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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
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
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.
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
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
Effects of upwelling on short-term variability in microbial and biogeochemical processes in estuarine sediments from Elkhorn Slough, California, USA
Caffrey, J. M., Hollibaugh, J. T., Bano, N., & Haskins, J. (2010). Effects of upwelling on short-term variability in microbial and biogeochemical processes in estuarine sediments from Elkhorn Slough, California, USA. Aquatic Microbial Ecology, 58(3), 261-271. doi:10.3354/ame01387
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
Biogeochemical processes in a small California estuary. 2. Nitrification activity, community structure and role in nitrogen budgets
Caffrey, J. M., Harrington, N., Solem, I., & Ward, B. B. (2003). Biogeochemical processes in a small California estuary. 2. Nitrification activity, community structure and role in nitrogen budgets. Marine Ecology Progress Series, 248, 27-40. doi:10.3354/meps248027
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
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.
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.
Seasonal and inter-annual patterns in primary production, respiration, and net ecosystem metabolism in three estuaries in the Northeast Gulf of Mexico
Caffrey, J. M., Murrell, M. C., Amacker, K. S., Harper, J. W., Phipps, S., & Woodrey, M. S. (2014). Seasonal and inter-annual patterns in primary production, respiration, and net ecosystem metabolism in three estuaries in the Northeast Gulf of Mexico. Estuaries and Coasts, 37, S222-S241. doi:10.1007/s12237-013-9701-5
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.
Seagrass abundance and productivity in Pensacola Bay and Santa Rosa Sound
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.
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.