People

Scott Miller

Scott Miller

Associate Professor

Office: HEALTH SCIENCES 302
Email: Scott.Miller@mso.umt.edu

Personal Website

Courses

BIOM 135N:  Biology of Yellowstone Hot Springs

Research Interests

Our research takes an integrative approach to address central questions in microbial evolution and ecology regarding the origins, maintenance and distribution of microbial diversity, with a particular emphasis on the evolution of environmental tolerance in cyanobacteria.  How do microorganisms adapt to novel environments?  Does adaptation come with evolutionary costs?  How do evolutionary processes, environmental variation and geography contribute to the patterns of microbial diversity observed at local, regional and global scales?  Current projects investigate: (1) the genetic basis of temperature adaptation in a group of hot spring cyanobacteria (Synechococcus) living at or near the thermal limit for photosynthetic life; (2) the population genomics of niche differentiation in ecological specialist lineages of the cyanobacterium Mastigocladus laminosus; (3) the roles of competition and character displacement for shaping the realized distributions of photosynthetic bacteria along hot spring thermal gradients; and (4) the molecular evolution of a novel cyanobacterial light harvesting system based on chlorophyll d.


 

Selected Publications

Miller, S. R., M. A. McGuirl and D. Carvey. 2013. The evolution of RuBisCO stability at the thermal limit of photoautotrophy. Mol. Biol. Evol. 30:752-60. (Fast Track publication)

Weltzer, M. L. and S. R. Miller. Ecological divergence of a novel group of Chloroflexus strains along a geothermal gradient. 2013. Appl. Environ. Microbiol.79:1353-1358. (AEM Spotlight)

Weltzer, M. L. and S. R. Miller. 2013. Division-specific differences in community assembly of two alkaline hot spring ecosystems from Yellowstone National Park. Microb. Ecol. 65:537-540.

Klatt, C.G., W. P. Inskeep, M. Herrgard, Z.J. Jay, D.B. Rusch, S.G. Tringe, M.N. Parenteau, D.M. Ward, S.M. Boomer, D.A. Bryant and S.R. Miller. 2013. Community structure and function of high-temperature phototrophic microbial mats inhabiting diverse geothermal environments. Front. Microbiol. doi: 10.3389/fmicb.2013.00106.

Inskeep, W. P. et al. 2013. The YNP metagenome project:  environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem. Front. Microbiol. doi: 10.3389/fmicb.2013.00067.

Ward, D. M., R. W. Castenholz and S. R. Miller. 2012. Cyanobacteria in geothermal habitats. In: The Ecology of Cyanobacteria, 2nd ed.

Miller, S. R., A. M. Wood, R. E. Blankenship, M. Kim and S. Ferriera. 2011. Dynamics of gene duplication in the genomes of chlorophyll d-producing cyanobacteria: Implications for the ecological niche. Genome Biol. Evol. 3:601-613.

Boyd, E. S., A. D. Anbar, S. R Miller, T. L. Hamilton, M. Lavin and J. W. Peters. 2011. A late methanogen origin for molybdenum-dependent nitrogenase. Geobiol. 9:221-232. (Editor’s Choice in Science)

Miller, S. R., A. L. Strong, K. L. Jones and M. C. Ungerer. 2009. Barcoded pyrosequencing reveals shared bacterial community properties along two alkaline hot spring temperature gradients in Yellowstone National Park. Appl. Environ. Microbiol. 75:4565-4572..

Miller, S. R., C. Williams, A. L. Strong and D. Carvey.  2009. Ecological specialization in a spatially structured population of the thermophilic cyanobacterum Mastigocladus laminosus. Appl. Environ. Microbiol. 75:729-734.

Miller, S. R., R. W. Castenholz and D. Pedersen. 2007. Phylogeography of the thermophilic cyanobacterium Mastigocladus laminosusAppl. Environ. Microbiol. 73:4751-4759.

Miller, S. R., M. D. Purugganan and S. E. Curtis. 2006.  Molecular population genetics and phenotypic diversification of two populations of the thermophilic cyanobacterium Mastigocladus laminosus. Appl. Environ. Microbiol. 72:2793-2800.

Ley, R. E., J. K. Harris, J. Wilcox, J. R. Spear, S. R. Miller, B. M. Bebout, J. A. Maresca, D. A. Bryant, M. L. Sogin and N. R. Pace. 2006. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl. Environ. Microbiol. 72:3685-3695.

Miller, S. R., S. Augustine, T. Le Olson, R. E. Blankenship, J. Selker, and A. M. Wood. 2005. Discovery of a free-living, chlorophyll-d producing cyanobacterium with a hybrid proteobacterial/cyanobacterial SSU rRNA gene. Proc. Natl. Acad. Sci. U.S.A. 102:850-855. (Must Read rating by Faculty of 1000)

Miller, S. R. and R. W. Castenholz. 2000.  The evolution of thermotolerance in hot spring cyanobacteria of the genus SynechococcusAppl. Environ. Microbiol. 66:4222-4229. (ASM News Journal Highlight)

 

Publications

Wall, C.A., G. J. Koniges and S. R. Miller. 2014. Divergence with gene flow in a population of thermophilic bacteria: a potential role for spatially varying selection. Mol. Ecol. 23:3371-3383.

Miller, S. R., M. A. McGuirl and D. Carvey. 2013. The evolution of RuBisCO stability at the thermal limit of photoautotrophy. Mol. Biol. Evol. 30:752-60.

M. L. Weltzer and S. R. Miller. 2013. Ecological divergence of a novel group of Chloroflexus strains along a geothermal gradient. Appl. Environ. Microbiol.79:1353-1358.

M. L. Weltzer and S. R. Miller. 2013. Division-specific differences in community assembly of two alkaline hot spring ecosystems from Yellowstone National Park. Microb. Ecol. 65:537-540.

C.G. Klatt, W. P. Inskeep, M. Herrgard, Z.J. Jay, D.B. Rusch, S.G. Tringe, M.N. Parenteau, D.M. Ward, S.M. Boomer, D.A. Bryant and S.R. Miller. 2013. Community structure and function of high-temperature phototrophic microbial mats inhabiting diverse geothermal environments. Front. Microbiol. doi: 10.3389/fmicb.2013.00106.

W. P. Inskeep et al. 2013. The YNP metagenome project:  environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem. Front. Microbiol. doi: 10.3389/fmicb.2013.00067.

T. Bauersachs, S. R. Miller, M.T.J. van der Meer, E.C. Hopmans, S. Schouten, J.S. and Sinninghe Damsté. 2013. Distribution of long chain heterocyst glycolipids in cultures of the thermophilic cyanobacterium Mastigocladus laminosus and a hot spring microbial mat. Organic Geochem.56:19-24.

Ward, D. M., R. W. Castenholz and S. R. Miller. Cyanobacteria in geothermal habitats.  2012. In: The Ecology of Cyanobacteria, 2nd ed. (B. A. Whitton and M. Potts, eds., Kluwer).

Miller, S. R., A. M. Wood, R. E. Blankenship, M. Kim and S. Ferriera. 2011. Dynamics of gene duplication in the genomes of chlorophyll d-producing cyanobacteria: Implications for the ecological niche. Genome Biol. Evol. 3:601-613.

Boyd, E. S., A. D. Anbar, S. R Miller, T. L. Hamilton, M. Lavin and J. W. Peters. 2011. A late methanogen origin for molybdenum-dependent nitrogenase. Geobiol. 9:221-232.

Miller, S. R. and M. Weltzer. 2011. Investigating bacterial diversity along alkaline hot spring thermal gradients by barcoded pyrosequencing. In: Handbook of Molecular Microbial Ecology II:  Metagenomics in Different Habitats (F. J. de Bruijn, ed.,  John Wiley & Sons).

A. Warren et al. 2011. Genotypic and phenotypic variation in P. aeruginosa reveals signatures of secondary infection and mutator activity in certain cf patients with chronic lung infections. Infect. Immun. 79:4802-4818.

Miller, S. R.  2010. Population genetics of cyanobacteria. Pp. 97-107. In: Microbial Population Genetics (J. Xu, ed., Horizon Press).

Miller, S. R., A. L. Strong, K. L. Jones and M. C. Ungerer. 2009. Barcoded pyrosequencing reveals shared bacterial community properties along two alkaline hot spring temperature gradients in Yellowstone National Park. Appl. Environ. Microbiol. 75:4565-4572.

Miller, S. R., C. Williams, A. L. Strong and D. Carvey.  2009. Ecological specialization in a spatially structured population of the thermophilic cyanobacterum Mastigocladus laminosus. Appl. Environ. Microbiol. 75:729-734.

Dillon, J. G., S. R. Miller, B. M. Bebout, M. Huller, N. Pinel and D. A. Stahl. 2009. Spatial and temporal variability in a stratified hypersaline microbial mat community. FEMS Microbiol. Ecol. 68:46-58.

Miller, S. R., R. W. Castenholz and D. Pedersen. 2007. Phylogeography of the thermophilic cyanobacterium Mastigocladus laminosusAppl. Environ. Microbiol. 73:4751-4759.

Miller, S. R. 2007. Diversity of the cosmopolitan thermophile Mastigocladus laminosus at global, regional and local scales. Pp. 401-410, In: Algae and Cyanobacteria in Extreme Environments. (J. Seckbach, ed., Springer Verlag).

Dillon J. G., S. Fishbain, S. R. Miller, B. M. Bebout, K. S. Habicht, S. M. Webb and D. A. Stahl. 2007. High rates of sulfate reduction in a low sulfate hot spring microbial mat driven by a low diversity of sulfate-respiring microorganisms Appl. Environ. Microbiol. 73:5218-5226.

Raghavan, R., S. R. Miller, L. D. Hicks and M. F. Minnick. 2007. The unusual 23S rRNA gene of Coxiella burnetii: Two self-splicing Group I introns flank a 34-bp exon, and one element lacks the canonical WG. J. Bacteriol. 189:6572-6579.

Miller, S. R., M. D. Purugganan and S. E. Curtis. 2006.  Molecular population genetics and phenotypic diversification of two populations of the thermophilic cyanobacterium Mastigocladus laminosus. Appl. Environ. Microbiol. 72:2793-2800.

Ley, R. E., J. K. Harris, J. Wilcox, J. R. Spear, S. R. Miller, B. M. Bebout, J. A. Maresca, D. A. Bryant, M. L. Sogin and N. R. Pace. 2006. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl. Environ. Microbiol. 72:3685-3695.

Miller, S. R., S. Augustine, T. Le Olson, R. E. Blankenship, J. Selker, and A. M. Wood. 2005. Discovery of a free-living, chlorophyll-d producing cyanobacterium with a hybrid proteobacterial/cyanobacterial SSU rRNA gene. Proc. Natl. Acad. Sci. U.S.A. 102:850-855.

Decker, K., C. Potter, B. Bebout, D. Des Marais, S. Carpenter, M. Discipulo, T. Hoehler, S. R. Miller, B. Thamdrup, K. Turk and P. Visscher. 2005. Mathematical simulation of the diel O, S, and C biogeochemistry of a hypersaline microbial mat. FEMS Microbiol. Ecol. 52:377-395.

Miller, S. R. and B. M. Bebout. 2004. Variation in sulfide tolerance of photosystem II in phylogenetically diverse cyanobacteria from sulfidic habitats. Appl. Env. Microbiol. 70:736-744.

Miller, S. R.  2004. Testing for evolutionary correlations in microbiology using phylogenetic generalized least squares.  Pp. 341-354, In: Environmental Microbiology (F. Spencer and A. Ragout de Spencer, eds.), Humana Press, Totowa, N.J..

Miller, S. R.  2003. Evidence for the adaptive evolution of the carbon fixation gene rbcL during diversification in temperature tolerance of a clade of hot spring cyanobacteria.  Mol. Ecol. 12:1237-1246.

Dillon, J., S. R. Miller and R. W. Castenholz.  2003. UV-acclimation responses in natural populations of cyanobacteria (Calothrix sp.). Environ. Microbiol. 5:473-483.

Bebout, B. M., S. P. Carpenter, D. J. Des Marais, M. Discipulo, T. Embaye, F. Garcia-Pichel, T. M. Hoehler, M. Hogan, L. L. Jahnke, R. M. Keller, S. R. Miller, L. E. Prufert-Bebout, C. Raleigh, M. Rothrock and K. Turk. 2002. Long term manipulations of intact microbial mat communities in a greenhouse collaboratory: Simulating Earth’s present and past field environments. Astrobiol.2:383-402.

Miller, S. R., M. Martin, J. Touchton and R. W. Castenholz.  2002.  Effects of nitrogen availability on pigmentation and carbon assimilation in the cyanobacterium Synechococcus sp. strain SH-94-5. Archives Microbiol. 177:392-400.

Wingard, L., S. R. Miller, E. Stenn, J. Selker and A.M. Wood.  2002.  Cyanophycin production in a marine Synechococcus strain of unusual phylogenetic affinity.  Appl. Environ. Microbiol. 68:1772-1777.

Wood, A. M., S. R. Miller, W. Li, R. W. Castenholz.  2002.  Preliminary studies of cyanobacteria, picoplankton, and virioplankton in the Salton Sea with special attention to phylogenetic diversity among eight strains of filamentous cyanobacteria.  Hydrobiologia 473:77-92.

Miller, S. R. and R. W. Castenholz.  2001.  Ecological physiology of Synechococcus sp. strain SH-94-5, a naturally occurring cyanobacterium deficient in nitrate assimilation.  Appl. Environ. Microbiol. 67:3002-3009.

Miller, S. R. and R. W. Castenholz. 2000.  The evolution of thermotolerance in hot spring cyanobacteria of the genus SynechococcusAppl. Environ. Microbiol. 66:4222-4229.

Miller, S. R., C. E. Wingard and R. W. Castenholz.  1998.  Effects of visible light and UV radiation on photosynthesis in a population of a hot spring cyanobacterium, a Synechococcus sp., subjected to high-temperature stress. Appl. Environ. Microbiol. 64:3893-3899.