Murrell, M.C., J.M. Caffrey, D.T. Marcovich, M.W. Beck, B.M. Jarvis,
J.D. Hagy III. Seasonal oxygen dynamics in a warm temperate estuary: effects of
hydrologic variability on measurements of primary production, respiration, and
net metabolism. Estuaries and Coasts DOI 10.1007/s12237-0328-9.
Caffrey, J.M., J.T. Hollibaugh, B. Mortazavi. 2016. Living oysters and
their shells as sites of nitrification and denitrification. Marine Pollution Bulletin.
112:86-90. http://dx.doi.org/10.1016/j.marpolbul.2016.08.038
Hester, C.M., H. M. Smith, M. Head, H. Langsten, S. Linder, L. Sartory,
E. Manor, J. Norman and J. M. Caffrey. 2016. Comparing production and biogeochemistry
of native and transplanted Thalassia testudinum and Halodule wrightii in Big Lagoon,
Florida, USA. Gulf of Mexico Science. 33:14-25.
Caffrey, J.M. and M.C. Murrell. 2016. A historical perspective on eutrophication
in the Pensacola Bay estuary, FL, USA. pp. 199-213 In P. Glibert and T. Kana (eds).
Aquatic Microbial Ecology and Biogeochemistry: A Dual Perspective. Invited book chapter.
Caffrey, J.M., M.C. Murrell, K.R.S Amacker, J. Harper, S. Phipps, and M. Woodrey.
2014 Sustained observations of estuarine metabolism in 3 estuaries in the northeast Gulf of
Mexico. Estuaries and Coasts invited Special Issue, “Drivers of Change in Shallow Coastal
Photic Systems" 37: 222-241. http://dx.doi.org/10.1007/s12237-013-9701-5
Yvon-Durocher, G., J. M. Caffrey, A. Cescatti, M. Dossena, P. del Giorgio,
J.M. Gasol, J.M. Montoya, J. Pumpanen, P.A. Staehr, M. Trimmer, G. Woodward & A.P.
Allen. 2012. Reconciling differences in the temperature-dependence of ecosystem respiration
across time scales and ecosystem types. Nature Nature 487: 472-476.
Mortazavi, B., A.A. Riggs, J.M. Caffrey, H. Genet, and S.W. Phipps. 2012. The
contribution of benthic nutrient regeneration to primary production in a shallow
eutrophic estuary, Weeks Bay, Alabama. Estuaries and Coasts. 35:862-877.
Bagui, S., J. Brown, J. Caffrey, S. Bagui. Designing a relational
database for tracking and analysis of atmospheric deposition of mercury
and trace metals in the Pensacola Bay Watershed. accepted to
Computers and Geosciences
Caffrey, J.M., W.M. Landing, S.D. Nolek, K.J. Gosnell, S.S Bagui,
and S.C. Bagui. 2010 Atmospheric deposition of mercury and major ions to
the Pensacola (Florida) watershed: spatial, seasonal, and inter-annual variability.
Atmospheric Chemistry and Physics 10:1-24
Landing, W.M., J.M. Caffrey, S.D. Nolek, K.J. Gosnell and W.C. Parker.
2010 Atmospheric deposition of mercury and other trace elements in Pensacola,
Florida. Atmospheric Chemistry and Physics 10:4867-4877.
Caffrey, J.M., N. Bano, J.T. Hollibaugh and J. Haskins. 2010 The effect of upwellling
on short-term variability in sediment biogeochemistry in Elkhorn Slough, CA. In
Aquatic Microbial Ecology. 58: 261-271
Murrell, M.C., J. Campbell, J.E Hagy, and J.M. Caffrey. 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. 81:501-512
Smith, K.A. and J.M. Caffrey.2009
The effects of human activities and extreme meterological events on sediment
nitrogen dynamics in an urban estuary, Escambia Bay, Florida, USA.
Hydrobiologia.
Caffrey, J.M., N. Bano, K. Kalanetra and J. T. Hollibaugh. 2007.
Environmental factors controlling ammonia-oxidation by ammonia oxidizing
Bacteria and Archaea.
ISME Journal 1:660-662.
Caffrey, J.M., T.P. Chapin, H.W. Jannasch, and J.C. Haskins. 2007.
High nutrient pulses, tidal mixing and biological response in a small
California estuary, Elkhorn Slough, CA, USA: variability in nutrient
concentrations from hourly to decadal time scales.
Estuarine, Coastal and Shelf Science 71:368-380
Caffrey, J.M., M.C. Murrell, C. Wigand and R. McKinney. 2007.
Effect of nutrient loading on biogeochemical and microbial processes in
a New England high salt marsh.
Biogeochemistry 82:251-264.
DiDonato G.T., E.M. Lores, M.C. Murrell,
L.M. Smith, and J.M. Caffrey. 2006.
Benthic nutrient flux in a small estuary in northwestern Florida (USA).
Gulf and Caribbean Research.
Murrell, M.C. and J.M. Caffrey. 2005.
High cyanobacterial abundance in three Gulf of Mexico estuaries.
Gulf and Caribbean Research. 17:95-106.
Chapin, T.P., J.M. Caffrey, H.W. Jannasch, L. Coletti,
J.C. Haskins and K. Johnson. 2004.
Nitrate sources and sinks in Elkhorn Slough, CA: results from continuous
in situ nitrate analyzers.
Estuaries 27:882-894
Caffrey, J.M. 2004
Factors controlling net ecosystem metabolism in U.S. estuaries.
Estuaries 27: 90-101
Caffrey, J.M. 2003.
Production, Respiration and Net Ecosystem Metabolism in U.S. Estuaries.
Environmental Monitoring and Assessment. 81: 207-219.
Caffrey, J.M., N.E. Harrington, I. Solem, and B.B. Ward. 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.
Caffrey, J.M., N.E. Harrington, and B.B. Ward. 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.
Caffrey, J.M., M. Brown, B. Tyler, M. Silberstein (eds.) 2002.
Changes in a California Estuary: an Ecosystem Profile of Elkhorn Slough.
Elkhorn Slough Foundation. Moss Landing, CA.
Mortazavi B., R.L. Iverson, W. Huang, F.G. Lewis, J.M. Caffrey. 2000.
Nitrogen Budget of Apalachicola Bay, a Bar-built Estuary in the
Northeastern Gulf of Mexico.
Marine Ecology Progress Series. 195:1-14.