Work Description

Title: Dataset related to 'Effects of Metamorphism and Metasomatism on Manganese Mineralogy: Examples from the Transvaal Supergroup' Open Access Deposited
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  • X-ray absorption spectroscopy (XAS) data was collected on manganese standards at beam line 4-1 at the Stanford Synchrotron Radiation Lightsource (SSRL). Data collection and analysis is described in detail in the accompanying manuscript and in the ReadMe file associated with this dataset.
  • Manganese in the sedimentary record has been interpreted by many as a powerful redox proxy for paleoenvironments, and yet very little work has been done to ensure that the manganese-rich minerals in the rock record are actually recording primary signals. In the accompanying manuscript, we present an in-depth characterization of the manganese mineralogy from two correlated regions recording the Transvaal Supergroup in South Africa with markedly different alteration histories to investigate if there can be post-depositional emplacement of manganese-rich minerals. The data uploaded here are X-ray absorption spectra of (1) manganese standard minerals that were useful in our analyses and (2) minerals from an important well-characterized sample that may be useful as comparative standards in future studies.
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Funding agency
  • Other Funding Agency
Other Funding agency
  • Packard Foundation
  • Lewis and Clark Foundation
Citations to related material
  • J.E. Johnson, S.M. Webb, C.B. Condit, N.J. Beukes, W.W. Fischer; Effects of metamorphism and metasomatism on manganese mineralogy: Examples from the Transvaal Supergroup. South African Journal of Geology doi:
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Last modified
  • 01/20/2020
  • 06/17/2019
To Cite this Work:
Johnson, J., Webb, S., Condit, C., Beukes, N., Fischer, W. (2019). Dataset related to 'Effects of Metamorphism and Metasomatism on Manganese Mineralogy: Examples from the Transvaal Supergroup' [Data set]. University of Michigan - Deep Blue.


Files (Count: 16; Size: 21.9 MB)

Effects of Metamorphism and Metasomatism on Manganese Mineralogy: Examples from the Transvaal Supergroup

Jena E. Johnson, Samuel M. Webb, Cailey B. Condit, Nicolas J. Beukes, Woodward W. Fischer

DOI: ----------------------


The enclosed is a partial deposit of raw data collected at the Stanford Synchrotron Radiation Lightsource and associated with the figures shown in Johnson et al (2019), published by the South African Journal of Geology.


Data collection was described in detail in the accompanying manuscript (Johnson et al, 2019, SAJG) and also in (Johnson et al., 2013, 2016), but will be summarized here as well.

X-ray absorption spectroscopy (XAS) data was collected on manganese standards at beam line 4-1 at the Stanford Synchrotron Radiation Lightsource (SSRL). Energy was chosen using a Silicon 220 phi=90 monochromator, with a collimating mirror used to reduce harmonics in the beam, and emitted fluorescence was collected using a Lytle detector. Calibration was performed using the pre-edge peak of a potassium permanganate standard (centroid set to 6543.34). Duplicates were run on all standards, scanning from 6310 to 7108 eV across the Mn K-edge. Spectral data were subsequently background-corrected and normalized using the SixPack software suite (Webb, 2005). In general, the pre-edge spectrum was fit to a Gaussian curve and the post-edge was fit linearly, but spectra were examined and adjusted individually to optimize normalization. Standards are labeled by mineral name or formula, with the exception of two standards that begin with ÔHotazelÕ; these are well-characterized minerals from the Hotazel Formation in South Africa (Johnson et al., 2013, 2016) that have become lab standards for the minerals kutnohorite and braunite. Standards included contain the prefix ÔStandardÕ.

With samples from the Transvaal Supergroup described in Johnson et al. (2019, SAJG), we applied X-ray spectroscopic imaging to create Mn speciation maps by leveraging the X-ray fluorescence differences at energies that distinguish relevant phases in a sample (Mayhew et al., 2011; Johnson et al., 2013, 2016). Maps were collected at a resolution of 2-10 micrometers at beam line 2-3 at SSRL. Incident energy was selected using a Silicon 111 double crystal monochromator and the beam was focused to ~ 2 micrometers using Kirkpatrick Baez mirrors. Calibration was performed on the pre-edge peak of potassium permanganate as described above. We produced maps by rastering the beam across target areas at the energies 6551 eV, 6556 eV, 6562 eV, and 6590 eV. XAS spectra of 2 micrometer x 2 micrometer pixels were taken in areas highlighted as distinct Mn phases by principal component analyses of these four energy maps. Maps were fit to internal spectral endmembers after normalization following the procedure described above.

For sample PA-2014, the locations of distinct endmember spectra are shown on the enclosed image ÔPA2014_point-spectra-markedÕ, with points labeled on the 6590 eV X-ray fluorescence map of the sampleÕs region of interest. The fluorescence map indicates that Mn abundance is variable throughout the region, with the highest Mn concentrations shown as red and the lowest (negligible) concentrations of Mn shown in deep blue. The XAS spectra of distinct endmembers are included in this subfolder as well, labeled with their mineralogical identification. The spectra were identified using the Mn standards measured above (for carbonate) or by independent analyses of elemental abundance (using energy or wavelength dispersive spectrometry in a scanning electron microscope or an electron microprobe) and/or by Raman spectroscopy. The identifications are described in greater detail in Johnson et al. (2019, SAJG). Mineral names in the enclosed spectra (starting with PA2014) are abbreviated as follows: carb = carbonate; grun = grunerite; grt = garnet.


Portions of this research were carried out at the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, which is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract DE-AC02-76SF00515.


Johnson, J.E., Webb, S.M., Ma, C., and Fischer, W.W., 2016, Manganese mineralogy and diagenesis in the sedimentary rock record: Geochimica Et Cosmochimica Acta, v. 173, p. 210Ð231.

Johnson, J.E., Webb, S.M., Thomas, K., Ono, S., Kirschvink, J.L., and Fischer, W.W., 2013, Manganese-oxidizing photosynthesis before the rise of cyanobacteria: Proceedings of the National Academy of Sciences of the United States of America, v. 110, p. 11238Ð11243, doi:10.1073/pnas.1305530110.

Mayhew, L.E., Webb, S.M., and Templeton, A.S., 2011, Microscale imaging and identification of Fe speciation and distribution during fluid-mineral reactions under highly reducing conditions: Environmental Science & Technology, v. 45, p. 4468Ð4474, doi:10.1021/es104292n.

Webb, S.M., 2005, SIXpack: a graphical user interface for XAS analysis using IFEFFIT: Physica Scripta, v. 2005, p. 1011, doi:10.1238/Physica.Topical.115a01011.

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