It is shown that polytypes or stacking sequences of cronstedtite, an Fe-bearing trioctahedral 1:1 phyllosilicate, can be determined using near-atomic high-resolution transmission electron microscopy (HRTEM). By viewing along the [010], [310] and directions (orthohexagonal indexing), the four groups of the standard polytypes can be distinguished. Imaging along the [100], [110] and directions allows determination of the polytypes in each group. The polytypic sequences of groups A and C are intergrown at the monolayer level in cronstedtite from Lostwithiel, England, which is a new insight if compared with previous suggestions that layer stackings characteristic of different groups do not occur together. The HRTEM images also revealed the relationship between the layer polarity and the morphology of the cronstedtite crystals, where the tetrahedral sheet side points towards the top of the truncated pyramidal shape of the crystal.

Transmission electron microscopy (TEM) observation shows narrow regions in a Ti-containing Mg-rich annite of composition (K0.90Na0.02)(Mg0.72Fe2+1.78Mn0.03Ti0.27Al0.05)(Si2.77Al1.23)O10(OH,F)2 from a granitic rock, where the ±60° and 180° stacking angles occur extensively. These regions are a few hundreds of nanometers thick along the [001]* direction and are within 1M or 2M1 annite. The stacking sequence in one of these regions was determined by two atomic-resolution images recorded along [1̄10] and [010] of the same crystal. Stacking sequences with ± 120° or 180° rotations are dominant, although those with ±60° rotations occur also. Locally 2O and more complex sequences exist. Compositional analysis by TEM indicated no difference in the chemical compositions between these regions and the adjacent ones with regular 1M or 2M1 stacking sequence. The origin of these unusual stacking sequences in annite is discussed.

The objective of this paper is to describe the new serpentine group mineral, guidottiite, which is analogous to cronstedtite. Guidottiite has an ideal chemical composition of (Mn2Fe3+)(SiFe3+)O5(OH)4. The sample is from the N’chwaning 2 mine, Kalahari manganese field, Republic of South Africa, and apparently forms from hydrothermal solutions. Grains are optically near opaque [average index of refraction 1.765, with variable extinction on the (001)], vitreous, and black, with perfect {001} platy cleavage. A non-separable fibrous substructure exists perpendicular to cleavage that results in a silky luster under optical examination. The average chemical analysis determined from electron microprobe based on four grains with ten analyses each resulted in a structural formula of (Mn1.86Fe0.613+Mg0.54)Σ=3.01(Si1.36Fe0.643+)Σ=2.00O5(OH)4, with calculated density of 3.236 g/cm3. Analysis from another area of the sample showed a slightly different chemical composition and resulted in a formula of (Mn1.70Fe0.963+Mg0.24Σ=2.89(Si1.26Fe0.743+)Σ=2.00O5(OH)4, with calculated density of 3.291 g/cm3. The measured density on a bulk sample (with impurities) was 3.33 g/cm3. Thermal analysis suggested a dehydroxylation temperature of 535°C, a decomposition/recrystallization temperature of 722°C, and weight loss (= H2O loss) of 9.4%. The derived Mohs hardness from nano-indentation is H = 4.25.

The sample is mostly the 2H1 polytype with minor amounts of the 2H2 polytype. Using a predominantly 2H2 crystal, which has better crystallinity, the strongest observed X-ray peaks are: 7.21 Å (Io/Io = 100%), 3.543 (50), 2.568 (39), 1.982 (26), and 2.381 (25). All Gandolfi simulations, even with three crystal remountings, showed preferred orientation effects. Transmission electron microscope (TEM) analysis showed stacking disorder within Group D serpentine polytypes. Thus, a regular alternation of the occupancy of octahedral sets within each layer along the stacking exists, but disorder of the layer displacements of 0 and ±b/3 (b defined here as the orthohexagonal cell) exists. Ordered 2H1 (no layer displacement) and 2H2 (alternating + and —b/3 displacement) domains were also frequently observed. X-ray diffraction analysis showed that even apparent single crystals contain impurity phases, presumably Mn-rich and Ca phases that were detected in the microprobe study. The single-crystal structure refinement used a well (stacking) ordered apparent 2H2 crystal with little to no streaking in the diffraction pattern. Results showed that the crystal has a random interstratification of 2H2 and 2H1. The 2H2 polytype is hexagonal, space group P63, with a = 5.5472(3), c = 14.293(2) Å, and Z = 2, and was refined to R1 = 0.072 and wR = 0.108 from 656 unique reflections. Because the two polytypes in the composite have only small differences in the lower 1:1 layer, a large displacement parameter for the basal oxygen atom results, which was constrained to B = 1.5 Å2 (Ueq = 0.0190) in the refinement. Half of the tetrahedral sites in the 2H1 upper layer superpose over half of the tetrahedral sites in the 2H2 upper layer (T1 sites only) per unit cell. This superposition produces an apparent excess of electron densities of the T1 site relative to the T2 site (T1 = 21.9 electrons, T2 = 15.8). Comparison with the microprobe data indicates that observed tetrahedral bond lengths are generally not affected by this intergrowth. Tetrahedral bond lengths indicated that the tetrahedral sites contain T1 = Si0.678 Fe0.3223+ and T2 = Si0.631Fe0.3693+. This excess of electron densities and other refinement problems associated with the guidottiite single-crystal refinement closely parallel all single-crystal cronstedtite-2H2 refinements to date, suggesting that these refinements also involve random interstratifications of 2H2 and 2H1 polytypes.

Cronstedtite is a member of the kaolin-serpentine group. It yields a wealth of more or less disordered polytypes. The crystals of polytype 1T (space group P31m, a = 5.512, c = 7.106 Å) contain, within coherently scattering blocks, variable concentrations of stacking faults so that domains of the basic 3D periodic structure can be shifted by 1/3 (a2 − a1) or 1/3(a1 − a2). These so-called OD parallel intergrowths have been confirmed by high-resolution transmission electron microscopy. The effect manifests itself in the diffraction pattern so that reflections with h-k = 3n — the family reflections — are always sharp, whereas remaining reflections — the characteristic polytype reflections — may be smeared out parallel to c*. The intensities of the latter are thus underestimated during diffractometer measurements. An analysis of such multiple OD intergrowths reveals that the moduli of structure factors for all characteristic (i.e. non-family) polytype reflections are reduced relative to those calculated for the non-intergrown basic structure, by a common factor. This fact usually leads to the appearance of ghost peaks in Fourier maps and to their erroneous interpretation. The structure of the basic model can, however, be refined much better if two scale factors are assigned to the family and non-family reflections, respectively.

Low-temperature FTIR spectroscopy was used to characterize the v(OH) region of kaolin-group minerals including well ordered to poorly ordered kaolins from Georgia, Brazil, and England, along with samples of discrete dickite and nacrite. Low-temperature FTIR spectra were useful in resolving dickite- and nacrite-like features present in the spectra of kaolins when cooled to <30 K. These features were not resolved at room temperature and only partially resolved at liquid N2 temperature (77 K). The room-temperature and low-temperature positions of the ν(OH) bands of kaolinite, dickite, and nacrite were linearly correlated with the interatomic OH⋯O distances and this relationship served as the basis for polytype/disorder identification. Dickite or dickite-like disorder was found in high Hinckley-Index kaolinite from Keokuk, Iowa, and from Cornwall, England. Dickite- and nacrite-like features were observed in both high- and low-Hinckley-index kaolinite and the amounts of these stacking sequences generally increased with decreasing Hinckley Index.

Stacking disorder in celadonite, a dioctahedral mica with Fe and Mg as major octahedral cations and which generally adopts the 1M stacking sequence, was investigated mainly by using transmission electron microscopy (TEM). The selected-area electron diffraction patterns with 0kl reflections along the [100] beam direction correspond to the 1M stacking but those along the [110], $\left[1\overline{1}0\right]$\$\end{document}, [010], [310], and $\left[3\overline{1}0\right]$\$\end{document} directions are frequently streaked along the [001]* direction or contain extra spots from twinned domains. Three-dimensional stacking analyses using sets of two high-resolution TEM images along different directions of the same area of one crystal indicate that all stacking faults involve only 180° layer rotations. These stacking faults produce greater peaks of 0kl reflections than expected in powder X-ray diffraction (XRD) patterns. Simulation of the XRD patterns indicated that 180° layer rotations occur at >10% of total interlayer regions in one celadonite specimen. The interlayer region of celadonite is characterized by a near-zero ditrigonal rotation angle, a small surface corrugation of the basal oxygen plane, and a small amount of Al substitution in the tetrahedral sheets. These features suggest that there is no preference for any of the six stacking angles around the interlayer region. The abundance of 180° layer rotation rather than ±60° and ±120° in the present specimens may be related to their ribbon-like morphologies elongated along the a axis.

The electron back-scattered diffraction (EBSD) technique has been applied to fine-grained kaolin minerals to determine the polytypes (kaolinite, dickite and nacrite) of individual grains and their crystallographic orientations in a scanning electron microscope (SEM). Because kaolin minerals are prone to radiation damage by the intense electron beam necessary to obtain EBSD patterns, the beam has to be rastered across the specimens during pattern acquisition. Kaolinite-dickite and nacrite are easily distinguished by their trigonal or hexagonal symmetry about the [001]* direction, respectively, of the Kikuchi bands with k = 3n. Dickite can be differentiated from kaolinite by mirror symmetry parallel to the a-c plane, and by the characteristic contrast of HOLZ rings.

As EBSD analysis is performed using a SEM, morphological characters can be correlated with polytypes. Dickite fragments could be discerned as oriented overgrowths on nacrite plates. Dickite was observed to always adopt euhedral shapes in a diagenetic mixture of kaolinite and dickite. Lath-shaped dickite is elongated along the a axis direction. Rhombohedral dickite consists of crystals with {1̄11} indexed to the side facets.

High-resolution transmission electron microscopy (HRTEM) images of two dioctahedral micas, celadonite and cis-vacant (cv) illite, were examined in detail to understand the effects of electron radiation on their structures during image acquisition. Celadonite, a dioctahedral mica with Fe and Mg as major octahedral cations, originally has a trans-vacant (tv) octahedral sheet but the contrast in the highresolution transmission electron microscopy (HRTEM) images indicates a different cation distribution in the sheet. Furthermore, the β angle for the 1M polytype derived from the HRTEM images is ~98.5º, which is considerably smaller than that (~100.5º) reported for celadonite. In previous works, cation migration from the tv to cv-like configurations and a decrease in the β angle after dehydroxylation of celadonite/ glauconite by heating were reported. The same phenomenon, dehydroxylation and subsequent cation migration, probably occurs by electron radiation in TEM. However, the new cation-distribution models derived from HRTEM images along the [100] and [110] directions are not in agreement. On the other hand, the contrast in a number of HRTEM images from an illite specimen in which cv-illite is dominant is the same as that for the tv-dioctahedral layer. This result is also interpreted as cation migration accompanied by dehydroxylation in TEM, as reported in heated cv-illite. The increased β angle (~102.5º) from that in the natural state (101.5º) estimated from the HRTEM images also supports this interpretation. This phenomenon is a large obstacle to the investigation of phyllosilicates containing Al-rich cv and Mg,Fe-rich tv 2:1 layers, using HRTEM.

To determine the relationships between the symmetry of the overall pyrophyllite and talc structure and the symmetry of individual layers, the geometry and symmetry of each 2:1 layer of pyrophyllite and talc were analyzed. For each, the previously published, refined unit cell may be rotated clockwise by ~60° for comparison to a layer unit cell. In pyrophyllite, the layer unit cell is ideal and shown to be orthogonal with C2/m symmetry. The agreement between the refined atomic coordinates and those calculated for the layer with C2/m symmetry confirms that the symmetry of the pyrophyllite layer is C2/m. The obliquity of the pyrophyllite refined cell results from the layer stacking and the choice of unit cell, but the interlayer stacking sequence does not disturb the layer symmetry. In contrast, talc has an oblique layer cell, without a mirror plane. For the most part, the distortion of the talc 2:1 layer is probably caused by an elongation of unshared O-O lateral edges around M1 that creates a slight corrugation of the octahedral sheet surface. Perhaps of lesser importance, the distortion of the talc layer cell may result from Coulombic interactions between cations of adjacent layers, and these cation-to-cation distances are sufficiently large (~6–7.5 Å) that the weak van der Waals forces that stabilize the stacking are not overcome. Because pyrophyllite has a vacant octahedral site, similar interactions are not present, and this results in a more idealized layer symmetry.

Phyllosilicates consisting of layers with an orthogonal cell and mirror plane (pyrophyllite, kaolinite, sudoite) were shown to have similar stacking faults. In these structures, the 2:1 or 1:1 layers have uniform orientation, and stacking faults occur owing to interstratifications of two alternative interlayer displacements in the same crystal that are related by a mirror plane in the projection on the (001) plane. In talc, stacking faults are associated with layer rotations by ±120°, whereas the lateral displacement between the adjacent tetrahedral sheets across the interlayer region is relatively ordered.

Cronstedtite from Lostwithiel, Cornwall, England, in which two polytypic groups (A and C) are present within the same crystal, has been investigated using various techniques to reveal the distribution of the two groups and the relationship between polytypic structure and chemical composition. X-ray precession photographs from cleaved fragments of pyramidal crystals revealed the variable proportions of the two groups from the top to the base. Near the top, the crystal consists entirely of group C, with 1T as the dominant polytype. Near the base, both groups A and C are present. Back-scattered electron images from cross-sections parallel to the pyramidal axis showed mosaic contrast near the base, suggesting that two compositionally-different domains of several tens of microns in size are present, whereas the contrast was uniform near the top. Electron microprobe chemical analysis indicated the compositions $\left({\text{Fe}}_{2.31}^{2+}{\text{Fe}}_{0.69}^{3+}\right)\left({\text{Si}}_{1.31}{\text{Fe}}_{0.69}^{3+}\right){\text{O}}_5{\left(\text{OH}\right)}_4$ and $\left({\text{Fe}}_{2.16}^{2+}{\text{Fe}}_{0.84}^{3+}\right)\left({\text{Si}}_{1.16}{\text{Fe}}_{0.84}^{3+}\right){\text{O}}_5{\left(\text{OH}\right)}_4$. Electron back-scattered patterns (EBSPs) confirmed that the domain with Si-rich composition belongs to group C and that with Si-poor composition to group A. This is the first evidence that specific chemical compositions are related to the polytypic structures in cronstedtite. Transmission electron microscopy revealed that intergrowth of groups A and C at the monolayer level is also present as stacking disorder in both domains near the base, whereas such intergrowth was not observed in the region near the top.

Mineralization of microbial biomass is a common phenomenon in geothermal habitats, but knowledge of the structure of the minerals formed in these environments is limited. A combination of spectroscopic, microscopic, and stable isotopic methods, as well as the chemical analysis of spring water, were employed in the present study to characterize calcium carbonate minerals deposited in filamentous cyanobacterial mats in different locations of La Duke hot spring, a circumneutral thermal feature near the north entrance of Yellowstone National Park, Montana, USA. Calcite was the primary crystalline mineral phase associated with biofilm-containing deposits closest to the source of the spring and the suspended microbial biomass in a pool further from the source. The carbonate minerals at all sites occurred as aggregated granules, ~2 μm in diameter, in close association with the microbial biomass. Only in the deposits closest to the source were the granules organized as laminated structures interspersed with microbial biomass. The calcium carbonate grains contained two distinct regions: a dense monolithic calcite core and a porous dendritic periphery containing organic matter (OM). Electron energy loss spectroscopy (EELS) indicated that the voids were infilled with OM and carbonates. The EELS technique was employed to distinguish the source of carbon in the organic matter and carbonate mixture. The studies of carbon isotope compositions of the calcium carbonates and the saturation indices for calcite in the spring waters suggest that processes (abiotic vs. biotic) controlling the carbonate formation may vary among the sampling sites.

Alteration of basalt is a ubiquitous process on the vast oceanic crust surface and results in the formation of secondary-phase minerals that include clay minerals and Fe-(oxyhydr)oxides. Thus, this process is a significant consequence of water/rock interactions that could reveal the (bio)geochemical conditions of formation. Core samples at the basalt/sediment interface from a depth of 74.79 m below sea floor (mbsf) were recovered during the International Ocean Discovery Program (IODP) expedition 329 (2010.10.10–2010.12.13) in the South Pacific Gyre (SPG). Two distinct regions of yellow- and red-colored sediment were observed. The mineralogy, elemental composition, Fe oxidation state, and mineral structure of the altered basalt samples were analyzed using transmission electron microscopy (TEM) with selected area electron diffraction (SAED) patterns, energy dispersive spectroscopy (EDS), electron energy loss spectroscopy (EELS), and micro X-ray fluorescence (μ-XRF). In the yellow sediment, K-nontronite and feroxyhyte (δ’-FeO(OH)) were the dominant mineral phases, while Mg-rich smectite (saponite), chlorite, and hematite were found predominantly in the reddish sediment. The appearance of K-nontronite and feroxyhyte mineral assemblages in altered sediment indicated that oxidative conditions prevailed during basalt alteration. Variation in the Fe-oxidation states in the K-nontronite structure, however, may indicate that local reducing conditions persisted throughout the biogeochemical reactions.

The structures of Fe-rich chlorite and berthierine and the formation mechanisms of 7 Å–14 Å interstratified minerals were not previously fully understood owing to the difficulties in analyzing them by X-ray diffraction (XRD). The present study characterizes Fe-rich chlorites in quartz veins of epithermal to xenothermal vein-type ore deposits without later structural modifications, based on high-resolution transmission electron microscopy (HRTEM) along with XRD examination and chemical analysis. Samples have a wide range of Fe/(Fe+Mg) ratios from 0.38 to 0.98 and tetrahedral Al substitution for Si from 0.94 to 1.44 atoms per formula unit (apfu). The variation in Fe content nearly parallels the tetrahedral Al content. The formation temperatures estimated by chlorite geothermometry range from 190°C to 320°C. In HRTEM, most of the samples showed interstratification between 7 Å, 14 Å, and/or (in some samples) smectite layers. Chlorites with relatively low Fe contents (Fe/(Fe+Mg) ≈ 0.4) were characterized by mostly 14 Å periodicity with the polytype IIbb. In contrast, interstratification of 7 Å and 14 Å layers predominated with increasing Fe content and the proportion of 7 Å layers exceeds 80% in Fe-rich samples with Fe/(Fe+Mg) > 0.9. The 7 Å component layer approximated Fe-rich berthierine based on the chemical composition. Layer stacking structures in the Fe-rich samples were complex, and characterized by disorder of 7 Å and 14 Å layers, differences in the polarity of the tetrahedral sheets, variations of the slant of the octahedral sheets, and positional disorder between octahedral and tetrahedral sheets involving the hydrogen bonding, as indicated from HRTEM observations along the Yi directions of the phyllosilicates. The complex stacking structures observed in Fe-rich samples suggest that irregularity was controlled by neither the Fe/(Fe+Mg) ratio nor the formation temperature; stacking was controlled by kinetic factors in the process of mineral precipitation under disequilibrium conditions.

Polytypism in gümbelite and its relationship to the fibrous or ribbon-like morphology exhibited by this Mg-rich illite were investigated by powder X-ray diffraction (XRD), electron back-scattered diffraction (EBSD) and transmission electron microscopy (TEM). Comparison between the XRD pattern from oriented fibers using a conventional powder diffractometer and a randomly oriented pattern using a Gandolfi camera suggested that 2M2 is dominant but other polytypes belonging to subfamily A also exist, and that the fiber axis of gümbelite is parallel to <110> in 2M2, <110> in 2M1, and <100> in 1M. The EBSD analyses confirmed these crystallographic directions directly from individual crystals. Electron diffraction and high-resolution TEM showed that twinning and intergrowths of various polytypes including both subfamilies are common in a single crystal and that the two types of rotations [2n60° and (2n+1)60°] between adjacent layers are often randomly mixed at the monolayer level. The data suggest that high densities of twinning and intergrowths account for the origin of the fibrous morphology along <110> for 2M1 and 2M2 polytypes. Volume restriction in a confined vein space may also play a role.

The dissolution of brucke, Mg(OH)2, on the (001) surface was investigated using in situ atomic force microscopy in solutions at near-neutral pH. Dissolution proceeded by the formation of crystallographically oriented triangular etch pits with monolayer step and expansion of the pits. The sides of the triangle are parallel to the [100], [110] and [010] directions of the brucite structure, and the orientation of lines from the center of the triangle to the three apices are along the [210], $[\overline{1}10]$$[\bar 110]$ and $[\overline{1}\overline{2}0]$$[\bar 1\bar 20]$ directions. This orientation may produce pit edges where OH groups coordinate to two Mg2+. Although triangular etch pits with monolayer depth formed mostly at random on the (001) surface, concentric pits penetrating several layers were also observed. Etch pits with spiral steps were rarely observed. Coalescence of the pits resulted in stranded terraces that diminished in size rapidly and formed a rounded irregular form. The step-retreat velocity around the triangular pit is 0.015–0.04 nm/s at pH 5–8. The retreat velocity around the stranded terraces was about three times more rapid than that around the triangular etch pits.

Although structural disorder in kaolinite has been investigated extensively, it is still not understood properly. To investigate the problem, a kaolinite specimen of sedimentary origin from Capim, Brazil, was examined, mainly by transmission electron microscopy (TEM). Selected-area electron diffraction (SAED) along the Xi ([100], [110], and []) directions shows various features, from completely discrete patterns to heavily streaked ones along the c* direction, suggesting that the degree of stacking disorder is variable among individual grains. High-resolution TEM images indicate that stacking faults are mainly caused by disorder of alternating t1 (~ −a/3) and t2 (−a/3 +b/3) layer displacements. Furthermore, stacking faults have been observed (1) as isolated stacking faults (e.g. insertion of an isolated t2 `fault' in an ordered sequence with t1 layer displacement) and (2) as interstratification of two kinds of multilayer blocks having regular t1 and t2 layer displacements. A mixture of grains with various degrees and modes of disorder with alternating t1 and t2 layer displacements may explain the experimental profile of the 02, 11 X-ray diffraction band.

Faults related to displacement of the octahedral vacancy and/or to layer rotation were also observed in HRTEM images. The SAED patterns along the Yi ([010], [310], and []) directions occasionally have extra spots and/or streaks, suggesting the presence of stacking sequences with (±60°, 180°) mutual layer rotation and/or with (0, ±b/3) layer displacements. The local dickite or nacrite-like fragments formed by these faults are in qualitative agreement with recent low-temperature FTIR results from this sample, where distinct ν(OH) absorption bands reflect multiple interlayer O-H⋯O environments that are possibly ascribed to dickite and nacrite.

Mass transport in suspensions of swimming microorganisms is one of the most important factors for the colonisation and growth of microorganisms. Hydrodynamic interactions among swimming microorganisms play an important role in mass transport, especially in highly concentrated suspensions. To elucidate the influence of highly concentrated cells on mass transport, we numerically simulated mass transport in lattices of squirmers that were fixed in space and oriented in the same direction. The effects of different volume fractions, Péclet numbers ($Pe$) and lattice configurations on mass transport were quantified by tracking Lagrangian material points that move with background flow with Brownian diffusivity. Although the flow field became periodic in space and each streamline basically extended in one direction, the motion of tracer particles became diffusive over long durations due to Brownian motion and cross-flows. Flow-induced diffusion was anisotropic and significantly enhanced over Brownian diffusion in the longitudinal direction. We also investigated mass transport in random configurations of squirmers to reproduce more general conditions. Similar enhanced diffusion was also observed in the random configurations, indicating that the flow-induced diffusion appears regardless of the configurations. The present flow-induced diffusion did not follow $Pe$ dependency of the conventional Taylor dispersion due to the cross-flows. The time and velocity scales were proposed, which enabled us to predict the flow-induced diffusivity from the data of the flow field and Brownian diffusivity without solving the mass conservation equation. The findings reported here improve our understanding of the transport phenomena in packed suspensions of swimming microorganisms.

This review demonstrates that high-resolution transmission electron microscopy (HRTEM) imaging of clay minerals or phyllosilicates with an incident electron beam along the major zone axes parallel to the constituting layers, in which the contrast corresponds to individual cation columns in the images obtained, is indispensable for elucidating the enigmatic structures of these minerals. Several kinds of variables for layer stacking, including polytypes, stacking disorder and the interstratification of various kinds of unit layers or interlayer materials, are common in phyllosilicates. Local and rigorous determination of such variables is possible only with HRTEM, although examination as to whether the results obtained by the HRTEM images from limited areas represent the whole specimen should be made using other techniques, such as X-ray diffraction. Analysis of these stacking features in clay minerals provides valuable insights into their origin and/or formation processes. Recent state-of-the-art techniques in electron microscopy, including incoherent imaging, superior resolutions of ~0.1 nm and low-dose imaging using new recording media, will also contribute significantly to our understanding of the true structures of clay minerals.