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Scott Miller, Associate Professor


Phone: (406) 243-5149

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)



BIOM 135N:  Biology of Yellowstone Hot Springs