272  2002 Estuarine Research Federation Estuaries Vol. 25, No. 2, p. 272–281 April 2002 Denitrification and the Stoichiometry of Nutrient Regeneration in Waquoit Bay, Massachusetts MICHAEL G. LAMONTAGNE 1, *, VALERIA ASTORGA 2 ,ANNE E. GIBLIN 3 , AND IVAN VALIELA 1 1 Boston University Marine Program, Marine Biological Laboratory, Woods Hole, Massachusetts 02543 2 University of Barcelona, Department of Ecology, Diagonal 645, 08028 Barcelona, Spain 3 Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts 02543 ABSTRACT: To determine the removal of regenerated nitrogen by estuarine sediments, we compared sediment N 2 fluxes to the stoichiometry of nutrient and O 2 fluxes in cores collected in the Childs River, Cape Cod, Massachusetts. The difference between the annual PO 4 3- (0.2 mol P m -2 yr -1 ) and NH 4  (1.6 mol N m -2 yr -1 ) flux and the Redfield N : P ratio of 16 suggested an annual deficit of 1.5 mol N m -2 yr -1 . Denitrification predicted from O 2 : NH 4  flux ratios and measured as N 2 flux suggested a nitrogen sink of roughly the same magnitude (1.4 mol N m -2 yr -1 ). Denitrification accounted for low N : P ratios of benthic flux and removed 32–37% of nitrogen inputs entering the relatively highly nutrient loaded Childs River, despite a relatively brief residence time for freshwater in this system. Uptake of bottom water nitrate could only supply a fraction of the observed N 2 flux. Removal of regenerated nitrogen by denitrification in this system appears to vary seasonally. Denitrification efficiency was inversely correlated with oxygen and ammonium flux and was lowest in summer. We investigated the effect of organic matter on denitrification by simulatingphytoplankton deposition to cores incubated in the lab and by deploying chambers on bare and macroaglae covered sediments in the field. Organic matter addition to sediments increased N 2 flux and did not alter denitrification efficiency. Increased N 2 flux co-varied with O 2 and NH 4  fluxes. N 2 flux (261  60 mol m -2 h -1 ) was lower in chambers deployed on macroalgal beds than deployed on bare sediments (458  70 mol m -2 h -1 ), and O 2 uptake rate was higher in chambers deployed on macroalgal beds (14.6  2.2 mmol m -2 h -1 ) than on bare sediments (9.6  1.5 mmol m -2 h -1 ). Macroalgal cover, which can retain nitrogen in the system, is a link between nutrient loading and denitrification. Decreased denitrification due to increasing macroalgal cover could create a positive feedback because decreasing denitrification would increase nitrogen availability and could increase macroalgae cover. Introduction Nitrogen limits primary productivity in temper- ate estuaries (Ryther and Dunstan 1971) despite high nitrogen loading rates (Nixon et al. 1986) and in contrast to most freshwater systems where phosphorus limits primary production (Howarth 1988). Denitrification contributes to the relative scarcity of nitrogen by consuming nitrate from overlying water (direct denitrification) or nitrate produced by sediment nitrification (coupled nitri- fication-denitrification). Mesocosm experiments indicate nutrient loading will increase direct de- nitrification (Seitzinger 1988) and denitrification appears positively correlated to sediment organic matter content (Yoon and Benner 1992; Nowicki et al. 1999). Increased organic matter deposition, associated with nutrient loading, could inhibit cou- pled nitrification-denitrification (Kemp et al. 1990). The percentage of mineralized nitrogen * Corresponding author; current address: Donald Bren School of Environmental Science and Management, University of California, Santa Barbara, California 93106-5131; tele: 805/ 893-5652; e-mail: lamontag@bren.ucsb.edu. that is denitrified appears to decrease with increas- ing benthic metabolism (Berelson et al. 1998). Nu- trient loading also increases biomass and cover of macroalgae in shallow estuaries (Hersh 1996), and increased macroalgal biomass changes benthic ox- ygen availability (D’Avanzo and Kremer 1994). The relationship between macroalgal cover and oxy- gen-dependent coupled nitrification-denitrifica- tion appears complex (Krause-Jensen et al. 1999). Nitrogen limitation of primary production in es- tuaries could also reflect increased availability of phosphorus in estuaries. Estuarine sediments im- mobilize less phosphate than freshwater sediments (Caraco et al. 1990), and in estuaries with high fluvial particle loads, desorption of phosphate from particles could provide a phosphate source (Froelich 1988). Nitrogen limits phytoplankton (Tomasky and Valiela 1995) and macroalgal (Peck- ol et al. 1994) growth in the Childs River, a shallow ( 1.5 m), small (687 ha), highly nitrogen loaded (3.8 mol N m -2 yr -1 ; Valiela et al. 1992) estuary in Waquoit Bay, Cape Cod, Massachusetts, even though N : P of the groundwater as it nears the Childs River ranges from 131 (LaMontagne 1996)