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The contribution of benthic nutrient regeneration to primary production in a shallow eutrophic estuary, Weeks Bay, Alabama
Mortazavi, B., Riggs, A. A., Caffrey, J. M., Genet, H., & Phipps, S. W. (2012). The contribution of benthic nutrient regeneration to primary production in a shallow eutrophic estuary, Weeks Bay, Alabama. Estuaries and Coasts, 35(3), 862-877. doi:10.1007/s12237-012-9478-y
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
Comparing productivity and biogeochemistry of native and transplanted Thalassia testudinum and Halodule beaudettei in Big Lagoon, Florida, USA
Hester, C. M., Smith, H. M., Head, M. E., Langsten, H., Linder, S., Manor, E., Norman, J., Sartory, L., & Caffrey, J. M. (2016). Comparing productivity and biogeochemistry of native and transplanted Thalassia testudinum and Halodule beaudettei in Big Lagoon, Florida, USA. Gulf of Mexico Science: An International Journal, 33(1), 14-25.
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
Patterns in phytoplankton and benthic production on the shallow continental shelf in the northeastern Gulf of Mexico
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.
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).
Effect of organic loading on nitrification and denitrification in a marine sediment microcosm
Caffrey, J. M., Sloth, N. P., Kaspar, H. F., & Blackburn, T. H. (1993). Effect of organic loading on nitrification and denitrification in a marine sediment microcosm. FEMS Microbiology Ecology, 12(3), 159-167.
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 comparison of two nitrification inhibitors used to measure nitrification rates in estuarine sediments
Caffrey, J. M., & Miller, L. G. (1995). A comparison of two nitrification inhibitors used to measure nitrification rates in estuarine sediments. FEMS Microbiology Ecology, 17, 213-220. doi:10.1016/0168-6496(95)00026-7
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.
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
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Biogeochemical processes in a small California estuary.
Caffrey, J. M., Harrington, N., & Ward, B. (2002). Biogeochemical processes in a small California estuary.: 1. Benthic fluxes and pore water constituents reflect high nutrient freshwater inputs. Marine Ecology - Progress Series, 233, 39-53.
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
Spatial and seasonal patterns in sediment nitrogen remineralization and ammonium concentrations in San Francisco Bay, California
Caffrey, J. M. (1995). Spatial and seasonal patterns in sediment nitrogen remineralization and ammonium concentrations in San Francisco Bay, California. Estuaries, 18(1), 219-233.
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
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.
Living oysters and their shells as sites of nitrification and denitrification
Caffrey, J. M., Hollibaugh, J. T., & Mortazavi, B. (2016). Living oysters and their shells as sites of nitrification and denitrification. Marine Pollution Bulletin, 112, 86-90. doi:10.1016/j.marpolbul.2016.08.038
Nitrogen cycling in sediments with estuarine populations of Potamogeton perfoliatus and Zostera marina
Caffrey, J. M., & Kemp, W. M. (1990). Nitrogen cycling in sediments with estuarine populations of Potamogeton perfoliatus and Zostera marina. Marine Ecology Progress Series, 66(1), 147-160.

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