SAN JOAQUIN RIVER Dissolved Oxygen Total Maximum Daily Load (SJR DO TMDL) Stakeholder Process

CURRICULUM VITAE JAMES T. HOLLIBAUGH

EDUCATION

1971 B.S. Biochemistry (with High Honor)
University of California, Davis

1977 Ph.D. Oceanography
Dalhousie University, Halifax, Nova Scotia, Canada

EXPERIENCE

Since UNIVERSITY OF GEORGIA - Department of Marine Sciences and
July 1997 School of Marine Programs, Athens, Georgia, USA

Professor and Associate Director

Share administrative responsibility with the Director for the Department of Marine Sciences, the Institute of Marine Sciences on Sapelo Island; Georgia Sea Grant; and the University of Georgia Marine Extension Service with 2 marine facilities on the Georgia coast and a seafood technology center in Atlanta. Total personnel involved in the program: approximately 100, annual budget, approximately $10,000,000.

Physiological ecology and trophic role of bacteria and phytoplankton in coastal systems, microbial processes in the Arctic Ocean. Role of bacteria in selenium geochemistry, primarily selenate respiration and assimilation. Relationship between bacterioplankton community metabolic capabilities and community composition. Trophic role of bacteria in San Francisco Bay.

PI/PD or co-PI on 3 NSF awards; OCE 98-07588, MCB 99-77886, OCE 99-82133 (LTER) and a contract from the State of California, Department of water Resources.

Teaching: Freshman seminars in Marine Biology, Honors seminar in Biology, Honors seminar, Advisor for the Biology program, guest lecturer in various Marine Sciences courses.

Since UNIVERSITY OF CALIFORNIA, SANTA CRUZ - Institute of Marine
May, 1997 Sciences, Santa Cruz, California, U.S.A.

Research Associate

1983 - SAN FRANCISCO STATE UNIVERSITY - Center for Environmental
1997 Studies, Tiburon, California, U.S.A.

Assistant, Associate and Senior Research Scientist; Lecturer.

Physiological ecology and trophic role of bacteria and phytoplankton in coastal systems around San Francisco, primarily San Francisco and Tomales Bays. Role of bacteria in selenium geochemistry, primarily selenate respiration and assimilation. Geochemistry of C, N, S and P in Tomales Bay. Effects of invading species and fresh water diversion on San Francisco Bay. Microbial processes in polar seas. Relationship between bacterioplankton community metabolic capabilities and community composition.

Most of the funding for this work was obtained from the National Science Foundation (OCE 82-14835, OCE 87-16469, OCE 89-14921, DPP 90-16446, DPP 91-14414, OCE 93-15639, OPP 95-00237, OCE 95-21983, OPP 96-25131, OPP 96-17337. PI or co-PI on 7 facilities grants to RTC; PI on 1 planning grant to RTC), and the State of California, Dept. of Water Resources. Other funding has been obtained from the U.S. Geological Survey, the Gulf of the Farallones National Marine Sanctuary, the San Francisco Foundation, and Contra Costa County Water Agency.

Taught graduate and undergraduate courses in Biological Oceanography, Marine Ecology, Radioisotope Methodology,and Marine Microbiology.

1990 - Acting Director.
1995

Responsible for administering a 32-acre facility with an annual budget of $1.5 million and a staff (scientists and support staff) of 30. Coordinated the instructional program. Purchased, refit and managed operations of a 38' research vessel and a number of small boats. Managed a conference center facility and rental property. Prepared facilities proposals, master plans, annual reports, and other administrative documents.

1980 - LAVALIN, Halifax, Nova Scotia and Vancouver, British Columbia,
1983 Canada.

Senior Scientist, Oceanographer.

Primary responsibility was a 1.5-year baseline study of the Grand Banks of Newfoundland supervising a staff of 25. Included biological, chemical and physical oceanographic components, sample collection and analysis, data analysis and report preparation. Funded mainly by private industry with some support from the Canadian government. Conducted other studies related to potential impacts of offshore oil development.

1977 - UNIVERSITY OF CALIFORNIA, SAN DIEGO - Scripps Institution of
1980 Oceanography, Institute of Marine Resources, La Jolla, California, U.S.A.

Postgraduate Research Biologist V and VI.

Studied the effects of heavy metals on phytoplankton and on plankton ecosystems, the role of resting spores in the life cycle and ecology of diatoms, and the physiological ecology and trophic role of bacteria in plankton ecosystems. Drs. W.H. Thomas and F. Azam, supervisors.

1976 BEDFORD INSTITUTE OF OCEANOGRAPHY - Atlantic Oceanographic
Laboratory, Dartmouth, Nova Scotia, Canada.

Research Assistant.

Chemical Oceanography program on C.S.S. Baffin Cruise 76001, "Senegal Survey," chemical and biological oceanographic studies off Senegal. Dr. R. Pocklington, supervisor.

1973 - DALHOUSIE UNIVERSITY - Departments of Biology and Oceanography,
1975 Halifax, Nova Scotia, Canada.

Research Assistant.

Project involved single cell isolation and culture of non-pigmented flagellates.
Dr. R.O. Fournier, supervisor.

Teaching Assistant.

Invertebrate zoology and a marine ecology summer course taught at Huntsman Marine Laboratory, St. Andrews, New Brunswick, Canada.

GRADUATE STUDENTS AND POSTDOCS

Supervisor for: Ms. Inge Werner (M.S.); Ms. Alison Murray (M.A.); Mr. Michael Murrell (Ph.D); Ms. Victoria Ferrari (M.A); Mr. Gary LeCleir (Ph.D.); Ms Erin Biers (M.S.)
Committee member for: Ms. Sue Vink (Ph.D.); Ms. Samantha Joye (Ph.D.); Ms. Inge Werner (Ph.D.); Ms. Kristin Nutile (M.S.), Ms. Alison Murray (Ph.D.), Ms Francoise Lucas (Ph.D.); Mr. Joe Covert (Ph.D.); Ms Alison Buchan (Ph.D.); Ms Deidre Gibson (Ph.D.). Mr Dirk Koopmans (M.S.); Mr Andy Allen (Ph.D.)
Postdoctoral research associates: Dr. Randolf Chambers; Dr. James Fourqurean; Dr. Samantha Joye; Dr. Nasreen Bano; Dr. Francoise Lucas

OTHER ACTIVITIES

Associate Editor, Limnology and Oceanography, Sept. 1991 to Oct. 1994.
Editorial Board, Marine Microbial Foodwebs (now Aquatic Microbial Ecology), Sept. 1992 to May 1996
Associate Editor, Estuaries, Jan. 1997 to present
Editor, Aquatic Microbial Ecology, Sept. 1999 to present
Reviewer for the following journals: Applied and Environmental Microbiology, Deep-Sea Research, FEMS Microbiology Ecology, Journal of Geophysical Research - Oceans, Limnology and Oceanography, Marine Biology, Marine Ecology Progress Series, Microbial Ecology, Nature, Science, Water Research.
Reviewer and/or panelist for the National Science Foundation: Biological Oceanography, Marine Chemistry, Oceanographic Facilities, Polar Biology and Medicine, International Programs, Small Business Innovative Research, Ecosystems/Division of Environmental Biology.
Reviewer and panelist for Department of Energy.
Reviewer for California, Delaware, Hawaii, Maryland, New York, and Wisconsin Sea Grant Programs.
LMER Coordinating Committee. October 1989 to October 1994.
Visiting Scholar, Memorial University of Newfoundland, Institute for Cold Ocean Studies. October, 1989.
Visiting Scholar; Laboratoire d'Evolution des Systemes Naturels et Modifies; Université Rennes 1; Rennes France. June and September 1997.
Technical Advisory Committee, California State Department of Fish and Game, San Francisco Bay Study. May 1991 to November 1994.
Technical Advisory Committee - Aquatic Ecology, Bay-Delta Oversight Council: a committee advising the Governor of the State of California on water policy issues. March to November 1994.
Technical Advisory Committees, San Francisco Bay Regional Water Quality Control Board. Gambonini mercury mine cleanup and fecal coliform contamination in Tomales Bay watershed.
Invited participant, National Research Council (NAS/NAE) workshop on Marine Biodiversity, NAS/NAE Beckman Conference Center, Irvine, CA 17-19 May 1994.
Organizer and convenor, San Francisco Bay Symposium, 75th Annual Meeting, Pacific Division AAAS. San Francisco, 20-24 June 1994.
Invited participant, SCOPE workshop on Estuarine Comparisons. NAS/NAE Beckman Conference Center, Irvine CA 22-25 February 1995.
Program committee member, AGU/ASLO Ocean Sciences Meeting, San Diego, 12-16 February 1996.
Invited participant, EPA's Morro Bay National Estuary Program workshop on estuarine management. Morro Bay CA, 2 March, 1996
Co-convenor, 1997 ASLO Annual Meeting, Santa Fe, New Mexico
Invited participant, USGS/Interagency Ecological Program workshop on Suisun Bay, Sacramento 9 May 1996
Invited participant, NSF workshop on the fate of LMER and the future of marine and estuarine Long Term Ecological Research (LTER) sites. Madison Wisconsin, July 18-20, 1996.
Invited participant, NOAA Coastal GOOS (Global Ocean Observing System) workshop. Bethesda MD, 10-12 December, 1996
Invited participant, EPA's San Francisco Bay National Estuary Program's annual "State of the Bay Conference" San Francisco CA, 10 October, 1996
External Science Advisory Committee, University of California System-wide Lead Campus Program in Environmental Toxicology at UC Davis.
Invited participant, NSF-sponsored EDOCC (Ecological Determinants of Organic Carbon Cycling) workshop, Timberline, OR 12-16 March, 2000
Mentor at local pre-, elementary and high schools

ASSOCIATIONS

American Association for the Advancement of Science
American Geophysical Union
American Society of Limnology and Oceanography
American Society of Microbiology
Estuarine Research Federation

CONTACT INFORMATION

Address: Department of Marine Sciences
University of Georgia
Athens GA 30602-3636
Phone: (706) 542-3016
Fax: (706) 355-9993
Email: aquadoc@uga.edu

PUBLICATIONS

Hollibaugh, J.T. 1977. Nitrogen regeneration during amino acid degradation and the activity of bacteria in plankton communities of Halifax Harbor, Nova Scotia, Canada. Ph.D. thesis. Dalhousie University, Halifax, Nova Scotia, Canada.
Hollibaugh, J.T. 1976. The biological degradation of arginine and glutamic acid in seawater in relation to the growth of phytoplankton. Marine Biology 36: 303-312.
Hollibaugh, J.T. 1978. Nitrogen regeneration during the degradation of several amino acids by plankton communities collected near Halifax, Nova Scotia, Canada. Marine Biology 45: 191-201.
Hollibaugh, J.T. 1979. Metabolic adaptation in natural bacterial populations supplemented with selected amino acids. Estuarine and Coastal Marine Science 9: 215-230.
Hollibaugh, J.T., D.L.R. Seibert and W.H. Thomas. 1980. A comparison of the acute toxicities of ten heavy metals to phytoplankton from Saanich Inlet, B.C., Canada. Estuarine and Coastal Marine Science 10: 92-105.
Hollibaugh, J.T. 1980. Amino acid fluxes in marine plankton communities contained in CEPEX bags. In: J.D. Farmer and H.J. Freeland (eds.) Fjord Oceanography. NATO Conference Series IV in Marine Sciences. Plenum Publishing Corporation, NY. pp. 439-445.
Hollibaugh, J.T., J.A. Fuhrman and F. Azam. 1980. Radioactively labeling of natural assemblages of bacterioplankton for use in trophic studies. Limnology and Oceanography 25: 172-181.
King, K.R., J.T. Hollibaugh and F. Azam. 1980. Predator- prey interactions between a larvacean, Oikopleura dioica and bacterioplankton in enclosed water columns. Marine Biology 56: 49-57.
Davis, C.O., J.T. Hollibaugh, D.L.R. Seibert, W.H. Thomas, and P.J. Harrison. 1980. Formation of resting spores by Leptocylindrus danicus Cleve (Bacillariophyceae) in a controlled experimental ecosystem. Journal of Phycology 16: 296-302.
Thomas, W.H., J.T. Hollibaugh, D.L.R. Seibert and G.T. Wallace. 1980. The toxicity of a mixture of ten metals to phytoplankton from Saanich Inlet, B.C. Canada. Marine Ecology: Progress Series 2: 213-220.
Hollibaugh, J.T., A.B. Carruthers, J.A. Fuhrman, and F. Azam. 1980. Cycling of organic nitrogen in marine plankton communities studied in enclosed water columns. Marine Biology 59: 15-21.
Thomas, W.H., J.T. Hollibaugh, and D.L.R. Seibert. 1980. Effects of heavy metals on the morphology of some marine phytoplankton. Phycologia 19: 202-209.
Hollibaugh, J.T., D.L.R. Seibert and W.H. Thomas. 1981. Observations on the survival and germination of resting spores of three Chaetoceros (Bacillariophyceae) species. Journal of Phycology 17: 1-9.
Hollibaugh, J.T. and F. Azam. 1983. Microbial degradation of dissolved proteins in seawater. Limnology and Oceanography 28: 1104-1116.
Smith, S.V., W.J. Wiebe, J.T. Hollibaugh, S.J. Dollar, S.W. Hager, B.E. Cole, G.W. Tribble and P.A. Wheeler. 1987. Stoichiometry of C, N, P, and Si fluxes in a temperate- climate embayment. Journal of Marine Research 45: 427-460.
Hollibaugh, J.T. 1988. Limitations on the [3H]thymidine method for estimating bacterial productivity due to thymidine metabolism. Marine Ecology: Progress Series 43: 19-30.
Hollibaugh, J.T., B.E. Cole, S.J. Dollar, S.W. Hager, W.J. Kimmerer, S. Obrebski, S.V. Smith, M. Valentino, S.M. Vink, and T.W. Walsh. 1988. Tomales Bay, California: a natural macrocosm for examining biogeochemical coupling at the land-sea interface. Eos 36: 843-845.
Friedman, C.S., T. McDowell, J.M. Groff, J.T. Hollibaugh, D. Manzer and R.P. Hedrick. 1988. Presence of Bonamia ostreae among populations of the European flat oyster, Ostrea edulis Linne, in California, USA. Journal of Shellfish Research 8: 1033-1037.
Smith, S.V., J.T. Hollibaugh, S.J. Dollar and S.M. Vink. 1989. Tomales Bay, California: a case for carbon controlled nitrogen cycling. Limnology and Oceanography 34: 37-52.
Smith, S.V. and J.T. Hollibaugh. 1989. Carbon-controlled nitrogen cycling in a marine "macrocosm": an ecosystem-scale model for managing cultural eutrophication. Marine Ecology: Progress Series 52: 103-109.
Oremland, R.S., J.T. Hollibaugh, A.L. Maest, T.S. Presser, L.G. Miller and C.W. Culbertson. 1989. Selenate reduction to elemental selenium by anaerobic bacteria in sediments and in culture: biogeochemical significance of a novel, sulfate- independent respiration. Applied and Environmental Microbiology 55: 2333-2343
Oremland, R.S., N.A. Steinberg, A.S. Maest, L.G. Miller and J.T. Hollibaugh. 1990. Measurement of in situ rates of selenate removal by dissimilatory bacterial reduction in sediments. Environmental Science and Technology 24: 1157-1164.
Hollibaugh, J.T., R.W. Buddemeier and S.V. Smith. 1991. Contribution of colloidal and high molecular weight dissolved material to alkalinity and nutrient concentrations in shallow marine and estuarine systems. Marine Chemistry 34: 1-27.
Smith, S.V., J.T. Hollibaugh, S.J. Dollar and S. Vink. 1991. Tomales Bay Metabolism: C-N-P stoichiometry and ecosystem heterotrophy at the land-sea interface. Estuarine, Coastal and Shelf Science 33: 223-257.
Dollar, S.J., S.V. Smith, S.M. Vink, S. Obrebski and J.T. Hollibaugh. 1991. Annual cycle of benthic nutrient fluxes in Tomales Bay, California, and contribution of the benthos to total ecosystem metabolism. Marine Ecology Progress Series 79: 115-125.
Azam, F., D.C. Smith and J.T. Hollibaugh. 1991. Role of the microbial loop in Antarctic pelagic ecosystems. Polar Research 10: 239-243.
Prasad, K.S. and J.T. Hollibaugh. 1992. Quantum yield estimates of phytoplankton on the Grand Bank of Newfoundland for use in remote sensing production models. Limnology and Oceanography 37: 1271-1279.
Prasad, K.S., J.T. Hollibaugh, D.C. Schneider and R.L Haedrich. 1992. A model for determining primary production on the Grand Banks. Continental Shelf Research 12: 563-575.
Hollibaugh, J.T. and P.S. Wong. 1992. Ethanol extractable substrate pools and the incorporation and metabolism of thymidine, L-leucine and other low molecular weight substrates by bacterioplankton. Canadian Journal of Microbiology 38: 605-613.
Hollibaugh, J.T., P.S. Wong, F. Azam, D.C. Smith, G.F. Steward and B.E. Cole. 1992. Measurement of bacterioplankton production in Antarctic coastal waters: Comparison of thymidine and L-leucine methods and verification of labeling patterns. Antarctic Journal of the U.S. 27: 127-128.
Smith, D.C., G.F. Steward, F. Azam and J.T. Hollibaugh. 1992. Virus and bacteria abundance in the Drake Passage during January and August 1991. Antarctic Journal of the U.S. 27: 125-127.
Boynton, W., J.T. Hollibaugh, D. Jay, M. Kemp, J. Kremer, C. Simenstad, S.V. Smith and I. Valiela. 1992. Understanding changes in coastal ecosystems: the Land Margin Ecosystems Program. Eos 73: 481, 484-485.
Smith, S.V. and J.T. Hollibaugh. 1993. Role of coastal ocean organic metabolism in the oceanic organic carbon balance. Reviews of Geophysics 31: 75-89.
Hollibaugh, J.T. 1993. Consistent patterns of thymidine metabolism by bacterioplankton communities: A clue to community composition and to the carbon sources used for growth? In: C. Pedrós-Alió and R. Guerrero, [Eds]; Trends in Microbial Ecology. Proceedings of the Sixth International Symposium on Microbial Ecology, Barcelona Spain, 7-11 September, 1992. pp. 471-474.
Werner, I. and J.T. Hollibaugh. 1993. Potamocorbula amurensis (Mollusca, Pelecypoda): Comparison of clearance rates and assimilation efficiencies for phytoplankton and bacterioplankton. Limnology and Oceanography 38: 949-964.
Kimmerer, W.J., S.V. Smith and J.T. Hollibaugh. 1993. A simple heuristic model of nutrient cycling in an estuary. Estuarine, Coastal and Shelf Science 37: 145-159.
Chambers, R.M., J.T. Hollibaugh and S. Vink. 1994. Sulfate reduction and sediment metabolism in Tomales Bay, California. Biogeochemistry 25:1-18.
Sansone, F., J.T. Hollibaugh, S.M. Vink, R.M. Chambers, S.B. Joye and B.N. Popp. 1994. Diver-operated piston corer for nearshore use. Estuaries 17: 716-720
Chambers, R.M., S.V. Smith and J.T. Hollibaugh. 1994. An ecosystem-level context for tidal exchange studies in salt marshes of Tomales Bay, California, USA. In: W.J. Mitsch, [Ed.] Global Wetlands, Old World and New. Elsevier, New York. pp. 265-276.
Hollibaugh, J.T. 1994. Relationship between thymidine metabolism, bacterioplankton community metabolic capabilities and sources of organic matter used for growth. Microbial Ecology 28: 117-131.
Chambers, R.M., J.W. Fourqurean, J.T. Hollibaugh and S.M. Vink. 1995. Importance of terrestrially derived, particulate phosphorus to P dynamics in a west coast estuary. Estuaries 18: 518-526.
Joye, S.B. and J.T. Hollibaugh. 1995. Sulfide inhibition of nitrification influences nitrogen regeneration in sediments. Science 270: 623-625.
Smith, S.V., R.M. Chambers, and J.T. Hollibaugh. 1996. Dissolved and particulate nutrient transport through a coastal watershed-estuary system. Journal of Hydrology 176: 181-203.
Murray, A.E., J.T. Hollibaugh and C. Orrego. 1996. Comparison of the phylogenetic compositions of bacterioplankton in two California estuaries by denaturing gradient gel electrophoresis of 16S rRNA gene fragments. Applied and Environmental Microbiology 62: 2676-2680.
Joye, S.B., S.V. Smith, J.T. Hollibaugh and H.W. Paerl. 1996. Estimating denitrification rates in estuarine sediments: A comparison of stoichiometric and acetylene based methods. Biogeochemistry 33: 197-215.
Hollibaugh, J.T. and P.S. Wong. 1996. Distribution and activity of bacterioplankton in the San Francisco Bay estuary. In: J.T. Hollibaugh, [Ed.]; San Francisco Bay: The Ecosystem. Pacific Division, AAAS, San Francisco, California. pp. 263-288.
Hollibaugh, J.T. (ed). 1996. San Francisco Bay: The Ecosystem. Further investigations into the natural history of San Francisco Bay and Delta with reference to the influence of man. Proceedings of the San Francisco Bay Symposium, 75th Annual Meeting, Pacific Division AAAS, June 20-24, 1994. Published by Pacific Division, AAAS, San Francisco California. 542 pp.
Fourqurean, J.W., K.L. Webb, J.T. Hollibaugh and S.V. Smith. 1997. Contribution of the plankton community to ecosystem respiration, Tomales Bay, California. Estuarine, Coastal and Shelf Science 44: 493-505.
Joye, S.B., M.L. Mazzotta and J.T. Hollibaugh. 1996. Community metabolism in microbial mats: the occurrence of biologically-mediated iron and manganese reduction. Estuarine, Coastal and Shelf Science 43: 747-766
Largier, J.L, J.T. Hollibaugh and S.V. Smith. 1997 Seasonally hypersaline estuaries in Mediterranean-climate regions. Estuarine, Coastal and Shelf Science 45: 789-797.
Smith, S.V. and J.T. Hollibaugh. 1997. Annual cycle and interannual variability of ecosystem metabolism in a temperate climate embayment. Ecological Monographs 67: 509-533
Fourqurean, J.W., T.O. Moore, B. Fry and J.T. Hollibaugh. 1997. Spatial and temporal variation in C:N:P ratios, 15N, and morphology of eelgrass (Zostera marina L.) as indicators of ecosystem processes, Tomales Bay, CA, USA. Marine Ecology Progress Series 157: 147-157.
Murrell, M.C. and J.T. Hollibaugh. 1998. Microzooplankton grazing in northern San Francisco Bay measured by the dilution method. Aquatic Microbial Ecology 15: 53-63.
Werner, I., K.F. Kline and J.T. Hollibaugh. 1998. Stress proteins expression in Ampelisca abdita (Amphipoda) exposed to sediments from San Francisco Bay. Marine Environmental Research 45: 417-430.
Smith, S.V. and J.T. Hollibaugh. 1998. Carbon-Nitrogen-Phosphorus cycling in Tomales Bay, California. Aquatic Geochemistry 4: 395-402.
Murrell, M.C., J.T. Hollibaugh, M.W. Silver and P.S. Wong. 1999. Bacterioplankton dynamics in northern San Francisco Bay: Role of particle association and seasonal freshwater flow. Limnology and Oceanography 44: 295-308.
Hollibaugh, J.T. 1999. Bacteria and the microbial loop in northern San Francisco Bay and the Sacramento-San Joaquin Delta. IEP Newsletter 12: 8-11.
Hollibaugh, J.T. and P.S. Wong. 1999. Microbial processes in the San Francisco Bay estuarine turbidity maximum. Estuaries 22: 848-862
Ferrari, V.C. and J.T. Hollibaugh. 1999. Distribution of microbial assemblages in the central Arctic Ocean basin studied by PCR/DGGE: Analysis of a large data set. Hydrobiologia 401: 55-68.
Fisher, T.R., D. Correll, R. Costanza, J.T. Hollibaugh, C.S. Hopkinson, R.W. Howarth, N. Rabalais, J.E. Richey, C. Vorosmarty and R. Wiegert. 2000. Chapter 4. Synthesizing drainage-basin inputs to coastal systems. In: J.E. Hobbie (ed.), Estuarine Science: A Synthetic Approach To Research And Practice . Island Press. pp 81-101.
Hollibaugh, J.T., P.S. Wong and M.C. Murrell. 2000. Similarity of particle-associated and free-living bacterial communities in northern San Francisco Bay, California. Aquatic Microbial Ecology 21: 103-114.
Chambers, R.M., J.T. Hollibaugh, C.S. Snively and J.N. Plant. 2000. Iron, sulfur and carbon diagenesis in sediments of Tomales Bay, California. Estuaries 23:1-9.
Hollibaugh, J.T.; J. Pages; J.-P Torreton and P.S. Wong. In press. Phylogenetic variation in bacterial populations from 10 atoll lagoons in the Tuamotu Islands, French Polynesia. In: M.J. Brylinsky [Ed]; Trends in Microbial Ecology. Proceedings of the Eighth International Symposium on Microbial Ecology; Halifax, Nova Scotia, Canada, 9-14 August, 1998.
Bano, N. and J.T. Hollibaugh. In press. Diversity and distribution of DNA sequences with affinity to ammonia-oxidizing bacteria of the -Subdivision of the Class Proteobacteria in the Arctic Ocean. Applied and Environmental Microbiology.
Murrell, M.C. and J.T. Hollibaugh. In press. Distribution and composition of dissolved and particulate organic carbon in northern San Francisco Bay during low flow conditions. Estuarine, Coastal and Shelf Science.

PAPERS IN REVIEW

Joye, S.B., J.T. Hollibaugh, H.W. Paerl and S.V. Smith. Nitrification and denitrification in the subtidal sediments of Tomales Bay, California, USA. Estuaries.
Hepperle, D., L. Krienitz, R. Goericke, J.T. Hollibaugh, H. Takeda and R.A. Lewin. Picocystis salinarum gen. et. sp. nov. (Chlorophyta) - a new picoplanktonic green alga. Journal of Phycology.
Lucas, F. and J.T. Hollibaugh. Shifts in the composition of estuarine sediment bacterial assemblages in response to amendments with selenate and acetate. Environmental Science and Technology
Hollibaugh, J.T., .P.S. Wong, N. Bano, S.K. Pak and C. Orrego. Stratification of microbial assemblages in Mono Lake, California, and response to a mixing event. Hydrobiologia

TECHNICAL REPORTS

Hollibaugh, J.T. and J.N. Booth. 1981. The dynamics and distribution of phytoplankton and primary production on the Grand Banks. Chapter 4 in Grand Banks Oceanographic Studies, Vol. 1. Final report prepared for Mobil Oil Canada Ltd. and Partners by MacLaren Plansearch, July 1981, 65 pp.
Hollibaugh, J.T. 1981. Overview of the biological oceanography of the Grand Banks. Chapter 9 in Grand Banks Oceanographic Studies, Vol. 4. Final report prepared for Mobil Oil Canada Ltd. and Partners by MacLaren Plansearch, July 1981, 60 pp.
Williams, P.B. and J.T. Hollibaugh. 1987. A salinity standard to maximize phytoplankton abundance by positioning an entrapment zone in Suisun Bay. Report prepared for Contra Costa County Water Agency and the Environmental Defense Fund, submitted as CCCWA/EDF Exhibit 1 to the State Water Resources Control Board Bay/Delta Hearings. 45 pp.
Williams, P.B. and J.T. Hollibaugh. 1987. A salinity standard to maximize phytoplankton abundance by limiting the intrusion of marine benthic organisms in Suisun Bay. CCCWA/EDF Exhibit 2, State Water Resources Control Board Bay/Delta Hearings. 36 pp.
Williams, P.B. and J.T. Hollibaugh. 1987. A flow standard to maximize phytoplankton abundance by positioning an entrapment zone in San Pablo Bay. CCCWA/EDF Exhibit 3, State Water Resources Control Board Bay/Delta Hearings. 57 pp.
Williams, P.B. and J.T. Hollibaugh. 1987. A salinity standard to maximize phytoplankton abundance in South San Francisco Bay. CCCWA/EDF Exhibit 4, State Water Resources Control Board Bay/Delta Hearings. 63 pp.
Hollibaugh, J.T. 1988. Water quality and oyster grow-out. IN: R.Amidei, ed., West Coast Mollusc Culture: A present and future perspective. California Sea Grant College Program, San Diego CA. pp 40-43.
Cole, B.E., S.W. Hager and J.T. Hollibaugh. 1990. Hydrographic, biological and nutrient properties of Tomales Bay, California, March 1985 to May 1986. U.S. Geological Survey Open File Report 90-178.
Dubrovsky, N.M., J.M. Neil, R. Fujii, R.S. Oremland and J.T. Hollibaugh. 1990. Influence of redox potential on selenium distribution in ground water, Mendota, western San Joaquin Valley, California. U.S.Geological Survey Open File Report 90-138.
Smith, S.V. and J.T. Hollibaugh,. 1990. Nutrient status of the Estero Americano. NOAA Technical Memorandum prepared for the Gulf of the Farallones National Marine Sanctuary. 18 pp.
Hollibaugh, J.T., M.N. Josselyn and S.V. Smith. 1990. Wastewater reclamation studies for proposed discharge of treated wastewater to Estero Americano. Review of Technical Memoranda. NOAA Technical Memorandum prepared for the Gulf of the Farallones National Marine Sanctuary. 47 pp.
Hollibaugh, J.T. and I. Werner. 1991. Potamocorbula amurensis: Comparison of clearance rates and assimilation efficiencies for phytoplankton and bacterioplankton. Interagency Ecological Program Technical Report 91-29. 42 pp.
Hollibaugh, J.T., W.J. Kimmerer and P.S. Wong. 1992. Relationship between the spring phytoplankton bloom and foodweb dynamics in South San Francisco Bay. Final report prepared for The San Francisco Foundation, grant 910326. 42 pp.
Kimmerer, W. et al. 1995. Working conceptual model for the food web of the San Francisco Bay/Delta estuary. Interagency Ecological Program Technical Report 95-42. 30 pp.
Committee on Biological Diversity in Marine Systems, Ocean Sciences Board, National Research Council, 1995. Understanding Marine Biodiversity: A Research Agenda for the Nation 128 pp
Werner, I., K.F. Kline and J.T. Hollibaugh. 1996. Stress proteins in amphipods as biomarkers of sediment pollution in San Francisco Bay. Interagency Ecological Program for the San Francisco Bay/Delta Estuary Technical Report 96-48. State of California, Department of Water Resources, Sacramento, CA. 78 pp.
Hollibaugh, J.T and P.S. Wong 1998. Chapter 3. Microbial production in the San Francisco Bay entrapment zone. In: W.J. Kimmerer, ed: Report of the 1994 Entrapment Zone Study. Interagency Ecological Program for the San Francisco Bay/Delta Estuary Technical Report 98-56. State of California, Department of Water Resources, Sacramento, CA. pp. 63-82.
Lucas, F. and J.T. Hollibaugh. 1999. Diversity of selenate-reducing bacteria in the sediment of the Olentangy River experimental wetlands: Potential reduction under anaerobic and aerobic conditions. In: Mitsch, W.J. and V. Bouchard, eds: Olentangy River Research Park at the Ohio State University 1999 Annual Report. pp. 125-128
Smith, S.V. and J.T. Hollibaugh. 1999. Water, salt and nutrient exchanges in San Francisco Bay. Interagency Ecological Program for the San Francisco Bay/Delta Estuary Technical Report 99-66. State of California, Department of Water Resources, Sacramento, CA. 34 pp.

PUBLISHED ABSTRACTS

This list contains only papers that I presented. Co-authors are not listed and papers for which I was a co-author but that I did not present are not listed as including them would double or triple the number of entries.

On amino acids and phytoplankton nutrition: Heterotrophic decomposition of amino acids by natural marine plankton populations. PSA annual meeting, Corvallis, Oregon. August 17, 1975.
Amino acid fluxes in marine plankton communities contained in CEPEX bags. ASM meeting Los Angeles, California. May 6, 1979.
Utilization of dissolved proteins by bacterioplankton. ASLO meeting, Seattle, Washington. December, 1979.
Relations between primary productivity and physical oceanographic features on the Grand Banks during 1980. AGU/ASLO meeting, San Francisco, California. December 9, 1982.
Specificity of bacterioplankton amino acid and glucose uptake systems. AGU/ASLO meeting, San Francisco, California. December 6, 1984.
San Francisco Bay bacterioplankton extensively degrade thymidine. AGU/ASLO annual meeting, New Orleans, Louisiana. January 23, 1986.
Mono Lake 2. Thymidine incorporation by bacterioplankton populations. AGU/ASLO annual meeting, San Francisco, California. December 12, 1986.
Reduction of selenate and selenite by a marine isolate. ASM annual meeting, Atlanta, Georgia. March 6, 1987.
They love that dirty water: Microbial processes in San Francisco Bay. Invited paper, Microbial Foodwebs, Session II, AGU/ASLO annual meeting, New Orleans, Louisiana. H. Ducklow, convenor. January 20, 1988.
Conversion factors for thymidine and leucine in San Francisco Bay bacterioplankton. Fifth International Symposium on Microbial Ecology, Kyoto, Japan. 29 August, 1989.
Bacterioplankton production in Suisun Bay during the 1988 drought. Estuarine Research Federation Biannual Meeting, Baltimore, Maryland. 13 October, 1989.
Non-conservative behavior of N and P at the land-sea interface: Lessons from Tomales Bay. Invited paper, ERF, symposium session on Nutrient Transport from Land to the Ocean: The Role of Estuaries, Bays and Coastal Seas. S.W. Nixon, convenor. 11 October, 1989.
Spatial and temporal variation in thymidine and leucine conversion factors in San Francisco Bay bacterioplankton. Invited paper, ERF, special session on Role of Pelagic Bacteria and Microbial Loops. K.G. Sellner, convenor. 10 October, 1989.
Exoenzyme expression in Antarctic microbial populations: changes during shift-up experiments and response to phytoplankton growth. ASLO, Halifax, Nova Scotia. 11 June, 1991.
Impact of Potamocorbula amurensis on the San Francisco Bay foodchain: Clearance rates and assimilation efficiencies for phytoplankton and bacterioplankton. ERF, San Francisco, CA. 13 November, 1991.
Contribution of bacteria to DOM fluxes in Tomales Bay, California. ERF biannual meeting, San Francisco, CA. 14 November, 1991.
Bacterial production in estuaries: Measurement and relationship to carbon sources. Invited presentation, Microbial Foodwebs symposium, F. Azam convenor. Sixth International Symposium on Microbial Ecology. Barcelona, Spain, 11 September 1992.
Tomales Bay, California: Temporal trends in biogeochemical variables, a possible drought response. Estuarine and Coastal Sciences Association (UK)/ERF Joint Meeting, Plymouth, UK. 17 September, 1992.
Consistent differences in the patterns of thymidine metabolism in two west coast estuaries: a clue to the relative importance of allochthonous carbon? Invited paper, Microbial Loop session, ASLO Annual Meeting, Edmonton, Alberta, Canada. 31 May, 1993.
Tomales Bay, California: Environmental forcing and temporal trends in estuarine variables. Invited paper, Land/Ocean interactions session, ASLO Annual Meeting, Edmonton, Alberta, Canada. 1 June, 1993.
Bacterioplankton distributions and community metabolic characteristics in the Arctic Ocean during March and April of 1996: SCICEX 95. ASLO/AGU Ocean Sciences Meeting, San Diego, CA 13 February, 1996.
Importance of particle-associated bacteria in the San Francisco Bay estuarine turbidity maximum. ASLO/AGU Ocean Sciences Meeting, San Diego, CA 14 February, 1996.
Biogeochemical reactions at the land-sea interface: LMER research in Tomales Bay, California. Pacific Division, AAAS annual meeting, San Jose, CA 25 June, 1996.
Annual cycle and interannual variability of ecosystem metabolism in a temperate climate embayment. ECSA/ERF Joint Meeting, Middleburg, The Netherlands, 19 September, 1996.
Seasonal variation in the composition of Mono Lake microbial communities studied by DGGE. ASLO Aquatic Sciences Meeting, Santa Fe, NM, 11 February, 1997.
Relationship between particle-associated and free-living microbial communities in the San Francisco bay ETM. ASLO Aquatic Sciences Meeting, Santa Fe, NM, 11 February, 1997.
Phylogenetic variation in bacterial populations from 10 atoll lagoons in the Tuamotu Islands, French Polynesia. Invited paper, ISME 8, Halifax NS Canada, 10 August, 1998.
Biogeography of Arctic Ocean microbial assemblages. ISME 8, Halifax NS Canada, 13 August, 1998.
Stratification of microbial assemblages in Mono Lake, California, and response to a mixing event. Saline Lakes Conference, Furnace Creek, Death Valley CA, 13 Sept, 1999.
Nutrient budgets and net ecosystem metabolism in San Francisco Bay. Estuarine Research Federation Annual Meeting, New Orleans LA , 29 September, 1999

SEMINARS AND OTHER PRESENTATIONS

I have given numerous seminars at academic institutions, small association meetings and government laboratories. A partial list of titles, (co-authors, if any, are not listed), includes:

Protein degradation and amino acid cycling in plankton ecosystems. Invited seminar, Department of Oceanography, Texas A & M University, College Station, Texas. April, 1980.
Role of bacterioplankton in material cycling in the upper water column. Invited seminar, Department of Oceanography, University of British Columbia, Vancouver, B.C. March, 1983.
Ecological relationships in heterotrophic marine bacterioplankton: What don't we know? Center for Coastal Marine Studies, University of California, Santa Cruz. January 11, 1984.
Degradation of dissolved protein by bacterioplankton. Bodega Marine Laboratory, University of California, Bodega Bay, California. February 9, 1984.
Confining water samples as a means of studying microbial ecology: Artifacts or perturbation experiments. Water Resources Division, U.S. Geological Survey, Menlo Park, California. March 7, 1984.
Production and biomass of bacterioplankton in San Francisco Bay. San Francisco Bay and Estuary Association, spring meeting, San Francisco, California. April 5, 1985
Distribution of bacteria and bacterial activity in the San Francisco Bay Estuary. Pacific Estuarine Research Society meeting, Monterey, California. April 26, 1985.
Population dynamics of bacterioplankton and phytoplankton in San Francisco Bay. Seminar presented at the University of Maryland's Chesapeake Biological Laboratory in Solomons, Maryland. November 19, 1985. A similar seminar was presented at the Horn Point Laboratory on November 20, 1985.
Dynamics of phytoplankton and bacterioplankton in San Francisco Bay. Invited presentation at NOAA's Estuary of the Month seminar series, NOAA Estuaries Program Office, Washington, D.C. November 22, 1985.
Microscale microbiology. Invited speaker, Central California marine science workshop. Bodega Marine Laboratory, University of California, Bodega Bay, California. October 17, 1987.
Bacteria and selenium: physiology and biogeochemistry. Invited seminar, Department of Oceanography, Texas A&M University, College Station, Texas. 6 June, 1988.
Environmental implications of selenate reduction in anaerobic sediments. Department of Biology, San Francisco State University, San Francisco, California. 27 October, 1988.
Bacterioplankton production in San Francisco Bay during the 1988 drought. San Francisco Bay and Estuary Association, spring meeting, Concord, California. 26 January, 1989.
Precipitation of elemental selenium from selenate by anaerobic cultures of bacteria. Invited speaker, Northern California Electron Microscopy Society annual meeting, San Francisco California. 9 March, 1989.
Selenate respiration and the marine selenium cycle revisited (again). Moss Landing Marine Laboratory, Moss Landing, California. 15 March, 1989.
Microbial activity in San Francisco Bay: Comparison of methyl- and 6-3H-TdR and L-leucine incorporation with growth in dilution cultures. Invited speaker, Dept. Oceanography, Oregon State University, Corvallis Oregon. 21 August, 1989.
Measuring bacterial production in San Francisco Bay: comparison of thymidine and L-leucine. Invited seminar, Marine Science Center, Memorial University of Newfoundland, St John's, Newfoundland. 17 October, 1989. A similar seminar was presented at the Atlantic Oceanographic Laboratory, Bedford Institute of Oceanography, Dartmouth, Nova Scotia on 20 October, 1989.
Biogeochemical processes in estuaries: N and P fluxes in Tomales Bay, California. Invited seminar, Newfoundland Institute for Cold Ocean Studies, Memorial University of Newfoundland, St. John's, Newfoundland. 18 Oct. 1989.
Role of bacteria in estuarine biogeochemistry. Invited speaker, Department of Biology, Western Washington University, Bellingham, Washington. April 27, 1990.
The Tomales Bay LMER program. Invited speaker, Central California marine biology workshop, University of California, Santa Cruz, California. May 19, 1990.
Bacterioplankton as dissolved organic matter. Invited seminar, Institute of Marine Studies, University of California, Santa Cruz. February 27, 1991.
Relationship between thymidine metabolism, bacterioplankton community metabolic capabilities and sources of organic matter used for growth. Invited speaker, symposium honoring Dr. Lawrence Pomeroy at his retirement. Department of Marine Science, University of Georgia, Athens, GA. 28 October, 1993.
Structure of bacterioplankton communities: A novel molecular approach reveals relationships between community composition, metabolic capabilities and organic matter. Invited seminar, University of California Bodega Marine Laboratory, Bodega Bay, CA. 5 May, 1994.
Comparison of the metabolic characteristics and composition of bacterioplankton communities from San Francisco Bay and Tomales Bay. Invited seminar, Department of Integrative Biology, University of California, Berkeley CA. 1 December, 1994.
A comparison of bacterioplankton in San Francisco Bay and Tomales Bay: metabolic characteristics and taxonomic composition. Invited seminar, Water Resources Division, U.S. Geological Survey, Menlo Park, CA. 31 March 1995.
Relationship between organic matter composition, bacterioplankton community composition, bacterioplankton diversity and assimilation efficiencies. Invited seminar, Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME. 16 August, 1995
DOM composition, bacterioplankton community composition and bacterioplankton assimilation efficiency: So what? Invited seminar, Horn Point Environmental Laboratory, University of Maryland, Cambridge MD. 21 September, 1995.
Influence of human activity on carbon metabolism in coastal ecosystems: case studies from Tomales Bay and San Francisco Bay, California. Invited seminar, Department of Biology, University of Southern California. Los Angeles CA, 19 March, 1996.
What's for lunch? Life in the SF Bay ETM as seen from the perspective of a microbiologist. Invited seminar, Horn Point Environmental Laboratory, University of Maryland, Cambridge MD. 4 June, 1996.
Composition of microbial communities studied by denaturing gradient gel electrophoresis. Invited seminar, Department of Marine Science, University of Georgia, Athens GA, 14 January, 1997. Similar seminars were presented at the Sapelo Island Marine Laboratory and the Skidaway Institute of Oceanography, Savannah GA on 16 and 17 January, 1997.
Bacteria in the Arctic Ocean: towards a basin-scale biogeography. Invited seminar, Skidaway Institute of Oceanography, Savannah GA, 13 November, 1998.
Phylogenetic variation in bacterial populations from 10 atoll lagoons in the Tuamotu Islands, French Polynesia. Invited seminar, Centre Oceanologie Marseille, Centre Natl. de la Recherche Scientifique, Universite Marseille - Campus de Luminy. Marseille France, 11 March, 1999.
Examining the composition of microbial communities - what can it tell us about an ecosystem? Plenary address, Atlantic Estuarine Research Society and Invited Seminar, College of William and Mary, Virginia Institute for Marine Science, Gloucester Point VA, 23 April, 1999.