3.3 Biological Condition 
3.3.1 Benthic Infauna 
A total of 217 samples were taken in the three states, with 60 samples taken in 
California other than San Francisco Bay, 30 in San Francisco Bay, 66 in Oregon, and 
61 in Washington. Twelve of the 30 San Francisco Bay samples were allocated to the 
“high marsh” frame. The West survey was defined as the 205 samples from the three 
states other than 12 high marsh samples in San Francisco Bay. Although the goal was 
to obtain 0.1 m 2 samples at all these sites, the large volume of detritus retained 
necessitated subsampling 78 (36%) of the benthic samples. Additionally, the actual 
interior area of the post-hole sampler was 0.09 m 2 rather than 0.1 m 2 . These two 
factors resulted in a total of twelve functional sample sizes with sizes ranging from 
0.0028 to 0.1 m 2 . While there was a wide range of sample sizes, the majority of the 
samples (122) were taken with the 0.09 m 2 post-hole digger and 196 of samples fell 
within four sizes (0.0056, 0.0225, 0.09, and 0.1 m 2 ). To account for the differences in 
sample size, all benthic abundances were normalized to 0.09 m 2 . Abundance generally 
increases linearly with area, so this normalization should not introduce much additional 
uncertainty in densities. Flowever, the number of species per sample does not increase 
linearly and accordingly we did analyze absolute species richness or FT on a per sample 
basis. 
The median abundance in the West wide survey was 503 individuals per 0.09 m 2 
(= 5589 m 2 ) with an average density of 1,802 individuals per 0.09 m 2 (=20,022/m 2 ). 
This intertidal density is approximately within the range found in the previous survey of 
primarily subtidal assemblages in the small and moderate sized West Coast estuaries 
(Nelson et al., 2004). Median benthic densities were highest in Oregon at about 1,245 
individuals per 0.09 m 2 (=13,833/m 2 ) and lowest in Washington with 373 individuals per 
0.09 m 2 (=4,144/m 2 ). Average densities showed the same trend, with Oregon having 
the highest average abundance, California and San Francisco having similar 
abundances, and Washington having the lowest average abundance (Figure 3.3.1). 
The lower density in Washington partially reflects the low density in Puget Sound 
(average = 617 individuals per 0.09 m 2 ) compared to the coastal estuaries (average = 
1,256 individuals per 0.09 m 2 ). 
A total of 420 taxa were identified from all 217 samples of which 248 were 
identified to the species level. Presumably the total number of species would have 
been greater if all the samples had been 0.1 m 2 in area and if the “problematic” taxa 
(e.g., oligochaetes, insect larvae) had been identified to species. Taxa were classified 
as native, nonindigenous, cryptogenic, indeterminate taxa, cosmopolitan, or 
unclassified. Cryptogenic species are species of unknown origin (Carlton, 1996) while 
indeterminate taxa are those not identified with sufficient taxonomic resolution to 
classify as native, nonindigenous, or cryptogenic (Lee et al., 2003). Cosmopolitan is 
used primarily for pelagic taxa that are widely dispersed across several oceans, while 
unclassified species are those that have yet to be sufficiently analyzed to render a final 
classification. The classifications used here follow the Pacific Ecosystem Information 
System (PCE/S), a georeferenced database of native and nonindigenous species of the 
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