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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.
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
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
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.
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
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.
Production, respiration and net ecosystem metabolism in U.S. estuaries
Caffrey, J. M. (2003). Production, respiration and net ecosystem metabolism in U.S. estuaries. Environmental Monitoring and Assessment, 81(1), 207-219.
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.
Nitrate sources and sinks in Elkhorn Slough, California
Chapin, T. P., Caffrey, J. M., Jannasch, H. W., Coletti, L. J., Haskins, J. C., & Johnson, K. S. (2004). Nitrate sources and sinks in Elkhorn Slough, California: Results from long-term continuous in situ nitrate analyzers. Estuaries, 27(5), 882-894.
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.
Progress report submitted to the U.S. Environmental Protection Agency, Region 4
Caffrey, J. M., & Landing, W. M. (2006). Progress report submitted to the U.S. Environmental Protection Agency, Region 4: Atmospheric deposition of mercury and trace metals to the Pensacola Bay watershed.
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
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
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
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
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
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
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
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).

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