THOMAS L. BOTT
Senior Research Scientist and Vice President, Stroud Water Research Center and Adjunct Professor of Biology, Department of Biology, University of Pennsylvania.

Stroud Water Research Center
970 Spencer Road
Avondale, PA 19311 
Phone: 610-268-2153, ext. 224
Fax: 610-268-0490
E-mail: tlbott@stroudcenter.org  

Research interest and area of expertise

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.

Research

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.

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.

Exemplary abstracts from publications or presentations are presented below- two from basic research projects and two from work on more applied questions.

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. [View PDF; 1467KB]

We measured the impact of riparian zone vegetation on ecosystem metabolism in paired forested and meadow reaches on 13 streams in southeastern Pennsylvania and Maryland, USA. Metabolism estimates were based on open-system measurements of dissolved oxygen changes, with reaeration determined from propane evasion. Daily gross primary productivity (GPP) in meadow and forested reaches averaged 2.85 and 0.86 g O₂·m^-2·d^-1, respectively, at water temperatures of 12°C or greater when the forest canopy was developed, and 1.74 and 1.09 g O₂·m^-2·d^-1, respectively, at temperatures below 12°C when the canopy was bare. Community respiration (CR24) also was greater in meadow reaches than in forested reaches, averaging 5.58 and 3.57 g O₂·m^-2·d^-1, respectively, in the warm season and 4.87 and 2.88 g O₂·m^-2·d^-1, respectively, during the cold season. Thus, both meadow and forested reaches were heterotrophic. Forested reaches were always wider and nearly always shallower than companion meadow reaches. When ecosystem function was assessed per unit of stream length, the difference in average GPP between meadow and forested reaches was reduced from 3-fold to 1.9-fold in the warm season and mean GPP was greater in the forested reaches during the cold season. Mean CR24 per meter stream length was greater in forested reaches during both seasons. Even though riparian shading reduced primary productivity per unit area of streambed, the greater stream width of the forested reaches counteracted that reduction in part. Thus, when rates of ecosystem function were expressed per length of stream, differences between reaches were always smaller than when expressed per area, and activity per unit stream length was sometimes greater in forested reaches than in meadow reaches.

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. [View PDF; 449KB]

Ecosystem metabolism was measured in 10 streams flowing into New York City drinking-water reservoirs. Six of the streams were located west of Hudson River (WOH) in the Catskill Mountains and 4 were in the Croton River watershed east of Hudson River (EOH). Measurements were made for 3-d periods between June and November in each of 3 y using an open-system O₂ technique with reaeration determined from propane evasion. Chlorophyll a concentrations, algal cover types, and nutrient uptake were measured concurrently. Gross primary productivity ranged from 2.02 to 4.32 g O₂·m^-2·d^-1 in the WOH streams and from 0.23 to 1.13 g O₂·m^-2·d^-1 in the EOH streams. Community respiration ranged from 3.94 to 8.30 g O₂·m^-2·d^-1 in the WOH streams and from 1.39 to 6.12 g O₂·m^-2·d^-1 in the EOH streams. All streams were heterotrophic. The WOH streams were larger and more open than the EOH streams. Metabolism was strongly correlated with instream environmental and water-chemistry variables and riparian shade. Land use was largely forested with some agriculture in the WOH watersheds, and it was forested or urbanized in EOH watersheds. Landuse impacts were confounded by the smaller size and denser shade along EOH streams than along WOH streams.

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. [View PDF; 690KB]

Primary productivity and chlorophyll a concentrations were measured in 8 reservoirs in the New York City drinking-water-supply watersheds. The light-and-dark bottle O₂-change procedure was used to measure gross primary productivity (GPP) once each summer from 2000 to 2002. GPP normalized for photosynthetically active radiation (PAR) in the Neversink and Schoharie averaged only 0.025 and 0.035 g O₂/mol quanta, respectively. Values for the New Croton and Cannonsville averaged 0.118 and 0.125 g O₂/mol quanta, respectively. Values in the other reservoirs (west basin Ashokan, Pepacton, Rondout, and Kensico) were intermediate. Chlorophyll a concentrations in reservoir photic zones ranged from mean values of <10 to 100 mg/m², with highest values in the New Croton and Cannonsville and lowest concentrations in the Neversink, Pepacton, and Schoharie. The Cannonsville was eutrophic, and the New Croton was at the mesotrophic–eutrophic boundary. The Neversink, Schoharie, and Pepacton were at the oligotrophic–mesotrophic boundary, and the remaining reservoirs (Kensico, Rondout, and west basin Ashokan) were mesotrophic. Reservoir conditions were related to watershed-scale land use. Gradients within reservoirs in chlorophyll a, depth of photic zone, and primary productivity indicated an influence of the major tributary on reservoir conditions in several of the reservoirs.

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.

Feeding interactions between microorganisms and their grazers range from broad and general to very specific. Here we examined routes of transfer of [³H]benzo[a]pyrene (BaP) and 2,2',5,5'[¹⁴C]tetrachlorobiphenyl (PCB-52) from microorganisms in freshwater sediments to oligochaetes (Lumbriculus variegatus) and chironomid larvae (either Stictochironomus sp. or a mix of smaller taxa) when exposed to the compounds added either directly to sediments or to bacteria or diatoms previously labeled and then added to sediments. The appearance of radiolabel in animals after a gut clearing step to differentiate between ingested and absorbed compound was followed in time course experiments. Relative to the added radiolabel, BaP concentrations were greater than PCB concentrations in L. variegatus and were greater in animals fed radiolabeled sediments or bacteria than those offered diatoms. In contrast, the chironomids accumulated more PCB than BaP. The mix of small chironomids bioaccumulated more PCB when fed pre-labeled algae than when fed sediment or bacteria. However, Stictochironomus sp. bioaccumulated more from sediments and/or bacteria. Food selection influences pathways of contaminant transfer, even to small animals at the base of the food web. We also tested whether the bioaccumulation of BaP and PCB would be predicted by the Koc for the sediment (i.e., BCF/Koc=1). The quotients, averaged over experiments, were 1.08 and 1.53 for PCB-52 and BaP, respectively, but error terms were large, with coefficients of variation being 83% and 135%, respectively.

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Current Grants

Co-Principal Investigator. “Water quality and stream health in Eastern Pennsylvania (Bucks County): 40 Years of Progress”. Studies of coliform bacteria, phytoplankton and periphyton in Bucks Co., PA streams. Funded by NASA.

Co-Principal Investigator. “Reducing nutrient levels in the Chesapeake Bay: The role of acid mine drainage mitigation”. Studies of ecosystem metabolism in PA streams, AMD impacted and control. Funded by Campbell Foundation, National Fish and Wildlife Foundation, Degenstein Foundation, Western PA Watershed Association.

Co-Principal Investigator. “LTREB: Stream ecosystem structure and function within a maturing deciduous forest” Studies of ecosystem metabolism in White Clay Creek. Funded by NSF.

Education

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.

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Previous Positions Held

Curator, Stroud Water Research Center, Academy of Natural Sciences of Philadelphia, 1986-1999; Associate Curator, 1978-1986; Assistant Curator, 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. 

Selected Publications (last 10 years, 83 total)

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. [View PDF; 1467KB]

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. [View PDF; 449KB]

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. [View PDF; 690KB]

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.  [View PDF; 237KB]

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.  [View PDF; 263KB]

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.  [View PDF; 584KB]

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.  [View PDF; 440KB]

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.  [View PDF; 1793KB]

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Recent Presentations

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 (last 10 years)

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.

Society Memberships

American Academy of Microbiology

American Association for the Advancement of Science

American Society for Microbiology

North American Benthological Society

Sigma Xi

Society for Environmental Chemistry and Toxicology

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