Alteration and Non-Formula Elements Uptake of Zircon from Um Ara Granite, South Eastern Desert, Egypt

Abstract

The Um Ara granites are a suite of granitoid rocks located in the southern part of the Eastern Desert of Egypt. The integration of various electron probe micro analyzer (EPMA) techniques, such as backscattered electron (BSE) imaging, X-ray compositional mapping, and wavelength dispersive spectrometry (WDS), has provided valuable insights into the alteration process of zircon in the Um Ara granite. The zircon exhibits high concentrations of non-formula elements such as P, Al, Ca, Fe, Ti, and REEs, suggesting that the alteration involved coupled dissolution-reprecipitation processes influenced by aqueous fluids. The negative correlations between Zr and the non-formula elements indicate that these elements were incorporated into zircon at the expense of Zr and Si, significantly affecting the distribution and fractionation of REEs in the original zircon. Based on the presented data and literature knowledge, the sequence of alteration events is proposed as follows: (1) initial zircon crystallization around 603 Ma accompanied by the formation of other U- and Th-bearing minerals like xenotime, thorite, monazite, and apatite; (2) long-term metamictization leading to fractures and cracks that facilitated fluid circulation and chemical changes; (3) a major hydrothermal event around 20 Ma that released a suite of non-formula elements from the metamicted zircon and associated minerals, with the enriched hydrothermal fluids subsequently incorporating these elements into the modified zircon structure; and (4) further low-temperature alteration during subsequent pluvial periods (around 50,000–159,000 years ago), facilitated by the shear zones in the Um Ara granites, may have allowed further uptake of non-formula elements. The interplay between hydrothermal fluids, meteoric water, and the shear zone environments appears to have been a key driver for the uptake of non-formula elements into the altered zircon.

1. Introduction

While zircon is generally considered a refractory mineral, it can undergo fluid-assisted alteration under different P-T conditions in the Earth’s crust. Metamict zircon, in particular, exhibits enhanced reactivity towards fluids due to its amorphous or disrupted crystal lattice structure. Several studies have indicated that metamict zircon is predominantly affected by fluid-aided alteration, even under fairly low P-T conditions [1,2,3]. Metamict zircon, with its amorphous or disturbed crystal lattice, provides more accessible pathways for fluid infiltration and alteration than the original zircon. The susceptibility of zircon to fluid-assisted alteration can lead to changes in its mineralogical and chemical composition. This includes the incorporation or loss of certain elements as the fluid interacts with the zircon lattice. These alterations can have significant implications for interpreting geochronological, geochemical, and isotopic data obtained from zircon. A recent study by [4] highlights that even zircon with low levels of radiation effect can undergo metasomatic alteration when exposed to alkali- and F-bearing solutions, which can induce chemical changes and modify the zircon structure. They demonstrated that zircon can be metasomatically altered under high P-T conditions within the lower crust. These solutions can induce chemical changes in zircon, leading to compositional modifications within the zircon structure.

During the initial stages of granite formation, non-metamict zircon crystallizes from the magma as a durable and resistant mineral. Compared to zircon with low radiation damage, metamict zircon is more susceptible to fluid-assisted alteration, even at relatively low pressure and temperature conditions. The metamictization process, caused by the alpha decay of radioactive elements within the zircon, could have eventually weakened this mineral, rendering it susceptible to modification by a later hydrothermal alteration. Multiple zircon alteration mechanisms have been proposed, including dissolution–reprecipitation and solid-state reaction processes [3,5,6,7]. These alteration processes require fluid access to the radiation-damaged areas of the zircon. As temperature increases, the dissolution-reprecipitation process appears to become the dominant replacement mechanism [5]. This process can lead to the partial or complete dissolution of zircon in hydrothermal fluids, followed by the reprecipitation of new zircon domains or overgrowths [8]. Fluids can also interact with zircon through exchange reactions, where elements are added or removed from the zircon structure, including the uptake of non-formula elements like HREE, Y, Ca, or P, or the release of Zr and Si [9,10,11,12]. Solid-state diffusion of elements, such as Pb, U, or Th, can occur in zircon, especially in metamict or partially damaged domains, altering its composition and isotopic signatures. Zircon can also undergo phase changes through solid-state phase transformations, and structural defects can accumulate in the zircon structure, altering its physical and chemical properties. Mechanical deformation can promote the recrystallization of zircon, leading to the formation of new zircon domains with different compositions and textures. The relevance and importance of these alteration mechanisms can vary depending on the specific geological context and the nature of the altering fluids. These fluids are often enriched in volatile components such as fluorine (F) and boron (B), which can be derived from the magmatic or metamorphic source rocks [13]. Additionally, hydrothermal fluids may contain elevated concentrations of REEs and other trace elements such as U, Th, and Hf.

The zircon occurrence in the Um Ara area is associated with alkali-feldspar granites that were emplaced between 620 and 530 Ma and intruded the older metavolcanics and Dokhan volcanics. The study of zircon alteration is indeed a valuable approach for gaining insights into complex geological processes occurring in the Earth’s crust. The researcher employed a multifaceted microanalytical approach to investigate various aspects of the zircon, including morphology, growth zoning, and compositional variations in major, trace, and REEs. This multi-technique analysis is crucial for elucidating the mechanisms and conditions of zircon alteration. The zircon from Um Ara exhibits a broad range of major element compositions, with low ZrO₂ and SiO₂ contents, along with high contents of “non-formula” elements such as P, Al, Ca, Fe, Ti, and REEs. This research contributes to the broader understanding of the interplay between zircon alteration, fluid–mineral interactions, and the mobilization and concentration of valuable elements within the Earth’s crust. Continued research in this field has the potential to yield further insights that can be applied across a range of geological disciplines, from mineralogy and petrology to geochemistry and geochronology.

2. Geological and Mineralogical Background

In the present study, zircon crystals have been examined from specimens collected from alkali-feldspar granites of the Um Ara area (Figure 1). This area consists predominantly of granite intrusions that are associated with metavolcanic and Dokhan volcanic. Petrographically, these granites are classified as monzogranite and alkali-feldspar granite. The monzogranite typically has a homogeneous, pinkish, coarse-grained, and equigranular texture, but in some areas, a porphyritic variety is observed. Monzogranite is composed of microcline, microcline perthite, plagioclase (An15-28), quartz, and biotite. Sparse muscovite flakes are also present. Common accessory minerals are sphene and magnetite. Occasionally, small mafic xenoliths (up to 10 cm in diameter) can be found within these granites.

The alkali-feldspar granites exhibit a distinct zonal structure. The lower zone consists of an unaltered, magmatic, pink alkali-feldspar granite. This zone gradually transitions into a middle, altered amazonitized granite zone, and then into an upper, highly metasomatized albitized granite zone. This zonal structure is the result of metasomatic enrichment in K-Na-Si fluids [14,15]. The placement of the altered phases at the top of the intrusion is physically plausible, as metasomatic fluids are buoyant and tend to escape upwards. The mineral constituents of the alkali-feldspar granites are microcline, microperthite, albite (An5-12), commonly micrographic quartz, and minor white mica.

The Um Ara granites exhibit A-type characteristics [14,16]. The amazonitized and albitized granites are characterized by high radioactivity compared to the lower, unaltered alkali-feldspar granite. This indicates that the alkali-metasomatic alteration played a role in localizing radioactive mineralization within the Um Ara granite. The metasomatized alkali-feldspar granites contain accessory amounts of zircon, thorite, monazite, xenotime, uranothorite, and uranophane. The formation of these accessory minerals has been attributed to either magmatic processes or post-magmatic, high-temperature metasomatic processes. Geochronological studies have confirmed that the zircon crystals in the Um Ara granite have a magmatic origin, dating them to 603 ± 14 Ma [16]. This zircon age is consistent with a K-Ar age of 589 Ma obtained from mica separates in the same granite [14].

Fluid inclusion data indicates that the exsolved mineralizing fluids were moderately saline, but rich in CO₂ [14]. It is proposed that the key stage of rare metal mineralization in the Um Ara granites was the late magmatic stage. During this stage, orthomagmatic fluids enriched in ligands like CO₂ and F exsolved from the granitic magma and interacted with the rare metal-rich residual magma to form complexes with the rare metals. During the waning hydrothermal stage, the decreasing solubility of CO₂ and F with falling temperature and increasing fluid pH led to the destabilization of these rare element complexes in the fluids. This favored the precipitation of Zr as zircon, Y as xenotime, Nb as columbite, Th as thorite, REEs as monazite, and U as uranophane. The close association of uranophane, calcite, and fluorite on the fracture surfaces of the albitized alkali-feldspar granite suggests that the precipitation of calcite, fluorite, and uranium mineralization occurred during this period of CO₂ and F loss.

The investigated rock samples, collected from the alteration zones (K- and Na- metasomatism), consist of colorless to little brown and minute zircon crystals that show a pronounced variation in morphology and are commonly metamictized towards the core. Based on field observations and microscopic examinations of both reflected and transmitted light, it has been found that zircon is closely associated with disseminated xenotime, thorite, monazite, apatite, ilmenite, and uranophane. Uranophane occurs as yellow fine acicular crystals that are assembled in fibrous masses. Prismatic to tabular crystals of thorite were recorded in association with zircon and other accessory minerals. Monazite occurs as brown rounded and fractured crystals. Fluorite of violet and colorless occurs as veinlets in the altered zone of the granitic rocks.

3. Sample Preparation and Analytical Procedures

Five samples were collected from the alkali feldspar granites of the Um Ara area at five different locations (Figure 1). The collected samples were initially washed with distilled water to remove any salts. The dried samples were crushed to the sand size fraction and then sieved using 500 µm, 250 µm, 125 µm, and 63 µm sieves. The fine and very fine sand sizes were combined in one fraction, and later subjected to heavy liquid separation using bromoform. The magnetite grains were removed from the heavy fractions by a hand magnet, with the remainder being split into four subfractions using a Frantz isodynamic separator at 0.2, 0.5, and 1.5 A. These subfractions were mounted on glass slides for mineral identification using a polarizing microscope. Mostly zircon grains were identified in the 1.5 A non-magnetic fraction. Several zircon grains from this fraction were hand-picked using a binocular reflected light microscope, mounted, and polished for further microprobe analyses.

BSE, X-ray peak intensity mapping, and WDS analyses of zircon grains and associated uranophane were performed on a JEOL JXA-8200 EPMA available at the Faculty of Earth Sciences, King Abdulaziz University, Saudi Arabia. All analyses were performed using an acceleration voltage of 20 kV, analytical beam current of 60 nA, and beam diameter of 2–10 µm. The counting time was 20 s on peak and 10 s on background. Relative analytical errors were 1% for major elements and 5% for minor elements. The setup and operating conditions for EPMA analyses for each element are given in Table 1. Interference corrections were applied to U Mα1 for interference by Th Mα1, and to Hf Lα1 for interference by Lu Lα1 and Ti Kα1, and to Pb Mα1 for interference by Y Lα1, and to Fe Kα1 for interference by Dy Lβ1, and to Al Kα1 for interference by Ti Kα1, and to Ca Kα1 for interference by Pb Mα1 and Yb Lα1, and to La Lα1 for interference by Nd Lβ1, and to Nd Lβ1 for interference by Ce Lα1, and to Eu Lβ1 for interference by Nd Lβ1, and to Gd Lβ1 for interference by Nd Lβ1, Ce Lα1, and La Lα1, and to Dy Lβ1for interference by Eu Lβ1, and to Ho Lβ1 for interference by Gd Ho Lβ1 and Lu Lα1, and to Er Lβ1 for interference by Tb Lβ1, and to Tm Lα1 for interference by Dy Lβ1 and Gd Lβ1, and to Yb Lα1 for interference by Eu Lβ1, Dy Lβ1, and Tb Lβ1, and to Lu Lα1 for interference by Dy Lβ1 and Ho Lβ1. Corrections were applied to minimize the analysis uncertainties resulting from these interferences using the method supplied by JEOL. Fifty analyses on zircon and six analyses on the associated uranophane were performed, using natural and synthetic standards. Data reduction for the various elements was performed by taking into account the matrix corrections between standards and samples and the analytical parameters. The matrix effects were corrected by the conventional ZAF method which is employed by JEOL 8200 EPMA instrument.

4. Results

4.1. Textural Observations

The majority of the zircon grains in the samples are euhedral and have a porous texture (Figure 2). The dark areas in this figure correspond to micropores within the zircon grains. However, some of the dark regions are not micropores, but rather apatite inclusions within the zircon grains. In addition to the apatite inclusions, the zoned zircon grains also contain inclusions of uranothorite and uranophane minerals (Figure 3 and Figure 4). There are two distinct textural types of zircon grains observed in the studied samples. The first type is referred to as the zoned zircon grains (Figure 2c, Figure 3 and Figure 4), which are the more prevalent type of zircon observed. They exhibit a distinct zonal texture, with a less altered core and a more altered outer rim. The contrast in BSE intensity between the inner and outer parts indicates different degrees of alteration. The more altered outer part of the zoned zircon is enriched in elements like Th, U, Hf, and REEs. Conversely, this outer altered part is depleted in Zr and Si compared to the less altered inner core (Figure 5). The less altered inner core has significantly lower concentrations of trace and rare earth elements compared to the outer region, but higher Zr and Si contents. The second type is referred to as the unzoned zircon grains, which exhibit mottled textures with numerous micropores (Figure 2a,b).

4.2. Major and Trace Elements Composition

The zircon from the Um Ara locality has a chemical composition and crystal structure that deviates significantly from typical zircon. The total amount of major elements in the Um Ara zircon varies widely, from 80% to almost 100%, with decreasing ZrO₂ and SiO₂ contents linearly with decreasing analytical totals (Figure 6a). The sums of cations in the zircon analyses generally increase from around 2.002 to 2.098 atoms per formula unit (apfu) as the overall analytical total decreases from around 99 to 88 wt% (Table 2). This is clear evidence that the studied zircon grains have substantially deviated from the ideal zircon stoichiometry. Several hypotheses have been proposed to explain the low analytical totals observed in the microprobe data, including (1) the presence of water and hydroxyl groups that degrade the mineral under the electron beam [17,18,19]; (2) the presence of numerous micropores, voids, or structural vacancies [20,21,22]; and (3) charge-compensating oxygen defects associated with divalent and trivalent cations, such as Ca, Fe, and REEs [23]. However, there is no consensus on the primary cause(s), and it may involve a combination of these factors.

In contrast to typical igneous zircons, which generally contain around 1 wt% REEs, 1.5 wt% Hf, and less than 3 wt% U and Th, the Um Ara zircons can exceed 2 wt% REEs, 9 wt% Hf, 7 wt% U, and 9 wt% Th. This level of enrichment in these elements is considered extreme compared to normal igneous zircons. The next discussion section will explore the complex substitution mechanisms and alteration processes that may be responsible for the incorporation of these variable and unusually high amounts of REEs, Hf, U, and Th into the zircon crystal structure.

EPMA data (Table 2) reveals a spectrum of alteration in zircon grains. A small subset of zircons is nearly pristine, showing minimal alteration, and major element totals close to 100 wt% (Figure 6a). However, most zircons exhibit greater alteration, reflected in lower total weights (80–98 wt%). The decline in ZrO₂ and SiO₂ content alongside decreasing total weight suggests progressive zircon alteration and the loss of major elements during this process. A clear linear correlation between ZrO₂, SiO₂, and total weight percent across the dataset emphasizes the substantial compositional variation among the zircon grains. It has high and variable concentrations of elements, including HfO₂ (3.80 wt%, on average), ThO₂ (1.74 wt%, on average), UO₂ (1.24 wt%, on average), FeO (1.18 wt%, on average), Al₂O₃ (0.96 wt%, on average), CaO (1.00 wt%, on average), P₂O₅, (0.55 wt%, on average), Y₂O₃ (0.49 wt%, on average), TiO₂ (0.23 wt%, on average), and As₂O₃ (0.14 wt%, on average), in addition to a negligible amount of PbO (0.07 wt%, on average) and MgO (0.03 wt%, on average). Compared to the highly altered variety, the less altered variety is characterized by lower amounts of UO₂, ThO₂, PbO, FeO, Al₂O₃, CaO, MgO, TiO₂, P₂O₅, and As₂O₃ concentrations, and higher ZrO₂, SiO₂, and Y₂O₃ concentrations, with REE below the detection limit.

The studied zircon samples exhibit a wide range of Th/U ratios, from 0.08 to 4.31, with an average of 1.2 (Figure 6b). These Th/U ratios deviate significantly from the typical compositional ranges reported for magmatic zircons (>0.5) and metamorphic zircons (approximately ≤0.1) [24,25,26,27,28,29]. Instead, the Th and U compositions of the studied zircons are more similar to those previously reported for hydrothermal zircons. Highly variable Th/U ratios ranging from 0.13 to 5.68 have been documented in hydrothermal zircons from the Baishitouquan pluton in Eastern Tianshan, NW China [30]. Similarly, hydrothermal zircon phases associated with the Dexing porphyry Cu deposit in China exhibited Th/U ratios between 0.24 and 1.14 [31], and zircons from W and Sn mineralized systems in the Mole Granite- and Boggy Plain-zoned pluton in Australia had Th/U ratios between 0.06 and 0.94 [32,33]. The generally higher Th/U ratios observed in the studied zircons are comparable to those reported for zircons of hydrothermal origin in highly evolved magmatic systems.

4.3. REE Pattern of Zircon

Figure 7 shows the REE patterns of the altered zircons in comparison with the pattern of unaltered magmatic zircon as reported by [34]. The REE distribution in the unaltered magmatic zircon shows a strong fractionation, with a steady increase from LREEs to HREEs and a moderately negative Eu anomaly (Figure 7). The studied altered zircon has an anomalously high REE content (Figure 7). The average LREE content of altered zircons is high (6155) ppm and the average HREE is higher than LREE (8582 ppm). The REE patterns of altered zircon are almost flat at the entire range (Lu_N/La_N averages 8.99). There is a positive Ce and Eu anomaly (Figure 7), with an average Eu/Eu* of 1.88. The (La/Lu)_N ratio is less than 1 (averages 0.35). This suggests that the zircons experienced a secondary enrichment event that preferentially increased the LREE and HREE concentrations, resulting in a flat REE pattern. The positive Ce and Eu anomalies indicate oxidizing conditions during this alteration [35,36].

The average of the (Sm/La)_N ratios observed in the studied altered zircons is 1.78. These ratios are significantly lower than the (Sm/La)_N ratios typically observed in unaltered magmatic zircon, ranging from 33 to 653 [32]. The La–Sm_N/La_N discrimination diagram (Figure 8) represents the compositions of porous, hydrothermal, and unaltered igneous zircons, as indicated by previous studies [32,38,39]. In this diagram, the studied zircon grains are located beyond the established compositional ranges, but close to the field of hydrothermal zircon. This positioning suggests that the parental zircon has undergone fluid-driven alteration, resulting in higher La contents (384–4093 ppm) and lower (Sm/La)_N ratios (0.208–5.47) in the altered zircon. Furthermore, the REE patterns of the studied zircon indicate that the incorporation of dissolved REEs during a hydrothermal stage has led to substantial variations in the REE distribution compared to the parental zircon. In general, the altered zircon grains exhibit higher total REE concentrations than the unaltered magmatic zircon.

5. Discussion

5.1. Zircon Alteration

Zircon is widely recognized as a highly resistant and durable mineral. However, despite its renowned chemical and physical stability, zircon can experience remarkable structural and chemical modifications through a combination of processes: (a) the incorporation of radioactive elements like U and Th can induce radiation damage to the zircon crystal structure, a process known as metamictization [40,41,42]. This radiation-induced damage can cause the zircon crystal lattice to expand in volume and generate internal stresses within the crystal [43]. These internal stresses can ultimately lead to the formation of fractures and cracks within the zircon crystal [44]. Importantly, these fractures provide additional and significant pathways for alteration fluids to penetrate and interact with the interior of the zircon grains; and (b) interaction with hydrothermal fluids can result in the partial dissolution of the original zircon mineral. This is followed by the reprecipitation of new zircon material [1,45,46]. These various alteration processes—radiation damage, deformation, and hydrothermal alteration—can substantially alter the characteristics of zircon, despite its generally accepted reputation as a robust and durable mineral.

The research conducted by [7,22,45] provides further evidence for the involvement of alteration processes in zircon crystals. [45] investigated the alteration effects on zircon crystals from an alkaline pegmatite in Malawi. They found that both interface-controlled and diffusion-controlled processes can operate simultaneously to modify the zircon. The participation of a fluid phase has been recognized in the formation of porous, inclusion-bearing zircon crystals from blueschist rocks in Greece [7]. The zircon crystals from these blueschist rocks contain mineral inclusions, such as xenotime and an unknown Y-REE-Th silicate phase. The presence of these mineral inclusions within the zircon indicates that fluid-mediated processes play a role in the alteration and formation of these inclusions. Furthermore, [22] concluded that alteration domains observed in heavily radiation-damaged zircon grains contain water and exhibit a distinct microtexture and composition compared to pristine areas. This implies that water and other elements can diffuse into radiation-damaged zircon, triggering alteration processes that can lead to structural recovery or recrystallization, depending on the temperature conditions [1,19]. Overall, these studies collectively support the idea that alteration processes in zircon can involve the interaction of fluids, the diffusion of elements, and structural changes. The presence of water and the diffusion of hydrous species play important roles in these alteration processes, which can lead to the formation of altered domains within zircon crystals.

The zircon samples examined in this study were extracted from a granite located within the Gabel Um Ara area in the southern part of the Egyptian Eastern Desert. This region is part of the Arabian-Nubian Shield, which holds significant structural and economic importance due to the presence of valuable mineral deposits. Along the western coastline of the Red Sea and in the Sinai Peninsula of Egypt, there are several mineral occurrences of Mn-Ba-Fe and Zn-Pb-U that are attributed to hydrothermal processes genetically linked to the Oligo-Miocene volcanic activity associated with the rifting of the Red Sea [47,48]. Consequently, despite the typically robust weathering resistance of zircon, it is interpreted that the Um Ara zircons have undergone a prolonged process of metamictization followed by a distinct stage of hydrothermal alteration. This alteration is associated with the main rifting phase of the Red Sea (ca. 20 Ma), as reported by [6]. This lengthy alteration process has led to the potential release and concentration of certain elements from within the crystal structure. During this alteration, the zircon becomes susceptible to the preferential loss of Zr and Si, as evidenced by the linear decreases in ZrO₂ and SiO₂ contents with decreasing analytical totals (Figure 6a). The hydrothermal alteration event also appears to have been accompanied by the breakdown of accessory minerals like xenotime, thorite, monazite, and apatite, which are recorded in the Um Ara granites. This mineral breakdown has enriched the hydrothermal fluids with a variety of non-formula elements, including Fe, Al, Ca, Ti, P, As, and REEs. As this hydrothermal alteration progresses, voids or altered remnants are left behind within the zircon grains. The release of these concentrated trace elements into the infiltrating hydrothermal fluids has facilitated their incorporation into the modified zircon crystal structure, filling the voids and altered zones. This observed alteration process is consistent with the findings reported by [6], who investigated the chemical and structural changes in metamict zircon crystals from the Gabel Hamradom in the Egyptian Eastern Desert. They found that the metamict-, U-, and Th-rich areas of the zircon exhibited significant enrichment in elements like Ca, Al, Fe, Mn, light REEs, and water species while experiencing the depletion of Zr, Si, and radiogenic lead (Pb). Ref. [6] attributed these chemical changes to an intensive reaction with a low-temperature aqueous solution, with temperatures varying from 120 to 200 °C. The presence of this aqueous solution facilitated the alteration process, leading to the enrichment of certain elements and the loss of others within the metamict zircon domains.

The negative correlation observed between ZrO₂ and elements such as ThO₂, UO₂, and Hf suggests a simple substitution mechanism (Figure 9a–c): (Th⁴⁺, U⁴⁺) = Zr⁴⁺; Hf⁴⁺ = Zr⁴⁺ [49]. This implies that these elements replace Zr in the zircon structure, where their effective ionic size and charge are compatible with the crystal lattice. The suggestion made by [50] regarding the incorporation of (UO₂)²⁺ into the zircon lattice at octahedral interstitial positions is an important insight into the crystal–chemical considerations of zircon alteration. This implies that the (UO₂)²⁺ molecular group could potentially be incorporated into the altered zircon variety during the alteration process. In addition to the incorporation of (UO₂)²⁺, the chemistry of zircon supports the possibility of the formation of secondary minerals such as uranophane. Uranophane commonly appears as distinct nano- and micro-inclusions within the zircon or at its peripheries (Figure 4a). The presence of uranophane, xenotime, uranothorite, and apatite inclusions within zircon suggests that the alteration process involves the interaction of aqueous fluids carrying U, Th, Ca, P, and REEs.

In addition to the previous simple substitution, trivalent rare earth elements (REEs) and yttrium (Y) can also substitute for Zr⁴+ (Figure 9d), while pentavalent phosphorus (P) can substitute for Si⁴⁺, according to coupled substitution ((Y, REE)³⁺ + P⁵⁺ = Zr⁴⁺ + Si⁴⁺, [51]). However, it has been observed that trivalent REEs are typically more abundant than P in natural zircons on an atomic basis. This suggests that additional elements must participate in balancing the trivalent REEs in the zircon structure. [52] proposed that interstitial elements such as Mg²⁺, Fe²⁺, Fe³⁺, and Al³⁺ could offer charge stability for REE replacement beyond what is allowed by P replacement. They proposed two “xenotime-type” reactions, as shown in Figure 9e_,f, to explain this charge balancing. The first reaction involves (Al, Fe)³⁺ + 4(Y, REE)³⁺ + P⁵⁺ = 4Zr⁴⁺ + Si⁴⁺, while the second reaction involves (Mg, Fe)²⁺ + 3(Y, REE)³⁺ + P⁵⁺ = 3Zr⁴⁺ + Si⁴⁺. Importantly, the incorporation of Mg, Al, and Fe cations within interstitial sites helps preserve local charge neutrality. In cases where the charge of REE is not fully balanced by P, the remaining charge is compensated by these cations occupying interstitial positions within the lattice structure. Furthermore, the combination of water and hydroxyl into parental zircon is probable through the reaction (Mn⁺ + n(OH)⁻ + (4–n)H₂O = Zr⁴⁺ + (SiO₄)⁴⁻, where M is a metal cation and n is an integer [53]. This suggests that water and hydroxyl groups can be integrated into the zircon structure by replacing Zr and Si.

The alteration processes significantly affect the distribution pattern of REEs in the parental zircon. The altered zircon exhibits distinct fractionation behavior compared to unaltered magmatic zircon, as shown in Figure 7. The irregular chondrite-normalized REE patterns observed in altered zircon may indicate a selective substitution of specific REEs within the crystal lattice of the mineral. This suggests that certain REEs are preferentially incorporated into the zircon structure during the alteration process.

Analysis of the Um Ara zircons reveals several key features that contradict a primary igneous origin as described by [24]). These zircons exhibit high and variable levels of elements not typically found in their crystal structure (often referred to as “non-formula” elements). Additionally, they have low concentrations of SiO₂ and ZrO₂. These characteristics are instead characteristic of zircons that have undergone metamictization or radiation damage [42,54,55]. This conclusion is supported by the BSE images of the Um Ara zircons that reveal textural evidence of extensive radiation damage. This damage manifests as voids, fractures, and highly porous regions throughout the zircon grains, with features ranging from micrometer to nanometer in size (Figure 2).

The accommodation of non-formula elements in metamict zircon can occur through a dissolution-reprecipitation mechanism, where the porous, damaged structure of metamict zircons facilitates the dissolution of the zircon lattice. This allows non-formula elements to be incorporated during the reprecipitation of the zircon. The porous ‘sponge-like’ texture observed in the Um Ara zircon supports this mechanism (Figure 2b). Diffusion–reaction mechanisms could also play a role in the absorption of non-formula elements, where these elements can diffuse into the radiation-damaged parts of the zircon structure. Chemical reactions then incorporate these elements into the zircon.

Regardless of the exact mechanism, the key point is that the extensive incorporation of additional elements into the zircon structure will significantly obscure and alter the primary chemical composition of the original zircon. The initial igneous signature has been overprinted by these secondary alteration processes. The initial zircon crystals likely formed around 603 Ma [16]. However, prolonged metamictization and hydrothermal alteration have dramatically transformed the original zircon structure and composition. The incorporation of substantial amounts of elements like U, Th, REEs, Fe, and Al into the zircon lattice indicates that the original zircon has been extensively modified. A continuum of alteration likely exists, where the original zircon has been progressively transformed. Some cores or domains may retain more of the original zircon structure, while other regions have been completely recrystallized or replaced by new mineral phases. Detailed mineralogical and crystallographic analyses would be needed to fully characterize the nature and extent of alteration in these grains. Zircons that have experienced fluid-assisted alteration have been the subject of numerous studies. Their rare and/or unusual textures, distinct trace element compositions, and REE distribution patterns have been linked to these fluid-mediated processes. For example, the formation of “spongy” zircon grains has been ascribed to dissolution-reprecipitation reactions, while LREE-rich, porous hydrothermal rims have been associated with direct crystallization from zircon-saturated aqueous fluids [7,32]. The selective enrichment in non-formula elements like Ca and Fe within the altered cores has been related to diffusion–reaction processes introducing these incompatible elements [1]. Additionally, the presence of mineral inclusions within the spongy cores may have also contributed to the observed geochemical signatures.

5.2. Timing of ‘Non-Formula’ Element Uptake in Um Ara Zircon

There are three potential events that may have contributed to the alteration of Um Ara granites:

• (i). An early stage of hydrothermal activity took place between 603 and 530 Ma ago. The granitic rocks in the Um Ara area formed during this period, following intense mountain-building. Zircon crystals extracted from these granites have been dated to 603 ± 14 Ma, confirming this timeframe [16]. The intrusion of these granites seems to be influenced by deep shear zones and faulting in the Earth’s crust. These shear zones acted as pathways for rare metal-bearing hydrothermal fluids. The granites contain various accessory minerals, like columbite, ilmenite, zircon, xenotime, thorite, monazite, and apatite. These minerals behave differently when they are altered by fluids. Some zircon crystals have compositions close to ideal stoichiometry, while others show signs of alteration. Normally, elements like uranium, thorium, and REEs would not be easily incorporated into zircon crystals, especially at low temperatures. So, it is likely that something changed the zircon crystals (metamictization) to allow them to accommodate these elements. This event likely involved the release of hot fluids during the final stages of magma cooling and crystallization, leading to Na- and K-metasomatism within the granite [14]. However, this phase was insufficient to alter zircon and other refractory minerals (xenotime, thorite, monazite, and apatite) due to their inherent resistance to alteration.

• (ii). Late-stage hydrothermal event (ca. 20 Ma), linked to the main rifting phase of the Red Sea. The prolonged metamictization of the refractory minerals could have eventually weakened them, rendering them susceptible to modification by this later hydrothermal event. This event may have led to the uptake of non-formula elements in the zircon, as supported by previous studies on metamict zircon crystals from the Gabel Hamradom in the Egyptian Eastern Desert. The time of this hydrothermal event is determined to be around 17.9 + 6.9 − 7.4 to 22.2 + 5.4 − 4.8 Ma [6].

• (iii). Surficial weathering event that led to the alteration of the Um Ara granites. Low-temperature alteration by oxic groundwater may have contributed to further uptake of non-formula elements in the zircon. The ²³⁰Th/²³⁴U ages of 50,000 to 159,000 years for uranophane from the Um Ara granites match up with periods of heavy rainfall (pluvial periods) known as the Kubbaniyan and Nabtian that occurred in the Egyptian Eastern Desert [56]. A similar low-temperature weathering event has been suggested as a mechanism for element uptake in metamict zircons [57,58].

The late-stage hydrothermal event around 20 Ma ago is likely the primary driver of zircon and refractory mineral alteration within the Um Ara granite. This event, occurring after prolonged metamictization had weakened these minerals, was able to significantly modify their composition. While supergene alteration might have played a secondary role in element incorporation within zircon, its impact is considered less significant compared to the hydrothermal event.

6. Conclusions

The EPMA data provides valuable insights into the elemental and mineralogical changes that occurred during the alteration of zircon. The zircon from the Um Ara alkali-feldspar granites exhibits high concentrations of non-formula elements such as REEs, P, Al, Ca, Fe, and Ti. They also display extensive structural features indicative of radiation damage, including porous and amorphous domains, cavities, and voids. These characteristics are consistent with the zircon undergoing significant hydrothermal alteration following their initial crystallization. The observed textures and presence of both simple and coupled substitutions suggest that the alteration occurred through coupled dissolution-reprecipitation processes influenced by aqueous fluids. Negative correlations between Zr and the non-formula elements indicate that these elements were incorporated into zircon at the expense of Zr and Si. The alteration processes have significantly affected the distribution and fractionation of REEs in the original zircon, leading to distinct REE patterns and anomalies.

Based on the presented mineralogical and geochemical data, as well as the current literature knowledge, the sequence of events that led to the alteration of the Um Ara zircons and the high concentrations of non-formula elements can be summarized as follows:

1. Initial zircon crystallization occurred around 603 Ma in the Um Ara granitic source, accompanied by the formation of other U- and Th-bearing minerals such as xenotime, thorite, monazite, and apatite.

2. Long-term metamictization of the primary zircon crystals, as well as the associated U- and Th-bearing minerals, resulted in the formation of fractures and cracks within these minerals. These fractures and cracks facilitated the subsequent alteration processes by allowing fluid circulation and chemical changes.

3. A major hydrothermal event, contemporaneous with the rifting of the Red Sea around 20 Ma, led to fluid-rock interaction and the release of Zr, Si, U, Th, Hf, Fe, Al, Ca, Ti, P, As, and REEs from the metamicted zircon and associated U- and Th-bearing minerals. As the hydrothermal alteration progressed, voids or altered remnants were left behind within the zircon grains. The enrichment of the hydrothermal fluids with non-formula elements, such as REEs, P, Al, Ca, Fe, and Ti, facilitated their incorporation into the modified zircon crystal structure, filling the voids and altered zones.

4. Subsequent pluvial periods in the Kubbaniyan and Nabtian periods (around 50,000–159,000 years ago) may have allowed further uptake of non-formula elements during low-temperature alteration. The shear zones within the Um Ara granites facilitated the mobilization and transport of non-formula element-bearing fluids, likely as carbonate and fluoride complexes.

5. Subsequent pluvial periods in the Kubbaniyan and Nabtian periods (around 50,000–159,000 years ago) may have had a limited role in incorporating additional elements into zircon. The shear zones within the Um Ara granites facilitated the mobilization and transport of non-formula element-bearing fluids, likely as carbonate and fluoride complexes.

Data Availability Statement

The data presented in this study are contained within the article.

Acknowledgments

The authors gratefully acknowledge technical and financial support from the Ministry of Education and King Abdulaziz University, Jeddah, Saudi Arabia. The Faculty of Earth Sciences, King Abdulaziz University, KSA, is acknowledged for using its mineral separation machine and EPMA facilities. Critical comments on the manuscript by James K.W. Lee and an anonymous reviewer are gratefully acknowledged. Their review has greatly contributed to improving the quality of this manuscript.

Conflicts of Interest

The author declares no conflict of interest.

Footnotes

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Figures and Tables

Figure 1. Geological map of Um Ara area (modified from [14]).

Figure 2. BSE imaging showing morphological characteristics of zircon grains separated from Um Ara granites, south Eastern Desert of Egypt. (a,b) show unzoned zircon grains that exhibit a porous texture. (c) Zoned zircon grains containing apatite inclusions.

Figure 3. (a) BSE showing zoning in zircon. It contains inclusions of apatite, uranothorite, and many micropores (dark areas). (b–g) peak intensity mappings showing the distribution of Zr, Th, U, Hf, Al, and Ca in the grain of image (a). Outer rims show a higher concentration of Th, U, Hf, and Al and a lower concentration of Zr.

Figure 4. (a) BSE showing inclusions of apatite, uranothorite, uranophane, and many micropores (dark areas). (b–g) peak intensity mappings showing the distribution of Zr, U, Th, Hf, Ca, and Ali in the grain of image (a).

Figure 5. Analyses of the different sectors along the lines X–Y in Figure 2c reveal variations in SiO2, ZrO2, HfO2, UO2+ThO2, Al2O3, FeO, CaO, and REE2O3.

Figure 6. (a) Binary plot of total major elements (wt%) versus SiO2 and ZrO2 for the Um Ara zircon. Theoretical endmember pure zircon indicated by the orange asterisk (where total major elements = 100 wt%, SiO2 = 32.8 wt%, and ZrO2 = 67.2 wt%, [24]). (b) ThO2 vs. UO2 diagram that reveals a wide range of Th/U ratios for the Um Ara zircon.

Figure 7. Rare earth element patterns of Um Ara-altered zircon, normalized to the C1 chondrite values of [37]. The dashed black line represents the mean chondrite pattern of Um Ara-altered zircon. The chondrite pattern of unaltered magmatic zircon is shown for comparison.

Figure 8. Chondrite-normalized Sm/La ratio vs. La (ppm) discrimination diagram (after [32,38,39]) with zircons from granitoids of the Um Ara area (red circles). The positioning of the studied zircon grains, along with their elevated La contents and lower (Sm/La)N ratios, indicates that the primary zircon has been subjected to fluid-driven alteration processes.

Figure 9. Dominant simple and coupled substitution in zircon from the Um Ara granite: (a) Zr4+ vs. Th4+; (b) Zr4+2 vs. U4+; (c) Zr4+ vs. Hf4+; (d) (Y, REE)3+ + P5+ vs. Zr4++Si4+; (e) (Al, Fe)3+ + 4(Y, REE)3+ + P5+ vs. 4Zr4++Si4+; (f) (Mg, Fe)2+ + 3(Y, REE)3+ + P5+ vs. 3Zr4++Si4+. Negative correlations in these diagrams indicate that Th, U, Hf, Al, Fe, Mg, P, Y, and REE were incorporated in the parental zircon at the expense of Zr and Si, leading to the non-formula elements uptake of the Um Ara-altered zircon.

Table 1

Setup and operating conditions for EPMA analyses.

Element	Emission Line	Std.	Analyzer Crystal	Limit of Quantification (LOQ) (wt.%)
Si	Kα1	Wollastonite	PETH	0.066
Zr	Lα1	Zr oxide	PETJ	0.042
U	Mα1	UO2	PETH	0.081
Th	Mα1	ThO2	PETH	0.102
Hf	Lα1	HfO2	LIFH	0.033
Pb	Mα1	PbVGe oxides	PETH	0.015
Fe	Kα1	Fe2O3	LIFH	0.033
Al	Kα1	Y-garnet	TAP	0.027
Ca	Kα1	Wollastonite	PETJ	0.051
Mg	Kα1	MgO	TAP	0.051
Ti	Kα1	Ilmenite	PETJ	0.024
P	Kα1	LaPO4	TAP	0.081
Y	Lα1	Y-garnet	TAP	0.039
As	Lα1	Cal-STD	LIF	0.039
La	Lα1	LaPO4	LIF	0.045
Ce	Lα1	CePO4	LIFH	0.069
Nd	Lβ1	NdPO4	LIFH	0.036
Sm	Lβ1	SmPO4	LIFH	0.057
Eu	Lβ1	EuPO4	LIFH	0.036
Gd	Lβ1	GdPO4	LIF	0.075
Tb	Lβ1	TbPO4	LIFH	0.036
Dy	Lβ1	DyPO4	LIFH	0.075
Ho	Lβ1	HoPO4	LIFH	0.018
Er	Lβ1	ErPO4	LIFH	0.018
Tm	Lα1	TmPO4	LIFH	0.018
Yb	Lα1	YbPO4	LIFH	0.039
Lu	Lα1	LuPO4	LIFH	0.021

Table 2

Representative EPMA analyses of zircon and associated uranophane from Um Ara alkali-feldspar granite.

Mineral Type	Less Altered Zircon		Altered Zircon						Uranophane
Sample	SP1 (N* = 1)	SP2-1 (N* = 2)	SP2-2 (N* = 8)	SP3-1 (N* = 7)	SP3-2 (N* = 8)	SP4-1 (N* = 8)	SP5(N* = 8)	SP4-2B(N* = 8)	U1 (N = 3)	U3 (N = 3)
	Oxides (wt.%)
SiO2	32.853	32.846	30.518	30.913	28.44	26.48	25.84	26.66	14.327	13.696
ZrO2	66.273	64.848	63.184	62.605	50.04	41.08	39.2	36.52	0.037	0.006
UO2	0.083	0.118	0.085	0.013	2.195	3.166	2.262	5.518	66.685	60.288
ThO2	0.103	0.05	-	0.038	1.035	8.685	6.73	8.01	-	-
HfO2	-	0.075	1.716	1.275	3.342	2.931	6.257	2.905	0.157	-
PbO	-	-	-		0.092	-	-	0.104	-	-
FeO	0.152	0.145	0.035	0.625	0.992	1.086	2.035	1.662	0.219	0.284
Al2O3	-	-	0.029	-	0.813	2.062	1.768	3.224	0.15	0.289
CaO	0.057	0.043	-	0.051	1.368	1.597	1.416	1.426	6.764	6.143
MgO	-	-	-	-	0.059	0.055	-	0.074	0.029	0.069
TiO2	-	-	0.053	0.064	0.026	-	-	-	0.014	-
P2O5	-	-	-	-	0.248	0.417	0.39	0.128	-	-
Y2O3	-	-	-	-	0.518	-	0.564	-	-	-
As2O3	-	-	-	-	0.06	0.061	0.22	0.128	0.034	0.055
La2O3	-	-	0.046	0.047	0.07	0.15	0.25	0.054	-	0.056
Ce2O3	-	-	0.079	0.07	0.103	1.024	0.941	0.856	0.183	-
Nd2O3	-	-	0.106	0.126	0.04	0.039	0.037	0.036	0.118	0.06
Sm2O3	-	-	0.059	0.075	0.063	0.184	0.144	0.066	-	-
EU2O3	-	-	0.056	0.091	0.04	0.037	0.038	0.045	-	-
Gd2O3	-	-	0.198	0.175	0.081	0.164	0.11	0.078	-	-
Tb2O3	-	-	0.037	0.037	0.037	0.039	0.037	0.039	-	0.089
Dy2O3	-	-	0.077	0.162	0.288	0.328	0.177	0.241	-	-
Ho2O3	-	-	0.175	0.104	0.082	0.02	0.018	0.018	-	-
Er2O3	-	-	0.02	0.02	0.356	0.053	0.413	0.076	-	-
Tm2O3	-	-	0.062	0.023	0.193	0.018	0.037	0.072	-	0.035
Yb2O3	-	-	0.26	0.078	0.489	0.393	0.395	0.044	-	-
Lu2O3	-	-	0.112	0.033	0.182	0.089	0.03	0.021	-	0.075
Total	99.52	98.13	96.91	96.56	91.25	90.16	89.31	88.01	88.72	81.15
Structuralformula	Based on O = 4								Based on O = 7
Si	1.007	1.017	0.982	0.991	0.991	0.976	0.969	1.000	1.508	1.549
Al	-	-	0.001	-	0.033	0.090	0.078	0.142	0.019	0.039
P	-	-	-	-	0.007	0.013	0.012	0.004	-	-
As	-	-	-	-	0.001	0.001	0.005	0.003	0.002	0.004
T-site	1.007	1.017	0.982	0.991	1.033	1.080	1.064	1.150
Zr	0.990	0.979	0.991	0.979	0.850	0.738	0.717	0.668	0.002	0.000
U	0.001	0.001	0.001	0.000	0.017	0.026	0.019	0.046	1.562	1.517
Th	0.001	0.000	-	0.000	0.008	0.073	0.057	0.068	-	-
Hf	-	0.001	0.016	0.012	0.033	0.031	0.067	0.031	0.005	-
Pb	-	-	-	-	0.001	0.000	-	0.001	-	-
Fe	0.004	0.004	0.001	0.017	0.029	0.034	0.064	0.052	0.019	0.027
Ca	0.001	0.001	-	0.002	0.051	0.063	0.057	0.057	0.763	0.744
Mg	-	-	-	-	0.003	0.001	-	0.004	0.005	0.012
Ti	-	-	0.001	0.002	0.000	-	-	-	0.001	-
Y	-	-	-	0.000	0.010	-	0.011	-	-	-
La	-	-	0.000	0.000	0.001	0.002	0.004	0.000	-	0.002
Ce	-	-	0.001	0.001	0.001	0.014	0.013	0.012	0.007	-
Nd	-	-	0.001	0.001	0.000	0.000	0.000	0.001	0.004	0.002
Sm	-	-	0.001	0.001	0.000	0.002	0.002	0.001	-	-
Eu	-	-	0.001	0.000	0.000	0.000	0.000	0.000	-	-
Gd	-	-	0.002	0.001	0.000	0.002	0.001	0.001	-	-
Tb	-	-	0.000	0.000	0.000	0.000	0.000	0.000	-	0.003
Dy	-	-	0.000	0.000	0.003	0.004	0.002	0.003	-	-
Ho	-	-	0.002	0.002	0.001	0.000	0.000	0.000	-	-
Er	-	-	0.000	0.000	0.004	0.001	0.005	0.001	-	-
Tm	-	-	0.001	0.000	0.002	0.000	0.000	0.001	-	0.001
Yb	-	-	0.003	0.001	0.005	0.004	0.005	0.000	-	-
Lu	-	-	0.001	0.001	0.002	0.001	0.000	0.000	-	0.003
A-Site	0.996	0.986	1.022	1.019	1.023	0.996	1.025	0.948
Total	2.002	2.003	2.004	2.010	2.056	2.076	2.089	2.098	3.896	3.904

(*) means number of analyses. (-) means below detection limit.

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