Mary McGann 20240722 2.0 comma-delimited text data release DOI: 10.5066/P13UOJDV Pacific Coastal and Marine Science Center, Santa Cruz, California U.S. Geological Survey 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. https://doi.org/10.5066/P13UOJDV https://www.sciencebase.gov/catalog/item/661415dad34e633466530203 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. 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. 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. 19830419 20241108 Ground condition at time data were collected. Complete None planned -123.0245 -121.8075 38.1269 37.4258 ISO 19115 Topic Category biota environment society geoscientificInformation Data Categories for Marine Planning Habitat Invertebrates Substrate USGS Thesaurus organisms animals invertebrates protists Marine Realms Information Bank (MRIB) keywords bay sediment deposition None U.S. Geological Survey USGS Coastal and Marine Hazards and Resources Program CMHRP Pacific Coastal and Marine Science Center PCMSC foraminifera benthic foraminifera USGS Metadata Identifier USGS:661415dad34e633466530203 Geographic Names Information System (GNIS) San Francisco Bay No access 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. U.S. Geological Survey, Pacific Coastal and Marine Science Center PCMSC Science Data Coordinator mailing and physical

2885 Mission Street

Santa Cruz CA 95060 831-427-4747 pcmsc_data@usgs.gov Mac OSX 15.3.2, Microsoft Excel 16.95.4 for Mac M. McGann L. Erikson E. Wan C. Powell, II R.F. Maddocks 2013 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. http://doi.org/10.1016/j.margeo.2013.05.006 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. 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. 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. 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. 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. 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. 2013 Samples collected during the R/V Jewell cruise 2024-662-FA were analyzed and added to this dataset following the same process. 2025 Mary McGann U.S. Geological Survey Research Geologist mailing and physical

2885 Mission Street

Santa Cruz CA 95060 831-427-4747 pcmsc_data@usgs.gov Point Point 386 0.0001 0.0001 Decimal degrees North American Datum of 1927 Clarke 1866 6378206.4 294.978698214 SF_Bay_T_hadai_1983-2010_counts_v2.csv Results of census counts of the non-indigenous benthic foraminiferal species Trochammina hadai Producer defined. Sampling_institution Institution which collected the sediment sample. Producer defined USGS, Water Mission Area Sampling institution Producer defined USGS, Pacific Coastal and Marine Science Center Sampling institution Producer defined San Francisco Estuary Institute Sampling institution Producer defined USGS_field_activity_number Unique alphanumeric identifier given to the USGS field activity. Producer defined. USGS field activity number USGS_sample_identification_number 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. Producer defined. USGS sample identification number SFEI_sample_identification_number Unique alphanumeric identifier given to the sediment sample collected by the San Francisco Estuary Institute (SFEI). NAN indicates the parameter was not determined. SFEI SFEI sample identification number Site_description Geographic description of the sample site in San Francisco Bay. The seven provinces are presented in McGann and others, 2013. Producer defined. Site description Date_Collected Date Producer defined. 4/19/1983 11/08/2024 MM/DD/YYYY Latitude Latitude of the site at which the surface sediment sample was collected. Producer defined. 37.4258 38.1269 decimal degrees 0.0001 Longitude Longitude of the site at which the surface sediment sample was collected. Producer defined. -123.0245 -121.8075 decimal degrees 0.0001 Water_Depth_m Water depth of surface sample collected. 9999 indicates the parameter was not determined. Producer defined. 0.0 70.0 meters 0.1 Total_Trochammina_hadai_counted Total number of Trochammina hadai specimens recovered in each sample. Trochammina hadai represents Trochammina hadai Uchio, 1962. Producer defined 0 1342 each 1 Trochammina_hadai_percent_abundance 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. Producer defined 0.0 100.0 percentage 0.1 Total_foraminifera_counted Total number of benthic foraminiferal specimens recovered in each sample. Producer defined 0 1550 each 1 The first line of the comma-separated values file is a header line. U.S. Geological Survey U.S. Geological Survey - ScienceBase mailing and physical

Denver Federal Center, Building 810, Mail Stop 302

Denver CO 80225 1-888-275-8747 sciencebase@usgs.gov 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. 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. comma-delimited text Microsoft Excel 16.95.4 for Mac .csv file none 0.005000 https://www.sciencebase.gov/catalog/file/get/661415dad34e633466530203 https://doi.org/10.5066/P13UOJDV 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. None. These data can be viewed with any text editor software. 20250515 U.S. Geological Survey, Pacific Coastal and Marine Science Center PCMSC Science Data Coordinator mailing and physical

2885 Mission Street

Santa Cruz CA 95060 831-427-4747 pcmsc_data@usgs.gov Content Standard for Digital Geospatial Metadata FGDC-STD-001-1998