Lithostratigraphy
The sequence stratigraphy in the study area is represented by three stratigraphic rock units, belonging to the late Early to Middle Eocene time. These rock units are, from older to younger, Minia Formation, Gebel Hof Formation, and Observatory Formation (Fig. 2). A detailed description of each rock unit in the study area is given below.
Minia Formation was first introduced by Said36 to describe a 35-meter-thick section of thick-bedded, white, alveolinid limestone containing Alveolina frumentiformis Schwager and Orbitolites cf. complanatus Lamarck at Zawiet Saada area, opposite to Minia City. In the study area, it is only recorded at Wadi El-Qanaa area, with a thickness of about 200 m, representing the oldest Eocene rock unit, unconformably overlying the Upper Cretaceous (Cenomanian) Galala Formation (Fig. 2).
The lower part of Minia Formation consists of white marl, grading into greyish-white, thinly-bedded marly limestone, and capped by cavernous limestone (Fig. 3a). The middle part is characterized by chalky limestone, intercalated with white sandy limestone, while the upper part is entirely made up of limestone (Fig. 2). Furthermore, Minia Formation yields several planktonic foraminiferal species, such as Acarinina pentacamerata (Subbotina) and Turborotalia frontosa (Subbotina). Therefore, Minia Formation can be assigned to the late Ypresian age. This is in alignment with the work of El-Dawoody and Galal16 that proposed a late Early Eocene (Ypresian) age for Minia Formation. Minia Formation conformably underlies the Middle Eocene Gebel Hof Formation (Fig. 2).
Field photographs of the studied lithostratigraphic units. (a) The lower part of Minia Formation at Wadi El-Qanaa area, marking the transition among the marl, marly limestone, and the overlying cavernous limestone. (b) The upper part of Observatory Formation at El-Hamma area, consisting of thick oyster bed followed by cavernous limestone. 1: Nummulites beaumonti (d’Archiac & Haime). 2: Nummulites gizehensis (Forskal). 3: Nummulites perforatus (de Montfort). 4: Nummulites discorbinus (Schlotheim). (c) The exposed rock units at the El-Moniedra area, showing the Observatory Formation unconformably overlying the Galala Formation, the glauconite bed marked by the green lines.
Gebel Hof Formation was proposed by Farag and Ismail37 to describe a 120-meter-thick section of white limestone, chalky at the base, and interspersed with thin bands of hard dolomitic limestone at Gebel Hof area, near Helwan City. In the study area, it is prominently exposed at the top of Wadi El-Qanaa area, where its thickness reaches about 130 m (Fig. 2).
The basal part of Gebel Hof Formation at Wadi El-Qanaa area consists of cherty limestone, followed by a thick marly limestone bed intercalated with limestone (Fig. 2). The uppermost part is made up of snow-white chalky limestone, creating a striking visual contrast (Fig. 2). Gebel Hof Formation at Wadi El-Qanaa area is assigned to the Middle Eocene (early-middle Lutetian) age according to El-Dawoody and Galal16, based on the presence of Nummulites beaumonti (de Montfort), Nummulites discorbinus (Schlotheim), and Operculina sp.
Observatory Formation was introduced by Farag and Ismail37 to describe an approximately 80-meter-thick section of white to golden-tan, marly, and nodular limestone at the Observatory Plateau, east of Helwan City. In the study area, it is recorded at El-Hamma area, with a thickness of about 15 m, and at El-Moniedra area, where its thickness reaches about 50 m (Fig. 2).
At El-Hamma area, Observatory Formation is characterized by highly fossiliferous limestone followed by a thin sandy limestone layer. The upper part consists of a distinctive oyster bed capped by white to yellow, cavernous limestone (Fig. 3b). Observatory Formation is characterized by rich faunal content, including significant elements such as oyster bivalves, gastropods, bryozoans, corals, echinoids, algae, and larger benthic foraminifera. Among the identified larger benthic foraminifera, Nummulites gizehensis (Forskal), Nummulites discorbinus (Schlotheim), Nummulites beaumonti (d’Archiac & Haime), and Nummulites perforatus (de Montfort) (Fig. 3b).
At El-Moniedra area, the lower part is made up of intercalations between limestone and dolomite (Fig. 3c). The middle part consists of a thick dolomite bed overlain by golden-tan, limestone, containing a green gluaconite bed. The upper part is characterized by a distinctive oyster bed capped by thin dolomite layer (Fig. 3c). Observatory Formation can be attributed to the Middle Eocene age based on the included larger benthic foraminifera, e.g., Nummulite gizehensis (Forskal), Nummulite perforatus (de Montfort), and Nummulite beaumonti (d’Archiac & Haime).
Microfacies analysis
The microfacies analysis of the carbonate beds of Minia, Gebel Hof, and Observatory formations allowed the identification of seven microfacies types. The recognized microfacies types are compared with the standard microfacies types of Flügel32 and the facies zones of Wilson33.
The bioclastic floatstone microfacies (MFT-1) is recorded from the uppermost part of Observatory Formation at El-Hamma area and the lowermost part of Observatory Formation at El-Moniedra area (Fig. 4). It comprises rich faunal content with high diversity in microsparite cement, along with a few, fine to medium, subangular quartz grains, peloids, glauconite grains, and ferruginous patches (Fig. 5a–c). The faunal content includes bivalve oyster shells, gastropod shell fragments, serpulid worms, bryozoan fronds, miliolid and larger foraminiferal tests, coral fragments, echinoid plates, and various algal plates.
Lithostratigraphic sections from the study area showing the microfacies types, depositional sequences and environments, and the distribution of the common carbonate diagenetic features throughout the recognized rock units.
(a–c) Bioclastic floatstone (MFT-1), with bivalves (Bv), echinoids (Ec), algae (Al), and bryozoa (Br). (d–f) Ferruginous dolomite (MFT-2), showing medium-grained, zoned dolomite crystals, filling the dissolution pores.
The ferruginous dolomite microfacies (MFT-2) is reported at various intervals within Observatory Formation at El-Moniedra area (Fig. 4). This microfacies consists of fine- to medium-grained, zoned, subhedral to euhedral dolomite crystals, with ferruginous material, iron oxides, and fine to medium, subangular quartz grains. Additionally, a few bivalve shell fragments are recorded (Fig. 5d–f).
The bioclastic packstone microfacies (MFT-3) is recorded from the lower part of Observatory Formation at El-Moniedra area (Fig. 4). The groundmass of this microfacies is represented by micrite cement, containing fine to medium, subangular quartz grains, yellowish glauconite pellets, ferruginous material, and some subhedral, zoned dolomite crystals (Fig. 6a–c).
(a–c) Bioclastic packstone (MFT-3), with bivalves, gastropod shells (Gs), and algal plates. (d–f) Ferrigenous peloidal bioclastic grainstone (MFT-4), with bryozoa (e) and phosphate grains (f).
Skeletal components include bivalve shell fragments, gastropod shells, and various algal plates, with some algae encrusting the bivalve shells.
The ferruginous peloidal bioclastic grainstone microfacies (MFT-4) is reported in the middle part of Observatory Formation at El-Hamma and El Moniedra areas (Fig. 4). This microfacies includes a highly diversified biota in a groundmass of microsparite. It has moderately-sorted, fine to medium, subangular to angular quartz grains, ooids, peloids, some subhedral, zoned dolomite crystals, phosphate grains, few ferruginous patches, glauconite grains, and iron oxides (Fig. 6d–f). The main skeletal components are bivalve shell fragments, gastropod shells, echinoid spines, bryozoan fronds, coral fragments, benthic foraminiferal tests, and various algal plates (Fig. 6e).
The sandy peloidal bioclastic rudstone microfacies (MFT-5) is recorded from various intervals within Observatory Formation at El-Hamma and El-Moniedra areas (Fig. 4). This microfacies is characterized by a highly diverse faunal content in microsparite cement, with a few ferruginous patches, ooids, peloids, fine subangular quartz grains, euhedral zoned dolomite crystals, glauconite grains, and a few phosphate grains (Fig. 7a–c). The faunal content consists of bivalve oyster shells, gastropod shells, coral fragments, echinoid plates with microbial encrustation, larger foraminiferal tests, bryozoan fronds, and various algal plates.
(a–c) Sandy peloidal bioclastic rudstone (MFT-5), with bryozoa, oyster bivalves, and the larger benthic foraminifer Nummulite beaumonti (d’Archiac & Haime) (b). (d-f) Foraminiferal wackestone (MFT-6), with Acarinina pentacamerata (Subbotina) (d) and echinoid fragments.
The foraminiferal wackestone microfacies (MFT-6) is recorded from the lowermost part of Gebel Hof Formation at Wadi El-Qanaa area (Fig. 4). This microfacies is made up of a highly diversified biota in a groundmass of micrite. The main skeletal components are planktonic and benthic foraminiferal tests, including miliolids, bivalve and gastropod shells, echinoid plates and spines, serpulid worms, and various algal plates (Fig. 7d–f).
The bioclastic packstone microfacies (MFT-7) is recorded from various intervals within Minia Formation and from the middle and upper parts of Gebel Hof Formation at Wadi El-Qanaa area (Fig. 4). The groundmass of this microfacies consists of micrite cement, with skeletal components including planktonic and benthic foraminiferal tests, gastropod shells, and bivalve shell fragments (Fig. 8).
Bioclastic packstone (MFT-7), with bivalves, echinoids, and planktonic foraminifera.
Sequence stratigraphy
The sequence stratigraphy of the study area, which spans from the late Early to Middle Eocene, was developed by integrating lithostratigraphic observations with detailed microfacies analysis, revealing important insights into the relative sea-level changes and accommodation space variations during the deposition of the Minia, Gebel Hof, and Observatory formations.
Minia Formation: This formation corresponds to the Transgressive Systems Tract (TST) of the first depositional sequence (YpM-Sq1; Fig. 4). The lower part, composed of white marl and marly limestone, reflects low-energy outer ramp conditions, while the middle section, marked by chalky limestone, indicates increased carbonate production during sea-level rise, reaching the maximum flooding surface (MFS). The upper part transitions to the early Highstand Systems Tract (HST), reflecting shallowing-upward conditions as accommodation space decreased.
A well-defined sequence boundary (SB Yp/Lu) separates the Minia Formation (YpM-sq1) and the overlying Gebel Hof Formation (LuGH-sq2) in Wadi El Qanaa area. This boundary is marked by a sharp lithological shift from the HST of YpM-sq1 (shallowing-upward pure limestone) to the basal cherty limestone of LuGH-sq2 (Fig. 4). The SB reflects a fall in relative sea level, culminating in the exposure of the carbonate platform and a basinward shift in facies prior to the renewed transgression recorded in LuGH-sq2. This boundary aligns with regional Late Ypresian–Early Lutetian eustatic fluctuations, emphasizing the interplay between tectonics and eustasy in controlling accommodation1.
Gebel Hof Formation: This formation represents the Highstand Systems Tract (HST) of the second depositional sequence (LuGH-Sq2; Fig. 4). The basal cherty limestone reflects mid-ramp deposition with episodic siliciclastic influx, transitioning upward into marly limestone, indicating a shallowing trend. The upper part, dominated by pure limestone, represents a low-energy lagoonal to shoal environment, marked by benthic foraminiferal assemblages.
Observatory Formation: The Observatory Formation includes both the Transgressive Systems Tract (TST) and Highstand Systems Tract (HST) within the third sequence (LuOb-Sq3; Fig. 4). At the El-Hamma area, highly fossiliferous limestone marks the initial transgression, while sandy limestone reflects increased siliciclastic input. The upper oyster beds and cavernous limestone signify a reduced accommodation space and regression, consistent with the HST. At the El-Moniedra area, glauconite-rich layers and ferruginous dolomites indicate a maximum flooding event followed by shoaling and progradation.
Carbonate diagenetic analysis
Petrographical analysis of the studied carbonate rocks revealed multiple diagenetic processes, altering their original depositional textures, such as micritization, glauconitization, dolomitization, and neomorphism (Fig. 4; Table 1). Micritization refers to the process whereby carbonate allochems undergo replacement by crypto- and microcrystalline calcite, leading to a gradual obliteration of their original textures38,39. This phenomenon is most pronounced in the shallow subtidal, including shoal, inner ramp carbonate sediments of Observatory Formation at El-Hamma and El Moniedra areas (Fig. 4).
Micritization
Skeletal particles such as echinoderms and mollusks exhibit various degrees of susceptibility to micritization. This process entails the partial replacement of their internal structures by microstructure-controlled minute patches of dark-colored micrite. Despite these alterations, the overall size, outer margins, and remnants of the internal structures of micritized fossils remain discernible (Fig. 9a, b). Micritization also led to the formation of micrite envelopes, typically 18–46 μm-thick, outlining the peripheries of bivalve shells and echinoid plates (Fig. 9c). In these instances, micritization initiated from the outer margins of the skeletal grains and progressed inward toward the center. These micrite envelopes serve to stabilize the carbonate grains, preventing further diagenetic alterations.
(a) and (b) Thin-section photomicrographs show the micritization of a gastropod shell. (c) Micrite envelope around the periphery of bivalves and echinoidal plates. (d) Glauconitic grains scattered in a micrite matrix. (e) Glauconites partially replace ooids. (f) Infilling of a nummulite chamber by glauconites. (g) and (h) Thin-section photomicrographs demonstrate fibrous calcite cement. (i) Filling of a dissolution pore by granular spar cement.
Glauconitization
Glauconites are volumetrically-infrequent in the analyzed carbonates. The glauconitic grains are dispersed throughout the matrix (Fig. 9d). They are prevalent in the shallow subtidal inner ramp carbonates of Observatory Formation at El-Hamma and El Moniedra areas (Fig. 4). The glauconites exhibit yellowish to reddish-green color, poor to moderate sorting, and subrounded to subangular shape. Additionally, glauconite partially replaces ooids and larger foraminifera (Fig. 9e, f).
Calcite cementation
Calcite cement is the most prevalent cement type in the examined carbonates, exhibiting numerous fabric varieties that reflect diverse diagenetic environments. Fibrous calcite cement is uncommon in the studied carbonates due to its deterioration by compaction processes over time. It has been identified in the shallow subtidal inner ramp carbonates of Observatory Formation at El-Hamma area (Fig. 4). The fibrous calcite cement is composed of fine-crystalline, needle-shaped, planar, tightly-packed calcite crystals, with translucent to cloudy fringes (Fig. 9g, h).
Sparry calcite cement represents the most significant porosity-destructive cement. It displays two main fabrics; granular spar and blocky calcite. The granular spar occupies interparticle pore spaces, consisting of inclusion-free, transparent, subhedral to anhedral crystals (Fig. 9i). Blocky calcite cement refers to limpid, transparent, mud-free, subhedral, non-equidimensional, and coarse calcite crystals with distinct planar intercrystalline boundaries.
Two phases of blocky calcite cement were identified in the studied carbonates. The earlier phase fills solution pore spaces, with crystal size increasing towards the center of the pore space (Fig. 10a). This phase is commonly observed in the shallow subtidal inner ramp carbonates of Observatory Formation at El-Moniedra and El-Hamma areas, as well as in the middle ramp carbonates of Minia and Gebel Hof formations at Wadi El-Qanaa area (Fig. 4). The second phase consists of blocky crystals with undulatory extinction occurring within fractures (Fig. 10b). It is mainly recorded in the shallow subtidal inner ramp carbonates of Observatory Formation at El-Moniedra area (Fig. 4).
(a) Blocky calcite cement fills a pore-space formed by dissolution of matrix. (b) Thin-section photomicrograph displays granular calcite fills a microfracture. (c) and (d) Thin-section photomicrographs show the fine-crystalline, replacive dolomites. (e) and (f) Thin-section photomicrographs display the occlusion of open void by medium-grained, zoned, euhedral dolomite cement. (g) Aggrading neomorphism of the micitic matrix into neomorphic spar. (h) Thin-section photomicrograph shows the neomorphic calcitization of gastropod shell into inclusion-rich, granular neomorphic spar. (i) The partial infilling of a void space by quartz cement.
Dolomitization
The petrographical investigation of the recorded dolomites reveals two modes of emplacement; replacive dolomites and void-filling dolomites. The matrix replacive dolomites are gray to yellowish-gray, hard, and burrowed. They are fine- to very fine-crystalline, displaying primary intercrystalline porosity (Fig. 10c, d).
These dolomites show uniform extinction, and unimodal crystal size distribution. Most of these dolomites are unzoned, exhibiting cloudy cores due to inclusions of precursor lime mud relicts. This phase is commonly observed in the intertidal and shallow subtidal shoal inner ramp carbonates of Observatory Formation at El-Hamma and El-Moiendra areas (Fig. 4).
Void-filling dolomite shows limited distribution in the studied carbonates. It is identified as a filling material that partially to entirely occludes open voids and dissolution pores. Dolomite cement has been observed in the intertidal carbonates of Observatory Formation at El-Moniedra area (Fig. 4). The examined dolomite cement is characterized by fine to medium crystalline, well-developed, idiomorphic dolomite rhombs and undulose extinction. Most of these rhombs are distinctly zoned, featuring dark reddish iron-oxide rhombic cores with clear rims, while some are completely limpid (Fig. 10e, f).
Neomorphism
Aggrading neomorphism of the micritic matrix is a prominent characteristic in the studied mud-supported carbonates (Fig. 4). This process involves the recrystallization of fine-crystalline micritic matrix into coarser neomorphic spar (Fig. 10g). The neomorphic spar consists of impure, granular, patchy, anhedral calcite crystals with curved to irregular intercrystalline contacts. It typically retains small remnants of the original unreplaced micritic matrix.
Neomorphic calcitization of skeletal allochems is a stabilization process that affects the bioclasts of gastropods and bivalves in different degrees, resulting in partial to complete obliteration of their original structures. During the progression of neomorphic calcitization, the internal structures of skeletal allochems are replaced by brownish-colored, non-planar, roughly-distributed granular calcite mosaics with curved boundaries (Fig. 10h).
Aggrading neomorphism of matrix and neomorphic calcitization of skeletal allochems are both documented in the shallow subtidal, including shoal, inner ramp carbonates of Observatory Formation at El-Hamma and El-Moiendra areas (Fig. 4).
Silicification
Silica is present as a cement filling pore spaces in the middle ramp carbonates of Minia and Gebel Hof formations at Wadi El-Qanaa area and the shallow subtidal shoal inner ramp carbonates of Observatory Formation at El-Hamma and El-Moiendra areas (Fig. 4). The silica cement in these rocks consists of fine to medium, anhedral quartz crystals, and dispersed throughout the matrix (Fig. 9g, h). The quartz crystals partially to entirely occlude open voids and dissolution pores (Figs. 10i and 11a). Some skeletal particles such as bivalves show partial replacement of their internal structures by silica (Fig. 11b).
(a) Quartz cement fills a cavity in micrite matrix. (b) Quartz cement fills biomoldic porosity of bivalve shell formed by dissolution of its internal structure. (c) A fracture in a nummulitic grain due to mechanical compaction. (d) Thinsection photomicrograph displays rearrangement of grains as result of mechanical compaction. (e) and (f) Iron-oxide replaces the matrix. (g) and (h) Iron-oxide envelope around the periphery of gastropod shells. (i) Moldic pore formed as result of selective dissolution of the calcite cement.
Mechanical compaction
Compaction is a post-depositional process resulting from a progressive increase in burial load or from crustal tectonic stresses32. It leads to the loss of interparticle porosity, dewatering, and reduction in bed thickness. The style of compaction is primarily influenced by rock texture, mineral stabilization, sedimentation rate, cementation, and overburden burial depth14. The mechanical compaction involves grain rearrangement, contortion, fracturing, and breakage of allochemical constituents (Fig. 11c, d). This phenomenon is most pronounced in the shallow subtidal shoal inner ramp carbonates of the Observatory Formation at El-Hamma and El-Moiendra areas (Fig. 4).
Iron oxides
The presence of iron oxides is quite limited in the examined rocks. It is recorded in the shallow subtidal shoal inner ramp carbonates of Observatory Formation at El-Hamma and El-Moiendra areas (Fig. 4). It manifests as brownish to reddish-black pockets and patches that impregnate the matrix, replace shells, and coat some allochemical constituents (Fig. 11e–h). Algae and echinoid plates are particularly susceptible to iron-oxide pigmentation.
Fracturing
Fractures are sparsely distributed throughout the studied sequence, observed at both macroscopic and microscopic scales (Figs. 10b, e and f and 11c). Macroscopic fractures were identified within the intertidal and shallow subtidal shoal inner ramp carbonates of Observatory Formation at El-Hamma and El-Moniedra area, and in the middle ramp carbonates characterizing Minia and Gebel Hof formations at Wadi El-Qanaa area (Fig. 4).
Dissolution
Dissolution is a prevalent feature observed in the studied carbonates. It impacts the matrix, cement, and skeletal allochems, leading to the obliteration of original textures and the formation of secondary porosity40. This process occurs as carbonate constituents are leached out by diagenetic fluids that are undersaturated with respect to CaCO341,42. This phenomenon is most pronounced in shallow subtidal inner ramp carbonates of Observatory Formation at El-Moniedra and El-Hamma areas (Fig. 4). As a result of the selective dissolution of cement and skeletal allochems, leaving behind open moldic pores, many pores are later filled or partially occluded by meteoric or burial cements during subsequent diagenetic stages (Figs. 9c and e and 11i).
