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Kathleen  Scott

Kathleen Scott

Kathleen Scott
Associate Professor


Office: BSF 132
Phone: 813-974-5173
Lab: BSF 122, BSF 124
Fax: 974-3263


Personal Bio



Ph.D. Biology, Penn State at University Park, 1998.
Post Doctoral Fellow, Harvard University.


Microbial physiology and biogeochemistry

Autotrophic microorganisms from all three domains of life (Bacteria, Archaea, and Eukarya) proliferate under a dizzying array of conditions. These organisms fix carbon dioxide while growing in more familiar habitats like lakes and oceans, but also thrive in extreme environments such as terrestrial hot springs, deep-sea hydrothermal vents and hydrocarbon seeps, acid rock drainage, and the subsurface biosphere.
Added to this breadth in habitats is a breadth in history. The three domains of life are believed to have originated rather early in Earth history, by 2.7 billion years ago. Since that time, the atmospheric concentration of carbon dioxide has fallen by nearly three orders of magnitude, while atmospheric oxygen, which inhibits some carbon fixing enzymes, has risen from nil to its current level of 21% by volume.

My major research question is, how have these organisms adapted to these changes? How do they fix carbon despite low concentrations of carbon dioxide, and elevated concentrations of oxygen? Have organisms within Bacteria and Archaea devised many different mechanisms for coping with these conditions, or did a few efficient methods (e.g., carbon concentrating mechanisms, carbonic anhydrases) originate fairly early on and are currently used by phylogenetically broad groups of organisms?
Given that many key autotrophic organisms are uncultivable, it is necessary for me to use a rather broad arsenal of methods to study them, including molecular tools and mass spectrometry. Elucidating the answers to the questions I raise above promises to have a substantial effect on our understanding of geochemical cycles and autotroph physiology, as well as their response to anthropogenic increases in atmospheric carbon dioxide.

Specialty Area


Microbial Physiology and Biogeochemistry

Current Courses

RefCourseSecCourse TitleCRDayTimeLocation
88129BSC 4910038Undergraduate Research

TBA 100
87617BSC 6910030Directed Research

83309BSC 7910027Directed Research

87111BSC 7980033Dissertation: Doctoral


Recent Journal Articles


Honors and Award






Recent Publications


Mangiapia M., Scott K.M. (2016) From CO2 to cell: Energetic expense of creating biomass using the Calvin-Benson-Bassham and reductive citric acid cycles based on genome data. FEMS Microbiology Letters 363: Doi: 10.1093/femsle/fnw054.

Menning K. J., Menon B. B., Fox, G., USF MCB4404L 2012, and Scott K.M. (2016) Dissolved inorganic carbon uptake in Thiomicrospira crunogena XCL-2 is delta-p- and ATP-sensitive and enhances RubisCO-mediated carbon fixation. Arch. Microbiol. 198: 149-159.

Diaz-Torres N., Mahon B., Boone C., Pinard M., Tu C., Ng R., Agbandje-McKenna M., Silverman D., Scott K, McKenna R. (2015) Structural and Biophysical Characterization of the alpha-Carbonic Anhydrase from Thiomicrospira crunogena XCL-2 Gammaproteobacterium: Insights into Engineering Thermostable Enzymes for CO2 Sequestration. Acta Crystallographica D71: 1745-1756.

Mahon B. P., Diaz-Torrez, N. A., Pinard M. A., Tu C., Silverman D. N., Scott K. M., McKenna R. (2015). Activity and anion inhibition studies of the & #945;-carbonic anhydrase from Thiomicrospira crunogena XCL-2 gammaproteobacterium. Bioinorganic & Medical Chemistry Letters 25: 4937-4040.

Boller A. J., Thomas P. J., Cavanaugh C. M., Scott K. M. (2015). Isotopic discrimination and kinetic parameters of RubisCO from the marine bloom-forming diatom Skeletonema costatum. Geobiology 13: 33-43.

Dobrinski K. P., Enkemann, S. A., Yoder, S. J., Haller E., and Scott K.M. (2012). Transcription response of the sulfur chemolithoautotroph Thiomicrospira crunogena to dissolved inorganic carbon limitation. Journal of Bacteriology 194: 2074-2081.

Scott K. M., Dobrinski K., Boller A., Le Bris N. (2011). Response of hydrothermal vent vestimentiferan Riftia pachyptila to differences in habitat chemistry. Marine Biology 159:435-442.

Hendrix W., Rocha A. M., Padmanabhan K., Choudhary A., Scott K., Mihelcic J. R. and Nagiza F Samatova (2011). DENSE: Efficient and Prior Knowledge-driven Discovery of Phenotype-associated Protein Functional Modules. BMC Systems Biology 5:172.

Boller A. J., Thomas P. J., Cavanaugh C. M., Scott K. M. (2011). Low stable carbon isotope fractionation by coccolithophore RubisCO. Geochimica et Cosmochimica Acta 75: 7200-7207.

Kerfeld C. and Scott K. M. (2011). Using BLAST to teach 'E-value-tionary' concepts. PLoS Biol. 9(2): e1001014.

Scott K. M., Fox G., and Girguis P. R. (2011). Measuring isotope fractionation by autotrophic microorganisms and enzymes. In “Methods in Methane Metabolism”, Methods in Enzymology, 494:281-99. (ed. S. Ragsdale). Elsevier Inc., Cambridge.

Schmidt, M. C., A.M. Rocha, K. Padmanabhan, Z. Chen, K. Scott, J. R. Mihelcic, and N. F. Samatova (2011). Efficient a, ß- motif Finder for Identification of Phenotype-related Functional Modules. BMC Bioinformatics 12:440.

Ditty, J. L., Kvaal, C. A., Axen, S., Kim, E., Kerfeld, C. A., Bailey, C., Britton, R. A., Goodner, B. W., Freyermuth, S. K., Gordon, S. G., Heinhorst, S., Johns, M. A., Reed, K., Sanders-Lorenz, E. R., Scott, K., Xu, Z. (2010). Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum. PLoS Biol 8(8): e1000448. doi:10.1371/journal.pbio.1000448

Dobrinski K., Boller A., and Scott K. M. (2010). Expression and function of four carbonic anhydrase homologs in deep-sea hydrothermal vent chemolithoautotroph Thiomicrospira crunogena.Applied and Environmental Microbiology 76: 3561-3567.

Scott K. M., Sievert S. M., Klotz M. G., Chain P. S. G., Hauser L. J., Hemp J., Hügler M., Land M., Lapidus A., Larimer F. W., Lucas S., Malfatti S. A., Meyer F., Paulsen I. T., Ren Q., Simon J., and the USF Genomics class (2008). Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans. Applied and Environmental Microbiology 74: 1145-1156.

Scott, K.M., Henn-Sax, M., Longo, D., and Cavanaugh, C.M. (2007) Kinetic isotope effect of RubisCO from marine picophytoplankton. Limnology and Oceanography 52: 2199-2204.

Scott, K.M. and Cavanaugh, C.M. (2007) CO2 uptake and fixation by endosymbiotic chemoautotrophs from the bivalve Solemya velum. Applied and Environmental Microbiology 73: 1174-1179.

Scott K.M., Sievert SM, Abril FN, Ball LA, Barrett CJ, Blake RA, Boller AJ, Chain PS, Clark JA, Davis CR, Detter C, Do KF, Dobrinski KP, Faza BI, Fitzpatrick KA, Freyermuth SK, Harmer TL, Hauser LJ, Hugler M, Kerfeld CA, Kong WW, Land M, Lapidus A, Larimer FW, Longo DL, Lucas S, Malfatti S, Massey SE, Martin DD, McCuddin Z, Meyer F, Moore JL, Ocampo LH, Paul JH, Paulsen IT, Reep DK, Ren Q, Ross RL, Sato PY, Thomas P, Tinkham LE, Zeruth GT (2006) The genome of the deep-sea vent chemolithoautotroph Thiomicrospira crunogena. Plos Biol 4: 1-17.

Dobrinski, K., Longo, D., and Scott, K.M. (2005) A hydrothermal vent chemolithoautotroph with a carbon concentrating mechanism. J. Bact. 187: 5741-5766.

Scott, K.M. (2005) Allometry of gill masses, gill surface areas, and foot biomass d13C values of the chemoautotroph-bivalve symbiosis Solemya velum. Mar. Biol. 147: 935-941.

Scott, K.M., Schwedock, J., Schrag, D. P., and Cavanaugh, C.M. (2004) Kinetic isotope effect of RubisCO from the chemoautotrophic symbionts of Solemya velum. Environ. Microbiol. 6: 1210-1219.

Schwedock, J., Harmer, T.L., Scott, K.M., Hektor, H.J. Seitz, A.P., Fontana, M.C., Distel, D.L., and Cavanaugh, C.M. (2004) Characterization and expression of genes from the RubisCO gene cluster of the chemoautotrophic symbiont of Solemya velum: cbbLSQO. Arch. Microbiol. 182: 18-29.

Scott, K.M., Lu, X., Cavanaugh, C.M., and Liu, J. (2004) Optimal methods for estimating kinetic isotope effects from different forms of the Rayleigh distillation equation. Geochim. Cosmochim. Acta 68: 433-442.

Scott, K.M. (2003) A d13C-based carbon flux model for the hydrothermal vent chemoautotrophic symbiosis Riftia pachyptila predicts sizeable CO2 gradients at the host-symbiont interface. Environ. Microbiol. 5: 424-432.

Robinson, J.J., Scott, K.M., Swanson, S.T., O'Leary, M.H., Horken, K., Tabita, F.R., and Cavanaugh, C.M. (2003) Kinetic isotope effect and characterization of form II RubisCO from the chemoautotrophic endosymbionts of the hydrothermal vent tubeworm Riftia pachyptila. Limnology and Oceanography 48: 48-54.

Smith, E., Scott, K.M., Nix, E., Korte, C., and Fisher, C. (2000) Growth and condition of seep mussels (Bathymodiolus childressi) at a Gulf of Mexico brine pool. Ecology 81: 2392-2403.

Scott, K.M., Bright, M., Macko, S.A., and Fisher, C.R. (1999) Carbon dioxide use with different affinities by chemoautotrophic endosymbionts of the hydrothermal vent vestimeniferans Riftia pachyptila and Ridgeia piscesae. Marine Biology 135: 25-34.

Scott, K.M., and Fisher, C.R. (1998) The burden of independence: Inorganic carbon utilization strategies of the sulfur chemoautotrophic hydrothermal vent isolate Thiomicrospira crunogena and the symbionts of hydrothermal vent and cold seep vestimentiferans. Cahiers de Biologie Marine 39: 379-381.

Nix, E., Fisher, C., Vodenichar, J., and Scott, K. (1995) Physiological ecology of a mussel with methanotrophic endosymbionts at three hydrocarbon seep sites in the Gulf of Mexico. Marine Biology 122: 605-617.

Scott, K., and Fisher, C. (1995) Physiological ecology of sulfide metabolism in hydrothermal vent and cold seep vesicomyid clams and vestimentiferan tube worms. American Zoologist 35: 102-111.

MacDonald, I., Guinasso, N., Sassen, R., Brooks, J., Lee, L., and Scott, K.M. (1994) Gas hydrate that breaches the sea floor on the continental slope of the Gulf of Mexico. Geology 22: 699-702.

Scott, K.M., Fisher, C.R., Vodenichar, J.S., Nix, E., and Minnich, E. (1994) Inorganic carbon and temperature requirements for autotrophic carbon fixation by the chemoautotrophic symbionts of the giant hydrothermal vent tube worm, Riftia pachyptila. Physiological Zoology 67: 617-638.