3D Reconstruction of Microbialites


Microbialites (rocks influenced by microbial growth when they formed) provide some of the earliest evidence of life on Earth. However, ancient microbialites rarely preserve microfossils and are often too geochemically altered to provide signatures of microbial metabolism. Thus, microbialite morphology is often the only indicator of possible past life, and it provides clues to both biological and environmental processes. Refined interpretations of morphology can substantially improve our understanding of the processes influencing microbialite growth and the ecology of early microbial communities.

Sumner and her lab group are developing a refined understanding of microbialite morphology by comparing modern microbialites, where growth processes can be observed, to microbialite fossils. For the modern microbialites (left: dcm-scale microbialite from Lake Joyce, Antarctica), we use x-ray computed tomography to map density variations that reflect concentrations of minerals preserving the otherwise soft mats. For ancient microbialites, density differences are too small to provide useful morphological information so we reconstruct their geometry by serial sectioning the rocks, scanning each surface, and reconstructing a 3D virtual representation of the microbialite from the scans (right: reconstruction of a 2.5 billion year old fossil microbial structure from South Africa). Both methods allow investigations of intricate 3D structures, including quantitative characterization of the dips of surfaces, the sizes of features, and various microbial growth features. These methods use 3DVisualizer.

In addition to reconstructing the internal morphology of microbialites, Sumner and her lab group are experimenting with an underwater laser scanner to map the intricate topography on modern microbial mats in Antarctic lakes (using LidarViewer). We are comparing results to 3d reconstructions of the mats from stereo video.



  • Dawn Sumner, Professor
  • Cara Harwood, Graduate Student
  • Tyler Mackey, Graduate Student
  • Marisol Juarez Rivera, Undergraduate
  • Eric Stevens, Former Undergraduate (now a graduate student at University of Minnesota)
  • Megan Murphy, Former Graduate Student (now at Chevron)
  • James Bishop, Former Graduate Student (now at Chevron)
  • Nic Huerta, Former Graduate Student (now a graduate student at UT Austin)
  • Rebekah Shepard, Former Graduate Student
  • Patrick Senge, Former Undergraduate (now at a mining company)

Computer Scientists

  • Oliver Kreylos, Research Scientist
  • Xin Wang, Visiting Professor
  • Bernd Hamann, Professor
  • Jesus Pulido, Graduate Student



  • Stevens*, Eric W., Dawn Y. Sumner, Cara L. Harwood*, James Crutchfield, Bernd Hamann, Oliver Kreylos, Edward Puckett and Patrick Senge*, 2011. Understanding microbialite morphology using a comprehensive suite of three dimensional analysis tools. Astrobiology, v. 11, in press.
  • Andersen, Dale T., Dawn Y. Sumner, Ian Hawes, Jenny Webster-Brown, and Christopher P. McKay, 2011. Discovery of large conical stromatolites in Lake Untersee, Antarctica. Geobiology, v.9. 280–293, DOI: 10.1111/j.1472-4669.2011.00279.x
  • Harwood*, Cara L., and Dawn Y. Sumner, 2011. Microbialites of the Neoproterozoic Beck Spring Dolomite, southern California. Sedimentology. DOI: 10.1111/j.1365-3091.2011.01228.x
  • Shepard*, Rebekah N., and Dawn Y. Sumner, 2010. Undirected motility of filamentous cyanobacteria produces reticulate mats. Geobiology, v. 8, p. 179-190. DOI: 10.1111/j.1472-4669.2010.00235.x
  • Murphy*, Megan, and Dawn Y. Sumner, 2007. Tube structures of probable microbial origin in the Neoarchean Carawine Dolomite, Hamersley Basin, Western Australia. Geobiology, v. 6, p. 83-93. DOI: 10.1111/j.1472-4669.2007.00114.x
  • Bishop*, James W., Dawn Y. Sumner, and Nicolas J. Huerta*, 2006. Molar tooth structures of the Neoarchean Monteville Formation, Transvaal Supergroup, South Africa: II. A Fluid Flow Model. Sedimentology, v. 53, p. 1069-1082. DOI: 10.1111/j.1365-3091.2006.00802.x