Research Interests

Understanding the origins, maintenance and distribution of biological diversity is a central goal of evolutionary biology. How do organisms adapt to novel environments? Does adaptation come with evolutionary costs? What is the functional significance of adaptive variation? In the Miller lab, we take an integrative approach to address these fundamental questions, with a focus on cyanobacteria, an ancient and widespread group of photosynthetic bacteria. Current projects investigate: (1) the genetic and physiological mechanisms of temperature adaptation in a group of hot spring cyanobacteria that include the most thermotolerant phototrophs on Earth; (2) the genetic basis of local adaptation of the thermophilic cyanobacterium Fischerella thermalis; (3) the consequences of gene duplication for the diversification of a novel genus of cyanobacteria (Acaryochloris) with a photosynthetic apparatus based on Chlorophyll d, a far-red light absorbing structural relative of the ubiquitous Chlorophyll a; and (4) the evolution and function of a cyanobacterial endosymbiont of diatoms that is in the process of becoming a nitrogen-fixing organelle. 

Selected Publications

N. J. Ulrich, H. Uchida, Y. Kanesaki, E. Hirose, A. Murakami, and S.R. Miller. 2021. Reacquisition of light-harvesting genes in a marine cyanobacterium confers a broader solar niche. Curr. Biol. DOI:https://doi.org/10.1016/j.cub.2021.01.047

S. R. Miller, P. R. Hutchins, R. Longley and T. Bauersachs. 2020. Cellular innovation of the cyanobacterial heterocyst by the adaptive loss of plasticity. Curr. Biol. 30:344-350.

Miller, S. R. and D. Carvey. 2019. Ecological divergence with gene flow in a thermophilic cyanobacterium. Microb. Ecol. 78:33-41.

Peipoch, M., S. R. Miller, T. Antão and H. M. Valett. 2019. Niche partitioning of microbial communities in riverine floodplains. Sci. Reports 9:16384.

Gallagher, A. L. and S. R. Miller. 2018. Expression of novel gene content drives adaptation to low iron in the cyanobacterium Acaryochloris. Genome Biol. Evol. 10:1484-1492.

Sano, E. B., C. A. Wall, P. R. Hutchins and S. R. Miller. 2018. Ancient balancing selection on heterocyst function in a cosmopolitan cyanobacterium. Nature Ecol. Evol. doi:10.1038/s41559-017-0435-9.

Miller, S. R. 2017. An appraisal of the enzyme stability-activity trade-off. Evolution 71:1876-1887.

Pedersen, D. and S. R. Miller. 2017. Photosynthetic temperature adaptation during niche diversification of the thermophilic cyanobacterium Synechococcus A/B clade. ISME J.11:1053-1057.

Hutchins, P. R. and S. R. Miller. 2017. Genomics of variation in nitrogen fixation activity in a population of the thermophilic cyanobacterium Mastigocladus laminosus. ISME J.11:78-86.

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. (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 laminosus.  Appl. 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 Synechococcus.  Appl. Environ. Microbiol. 66:4222-4229. (ASM News Journal Highlight)