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Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia
Caffrey, J. M., Bano, N., Kalanetra, K., & Hollibaugh, J. T. (2007). Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia. International Society for Microbial Ecology, 1(7), 660-662. doi:10.1038/ismej.2007.79
Atmospheric deposition of mercury and major ions to the Pensacola (Florida) watershed
Caffrey, J. M., Landing, W. M., Nolek, S. D., Gosnell, K. J., Bagui, S. S., & Bagui, S. C. (2010). Atmospheric deposition of mercury and major ions to the Pensacola (Florida) watershed: Spatial, seasonal, and inter-annual variability. Atmospheric Chemistry and Physics, 10, 5425-5434. doi:10.5194/acp-10-5425-2010
Changes in production and respiration during a spring phytoplankton bloom in San Francisco Bay, California, USA
Caffrey, J. M., Cloern, J. E., & Grenz, C. (1998). Changes in production and respiration during a spring phytoplankton bloom in San Francisco Bay, California, USA: Implications for net ecosystem metabolism. Marine Ecology Progress Series, 172, 1-12. doi:10.3354/meps172001
Patterns in phytoplankton and benthic production on the shallow continental shelf in the northeastern Gulf of Mexico
Factors controlling net ecosystem metabolism in U.S. estuaries
Caffrey, J. M. (2004). Factors controlling net ecosystem metabolism in U.S. estuaries. Estuaries, 27(1), 90-101.
Mass independent fractionation of mercury isotopes as source tracers in sediments
Das, R., Landing, W., Bizimis, M., Odom, L., & Caffrey, J. (2015). Mass independent fractionation of mercury isotopes as source tracers in sediments. Procedia Earth and Planetary Science, 13, 151-157. doi:10.1016/j.proeps.2015.07.036
Atmospheric wet deposition of mercury and other trace elements in Pensacola, Florida
Landing, W. M., Caffrey, J. M., Nolek, S. D., Gosnell, K. J., & Parker, W. C. (2010). Atmospheric wet deposition of mercury and other trace elements in Pensacola, Florida. Atmospheric Chemistry and Physics, 10, 4867-4877. doi:10.5194/acp-10-4867-2010
Effect of nutrient loading on biogeochemical and microbial processes in a New England salt marsh
Caffrey, J. M., Murrell, M. C., Wigand, C., & McKinney, R. (2007). Effect of nutrient loading on biogeochemical and microbial processes in a New England salt marsh. Biogeochemistry, 82, 251-264. doi:10.1007/s10533-007-9068-4
Influence of the submersed plant, Potamogeton perfoliatus, on nitrogen cycling in estuarine sediments
Caffrey, J. M., & Kemp, W. M. (1992). Influence of the submersed plant, Potamogeton perfoliatus, on nitrogen cycling in estuarine sediments. Limnology and Oceanography, 37(7), 1483-1495. doi:10.4319/lo.1992.37.7.1483
Atmospheric deposition of mercury, trace elements, and major ions around a coal-fired power plant (3002001018)
Caffrey, J., & Landing, W. (2013). Atmospheric deposition of mercury, trace elements, and major ions around a coal-fired power plant (3002001018).
Short exposure to oxygen and sulfide alter nitrification, denitrification, and DNRA activity in seasonally hypoxic estuarine sediments
Jane M., C., Stefano, B., & Conley, D. J. (2019). Short exposure to oxygen and sulfide alter nitrification, denitrification, and DNRA activity in seasonally hypoxic estuarine sediments. FEMS Microbiology Letters, 336(1). doi:10.1093/femsle/fny288
Seasonal and spatial patterns of oxygen production, respiration and root-rhizome release in Potamogeton perfoliatus L. and Zostera marina L.
Caffrey, J. M., & Kemp, W. M. (1991). Seasonal and spatial patterns of oxygen production, respiration and root-rhizome release in Potamogeton perfoliatus L. and Zostera marina L. Aquatic Botany, 40(2), 109-128. doi:10.1016/0304-3770(91)90090-R
A historical perspective on eutrophication in the Pensacola Bay estuary, FL, USA
Caffrey, J. M., & Murrell, M. C. (2016). A historical perspective on eutrophication in the Pensacola Bay estuary, FL, USA. Aquatic Microbial Ecology and Biogeochemistry: A Dual Perspective, 199-213. doi:10.1007/978-3-319-30259-1_16
Thunderstorms increase mercury wet deposition
Holmes, C. D., Krishnamurthy, N. P., Caffrey, J. M., Landing, W. M., Edgerton, E. S., Knapp, K. R., & Nair, U. S. (2016). Thunderstorms increase mercury wet deposition. Environmental Science & Technology, 50(17), 9343-9350. doi:10.1021/acs.est.6b02586
Effects of irradiance on benthic and water column processes in a Gulf of Mexico estuary
Murrell, M. C., Campbell, J. G., Hagy, III, J. D., & Caffrey, J. M. (2009). Effects of irradiance on benthic and water column processes in a Gulf of Mexico estuary: Pensacola Bay, Florida, USA. Estuarine, Coastal and Shelf Science, 81(4), 501-512. doi:10.1016/j.ecss.2008.12.002
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High cyanobacterial abundance in three northeastern Gulf of Mexico estuaries
Murrell, M. C., & Caffrey, J. M. (2005). High cyanobacterial abundance in three northeastern Gulf of Mexico estuaries. Gulf and Caribbean Research, 17(1), 95-106. doi:10.18785/gcr.1701.08
Benthic nutrient flux in a small estuary in northwest Florida (USA)
DiDonato, G. T., Lores, E. M., Murrell, M. C., Smith, L. M., & Caffrey, J. M. (2006). Benthic nutrient flux in a small estuary in northwest Florida (USA). Gulf and Caribbean Research, 18(1), 15-25.
Benthic processes in South San Francisco Bay
Caffrey, J. M., Hammond, D. E., Kuwabara, J. S., Miller, L. G., & Twilley, R. R. (1996). Benthic processes in South San Francisco Bay: The role of organic inputs and bioturbation. San Francisco Bay: The Ecosystem, 425-442.
High nutrient pulses, tidal mixing and biological response in a small California estuary
Caffrey, J. M., Chapin, T. P., Jannasch, H. W., & Haskins, J. C. (2007). High nutrient pulses, tidal mixing and biological response in a small California estuary: Variability in nutrient concentrations from decadal to hourly time scales. Estuarine, Coastal and Shelf Science, 71(3), 368-380. doi:10.1016/j.ecss.2006.08.015

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