John R. Spear

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)


  • 2014 – Present: Professor
  • 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 498 / 560 – Microbiology of Engineered Environmental Systems
  • CEEN 595 – Introduction to NEPA, The National Environmental Policy Act (a policy class)
  • CEEN 573 – Reclamation of Disturbed Lands (a policy class)
  • HNRS 445 – McBride Honors Program, The Evolution Revolution
  • HNRS 450 – McBride Honors Program, Science, Technology and Ethics: Unnatural Disasters
  • CEEN 302 – Environmental Engineering

Selected Publications

  • Oetjen, K., K.E. Chan, K. Gulmark, J.H. Christensen, J. Blotevogel, T. Borch, J.R. Spear, T.Y.Cath and C.P Higgins.  2018. “Temporal Characterization and Statistical Analysis of Flowback and Produced Waters and Their Potential for Reuse.”  Science of the Total Environment, 619-620: 654-664; doi: 10.1016/j.scitotenv.2017.11.078.
  • Bradley, J.A., L.K. Daille, C.B. Trivedi, C.L. Bojanowski, B.W. Stamps, B.S. Stevenson, H.S. Nunn, H.A. Johnson, S.J. Loyd, W.M. Berelson, F.A. Corsetti and J.R. Spear.  2017.  “Carbonate-Rich Dendrolitic Cones: Insights into a Modern Analogue for Incipient Microbialite Formation, Little Hot Creek, Long Valley Caldera, California.”  npj Biofilms and Microbiomes, 3(32): doi: 10.1038/s41522-017-0041-2.
  • Colman, D.R., S. Poudel, B.W. Stamps, E.S. Boyd and J.R. Spear.  2017.  “The Deep Hot Biosphere: Twenty-Five Years of Retrospection.”  Proceedings of the National Academy of Sciences, 114(27): 6895-6903; doi: 10.1073/pnas.1701266114.
  • Maloy, S., M. Moran, M.R. Mulholland, H.M. Sosik and J.R. Spear.  2017.  “FAQ:  Microbes and Climate Change.”  American Academy of Microbiology.
  • Freedman, D.E., S.M. Riley, Z.L. Jones, J.S. Rosenblum, J.O. Sharp, J.R. Spear and T.Y. Cath.  2017.  “Biologically Active Filtration for Fracturing Flowback and Produced Water Treatment.” Journal of Water Process Engineering, 18(2017): 29-40; doi: 10.1016/jwpe.2017.05.008.
  • Frank, V.B., J. Regnery, K.E. Chan, D.F. Ramey, J.R. Spear and T.Y. Cath.  2017.  “Co-treatment of Residential and Oil and Gas Production Wastewater with a Hybrid Sequencing Batch Reactor-Membrane Bioreactor Process.” Journal of Water Process Engineering, 17(2017): 82-94.
  • Lau, G.E., J. Cosmidis, S.E. Grasby, C.B. Trivedi, J.R. Spear and A.S. Templeton.  2017.  “Low-temperature Formation and Stabilization of Rare Allotropes of Cyclooctasulfur (β-S8 and γ-S8) in the Presence of Organic Carbon at a Sulfur-rich Glacial Site in the Canadian High Arctic.”  Geochimica et Cosmochimica Acta, 200: 218-231; doi: 10.1016/j.gca.2016.11.036.
  • Lindsay, M.R., C. Anderson, N. Fox, G. Scofield, J. Allen, E. Anderson, L. Bueter, S. Poudel, K. Sutherland, J.H. Munson-McGee, J.D. Van Nostrand, J. Zhou, J.R. Spear, B.K. Baxter, D.R. Lageson and E.S. Boyd.  2017.  “From the Cover: Microbialite Response to an Anthropogenic Salinity Gradient in Great Salt Lake, Utah.”  Geobiology, 15(1): 131 – 145; doi: 10.1111/gbi.12201.
  • Stoll, Z.A., Z. Ma, C.B. Trivedi, J.R. Spear and P. Xu.  2016.  “Sacrificing Power for More Cost-Effective Treatment: A Techno-Economic Approach for Engineering Microbial Fuel Cells.”  Chemosphere, 161: 10-18.
  • Shelton, J.L., D.M. Akob, J.C. McIntosh, N. Fierer, J.R. Spear, P.D. Warwick and J.E. McCray.  2016.  “Environmental Drivers of Differences in Microbial Community Structure in Crude Oil Reservoirs Across a Methanogenic Gradient.”  Frontiers in Microbiology, 7: 1 – 12 #1535; doi: 10.3389/fmicb.2016.01535.
  • Kenwell, A., A. Navarre-Sitchler, R. Prugue, J.R. Spear, R.M. Maxwell, A.S. Hering, R.W.H. Carroll and K.H. Williams.  2016.  “Using Geochemical Indicators to Distinguish High Biogeochemical Activity in Floodplain Soils and Sediments.”  Science of the Total Environment, 563: 386-395; doi: 10.1016/j.scitotenv.2016.04.014.
  • Stanish, L.F., N.M. Hull, C.E. Robertson, J.K. Harris, M.J. Stevens, J.R. Spear and N.R. Pace.  2016.  “Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA.”  PLoS ONE, 11(6): e0157966.
  • Vollmer, N.L., J.R. Spear and R.A. Ayers.  2016.  “Antimicrobial Activity and Biologic Potential of Silver-Substituted Calcium Phosphate Constructs Produced with Self-Propogating High-Temperature Synthesis.”  Journal of Materials Science: Materials in Medicine, 27: 1-12, #104; doi: 10.1007/s10856-016-5715-4.
  • Battalora, L., K. Buchacz, C. Armon, E.T. Overton, J. Hammer, P. Patel, J.S. Chmiel, K. Wood, T.J. Bush, J.R. Spear, J.T. Brooks and B. Young for the HIV Outpatient Study (HOPS) and SUN Study Investigators.  2015.  “Low Bone Mineral Density and Risk of Incident Fracture in HIV-infected Adults.”  Antiviral Therapy, 21(1): 45-54, doi: 10.3851/IMP2979.
  • Vuono, D.C., J. Munakata-Marr, J.R. Spear and J.E. Drewes.  2016.  “Disturbance Opens Recruitment Sites for Bacterial Colonization in Activated Sludge.”  Environmental Microbiology, 18(1): 87 – 99; (doi: 10/1111/1462-2920.12824).
  • Carr, S.A., B.N. Orcutt, K.W. Mandernack and J.R. Spear.  2015.  “Abundant Atribacteria in Deep Marine Sediment from the Adélie Basin, Antarctica.”  Frontiers in Microbiology, 6: #877, doi: 10.3389?fmicb.2015.00872.
  • Williamson, C.H.D., L.A. Jain, B. Mishra, D.L. Olson and J.R. Spear.  2015.  “Microbiologically Influenced Corrosion Communities Associated with Fuel-grade Ethanol Environments.”  Applied Microbiology and Biotechnology, 99(16): 6945-6957, doi: 10.1007/s00253-015-6729-4, pgs. 1 – 13.
  • Lynch, K.L., B.H. Horgan, J. Munakata-Marr, J. Hanley, R.J. Schneider, K.A. Rey, J.R. Spear, W.A. Jackson and S.M. Ritter.  2015.  “Near-Infrared Spectroscopy of Lacustrine Sediments in the Great Salt Lake Desert: An Analog Study for Martian Paleolake Basins.”   JGR Planets, 120(3): 599-623, doi:  10.1002/2014JE004707.
  • Vuono, D.C., J. Benecke, J. Henkel, W.C. Navidi, T.Y. Cath, J. Munakata-Marr, J.R. Spear and J.E. Drewes.  2014.  “Disturbance and Temporal Partitioning of the Activated Sludge Metacommunity.”  ISME Journal, 9(2): 425-235, (doi: 10.1038/ismej.2014.139).
  • Lee, J.Z., A. Logan, S. Terry and J.R. Spear.  2015.  “Microbial Response to Single Cell Protein Production and Brewery Wastewater Treatment.”  Microbial Biotechnology, 8(1): 65-76, (doi: 10.1111/1751-7915.12128).
  • Stamps, B.W., F.A. Corsetti, J.R. Spear, and B.S. Stevenson.  2014.  “Draft Genome of a Novel Chlorobi Assembled by Tetranucleotide Binning of a Hot Spring Metagenome.”  Genome Announcements, September / October 2014 2: e-00897-14; doi: 10.1128/genomeA.00897-14.
  • Bhola, S.M., F.M. Al-Abbas, J.R. Spear, and B. Mishra.  2014.  “Neem Extract as an Inhibitor for Biocorrosion Influenced by Sulfate Reducing Bacteria: A Preliminary Investigation.”  Engineering Failure Analysis, 36: 92 – 103.
  • Sowards, J.W., C.H.D. Williamson, T.S. Weeks, J.D. McColskey, and J.R. Spear.  2014.  “The Effect of Acetobacter sp. and a Sulfate-Reducing Bacterial Consortium from Ethanol Fuel Environments on Fatigue Crack Propagation in Pipeline and Storage Tank Steels.”  Corrosion Science, 79: 128-138.
  • Ricci, J.N., M.L. Coleman, P.V. Welander, A.L. Sessions, R.E. Summons, J.R. Spear and D.K. Newman.  2014.  “Diverse Capacity for 2-methylhopanoid Production Correlates with a Specific Ecological Niche.”  ISME Journal, 8(3): 675-684, (doi: 1751-7362/13).
  • Al-Abbas, F.M., C. Williamson, S.M. Bhola, J.R. Spear, D.L. Olson, B. Mishra and A. Kakpovbia.  2013.  “Microbial Corrosion in Linepipe Steel under the Influence of Sulfate Reducing Consortium Isolated from an Oil Field.”  J. Materials Eng. and Performance, 22(11): 3517-3529, (doi 10.1007/s11665-013-0627-7).
  • Al-Abbas, F.M., S.M. Bhola, J.R. Spear, D.L. Olson and B. Mishra.  2013.  “The Shielding Effect of Wild-Type Iron Reducing Bacterial Flora on the Corrosion of Linepipe Steel.”  Engineering Failure Analysis, 33: 222-235.
  • Carr, S.A., S.W. Vogel, R.B. Dunbar, J. Brandes, J.R. Spear, R. Levy, T.R. Naish, R.D. Powell, S.G. Wakeham and K.W. Mandernack.  2013.  “ Bacterial Abundance and Composition in Marine Sediments Beneath the Ross Ice Shelf, Antarctica.”  Geobiology, 11(4): 377-395, (doi: 10.1111/gbi.12042). 
  • 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.