Local Crystallographic Texture of Alpha Quartz in Silicified Wood (Late Triassic, Madagascar)

Abstract

Compositional and anatomical studies of silicified wood have been carried out extensively all around the world. The classification of silicified wood as such deals with all the forms and phases of silica that come under its umbrella. One such class of silicified wood is fossil wood with a high content of quartz, and there are very limited mentions of this category of fossilized wood. The examined wood belongs to gymnosperm and comes from the Upper Triassic deposits of Madagascar. A fresh approach to such samples is adopted by studying the crystallographic texture of the fossil wood to understand the orientation of the crystals replacing the organic matter within the sample. This work focuses on crystallographic texture analysis based on pole figures measured by X-ray diffraction. The intensity of the pole density maxima on the pole figures measured on the heartwood surface part of the analyzed samples is higher than that on the sapwood. This affirms that the crystallographic texture is sharper at the heartwood part compared to the sapwood. The X-ray tomography study, conducted to understand the difference in mineral distribution within the sample, reveals a greater X-ray absorbing phase on the sapwood of both samples. This is due to the concentration of iron compounds, which both replace the remaining conductive structures of the wood and fill the cavities inside them. We believe that this research on silicified wood is the first research work that encompasses crystallographic texture analysis with pole figures, an approach not previously undertaken in similar studies. We hope that our research can be useful in understanding the processes of replacement of organic matter by minerals.

1. Introduction

Woody plants have been present on the Earth’s surface for hundreds of millions of years. Fossil wood plays an important role in paleontological and geological studies, providing valuable insights into ancient ecosystems and environmental conditions. Cenozoic fossil wood from Thailand is significant for understanding past environmental conditions [1]. Additionally, the authors of the paper [2] discussed how petrified wood can enhance public understanding of geologic time and evolution. Silicified wood is a fossil formed by minerals containing silica substituting the organic material, which is turned into a fossil over time by various processes. They typically form polycrystalline materials and can be composed of a single mineral or different combinations of minerals. There are many minerals that could replace fossil wood, for example, pyrite, quartz, opal, volkonskoite, marcasite, siderite, malachite, apatite, azurite, chalcedony, calcite, dolomite, hematite, goethite, hollandite, chalcopyrite, lepidocrocite, chalcocite), covellite, fluorite, barite, bornite, natrolite, and vivianite [3,4]. Many forms of fossilized wood, including petrified [5,6], silicified [7,8,9], pyritized [10], permineralized, and char wood, have been found all over the world [6,7,8,11,12,13,14].

These types of wood vary based on the location, the availability of specific materials, and the type of preservation that the wood has undergone. The discovery and study of this kind of fossilized wood have been the subjects of numerous research projects, with the characterization and classification of the wood receiving most of the attention. Certain publications also delve into comprehending the sample’s composition [14], internal structure [13], pores [5], paleoenvironmental information [7], and so on. Since fossilized wood has a distinct morphology and replaces organic material with minerals inside the newly formed rock structure, it is an intriguing category with a plethora of research potential.

Silicified fossil wood is a significant find in paleontological studies, providing insights into ancient ecosystems and environmental conditions. The process of silicification, where wood is replaced by silica, can preserve intricate details of the wood’s structure and composition over millions of years [15]. Silicified wood has been discovered in various locations worldwide, such as the Pleistocene Touro Passo Formation in Brazil [16], the Cenomanian of Vienne in France [17], and the Miocene Bruneau Woodpile in Idaho, USA [18]. These findings indicate the widespread occurrence of silicified wood across different geological periods.

Studies have shown that silicified wood can contain not only the wood structure but also other elements, like fungi, foliage fossils, spores, pollen grains, and flowers, providing a more comprehensive view of past ecosystems [19]. The presence of fungal hyphae in silicified wood is not uncommon in the fossil record, further highlighting the diverse interactions and preservation potential of silicified wood [20]. Additionally, the chemical composition of silicified wood can be analyzed to determine its botanical origin, as seen in the Cupressaceae family from the Noto Peninsula in Japan [21]. Silicified wood has also been used in material science research, with studies mimicking the microstructure of natural silicified wood to create porous ceramics [22]. Furthermore, the mineralogy of silicified wood specimens can be evaluated through density measurements, providing insights into the silicification process [23]. Observations from volcaniclastic deposits, like those from Mount St. Helens, have contributed to understanding the burial and silicification processes of fossil forests [24]. One of these research areas pertains to the way the wood is encased in the fossil and how the crystals arrange around it in a particular orientation, making the crystallographic texture of the formed fossilized wood. The orientation that the crystallites choose to arrange themselves in within the matrix depends on how the wood influences the crystallites. This property may be utilized in the future to grow crystallites in the required orientation by using an appropriate organic matrix [10]. The organized crystal matrix around the wood can be investigated for the crystallographic texture since the wood contributes to this specific attribute of crystal arrangement.

Numerous studies and data exist regarding the identification and characteristics of silicified wood, which is primarily composed of silica or its various forms, such as quartz, quartz-silica, opal-A, opal-C, and so forth. The term “Silicified wood” refers to a broad category of fossilized wood that contains silica in all its forms and phases.

Characterization studies, for example, composition analysis, morphological [6], anatomical [5,25], structural [26], content analysis, defects, etc., were also carried out. There have been previous studies on silicified wood with alpha quartz crystallization reported in [8,12].

This is one of the first observations with pole figure studies, even though there are some studies that employed X-ray diffraction (XRD) for phase analysis [8,14,27,28]. There have not been any prior records that emphasize the crystallographic texture analysis of silicified wood samples and adequately describe the importance of the study in the field. The quantitative study of silicified wood has been extensively explored by various researchers across multiple disciplines. The biochemistry of silicified wood of Angiosperms and Gymnosperms from Kirk was investigated in [29]. Cathodoluminescence studies were conducted on silicified wood from the Permo-Carboniferous basins of the Czech Republic [30,31] in Central Europe. The authors of [32] employed micro-CT imaging and image analysis to quantitatively characterize the porosity of silicified wood. SEM and optical microscope techniques were utilized for microstructural characterization in [33]. About 75 fossil wood specimens from Australia were examined using different techniques like X-ray diffraction, differential thermal analysis, electron probe techniques, and optical and scanning electron microscopy [34]. Light microscopy, SEM, electron probe X-ray microanalysis (EPMA), polarizing microscopy, and X-ray diffraction were used to study the anatomy and mineralization of Pliocene and Miocene silicified woods from Japan [35,36]. The mineralogy of silicified wood was studied using XRD [4,37] and SEM EDS [37]. Raman and cathodoluminescence spectroscopy for understanding the chemical composition and structure of silicified plants from the 290-million-year-old Chemnitz Petrified Forest were used in [38].

Most of the crystallographic texture research traditionally focuses primarily on metals, alloys and ceramics [39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57]. However, especially recently, there has been a great deal of curiosity concerning the study of the crystallographic texture of biological objects [58,59,60,61,62,63,64,65,66,67,68,69].

2. Materials and Methods

The silicified wood samples from the Republic of Madagascar, which is located off the coast of Southeast Africa, have been studied (Figure 1). The wood comes from the Late Triassic sediments. The wood samples belong to the gymnosperms. The studied material is stored at the Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research (Dubna, Moscow region, Russia).

One of the most commonly used tools for studying the structure and texture of crystal phases is XRD [70]. This technique is a non-destructive way to determine the crystalline structure and texture, since it relies on irradiating the sample with X-rays that do not damage it. Following the observation of the intensity of the rays scattered from the sample, the angle at which diffraction occurs is determined. By examining the diffracted peaks’ intensity and location, one can ascertain the material’s structure. To enable accurate XRD measurements, the samples were polished to have a smooth, flat surface. The X-ray diffraction study at λ = 1.54 Å was carried out using Cu-Kα radiation with the instrument EMPYREAN from Malvern PANalytical (Worcestershire, UK), which is housed at the Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research (Dubna, Moscow region, Russia) (Figure 2).

The bulk sample with the smooth, flat surface was used for the measurements. It was set up on the sample holder and left in the course of the X-ray once it was emitted from the source and reflected onto the detector. A scan, carried out by adjusting the height of the sample holder with the sample, is crucial because it precisely ascertains the ideal height at which the best measurement accuracy will occur.

After determining the sample’s necessary height—which is optimal for X-ray diffraction—a scan was conducted to assess the phases present in the sample prior to the X-ray measurements for the texture analysis. This was accomplished by using the PDF-2 database and the PANalytical HighScorePlus software package, version 4.1, which allows identification of the substances present in the sample based on the results of the scan. An Ni filter was used to get rid of K_β lines of the X-rays. The phase analysis scan parameters were the following: a voltage of 40 kV, a current of 40 mA, a 10 mm mask, slits of 0.25° and 0.5°, and an exposure time of 300 s per frame.

Pole figures, alternatively referred to as stereographic projections or pole plots, serve as visual aids in materials science and geology for illustrating the distribution of the crystal orientations in each specimen [71]. Their utility is especially evident in the examination of polycrystalline substances, including metals, minerals, and ceramics. The multiples of random distribution (mrd) is the term used to describe the pole density intensity of the samples measured. The multiples of random distribution for intensity representation involve adjusting the randomness of a distribution using a scaling factor k, where k is a positive real number.

When measuring the pole figures of the crystallographic plane hkl, the 2θ value takes a value in accordance with Bragg’s law for the reflection from this plane and is kept constant. In order to measure the pole figure, the sample has to be rotated about two mutually perpendicular axes while maintaining one fixed axis (ω) (Figure 3).

The rotation about the vertical axis perpendicular to the sample surface is carried out by the angle φ and is instrumental in examining the orientations within the plane of the sample surface. The rotation about the horizontal axis of the sample holder is carried out by the angle χ. The Chi (χ) scans are employed to explore the orientations during sample tilting. The intensity of the reflected beam from the sample is measured by the detector present to collect the reflected rays.

During an XRD texture experiment, only incomplete pole figures up to an χ angle of 70° can be measured. The primary cause of this can be linked to the following issues. The sample’s texture is measured for a predetermined, fixed area irradiated by the incident beam that hits the sample. The sample is rotated by an angle of 5°, and then at this position the reflected intensity is determined by counting for a given time, equal to 15 s in our case. This area stays the same until the sample is tilted from its initial position. However, once the sample is tilted from its starting angle, the pre-set area changes. This causes variations in the reflected intensity that the detector records. This means that to make up for the intensity loss, some corrections must be added. When the tilt angle increases, the problem with the beam focusing occurs. This phenomenon is called defocusing. As a result, an intensity correction for defocusing is also necessary. In addition, defocusing causes the diffraction lines to become broader. Since the defocusing corrections do not yield improved results at tilt angles greater than 70°, the measurements must be stopped at 70°, yielding only incomplete pole figures.

Based on the results of the 2θ scan recorded between 20° and 70°, it was found that the surface layer of the sample contains only one alpha quartz phase and the crystallographic planes (100), (110), (011) and (102) were selected for the PF measurement. These specific planes were chosen because, in comparison to the other detected peaks, they had the highest reflected intensity and an appropriate signal to background ratio. Moreover, these planes have simple Miller indices, which make the PFs measured for these planes convenient for interpretation. Since the reflection from the (006) plane was not recorded, the PF for this plane was recalculated using the ODF reconstructed from other measured and corrected PFs. This method for the pole figure finding for the plane, the reflection on which is typically not measured or not very intense, was chosen since (006) is the typical plane for trigonal crystals and is hence one of the favored pole figures for interpretation. It took around 4 h 36 min to measure the one pole figure for each crystallographic plane of the samples, and 12 min to carry out the background measurements, requiring approximately 15 s and 12 s per step, respectively. The complete pole figures have been reconstructed using the orientation distribution function (ODF) from the measured ones by means of the WIMV approach (first letters of the authors’ surnames: Williams, Imhof, Matthies and Vinel) [72,73,74,75] because XRD gives incomplete pole figures only. The program X’Pert Texture version 1.3 from PANalytical was used to calculate the ODF and complete pole figures [76].

The ODF is a three-dimensional probability density function that associates to each orientation the volume percentage of crystals in a polycrystalline specimen that are in this particular orientation. Since the pole figures obtained from XRD are incomplete and only measured up to 70°, the ODF can be used to compute the complete pole figures because it contains complete information about the crystallographic texture. Additionally, the ODF allows us to calculate the pole figures, which are significant but challenging to measure because small peaks or poor signal-to-background ratios interfere with the observations. The ODF is computed using the corrected PFs, considering the defocusing.

The incomplete pole figures are recalculated using the ODF to form complete pole figures as only these can be normalized. Once normalization is performed, the maximum and minimum pole densities can be obtained for the measured sample area and studied. For a normalized pole figure, the following expression is valid:

$${\displaystyle \underset{S^2}{\int }{P}_{\overrightarrow{h}}}(\overrightarrow{y})d\overrightarrow{y}={\displaystyle \underset{0}{\overset{2\pi }{\int }}{\displaystyle \underset{0}{\overset{\pi }{\int }}{P}_{\overrightarrow{h}}}}(\chi ,\varphi )\sin \chi d\chi d\varphi =4\pi$$

(1)

The samples were examined at the heartwood and sapwood using XRD. Since X-rays do not have a very strong penetration power, most of the points measured were not very deep but rather only on the surface of the samples. To investigate the interior makeup of the samples, namely the mineral distribution that makes up the samples, an X-ray tomography (XRT) study was conducted. Every chemical element included in minerals has a unique X-ray absorption coefficient, which is reflected in the results by contrasting. The contrast of these minerals depends on their elemental composition. At the Joint Institute of Nuclear Research’s (JINR’s) Frank Laboratory of Neutron Physics (FLNP), Prodis.NDT micro computerized tomography Russia, Moscow (https://prodis-tech.ru/en/prodis-kompakt/, accessed on 10 September 2024) was used to examine the samples’ internal makeup. The parameters that were utilized for the sample measurements were the following: voltage 80 kV, current 450 mA, rotation step 0.2°, Cu filter 140 µm, pixel size 50 µm and rotation by 360°. Moreover, the X-ray microtomograph Neoscan N80, Belgium, Mechelen (Borissiak Paleontological Institute, Russian Academy of Science, PIN RAS, Moscow, Russia) was used for a more detailed tomographic examination. The investigation parameters were the following: voltage 101 kV, current 159 mA, Cu filter 0.5 mm, rotation step 0.4°, pixel size 26.7 µm and rotation by 180°.

The microstructure and elemental composition were studied using a Tescan/Vega2 scanning electron microscope with an Inca microanalyzer, Brno, Czech Republic (PIN RAS).

3. Results

In this study, we employed XRT and XRD techniques to examine the mineral composition and crystallographic texture of silicified wood samples. The characterization of these samples is crucial to understanding their composition and texture. By analyzing the XRD diffraction patterns and XRT images, we aimed to elucidate the phases and texture of the mineral matter present in the samples. These findings will contribute to a comprehensive understanding of the texture within the samples in a better way.

3.1. XRD

The XRD measurements and the subsequent analysis revealed that the primary constituent of the samples is alpha quartz. It has trigonal crystal system. It was confirmed that the quartz in the samples has the space group P3221 with number 154. This was determined by comparing the initial scan data with the PDF-2 database for quartz. The reference code for quartz card in the PDF-2 database is 01-085-0930, with unit cell parameters a = 4.9110 Å, b = 4.9110 Å, and c = 5.4070 Å, α = 90°, β = 90°and γ = 120°. The XRD patterns presented in Figure 4 show the comparison of the data obtained for the two samples and how the intensity varies when the area of measurement changes from the heartwood of the samples to the sapwood.

The figure clearly points out the relative difference in the minute changes in the intensity of the diffraction patterns obtained from different areas of the sample and the comparison between the areas. The pattern provides information about the peaks selected for the PF measurements and analysis and their corresponding Miller indices. As we can see from the pattern, the graphs almost coincide with each other, revealing that the substance of the samples is pure alpha quartz. There were some other, very small background peaks within the scan that are not discussed in this study, which could possibly be of another phase. However, this phase is not more than 5% of the total matter in the irradiated area and does not interfere in the subsequent analysis of the data obtained.

The measured data provide information about the texture by plotting the incomplete pole figures, which were corrected when dealing with defocusing and then taken for ODF reconstruction. Then, the ODF was used to recalculate the complete pole figures. We were also able to recalculate the pole figure (006), which is the axial pole figure of a trigonal crystal in our case. It provides information about the distribution of the basal crystal planes within the sample. The pole figures (100), (011) also have a fiber texture, which can be judged from the isoline pattern representation. The pole figures were measured for two areas in both of the samples, which are the heartwood and the sapwood. In the plotted pole figures, it is also evident that there is a slight axial shift for the pole figures measured in the sapwood. This is expected due to the measurement point selected in the sapwood not being exactly symmetrical compared to the heartwood, which shows a not perfect pole figure symmetry. The measured intensities of both pole figures (100), (011) are close in values to each other and to the (006) pole figure values.

3.1.1. Wood Heartwood and Sapwood—Sample A

The pole density maximum of the pole figure (100) of the sample in the heartwood is observed to be 1.68 mrd, while the sapwood has a maximum intensity of 1.99 mrd (see

Table 1. Pole density maximum and minimum of the calculated pole figures for sample A in the heartwood and sapwood.

Pole Figure	Heartwood (mrd)		Sapwood (mrd)
	Maximum	Minimum	Maximum	Minimum
(100)	1.68	0.55	1.99	0.51
(011)	2.32	0.59	2.35	0.56
(006)	1.85	0.39	2.24	0.36

). The pole figure (011) has the maximum pole density for the heartwood sample, with a value of 2.32 mrd, and a value of 2.35 mrd at the sample sapwood.

The pole density of the axial (006) pole figure, calculated using the ODF reconstructed from the measured pole figures, is observed with a maximum value of 1.85 mrd for the heartwood, while this value is 2.24 mrd for the sapwood (Figure 5).

The calculated pole figure (006) has the maximum pole intensity at the periphery. The pole figures (100), (011) and (006) calculated for the edge seem to have a slight axial shift from the center of the pole figures. This can be justified when comparing it to the pole figures (100), (011) and (006) for the heartwood, which has better symmetry compared to the sapwood. The results also reveal that the sample has a slightly sharper texture at the edge compared to the heartwood.

3.1.2. Wood Heartwood and Sapwood—Sample B

The pole density maximum on the pole figure (100) of the sample heartwood is observed to be 1.83 mrd, while the one in the sample sapwood has a value of 1.91 mrd (see

Table 2. Pole density maximum and minimum of sample B in the heartwood and sapwood.

Pole Figure	Heartwood (mrd)		Sapwood (mrd)
	Maximum	Minimum	Maximum	Minimum
(100)	1.83	0.49	1.91	0.46
(011)	2.28	0.58	2.54	0.47
(006)	2.19	0.38	2.09	0.25

).

The pole figure (011) has the pole density maximum for the heartwood sample at a value of 2.28 mrd, while for the sapwood sample it is a value of 2.54 mrd. The pole density maximum of the axial (006) pole figure is 2.19 mrd for the heartwood, while it is 2.09 mrd for the sapwood. The pole figures (100), (011) and (006) calculated for the heartwood have no such shift and the isolines on them are arranged symmetrically (Figure 6). It is important to notice that the maximum and minimum values are just some quantitative characteristic of the crystallographic texture. In addition, the appearance of the pole figures also matters. As one can see from Figure 6, the isoline patterns differ in the central part of the pole figures as well as at the edges of them.

The pole figures in Figure 6 clearly evidence that the sample has a sharper texture in the sapwood than in the heartwood.

3.2. XRT

Based on the X-ray tomography studies, areas of different contrast were identified in both wood samples. There are three such contrasting phases, namely black, dark and light gray, in sample A (Figure 7. The first corresponds to quartz. It predominates in the sample. The other two are very different in contrast and therefore contain minerals with chemical elements that have a significantly higher atomic number than silicon and oxygen and, accordingly, different absorption coefficients. That is, fossil wood was replaced by at least two minerals. Two contrasting phases were also found in wood sample B (Figure 7). However, XRD analysis of the mineral composition of the expected areas of contrast did not reveal the presence of a second mineral phase. This may be due to the peculiarities of the method, namely the limited study area and low penetration depth of X-rays or a mineral concentration of less than 5% of the total mass of the substance. Therefore, only alpha quartz was found in these areas.

A more detailed microtomographic study of sample B using a Neoscan N80 microtomograph revealed the detailed structure of the wood section. The presence of marginal contrast areas was confirmed. However, the contrast agent is distributed unevenly in them. Most of it is along the very edge of the wood. Lines of increased contrast were found, running along the periphery of the sample at a distance from its edge. They correspond to growth rings. As in sample A, there are dark gray and light gray areas, probably belonging to different minerals (Figure 8).

3.3. SEM

It is clearly visible that the sapwood areas of sample B differ in structure. There are light areas with light lines extending from them at the very edge (Figure 9). They are not artifacts that appeared during sample grinding, since they can contain moderately well-preserved anatomical elements of the wood structure. The conductive elements are well preserved in some areas. In addition to them, there are thickened cells on the outer surface of the trunk. They are rectangular and flattened. They can correspond to cells of secondary wood (cross-sections of thickened tracheids) or bark (Figure 10 and Figure 11). The wood is similar to that of gymnosperms, for example, araucaria [77,78,79]. There are also dark gray inclusions (Figure 9).

In terms of the elemental composition, silicon (Si) and oxygen (O₂) predominate in the bulk of the sample (Figure 9). Aluminum (Al) is also present, and sodium (Na) is found in a separate point. In addition to the listed elements, iron (Fe) is also present in the light areas. It is the iron minerals that cause the high contrast along the sapwood of the sample. Cobalt (Co) and chromium (Cr) are also present in separate points. In addition to Si and O₂, calcium (Ca) and carbon (C) are present in the dark gray inclusion, as well as in some other areas of the sample (Figure 9). The distribution of elements in some areas of the wood surface is shown in the element maps. The concentration of Fe in the light areas ranges from 8.44 to 33.68 weight percent or from 3.10 to 14.55 atomic percent. The concentration values of the other identified elements can be seen in

Table 3. The results of the elemental analysis of sample B.

Element	The Range of Element Concentration
	Weight %	Atomic %
Si	1.82–35.42	1.11–25.86
O	35.39–66.04	34.07–82.64
Al	0.67–26.33	0.35–19.37
Fe	8.44–33.68	3.10–14.55
Na	0.94	0.81
Ca	2.37–32.11	1.09–16.04
C	43.46–49.34	55.73–58.01
Co	0.67	0.28
Cr	1.65	0.78

.

From the above description, one can conclude that the main mineral replacing the wood is quartz. However, the plant bark has been partially replaced by iron minerals (Figure 12) and calcium carbonate in the sapwood of the sample. The iron minerals are displayed in tomographic sections as light inclusions, while the darker inclusions probably correspond to calcium carbonate. Nevertheless, it is not clear which particular iron minerals are present in the sample. The X-ray diffraction method turned out to be insensitive to the amount of iron minerals contained in the sample. It is possible that areas with a high iron content were not included in the analyzed field since a small area is irradiated in the diffraction measurement.

4. Discussion

The wood samples that were collected here for examination include a significant amount of quartz in its alpha phase, according to the XRD findings. The XRD studies reveal an axial shift for the pole figures that were measured in the sapwood of the samples due to the asymmetry of the sample in that area, thus showing the difference in the crystallite distribution in that area. This can be due to the different symmetries of the wood samples at various areas, which results in such shifts. Based on the study, quartz and other minerals make up the fossil wood matrix. The results of the XRT measurements were different from those of the XRD study, even though no additional minerals or unusual peaks were found by XRD. Sample A included some white patches, and sample B included a lining, as shown by XRT, which effectively demonstrate the presence of another mineral by virtue of their contrast difference. The samples were studied again to search for any alternate phases present in them, but no other phases were determined from the XRD scans performed for both samples. When the samples were studied using the instrument, no other significant differences in the peaks obtained were observed.

It seems interesting that the pole densities’ intensities in the heartwood and the sapwood of the samples are close to each other. The pole densities’ maximum in the heartwood of the samples were obtained as 1.68 mrd and 1.83 mrd for pole figure (100), 2.32 mrd and 2.28 mrd for pole figure (011) and 1.85 mrd and 2.19 mrd for pole figure (006). The pole densities’ maximum in the sapwood of the samples were found to be 1.99 mrd and 1.91 mrd for pole figure (100), 2.35 mrd and 2.54 mrd for pole figure (011) and 2.24 mrd and 2.09 mrd for pole figure (006). The values of the pole density maximum seem to be so close between the samples for both the heartwood and the sapwood.

The wood’s contents are thought to have been partially replaced by the quartz, which then gradually mineralized to form the silicified wood. One might expect the quartz crystal arrangement to be random because of the absence of the oriented impact. However, the analysis shows that the samples had the more ordered crystallites in the sapwood than in the heartwood. The crystals may have chosen to be oriented in this manner because of the wood’s influence, if not randomly arranged. It therefore matters to note that the quartz crystals not only filled any gaps or cavities in the wood but also formed a full matrix by replacing the wood with an ordered crystal arrangement.

However, this process should not be treated as exclusively silicification. At least two more mineral components were found in the wood, namely iron and calcium minerals. They are distributed along the periphery of the samples. High-contrast iron minerals are located in the form of rings enveloping the heartwood of the samples. These structures probably do not belong to xylem rays, since they do not go from the center of the samples to the periphery. They are growth rings.

Replacement of iron minerals occurred along these rings. Iron compounds were found in the cell walls, conductive elements of the wood (these are tracheids) (Figure 10 and Figure 12), or along the periphery of the sample in the lumen of the cells (Figure 11). The appearance of contrasting rings on the periphery of the wood reflects one of the stages of its mineralization. At the initial stage of its silicification, active diffusion of iron ions occurred in the gel of silicic acid. Some of the iron compounds remained at the level of the growth rings, and this is clearly visible in the tomography. But a significant part of the iron ions moved to the periphery of the trunk. In sample B, flattened and thickened cells are located along the periphery of the trunk, which may belong to the bark or secondary wood (Figure 11). The appearance of calcium-containing mineral regions is not entirely clear. Most likely, it occurred after the completion of silicification and is associated with secondary calcination of some wood regions. This is just our assumption.

In the comprehensive study in [33] on the mineralization of fossil wood, the author categorizes silicified wood into two primary types: wood-opal (disordered tridymite) and chalcedonic silicifications. The research emphasizes that wood-opals demonstrate exceptional structure preservation, suggesting a replacement process where silica substitutes the original organic material. In contrast, chalcedonic silicifications are associated with permineralization, where minerals fill spaces within the wood. The study also examines other mineralization processes, such as phosphatization, carbonatization, and iron oxide impregnation, highlighting their roles in both terrestrial and marine environments. Buurman [33] concludes that most fossil wood undergoes permineralization, with the preservation of wood structures largely dependent on the mineral type and the environmental conditions during fossilization. The geochemical processes involved in the silicification of wood in the Petrified Forest National Park, focusing on the Triassic Chinle Formation, were investigated in [80,81], where abundant fossilized wood is preserved within bentonitic sandstones and shales. The study proposes that silicification occurred through a void-filling mechanism, where silica infiltrated and preserved the structure of the wood rather than replacing the organic material entirely. The geochemical analysis of the surrounding sediments reveals the presence of montmorillonite clay, formed from the weathering of volcanic ash, which provided the silica necessary for the fossilization process. The environmental conditions during silicification were mildly acidic and anoxic, typical of swampy environments where organic matter is decomposing. The study concludes that silicification occurred under normal surface and groundwater conditions, with volcanic ash serving as the primary silica source. The fossilized wood found across Thailand, dating from the Mesozoic and Cenozoic eras, were explored in [11]. The research highlights the significance of volcanic activity in the silicification process, where silica from volcanic ash infiltrated the trees and preserved them as fossils. The study discusses various environments where this fossilization occurred, including floodplains, swamps, and lakes, and emphasizes the role of Thailand’s dynamic geological history in shaping these preservation processes. The petrified wood found in Thailand provides important insights into the region’s ancient ecosystems and climates. The study suggests that these fossilized trees help reconstruct the paleoenvironments of Southeast Asia, revealing the impact of climate and geological changes over millions of years. Through this research, the authors contribute to a deeper understanding of the processes that preserved these ancient trees and the broader environmental contexts in which they existed. This is not the only work devoted to paleoclimatological analysis carried out on the basis of fossil wood. For example, in the article [82], the wood of modern dicotyledonous and Eocene-Miocene plants is compared and attempts are made to reconstruct the climate of the past.

5. Conclusions

The results of this study showed that the silicified wood samples had a highly organized matrix, with alpha quartz making up most of the sample. In addition to quartz, iron compounds played an important role in the mineralization of the wood, including in the anatomical structures. This further demonstrates the impact of the wood matrix on the orientations of the replacement crystals in the two examined samples. The samples have an internal anisotropy. This property leads to the difference in the pole density intensities measured at different areas in the samples, i.e., the heartwood and the sapwood, as evident from the results. The pole densities, although slightly different, indicate similar values of the maxima and minima from the measured data of the samples. These data hence confirm that the sapwood of the samples is more ordered and textured than the heartwood of the samples, although the difference in the sharpness values is insignificant. We hope that our research can be useful in understanding the processes of replacement of organic matter by minerals.