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Short Citation:
National Centers for Coastal Ocean Science, 2023: National Status and Trends: Bioeffects Program - San Francisco Bay Database,

Item Identification

Title: National Status and Trends: Bioeffects Program - San Francisco Bay Database
Short Name: SFB_metadata
Status: Completed
Publication Date: 2008-05

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.



Supplemental Information:

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.


Theme Keywords

Thesaurus Keyword
ISO 19115 Topic Category
ISO 19115 Topic Category
NOS Data Explorer Topic Category Environmental Monitoring
None amphipod
None analytes
None benthic
None bioassay
None butyltins
None chemical
None contaminants
None date
None estuary
None infauna
None inorganic
None latitude
None location
None longitude
None Microtox
None NCCOS Research Data Type > Field Observation
None NCCOS Research Priority > Long-term Monitoring
None NCCOS Research Priority > Stressors, Impacts, Mitigation, and Restoration (SIMR)
None NCCOS Research Topic > Bioeffects/Toxicity
None NCCOS Research Topic > Chemical Contaminants
None NCCOS Research Topic > Monitoring
None organic
None organochlorines
None P450 human reporter gene system
None PAH
None parameter
None PCB
None pesticides
None polychlorinated biphenyls
None polynuclear aromatic hydrocarbons
None region
None sea urchin fertilization
None sediment
None Site
None state
None station
None TBT
None toxicity

Spatial Keywords

Thesaurus Keyword
None NCCOS Research Location > Geographic Area > Coastal Ocean
None NCCOS Research Location > Region > West Coast
None NCCOS Research Location > U.S. States and Territories > California
None Pacific Ocean
None San Francisco Bay
None United States

Physical Location

Organization: National Centers for Coastal Ocean Science
City: Silver Spring
State/Province: MD

Data Set Information

Data Set Scope Code: Data Set
Maintenance Frequency: None Planned
Entity Attribute Overview:

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 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

Entity Attribute Detail Citation:

NOAA National Status and Trends

Distribution Liability:

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.

Data Set Credit: The partners in the partners in the San Francisco Bay Estuary Project were: (1) National Oceanographic and Atmospheric Administration (NOAA); (2) Environmental Protection Agency (EPA); (3) San Francisco Estuary Inst. The National Oceanographic and Atmospheric Administration (NOAA) was responsible for collection, final assembly and review of all data.

Support Roles

Data Steward

CC ID: 459560
Date Effective From: 2008-05
Date Effective To:
Contact (Position): NCCOS Scientific Data Coordinator
Email Address:


CC ID: 459562
Date Effective From: 2008-05
Date Effective To:
Contact (Position): NCCOS Scientific Data Coordinator
Email Address:

Metadata Contact

CC ID: 459563
Date Effective From: 2008-05
Date Effective To:
Contact (Position): NCCOS Scientific Data Coordinator
Email Address:

Point of Contact

CC ID: 459561
Date Effective From: 2008-05
Date Effective To:
Contact (Position): NCCOS Scientific Data Coordinator
Email Address:

Principal Investigator

CC ID: 459564
Date Effective From: 2008-05
Date Effective To:
Contact (Person): Piniak, Greg
Email Address:


Currentness Reference: Ground Condition

Extent Group 1

Extent Group 1 / Geographic Area 1

CC ID: 459567
W° Bound: -122.53297
E° Bound: -121.81588
N° Bound: 38.1591
S° Bound: 37.4407

Extent Group 1 / Time Frame 1

CC ID: 459566
Time Frame Type: Range
Start: 2000
End: 2001

Access Information

Security Class: Unclassified
Data Access Constraints:


Data Use Constraints:

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)"

Distribution Information

Distribution 1

CC ID: 459569
Download URL:

Live Data and Maps

File Type (Deprecated): XML
Distribution Format: XML (Structured Text)

Distribution 2

CC ID: 459568
Download URL:

Live Data and Maps

File Type (Deprecated): ASCII
Distribution Format: Text (Unstructured)



CC ID: 459558
URL Type:
Online Resource

Activity Log

Activity Log 1

CC ID: 459622
Activity Date/Time: 2016-11-16

Date that the source FGDC record was last modified.

Activity Log 2

CC ID: 459621
Activity Date/Time: 2017-04-05

Converted from Content Standard for Digital Geosptial Metadata (version FGDC-STD-001-1998) using '' script. Contact Tyler Christensen (NOS) for details.

Data Quality


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%.

Completeness Report:

Data are believed to be complete.

Conceptual Consistency:

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.


Process Steps

Process Step 1

CC ID: 459554

DATA ACQUISITION/FIELD SAMPLING Sediment sampling procedures are available for download ( PREPARATION AND SAMPLE PROCESSING Fields are arranged as follows:Sample Type; Container; Field Holding; Lab Storage; Max Holding SEDIMENT Organic contaminants; I-Chem glass jars; Wet ice (4C); Freezer (-20C); 1 year; Inorganic contaminants; I-Chem glass jars; Wet ice (4C); Freezer (-20C); 1 year; Total organic Carbon; I-Chem glass jars; Wet ice (4C); Freezer (-20C); 1 year; Grain size; Whirl paks; Wet ice (4C); Refrigerated (4C); 1 year; TOXICITY BIOASSAY Whole sediment and porewater bioassays; Plastic jars; Wet ice (4C); Refrigerated (4C);2 weeks; Organic extract (P450 and Microtox); I-Chem glass jars;Wet ice (4C); Freezer (-20C); 1 year; BENTHOS Taxonomy; Plastic jars; 10% buffered formalin; Transfer to 70% ethanol; Indefinitely

Process Date/Time: 2001-01-01 00:00:00

Process Step 2

CC ID: 459555

Chemicals with similar structural properties were summed and reported as "Totals" in addition to their individual measured concentrations. The components of these totals are as follows:Total DDT = sum of concentrations of ortho and para forms of parent and metabolites 2,4'DDE; 4,4'DDE; 2,4'DDD; 4,4'DDD; 2,4'DDT and 4,4'DDT.Total Chlordane = sum of concentrations of four compounds alpha-chlordane, trans-nonachlor, heptachlor, heptachlorepoxide.Total Chlorinated benzenes = 1,2,4,5-Tetrachlorobenzene, 1,2,3,4-Tetrachlorobenzene, Pentachlorobenzene, Hexachlorobenzene and PentachloroanisoleTotal Dieldrin = sum of concentrations of two compounds aldrin and dieldrin.Total cyclodines = sum of Heptachlor, Heptachlor Epoxide, Oxychlordane, Alpha Chlordane, Gamma Chlordane, Cis-Nonachlor, Trans-Nonachlor, Aldrin, Dieldrin, Endrin, Endosulfan IITotal HCH = Alpha HCH, Beta HCH, Gamma HCH, Delta HCHTotal Butyl tin = sum of concentrations of parent compound and metabolites monobutyltin, dibutyltin, tributyltin, tetrabutyltin [concentrations are in terms of tin].Total PCB = the sum of the concentrations of eighteen congeners: PCB8, PCB18, PCB28, PCB44, PCB52, PCB66, PCB101, PCB105, PCB118, PCB128, PCB138, PCB153, PCB170, PCB180, PCB187, PCB195, PCB206, and PCB209.High Molecular Weight PAHs = Fluoranthene, Pyrene, Benz(a)anthracene, Chrysene, Benzo(b)fluoranthene, Benzo(k)fluoranthene, Benzo(e)pyrene, Benzo(a)pyrene, Perylene, Indeno(1,2,3-c,d)pyrene, Dibenzo(a,h)anthracene, Benzo(g,h,i)perylene High Molecular Weight Substituted PAHs = C1-Fluoranthenes/Pyrenes, C1-Chrysenes, C2-Chrysenes, C3-Chrysenes, C4-Chrysenes Low MW PAHs = Naphthalene, Biphenyl Acenaphthylene, Acenaphthene, Fluorene, Anthracene, Phenanthrene, Dibenzothiophene Low Molecular Weight Substituted PAHs = C1-Naphthalenes, C2-Naphthalenes, C3-Naphthalenes, C4-Naphthalenes, C1-Fluorenes, C2-Fluorenes, C3-Fluorenes, C1-Phenanthrenes/Anthracenes, C2-Phenanthrenes/Anthracenes, C3-Phenanthrenes/Anthracenes, C4-Phenanthrenes/Anthracenes, C1-Dibenzothiophenes, C2-Dibenzothiophenes, C3-DibenzothiophenesSeveral numerical indices were chosen for analysis and interpretation of the macroinfaunal data. Infaunal abundance is reported as the total number of individuals per station and the total number of individuals per square meter (= density). Taxa richness is reported as the number of taxa represented in a given site location. Taxa diversity, which is often related to the ecological stability and environmental "quality" of the benthos, was estimated by the Shannon-Weiner Index (Shannon and Weaver, 1949).In order to quantify and compare the equitability in the fauna to the taxa diversity for a given area, Pielou's Evenness Index J' (Pielou, 1966) was calculated as J' = H'/lnS, where lnS = H'max, or the maximum possible diversity, when all taxa are represented by the same number of individuals; thus, J' = H' /H' max.

Process Step 3

CC ID: 459556

Project Related References: Pielou, E.C. 1966. The Measurement of Diversity in Different Types of Biological Collections. J. Theoretical Biology 13:131-144. Shannon, L.C. and W. Weaver. 1949. The Mathematical Theory of Communication. Univ. of Illinois Press, Urbana, Ill. 117 p.

Catalog Details

Catalog Item ID: 39186
GUID: gov.noaa.nmfs.inport:39186
Metadata Record Created By: Tyler Christensen
Metadata Record Created: 2017-04-05 12:51+0000
Metadata Record Last Modified By: SysAdmin InPortAdmin
Metadata Record Last Modified: 2023-10-17 16:12+0000
Metadata Record Published: 2017-04-17
Owner Org: NCCOS
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Last Review Date: 2017-04-17
Metadata Review Frequency: 1 Year
Metadata Next Review Date: 2018-04-17