Berg GM, Thomas S, Hayashi K, Ross M, Kudela R (2017) Variation in growth rate, carbon assimilation, and photosynthetic efficiency in response to nitrogen source and concentration in phytoplankton isolated from upper San Francisco Bay. Journal of Phycology (in press).
Factors Affecting Growth of Cyanobacteria – With Special Emphasis on the Sacramento-San Joaquin Delta, AMS. Commissioned by: Southern California Coastal Water Research Project for The Central Valley Regional Water Quality Control Board and The California Environmental Protection Agency State Water Resources Control Board, August 2015: SCCWRP Technical Report no. 869. Principal Author.
Impact of Nutrient Concentrations and Ratios on Phytoplankton Community Composition – With special emphasis on the San Francisco Bay Estuary, AMS. Prepared for: The San Francisco Estuary Institute in support of The San Francisco Bay Nutrient Management Strategy, 2015. Principal Author.
Scientific Basis to Assess the Effects of Nutrients on San Francisco Bay Beneficial Uses, AMS. Prepared for San Francisco Bay Regional Water Quality Control Board. June 2015. Technical Report no. 864. Contributing Author.
Literature Review on Factors Influencing Phytoplankton Nutrient Uptake and Metabolism: Molecular and Phytoplankton Ecology Perspectives, AMS. Prepared for the Suisun Bay Ammonium Synthesis Report, 2014, Eds: Senn, D.B. and Novick E., Contribution no. 706. San Francisco Estuary Institute, Richmond, CA. Chapter Author.
Esparza ML, Farrell AE, Craig DJ, Swanson C, Dhaliwal BS, Berg GM (2014) Impact of atypical ammonium concentrations on phytoplankton abundance and composition in fresh versus estuarine waters. Aquat Biol 21:191-204.
Assmy P, Smetacek V, Montresor M and 21 others (2013) Thick-shelled, grazer-protected diatoms decouple ocean carbon and silicon cycles in the iron-limited Antarctic Circumpolar Current. PNAS 110:20633-20638.
Smetacek V, Klaas C, Strass VH and 27 others (2012) Deep carbon export from a Southern Ocean iron-fertilized diatom bloom. Nature 487:313-319 doi:10.1038/nature11229.
Chan CX, Zauner S and 14 others (2012) Analysis of Porphyra membrane transporters demonstrates gene transfer among photosynthetic eukaryotes and numerous sodium-coupled transport systems. Plant Physiology 158:2001-2012.
Berg GM, Shrager J, VanDijken G, Mills MM, Arrigo KR, Grossman AR (2011) Responses of hli, ptox and psbA genes to changes in irradiance in marine Synechococcus and Prochlorococcus. Aquatic Microbial Ecology 65:1-14.
Berg GM, Mills MM, Long MC, Bellerby R, Strass V, Savoye N, Rottgers R, Croot PL, Webb A, Arrigo KR (2011) Variation in particulate C and N isotope composition following iron fertilization in two successive phytoplankton communities in the Southern Ocean. Global Biogeochemical Cycles 25, GB3013, doi:10.1029/2010GB003824.
Gobler CJ, Berry DL and 31 others (2011) Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics. PNAS 108:4352-4357.
Kropuenske LR, Mills MM, van Dijken GL, Alderkamp AC, Berg GM, Arrigo KR, Robinson DH and NA Welschmeyer (2010) Strategies and rates of photoacclimation in two major Southern Ocean phytoplankton taxa: Phaeocystis antarctica (Haptophyta) and Fragilariopsis cylindrus (Bacillariophyceae). Journal of Phycology 46: 1138-1151.
Mills MM, Kropuenske LR, Alderkamp AC, van Dijken GL, Robinson DH, Berg GM Welschmeyer NA and KR Arrigo (2010) Photophysiology in two major Southern Ocean phytoplankton taxa: Photosynthesis of Phaeocystis antarctica (Prymnesiophyceae) and Fragilariopsis cylindrus (Bacillariophyceae) under simulated mixed layer irradiance. Journal of Phycology 46: 1114-1127.
Gantt E, Berg GM and 26 others (2010) Porphyra: complex life histories in a harsh environment. In: J. Seckback and D. Chapman (eds) Red Algae in the Genomic Age. (volume 13 of Cellular Origins Life in Extreme Habitats and Astrobiology) Springer.
Solomon CM, Collier JL, Berg GM and PM Glibert (2010) Role of urea in microbe metabolism in aquatic systems: a biochemical and molecular review. Aquatic Microbial Ecology 59:67-88.
Leblanc K, Hare CE, Feng Y, Berg GM, DiTullio J, Neeley A, Benner I, Sprengel C, Beck A, Sanudo-Wilhelmy SS, Passow U, Schreiber K, Rowe JM, Wilhelm SW, Brown CW, and DA Hutchins (2009) Distribution of calcifying and silicifying phytoplankton in relation to environmental and biogeochemical parameters during the late stages of the 2005 North East Atlantic Spring Bloom. Biogeosciences 6:2155-2179.
Glibert PM and GM Berg (2008) Nitrogen and phytoplankton blooms. In: Experimental Ecosystems and Scale: tools for understanding and managing coastal ecosystems. Edited by JE Petersen, VS Kennedy, WC Dennison and WM Kemp. Springer Science and Business media, New York, NY, pp. 183-190.
Rowe JM, Saxton MA, Cottrell MT, DeBruyn JM, Berg GM, Kirchman DA, Hutchins DA and SW Wilhelm (2008) Constraints on viral production in the Sargasso Sea and North Atlantic. Aquatic Microbial Ecology. 52: 233-244.
Glibert PM, Azanza R, Burford M, Furuya K, Abal E, Al-Azri A, Al-Yamani F, Andersen P, Beardall J, Berg GM and 44 others (2008) Ocean urea fertilization for carbon credits poses high ecological risks. Marine Pollution Bulletin. 56: 1049-1056.
Berg GM, Shrager J, Gloeckner G, Arrigo KR and AR Grossman (2008) Understanding nitrogen limitation in Aureococcus anophagefferens (Pelagophyceae) through cDNA and qRT-PCR analysis. Journal of Phycology 44: 1235-1249.
Bailey S, Melis A, Mackey KRM, Cardol P, Finazzi G, van Dijken G, Berg GM, Arrigo KR, Shrager J and AR Grossman (2008) Alternative photosynthetic electron flow to oxygen in marine Synechococcus. Biochimica et Biophysica Acta 1777: 269-276.
Berg GM and NOG. Jørgensen (2006) Purine and pyrimidine metabolism by estuarine bacteria. Aquatic Microbial Ecology. 42: 215-226.
Berg GM, Repeta DJ and J LaRoche (2003a) The role of the picoeukaryote Aureococcus anophagefferens in cycling of marine high-molecular weight dissolved organic nitrogen. Limnology and Oceanography 48: 1825-1830.
Berg GM, Balode M, Purina I, Bekere S, Bechemin C and SY Maestrini (2003b) Plankton community composition in relation to availability and uptake of oxidized and reduced nitrogen. Aquatic Microbial Ecology 30: 263-274.
Berg GM, Repeta DJ and J LaRoche (2002) Dissolved organic nitrogen hydrolysis rates in axenic cultures of Aureococcus anophagefferens (Pelagophyceae): comparison with heterotrophic bacteria. Applied and Environmental Microbiology 68: 401-404.
Berg GM, Glibert PM, Jørgensen NOG, Balode M, and I Purina (2001) Variability in inorganic and organic nitrogen uptake associated with riverine nutrient input in the Gulf of Riga, Baltic Sea. Estuaries 24: 204-214.
Jørgensen NOG, Tranvik L and GM Berg (1999) Occurrence and bacterial cycling of dissolved nitrogen in the Gulf of Riga, the Baltic Sea. Marine Ecology Progress Series 191: 1-18.
Berg GM, Glibert PM, and C-C. Chen (1999) Dimension effects of enclosures on ecological processes in pelagic systems. Limnology and Oceanography 44: 1331-1340.
Mulholland MR, Glibert PM, Berg GM, VanHeukelem L, Pantoja S, and C Lee (1998) Extracellular amino acid oxidation by phytoplankton and cyanobacteria: a cross-ecosystem comparison. Aquatic Microbial Ecology 15: 141-152.
Berg GM, Glibert PM, Lomas MW, and M Burford (1997) Organic nitrogen uptake and growth by the Chrysophyte Aureococcus anophagefferens during a brown tide event. Marine Biology 129:377-387.
Miller CA, Glibert PM, Berg GM, Mulholland MR (1997) Effects of grazer and substrate amendments on nutrient and plankton dynamics in estuarine enclosures. Aquatic Microbial Ecology 12:251-261.
Lomas MW, Glibert PM, Berg GM, Burford M (1996) Characterization of nitrogen uptake by natural populations of Aureococcus anophagefferens (Chrysophyceae) as a function of incubation duration, substrate concentrations, light, and temperature. Journal of Phycology 32: 907-916.
Coats DW, Bockstahler KR, Berg GM, Sniezek JH (1994) Dinoflagellate infections of Favella panamensis from two North American estuaries. Marine Biology 119: 105-113.
Berg GM, Thomas S, Hayashi K, Ross M, Kudela R (2017) Variation in growth rate, carbon assimilation, and photosynthetic efficiency in response to nitrogen source and concentration in phytoplankton isolated from upper San Francisco Bay. Journal of Phycology (in press)
DeCarlo, E.H., M.S. Tomlinson, L.E. deGelleke, and S. Thomas (2013). Distribution and abundance of arsenic in the soils and sediments of O’ahu, Hawai’i. Aquatic Geochemistry DOI 10.1007/s10498-013-9212-9.
Bruno, B.C., S.Thomas, L. James, and M. Frazier (2011). Student perspectives on facilitating positive undergraduate research experiences. Council on Undergraduate Research Quarterly 32(2); 40-43.
S. Thomas (2010). Reflections of an MBARI 2010 summer intern. Ocean Carbon and Biogeochemistry Newsletter 3(3);9.
Lees, D. C. and J. L. Elliott. 2010. Pre-construction Survey Report and Videos of the Subtidal Environment Potentially Effected by Expansion of the Sitka Rocky Gutierrez Airport, Sitka, AK. Report prepared for PENTEC/Hart Crowser, Edmonds, WA
Elliott, J.L. 2009. Review of data from samples collected for bacterial analyses from coastal storm drains in Encinitas, Solana Beach, and Del Mar, CA. Report prepared for Coastal Environments.
Lees, D. C. and J. L. Elliott. 2007. Qualitative Nature of Subtidal Biota on Shallow Substrata Adjacent to Sitka Airport. Report Prepared for PENTEC Environmental.
Lees, D. C. and J. L. Elliott. 2006. Final Comparison for Pre- and Post-operations Kelp Assessment in Areas Associated With Demolition of Remnant Pier Structure and Construction of Bird Roosts in State of California Tidelands Lease PRC-421, Santa Barbara County, California. Prepared for Fairweather Pacific LLC and BP/ARCO for submittal to regulatory agencies.
L. Elliott and H. Elwany. 2006. Ground-Truth Of The Biological Resources Offshore Of San Clemente, California In Potential Areas For Expansion Of The San Onofre Artificial Reef. Report prepared for Coastal Environments and Southern California Edison Company.
Lees, D. C. and J. L. Elliott. 2003. Biological Survey Results for Ground-truth Surveys for the Nearshore San Diego Coastline Habitat Mapping Project. Prepared for Pelagos-Thales.
Elliott, J.L. 1979-1994. Report Coordinator and Editor for Annual and Semiannual Marine Environmental Monitoring, Technical Specifications, and NPDES Reports for the San Onofre Nuclear Generating Station. Prepared for Southern California Edison Company, Rosemead, California, 41 reports.
Elliott, J.L. 1992. “Perspectives on the Design of an Artificial Reef to Support Giant Kelp.” In Compendium of Papers Presented at the Special Artificial Reef Design Workshop, November 1991. Prepared for Southern California Edison Company.
Carter, J.W., M.S. Foster, and J.L. Elliott. 1986. Substratum Composition and Stability in the San
Onofre Kelp Forest. In: Report on 1985 Data, Marine Environmental Analysis and Interpretation, San Onofre Nuclear Generating Station. Prepared for Southern California Edison Company. Report number 86-RD-26.
Lester, W.C., D.C. Lees, and J.L. Elliott. 1985. Pre- and Post-construction Surveys and Impact Analysis of Pipeline Construction on Kelp Resources Along the Molino Pipeline Corridor
(PRC 2933), Tajiguas, California. Prepared for Phillips Oil Co. Lester, W.C., and J.L. Elliott. 1985. Marine Biological Survey of the Proposed Flowline Landfall at Arroyo Hondo, California. Prepared for Shell California Production Inc.
Elliott, J.L. South Bay Power Plant Receiving Water Monitoring Program. Multiple annual reports for NPDES requirements. Prepared for SDG&E, San Diego, California, 1977 to 1981; 1984.
L. Elliott and H. Elwany. 2006. Ground-Truth Of The Biological Resources Offshore Of San Clemente, California In Potential Areas For Expansion Of The San Onofre Artificial Reef.Report prepared for Coastal Environments and Southern California Edison Company.
Elliott, J.L. 2000. Observations on the Status of the Biological and Physical Intertidal Resources Along the Coastline of Encinitas and Carlsbad, CA. Prepared for Coastal Environments/Cities of Encinitas and Carlsbad.
Elliott, J.L., and P.C. Rusanowski. 1978. Report on 96-hour static bioassays on whole and settled effluent performed for the Oxnard sewage outfall. Prepared for CH2M HILL, San Diego, California. 13 p.
Gunther, A.J. 2015. Working with invalid boundary conditions: lessons from the field for communicating about climate change with public audiences. American Geophysical Union, Fall Meeting 2015
Connor, M.S, J. A Davis, J. Leatherbarrow, B. K. Greenfield, A. J. Gunther, D. Hardin, T. Mumley, J. J. Oram, and C. Werme. 2007. The slow recovery of the San Francisco Estuary from the legacy of organochlorine pesticides. Environmental Research 105:87-100.
Hoenicke, R., Davis, J.A., Gunther, A.J., Mumley, T.E., Abu-Saba, K., and K. Taberski. 2003. Effective application of monitoring information: the case of San Francisco Bay. Environmental Monitoring and Assessment 81:15-25.
Thompson, B.T., Hoenicke, R.H., Davis, J.A., and A.J. Gunther. 2000. An overview of contaminant-related issues identified by monitoring in San Francisco Bay. Environmental Monitoring and Assessment. 64:409-419.
Gunther, A.J., J.A. Davis, D.D. Hardin, J. Gold, D. Bell, J.R. Crick, G.M. Scelfo, J. Sericano, and M. Stephenson. 1999. Long-term bioaccumulation monitoring with transplanted bivalves in the San Francisco Estuary. Marine Pollution Bulletin 38(3):170-181.
Gunther, A.J., R.B. Spies, J.J. Stegeman, B. Woodin, D. Carney, J. Oakden, and L. Hain. 1997. EROD activity in fish as an independent measure of contaminant-induced mortality of invertebrates in sediment bioassays. Marine Environmental Research. 44:41-48.
Gunther, A.J. 1992. A chemical survey of remote lakes in the Alagnak and Naknek River Systems, Southwest Alaska. Arctic and Alpine Research. 24:64–68.
Davis, J.A., A.J. Gunther and J.M. O’Connor. 1992. Priority pollutant loads from effluent discharges to the San Francisco Estuary. Water Environment Research. 64:134–140.
Gunther, A.J. 1989. Nitrogen fixation by lichens in a subarctic Alaskan watershed. The Bryologist. 92:202–208.
Hart, S.C. and A. J. Gunther. 1989. In situ estimates of annual net nitrogen mineralization and nitrification in a subarctic watershed. Oecologia. 80:284–288.
Gunther, A.J. 1988. The effect of simulated acid deposition on acetylene reduction in the lichen genus Peltigera under field and laboratory conditions. Water, Air, and Soil Pollution. 38:379–385.
Daniels, M.E., J. Hogan, W.A. Smith, S.C. Oates, M.A. Miller, D. Hardin, K. Shapiro, M. Los Huertos, P.A. Conrad, C. Dominik, F.G.R. Watson. 2014. Estimating environmental conditions affecting protozoal pathogen removal in surface water wetland systems using a multi-scale, model-based approach. Science of the Total Environment. 493(2014):1036–1046.
Hogan, J.N., M.E. Daniels, F.G. Watson, S.C. Oates, M.A. Miller, P.A. Conrad, K. Shapiro, D. Hardin, C. Dominik, A. Melli, D.A. Jessup, W.A. Miller, 2013. Hydrologic and vegetative removal of Cryptosporidium parvum, Giardia lamblia, and Toxoplasma gondii surrogate mircrospheres in coastal wetlands. Applied Environmental Microbiology. 79(6):1859–1865.
Hogan, J.N., M.E. Daniels, F.G. Watson, P.A. Conrad, S.C. Oates, M.A. Miller, D. Hardin, B.A. Byrne, C. Dominik, A. Melli, D.A. Jessup, W.A. Miller. 2012. Longitudinal Poisson regression to evaluate the epidemiology of Cryptosporidium, Gardia, and fecal indicator bacteria in coastal California wetlands. Applied Environmental Microbiology. 78(10):3606–3613.
Oates, S.C., M.A. Miller, B.A. Byrne, N. Chouicha, D. Hardin, D. Jessup, C. Dominik, A. Roug, A. Schriewer, S.S. Jang, W.A. Miller. 2012. Epidemiology and potential land-sea transfer of enteric bacteria from terrestrial to marine species in the Monterey Bay region of California. Journal of Wildlife Diseases. 48(3):654–668.
Oates, S.C., M.A. Miller, D. Hardin, P.A. Conrad, A. Melli, D.A. Jessup, C. Dominik, A. Roug, M.T. Tinker, W.A. Miller. 2012. Prevalence, environmental loading, and molecular characterization of Cryptosporidium and Giardia isolates from domestinc and wild animals along the central California coast. Applied and Environmental Microbiology. 78(24):8762–8772.
Miller, M.A., R.M. Kudela, A. Mekebri, D. Crane, S.C. Oates, M.T. Tinker, M. Staedler, W.A. Miller, S. Toy-Choutka, C. Dominik, D. Hardin, G. Langlois, M. Murray, K. Ward, D.A. Jessup. 2010. Evidence for a novel marine harmful algal bloom: cyanotoxin (microcystin) transfer from land to sea otters. PLoS One, 2010 Sep 10;5(9).
Schriewer, A., W.A. Miller, B.A. Byrne, M.A. Miller, S. Oates, P.A. Conrad, D. Hardin, H.H. Yang, N. Chouicha, A. Melli, D. Jessup, C. Dominik, S. Weurtz. 2010. Presence of Bacteroidales as a predictor of pathogens in surface water of the central California coast. Applied Environmental Microbiology. 76(17):5802–5814.
Connor, M.S, J.A. Davis, J. Leatherbarrow, B.K. Greenfield, A. Gunther, D. Hardin, T. Mumley, J.J. Oram, C. Werme. 2007. The slow recovery of San Francisco Bay from the legacy of organochlorine pesticides. Environmental Research 105:87-100.
Nairn, R., J.A. Johnson, D. Hardin, J. Michel. 2004. A biological and physical monitoring program to evaluate long-term impacts from sand dredging operations in the United States outer continental shelf. Journal of Coastal Research. 20(1):126-137.
Foster, M.S., E.W. Nigg, L.M. Kiguchi, D.D. Hardin, J.S. Pearse. 2003. Temporal variation and succession in an algal-dominated high intertidal assemblage. Journal of Experimental Marine Biology and Ecology 289 (2003) 15– 39.
Gunther, A.J., J.A. Davis, D.D. Hardin, J. Gold, D. Bell, J.R. Crick, G.M. Scelfo, J. Sericano, M. Stephenson. 1999. Long-term Bioaccumulation Monitoring with Transplanted Bivalves in the San Francisco Estuary. Marine Pollution Bulletin. 38(3): 170-181.
Montagna, P.A., J.E. Bauer, D. Hardin, and R.B. Spies. 1995. Meiofaunal and microbial trophic interactions in a natural submarine hydrocarbon seep. Vie et Milieu, 45(1): 17–25.
Hardin, D.D., J. Toal, T. Parr, P. Wilde, and K. Dorsey. 1994. Spatial variation in hard-bottom epifauna in the Santa Maria Basin: The importance of physical factors. Marine Environmental Research, 37(2):165–193.
Hyland, J., D. Hardin, S. Steinhauer, D. Coats, R. Green, and J. Neff. 1994. Environmental impact of offshore oil development on the outer continental shelf and slope off Pt. Arguello, CA. Marine Environmental Research, 37(2):194–229.
Hardin, D.D., D. Graves, and E. Imamura. 1992. Investigating seafloor disturbances with a small ROV. Marine Technology Society Journal, 26(4):40–45.
Brewer, G., J. Hyland, and D. Hardin. 1991. Effects of oil drilling on deep-water reefs offshore California. American Fisheries Society Symposium, 11:26–38.
Coats, D., M. Savoie, and D. Hardin. 1991. Poleward flow on the Point Conception continental shelf and its relation to the distribution of oil-drilling particulates and biological impacts. EOS Transactions. American Geophysical Union, 72(44):254.
Foster, M.S., C. Harrold, and D.D. Hardin. 1991. Point vs. photo quadrat estimates of the cover of sessile marine organisms. Journal of Experimental Marine Biology and Ecology, 146:193–203.
Hyland, J., D. Hardin, E. Crecelius, D. Drake, P. Montagna, and M. Steinhauer. 1990. Monitoring long-term effects of offshore oil and gas development along the southern California outer continental shelf and slope: Background environmental conditions in the Santa Maria Basin. Oil & Chemical Pollution, 6:195–240.
Spies, R.B., J.E. Bauer, and D. Hardin. 1989. Stable isotope study of sedimentary carbon utilization by Capitella spp.: Effects of two carbon sources and geochemical conditions during their diagenesis. Marine Biology, 101:69–74
Montagna, P.A., J.E. Bauer, D. Hardin, and R.B. Spies. 1989. Vertical distribution of microbial and meiofaunal populations in sediments of a natural coastal hydrocarbon seep. Journal of Marine Research, 47:657–680.
Bauer, J.E., P.A. Montagna, R.B. Spies, M.C. Prieto, and D. Hardin. 1988. Microbial biogeochemistry and heterotrophy in sediments of a marine hydrocarbon seep. Limnology and Oceanography, 33(6):1493–1513.
Palmer, M.A., P.A. Montagna, R.B. Spies, and D. Hardin. 1988. Meiofauna dispersal near natural petroleum seeps in the Santa Barbara Channel: A recolonization experiment. Oil & Chemical Pollution, 4:179–189.
Spies, R., D. Hardin, and J. Toal. 1988. Organic enrichment or toxicity? A comparison of the effects of kelp and crude oil in sediments on the colonization and growth of benthic infauna. Journal of Experimental Marine Biology and Ecology, 124:261–282.
Caimi, F.M., R.F. Tusting, and D. Hardin. 1987. Laser-aided quantitative sampling of the sea bed. Proceedings of Oceans ‘87, pp 1234–1238.
Montagna, P.A., J.E. Bauer, J. Toal, D. Hardin, and R.B. Spies. 1987. Temporal variability and the relationship between benthic meiofaunal and microbial populations of a natural coastal petroleum seep. Journal of Marine Research, 45:761–789.
Harrold, C. and D. Hardin. 1986. Prey Consumption on land by the California sea otter, Enhydra lutris. Marine Mammal Science, 2(4):309–313.
Montagna, P.A., J.E. Bauer, M.C. Prieto, D. Hardin, and R.B. Spies. 1986. Benthic metabolism in a natural coastal petroleum seep. Marine Ecology – Progress Series, 34:31–40.
Toimil, L., E. Ticken, D. Hardin, D. White. 1982. Mapping significant rock habitats using seismic reflection techniques, Beaufort Sea, Alaska. Geophysics 47(4).
Hardin, D.D. 1968. A comparative study of lethal temperatures in the limpets Acmaea scabra and Acmaea digitalis. The Veliger (Supplement) 11:83–88.
Nairn, R., Johnson, J.A., Hardin, D., and Michel, J. 2002. Development and Design of a Biological and Physical Monitoring Program for the Evaluation of Long-term Impacts to the Marine Environment from Offshore Sand Dredging Operations in the U.S. Outer Continental Shelf. Journal of Coastal Research. 20:1 pp 126-137.
Boehm, P.D. Turton, A. Raval, D. Caudle, D. French, N. Rabalais, R. Spies, and J. Johnson. 2001. Deepwater Program: Literature Review, Environmental risks of Chemical Products Used in Gulf of Mexico Deepwater Oil and Gas Operations; Volume : Technical Report. OCS Study MMS 2001-011. U.S. Department of the Interior, Minerals Management Service, Gulf of Mexico OCS Region, New Orleans, LA. 326 pp.
Johnson, J.A., Hardin, D., Spies, R. 1985. An Investigation of the Effects of Discharged Drilling Fluids from Exploratory Drilling on Hard Bottom Communities in the Western Santa Barbara Channel. Symposium Proceedings, Oceans ’85, Marine Technology Society.
Johnson, J.A. 1984. The Use of a Manned Submersible in a Deep Water Hard Bottom Monitoring Program. Paper Presented at the American Academy of Underwater Sciences Symposium. November, 1984. La Jolla, CA.
Goncalves, P., Anderson, K., Thompson, E.L., Melwani, A.R., Parker, L., Ross, P.M., Raftos, D.A. 2016. Rapid transcriptional acclimation following transgenerational exposure of oysters to ocean acidification, Molecular Ecology 25(19): 4836-49.
Raftos, D.A., Melwani, A.R., Haynes, P.A., Muralidharan, S., Birch, G.F., Amaral, V., Thompson, E.L., Taylor, D. 2016. The Biology of Environmental Stress: Molecular biomarkers in Sydney rock oysters (Saccostrea glomerata), Environmental Science: Processes and Impacts 18: 1129-1139.
Melwani, A.R., Thompson, E.L., Raftos, D.A. 2016. Differential proteomic response of Sydney rock oysters (Saccostrea glomerata) to prolonged environmental stress, Aquatic Toxicology 173: 53-62.
Green, T. J., Chataway, T., Melwani, A. R., Raftos, D. A. 2016. Proteomic analysis of hemolymph from poly (I:C)-stimulated Crassostrea gigas. Fish & Shellfish Immunology 48: 39-42.
Anderson, K., Taylor, D.A., Thompson, E.L., Melwani, A. R., Nair, S.V., Raftos, D.A. 2015. Meta-analysis of studies using Suppression Subtractive Hybridization and Microarrays to investigate the effects of environmental stress on gene transcription in oysters, PLoS ONE 10(1): e0118839.
Birch, G., Melwani, A.R., Lee, J., Apostolatos, C. 2014. The discrepancy in concentration of metals (Cu, Pb and Zn) in oyster tissue (Saccostrea glomerata) and ambient bottom sediment (Sydney estuary, Australia). Marine Pollution Bulletin 80(1-2): 263-274.
Greenfield, B.K., Melwani, A.R., Bay, S. 2014. A tiered assessment framework to evaluate human health risk of contaminated sediment, Integrated Environmental Assessment and Management 11(3): 459-473.
Melwani, A.R., Gregorio, D., Jin, Y., Stephenson, M., Ichikawa, G., Siegel, E., Crane, D., Lauenstein, G. Davis, J.A. 2014. Mussel Watch Update: Long-term trends in selected contaminants from coastal California, 1977- 2010 Marine Pollution Bulletin 81(2): 291-302.
Thompson, B., Ranasinghe, J.A. Lowe, S., Melwani, A.R., Weisberg, S.B. 2013. Benthic macrofaunal assemblages of the San Francisco Estuary and Delta, USA Environmental Monitoring and Assessment 185: 2281-2295.
Greenfield, B.K., Melwani, A.R., Allen, R.M., Slotton, D.G., Ayers, S.M., Harrold, K.H., Ridolfi, K., Jahn, A., Grenier, J.L., Sandheinrich, S.B. 2013, Seasonal and annual trends in forage fish mercury concentrations, San Francisco Bay, Science of the Total Environment 444: 591-601.
Thompson, B., Weisberg S.B., Melwani, A.R., Lowe, S. Ranasinghe, J.A., Cadien D.B., Dauer D.M., Diaz, R.J., Fields, W., Kellogg, M., Montagne, D.E., Ode, P.R., Reish, D.J., Slattery, P.N. 2012. Low levels of agreement among experts using best professional judgment to assess mesohaline and limnetic benthic macrofaunal condition in the San Francisco Estuary. Ecological Indicators 12: 167-173.
Melwani, A.R., Greenfield, B.K., Byron, E.R. 2009. Empirical estimation of biota exposure range for calculation of bioaccumulation parameters. Integrated Environmental Assessment and Management. 5: 128-139.
Melwani, A.R., Bezalel, S.N., Hunt, J.A., Grenier, J.L., Davis, J.A. 2009. Spatial trends and impairment assessment of mercury in fish from the Sacramento-San Joaquin Delta watershed. Environmental Pollution. 157: 3137-49.
Melwani A.R, Kim S.L. 2008. Benthic infaunal distributions in shallow hydrothermal vent sediments. Acta Oecologica. 33(2): 162-75.
2016. with Burns, K.A. and M. Mukhtasor. 2017. The Montara Oil Spill: A 2009 well blowout in the Timor Sea”. Archiv. Environ. Contam. Toxicol. (in press).
2016. with S. Senner and C.S. Robbins. 2016.An overview of the northern Gulf of Mexico ecosystem. Gulf of Mexico Science. 33: 98-121.
2012. with Peterson, C.H. and 20 other co-authors. A tale of two spills: Novel science and policy implications of an emerging new oil spill model. Bioscience 62: 461-469.
2008. Kondolf, G.M., Angermeier, P.L., Cummins, K., Dunne, T., Healey, M., Kimmerer, W. , Moyle, P.B., Murphy, D. , Patten, D., Railsback, S., Reed, D.J., Spies, R., Twiss, R. Projecting cumulative benefits of multiple river restoration projects: An example from the Sacramento-San Joaquin river system in California. Environ. Manag. 42: 933-945.
2007. Oros, D.R., J.R.M. Ross, R.B. Spies and T. Mumley. Polycyclic aromatic hydrocarbon (PAH) contamination in San Francisco Bay: A 10-year retrospective of monitoring in an urbanized estuary. Environ. Res. 105: 101-118.
2006. Thompson, B., et al., Biological effects of anthropogenic contaminants in the San Francisco Estuary. Environ. Res. 105: 145-155.
2006. Spies, R.B. (editor/author). Long-term ecological change in the northern Gulf of Alaska. Elsevier, Amsterdam, 589 pp. (several chapters written by R. Spies).
2005. P.R. Mundy and R. Spies. Introduction, pp. 1-14, in The Gulf of Alaska. Biology and Oceanography, Alaska Sea Grant Publication, Fairbanks Alaska, 214 pp.
1997 R.B. Spies and P. Thomas. Reproductive and endocrine status of mature female kelp bass Paralabrax clathratus from a contaminated site in the Southern California Bight and estrogen receptor binding of DDTs, Chapter 9, in Chemically-induced alterations in functional development and reproduction of fishes, R.M. Rolland, M. Gilbertson and R.E. Peterson (Eds.) Society of Environmental Contamination and Toxicology, Technical Publication Series, SETAC Press, Pensacola, Fl.
1997. A.J.Gunther, R.B. Spies, J.J. Stegeman, B. Woodin, D. Carney, J. Oakden, and L. Hain. 1997. EROD activity as an independent measure of contaminant-induced mortality of invertebrates in sediment bioassays. Mar. Environ. Res. 44:41-49.
1996. R. B. Spies, S. D. Rice, D. A. Wolfe and B. A.Wright. The effects of the Exxon Valdez Oil spill on the Alaskan Coastal environment, pp. 1-16, in: Rice, S.D., R.B. Spies, D.A. Wolfe, and B.A. Wright (Eds.) Exxon Valdez Oil Spill Proceedings, Anchorage, Alaska, 2-5 February 1993. American Fisheries Society Symposium No. 18.
1996. R.B. Spies, P. Thomas, and M. Matsui. 1996. Effects of DDT and PCB on reproductive endocrinology of Paralabrax clathratus in southern California. Mar. Environ. Res. 42, 175-176. (abstract)
1996 R.B. Spies, R.B., J.J. Stegeman, D.E. Hinton, B. Woodin, M. Okihiro, R. Smolowitz and D. Shea. Biomarkers of hydrocarbon exposure and sublethal effects in embiotocid fishes from a natural petroleum seep in the Santa Barbara Channel. Aquatic Toxicol. 34:195-219.
1995. R. Spies. Restoring Prince William Sound. Science 269, 1328-1329. (letter)
1994 D.W. Rice, C.B. Seltenrich, M.L. Keller, .R.B. Spies, and J.S. Felton. Mixed-function oxidase-specific activity in wild and caged speckled sandabs Citharichtys stigmaeus in Elkhorn Slough. Environ. Poll. 84, 179-188.
1993 R.B. Spies. So why can’t science tell us more about the effects of the Exxon Valdez oil spill ?, pp. 1-5, In: Exxon Valdez oil spill symposium, EVOS Trustee Council, Anchorage Alaska.
1993. D.W. Rice, Seltenrich, C.P., Keller, M.L., Spies, R.B., Felton, J.S. Seasonal and annual distribution of organic contaminants in marine sediments from Elkhorn Slough, Moss Landing Harbor and nearshore Monterey Bay, California. Environmental Pollution 82: 79-91.
1993. J.W. Anderson, D.J. Reish, R.B. Spies, M.E. Brady and E.W. Segelhorst. Human impacts, pp. 682-766, In: Ecology of the Southern California Bight (M.D. Daily, J.W. Anderson, and D.J. Reish, eds.) University of California Press, Berkeley, 926 pp.
1992 M.J. Melanacon, R. Alscher, W. Benson, G. Kruzynski, R.F. Lee, H.C. Sikka, R.B. Spies. Metabolic products as biomarkers, In: Biomarkers: Biochemical, physiological and hstological markers of anthropogenic stress (Huggett et al., Eds) Lewis Publishers, Boca Raton, Florida.
1990 J.E. Bauer, R.B. Spies, J. S. Vogel, D.E. Nelson and J.R. Southon. Radiochemical evidence of fossil hydrocarbon cycling in sediments of a nearshore hydrocarbon seep. Nature 348, 230-232.
1990 R.B. Spies, J.J. Stegeman, D.W. Rice, Jr., B. Woodin, P. Thomas, J.E. Hose, J. Cross and M. Prieto. Sublethal responses of Platichthys stellatus to organic contamination in San Francisco Bay with emphasis on reproduction, pp. 87-122, in Biological Markers of Environmental Contamination. Lewis Publishers, Chelsea, Michigan .
1989 R.B. Spies, D.W. Rice Jr., P.J. Thomas, J.J. Stegeman, J.N. Cross and J.E. Hose. A field test for correlates of poor reproductive success and genetic damage in contaminated populations of starry flounder, Platichthys stellatus. Mar. Environ. Res. 28: 542-543.
1989 R. B. Spies, H. Kruger, R. Ireland and D.W. Rice, Jr. Stable isotope isotope ratios and contaminant concentrations in a sewage-distorted food web. Mar. Ecol. Prog. Ser. 54, 157-170.
1989 R.B. Spies, J.E. Bauer and D. H. Hardin. A stable isotope study of sedimentary carbon utilization by Capitella spp.: effects of two carbon sources and geochemical conditions during their diagenesis Mar. Biol. 101: 68-74.
1989 R.B. Spies, D.D. Hardin and J.P. Toal. Organic enrichment or toxicity? A comparison of the effects of kelp and crude oil in sediments on the colonization and growth of benthic infauna. J. Exp. Mar. Ecol. 124, 261-282.
1988 D.J. H. Phillips and R.B. Spies. Chlorinated hydrocarbons in the San Francisco estuarine ecosystem. Mar. Poll. Bull. 19, 445-453.
1988 J.E. Bauer, P.A. Montagna, R.B. Spies, D.H. Hardin and M. Prieto. Microbial
biogeochemistry and heterotrophy in sediments of a marine hydrocarbon seep. Limnol.
Oceanogr. 33, 1493-1513.
1988 R.B. Spies and D.W. Rice, Jr. The effects of organic contaminants on reproduction of starry flounder, Platichthys stellatus (Pallas) in San Francisco Bay. Part II. Reproductive success of fish captured in San Francisco Bay and spawned in the laboratory. Mar. Biol. 98, 191-202.
1988 R. B. Spies, D.W. Rice, Jr. and J.W. Felton. The effects of organic contaminants
on reproduction of starry flounder, Platichthys stellatus (Pallas) in San Francisco Bay. Part I. Hepatic contamination and mixed-function oxidase (MFO) activity during the reproductive season. Mar. Biol. 98, 181-189.
1987 Melzian, B. D., Zoffman, C. and R.B. Spies. Chlorinated hydrocarbons in lower
continental shelf fish collected near the Farallon Islands, California. Mar. Poll. Bull. 18,
1987 P.A. Montagna, J.E. Bauer, J. Toal, D.H. Hardin and R.B. Spies. Temporal variability and the relationship between benthic meiofaunal and microbial populations in a natural coastal petroleum seep. J. Mar. Res . 45, 761-789.
1987 R. B. Spies , B. Andresen and D.W. Rice, Jr. Benzthiazoles in estuarine sediments as indicators of street runoff. Nature 327: 697-699.
1987 R. B. Spies. The biological effects of petroleum hydrocarbons in the sea: Assessments from field and microcosms, pp. 411-467 in: Long-term environmental effects of offshore oil and gas development. D.F. Boesch and N.N. Rabalais, Eds. Elsevier-Applied Sciences, London.
1986 P.A. Montagna, J.E. Bauer, M.C. Prieto, D.H. Hardin and R. B. Spies. Benthic metabolism in a natural coastal petroleum seep. Mar. Ecol. Prog. Ser., 34, 31-40.
1985. P.A. Montagna and R.B. Spies. Meiofauna and chlorophyll associated with Beggiatoa mats of a natural submarine petroleum seeps. Mar. Environ. Res. 16, 231-242.
1984 R.B. Spies. Benthic-pelagic coupling in sewage affected ecosystems. Mar. Environm. Res. 13, 195-230.
1983 R.B. Spies and D.J. DesMarais. Natural isotope study of trophic enrichment of
marine benthic communities by petroleum seepage. Mar. Biol. 73, 67-71.
1982 D.H. Steurmer, R.B. Spies, P.H. Davis, D.J. Ng, C.J. Morris and S. Neal. The
hydrocarbon chemistry of the Isla Vista Marine Seep Environment. Mar. Chem. 11, 413-426.
1982 R.B. Spies, J.S.Felton and L.J. Dillard. Hepatic mixed-function oxidases in California flatfish are increased in contaminated environments and by oil and PCB ingestion. Mar. Biol. 70, 117-127.
1982 R.B. Spies and P.H. Davis. Toxicity of Santa Barbara seep oil to starfish embryos. III. Influence of parental exposure and the effects of other crude oils. Mar. Environ. Res. 6, 3-11.
1981 D.H. Steurmer, R.B. Spies and P.H. Davis. Toxicity of Santa Barbara seep oil to
starfish embryos. I. Hydrocarbon composition of test solutions and field samples. Mar. Environ. Res . 5, 275-286.
1981 R. B. Spies, K. Marsh and J. R. Kercher. Dynamics of radionuclide exchange in
the calcareous algae Halimeda at Enewetak Atoll. Limnol. Oceanogr. 26, 74-85.
1980 P.H. Davis and R.B. Spies. Infaunal benthos of a natural petroleum seep: a study of community structure. Mar. Biol. 59, 31-41.
1980 R.B. Spies, P.H. Davis and D. Stuermer. Ecology of a petroleum seep off the
California coast. in Marine Environmental Pollution (R. Geyer, Ed.). Elsevier,
Amsterdam, pp. 229-263.
1975 R.B. Spies Structure and function of the head of flabelligerid polychaetes.
J. Morph . 147, 187-208.