate rock, plane-polarized light; (B): Well LY1, 3631.3 m, grain carbonate rock, cross-polarized light; (C): Well FY1, 3458.57 m, grain carbonate rock, scanning electron microscope; (D): Well LY1, 3631.3 m, grain carbonate rock, scanning electron microscopy, asphaltite filling in dissolution pores; (E): Well FY1, 3128.6 m, grain carbonate rock, scanning electron microscopy, intercrystalline pores with pyrite development; (F): Well FY1, 3128.6 m, micritic carbonate rock, cross-polarized light; (G): Well NY1, 3294.3 m, micritic carbonate rock, plane-polarized light; (H): Well FY1, 3128.6 m, micritic carbonate rock, scanning electron microscope; (I): Well NY1, 3294.3 m, micritic carbonate rock, scanning electron microscopy, carbonate minerals dissolved, with pyrite filling in between.

SEM observations reveal well-developed microcracks and dissolution pores within the carbonate minerals. Some of these dissolution pores are filled with pyrite or organic matter (Fig. 6C, D). XRD analysis indicates that this rock type contains 49% carbonate, 28% quartz, and 3% feldspar. The clay content is 16%, and the pyrite content is 4% (Fig. 5). Additionally, this rock type exhibits a high organic matter content, typically ranging from 2 to 5%. It is relatively enriched in clay laminations, which are often conformable and continuous. Both the organic matter and pyrite contents are higher than those found in mudstone and shale.

Micritic carbonates rock

The core appears dark gray and vigorously bubbles upon contact with hydrochloric acid. The laminations exhibit alternating light and dark colors, with a continuous horizontal distribution (Fig. 2D–E). Microscopic observation reveals that the rock is primarily composed of organic-rich muddy laminations and carbonate laminations. The interfaces between the laminations are well-defined, with carbonate laminations generally thicker than the muddy laminations. Carbonate laminations typically range from 0.2 mm to 0.5 mm in thickness, while muddy laminations range from 0.1 mm to 0.3 mm (Fig. 6F–G).

SEM reveals plate-like calcite with well-developed dissolution pores (Fig. 6H–I). The edges of the calcite are filled with spherical pyrite, and microcracks, approximately 1.2 μm wide, are present at the edges of the muddy laminations (Fig. 6E, H).

XRD analysis indicates that the carbonate content is 53%, while quartz and feldspar comprise 11% and 7%, respectively. The clay content is 25%, and the pyrite content is 4% (Fig. 5). This rock type has a high organic matter content, typically ranging from 3 to 4%, and is relatively enriched in muddy laminations, which often exhibit a conformable and continuous distribution.

Geochemical features

Trace elements and rare earth elements

Eu and various trace and rare earth elements were analyzed in the clay and carbonate minerals of the two carbonate types. The results are presented in Tables 1 and 2.

Table 1 Trace element content in clay laminations and carbonate laminations of carbonate rocks.

Table 2 Rare earth element content in clay laminations and carbonate laminations of carbonate rocks.

C-O isotopes and Sr isotopes

The carbonate mineralogy and isotopic composition of two carbonate types (e.g., clay laminae and both grain and micritic carbonate layers) were analyzed. The results of these analyses are presented in Table 3.

Table 3 C-O and Sr isotopes of clay laminations and carbonate laminations in carbonate rocks.

TOC and reservoir space characteristics

The results of whole-rock TOC testing, presented in Table 4, indicate no significant difference in TOC content between grain carbonate rock and micritic carbonate rock, with average values of 2.47% and 2.34%, respectively. Micro-scale TOC testing reveals that in grain carbonate rock, the minimum TOC content of clay laminations is 4.26%, the maximum is 12.3%, and the average is 8.1%. In contrast, micritic carbonate rock shows a minimum TOC content of 4.87%, a maximum of 9.16%, and an average of 7.13% for its clay laminations. These findings suggest that grain carbonate rock has a higher organic matter content in its clay laminations compared to micritic carbonate rock.

Table 4 Data for TOC content, porosity, and permeability of carbonate rocks.

The results of porosity and permeability testing, presented in Table 4, show that the average porosity and permeability of grain carbonate rock are 7.75% and 0.464 mD, respectively. In contrast, micritic carbonate rock has average porosity and permeability values of 6.32% and 0.3 mD, respectively. This suggests that grain carbonate rock possesses greater reservoir potential and connectivity.

Nitrogen (N₂) adsorption tests, shown in Fig. 7, indicate that the pore size distribution ranges for crystalline carbonate and mudstone carbonate are similar, falling within 5–10 nm. According to the International Union of Pure and Applied Chemistry (IUPAC) classification (Fig. 7A), the pore structures of grain carbonate rocks are classified as H2 and H3 types, resembling "bottleneck," slit, or conical structures. In contrast, the pore structures in micritic carbonate rocks are classified as H3 and H4 types, resembling flat slit, conical, or slit pore structures^44,45.

Fig. 7

(A): Different types of carbonate rock pore structure characteristics; (B): Pore size distribution characteristics.

Discussion

Evidence of deep fluid activity

Petrological evidence

The Es3-3 and Es4-1 formations in the Dongying Depression have developed large-scale igneous rocks. Due to their differing formation locations and occurrences, these igneous rocks can be classified as intrusive and extrusive (Fig. 8A–F). Intrusive rocks are predominantly found in the Es3-3 formation, with gabbro and diabase as the main rock types. These rocks are located in the eastern part of the Boxing Depression (Fig. 1A). Extrusive rocks, on the other hand, are primarily associated with the Es4-1 formation and are mainly composed of basalt, which is distributed in the southern part of the Binnan Uplift and around the Boxing Depression^40,42 (Fig. 1A).

Fig. 8

Petrological and mineralogical characteristics of igneous rocks. (A): Well C102, gabbro, 2395 m, core photograph; (B): Well C102, gabbro, 2395 m, cross-polarized light, with a yellow arrow indicating the serpentinization of olivine; (C): Well C102, gabbro, 2395 m, scanning electron microscope image, with a yellow arrow indicating the alteration of volcanic minerals to kaolinite; (D): Well G81, basalt, 2448.9 m, core photograph showing yellow sulfur-filled fractures; (E): Well G81, basalt, 2448.9 m, cross-polarized light illustrating the alteration of volcanic minerals to chlorite, yellow arrow indicating chlorite; (F): Well B52, basalt, 1442 m, cross-polarized light, with a yellow arrow indicating the serpentinization of olivine.

Mineralogical evidence

Hydrothermal fluids exhibit strong chemical reactivity and can interact with the surrounding rocks, leading to the formation of hydrothermal minerals^{46,47,48,49,50}. Additionally, as hydrothermal fluids migrate and undergo changes in temperature and pressure conditions, minerals can precipitate directly from the solution. In this study, various hydrothermal minerals and their assemblage types were identified in the core samples and thin sections from the Es3-3 and Es4-1 formation units of the Shahejie Formation within the study area^47,48.

• a. Sericite

Sericite is a low- to medium-temperature hydrothermal alteration mineral that typically forms at temperatures between 200 and 350 °C. In the Gaoqing area, near the Gaoqing-Pingnan fault zone in the western part of the Dongying Depression, sericite alteration is frequently observed in the Es4-1 formation, where plagioclase is present (Fig. 9A–C). The Es4-1 formation in the Gaoqing area has been continuously buried since deposition, currently representing its maximum burial depth, with an estimated maximum burial temperature of approximately 140 °C^29,42. This temperature is insufficient for the formation of sericite, indicating that sericite development in this area is likely influenced by hydrothermal fluid activity.

Fig. 9

Microscopic characteristics of hydrothermal minerals. (A): Complete sericitization of plagioclase, PPL, plane polarized light, Well G81, 2442.8 m; (B): Also shows complete sericitization of plagioclase, PPL, : Well G81, 2442.8 m; (C): Another indication of complete sericitization of plagioclase, PPL, Well G80, 2203.5 m; (D): Cementation with dawsonite, accompanied by authigenic quartz (indicate that), PPL, Well B16, 1434.8 m; (E): Coexisting dawsonite and calcite, XN, Cross-polarized light, Well B80, 1434.8 m; (F): Dawsonite, under scanning electron microscope image, Well B77, 1502 m.

• b. Dawsonite

Dawsonite (NaAlCO₃(OH)₂) is a unique carbonate mineral that forms through continuous reactions between high concentrations of CO₂ and minerals such as potassium feldspar, plagioclase, and kaolinite under elevated partial pressures of CO₂. It is the only thermodynamically stable mineral under high CO₂ conditions and serves as a distinct indicator of the migration and accumulation of CO₂ from mantle sources^51,52. Dawsonite is commonly associated with deep thermal fluid activities and acts as an indicative mineral for recording magmatic events. In the Dongying Depression, multiple mantle-derived CO₂ reservoirs are present within the Neogene strata, where dawsonite is frequently observed in the reservoir formations (Fig. 9D–F). Under polarizing and scanning electron microscopy, dawsonite displays several distinctive characteristics: it typically forms radiating, bundled, hair-like, or flower-like aggregates, with larger aggregates ranging in size from 80 μm to 200 μm. It is often located in the pores of sandstones or replaces plagioclase and rock fragments, demonstrating high identification accuracy.

Geochemical evidence

In the western part of the Dongying Depression, multiple CO₂ reservoirs have developed along the Gaoqing-Pingnan Fault, including the Pingfangwang, Pingnan, Gaoqing, and Huagou gas fields. The volume fraction of CO₂ in these gas fields is generally high, typically exceeding 70%. Additionally, the carbon isotope δ13C shows a significant positive deviation, usually greater than -8‰⁵³. Based on the CO₂ genesis discrimination diagram developed by Dai Jinxing⁵⁴, the data points are projected onto the inorganic genesis area (Fig. 10A). Previous studies suggest that the CO₂ in the western part of the Dongying Depression has a mantle origin. As mantle-derived CO₂-rich fluids migrate, significant development of CO₂-rich fluid inclusions within mineral grains in the rocks occurs. Laser Raman spectroscopy reveals that the Raman scattering characteristic peaks of the host quartz exhibit high intensity, while the CO₂ Raman scattering peak is also strong, accompanied by a lower intensity peak of CH₄ (Fig. 10B). This evidence indicates that during the deposition of the Es4-1 in the Dongying Depression, deep fluid activity was more frequent compared to the Es3-3 interval. The deep fluids encompass various types, including magmatic activity, hydrothermal activity, and mantle-derived CO₂ activity.

Fig. 10

(A): CO₂ Genesis Types; (B): Laser Raman Characteristics of CO₂-Rich Fluid Inclusions in the Dongying Depression (modified after Dai et al.⁵⁴).

Genesis of the carbonate rock

Mineralogical characteristics

Grain carbonate rocks are present in all four core wells, primarily within the Es4-1 interval, where deep fluid activity is more frequent. In contrast, they are less developed in the Es3-3 interval. The carbonates principally consist of calcite, dolomite, and ankerite (Fig. 11A, C), with cube-shaped pyrite observed under scanning electron microscopy (Fig. 11D). The formation of dolomite and the occurrence of cube-shaped pyrite are often closely related to deep fluid activity in the basin. In the deeper parts of the Dongying Depression, a mid-crustal low-velocity, high-conductivity layer exists^29,38. This deep basin layer consists of serpentinized peridotite, which releases significant amounts of Mg²⁺ during serpentinization. Mg²⁺-rich hydrothermal fluids, originating from the serpentinite, migrate upward along fractures and interact with CaCO₃ in the basin’s carbonate rocks, leading to the formation of dolomite. Cathodoluminescence observations reveal that the interiors of carbonate grains appear darker, exhibiting a deep red color, while the edges display a brighter orange-red hue (Fig. 11A). Additionally, some crystals show signs of fracturing due to stress, with cracks developing nearly perpendicular to the carbonate bedding. These cracks are filled with calcite, which exhibits a blue-green fluorescence (Fig. 11A–B). These mineralogical characteristics suggest multi-stage crystallization of grain carbonates influenced by deep hydrothermal fluids.

Fig. 11

Microscopic characteristics of carbonate rocks. (A): Well FY1, 3458.57 m, grain carbonate rock, cathodoluminescence imagery; (B): Well FY1, 3458.57 m, grain carbonate rock, fluorescence imagery; (C): Well FY1, 3458.57 m, grain carbonate rock, scanning electron microscopy showing the coexistence of carbonate and ankerite; (D): Well FY1, 3458.57 m, grain carbonate rock, scanning electron microscopy revealing cubic-shaped pyrite crystals (Pr), indicate Cc is crystalline carbonate, I\S is IUite/smectite interstratified layer, with the energy spectrum analysis shown in the bottom left; (E): Well FY1, 3128.6 m, micritic carbonate rock, cathodoluminescence imagery; (F): Well FY1, 3128.6 m, micritic carbonate rock, fluorescence imagery; (G): Well FY1, 3128.6 m, micritic carbonate rock (Cc), scanning electron microscopy displaying spherical carbonate minerals, with the energy spectrum analysis shown in the bottom left; (H): Well FY1, 3128.6 m, micritic carbonate rock, scanning electron microscopy illustrating spherical pores on the sample surface indicate Cc is crystalline carbonate, Fs is ferrosilite; (I): Well NY1, 3294.3 m, micritic carbonate rock (Cc), scanning electron microscopy revealing filamentous and sheath-like carbonate minerals, with the energy spectrum analysis shown in the bottom left.

Micritic carbonate rocks are more prevalent in the studied strata than grain carbonate rocks, second only to mudstone in abundance. The carbonate laminae are relatively continuous and alternate with laminae of clay minerals. Under cathodoluminescence, they exhibit an orange-red coloration and are primarily composed of calcite (Fig. 11E), displaying blue-green fluorescence (Fig. 11F). SEM observations reveal diverse morphologies of calcite in micritic carbonate rocks, including spherical, filamentous, and sheath-like forms (Fig. 11D–I). Previous studies simulating mineralization under natural conditions, compared with carbonate minerals formed in completely inorganic environments, suggest that the spherical, filamentous, and sheath-like carbonate forms are associated with biogenic mineralization processes^55,56,57. Additionally, some carbonates exhibit dissolution features, such as bay-like and cavity-like features (Fig. 6I). These features are thought to be caused by organic acids secreted by organisms, providing direct evidence of microbial involvement in sedimentation.

REE and trace element geochemistry

Rare earth element and trace element analyses are commonly used methods in the study of sedimentary rocks to assess sedimentation rates, depositional environments, sediment sources, and other related aspects^5,12. The trace element data of clay and carbonate laminations in carbonate rocks, normalized against the UCC average values⁵⁸, reveal unusually high concentrations of Ni and Sr in the carbonate rocks of the study area. Significant variations in elemental content are observed among different sample types (Fig. 12).

Fig. 12

Spider diagrams of trace elements in the samples (A): micritic carbonate minerals; (B) grain carbonate laminae; (C): clay minerals in micritic carbonate rocks; (D): clay laminae in grain carbonate rocks. All data are normalized to the upper crustal average values for trace elements from Taylor and McLennan⁵⁸ UCC.

The Ni content in micritic calcite ranges from 79.6 to 301 ppm, with an average of 150.4 ppm. In grain calcite, Ni content varies from 100.9 to 411 ppm, with an average of 204.62 ppm. In micritic carbonate rocks, the Ni content in clay laminae ranges from 70.4 to 201.4 ppm, averaging 126.65 ppm. In grain carbonate rocks containing clay laminae, Ni content ranges from 89.6 to 201 ppm, with an average of 142.15 ppm. The Ni content in the carbonate rocks of the study area is significantly higher than the average Ni content in the Upper Continental Crust, which is 20 ppm.

The Sr content in the carbonate rocks also exhibits enrichment characteristics similar to those of Ni. The Sr/Ba ratio is often used to infer the salinity of the depositional environment during sedimentation. Generally, Sr/Ba ratios greater than 1 indicate a marine environment or a saline lake basin, while ratios less than 1 suggest a continental or freshwater depositional setting⁵⁹. The average Sr/Ba ratio in clay laminae of micritic carbonate rocks in the study area is 2.01, while the average Sr/Ba ratio in clay laminae of grain carbonate rocks is 4.09. This suggests that the carbonate rocks formed in a high-salinity saline lake basin environment, consistent with previous research findings.

Ni, a transition metal, is highly enriched in deep fluids. Consequently, its concentration levels can indicate the influence of deep fluids or magmatic processes⁶⁰. During the sedimentary periods of Es4-1 and Es3-3 in the study area, vigorous tectonic activity and significant faulting occurred, allowing deep fluids to migrate along these faults. The anomalous enrichment of Ni in this specific layer may be linked to these geological processes. Additionally, the concentration of Sr in calcite is generally higher than in clay laminae, as strontium exhibits a greater affinity for incorporation into the crystal lattice of carbonate minerals compared to clay minerals⁵⁶. Consequently, Sr is relatively enriched in carbonate minerals.

Furthermore, the higher concentration of strontium in grain calcite carbonate compared to micritic calcite carbonate suggests that the formation fluids responsible for the creation of grain calcite had a notably high strontium content. This enrichment is likely due to the infiltration of deep fluids into the strata, which altered the properties of the formation fluids. In two grain calcite samples, the data indicate unusually high concentrations of Ba, measuring 12,963 ppm and 12,784 ppm, respectively. Scanning electron microscopy and energy spectrum analysis revealed the presence of barite in these samples (Fig. 13), highlighting an association between the formation of grain calcite and deep hydrothermal activity.

Fig. 13

Images and energy spectrum of barite in grain calcite. (A): Well FYP1, 3457.5 m, scanning electron microscope, spherical barite is observed in the calcite grains. The red dots indicate positions for energy spectrum analysis; (B): Energy spectrum analysis from the red dot in (A), revealing the mineral’s main elemental composition as Ba, S, and O.

Normalization of various North American shale samples is presented in Fig. 14. Previous studies suggest that sedimentary rocks typically have δEu values around 0.65. In the study area, the average δEu values of clay minerals in micritic calcareous rocks and grain calcareous rocks were 0.68 and 0.65, respectively. The average δEu value for micritic calcareous minerals was 0.75, while that for grain calcareous minerals was 0.83^59,61. Different mineral types exhibited varying degrees of δEu values, particularly in grain calcareous minerals, where the δEu anomaly compared to typical sedimentary rocks was notably weaker.

Fig. 14

REE distribution patterns of samples. (A): Micritic carbonate mineral; (B): Grain carbonate minerals; (C): Clay laminae in micritic carbonate rocks; (D): Clay laminae in grain carbonate rocks; North American Shale Composite (NASC) values according to Haskin et al.⁶¹.

The (La/Yb)n ratio is commonly used to assess the fractionation of light and heavy rare earth elements in sedimentary rocks^5,59,61. There is limited variation among the different types of minerals in the study area concerning this indicator. However, compared to North American shale, distinct characteristics are observed in the mineral samples, indicating an enrichment of light rare earth elements and fractionation of heavy rare earth elements. The geochemical evidence suggests that grain calcareous rocks primarily formed under the influence of diagenetic fluids. Additionally, the notably high Ni and Sr values in grain calcareous rocks may be associated with deep hydrothermal activity.

C, O and Sr isotopes

As illustrated in Fig. 15, the carbon and oxygen isotope characteristics of the two carbonate minerals show significant differences. The δ18O values of clay minerals in micritic calcareous rocks are generally greater than -10‰, whereas the δ18O values of clay laminae in grain calcareous rocks are mostly less than -10‰^62,63. The negative shift in oxygen isotopes is typically attributed to fluid activity during the burial period of calcite. As a result, grain calcareous minerals are strongly associated with diagenetic fluids. When calculating the Z values of the samples using carbon and oxygen isotopes, the average Z values for both carbonate minerals exceed 120. This suggests a marine environment with elevated salinity levels.

Fig. 15

Carbon and oxygen isotope analysis of grain carbonate minerals and micritic carbonate mineral samples.

Due to their high stability and excellent traceability, Sr isotopes in sedimentary rocks provide direct evidence for determining the origin of rocks or minerals. Previous research indicates that Sr isotopes associated with thermal fluid sources from primary magmas have values around 0.703, those linked to volcanic activities in island arcs are approximately 0.706, Sr isotopes from deep cratonic thermal brines are around 0.711, and Sr isotopes from continental detritus sources are roughly 0.719^64,65,66. The average Sr isotope values of carbonate and clay minerals in the carbonate rock samples from this study are approximately 0.711. Thus, the formation of carbonate rocks in the study area is not related to magmatic processes and is not influenced by continental detritus. Given the trace element features of Ni and Sr in the carbonate rocks, it can be inferred that their formation is influenced by deep hydrothermal activity.

Correlation analysis of Sr isotopes in carbonate laminae and adjacent clay minerals reveals a strong correlation in micritic carbonate rocks, with a correlation coefficient of 0.842 (Fig. 16A). In contrast, there is minimal correlation between the two minerals in grain carbonate rocks (Fig. 16B). This suggests that the formation of micritic carbonate rocks is primarily governed by sedimentary processes, with no significant alteration by formation fluids during sedimentation. Conversely, the formation of clay minerals and carbonate minerals in grain carbonate rocks is influenced by fluids with different characteristics. Additionally, the presence of barite and its trace element features in grain carbonate indicate that the formation of carbonate minerals in these rocks is influenced by deep hydrothermal activity and subsequent diagenetic processes.

Fig. 16

Strontium isotope analysis of different mineral types in grain carbonate rocks and micritic carbonate rocks. (A): Micritic carbonate rocks; (B): Grain carbonate rock.

Origin and evolution process of carbonate minerals

The formation of grain carbonate rocks is primarily governed by diagenesis, as demonstrated by petrological and geochemical analyses. During the sedimentary period of Es4-1 in the Dongying Depression, rapid sedimentation rates led to the formation of two distinct rock types. mudstone and shale, at the base of the saline lake basin. Variations in sedimentation rates resulted in the formation of these distinct rock types. As mudstone and shale underwent compaction, fluids were expelled outward from the muddy sediment, simultaneously causing a decrease in sediment volume. This led to the development of diagenetic shrinkage fractures (Fig. 17A).

Fig. 17

Formation patterns of grain carbonate rocks and micritic carbonate rocks.

During the Es4-1 sedimentary period, the Dongying Depression experienced frequent tectonic activity and deep fluid movement^29,36. Intense compressional tectonic forces, combined with hydrocarbon generation pressure and compaction, resulted in widespread overpressure systems within the stratigraphy^34,38,39. The mechanically unstable nature of shale bedding planes made them susceptible to fracturing when residual pressure from the overpressure system exceeded the rock’s bearing capacity, resulting in microfractures.

Meanwhile, deep hydrothermal brines participated in the sedimentary processes. The fluid composition primarily consisted of deep cratonic thermal fluids, which introduced significant amounts of Ni and Sr into the system. The microfractures facilitated the entry of these fluids into diagenetic shrinkage fractures, leading to the formation of cathodoluminescent, deep red luminescent carbonate minerals within the grain carbonate rocks.

The high-salinity water environment of the Paleogene favored the precipitation of aragonite, which is rich in Sr. However, aragonite is an unstable mineral that rapidly transforms into stable calcite within a short period. During this transformation, significant amounts of Sr are released into the fluid, with later-stage diagenetic fluids largely inheriting the properties of the earlier sedimentary fluids. Consequently, this process led to the formation of grain calcite with orange-red luminescence around the periphery of the grain carbonate rocks (Fig. 17B).

The development of micritic carbonate rocks is primarily influenced by biogenic activities. Deep-sea hydrothermal processes increase the salinity of lake basin water, leading to the accumulation of elements such as Ni and Sr within the basin. During the sedimentation phase of the Es3-Es4 interval in the Dongying Depression, the climate was characterized by dry and warm summer conditions^34,38,39. This resulted in a significant temperature disparity between the lake’s surface and its depths, fostering the formation of water column stratification. In the shallower regions of the water body, oxidizing conditions promoted the flourishing of aquatic life. Upon the demise of these organisms, their remains settled and descended to the bottom of the lake basin, where a reducing environment prevailed, ultimately leading to sediment deposition.

During the cold and humid winter, the temperature difference between the shallow and deep parts of the lake basin was minimal, preventing water column stratification. Under the influence of biological processes, carbonate mineral deposition occurred (Fig. 17C). Additionally, seasonal climatic changes contributed to the deposition of thinner layers of carbonate and clay minerals in the micritic carbonate rocks, exhibiting periodic variation patterns.

The relations between carbonates and oil shale

Extensive research has focused on the enrichment mechanisms of continental oil shale. Previous studies suggest that organic content and the development of storage space within shale are key factors determining oil accumulation^1,7,8,16. A positive correlation exists between organic content and carbonate mineral content in shale, with carbonates acting as the primary reservoir for oil shale accumulation. This study further categorizes carbonate rock types and shows that micritic and grain carbonate rocks have significantly different effects on oil shale enrichment.

The formation of micritic carbonate rocks is mainly influenced by seasonal water column stratification. These rocks have higher clay mineral content and feature alternating thin layers of carbonate and clay laminae, a pattern more common in mudstone segments. Due to the faster sedimentation rate of organic matter in mudstone compared to shale, micritic carbonate rocks tend to have lower TOC content. The primary storage spaces in these rocks are “narrow slit” microcracks, which result in a higher density than shale.

Grain carbonate rocks, on the other hand, are primarily formed through diagenetic processes. They are more abundant within shale intervals, characterized by higher carbonate mineral content and thicker, granular grains. The slower sedimentation rate of shale leads to higher TOC content in grain carbonate rocks. Structural activity influences the development of bedding planes (foliation), and increased hydrocarbon generation under pressure causes granule fragmentation, resulting in fractures filled with asphaltenes. The main reservoir spaces in these rocks are dominated by “bottle neck” and “slit” microfractures, enhancing reservoir characteristics. The higher organic content and well-developed storage spaces make shale more conducive to oil shale enrichment, with the carbonate layers of grain carbonate rocks representing the “sweet spot” for oil shale development.

Conclusions

Deep hydrothermal activity has played a crucial role in the formation of carbonate minerals in shale. Intense tectonic activity has created deep faults connecting to the mantle, generating numerous microfractures along bedding planes of previously deposited shale. Some hydrothermal fluids infiltrate these microfractures during diagenesis, forming grain carbonate. Other fluids ascend along faults into the basin, contributing substantial amounts of elements such as Ni and Sr to the basin water.

In the hot, dry summer environment, a significant temperature gradient between the surface and the basin floor causes water stratification. The surface water, being warmer and lower in density, contains sufficient oxygen, promoting biological proliferation. When organisms die, their remains sink to the bottom of the basin, where the denser, oxygen-deficient environment preserves thin layers of clay minerals. In the cold, wet winter, the basin experiences an oxidizing environment, facilitating the formation of micritic carbonate minerals through biological processes. Due to the early influx of hydrothermal fluids, these micritic carbonates are enriched in elements such as Ni and Sr.

Grain carbonate minerals mainly develop in shale. Due to the slow sedimentation rate, shale retains relatively high organic matter content in its clay minerals. Structural activity and overpressure from hydrocarbon generation lead to the formation of "bottle-neck" and “slit” microfractures in shale, contributing to higher TOC content and enhancing reservoir quality and connectivity. This makes shale a favorable medium for oil shale accumulation.

Micritic carbonate minerals primarily form in mudstone. Due to the faster sedimentation rate of mudstone, organic matter enrichment is diluted, resulting in lower organic content. Water stratification leads to the alternation of thin layers of carbonate and clay minerals, forming “slit” microfractures. Consequently, the reservoir quality and connectivity in mudstone are poor, making it less favorable for oil shale accumulation.