estuarine landscape. DIN efflux (release) from sediments was estimated to be much greater than DIN 
uptake in the presence of burrowing shrimp, but in the absence of the shrimp DeWitt et al. (2004) 
estimated a net uptake of DIN by sediments. Most of the DIN efflux was projected to occur in U. 
pugettensis - dominated habitat, mostly due to enhanced NH4 efflux. Tide flats lacking burrowing 
shrimp or having low densities of N. californiensis were shown to have a net uptake of DIN, most of 
which is expected to be NO3 + NO2. DIN efflux was estimated to be much greater than DIN uptake in 
the lower portion of the estuary, mostly due to the presence of dense populations of U. pugettensis. 
Using this shrimp species- and density-dependent nutrient flux model, the benthos in the upper 
(mesohaline) regions of the Yaquina Estuary was estimated to have a large net uptake of DIN because 
of the spatial dominance of N. californiensis and scarcity of U. pugettensis. 
Much of the organic matter that is produced within, or advected into, the estuary is available for 
consumption by benthic herbivores, filter-feeders, or deposit feeders. The dominant benthic herbivores 
in Yaquina Estuary are ampithoid amphipods, isopods, and nereid polychaetes. Herbivores are not 
abundant among benthic infauna in Yaquina Estuary, with biomass 1-10% of filter-feeders and deposit 
feeders (Figure A.4). Deposit feeders are abundant throughout the estuary, and dominate the upper- 
estuary infauna. In lower and upper reaches, the most abundant deposit-feeder by biomass is N. 
californiensis. Organic matter consumption rates have not been calculated for the infaunal deposit- 
feeder guild in Yaquina Estuary. Filter-feeders are more abundant in the lower than in the upper 
estuary, primarily because that is the distribution pattern of the dominant species of this guild, U. 
pugettensis. Griffen et al. (2004) estimated that populations of the mud shrimp in the lower Yaquina 
Estuary pump the entire volume of water covering the tide flats through their burrows every day. 
Combining per-capita grazing rates for mud shrimp (Griffen et al., 2004), patterns of mud shrimp 
population distribution in the estuary (Figure A.2a), bathymetry, chlorophyll a data and a 
hydrodynamic model, it has been estimated that mud shrimp populations graze approximately 60% of 
the phytoplankton that enters the lower estuary. This estimate is similar to measured differences in 
flood- and ebb-tide chlorophyll a concentrations, suggesting that filter feeding is an important sink for 
phytoplankton in the lower estuary (see Section 7.1). 
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