Thomas L. Bott Ph.D.
Research Scientist Emeritus
970 Spencer Road
Avondale, PA 19311
610.268.2153 x 224
Adjunct Professor of Biology, Department of Biology, University of Pennsylvania
Microbial ecology of aquatic ecosystems, particularly streams and rivers, with focus on primary productivity and energy flow, microbes in food webs and trophic interactions, nutrient cycling, population dynamics and ecology of introduced bacteria, effects of perturbations on function.
- Previous Positions
- Professional Activities
B.S. Biology, Wheaton College, Wheaton, IL, 1962.
M.S. Bacteriology, University of Wisconsin, Madison, 1965.
Ph.D. Bacteriology/Zoology (Limnology), University of Wisconsin, Madison, 1968.
Vice President, Stroud Water Research Center, 1999-2011.
Senior Research Scientist, Stroud Water Research Center, Academy of Natural Sciences of Philadelphia, 1999-2008.
Curator, Stroud Water Research Center, Academy of Natural Sciences of Philadelphia, 1986-1998.
Associate Curator, Stroud Water Research Center, Academy of Natural Sciences of Philadelphia, 1978-1986.
Assistant Curator, Stroud Water Research Center, Academy of Natural Sciences of Philadelphia, 1969-1977.
Adjunct Associate Professor, Department of Biology, University of Pennsylvania, 1981-1992; Adjunct Assistant Professor, 1972-1981.
Research Fellow, Microbial Ecology; Department of Microbiology, Indiana University, Bloomington, IN, 1968-1969.
Current & Recent Research
Current research efforts address (1) the effect of acid mine drainage (AMD) and AMD remediation efforts on ecosystem metabolism and periphyton communities in Pennsylvania streams, (2) analysis of a 35 years of data concerning ecosystem metabolism in White Clay Creek, PA, and (3) changes in algal communities and coliform densities in Bucks Co., PA streams during the past 40 years.
Research programs have dealt with basic questions related to bacterial and algal productivity, litter decomposition, the microbial food web, i.e., bacteria and algae as food resources for protozoa and meiofauna, and ecosystem metabolism in streams and rivers. Other projects have focused on more applied issues such as the population dynamics of introduced bacteria (including genetically manipulated ones) in stream ecosystems, the effects of pollution on stream ecosystem metabolism, the roles of microorganisms in the transfer of toxic substances to invertebrates, and the effect of watershed management on ecosystem metabolism.
Questions are characteristically studied using a mix of field measurements and laboratory experiments, often conducted in microcosms in which a portion of the natural is reproduced. Currently, measures of ecosystem metabolism in Pennsylvania streams are performed using open system monitoring of diel changes in dissolved oxygen with determination of reaeration from propane evasion.
In other studies, we have performed experiments to parameterize a model of oxygen dynamics in the Jackson River, VA using mesocosms in the under controlled light, nutrient, and velocity conditions. Food web studies and population dynamics studies were performed in microcosms in water jackets in a greenhouse or laboratory. Radioisotopically labeled contaminants were used to radiolabel food sources or environmental compartments for uptake studies, and bacteria were enumerated using DNA-staining fluorochromes or fluorescent antibodies and epifluorescence microscopy.
Bott, T. L. and J. D. Newbold. 2013. Ecosystem metabolism and nutrient uptake in Peruvian headwater streams. International Review of Hydrobiology 98: 117-131.
Bott, T.L., J. K. Jackson, M. E. McTammany, J. D. Newbold, S. T. Rier, B. W. Sweeney and J. M. Battle. 2012. Abandoned coal mine drainage and its remediation: Impacts on stream ecosystem structure and function. Ecological Applications 22: 2144-2163.
Raymond, P. A., C. J. Zappa, D. Butman, T. L. Bott, J. Potter, P. Mulholland, A. E. Laursen, W. H. McDowell and J. D. Newbold. 2012. Scaling the gas transfer velocity and hydraulic geometry in streams and rivers. Limnology and Oceanography, Fluids and Environments 2: 41-53.
Kaplan, L. A., T. L. Bott, J. K. Jackson, J. D. Newbold and B. W. Sweeney. 2008. Protecting Headwaters: The scientific basis for safeguarding stream and river ecosystems. Sierra Club sponsored white paper. 18 pp.
Bott, T. L., J. D. Newbold and D. Arscott. 2006. Ecosystem metabolism in Piedmont streams: Reach geomorphology modulates the influence of riparian vegetation. Ecosystems 9: 398-401. Request PDF.
Bott, T. L. 2006. Primary productivity and community respiration, pp. 263-290. In: F. R. Hauer and G. A. Lamberti, eds. Methods in Stream Ecology, 2nd ed. Elsevier, New York.
Bott, T. L., D. S. Montgomery, D. B. Arscott, J. D. Newbold and C. L. Dow. 2006. Ecosystem metabolism in streams of the Catskill Mountains (Delaware and Hudson River watersheds) and Lower Hudson Valley. Journal of the North American Benthological Society 25:1018-1044. Request PDF.
Bott, T. L., D. S. Montgomery, D. B. Arscott and C. L. Dow. 2006. Primary productivity in receiving reservoirs: links to influent streams. Journal of the North American Benthological Society 25:1045-1061. Request PDF.
Newbold, J. D., T. L. Bott and L. A. Kaplan. 2006. Uptake of nutrients and organic C in streams in the New York City drinking-water-supply watersheds. Journal of the North American Benthological Society 25:998-1017. Request PDF.
Sweeney, B. W., D. B. Arscott, C. L. Dow, J. G. Blaine, A. K. Aufdenkampe, T. L. Bott, J. K. Jackson, L. A. Kaplan and J. D. Newbold. 2006. Enhanced source-water monitoring for New York City: summary and perspective. Journal of the North American Benthological Society 25:1062-1067.
Bately, G. E., R. G. Stahl, Jr., M. P. Babut, T. L. Bott, J. R. Clark, L. J. Field, K. T. Ho, D. R. Mount, R. C. Swartz and A. Tessier. 2005. Scientific Underpinnings of Sediment Quality Guidelines, pp. 39 – 119. In: R. W. Wenning, G. Batley, C. Ingersoll, and D. W. Moore, eds. Use of Sediment Quality Guidelines and related tools for the assessment of contaminated sediments. Society of Environmental Toxicology and Chemistry, Pensacola.
Sweeney, B. W., T. L. Bott, J. K. Jackson, L. A. Kaplan, J. D. Newbold, L. J. Standley, W. C. Hession and R. J. Horwitz. 2004. Riparian deforestation, stream narrowing, and loss of stream ecosystem services. Proceedings of the National Academy of Sciences 101: 14132-14137. Request PDF.
Bott, T. L. and L. A. Kaplan. 2002. Autecological properties of 3-chlorobenzoate-degrading bacteria and their population dynamics when introduced into sediments. Microbial Ecology 43: 199-216.
Zinabu, G. M. and T. L. Bott. 2000. The effect of formalin and Lugol's iodine solution on protozoal cell volume. Limnologica (Berlin) 30: 59-63. Request PDF.
Bott, T. L. and L. J. Standley. 2000. Transfer of benzo[a]pyrene and 2,2',5,5'-tetrachlorobiphenyl from bacteria and algae to sediment associated freshwater invertebrates. Environmental Science and Technology 34: 4936-4942.
Bott, T. L. and M. A. Borchardt. 1999. Grazing of protozoa, bacteria, and diatoms by meiofauna in lotic epibenthic communities. Journal of the North American Benthological Society 28: 499-513.
Bott, T. L. and L. J. Standley. 1999. Incorporation of trifluoroacetate, an atmospheric breakdown product of hydrofluorocarbon refrigerants, by freshwater benthic microbial communities. Water Research 33: 1538-1544.
Standley, L. J. and T. L. Bott. 1998. Trifluoroacetate, an atmospheric breakdown product of hydrofluorocarbon refrigerants: Biomolecular fate in aquatic organisms. Environmental Science and Technology 32:469-475.
Bott, T. L. and L. J. Standley. 1998. Effects of trifluoroacetate, an atmospheric breakdown product of hydrofluorocarbon refrigerants, on acetate metabolism by freshwater benthic microbial communities. Bulletin of Environmental Contamination and Toxicology 60: 472-479.
Newbold, J. D., T. L. Bott, L. A. Kaplan, B. W. Sweeney, and R. L. Vannote. 1997. Organic matter dynamics in White Clay Creek, Pennsylvania, U.S.A, pp. 46 – 50. In: J. R. Webster and J. L. Meyer (eds.). Stream organic matter budgets. Journal of the North American Benthological Society 16: 3-161. Request PDF.
Bott, T. L., J. T. Brock, A. Baattrup-Pedersen, P. Chambers, W. K. Dodds, K. Himbeault, J. R. Lawrence, D. Planas, E. Snyder, and G. M. Wolfaardt. 1997. An evaluation of techniques for measuring periphyton metabolism in chambers. Canadian Journal of Fisheries and Aquatic Sciences 54: 715-725. Request PDF.
Bott, T. L. and J. D. Newbold. 2007. Ecosystem metabolism in White Clay Creek, PA: A 35-year perspective. Annual Meeting, North American Benthological Society, Columbia, SC.
Bott, T. L., D. Montgomery, J.D. Newbold, D.B. Arscott, and C.L. Dow. 2006. Algal biomass and metabolic rates in New York City drinking water reservoirs and tributary streams. Annual Meeting, North American Benthological Society, Anchorage, AK.
Bott, T. “Transcending Boundaries: Challenges for holistic restoration in the Chesapeake Bay watershed”. AAAS Annual meeting, February 2005.
Selected Professional Activities
Appointed to Editorial Board of Applied and Environmental Microbiology, January 2001. Reappointed January 2004, January 2007.
Member, Expedition: Measuring watershed health: training conservation planners how to use biophysical tools for monitoring streams in temperate and neo-tropical ecosystems. Metabolism studies in Peruvian Amazonian headwater streams, 2006.
Invited speaker: AAAS Symposium, “Transcending Boundaries: Challenges for holistic restoration in the Chesapeake Bay watershed”. Annual meeting, February 2005.
Invited participant: SETAC Pellston Conference on Sediment Quality Criteria, August 2002.
Panel Member, Biocomplexity in the Environment: Dynamics of Coupled Natural and Human Systems Competition. National Science Foundation, May, 2001.
Commentary, with L. J. Standley. “Appropriate role of biology in establishing sediment criteria.” In SETAC Globe 2 (2): 29-30, 2001.
Invited speaker. Consider Microbial Ecology when Attempting Bioremediation. Society for Environmental Toxicology and Chemistry, April 25, 1998, Avondale, PA.
Councilor at Large, American Society for Microbiology, July 1998-2000.
Member, Editorial Board, Microbial Ecology, January, 1997-2006.
American Academy of Microbiology
American Association for the Advancement of Science
American Society for Microbiology
North American Benthological Society
Society for Environmental Chemistry and Toxicology