Census counts of the non-indigenous benthic foraminifera Trochammina hadai Uchio obtained in 1983-2010 in San Francisco Bay, California

Metadata also available as - [Questions & Answers] - [Parseable text] - [XML]

Metadata:

Identification_Information
Data_Quality_Information
Spatial_Data_Organization_Information
Spatial_Reference_Information
Entity_and_Attribute_Information
Distribution_Information
Metadata_Reference_Information

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 1983-2010 in San Francisco Bay, California

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 1983-2010 in San Francisco Bay, California: 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 San Francisco Bay, California from 1983-2010.

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, India, 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 2010 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 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: 20100320

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: 650-329-4979
Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov

Native_Data_Set_Environment: Mac OSX 13.6.6, Microsoft Excel 16.83 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. 113ï¿½142.

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 accuracyassessment 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, and a Garmin 4212 GPS for R/V Parke Snavely cruises S-7-10-SF and S-8-10-SF.

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.

Lineage:

Process_Step:

Process_Description:

Surface 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

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: 381

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:

A comma-separated values file with the first line being a header line.

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: 3/20/2010
Attribute_Units_of_Measure: M/D/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 fileï¿½(SF_Bay_T_hadai_1983-2010_counts.csv) which contains census counts of the non-indigenous benthic foraminifera Trochammina hadai obtained in 1987-2010 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 16.83 for Mac
Format_Information_Content: .csv file
File_Decompression_Technique: none
Transfer_Size: 0.04695

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: 20240722
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

This page is <https://cmgds.marine.usgs.gov/catalog/pcmsc/DataReleases/ScienceBase/DR_P13UOJDV/SF_Bay_T_hadai_1983-2010_metadata.html>