John R. Spear

Professor, Civil and Environmental Engineering

john-spear 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? It is in the pursuit of the answers to these questions that leads us to better understand our natural world that is filled with revelations and surprise—on a daily basis! Over the past twenty years the fields of Environmental Microbiology and Geobiology have progressed like no other in science! We are lucky to live, work and tell amazing stories of this microbial world in this time!


Coolbaugh Hall 334


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


  • 2014 – Present: Professor
  • 2015 – 2018: Associate Vice President for Research
  • 2010 – 2014: Associate Professor
  • 2005 – 2010: Assistant Professor
  • 2010 – 2016: Co – Director, International Geobiology Course
  • 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


  • CEEN 460 / 560 – Molecular Microbial Ecology & the Environment
  • CEEN 595 – Introduction to NEPA, The National Environmental Policy Act (a policy class)
  • CEEN 573 – Reclamation of Disturbed Lands (a policy class)
  • HNRS 440 – McBride Honors Program—Explorations in International Studies and Global Affairs: Nepal
  • HNRS 445 – McBride Honors Program—The Evolution Revolution
  • HNRS 450 – McBride Honors Program—Science, Technology and Ethics: Unnatural Disasters
  • CEEN 302 – Environmental Engineering: Air and Waste Management
  • CSM Senior Design: Various Projects in Various Countries

Research Areas

The Spear Research Group is primarily interested in microbes—in any environment. For the past 20 years or so, we have been engaged mostly with the geology : biology interface—Geobiology. We begin with skilled field work to different environments for sample collection that typically includes samples for subsequent geology, geochemistry and microbiology analyses. Upon return to the laboratory, we engage in microscopy (basic to complex), cultivation, ‘—omics’ technologies that include metagenomics, metatranscriptomics, metabolomics, single-cell genomics and overall microbiome analysis via advanced bioinformatics interpretation. Current research projects include:

  • Analysis of microbially influenced corrosion (MIC) on steel and other materials
  • The microbiome of snow
  • The characterization of subsurface microbiomes in zones of serpentinization in the Sultanate of Oman—part of the NASA Astrobiology Institute Rock Powered Life Team
  • The geobiology of silicification and stromatolite building in the world’s best example of living stromatolites in Yellowstone National Park, Wyoming
  • The microbiome of fire recovery after catastrophic wildland fire
  • The characterization of microbes associated with sulfur and ice at Borup Fiord Pass Glacier, Ellesmere Island, Nunavut, Canada
  • Subsurface microbiology in mines including the local Edgar Mine (hotlink to: ), the Golden Sun Mine and the Henderson Molybdenum Mine

Selected Publications

  • ASM Colloquium Report: Microbes & Climate Change—Science, People & Impacts, April, 2022. J.R. Spear, co-author. American Academy of Microbiology & American Society for Microbiology, Washington, D.C.,-People,-Impacts
  • Lau, G.E., C.B. Trivedi, S.E. Grasby, J.R. Spear, J. Cosmidis and A.S. Templeton. 2022. “Sulfur- and Iron-Rich Mineralogical Features Preserved in Permafrost in the Canadian High Arctic: Analogs for the Astrobiological Exploration of Mars.” Frontiers in Astronomy and Space Sciences. doi: 10.3389/fspas.2022.825019.
  • Medina-Ferrer, F., M.R. Rosen, J. Feyhl-Buska, V.V. Russell, F. Sønderholm, S. Loyd, R. Shapiro, B.W. Stamps, V. Petryshyn, C. Demirel-Floyd, J.V. Bailey, H.A. Johnson, J.R. Spear and F.A. Corsetti.  2021.  “From the Cover: Potential Role for Microbial Ureolysis in the Rapid Formation of Carbonate Tufa Mounds.” Geobiology, 20: 79 – 97; doi: 10.1111/gbi.12467.
  • Thieringer, P.H., A.S. Honeyman and J.R. Spear.  2021.  “Spatial and Temporal Constraints on the Composition of Microbial Communities in Subsurface Boreholes of the Edgar Experimental Mine.” Microbiol. Spectr., 9(3): e00631-21. doi: 10.1128/Spectrum.00631-21.
  • Templeton, A.S., E.T. Ellison, C. Glombitza, Y. Morono, K.R. Rempfert, T.M. Hoehler, S.D. Ziegler, E.A. Kraus, J.R. Spear, D.B. Nothaft, E.M. Fones, E.S. Boyd, R.M. Munro-Ehrlich, L.E. Mayhew, D. Cardace, J.M. Matter, P.B. Kelemen and the Oman Drilling Project Science Party. 2021. “Accessing the Subsurface Biosphere within Rocks Undergoing Active Low-temperature Serpentinization in the Samail Ophiolite, (Oman Drilling Project).” Journal of Geophysical Research: Biogeosciences. doi: 10.1029/2021JG006315.
  • Battalora, L., C. Armon, F. Palella, J. Li, E.T. Overton, J. Hammer, J. Fuhrer, R.M. Novak, J.R. Spear, K. Buchacz, for the HIV Outpatient Study (HOPS) Investigators.  2021.  “Incident Bone Fracture and Mortality in a Large HIV Cohort Outpatient Study, 2000 – 2017, USA.” Archives of Osteoporosis, 16: 117; doi.10.1007/s11657-021-00949-y.
  • Murphy, C.L., A. Sheremet, P.F. Dunfield, J.R. Spear, R. Stepanauskas, T. Woyke, M.S. Elshahed and N.H. Youssef.  2021.  “Genomic Analysis of the Yet-Uncultured Binatota Reveals Broad Methylotrophic, Alkane-Degradation, and Pigment Production Capacities.” mBio, 12: e00985-21; doi.10.1128/mBio.00985-21.
  • Petryshyn, V.A., E.N. Junkins, B.W. Stamps, J.V. Bailey, B.S. Stevenson, J.R. Spear and F.A. Corsetti.  2021.  “Builders, Tenants and Squatters: The Origins of Genetic Material in Modern Stromatolites.”  Geobiology, 19: 261 – 277; doi: 10.1111/gbi.12429.
  • Fones, E.M., D.R. Colman, E.A. Kraus, R. Stepanauskas, A.S. Templeton, J.R. Spear and E.S. Boyd. 2021. “Diversification of Methanogens into Hyperalkaline Serpentinizing Environments Through Adaptations to Minimize Oxidant Limitation.” ISME Journal. doi: 10.1038/s41396-020-00838-1.
  • Kraus, E.A., D. Nothaft, B.W. Stamps, K.R. Remphert, E.T. Ellison, J.M. Matter, A.S. Templeton, E.S. Boyd and J.R. Spear.  2021.  “Molecular Evidence for an Active Microbial Methane Cycle in Subsurface Serpentinite-hosted Groundwaters in the Samail Ophiolite, Oman.” Applied and Environmental Microbiology, 87(2): 1 – 18, e02068-20, doi: 10.1128/AEM.02068-20.

Complete Publication List

Awards and Honors

  • Faculty of the Year for CEE from the Senior Class, 2006, 2007, 2012, 2013, 2019
  • Colorado School of Mines, Martin Luther King Award for Diversity and Inclusion, 2010
  • Postdoctoral Fellow, The Agouron Institute, 2003 – 2005
  • NSF Microbial Biology Postdoctoral Fellow, 2001 – 2003
  • Eagle Scout, Boy Scouts of America