National Status and Trends: Bioeffects Program - San Francisco Bay Database

This study was based on the sediment quality triad (SQT) approach. A stratified probabilistic sampling design was utilized to characterize the San Francisco Bay system in terms of chemical contamination, sediment toxicity (Microtox, amphipod bioassays; sea urchin gamete bioassay; and P450 biomarker) and benthic infaunal community structure. The purpose was to define the extent and magnitude of toxicity and other biological effects associated with contaminants in the San Francisco estuary system from the delta to the south Bay and out to the Golden Gate. This file contains data measured in the San Francisco Bay Estuary in 2000 and 2001. Samples were collected for water and sediment analyses.

Specific objectives of the study were to: 1. Describe the levels and spatial distribution of contaminants in the San Francisco Bay estuary; 2. Describe the incidence, severity and spatial extent of contamination, toxicity, and characteristics of the benthic infaunal community; 3. Describe the study results in relation to known or suspected sources of contamination; 4. Describe statistical relationships between levels of contaminants and adverse biological effects, and identify chemicals of concern in terms of regional environmental quality and adverse biological effects; 5. Compare environmental conditions within sub-areas of San Francisco Bay and compare estimates of toxicity in San Francisco Bay with those in other estuaries based on comparable data. The dataset objective is to report information about chemical residues in sediment, sediment toxicity, and benthic infauna characteristics of the system.

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PRINCIPAL INVESTIGATORS S. Ian Hartwell, NOAA Ocean Service, National Status and Trends Program; Jawed Hameedi, NOAA Ocean Service, National Status and Trends Program; Ed Long, NOAA Ocean Service, National Status and Trends Program; Michelle Harmon, NOAA Ocean Service, National Status and Trends Program SAMPLE COLLECTION INVESTIGATORS Roger Fay, TDI-Brooks International, College Station, Texas;Ian Hartwell, NOAA Ocean Service, National Status and Trends Program;Michelle Harmon, NOAA Ocean Service, National Status and Trends Program;Ed Long, NOAA Ocean Service, National Status and Trends Program;W. Edward Johnson, NOAA Ocean Service, National Status and Trends Program SAMPLE PROCESSING INVESTIGATORS - Contaminant analyses:1) Organic and inorganic chemicals in sediment: TDI Brooks Inc., College Station, TXSAMPLE PROCESSING INVESTIGATORS - Benthos:Barry A. Vittor and Associates, Inc. Mobile, ALSAMPLE PROCESSING INVESTIGATORS - Toxicity and Bioassays:1. MicroTox Assay: Mike Fulton, CCEHBR, NOAA; 2. Sea Urchin Assay: Scott Carr, Marine Ecotoxicology Research Station, USGS3. Amphipod Assays: Bryn Phillips, U.C. Davis;4. P450 Human Reporter Gene System: Jack Anderson, Columbia Analytical Services, Inc.

The dataset is composed of two relational files each listed below. The "SITES" data file reports information regarding the planned sampling locations and the actual locations. The geographical information provided for a sampling site (the estuary stratum and site) is useful when interpreting the results of other data files. Link for the SITES data http://ccma.nos.noaa.gov/about/coast/nsandt/download.aspx The "INDICATOR" data file reports the results for chemical/microbial analytes, toxicity endpoints, benthic community indices and field measurements. Link for the INDICATOR data dictionary http://ccma.nos.noaa.gov/about/coast/nsandt/download.aspx

NOAA National Status and Trends

These data were prepared by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of their employees, make any warranty, expressed or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed in this report, or represents that its use would not infringe privately owned rights. Reference therein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. Any views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof. Although all data have been used by NOAA, no warranty, expressed or implied, is made by NOAA as to the accuracy of the data and/or related materials. The act of distribution shall not constitute any such warranty, and no responsibility is assumed by NOAA in the use of these data or related materials.

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NOAA requests that all individuals who download NOAA data acknowledge the source of these data in any reports, papers, or presentations. If you publish these data, please include a statement similar to: "Some or all of the data described in this article were produced by the "NOAA's Ocean Service through its National Status and Trends Program (NSandT)"

MEASUREMENT QUALITY OBJECTIVES: SITE LOCATION - Sampling sites were located by GPS with a manufacturer reported position accuracy of better than 3 meters in DGPS mode. Coordinates are expressed in units to the nearest 0.0001 decimal degrees. An acceptable tolerance goal for siting was that the sampling location be established within 0.2nm (+/- 120ft) of the given coordinates. In the event the vessel could not navigate to the site (i.e., too shallow) or the bottom type was not appropriate (i.e., rock or shellfish bed) then the first alternate site was substituted. In the event the first alternate could not be sampled then the second alternate site was sampled. ORGANIC AND INORGANIC CONTAMINANTS - The measurement quality objectives of the San Francisco Bay Project specify accuracy and precision requirements of 30% for organic analytes and 15% for inorganic analytes in sediment samples. WATER COLUMN MEASUREMENTS - Water column monitoring instrumentation was calibrated based on manufacturer's recommendations (YSI Corporation). Depth was recorded from the vessel fathometer. BENTHIC TAXONOMY - The minimum acceptable sorting efficiency was 95%. The minimum acceptable taxonomic efficiency was 95%.

Data are believed to be complete.

All chemical contaminant values have been rounded to three significant digits. To accommodate the wide range of values, all concentration values have been formatted to the thousandth unit (0.001). The actual precision is as listed below.Metals, variable ug/g; Butlytins 0.01 ng Sn/g; PAHs 0.1 ng/g; PCBs 0.01 ng/g; Pesticides 0.01 ng/g; DATA QUALITY ASSURANCE PROCEDURES Site location - Handheld GPS units were compared daily with vessel GPS units. Organic and Inorganic Contaminants - QA procedures include blanks, spiked samples, and standard reference materials with each batch of samples. Any batch failing to meet the specifications presented in Section 9.1 would be reanalyzed or rejected. Water column measurements - Fields are arranged as follows:Indicator; QA sample type or measurement; Data generated for measurement quality. DO; Water-saturated air calibration; Difference between probe value and saturation level. Salinity; Seawater standard; Difference between probe measurement and standard value. Specific Conductance; Seawater standard; Difference between probe measurement and standard value. Temperature; Thermometer; +/- 1C.Benthic taxonomy - At a minimum, 10 percent of all samples were resorted and recounted on a regular basis. Ten percent of samples were randomly selected and re-identified. A voucher collection composed of representative individuals of each species encountered in the project was accumulated and retained.