Metadata: Identification_Information: Citation: Citation_Information: Originator: Mary McGann Publication_Date: 20240722 Title: Census counts of the non-indigenous benthic foraminifera Trochammina hadai Uchio obtained in 1983-2024 in San Francisco Bay, California (ver. 2.0, May 2025) Edition: 2.0 Geospatial_Data_Presentation_Form: comma-delimited text Series_Information: Series_Name: data release Issue_Identification: DOI: 10.5066/P13UOJDV Publication_Information: Publication_Place: Pacific Coastal and Marine Science Center, Santa Cruz, California Publisher: U.S. Geological Survey Other_Citation_Details: Suggested Citation: McGann, M., 2024, Census counts of the non-indigenous benthic foraminifera Trochammina hadai Uchio obtained in 1983-2024 in San Francisco Bay, California (ver. 2.0, May 2025): U.S. Geological Survey data release, https://doi.org/10.5066/P13UOJDV. Online_Linkage: https://doi.org/10.5066/P13UOJDV Online_Linkage: https://www.sciencebase.gov/catalog/item/661415dad34e633466530203 Description: Abstract: This data release provides census counts of the non-indigenous benthic foraminifera Trochammina hadai Uchio in surface sediment samples obtained in San Francisco Bay, California from 1983-2024. Purpose: Biological invasions have greatly impacted ecosystems worldwide, particularly in urbanized ports of coastal bays and estuaries. However, few studies have documented the introduction of non-indigenous microorganisms. One of the most comprehensive studies to date of invasive foraminifera has focused on the benthic foraminifera Trochammina hadai Uchio 1962. The species is an estuarine inhabitant native to Asia, particularly Japan, South Korea, and China. Trochammina hadai is present in San Francisco Bay and the purpose of this data release is to provide census counts of this species from 1983 to 2024 in that bay. Supplemental_Information: Additional information about the field activity from which these data were derived is available online at: https://cmgds.marine.usgs.gov/services/activity.php?fan=1983-611-DD https://cmgds.marine.usgs.gov/services/activity.php?fan=1986-602-DD https://cmgds.marine.usgs.gov/services/activity.php?fan=P187SF https://cmgds.marine.usgs.gov/services/activity.php?fan=1993-602-DD https://cmgds.marine.usgs.gov/services/activity.php?fan=J198SF https://cmgds.marine.usgs.gov/services/activity.php?fan=S710SF https://cmgds.marine.usgs.gov/services/activity.php?fan=S810SF https://cmgds.marine.usgs.gov/services/activity.php?fan=2024-662-FA Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Time_Period_of_Content: Time_Period_Information: Range_of_Dates/Times: Beginning_Date: 19830419 Ending_Date: 20241108 Currentness_Reference: Ground condition at time data were collected. Status: Progress: Complete Maintenance_and_Update_Frequency: None planned Spatial_Domain: Bounding_Coordinates: West_Bounding_Coordinate: -123.0245 East_Bounding_Coordinate: -121.8075 North_Bounding_Coordinate: 38.1269 South_Bounding_Coordinate: 37.4258 Keywords: Theme: Theme_Keyword_Thesaurus: ISO 19115 Topic Category Theme_Keyword: biota Theme_Keyword: environment Theme_Keyword: society Theme_Keyword: geoscientificInformation Theme: Theme_Keyword_Thesaurus: Data Categories for Marine Planning Theme_Keyword: Habitat Theme_Keyword: Invertebrates Theme_Keyword: Substrate Theme: Theme_Keyword_Thesaurus: USGS Thesaurus Theme_Keyword: organisms Theme_Keyword: animals Theme_Keyword: invertebrates Theme_Keyword: protists Theme: Theme_Keyword_Thesaurus: Marine Realms Information Bank (MRIB) keywords Theme_Keyword: bay Theme_Keyword: sediment deposition Theme: Theme_Keyword_Thesaurus: None Theme_Keyword: U.S. Geological Survey Theme_Keyword: USGS Theme_Keyword: Coastal and Marine Hazards and Resources Program Theme_Keyword: CMHRP Theme_Keyword: Pacific Coastal and Marine Science Center Theme_Keyword: PCMSC Theme_Keyword: foraminifera Theme_Keyword: benthic foraminifera Theme: Theme_Keyword_Thesaurus: USGS Metadata Identifier Theme_Keyword: USGS:661415dad34e633466530203 Place: Place_Keyword_Thesaurus: Geographic Names Information System (GNIS) Place_Keyword: San Francisco Bay Access_Constraints: No access constraints Use_Constraints: USGS-authored or produced data and information are in the public domain from the U.S. Government and are freely redistributable with proper metadata and source attribution. Please recognize and acknowledge the U.S. Geological Survey as the originators of the dataset and in products derived from these data. Point_of_Contact: Contact_Information: Contact_Organization_Primary: Contact_Organization: U.S. Geological Survey, Pacific Coastal and Marine Science Center Contact_Person: PCMSC Science Data Coordinator Contact_Address: Address_Type: mailing and physical Address: 2885 Mission Street City: Santa Cruz State_or_Province: CA Postal_Code: 95060 Contact_Voice_Telephone: 831-427-4747 Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov Native_Data_Set_Environment: Mac OSX 15.3.2, Microsoft Excel 16.95.4 for Mac Cross_Reference: Citation_Information: Originator: M. McGann Originator: L. Erikson Originator: E. Wan Originator: C. Powell, II Originator: R.F. Maddocks Publication_Date: 2013 Title: Distribution of biologic, anthropogenic, and volcanic constituents as a proxy for sediment transport in the San Francisco Bay Coastal System Other_Citation_Details: McGann, M., Erikson, L., Wan, E., Powell, C., II, and Maddocks, R.F., 1977, Distribution of biologic, anthropogenic, and volcanic constituents as a proxy for sediment transport in the San Francisco Bay Coastal System: Marine Geology, v. 345, p. 113Ð142. Online_Linkage: http://doi.org/10.1016/j.margeo.2013.05.006 Data_Quality_Information: Attribute_Accuracy: Attribute_Accuracy_Report: Microscopes are operationally checked every year to assure optics are aligned and visual acuity can be maximized during sorting and identifications. Specimen identifications were compared to reference material (actual specimens and published monographs) to ensure identifications were accurate. Specimen enumeration (counts) were checked with original laboratory bench sorting sheets to assure numbers were correct, and the sorting and data entry into spreadsheets was rechecked at least once. Logical_Consistency_Report: Data were checked for logical consistency by the laboratory staff before release to confirm that numerical values were not outside a reasonable range for a particular field. Cumulative counts of percentage data for the total foraminiferal assemblage had to equal approximately 100 percent to ensure numbers were reported correctly. Completeness_Report: Dataset is considered complete for the information presented, as described in the abstract. Users are advised to read the metadata for each part of this data release carefully for additional details. Positional_Accuracy: Horizontal_Positional_Accuracy: Horizontal_Positional_Accuracy_Report: A formal accuracy assessment of the horizontal positional information in the data set has not been conducted. The horizontal accuracy was determined with a Leica GPS for R/V Polaris cruises 1983-611-DD, 1986-602-DD, and P-1-87-SF, a Garmin ProNav GPS 100 for R/V David Johnston cruises 1993-602-DD and J-1-98-SF, a Garmin 4212 GPS for R/V Parke Snavely cruises S-7-10-SF and S-8-10-SF, and a Garmin GPSmap XSV chartplotter and Garmin GPS19x antenna for the R/V Jewell cruise 2024-662-FA. Vertical_Positional_Accuracy: Vertical_Positional_Accuracy_Report: A formal accuracy assessment of the vertical positional information in the data set has not been conducted. Depth was determined using a Garmin GPSMAP with depth sounder for for R/V Polaris cruises 1983-611-DD, 1986-602-DD, and P-1-87-SF, and a Furuno FCV585 depth sounder for R/V David Johnston and R/V Parke Snavely cruises 1993-602-DD, J-1-98-SF, S-7-10-SF, and S-8-10-SF, and R/V Jewell cruise 2024-662-FA. Lineage: Process_Step: Process_Description: Surface or core-top sediment samples were analyzed for benthic foraminifera. These sediment samples were wet-sieved through stacked 0.063 mm, 0.150 mm, and 1.0 mm screens to remove the silt and clay-sized fractions (less than 0.063 mm). Sediment remaining on each screen was transferred to filter paper, air-dried, and then recombined with the other size fractions. Foraminifera were extracted from the greater than 0.063 mm to 1.0 mm fractions. Each sample was split with the aid of a microsplitter into an aliquot containing at least 300 benthic foraminifers. While viewing under a microscope, specimens were removed from the matrix with a small, moistened picking brush, and placed on pre-glued microfaunal slides. All specimens were picked, including the non-indigenous species Trochammina hadai, identified using the nomenclature registered in the World Foraminiferal Database, and tabulated. If the sample contained less than 300 foraminifera, all that were present were picked. The percent of Trochammina hadai was calculated by dividing the number of Trochammina hadai specimens in each sample by the total number of foraminiferal specimens collected in each sample, multiplied by 100. The foraminiferal slides and residues of this study are on file at the U.S. Geological Survey, Santa Cruz, California. Process_Date: 2013 Process_Step: Process_Description: Samples collected during the R/V Jewell cruise 2024-662-FA were analyzed and added to this dataset following the same process. Process_Date: 2025 Process_Contact: Contact_Information: Contact_Person_Primary: Contact_Person: Mary McGann Contact_Organization: U.S. Geological Survey Contact_Position: Research Geologist Contact_Address: Address_Type: mailing and physical Address: 2885 Mission Street City: Santa Cruz State_or_Province: CA Postal_Code: 95060 Contact_Voice_Telephone: 831-427-4747 Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov Spatial_Data_Organization_Information: Direct_Spatial_Reference_Method: Point Point_and_Vector_Object_Information: SDTS_Terms_Description: SDTS_Point_and_Vector_Object_Type: Point Point_and_Vector_Object_Count: 386 Spatial_Reference_Information: Horizontal_Coordinate_System_Definition: Geographic: Latitude_Resolution: 0.0001 Longitude_Resolution: 0.0001 Geographic_Coordinate_Units: Decimal degrees Geodetic_Model: Horizontal_Datum_Name: North American Datum of 1927 Ellipsoid_Name: Clarke 1866 Semi-major_Axis: 6378206.4 Denominator_of_Flattening_Ratio: 294.978698214 Entity_and_Attribute_Information: Detailed_Description: Entity_Type: Entity_Type_Label: SF_Bay_T_hadai_1983-2010_counts_v2.csv Entity_Type_Definition: Results of census counts of the non-indigenous benthic foraminiferal species Trochammina hadai Entity_Type_Definition_Source: Producer defined. Attribute: Attribute_Label: Sampling_institution Attribute_Definition: Institution which collected the sediment sample. Attribute_Definition_Source: Producer defined Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: USGS, Water Mission Area Enumerated_Domain_Value_Definition: Sampling institution Enumerated_Domain_Value_Definition_Source: Producer defined Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: USGS, Pacific Coastal and Marine Science Center Enumerated_Domain_Value_Definition: Sampling institution Enumerated_Domain_Value_Definition_Source: Producer defined Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: San Francisco Estuary Institute Enumerated_Domain_Value_Definition: Sampling institution Enumerated_Domain_Value_Definition_Source: Producer defined Attribute: Attribute_Label: USGS_field_activity_number Attribute_Definition: Unique alphanumeric identifier given to the USGS field activity. Attribute_Definition_Source: Producer defined. Attribute_Domain_Values: Unrepresentable_Domain: USGS field activity number Attribute: Attribute_Label: USGS_sample_identification_number Attribute_Definition: Unique alphanumeric identifier given to the sediment sample collected by the U.S. Geological Survey. BRP refers to the San Francisco Bar Province; CP refers to the Central Bay Province; GGP refers to the Golden Gate Province; OSP refers to the Offshore Province; SBP refers to the South Bay Province; SPP refers to the San Pablo Bay Province; and SSP refers to the Susuin Bay Province. These seven provinces are presented in McGann and others, 2013. NAN indicates the parameter was not determined. Attribute_Definition_Source: Producer defined. Attribute_Domain_Values: Unrepresentable_Domain: USGS sample identification number Attribute: Attribute_Label: SFEI_sample_identification_number Attribute_Definition: Unique alphanumeric identifier given to the sediment sample collected by the San Francisco Estuary Institute (SFEI). NAN indicates the parameter was not determined. Attribute_Definition_Source: SFEI Attribute_Domain_Values: Unrepresentable_Domain: SFEI sample identification number Attribute: Attribute_Label: Site_description Attribute_Definition: Geographic description of the sample site in San Francisco Bay. The seven provinces are presented in McGann and others, 2013. Attribute_Definition_Source: Producer defined. Attribute_Domain_Values: Unrepresentable_Domain: Site description Attribute: Attribute_Label: Date_Collected Attribute_Definition: Date Attribute_Definition_Source: Producer defined. Attribute_Domain_Values: Range_Domain: Range_Domain_Minimum: 4/19/1983 Range_Domain_Maximum: 11/08/2024 Attribute_Units_of_Measure: MM/DD/YYYY Attribute: Attribute_Label: Latitude Attribute_Definition: Latitude of the site at which the surface sediment sample was collected. Attribute_Definition_Source: Producer defined. Attribute_Domain_Values: Range_Domain: Range_Domain_Minimum: 37.4258 Range_Domain_Maximum: 38.1269 Attribute_Units_of_Measure: decimal degrees Attribute_Measurement_Resolution: 0.0001 Attribute: Attribute_Label: Longitude Attribute_Definition: Longitude of the site at which the surface sediment sample was collected. Attribute_Definition_Source: Producer defined. Attribute_Domain_Values: Range_Domain: Range_Domain_Minimum: -123.0245 Range_Domain_Maximum: -121.8075 Attribute_Units_of_Measure: decimal degrees Attribute_Measurement_Resolution: 0.0001 Attribute: Attribute_Label: Water_Depth_m Attribute_Definition: Water depth of surface sample collected. 9999 indicates the parameter was not determined. Attribute_Definition_Source: Producer defined. Attribute_Domain_Values: Range_Domain: Range_Domain_Minimum: 0.0 Range_Domain_Maximum: 70.0 Attribute_Units_of_Measure: meters Attribute_Measurement_Resolution: 0.1 Attribute: Attribute_Label: Total_Trochammina_hadai_counted Attribute_Definition: Total number of Trochammina hadai specimens recovered in each sample. Trochammina hadai represents Trochammina hadai Uchio, 1962. Attribute_Definition_Source: Producer defined Attribute_Domain_Values: Range_Domain: Range_Domain_Minimum: 0 Range_Domain_Maximum: 1342 Attribute_Units_of_Measure: each Attribute_Measurement_Resolution: 1 Attribute: Attribute_Label: Trochammina_hadai_percent_abundance Attribute_Definition: Abundance percent of Trochammina hadai in each sample. Trochammina hadai represents Trochammina hadai Uchio, 1962. The percent of Trochammina hadai was calculated by dividing the number of Trochammina hadai specimens in each sample by the total number of foraminiferal specimens collected in each sample, multiplied by 100. Attribute_Definition_Source: Producer defined Attribute_Domain_Values: Range_Domain: Range_Domain_Minimum: 0.0 Range_Domain_Maximum: 100.0 Attribute_Units_of_Measure: percentage Attribute_Measurement_Resolution: 0.1 Attribute: Attribute_Label: Total_foraminifera_counted Attribute_Definition: Total number of benthic foraminiferal specimens recovered in each sample. Attribute_Definition_Source: Producer defined Attribute_Domain_Values: Range_Domain: Range_Domain_Minimum: 0 Range_Domain_Maximum: 1550 Attribute_Units_of_Measure: each Attribute_Measurement_Resolution: 1 Overview_Description: Entity_and_Attribute_Overview: The first line of the comma-separated values file is a header line. Entity_and_Attribute_Detail_Citation: U.S. Geological Survey Distribution_Information: Distributor: Contact_Information: Contact_Organization_Primary: Contact_Organization: U.S. Geological Survey - ScienceBase Contact_Address: Address_Type: mailing and physical Address: Denver Federal Center, Building 810, Mail Stop 302 City: Denver State_or_Province: CO Postal_Code: 80225 Contact_Voice_Telephone: 1-888-275-8747 Contact_Electronic_Mail_Address: sciencebase@usgs.gov Resource_Description: These data are available in a comma-delimited text file (SF_Bay_T_hadai_1983-2024_counts_v2.csv) which contains census counts of the non-indigenous benthic foraminifera Trochammina hadai obtained in 1987-2024 in San Francisco Bay, California. Distribution_Liability: Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. Standard_Order_Process: Digital_Form: Digital_Transfer_Information: Format_Name: comma-delimited text Format_Version_Number: Microsoft Excel 16.95.4 for Mac Format_Information_Content: .csv file File_Decompression_Technique: none Transfer_Size: 0.005000 Digital_Transfer_Option: Online_Option: Computer_Contact_Information: Network_Address: Network_Resource_Name: https://www.sciencebase.gov/catalog/file/get/661415dad34e633466530203 Network_Resource_Name: https://doi.org/10.5066/P13UOJDV Access_Instructions: Data can be downloaded using the Network_Resource_Name links. This first link begins a direct download of the data and metadata. The second link points to the landing page for the data release. Fees: None. Technical_Prerequisites: These data can be viewed with any text editor software. Metadata_Reference_Information: Metadata_Date: 20250515 Metadata_Contact: Contact_Information: Contact_Organization_Primary: Contact_Organization: U.S. Geological Survey, Pacific Coastal and Marine Science Center Contact_Person: PCMSC Science Data Coordinator Contact_Address: Address_Type: mailing and physical Address: 2885 Mission Street City: Santa Cruz State_or_Province: CA Postal_Code: 95060 Contact_Voice_Telephone: 831-427-4747 Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov Metadata_Standard_Name: Content Standard for Digital Geospatial Metadata Metadata_Standard_Version: FGDC-STD-001-1998