Click on the following links to see the full list and additional publication information on Google Scholar or ResearchGate

2026

Howells, A., Santana, M., Cook, E., Orrill, B., Boyer, G., Debes II, R., Fecteau, K., Colman, D., Boyd, E. and Shock, E. 2026. Pushing the Upper Temperature Limit of Methanotrophy in Continental Hydrothermal Ecosystems, Active Biological Methane Oxidation in Hot Springs of Yellowstone National Park. Frontiers in Microbiology, 17, p.1736896.

Lai, D., Mosier, D., Palmer, M., Mayali, X., Johnston, J., Saldivar, W., Covington, J.K., Jiao, J.Y., Murali, R., Seymour, C.O. and Liu, L., Hua, Z., Li, W-J., Weber, P., Pett-Ridge, J., Colman, D., Boyd, E., Nunoura, T., Dodsworth, J., Hedlund, B. 2026. Branched-chain amino acid specialization drove diversification within Calditenuaceae (Caldarchaeia) and enables their cultivation. Nature Communications, Published Online 02/26.

Calhoun, A., Blewett, J., Colman, D., Amenabar, M., Harris, C., Boyd, E., Pearson, A. and Leavitt, W. 2026. Environmental controls on crenarchaeol distributions in hydrothermal springs. Environmental Microbiology, 28(2), p.e70248.

Keller, L., Colman, D., Stefánsson, A. and Boyd, E., 2026. Cross‐Feeding of Carbon and Nitrogen Between Aquificales and Thermus in Hot Springs. Environmental Microbiology, 28(1), p.e70225.

2025

Boyd, E., Colman, D., Menchaca, A., Spietz, R., Shoemaker, A., Finn, C., Mencin, D., Andrade-Barahona, E., Cox, A., Kieft, T. and Bilek, S., 2025. Seismic shifts in the geochemical and microbial composition of a Yellowstone aquifer. PNAS nexus, 4(11), p.pgaf344.

Colman, D., Templeton, A., Spear, J., and Boyd, E. (2025). Microbial Ecology Serpentinite-Hosted Ecosystems. Invited Review for The International Society for Microbial Ecology Journal, 9 (1), wraf029.

Keller, L., Colman, D., and Boyd, E. (2025). Simultaneous aerobic and anaerobic respiration in hot spring chemolithotrophic bacteria. Nature Communications, 16 (1), no. 1063.  

2024

Colman, D.R., Keller, L.M., Arteaga-Pozo, E., Andrade-Barahona, E.., St. Clair, B., Shoemaker, A., Cox, A., & Boyd, E.S. (2024). Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution. Nature Communications, 15 (1), no. 7506.

Fernandes-Martins, M. C., Springer, C., Colman, D. R., & Boyd, E. S. (2024). Acquisition of elemental sulfur by sulfur-oxidizing Sulfolobales. Environmental Microbiology, 26(9), no. e16691.

Payne, D., Keller, L.M., Larson, J., Bothner, B., Colman, D. R., & Boyd, E. S. (2024). Alternative sources of molybdenum for Methanococcus maripaludis and their implication for the evolution of molybdoenzymes. Communications Biology, 7(1), no. 1337.

Fernandes-Martins, M. C., Colman, D. R., & Boyd, E. S. (2024). Sulfide oxidation by members of the Sulfolobales. PNAS Nexus, 3(6), no. pgae201.

Massiot, C., Adam, L., Boyd, E.S., Cary, S.C., Colman, D.R., Cox, A., Hughes, E., Kilgour, G., Lelli, M., Liotta, D. & Lloyd, K.G. (2024). CALDERA: a scientific drilling concept to unravel Connections Among Life, geo-Dynamics and Eruptions in a Rifting Arc caldera, Okataina Volcanic Centre, Aotearoa New Zealand. Scientific Drilling, 33(1), 67-88. 

Templeton, A., Ellison, E., Leong, J., Colman, D.R., Boyd, E.S., Kelemen, P.B. & Matter, J.M. (2024). Low-temperature hydrogen production and consumption in partially-hydrated peridotites in Oman: implications for stimulated geological hydrogen production. Frontiers in Geochemistry, 2, no. 1366268.

Shoemaker, A., Maritan, A., Cosar, S., Nupp, S., Menchaca, A., Jackson, T., Dang, A., Baxter, B.K., Colman, D.R., Dunham, E.C. & Boyd, E.S. (2024). Wood–Ljungdahl pathway encoding anaerobes facilitate low-cost primary production in hypersaline sediments at Great Salt Lake, Utah. FEMS Microbiology Ecology, 100(8), no. fiae105.

Boyd, E.S., Colman, D.R. & Templeton, A.S. (2024). Perspective: Microbial hydrogen metabolism in rock-hosted ecosystems. Frontiers in Energy Research, 12, no. 1340410.

Power, J.F., Carere, C.R., Welford, H.E., Hudson, D.T., Lee, K.C., Moreau, J.W., Ettema, T.J., Reysenbach, A.L., Lee, C.K., Colman, D.R., Boyd, E.S., Morgan, X.C., McDonald, I.R., Cary, S.C. and Stott. M.B. (2024). A genus in the bacterial phylum Aquificota appears to be endemic to Aotearoa-New Zealand. Nature Communications, 15(1), no. 179.

2023

Sims, K. W., Messa, C. M., Scott, S. R., Parsekian, A. D., Miller, A., Role, A. L., Moloney, T.P., Shock, E.L., Lowenstern, J.B., McCleskey R.B., Charette, M.A., Carr, B.J., Pasquet, S., Heasler, H., Jaworowoski Ch., Holbrook, W.S., Lindsay, M.R., Colman, D.R. & Boyd, E. S. (2023). The dynamic influence of subsurface geological processes on the assembly and diversification of thermophilic microbial communities in continental hydrothermal systems. Geochimica et Cosmochimica Acta, 362, 77-103.

Colman, D.R., A. Veach, A. Stefánsson, L. Wurch, B.S. Belisle, P.T. Podar, Z. Yang, D. Klingeman, K. Senba, K. Murakami, J. Kristjánsson, S.H. Björnsdóttir, E.S. Boyd & M. Podar. 2023. Tectonic and geological setting influence hot spring microbiology. Environmental Microbiology, 25 (11), 2481-2497.  

Coe, G.L., Krout I.N., Munro-Ehrlich M., Beamish C.R., Vorojeikina D., Colman, D.R., Boyd, E.S., Walk, S.T., & M.R. Rand. (2023). Assessing the role of the gut microbiome in methylmercury demethylation and elimination in humans and gnotobiotic mice. Archives of Toxicology. 97 (9), 2399-2418. 

Upin, H., D.R. Newell, D.R. Colman & E.S. Boyd. (2023) Tectonic settings influence the geochemical and microbial diversity of Peru hot springs. Communications Earth and Environment. 4 (1), no. 112.

Blum, L.N., D.R. Colman, E.A. Eloe-Fadrosh, M. Kellom, E.S. Boyd, O. Zhaxybayeva & W.D. Leavitt. (2023). Distribution and abundance of tetraether lipid cyclization genes in terrestrial hot springs reflect pH. Environmental Microbiology 25(9), 1644-1658.

Keller, L., D.R. Colman & E.S. Boyd. (2023). An active microbiome in Old Faithful Geyser. Proceedings of the National Academy of Sciences Nexus. 2 (3), no. pgad066.

Fernandes-Martins, M.C., D.R. Colman & E.S. Boyd. (2023). Relationships between fluid mixing, biodiversity, and chemosynthetic primary productivity in Yellowstone hot springs. Environmental Microbiology. 25 (5), 1022-1040.

2022

Colman, D.R., Kraus, E.A., Thieringer, P.H., Rempfert, K., Templeton, A.S., Spear, J.R. & Boyd, E.S. (2022). Deep-branching acetogens in serpentinized subsurface fluids of Oman. Proceedings of the National Academy of Sciences, 119(42), no. e2206845119.

Boyd, E. S., Spietz, R.L., Kour, M. & Colman, D.R. (2022). Crystal Ball: A Naturalist perspective of microbiology: Examples from methanogenic Archaea. Environmental Microbiology, 25 (1). 

McCleskey, R.B., Nordstrom, D.K., Hurwitz, S., Colman, D.R., Roth, D.A., Johnson, M. & Boyd, E.S. (2022). The source, fate, and transport of arsenic in the Yellowstone hydrothermal system-an overview. Journal of Volcanology and Geothermal Research, 432, no. 107709.

Colman, D.R., Amenabar, M.J., Fernandes-Martins, M.C. & Boyd, E.S. (2022). Subsurface Archaea associated with rapid geobiological change in a model Yellowstone hot spring. Communications Earth & Environment, 3(1), 1-12. 

Buessecker, S., Palmer, M., Lai, D., Dimapilis, J., Mayali, X., Mosier, D., Jiao, J.Y., Colman, D.R., Keller, L.M., St John, E., Miranda, M., Gonzalez, C., Gonzalez, C., Sam, C., Villa, C., Zhuo, M., Bodman, N., Robles, F., Boyd, E.S., Cox, A.D., St. Clair, B., Hua, Z., Li, W., Reysenbach, A.L., Stott, M.B., Weber, P.K., Pett-Ridge, J., Dekas, A.E., Hedlund, B.P., & Dodsworth, J.A. 2022. An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea. Nature Communications, 13 (1), 1-13.

Colman, D.R., Labesse, G., Swapna G.V.T., Stefanakis J., Montelione, G.T., Boyd, E.S., & Royer, C.A. (2022) Structural evolution of the ancient enzyme, dissimilatory sulfite reductase. Proteins: Structure, Function, and Bioinformatics. 90 (6), 1331-1345.

Jiang, X., Van Horn, D.J., Okie, J.G., Buelow, H.N., Schwartz, E., Colman, D.R., Feeser, K. & Takacs-Vesbach, C.D. (2022) Limits to the three domains of life: Lessons from an Antarctic salinity gradient. Extremophiles. 26 (1), 1-14.

2021

Fernandes-Martins, M.C., Keller, L.M., Munro-Ehrlich, M., Zimlich, K.R., Mettler, M.K., England, A.M., Clare, R., Surya, K., Shock, E.L., Colman, D.R. & Boyd, E.S. (2021). Ecological dichotomies arise in microbial communities due to mixing of deep hydrothermal waters and atmospheric gas in a circumneutral hot spring. Applied and Environmental Microbiology, 87 (23), e01598-21.

Fones, E.M., Colman, D.R., Kraus, E.A., Stepanauskas, R., Templeton, A.S., Spear, J.R. & Boyd, E.S. (2021). Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation. The International Society for Microbial Ecology Journal, 15 (4), 1121-1135.

Johnson, C., England, A., Munro-Ehrlich, M., Colman, D.R., DuBois, J.L. & Boyd, E.S., 2021. Pathways of iron and sulfur acquisition, cofactor assembly, destination, and storage in diverse archaeal methanogens, methanotrophs, and alkanotrophs. Journal of Bacteriology, 203 (117), no. 00117-21. 

Ando, N., Barquera, B., Bartlett, D.H., Boyd, E., Burnim, A.A., Byer, A.S., Colman, D., Gillilan, R.E., Gruebele, M., Makhatadze, G. & Royer, C.A., 2021. The molecular basis for life in extreme environments. Annual Review of Biophysics, 50 (1), 343-372.

Colman, D.R., Lindsay, M.R., Harnish, A., Bilbrey, E.M., Amenabar, M.J.,, Selensky, M.J., Fecteau, K.M.,,  Debes, R.V., Stott, M., Shock, E.L. & Boyd, E.S. (2021). Seasonal hydrologic and geologic forcing of hot spring geochemistry and biodiversity. Environmental Microbiology, 23 (7), 4034-4053.

2020

Murray, A.E., J. Freudenstein, S. Gribaldo, R. Hatzenpichler, P. Hugenholtz, P. Kämpfer, K.T. Konstantinidis, C.E. Lane, R.T. Papke, D.H Parks, R. Rossello-Mora, M.B Stott, I.C. Sutcliffe, J.C. Thrash, S.N Venter, W.B Whitman, S.G Acinas, R.I. Amann, K. Anantharaman, J. Armengaud, B.J. Baker, R. Barco, H.B. Bode, E.S. Boyd, C.L Brady, P. Carini, P.S.G. Chain, D.R. Colman, K.M DeAngelis, M. Asuncion de los Rios, P. Estrada de los Santos, C.A. Dunlap, J.A Eisen, D. Emerson, T.J.G. Ettema, D. Eveillard, P.R Girguis, U. Hentschel, J.T Hollibaugh, L.A. Hug, W.P. Inskeep, E.P. Ivanova, H.-P. Klenk, W.-J. Li, K.G. Lloyd, F.E. Löffler, T. Makhalanyane, D.P. Moser, T. Nunoura, M. Palmer, V. Parro, C. Pedrós-Alió, A.J. Probst, T.H.M. Smits, A.D. Steen, E.T. Steenkamp, A. Spang, F.J Stewart, J.M Tiedje, P. Vandamme, M. Wagner, F.-P. Wang, B.P. Hedlund, & A.-L. Reysenbach. 2020. Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 5 (8), 987-994.  

Merino, N., Kawai, M., Boyd, E.S., Colman, D.R., McGlynn, S., Nealson, K., Kurokawa, K. & Hongo, Y. (2020) Single-cell genomic characterization of an uncultivated actinobacterial acetogen from a serpentinite-hosted hot spring. Frontiers in Microbiology, 11, no. 1031.  

Kanik, M., Munro-Ehrlich, M., Fernandes-Martins, M.C., Payne, D., Gianoulias, K., Keller, L., Kubacki, A., Lindsay, M., Baxter, B., Vanden Berg, M., Colman, D.R. & Boyd, E.S. (2020) Unexpected abundance and diversity of phototrophs in mats from morphologically diverse microbialites in Great Salt Lake, Utah. Applied and Environmental Microbiology, 86 (10), no. e00165-20.  

Colman, D.R., Lindsay, M.R., Amenabar, M.J., Fernandes-Martins, M.C., Roden, E. & Boyd, E.S. (2020). Phylogenomic analysis of novel Diaforarchaea is consistent with sulfite but not sulfate reduction in volcanic environments on early Earth. The International Society for Microbial Ecology Journal. 14 (5), 1316-1331.

2019

Dunham, E.C., Fones, E.M., Fang, Y., Lindsay, M.R., Steur, C., Fox, N., Willis, M., Walsh, A., Colman, D.R., Baxter, B.K., Lageson, D., Mogk, D., Rupke, A., Xu, H. & Boyd, E.S. An ecological perspective on dolomite formation in Great Salt Lake, Utah. Frontiers in Earth Science, 8, no. 24. 

Colman, D.R., Lindsay, M.R., Amenabar, M.J. & Boyd, E.S. The intersection of geology, geochemistry, and microbiology in continental hydrothermal systems. Astrobiology, 19 (12): 1505-1522.

Payne, D., Dunham, E.C., Mohr, E., Miller, I., Arnold, A., Erickson, R., Fones, E.M., Lindsay M.R., Colman, D.R. & Boyd, E.S. (2019). Geologic legacy spanning >90 years explains unique Yellowstone hot spring geochemistry and biodiversity, Environmental Microbiology, 21 (11): 4180-4195. 

Lindsay, M.R., Colman, D.R., Amenabar, M.J., Fristad, K.E., Fecteau, K.M., Debes, R.V., Spear, J.R., Shock, E.L., Hoehler, T. & Boyd, E.S. (2019). Subsurface source and biological fate of hydrogen in Yellowstone hot springs. Environmental Microbiology, 21 (10), 3816-3830.

Fones, E.M., Colman, D.R., Kraus, E.A., Nothaft, D.B., Poudel, S., Rempfert, K.R., Fox, N.R., Spear, J.R., Templeton, A.S. & Boyd, E.S. (2019) Physiological adaptations to serpentinization in the Samail Ophiolite, Oman. The International Society for Microbial Ecology Journal, 13 (7), 1750-1762.

Mus, F., Colman, D.R., Peters, J.W. & Boyd, E.S. (2019) Geobiological feedbacks, oxygen, and the evolution of nitrogenase. Free Radical Biology and Medicine 140, 250-259.

Colman, D.R., Lindsay, M.R. & Boyd, E.S. (2019) Mixing of end-member fluids supports hyperdiverse chemosynthetic hydrothermal communities. Nature Communications, 10 (1), no. 681.

2018

Colman, D.R., Poudel, S., Hamilton, T.L., Havig, J.R., Selensky, M.J., Shock, E.L. & Boyd, E.S. (2018) Geobiological feedbacks and the evolution of thermoacidophiles. The International Society for Microbial Ecology Journal. 12 (1), 225-236.

Feeser, K.L., Van Horn, D.J., Buelow, H.N., Colman, D.R., McHugh, T., Okie, J.G., Schwartz, E. & Takacs-Vesbach, C.D.  (2018). Local and regional scale heterogeneity drive bacterial community diversity and composition in a polar desert. Frontiers in Microbiology, 9, no. 1928.

Poudel, S., Dunham, E.C., Lindsay, M.L, Amenabar, M.A., Fones, E.M., Colman, D.R. & Boyd, E.S. (2018) Origin and evolution of flavin-based electron bifurcating enzymes. Frontiers in Microbiology, 9, no. 1762.

Amenabar, M.J., Colman, D.R., Poudel, S., Roden, E.E. & Boyd, E.S. (2018) Electron acceptor availability alters carbon and energy metabolism in a thermoacidophile. Environmental Microbiology, 7, 2523-2537.

Ziegler, M., Stone, E., Colman, D., Takacs-Vesbach C. & Shepherd, U. (2018) Patterns of Symbiodinium (Dinophyceae) diversity and assemblages among diverse hosts and the coral reef environment of Lizard Island, Australia. The Journal of Phycology, 54 (4), 447-460. 

Poudel, S., Colman, D.R., Fixen, K.R., Ledbetter, R.N., Zheng, Y., Pence, N., Seefeldt, L.C., Peters, J.W., Harwood, C.S. & Boyd, E.S. (2018) Electron transfer to nitrogenase in different genomic and metabolic backgrounds. Journal of Bacteriology. 200 (10), no. e00757-17.  

Berry, L., Poudel, S., Tokmina-Lukaszewska, M., Colman D.R., Schut, G.J., Adams, M.W.W., Peters, J.W., Boyd, E.S. & Bothner, B. (2018) H/D exchange mass spectrometry and statistical coupling analysis reveal a role for allostery in a ferredoxin-dependent bifurcating transhydrogenase catalytic cycle. Biochimica et Biophysica Acta, 1862 (1), 9-17.

Artz, J.H., Mulder, D.W., Poudel, S., Colman, D.R, Schut, G.J., Williams, S.G., Jones, A.K., Adams, M.W., Boyd, E.S., King, P.W. & Peters, J.W. (2018). Structure-function of [FeFe]-and [NiFe]-Hydrogenases: an overview of diversity, mechanism, maturation, and bifurcation. Microalgal Hydrogen Production, 31-66.

2017

Colman, D.R., Poudel, S., Stamps, B.W., Boyd, E.S. & Spear, J.R. (2017) The deep hot biosphere: Twenty-five years of retrospection. Proceedings of the National Academy of Sciences, U.S.A. 114 (27), 6895-6903.

Colman, D.R., 2017. The cooccurrence of Archaea and Bacteria among diverse globally distributed ecosystems. In Biocommunication of Archaea (pp. 17-26). Springer, Cham.

2016

Colman, D.R., Feyhl-Buska, J., Robinson, K.J., Fecteau K.M., Xu, H., Shock, E.L. & Boyd, E.S. (2016) Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs. FEMS Microbiology Ecology, 92 (9), no. fiw137.

Colman, D.R., Ferrera, I., Takacs-Vesbach, C.D. & Reysenbach, A.L. (2016) Archaeal ecology in Encyclopedia of Life Sciences. John Wiley & Sons Ltd, Chichester. 

Colman, D.R., Jay, Z.J., Inskeep, W.P., deM. Jennings, R., Maas, K., Rusch, D.B. & Takacs-Vesbach, C.D. (2016) Characterization of novel, deep-branching heterotrophic bacterial populations recovered from thermal spring metagenomes. Frontiers in Microbiology 7, no. 304.

Poudel, S., Tokmina-Lukaszewska M., Colman D.R, Refai M., Schut, G., King, P., Maness, P., Adams, M., Peters, J., Bothner, B., & Boyd E. (2016) Unification of [FeFe]-hydrogenases into three structural and functional groups. Biochimica et Biophysica Acta.1860 (9), 1910–1921. 

Van Horn, D., Wolf, C., Colman, D.R., Jiang, X., Kohler, T., Mcknight, D., Stanish, L., Yazzie, T. & Takacs-Vesbach, C.D. (2016) Patterns of bacterial biodiversity in the glacial meltwater streams of the McMurdo Dry Valleys, Antarctica. FEMS Microbiology Ecology. 92 (10), fiw148.

Crossey, L.J., Karlstrom, K.E., Schmandt, B., Crow, R.R., Colman, D.R., Cron, B., Takacs-Vesbach, C.D., Dahm, C.N., Northup, D.E., Hilton, D.R., Rickets, J., & Lowry, A.R. (2016) Continental smokers couple mantle degassing and unique microbiology within continents. Earth and Planetary Science Letters Frontiers, 435, 22-30.

2015

Saw, J.H., Spang, A.J., Zaremba-Niedzwiedzka, K., Juzokaite, L., Dodsworth, J.A., Murugapiran, S.K., Colman, D.R., Takacs-Vesbach, C.D., Hedlund, B.P., Guy, L. & Ettema, T.J.G. (2015) Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes. Philosophical Transactions of the Royal Society, Biology 370 (1678), no. 20140328.

Colman, D.R., Thomas, R., Maas, K.R. & Takacs-Vesbach, C.D. (2015) Detection and analysis of elusive members of a novel and diverse archaeal community within a thermal spring streamer consortium. Extremophiles, 19, 307-313.

2014-2012

Colman, D.R., Garcia, J.R., Crossey, L.J., Karlstrom, K., Jackson-Weaver, O. & Takacs-Vesbach, C.D. (2014) An analysis of geothermal and carbonic springs in the western United States sustained by deep fluid inputs. Geobiology, 12, 83-98.

Colman, D.R., Toolson, E.C. & Takacs-Vesbach, C.D. (2012) Do diet and taxonomy influence insect gut bacterial communities? Molecular Ecology, 21, 5124-5137.

Kirk, M.F., Martini, A.M., Breecker, D.O., Colman, D.R., Takacs-Vesbach, C., & Petsch S.T. (2012) Impact of commercial natural gas production on geochemistry and microbiology in a shale-gas reservoir. Chemical Geology. 332, 15-25.

FitzPatrick, S.K., Liberatore, K.L., Garcia, J.R., Burghardt, I., Colman, D.R., Moquin, S.A., Takacs-Vesbach, C.D. & Shepherd, U.L. (2012) Symbiodinium diversity in the soft coral Heteroxenia sp. and its nudibranch predator Phyllodesmium lizardensis. Coral Reefs, 31, 895-905.