Authigenic clays as precursors to carbonate precipitation in saline lakes of Salar de Llamara, Northern Chile

Published: 12 December 2022| Version 1 | DOI: 10.17632/fw63t9h56p.1
Erica Suosaari,
Ioan Lascu,
Amanda Oehlert,
Paola Parlanti,
Enrico Mugnaioli,
Mauro Gemmi,
Paul Machabee,
Alan Piggot,


In this study, we examined associations between microbial communities, Mg-clay minerals, and carbonates in microbial mat samples from the Puquios of the Salar de Llamara using scanning electron microscopy, energy dispersive X-ray spectroscopy, focused ion beam nanotomography, and transmission electron microscopy. Data shared here correspond to Figs. 4-6, and include the raw data used to create the Supplemental Videos 1 and 2.


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Samples were embedded in epoxy following the method of Nye et al. 1972, in an effort to examine microbe-mineral interactions. After samples were fully cured, the epoxy block from P163 was subsampled and used to prepare petrographic thin sections for optical microscopy examination, and also stained with crystal violet to highlight biomass. The remaining epoxy block from P163, as well as the epoxied sample from P31, were then polished in graduated steps up to 0.6 µm with diamond polishing compound to achieve a flat surface for examination using SEM. ROIs were selected for FIB-SEM nanotomography to reconstruct the 3D nanocrystal morphology of the Mg-clay minerals, their location around preserved cell sheaths, as well as the juxtaposition between Mg-clay and carbonate minerals. The surfaces of the SEM samples were coated with a ~15 nm-thick veneer of carbon. TEM imaging and SAED, and 3DED were used for mineral identification. FIB-SEM nanotomography was performed using a Helios NanoLab 660 dual beam focused ion beam SEM, and was conducted in three areas. In sample P163 we targeted an area with Mg-clay nanocrystals in the initial stages of formation around a cyanobacterial cell. In sample P31, we milled an area containing a dense aggregation of Mg-clay along a filamentous cell (P31a), and an area containing both Mg-clay and carbonate (P31b). The ROIs were prepared using ion beam induced deposition to lay down a 1 μm-thick platinum pad. Trenches were milled out on three sides of the ROI, with a large front trench to allow imaging of the cleaned cross-section and two side trenches to minimize the redeposition effects associated with the milling process. Fiducial markers were created on the sample surface and on the backwall of one of the side trenches to assist with FIB and electron beam alignment, respectively. FIB milling was done using an acceleration voltage of 30 kV and beam current 2.5-21 nA, at 52° stage tilt, and 4 mm working distance. Backscattered electron imaging was performed with the Through the Lens Detector in immersion mode, with an acceleration voltage of 2 kV and beam current 0.4 nA, at 45°stage tilt and working distance of 2.5 mm. The image acquisition parameters for the three datasets are listed in Table 2. The resulting images were aligned using the open-source platform FijiSalar de Mg-Si. The aligned image stacks were imported in the Object Research Systems Dragonfly software package, which was used to segment the stacks in order to define the mineral components, and subsequently reconstruct the ROIs.


Smithsonian Institution


Electron Microscopy, Scanning Electron Microscopy, Focused Ion Beam, Carbonate Sedimentology, Clay Mineral, Authigenic Mineral, Carbonate Mineral