John R. Spear

PhD, Professor, Civil and Environmental Engineering

John SpearThe great majority of life on Earth is microbial in size, things only visible through the microscope. Almost all of these microbes are harmless to humans and in fact, provide vital ecosystem services to just about every habitat on the planet—including our own bodies. We are interested in the who, what, when, where, why and how questions about microbial life—in essence, microbial ecology. We think and work with both the fundamentals of Basic Science and translate that into very Applied Science to make better and more favorable use of microbial-related processes. Who are they?—We are interested in the diversity of this microbial life in all three domains of life—Eucarya, Bacteria and Archaea. What do they do?—Are they interacting and / or changing their environment? What can they do for us?—Can we learn how to optimize a microbial process for bioremediation or for bioenergy? When are the microbiota of a particular environment active?—Can we manipulate that activity for stimulation in an engineered system or process? Where are they?—Is a certain microbe only found in one place or throughout the ecosystem / world? Why are they there? Why do they do what they do? This leads us to ask “how?” Do microbiota interact with their world? Do microbiota use energy flow in novel ways? Do microbiota process metal and /or heavy metals? Are these processes beneficial to humanity?


Coolbaugh Hall 252

Labs and Research Centers


  • PhD, Colorado School of Mines
  • MS, Colorado School of Mines
  • BA, University of California, San Diego (Animal Physiology/Biochemistry; Minor–Psychology)


  • 2005 – Present: Assistant Professor
  • 2001 – 2008: Instructor/Faculty, International Geobiology Course
  • 1999 – 2005: Postdoc, Molecular, Cellular and Developmental Biology, University of Colorado, Boulder; Laboratory of Dr. Norman R. Pace.
  • 1992 – 1999: Graduate Student, Division of Environmental Science and Engineering, Colorado School of Mines, Golden, CO
  • 1988 – 1992: Instructor / Operations Manager, National Outdoor Leadership School (NOLS), Lander, WY
  • 1986 – 1989: Manager, Keystone Ski Area, Keystone, Colorado
  • 1984 – 1986: Research Technician, The Scripps Research Institute, La Jolla, CA


  • ESGN 596–Microbiology of Engineered Environmental Systems
  • ESGN 586–Molecular Environmental Microbiology
  • ESGN 591–Introduction to NEPA, The National Environmental Policy Act (a policy class)
  • ESGN 522–Reclamation of Disturbed Lands (a policy class)
  • ESGN 498–Introduction to Geobiology
  • ESGN 354–Environmental Engineering
  • Co-Director, The International Geobiology Summer Course (More Information)

Selected Publications

  • Baumgartner, L.K., C. Dupraz, D.H. Buckley, J.R. Spear, N.R. Pace, and P.T. Visscher. 2009. “Microbial Species Richness and Metabolic Activities in Hypersaline Microbial Mats: Insight into Biosignature Formation Through Lithification.” Astrobiology, 9(9): 861-874.
  • Baumgartner, L. K., J.R. Spear, D.H. Buckley, N.R. Pace, R.P. Reid, C. Dupraz and P.T. Visscher. 2009. “Microbial Diversity in Modern Marine Stromatolites, Highborne Cay, Bahamas.” Environmental Microbiology, 11(10): 2710-2719.
  • Boyd, E.S., J.R. Spear and J.W. Peters. 2009. “[Fe-Fe]-hydrogenase Genetic Diversity Provides Insight into Molecular Adaptation in a Saline Microbial Mat Community.” Applied and Environmental Microbiology, 75(13): 4620-4623.
  • Tomaras, J.M.B., J.W. Sahl, J.R. Spear and R.L. Siegrist. 2009. “Microbial Diversity of Septic Tank Effluent and a Soil Biomat.” Applied and Environmental Microbiology, 75(10): 3348-3351.
  • Robertson, C.E., J.R. Spear, J.K. Harris and N.R. Pace. 2009. “Diversity and stratification of Archaea in a hypersaline microbial mat.” Applied and Environmental Microbiology, 75(7): 1801-1810.
  • Sahl, J.W., N.R. Pace and J.R. Spear. 2008. “Comparative Molecular Analysis of Endoevaporitic Microbial Communities.” Applied and Environmental Microbiology, 74(20): 6444-6446.
  • Kunin, V., J. Raes, J.K. Harris, J.R. Spear, J.J. Walker, N. Ivanova, C. von Mering, B.M. Bebout, N.R. Pace, P. Bork, P. Hugenholtz. 2008. “Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.” Molecular Systems Biology, 4:198: 1-6.
  • Feazel, L.M., J.R. Spear, A.B. Berger, J.K. Harris, D.N. Frank, R.E. Ley and N.R. Pace. 2008. “Eucaryotic Diverstiy in a Hypersaline Microbial Mat.” Applied and Environmental Microbiology, 74(1): 329 – 332.
  • Sahl, J.W., R. Schmidt, E.D. Swanner, K.W. Mandernack, A.S. Templeton, T.L. Kieft, R.L. Smith, W.E. Sanford, R.L. Callaghan, J.B. Mitton and J.R. Spear. 2008.
    “Subsurface Microbial Diversity in Deep Granitic Fracture Water in Colorado.” Applied and Environmental Microbiology, 74(1): 143 – 152.
  • Walker, J.J., J.R. Spear, and N.R. Pace. 2005. “Geobiology of a microbial endolithic community in the Yellowstone geothermal environment.” Nature, 434: 1011-1014.
  • Spear, J.R., J.J. Walker, T. McCollom and N.R. Pace. 2005. “From the Cover: Hydrogen and Bioenergetics in the Yellowstone Geothermal Ecosystem.” PNAS 102(7): 2555-2560.