The effect of inorganic nitrogen speciation on primary production in the San Francisco Estuary Alexander E. Parker * , Victoria E. Hogue, Frances P. Wilkerson, Richard C. Dugdale Romberg Tiburon Center for Environmental Studies, San Francisco State University, 3152 Paradise Drive, Tiburon, CA 94920, USA article info Article history: Received 31 August 2011 Accepted 1 April 2012 Available online xxx Keywords: San Francisco Estuary primary production phytoplankton carbon ammonium nitrate abstract We describe the results of a series of 96-h enclosure experiments conducted using water from stations in the northern San Francisco Estuary (SFE) along a gradient in ammonium (NH 4 ) and nitrate (NO 3 ) concentrations. Using dual-labeled 13 C/ 15 N tracers, we followed the timing and sequence of primary (carbon, C) production and phytoplankton nitrogen (N) use during experimental phytoplankton blooms. Our results show that diatoms consistently drive the phytoplankton blooms in the enclosures. By tracing both C and N uptake we provide clear evidence that high rates of C uptake are linked to phytoplankton NO 3 , and not NH 4 , use. Results from kinetics experiments demonstrated higher specific uptake rates (V MAx ) for NO 3 compared to NH 4 in the SFE. Finally, dissolved inorganic carbon and nutrient drawdown ratios in the enclosures from the chronically high NH 4 regions of the SFE were substantially lower than predicted from the Redfield ratio, suggesting suppressed C uptake, in relation to other elemental uptake. Our conceptual model of the DIN interactions that lead to higher primary production and phytoplankton blooms in the SFE suggests that higher rates of primary production that accompany phytoplankton NO 3 uptake are sufficient to outpace phytoplankton losses, leading to blooms, compared to the lower rates associated with NH 4 uptake (only 20% of that based upon NO 3 ). Historical changes in wastewater practices have increased the proportion of NH 4 to the DIN pool in the SFE leading to reduced access to NO 3 by phytoplankton. This may help to explain some of the reduced primary production and phyto- plankton biomass observed there since the 1970s. Ó 2012 Elsevier Ltd. All rights reserved. 1. Introduction The San Francisco Estuary (SFE) is the major west coast estuary of the U.S. and like many large estuaries worldwide has been modified as a result of urbanization (Nichols et al., 1986). Among the many manifestations of population growth and development are the diversion of freshwater from the Sacramento and San Joa- quin Rivers that feed the SFE to California’s Central Valley for agriculture and to southern California’s urban centers (Nichols et al., 1986), ballast water introductions of invasive species (Cohen and Carlton, 1998), and nutrient loading from agricultural and municipal wastewater sources (Nichols et al., 1986; Hager and Schemel, 1996; Jassby, 2008). In recent decades declines in phyto- plankton (Jassby et al., 2002) and zooplankton (Orsi and Mecum, 1996; Kimmerer and Orsi, 1996; Kimmerer, 2005) have been observed and since the early 2000’s several fish, including state and federally threatened species, have also declined (Feyrer et al., 2007). These changes have led to local concern that the estuary is experiencing a “pelagic organism decline” (POD) (Sommer et al., 2007). Historically, primary production was low in the SFE compared to other estuaries (Boynton et al., 1982; Cloern, 2001), due to high suspended sediment loads resulting in reduced photic zone depth (Cole and Cloern, 1984, 1987; Alpine and Cloern, 1988). A decline to now chronically low chlorophyll-a (chl-a) concentrations occurred in the northern SFE in the late 1980s and was attributed mainly to grazing by the overbite clam, Corbula amurensis (Carlton et al., 1990), which was introduced to the estuary in 1986 (Alpine and Cloern, 1992). However, C. amurensis abundance alone may be insufficient to explain annual chl-a trends, as winter chl-a in the northern estuary began to decline before the clam’s introduction (Jassby et al., 2002) and rare spring phytoplankton blooms have been observed in the northern SFE (Dugdale et al., submitted; Wilkerson et al., 2006; Glibert et al., 2011; Dugdale et al., submitted) since the clam’s introduction even while clam biomass has been relatively stable. * Corresponding author. E-mail addresses: aeparker@sfsu.edu (A.E. Parker), vhogue6417@gmail.com (V.E. Hogue), fwilkers@sfsu.edu (F.P. Wilkerson), rdugdale@sfsu.edu (R.C. Dugdale). Contents lists available at SciVerse ScienceDirect Estuarine, Coastal and Shelf Science journal homepage: www.elsevier.com/locate/ecss 0272-7714/$ e see front matter Ó 2012 Elsevier Ltd. All rights reserved. doi:10.1016/j.ecss.2012.04.001 Estuarine, Coastal and Shelf Science xxx (2012) 1e11 Please cite this article in press as: Parker, A.E., et al., The effect of inorganic nitrogen speciation on primary production in the San Francisco Estuary, Estuarine, Coastal and Shelf Science (2012), doi:10.1016/j.ecss.2012.04.001