important for estuaries adjacent to coastal upwelling regions, such as the west coast of the United 
States (e.g., de Angelis and Gordon, 1985; Roegner and Shanks, 2001; Roegner et al., 2002; 
Colbert and McManus, 2003; Brown and Ozretich, in review). 
2.2 Biotic Characteristics 
PNW estuaries, including Yaquina Estuary, are highly productive ecosystems, supporting 
several hundred species of macrophytes, macroinvertebrates, fish, birds, marine and terrestrial 
mammals. The Yaquina estuarine ecosystem contains six major habitats, three of which are 
defined by the presence of an ecosystem-engineering species: tidal channels (including water 
column and subtidal unvegetated sediments), eelgrass beds (lower intertidal and shallow subtidal 
sediments dominated by Zostera marina), mud shrimp beds (mid- to lower intertidal muddy 
sediments dominated by Upogebia pugettensis ), ghost-shrimp beds (lower- to upper intertidal 
sediments dominated by Neotrypaea californiensis), unvegetated intertidal sediments, and tidal 
marshes. Each habitat supports different floral and faunal communities (Seliskar and Gallagher, 
1983; Simenstad 1983; Phillips, 1984; Ferraro and Cole, 2006). 
One hundred twenty-eight species of macroalgae (Kjeldsen, 1967) and three species of 
seagrass have been recorded in Yaquina Estuary. The species diversity and biomass of 
macroalgae is greatest near the mouth of the estuary and decreases up river (Kjeldsen, 1967). 
From late spring to early fall, green macroalgae (principally Enteromorpha spp. [6 spp.], Ulva 
spp. [6 spp.], and Cheaetomorpha spp. [2 spp.]) form extensive intertidal and shallow subtidal 
mats in the lower portion of the estuary, but are largely absent upstream of Poole Slough (about 
11 km from mouth; Figure 2.4). Above Toledo, macroalgae diversity declines to <5 spp. and 
biomass is negligible (Kjeldsen, 1967; WED unpublished data). Large meadows and long 
patches of the native seagrass, Zostera marina (eelgrass), occur on the intertidal flats and along 
channel edges in the lower estuary. From Poole Slough upriver to Toledo, eelgrass occurs 
sporadically in the shallow subtidal, with the largest patches occurring near the Toledo public 
boat launch, which is about 18 km from the mouth of the estuary (Figure 2.4). The introduced 
seagrass, Z. japonica, occurs in the upper-to-mid intertidal zone from the lower estuary to 
Toledo, occasionally forming large beds; its abundance is increasing and it may eventually 
compete for space with the native eelgrass. Widgeon grass ( Ruppia maritima ), the third seagrass 
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