Archival biogenic micro- and nanostructure data analysis: Signatures of diagenetic systems

The present data in brief article provides additional data and information to our research article “Micro- and nanostructures reflect the degree of diagenetic alteration in modern and fossil brachiopod shell calcite: a multi-analytical screening approach (CL, FE-SEM, AFM, EBSD)” [1] (Casella et al.). We present fibre morphology, nano- and microstructure, as well as calcite crystal orientations and textures found in pristine, experimentally altered (hydrothermal and thermal), and diagenetically overprinted brachiopod shells. Combination of the screening tools AFM, FE-SEM, and EBSD allows to observe a significant change in microstructural and textural features with an increasing degree of laboratory-based and naturally occurring diagenetic alteration. Amalgamation of neighbouring fibres was observed on the micrometre scale level, whereas progressive decomposition of biopolymers in the shells and fusion of nanoparticulate calcite crystals was detected on the nanometre scale. The presented data in this article and the study described in [1] allows for qualitative information on the degree of diagenetic alteration of fossil archives used for palaeoclimate reconstruction.

whereas progressive decomposition of biopolymers in the shells and fusion of nanoparticulate calcite crystals was detected on the nanometre scale. The presented data in this article and the study described in [1] allows for qualitative information on the degree of diagenetic alteration of fossil archives used for palaeoclimate reconstruction.
& 2018 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Data accessibility
Data is with this article

Value of the data
The data provides fundamental, quantitative and qualitative information on the assessment of the degree of (diagenetic) alteration of brachiopod shells.
Hydrothermal alteration experiments mimicking diagenetic alteration may be applied to other biogenic hard tissues and inorganic mineral assemblages (e.g., rocks) in order to objectively compare the degree of diagenetic overprint.
Data analysed by multi-analytical screening methods (FE-SEM, EBSD, AFM) may provide crucial information on the history of fossils used in research fields such as reconstruction of the palaeoclimates and palaeoenvironments.
A comparison between microstructure and texture analyses of our data with isotope analysis may provide more detailed understanding of diagenetic overprint of fossil samples.

Thermal alteration
Thermal alteration was carried out in order to observe the decomposition of the enclosing organic membranes. Sample material used in thermal alteration experiments was heated in an oven at 100°C for 72 h and for three months, as well as at 400°C for 48 h.

Hydrothermal alteration
Hydrothermal alteration experiments were performed in the presence of either simulated meteoric (10 mM NaCl aqueous solution) or simulated burial (100 mM NaCl þ 10 mM MgCl 2 aqueous solution) fluid. Both solutions were prepared using high-purity deionised water [1,2,21]. Sample material and 10 ml of fluid were inserted into a polytetrafluoroethylene crucible which was placed inside a metal autoclave. Experiments were conducted at 100°C for 28 days using either simulated meteoric or burial fluid. Pressure conditions during the hydrothermal alteration experiments corresponded to the vapour pressure of water at the given temperature.   mimicking diagenetic alteration of biogenic carbonates. Sampling sites of both live collected brachiopods were Friday Harbor Laboratories, University of Washington, U.S.A., and Signy and Rothera Islands, Antarctica, for T. transversa and L. uva, respectively.

Investigated fossil brachiopods
Four fossil equivalents were chosen from basins which experienced different burial depths and diagenetic temperatures. Platystrophia laticostata (James, 1871) was collected from the Upper Ordovician Dillsboro Formation, Indiana, U.S.A. The Jurassic brachiopods Lobothyris punctata (Sowerby, 1812) and Quadratirhynchia attenuata (Dubar, 1931) were collected at the Bakony Mountains, Hungary, and Ait Athmane Formation of the Central Atlas Basin, Morocco, respectively. Digonella digona (Sowerby, 1815) is the youngest of all Jurassic brachiopod samples and its sampling site was located at Luc-Sur-Mer, Normandy, France. Further information on all utilised brachiopod specimens is given in [1]. Fig. 7. EBSD band contrast image of hydrothermally altered T. transversa shell. Alteration occurred at 175°C for 28 days and was carried out in simulated burial fluid. Shell areas where the original fibre morphology was distorted by alteration (yellow rectangle) can be observed close to regions where the shell microstructure was little affected (white rectangle). Note that amalgamation of fibres occurred occasionally (white arrows). Fig. 8. EBSD band contrast image of hydrothermally altered T. transversa shell. Alteration occurred at 175°C for 28 days and was carried out in simulated burial fluid. In some parts of the shell the original fibrous shell microstructure was distorted by amalgamation of fibres due to alteration (yellow dashed rectangles). The amalgamation of fibres can be explained by lateral growth of the inorganic rhombohedral calcite (IRC) of one nanocomposite mesocrystal biocarbonate (NMB) fibre growing into the neighbouring fibre. Note that altered shell areas are next to shell areas which appear to be little affected by alteration (white dashed rectangle).

Microtome cutting and polishing
Brachiopod shell fragments of pristine and fossil brachiopod species were mounted on 3 mm thick cylindrical aluminium rods using super glue. In order to obtain plane surfaces, the samples were  microtome cut using a Leica Ultracut ultramicrotome equipped with glass knives. Subsequently, the cut specimens were polished by stepwise removal of material in a series of slices with successively decreasing thicknesses (90 nm, 70 nm, 40 nm, 20 nm, 10 nm, and 5 nm) using a DiATOME diamond knife. Each step was repeated 15 times [22].

Selective biochemical etching
Microtome-polished shell surfaces were etched and the organic matter fixed, simultaneously, while immersed in a solution of 0.1 M HEPES (pH ¼ 6.5) and 2.5% glutaraldehyde for 180 seconds. The etching procedure was stopped by a dehydration step in 100% isopropyl 3 times for 10 minutes each. Subsequently, specimens were critical point dried using a BAL-TEC CPD 030 (Liechtenstein) device and rotary coated with 3 nm of platinum.

FE-SEM imaging
For FE-SEM imaging, selected sample material was prepared by microtome cutting and polishing following a selective biochemical etching treatment. However, the major preparation technique for SEM imaging and EBSD measurements of brachiopod samples was carried out as follows. Brachiopod shells were longitudinally cut from the umbo to the commissure and, subsequently, embedded in epoxy resin. Shell surfaces were conventionally ground and polished in sequential steps down to a grain size of 1 mm (particle size of polishing agent). The preparation was finalised by an etch-polishing step utilising colloidal alumina with particle sizes of approx. 0.05 mm in a vibratory polisher. Subsequently, sample surfaces were rotary coated with 4-6 nm of carbon.
FE-SEM imaging was carried out at 4, 5, or 10 kV using a Hitachi S5200 electron microscope.

EBSD measurements, band contrast and analysis of calcite orientation data
For EBSD measurements, brachiopod shells were conventionally ground and polished as described above. Sample surfaces were rotary coated with 4-6 nm of carbon. EBSD measurements were conducted at 20 kV using a Hitachi SU5000 FE-SEM equipped with a Nordlys II EBSD detector and AZTec acquisition. Obtained EBSD data was evaluated using CHANNEL 5 HKL evaluation software [23,24]. Data on crystal orientation is shown as band contrast images and colour-coded crystal orientation maps with corresponding pole figures. EBSD band contrast represents the quality of the Kikuchi diffraction pattern in each measured point, thus, strong EBSD signals result in a bright image point and weak or absent signals (e.g., due to pores, organic matter, amorphous phases) result in dark image points. Crystallographic orientation maps were derived from EBSD scans. A measure of coorientation within single crystals or ensembles of crystals are given by the multiple of uniform distribution (MUD). High MUD values indicate highly co-oriented crystallographic axes (e.g., MUD of 4 700 in inorganic single crystals [25]) and, thus, a strong texture. Low MUD values down to 1.0 reflect randomly oriented crystallographic axes, thus, a weak or no texture.

AFM imaging
For AFM imaging, brachiopod specimens were prepared by two different preparation techniques, i.e., microtome cutting using glass knives and polishing using a diamond knife, as well as by conventional grinding and polishing as is described above (see subchapters 2.3 and 2.5). The latter includes an additional step, i.e., cleaning of the highly polished sample surface for 10 min. using highpurity deionised water in an ultrasonic bath, rinsing with ethanol and subsequent air drying. Rotary coating was not applied prior to AFM imaging.
Atomic force microscopy was conducted on hydrothermally altered and fossil brachiopod shells. Images were taken in contact mode.