@article{miller_purugganan_curtis_2006, title={Molecular population genetics and phenotypic diversification of two populations of the thermophilic cyanobacterium Mastigocladus laminosus}, volume={72}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.72.4.2793-2800.2006}, abstractNote={We investigated the distributions of genetic and phenotypic variation for two Yellowstone National Park populations of the heterocyst-forming cyanobacterium Mastigocladus (Fischerella) laminosus that exhibit dramatic phenotypic differences as a result of environmental differences in nitrogen availability. One population develops heterocysts and fixes nitrogen in situ in response to a deficiency of combined nitrogen in its environment, whereas the other population does neither due to the availability of a preferred nitrogen source. Slowly evolving molecular markers, including the 16S rRNA gene and the downstream internal transcribed spacer, are identical among all laboratory isolates from both populations but belie considerable genetic and phenotypic diversity. The total nucleotide diversity at six nitrogen metabolism loci was roughly three times greater than that observed for the human global population. The two populations are genetically differentiated, although variation in performance on different nitrogen sources among genotypes could not be explained by local adaptation to available nitrogen in the respective environments. Population genetic models suggest that local adaptation is mutation limited but also that the populations are expected to continue to diverge due to low migratory gene flow.}, number={4}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Miller, SR and Purugganan, MD and Curtis, SE}, year={2006}, month={Apr}, pages={2793–2800} }
 @article{miller_2003, title={Evidence for the adaptive evolution of the carbon fixation gene rbcL during diversification in temperature tolerance of a clade of hot spring cyanobacteria}, volume={12}, ISSN={["0962-1083"]}, DOI={10.1046/j.1365-294X.2003.01831.x}, abstractNote={Determining the molecular basis of enzyme adaptation is central to understanding the evolution of environmental tolerance but is complicated by the fact that not all amino acid differences between ecologically divergent taxa are adaptive. Analysing patterns of nucleotide sequence evolution can potentially guide the investigation of protein adaptation by identifying candidate codon sites on which diversifying selection has been operating. Here, I test whether there is evidence for molecular adaptation of the carbon fixation gene rbcL for a clade of hot spring cyanobacteria in the genus Synechococcus that has diverged in thermotolerance. Amino acid replacements during Synechococcus radiation have resulted in an increase in the number of hydrophobic residues in the RbcLs of more thermotolerant strains. A similar increase in hydrophobicity has been observed for many thermostable proteins. Maximum likelihood models which allow for heterogeneity among codon sites in the ratio of nonsynonymous to synonymous nucleotide substitutions estimated a class of amino acid sites as a target of positive selection. Depending on the model, a single amino acid site that interacts with a flexible element involved in the opening and closing of the active site was estimated with either low or moderate support to be a member of this class. Site-directed mutagenesis approaches are being explored in order to directly test its adaptive significance.}, number={5}, journal={MOLECULAR ECOLOGY}, author={Miller, SR}, year={2003}, month={May}, pages={1237–1246} }
 @article{dillon_miller_castenholz_2003, title={UV-acclimation responses in natural populations of cyanobacteria (Calothrix sp.)}, volume={5}, ISSN={["1462-2912"]}, DOI={10.1046/j.1462-2920.2003.00435.x}, abstractNote={Phenotypic acclimation to changing conditions is typically thought to be beneficial to organisms in the environment. UV radiation is an important parameter affecting photosynthetic organisms in natural environments. We measured the response of photosynthetic carbon fixation in populations of cyanobacteria inhabiting a hot spring following acclimation to different UV treatments. These two very closely related populations of cyanobacteria, differing in their content of the extracellular UV-screening pigment scytonemin, were acclimated in situ under natural solar irradiance modified by filters that excluded both UVA/B, only UVB or transmitted both UVA/B. Cells from each preacclimation treatment were subsequently assayed for photosynthetic performance under all UV conditions (incubation treatment) giving a two-factor experimental design for each population. No acclimation filter treatment effects were observed even after two months under different acclimation treatments. This suggests that UV photoacclimation does not occur in either of these populations, regardless of the presence of scytonemin. By contrast, cells showed significant UV-inhibition during 1 h incubations under full sun. The population with high levels of scytonemin usually had lower rates of photosynthetic carbon fixation than the scytonemin-lacking population. However, the degree of UV inhibition, especially UVA inhibition, was higher for the cells without scytonemin pigment. These results suggest that closely related natural cyanobacterial populations respond differently to natural irradiance conditions and may be adopting different strategies of UV tolerance.}, number={6}, journal={ENVIRONMENTAL MICROBIOLOGY}, author={Dillon, JG and Miller, SR and Castenholz, RW}, year={2003}, month={Jun}, pages={473–483} }
 @article{miller_martin_touchton_castenholz_2002, title={Effects of nitrogen availability on pigmentation and carbon assimilation in the cyanobacterium Synechococcus sp strain SH-94-5}, volume={177}, ISSN={["1432-072X"]}, DOI={10.1007/s00203-002-0404-8}, number={5}, journal={ARCHIVES OF MICROBIOLOGY}, author={Miller, SR and Martin, M and Touchton, J and Castenholz, RW}, year={2002}, month={May}, pages={392–400} }
 @article{bebout_carpenter_des marais_discipulo_embaye_garcia-pichel_hoehler_hogan_jahnke_keller_et al._2002, title={Long-term manipulations of intact microbial mat communities in a greenhouse collaboratory: Simulating Earth's present and past field environments}, volume={2}, ISSN={["1531-1074"]}, DOI={10.1089/153110702762470491}, abstractNote={Photosynthetic microbial mat communities were obtained from marine hypersaline saltern ponds, maintained in a greenhouse facility, and examined for the effects of salinity variations. Because these microbial mats are considered to be useful analogs of ancient marine communities, they offer insights about evolutionary events during the >3 billion year time interval wherein mats co-evolved with Earth's lithosphere and atmosphere. Although photosynthetic mats can be highly dynamic and exhibit extremely high activity, the mats in the present study have been maintained for >1 year with relatively minor changes. The major groups of microorganisms, as assayed using microscopic, genetic, and biomarker methodologies, are essentially the same as those in the original field samples. Field and greenhouse mats were similar with respect to rates of exchange of oxygen and dissolved inorganic carbon across the mat-water interface, both during the day and at night. Field and greenhouse mats exhibited similar rates of efflux of methane and hydrogen. Manipulations of salinity in the water overlying the mats produced changes in the community that strongly resemble those observed in the field. A collaboratory testbed and an array of automated features are being developed to support remote scientific experimentation with the assistance of intelligent software agents. This facility will permit teams of investigators the opportunity to explore ancient environmental conditions that are rare or absent today but that might have influenced the early evolution of these photosynthetic ecosystems.}, number={4}, journal={ASTROBIOLOGY}, author={Bebout, BM and Carpenter, SP and Des Marais, DJ and Discipulo, M and Embaye, T and Garcia-Pichel, F and Hoehler, TM and Hogan, M and Jahnke, LL and Keller, RM and et al.}, year={2002}, pages={383–402} }