Analyses of benthic communities were performed with two methods: "traditional" 

 taxonomic analyses of animals collected with a grab sampler and retained on a 1-millimeter 

 (mm) screen; and analyses of horizontal sediment profiling photographs taken with a 

 remotely operated camera. The taxonomic analyses showed that the benthos were very 

 similar among the three stations sampled at each site, but quite distinct among the sites. 

 Total abundance, species richness, measures of total biomass, and indices of dominance and 

 species diversity all indicated significant differences among sites. Molluscs were dominant 

 at one site, polychaetes at another (the reference site), and crustaceans were dominant at 

 two others. No data are available thus far for the most contaminated site. The major 

 differences in benthos composition among sites could be attributable to "natural" types of 

 stress such as periods of lowered salinity or scouring, as well as to differences in chemical 

 contamination. 



A survey of 69 sites in the San Francisco Bay estuary was performed with a sediment 

 profiling camera. A variety of sedimentological and biological parameters was recorded 

 during analyses of the photographs. There were 4 of the 69 sites which corresponded with 

 those sampled for bioassays, benthos, and chemical analyses. Signs of sediment organic 

 enrichment or anoxia were recorded at very few of the sites. Some sites in the peripheral 

 waterways of Redwood Creek, Oakland Inner Harbor, and Richmond Harbor showed 

 indications of enriched sediments. Among the four sites sampled for toxicity, benthos, and 

 chemical analyses the most contaminated site showed several indications of slightly 

 elevated organic enrichment and contamination by bacterial indicators of sewage. The 

 successional stage in benthic communities at that site, however, was not remarkably 

 different from that at the other three sites. The sediment profiling photography technique 

 provided data quickly on important characteristics of the surficial sediments. 



The starry flounder (Platichthys stellatus), a bottom-dwelling flatfish, was collected at six 

 sites and tested for contamination of the tissues by chlorinated hydrocarbons and a variety 

 of measures of the health of the fish. The biological measures included analyses of hepatic 

 aryl hydrocarbon hydroxylase (AHH) activity, counts of micronucleated erythrocytes in the 

 blood, analyses of steroid hormone content in the plasma, and analyses of the induction of 

 the hepatic cytochrome P-450 enzyme system. All were performed on subsamples of the same 

 fish. Fish were collected during two periods: November and December 1986 and January and 

 February 1987. Fish caught in the latter period were spawned to also determine impaired 

 reproductive success in addition to the other measures. 



Fish from two sites in San Francisco Bay were generally more contaminated with a 

 mixture of compounds than those from a coastal reference site and a reference site in the 

 Bay. However, the distinction in the chemical concentrations between sites was not as clear 

 as with the sediments. The range in contaminant concentrations and the absolute values 

 were not particularly high among the sampling sites for both fish and sediments. This 

 observation corroborated the conditions that were anticipated, based upon previous 

 knowledge of contamination of San Francisco Bay and vicinity. It was presumed that the 

 sensitivity of various candidate measures of effects could be tested most accurately by 

 sampling locations that would not be grossly contaminated (i.e., where even the least 

 sensitive tests would indicate effects) and that would generally mimic conditions often 

 encountered in the NS&T Program (which, thus far, has mostly avoided highly 

 contaminated areas). 



The incidence of micronucleated erythrocytes in the fish was significantly lower in fish 

 from the coastal reference site than in fish from most of the sites in San Francisco Bay. 

 Incidences in fish among the sites in San Francisco Bay were not distinguishable. The 

 measures of micronuclei formation (especially detached micronuclei) appear to be sensitive, 

 applicable to several species, relatively high in between-site discriminatory power in some 

 species, and correlated with the concentrations of organic compounds, but also are relatively 

 highly variable among fish caught at the same site. Cytochrome "P-450E" content and 

 ethoxyresorufin-O-deethylase (EROD) activities in the liver microsomes of the fish were 

 significantly higher in fish from sites near urban centers than in fish from a coastal 



