Appendix A: Benthic Processes in Yaquina Estuary 
Benthic communities harboring actively burrowing, tube- or burrow-dwelling infaunal are 
often associated with elevated rates of DIN advection from sediments (e.g., Aller, 1988; Kristensen et 
al., 1991; Marinelli and Williams, 2003). Bioturbation and bioirrigation by infauna oxygenates 
sediments and mixes labile organic matter into sediments, stimulating the activity of microbial 
communities responsible for recycling of nutrients (Kristensen, 1988; Welsh, 2003). Benthic fauna 
consume organic matter from the water column (i.e., filter feeders), at the sediment surface (i.e., 
herbivores, surface deposit-feeders, carnivores), or below the sediment surface (i.e., sub-surface 
deposit feeders, carnivores). The presence of seagrasses (i.e., Zostera spp.), green macroalgae (i.e., 
Enteromorphci spp. and Ulva spp.), or microphytobenthic algae usually results in a net benthic uptake 
of DIN during daylight hours (Underwood and Kromkamp, 1999; Hansen et al., 2000; Sundback et al., 
2000; Sundback et al., 2003). Benthic primary producers are recycled into the benthos (i.e., consumed 
by benthic herbivores or surface deposit feeders, buried by bioturbators, decay at the sediment surface) 
or are transported out of the estuary by currents. 
Five studies of benthic nutrient flux have been conducted in Pacific estuaries north of San 
Francisco, but the reported benthic flux-chamber data in four (i.e., Dollar et al. 1991; Garber et al. 
1992; Thom et al. 1994; Lamed 2003) may not be appropriate for the purpose of estimating estuary- 
scale nutrient fluxes in Yaquina Estuary because they did not adequately take into account the presence 
of thalassinid burrowing shrimp. As described in Section 3.2.3 Benthic Processes, previous studies of 
benthic nutrient flux in PNW estuaries may have underestimated the nutrient fluxes from sediments by 
failing to account for the presence of burrowing shrimp. Both ghost shrimp and mud shrimp were 
present, or were likely to have been present, at field sites in all of the studies. Burrowing shrimp are 
very common, and frequently very abundant, in NE Pacific estuaries (DeWitt et al., 2004 and 
references therein), and they construct deep (>50 cm), branching burrows with openings 10’s of cm 
apart. These shrimp are prodigious bioturbators, actively irrigate their burrows, and thus greatly 
elevate nutrient flux from sediments (Waslenchuk et al., 1982; DeWitt et al., 2004; Webb and Eyre, 
2004; Papaspyrou et al., 2004). 
Failure to take the presence of burrowing shrimp into account can result in water inside the 
chamber being exchanged with water outside of the chamber via shrimp burrows (e.g., Hughes et al. 
2000), which violates the requirement that benthic chambers be closed microcosms (Hofman and de 
Jong, 1993, Forja and Gomez-Parra 1998). In the case of one study, benthic chamber treatments 
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