Exploring for Magnetofossils in the Buck Reef Chert

Barberton Greenstone Belt, South Africa

Elizabeth Desser

Paleomagnetic Research Group

Department of Earth and Environmental Sciences, University of Rochester

Recent work positing the onset of the geomagnetic field at ~4.2 Ga (~750 Ma earlier than previously thought) potentially provides earlier time constraints on the emergence of an atmosphere and water - both essential for life (Tarduno et al., 2015). Precambrian rocks, such as the 3.416 Ga Buck Reef Chert (BRC) within the Barberton Greenstone Belt (BGB) in South Africa (Fig. 1), may have hosted microorganism environments whose fossil remains might corroborate an earlier geomagnetic field.


Fig. 1. Modified from Lowe (2013). Location of the Buck Reef Chert (BRC) within (A) the Barberton Greenstone Belt (BGB) in (B) South Africa. The red arrows indicate the interface marking the general location of the Buck Reef Chert.

Magnetotactic bacteria (MTB) are microorganisms that precipitate biogenic magnetite (Fe3O4), or greigite (Fe3S4), inside rod-shaped magnetosomes (Chang and Kirschvinck, 1989). The crystals are arranged in chains of either single (Fig. 2) or multiple strands positioned along the length of the magnetosome. MTB crystals are approximately 50 nm in length (single-domain magnets), and, as such, possess sufficient magnetization strength to align themselves along magnetic flux lines in search of oxygen gradients, preferring oxic-anoxic transition zones (OATZ) (Butler, 1992). A section of a BRC core sample used in this study is from such a zone, interpreted to be a shallow water environment, such as a protected lagoon and evaporitic pool. (Tice and Lowe, 2006).

Figure 2: Micrograph of a modern magnetotactic bacterium and its secreted crystals of magnetite aligned within the magnetosome (Nature Education, 2010).


A core sample from the BRC is investigated for the presence of MTB in this study. Using microscopy techniques, the thin-section sample is explored for sites described as wavy laminations of microbial mats by Lowe and Byerly (1999). At these locations, the geologic interpretation suggests an OATZ environment. Focused Ion Beam (FIB) ablation to probe the interior of the thin-section is used to prepare for more advanced microscopy techniques, should there be positive identification of MTB.


A geologic thin-section was prepared from previously collected rock core extracted from the BRC.

Figure 3: Thin-section map with zones and transects indicated. Focused Ion Beam (FIB) ablation sites are shown.

The thin section was created by cutting a 100 μm-thick slab from a core sample, mounting it on a glass slide with epoxy, grinding it to 30 μm-thick, and polishing it in three phases with successively finer polishing agents. The thin-section was scanned at high resolution with light microscopy to mark zones of interest (Fig. 3). Ten zones were identified based on visible changes in stratigraphy, and five transects were marked to sample all zones with light microscopy and electron scanning microscopy.



Light Microscopy (LM) was completed on a Nikon Eclipse polarizing microscope to perform reconnaissance of the thin-section in each zone (Fig. 4a shows zone 5). Observations in reflected, transmitted, and cross-polarized light include extinction, twinning, inclusions, different crystalline shapes and colors, and apparent presence of microbial detritus. Fiji-imageJ software is used for image enhancements, and Fig. 4b shows the same image from Fig. 4a, but enhanced to highlight the wavy laminated facies using 8-bit grayscale sharpening, contrast enhancement, and illumination techniques.

Fig. 4. (a) Transmitted light image of zone 5 at 10x magnification. A quartz vein traverses the top, and the wavy laminated facies extends across the middle of the image; (b) the same image but processed with Fiji-ImageJ.


This study used the University of Rochester’s field emission source AURIGA© Modular Crossbeam Scanning Electron Microscope (SEM). The instrument hosts different electron detectors such as In-Lens (Figs. 8b and 8c), secondary electron (SE) (Fig. 7a) and backscatter electron (BSE) detectors (Fig. 6 and Fig. 8a), for which selection depends on imaging objectives and the specimen properties. Each zone in the thin-section was tested for elemental composition and underwent Electron Dispersive Spectroscopy (EDS) and Electron Dispersive X-ray detection (EDAX©), the results of which are shown in Figs. 6 and 7 for a crystal in zone 10.


The Electron Flight Simulator software program (EFS) was used to model the electron beam and thin-section interaction. EFS uses Monte Carlo statistical methods to make predictions of the size and shape of the interaction volume to determine the signal type that will be generated, and to display from which depth signals will be emitted using the electron energy color scale ranges.8 Fig. 5 shows the electron energies for SiO2.

Fig. 5. Electron energy simulation for pure SiO2, inferred rock matrix composition.

Energy-dispersive X-ray Spectrometry (EDS) and Energy Dispersive Analysis of X-rays (EDAX)©

The electron beam generates an x-ray photon and the excess energy released is characteristic of certain elements.8 EDS was performed in each zone to determine the elemental composition of crystals and the host matrix. The energy values and photon count are used to make spectra such as that shown in Fig. 6, taken from the inset image depicting a crystal from zone 10. Its distinctive composition may yield details about the depositional environment. EDAX methods allow quantitative analysis to obtain, by element detected, the weight and atomic percentages. In addition, EDAX performs corrections for atomic number (Z), absorption (A), and fluorescence (F).


Fig. 6. EDS spectrum for standardless quantitative interpretation generated in spot mode on a distinctive crystal from zone 10.

Elemental Maps

Elemental maps (Fig. 7) are generated with Genesis© software, from which composition estimates can be made. The same crystal from Fig. 6 was scanned in the area shown in Fig. 7a, and elemental maps derived from this region appear below.

Fig. 7. Elemental Maps: (a) Distinctive crystal from zone 10 upon which the areal elemental maps are based; (b) iron, present throughout the crystal and surrounding crystals; (c) sulfur, the primary element present in the crystal; (d) nickel, also an important component of the crystal; (e) silicon, comprises the background (and strongest signal), and (f) oxygen, also in the background. The results suggest an iron-nickel sulfide crystal in a chert (Si02 ) matrix.


Prior to SEM, the specimen was given an evaporative carbon coating to prevent charge buildup from the electron beam. This was performed a second time after Focused Ion Beam (FIB) ablation. The evaporative carbon coating apparatus works on “line of sight deposition” where the incoming carbon particles are evaporated upwards, and coat the sample mounted above the aperture.



Optimized siting for FIB ablation based upon previous reconnaissance methods are shown in Fig. 3. Two sites in zones 3 and 8 were chosen based on facies interpretation for preferred MTB habitats. For each, FIB ablation using a Gallium ion beam milled out a trapezoidal wedge which would be reworked to create a thin window for lift-out, should further microscopy be required.

Fig. 8. (a) Backscatter electron BSE image of locator crystal from zone 8. FIB ablation was completed about 100 μm to the left of the crystal; (b) Ablated FIB trench in zone 8; (c) Objects of interest observed on the vertical wall of the trench, and potential subject for future work. If transmission electron beam (TEM) and diffraction techniques follow, a trench would be ablated on the other side of this wall, leaving a “window” with the objects in it for lift-out and subsequent advanced microscopy methods.


Presumed oldest MTB are found in rocks dating to about 1.9 Ga.3 Locating older remains is significant, for it might provide an additional constraint for the postulated earlier presence of the geomagnetic field, and hence, associated implications for earlier life. The exploratory techniques with LM, SEM, EFS, and EDS/EDAX© confirmed initial guesses about composition, and in comparison with previous studies from former graduate students in the Paleomagnetic Research Group, this sample of the BRC is quite similar. FIB ablation sites were selected by careful analysis of the results from the other methods, and the small anomalies observed and imaged in Fig. 8c are encouraging, and might direct future research investigations using advanced microscopy techniques.


With much gratitude to my research advisor, Professor John Tarduno, and all of my colleagues in the UR-Paleomagnetic Research Group (UR-Pmag), especially Richard Bono and Rory Cottrell who provided essential guidance. I acknowledge former Pmag students Julia Voronov, Matt Dare, and Nick Hebdon who conducted earlier studies in the BRC upon which this one is based. Many thanks to Gerry Kloc who prepared the polished thin section, and patiently showed me the processes - even letting me try out a few myself. With deep appreciation to Brian McIntyre, our formidable SEM instructor, for introducing me to the wonder and beauty of the fascinating tiny universes observable through microscopy, and for his excellent instruction over the course. I also thank Caleb Whittier, our knowledgeable course Teaching Assistant, and my lab partner Cody Fagan, and classmates, for interesting discussions.

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Lowe, D. R. Crustal fracturing and chert dike formation triggered by large meteorite impacts, ca. 3.260 Ga, Barberton Greenstone Belt, South Africa. GSA Bulletin 125, 5/6, 894-912 (2013).

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Butler, R. F. Paleomagnetism: Magnetic Domains to Geologic Terranes. (Blackwell Scientific Publications, Oxford, UK, 1992).

Tice, M. M., & Lowe, D. R., The origin of carbonaceous matter in pre-3.0 Ga greenstone terrains: A review and new evidence form the 3.42 Ga Buck Reef Chert. Earth-Science Reviews 76, 259-300 (2006).

Nature education (2010). Retrieved on 24 April 2017. www.nature.com/scitable/knowledge/library/bacteria- that-synthesize-nano-sized-compasses-to-15669190.

Lowe, D. R., and Byerly, G. R. Stratigraphy of the west-central part of the Barberton Greenstone Belt, South Africa, in Geologic Evolution of the Barberton Greenstone Belt, South Africa (eds Lowe, D. R. and G. R. Byerly) 1-36 (Geol. Soc Am. Spec. Pap. 329, Geol. Soc. of Am., Boulder, CO, 1999).

Brian McIntyre, OPT 407 SEM, course notes and personal communication.