Papers in Peer Reviewed Journals, In-Press or Submitted:
Note: PDF reprints are provided below within the context of fair use.
Please obtain copies from the publisher if appropriate.
For a complete listing of Spear Lab publications, please see PubMed.
(32) Sahl, J.W., M.O. Gary, J.K. Harris and J.R. Spear. 2009. "A Comparative Molecular Analysis of Phreatic Limestone Sinkholes in Northeastern Mexico." Submitted to Environmental Microbiology.
(31) Harris, J.K., J.W. Sahl and J.R. Spear. 2009. “Comparison of normalization methods for construction of large multiplex amplicon pools.” Submitted to Applied and Environmental Microbiology.
(30) Sahl, J.W., N. Fairfield, J.K. Harris, D. Wettergreen, W.C. Stone, and J.R. Spear. 2009. “Novel Microbial Diversity Retrieved from an Autonomous Robotic Exploration of the World’s Deepest Phreatic Sinkhole.” Submitted to Astrobiology.
(29) 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: Potential Role in Mineral Biosignature Formation.” Accepted to Astrobiology.
(28) 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.” Accepted to Environmental Microbiology.
(27) 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. (PDF)
(26) 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. (PDF)
(25) 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. (PDF)
(24) 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. (PDF)
(23) 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. (PDF)
(22) 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. (PDF)
(21) 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. (PDF)
(20) Siegrist, R.L., K.S. Lowe, J.E. McCray, J. Munakata-Marr, J.E. Drewes, J.R. Spear, and J.E. Tomaras. 2007. “Advancing the Science and Engineering and Integration of On-Site Wastewater Systems,” in Innovation and technology for On-Site Systems: Proceedings of On-Site ‘07 Conference, R.A. Patterson and M.J. Jones, Eds. Lanfax Laboratories, Armidale, Australia. p. 27 - 34. (PDF)
(19) Spear, J.R., H.A. Barton, C.E. Robertson, C.A. Francis, and N.R. Pace. 2007. "Microbial Community Biofabrics in a Geothermal Mine Adit." Applied and Environmental Microbiology, 73(19): 6172-6180. (PDF)
(18) Lee, J.Z., D.M. Klaus, P-C. Maness and J.R. Spear. 2007. "The effect of butyrate concentration on hydrogen production via photofermentation for use in a Martian habitat resource recovery process." International Journal of Hydrogen Energy, 32: 3301 - 3307. (PDF)
(17) Ley, R.E., J.K. Harris, J. Wilcox, J.R. Spear, S.R. Miller, B.M. Bebout, J.A. Maresca, D.A. Bryant and N.R. Pace. 2006. “From the Cover: Unexpected Diversity and Complexity from the Guerrero Negro Hypersaline Microbial Mat.” Applied and Environmental Microbiology, 72(5): 3685 - 3695. (PDF)
(16) Spear, J.R., J.J. Walker, and N.R. Pace. 2006. “Microbial Ecology and Energetics in Yellowstone Hotsprings.” Yellowstone Science, Winter 2006, 14(1): 17 - 24. (PDF)
(15) Baumgartner, L.K., R.P. Reid, C. Dupraz, A.W. Decho, D.H. Buckley, J.R. Spear, K.M. Przekop, and P.T. Visscher. 2006. “Sulfate Reducing Bacteria in Microbial Mats: Changing Paradigms, New Discoveries.” Sedimentary Geology, 185: 131 - 145. (PDF)
(14) Robertson, C.E., J.K. Harris, J.R. Spear, and N.R. Pace. 2005. “Phylogenetic
diversity and ecology of environmental Archaea.” Current Opinion in
Microbiology, 8: 638-642. link (PDF)
(13) 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. link (PDF)
(12) 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. link (PDF)
(11) Spear, J.R. 2004. “Minimum Impact Research.” Conservation Biology, 18(4): 861. (PDF)
(10) Elshahed, M.S., J.M. Senko, F.Z. Najar, S.M. Kenton, B.A. Roe, T.A. Dewers, J.R. Spear, and L.R. Krumholz. 2003. “Bacterial Diversity and Sulfur Cycling in a Mesophilic Sulfide-Rich Spring.” Applied and Environmental Microbiology, 69(9): 5609-5621. link (PDF)
(9) Spear, J.R., R.E. Ley, A. Berger and N.R. Pace. 2003. “Complexity in Natural Microbial Ecosystems: The Guerrero Negro Experience. “ Biological Bulletin, 204: 168-173. link (PDF)
(8) Spear, J.R., J.J. Walker, S.M. Barns and N.R. Pace. 2002. “A Search for Life in Yellowstone’s Well Y-7: Portal to the Subsurface.” Yellowstone Science, 10(4): p. 15-21. (PDF)
(7) Spear, J.R. and N.R. Pace. 2001. “Molecular Survey of Microbial Diversity in Hypersaline Ecosystems. “ Abstract in Astrobiology, 1(3): 341-342.
(6) Barton, H.A., J.R. Spear, and N.R. Pace. 2001. “Microbial Life in the Underworld: Biogenicity in Secondary Mineral Formations.” Geomicrobiology Journal, 18: 1-10. ( PDF)
(5) Spear, J.R. 2000. “Conservation Medicine: The Changing View of Biodiversity.” Conservation Biology, 14(6): 1913-1917. ( PDF)
(4) Spear, J.R., L.A. Figueroa, and B.D. Honeyman. 2000. “Modeling Reduction of U(VI) Under Variable Sulfate Concentrations by Sulfate-Reducing Bacteria.” Applied and Environmental Microbiology. 66 (9): 3711-3721. link (PDF)
(3) Spear, J.R., L.A. Figueroa, and B.D. Honeyman. 1999. “Modeling the Removal of Uranium (U(VI)) from Aqueous Solutions in the Presence of Sulfate Reducing Bacteria.” Environmental Science and Technology, 33: 2667-2675. (PDF)
(2) Harnish, R., T. McKibben, J. Spear, S. Winkler, and B. Honeyman. 1999. “Actinide Migration Studies at the Rocky Flats Environmental Technology Site: The Effect of Soil-Water Redox Potential on 239,240Pu Solubility.” RFETS Contract #KH800022MW Report.
(1) Minden P., R.A. Houghten, J.R. Spear, and T.M. Shinnick. 1986. “A Chemically Synthesized Peptide Which Elicits Humoral and Cellular Immune Responses to Mycobacterial Antigens.” Infection and Immunity, 54(9): 560-564. link
Book Chapters
(5) Thermal Biology Institute, Montana State University, 2006. “Performing environmentally Sensitive Field Research in Yellowstone National Park: A Guide for Research Scientists.” Brochure for Distribution. (pdf)
(4) Spear, J.R. 2005. “What is Minimum Impact Research?,” in Geothermal Biology and Geochemistry in Yellowstone National Park, W. P. Inskeep and T. R. McDermott, eds. Thermal Biology Institute, Montana State University. Pgs. 343 - 352. (PDF)
(3) Spear, J.R., J.J. Walker and N.R. Pace. 2005. “Hydrogen and Primary Productivity: Inference of Biogeochemistry from Phylogeny in a Geothermal Ecosystem,” in Geothermal Biology and Geochemistry in Yellowstone National Park, W. P. Inskeep and T. R. McDermott eds. Thermal Biology Institute, Montana State University. Pgs. 113 - 128. ( PDF)
(2) Spear, J.R., and N.R. Pace. 2004. “Diversity of Life at the Geothermal Subsurface-Surface Interface: The Yellowstone Example”, in The Subseafloor Biosphere at Mid-Ocean Ridges, W.S.D. Wilcock, E.F. DeLong, D.S. Kelley, J.A. Baross and S.C. Cary, eds. American Geophysical Union Press, Geophysical Monograph Series, v. 144: 343-354. (PDF)
(1) Minden P., R.A. Houghten, J.R. Spear, and T.M. Shinnick. 1986. “A Chemically Synthesized Peptide That has Mycobacterial Antigenic Properties,” in Vaccines ‘86: New Approaches to Immunization. Cold Spring Harbor Laboratory.
Photographic Publications
(9) Spear, J.R. October, 2008. Cover Photo, Guerrero Negro Endoevaporite Crust. Applied and Environmental Microbiology, 74(20).
(8) Spear, J.R. May, 2007. Cover Photo, Guerrero Negro Hypersaline Microbial Mat. Applied and Environmental Microbiology, 73(9).
(7) Spear, J.R., 2007, Cenoté Zacatón, Mexico. Science Magazine, 315(5810): p. 323.
(6) Spear, J.R., 2006, Obsidian Pool Microbial Mat. Yellowstone Science, Table of Contents.
(5) Spear, J.R. 2003. Intertidal Microbial Mat. Marine Biological Laboratory, 2002 Annual Report, p. 30.
(4) Spear, J.R. 2003. Crystalline Gypsum Crust. Marine Biological Laboratory, 2002 Annual Report, p. 30.
(3) Spear, J.R. 2003. Cover Photo-Intertidal Microbial Mat. April. 2003. Biological Bulletin, 204: Cover.
(2) Spear, J.R. 2001. Cover Photo-Winogradsky Column. Systematic Biology, August 2001, 50(4): Cover.
(1) Spear, J.R. 2001. Cover Photo-Winogradsky Column, Department of Molecular, Cellular and Developmental Biology, Graduate Studies Brochure.
