All Things Microbial Group


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.

(67) Williamson, C.H.D., L. Jain, B. Mishra, D. Olson and J.R. Spear. 2014. "Microbial Communities Associated with Fuel-grade Ethanol Environments: Implications for Microbiologically Influenced Corrosion." Submitted to Fuel.

(66) Eydal, H.S.C., S.A. Carr, L. Øvreås and J.R. Spear. 2014. "In Situ Methanogenesis in Yellowstone National Park Hot Springs." Submitted to PLoS ONE.

(65) Vuono, D.C., J. Munakata-Marr, J.R. Spear and J.E. Drewes. 2014. "Disturbance Opens Recruitment Sites for Bacterial Colonization." Submitted to Environmental Microbiology.

(64) 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. 2014. "Low Bone Mineral Density is Associated with Increased Risk of Incident Fracture in HIV-infected Adults." Submitted to Clinical Infectious Disease.

(63) Lee, J.Z., A. Logan, S. Terry and J.R. Spear. 2014. "Proteins and Proteomics of ProFloc, a Sustainable Feed Produced from Brewery Wastewater Treatment." Submitted to Bioresource Technology.

(62) 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. 2014. "Near-Infrared Spectroscopy of Lacustrine Sediments in the Great Salt Lake Desert: An Analog Study for Martian Paleolake Basins." Submitted to JGR Planets.

(61) Stamps, B.W., J.R. Spear, F.A. Corsetti and B.S. Stevenson. 2014. "Draft Genome of a Novel Chlorobi Assembled by Tetranucleotide Binning of a Hot Spring Metagenome." Accepted to Genome Announcements.

(60) 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, August, 2014. (PDF)

(59) Lee, J.Z., A. Logan, S. Terry and J.R. Spear. 2014. "Microbial Response to Single Cell Protein Production and Brewery Wastewater Treatment" Microbial Biotechnology, doi: 10.1111/1751-7915.12128. (PDF)

(58) 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. (PDF)

(57) 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. (PDF)

(56) 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, doi: 1751-7362/13. (PDF)

(55) 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: doi 10.1007/s11665-013-0627-7. (PDF)

(54) 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. (PDF)

(53) 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, doi: 10.1111/gbi.12042. (PDF)

(52) Inskeep, W.P., Z.J. Jay, M.J. Herrgard, M.A. Kozubal, D.B. Rusch, S.G. Tringe, R.E. Macur, R. deM. Jennings, E.S. Boyd, J.R. Spear and F.F. Roberto. 2013. "Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages Between Metabolic Potential and Geochemistry." Frontiers in Microbiology, 4 #95: doi 10.3389/fmicb.2013.00095. (PDF)

(51) Inskeep, W.P., Z.J. Jay, S.G. Tringe, M.J. Herrgard, D.B. Rusch, J.R. Spear and YNP Metagenome Project Steering Committee and Working Group Members. 2013. "The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem." Frontiers in Microbiology, 4 #67: doi 10.3389/fmicb.2013.00067. (PDF)

(50) Stanish, L.F. and J.R. Spear. 2013. "Diatom Ecology and Microbial Mat Structure and Function in Antarctic Dry Valleys." Palaios, 28: 267-269. (PDF)

(49) Al-Abbas, F.M., C. Williamson, S.M. Bhola, J.R. Spear, D.L. Olson, B. Mishra and A. E. Kakpovbia. 2013. "Influence of Sulfate Reducing Bacterial Biofilm on Corrosion Behavior of Low-Alloy, High- Strength Steel (API-5L X80)." International Biodeterioration & Biodegradation, 78: 34-42. (PDF)

(48) Meuser, J.E., B.K. Baxter, J.R. Spear, J.W. Peters, M.C. Posewitz and E.S. Boyd. 2013. "Contrasting Patterns of Community Assembly in the Stratified Water Column of Great Salt Lake, UT." Microbial Ecology, 66: 268-280. (PDF)

(47) Reyes, K., N.I. Gonzalez, J. Stewart, F. Ospino, D. Nguyen, D. T. Cho, N. Ghahremani, J. R. Spear and H.A. Johnson. 2013. "Surface Orientation Affects the Direction of Cone Growth by Leptolyngbya sp. Strain C1, a Likely Architect of Coniform Structures Octopus Spring (Yellowstone National Park)." Applied and Environmental Microbiology, 79(4): 1302-1308. (PDF)

(46) Wright, K.E., C. Williamson, S.E. Grasby, J.R. Spear and A.S. Templeton. 2013. "Metagenomic Evidence for Sulfur Lithotrophy by Epsilonproteobacteria as the Major Energy Source for Primary Productivity in a Sub-aerial Arctic Glacial Deposit, Borup Fiord Pass." Frontiers in Microbiology, 4 #63: doi 10.3389/fmicb.2013.00063. (PDF)

(45) Al-Abbas, F.M., R. Bhola, J.R. Spear, D.L. Olson and B. Mishra. 2013. "Electrochemical Characterization of Microbiologically Influenced Corrosion on Linepipe Steel Exposed to Facultative Anaerobic Desulfovibrio sp." Int. J. of Electrochemical Science, 8: 859-871. (PDF)

(44) Nelson, A.W., L.M. Feazel, C.E. Robertson, J.R. Spear and D.N. Frank. 2012. "Microbiological Water Quality Monitoring in a Resource-limited Urban Area: A Study in Cameroon, Africa." Accepted to Journal of Public Health, Africa.(PDF)

(43) Harris, J.K., J.G. Caporaso, J.J. Walker, J.R. Spear, N.J. Gold, C.E. Robertson, P. Hugenholtz, J. Goodrich, D. McDonald, D. Knights, P Marshall, H. Tufo, R. Knight and N.R. Pace. 2012. "Phylogenetic Stratigraphy of the Most Diverse Microbial Community Known." ISME Journal, DOI: 10.1038/ismej.2012.79. (PDF)

(42) Gerea, A.L., K.M. Branscum, J.B. King, J. You, D.R. Powell, A.N. Miller, J.R. Spear and R.H. Cichewicz. 2012. "Secondary Metabolites Produced by Fungi Derived From a Microbial Mat encountered in an Iron-Rich Natural Spring." Tetrahedron Letters, 53: 4202-4205. (PDF)

(41) Al-Abbas, F.M., J.R. Spear, A. Kakpovbia, N.M. Balhareth, D.L. Olson and B. Mishra. 2012. "Bacterial Attachment to Metal Substrate and its Effects on Microbiologically-influenced Corrosion in Transporting Hydrocarbon Pipelines." Journal of Pipeline Engineering, 11(1): 63-72. (PDF)

(40) Mata, S.A., C.L. Harwood, F.A. Corsetti, N.J. Stork, K. Eilers, W.M. Berelson and J.R. Spear. 2012. "Influences of Gas Production and Filament Orientation on Stromatolite Microfabric." Palaios, 27: 206-219. (PDF)

(39) Ross, K.A., L.M. Feazel, C.E. Robertson, B.Z. Fathepoure, K.E. Wright, R.M. Turk, M.M. Chan, N.L. Held, J.R. Spear, and N.R. Pace. 2012. "Phototrophic Phylotypes Dominate Microbial Mats of Hotspring Mesothermic Zones in Yellowstone National Park." Microbial Ecology, DOI 10.1007/s00248-012-0012-3. (PDF)

(38) Pepe-Ranney, C., W.M. Berelson, F.A. Corsetti, M. Treants and J.R. Spear. 2012. "Cyanobacterial Construction of Hot Spring Siliceous Stromatolites in Yellowstone National Park." Environmental Microbiology, DOI 10.1111/j.1462-2920.2012.02698.x. (PDF) (Data)

(37) Berelson, W.M., F.A. Corsetti, C. Pepe-Ranney, D.E. Hammond, W. Beaumont and J.R. Spear. 2011. "Hot Spring Siliceous Stromatolites from Yellowstone National Park: Assessing Growth Rate and Laminae Formation." Geobiology, 9: 411-424. (PDF)

(36) Osburn, M.R., A.L.Sessions, C. Pepe-Ranney and J.R. Spear. 2011. "Hydrogen-Isotopic Variability in Fatty Acids from Yellowstone National Park Hot Spring Microbial Communities." Geochimica et Cosmochimica Acta, 75: 4830-4845. (PDF)

(35) Rhodes, M.E., J.R. Spear, A. Oren and C.H House. 2011. "Differences in Lateral Gene Transfer in Hypersaline versesThermal Environments." BMC Evolutionary Biology, 11: 199; (PDF)

(34) Gleeson, D.F., C. Williamson, S.E. Grasby, R.T. Pappalardo, J.R. Spear, A.S. Templeton. 2011. "Low temperature S0 biomineralization at a supraglacial spring system in the Canadian High Arctic." Geobiology, 9: 360-375. (PDF)

(33) Sahl, J.W., M.O. Gary, J.K.Harris and J.R. Spear. 2011. "A Comparative Molecular Analysis of Water-Filled Limestone Sinkholes in Northeastern Mexico." Environmental Microbiology, 13(1): 226-240. (PDF)

(32) Boyd, E.S., T.L. Hamilton, J.R. Spear, M. Lavin and J.W. Peters. 2010. "[Fe-Fe]-hydrogenase in Yellowstone National Park: Evidence for dispersal limitation and phylogenetic niche conservatism." International Society of Microbial Ecology, 4: 1485-1495. (PDF)

(31) Harris, J.K., J.W. Sahl, T.A. Castoe, B.D. Wagner, D.D. Pollock and J.R. Spear. 2010. "Comparison of normalization methods for construction of large multiplex amplicon pools for next-generation sequencing." Applied and Environmental Microbiology, 76(12): 3863-3868. (PDF)

(30) Sahl, J.W., N. Fairfield, J.K. Harris, D. Wettergreen, W.C. Stone, and J.R. Spear. 2010. "Novel Microbial Diversity Retrieved by Autonomous Robotic Exploration of the World's Deepest Vertical Phreatic Sinkhole." Astrobiology, 10(2): 201-213. (PDF)

(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: Insight into Biosignature Formation Through Lithification." Astrobiology, 9(9): 861-874. (PDF)

(28) Baumgartner, L.K., J.R. Spear, D.H. Buckley, N.R. Pace, P. Reid, C. Dupraz and P.T. Visscher. 2009. "Microbial Diversity in Modern Marine Stromatolites, Highborne Cay, Bahamas." Environmental Microbiology, 11(10): 2710-2719. (PDF)

(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.(PDF-missing)

(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

(6) Spear, J.R. and Corsetti, F.A. 2013. The Evolution of Geobiology in the Context of Living Stromatolites, in Bickford, M.E., ed., The Web of Geological Sciences: Advances, Impacts and Interactions. Geological Society of America Special Paper #500. (PDF)

(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. (PDF-missing)

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.

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