Carrie E. Givens, US Geological Survey Alexei R. Rose, US Geological Survey Tai Brass, US Geological Survey 20250701 spreadsheet Givens, C.E., Rose, A.R., Brass, T.D., 2025, Bacteria Enumerations from Surface Water and Bed Sediment Collected from a Mudflat in Palo Alto, California, 2021-2024: U.S. Geological Survey data release, https://doi.org/10.5066/P18QTMPK. https://doi.org/10.5066/P18QTMPK Daniel J Cain Marie-Noele Croteau Francis Parchaso Emily L Zierdt Smith Robin Stewart Le Kieu Matthew A Turner Shaun Baesman 2021 dataset https://www.sciencebase.gov U.S. Geological Survey Cain, D.J., Croteau, M., Parchaso, F., Stewart, R., Zierdt Smith, E.L., Thompson, J.K., Kieu, L., Turner, M., and Baesman, S.M., 2022, Data for monitoring trace metal and benthic community near the Palo Alto Regional Water Quality Control Plant in South San Francisco Bay, California (ver 2.0, November 2022): U.S. Geological Survey data release, https://doi.org/10.5066/P9IBQ23S. https://doi.org/10.5066/p9ibq23s USGS scientists enumerated bacteria, including bacterial pathogens, from surface water and sand/sediment collected at an intertidal site (mudflat) near the outfall the Palo Alto Regional Water Quality Control Plant (RWQCP). This site has been monitored for metal concentrations and benthic invertebrate community for the last 30 years. Continued efforts to document changes in pollutant concentrations, forms, and types over time is critical to assess ecosystem health. Environmental water and sand samples were analyzed at U.S. Geological Survey Michigan Bacteriological Research Laboratory for enumeration of halophilic bacteria, total coliforms, Escherichia coli, and enterococci, and the enrichment and isolation of Vibrio spp. The goal of this study is to assess aquatic ecosystem responses (including long-term responses) to wastewater-associated bacterial contaminants as a water quality metric documenting recovery after contaminant assault and physical disturbances at a site in South San Francisco Bay with a history of legacy contaminant exposure. 20210222 20241210 ground condition Planned As needed SAN FRANCISCO BAY -122.1015000 -122.1007000 37.4627000 37.4603000 ISO 19115 Topic Category biota Theme water quality environmental health recreational water quality bacteria microorganisms surface water sediment environment USGS Metadata Identifier USGS:68373aa0d4be0253791824f6 Geographic location Palo Alto, California California United States Bacteria species Escherichia coli Total coliforms Bacteria Halophilic bacteria Vibrionaceae Vibrio spp. Enterococci Kingdom Bacteria No access constraints. Please see 'Distribution Information' for details. These data are marked with a Creative Common CC0 1.0 Universal License. These data are in the public domain and do not have any use constraints. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations. Carrie E Givens USGS - MIDCONTINENT REGION Supervisory Research Microbiologist mailing and physical

Upper Midwest WSC Lansing Office,WRD MI District Office

5840 Enterprise Drive

Lansing MI 48911-4107 United States 517-512-9505 cgivens@usgs.gov Dean J. Cain, US Geological Survey Marie-Noele Croteau, US Geological Survey 2023 U.S. Geological Survey Open-File Report 2023–1017 publication U.S. Geological Survey Open-File Report 2023–1017 Cain, D.J., Croteau, M.-N., Thompson, J.K., Parchaso, F., Stewart, R., Zierdt Smith, E.L., Shrader, K.H., Kieu, L.H., and Luoma, S.N., 2023, Near-field receiving-water monitoring of trace metals and a benthic community near the Palo Alto Regional Water Quality Control Plant in south San Francisco Bay, California—2020: U.S. Geological Survey Open-File Report 2023–1017, 51 p., https://doi.org/10.3133/ofr20231017. ISSN: 2331-1258 (online) https://pubs.usgs.gov/publication/ofr20231017 A field blank was collected once to ensure that sample collection and handling procedures did not affect the corresponding chemical and microbial results. The field blank consisted of sterile deionized (DI) water which was collected and handled using the same field protocols as the environmental sample. The field blank did not yield any bacterial colony growth. Microbial laboratory blanks consisting of sterile deionized (DI) water for IDEXX (Westbrook, ME) analysis and sterile 1X phosphate buffered saline (PBS) for all culture enumerations and enrichment were processed with each set of samples received. Laboratory blanks did not yield any colony growth. Media blanks were incubated alongside environmental samples and laboratory blanks to ensure media reagents were not contaminated. Media blanks did not yield any growth. Positive and negative controls from IDEXX-QC Coliform and E. coli kit and IDEXX-QC Enterococci kit were run on each IDEXX Colilert and Enterolert lot to ensure assay accuracy. All reported values fall within the expected ranges. Data were checked for completeness, duplicate values, and omissions. All data is included Field sites were located by GPS. No formal vertical positional accuracy tests were conducted. IDEXX Laboratories 2022 1.4.4 application/service IDEXX Laboratories, IDEXX MPN Generator, 2022, 1.4.4 https://www.idexx.com/en/water/resources/mpn-generator/ Digital and/or Hardcopy 2021 2024 publication date IDEXX MPN Generator calculating IDEXX Most Probable Number (MPN) values D.N. Myers D.M. Stoeckel R.N. Bushon D.S. Francy A.G. Brady 2014 2.1 publication Techniques of Water-Resources Investigations 09-A7.1 Myers, D.N., Stoeckel, D.M., Bushon, R.N., Francy, D.S., and Brady A.M.G., 2014, Chapter A7.1, Fecal Indicator Bacteria: U.S. Geological Survey Techniques of Water-Resources Investigations, book 9, chap. A7.1, https://doi.org/10.3133/twri09A7.1. https://pubs.usgs.gov/twri/twri9a7/twri9a7_7.1_ver2.1.pdf Digital and/or Hardcopy 2021 2024 publication date USGS NWQM Methods and enumeration reference American Water Works Association, and Water Environment Federation 2017 23rd publication Standard Methods Committee of the American Public Health Association, American Water Works Association, and Water Environment Federation. standard methods committee In: Standard Methods For the Examination of Water and Wastewater. Lipps WC, Baxter TE, Braun-Howland E, editors. Washington DC: APHA Press. DOI: 10.2105/SMWW.2882.001 https://www.standardmethods.org/doi/full/10.2105/SMWW.2882.001 Digital and/or Hardcopy 2021 2024 publication date Standard Methods Standard methods for membrane filtration and isolation of total coliforms, Escherichia coli, enterococci, and Vibrio spp. Samples were shipped on ice overnight the day of collection to the Michigan Bacteriological Research Laboratory (MI-BaRL; Lansing, MI) and analyzed for halophilic bacteria, total coliform, Escherichia coli (E. coli), enterococci, and Vibrio spp. colony growth. Surface water (10 mL) was added to IDEXX Quanti-Tray/2000 System with either Colilert or Enterolert tests (IDEXX; Westbrook, ME) to detect and quantify total coliforms, E. coli, and enterococci, respectively. Additionally, surface water samples (50 mL, 10 mL, and 1 mL) were filtered in the laboratory using sterilized equipment and standard methods for membrane filtration (American Public Health Association, 2017) and subsequently enriched and enumerated on marine agar (MA; halophilic bacteria) and selectively enriched and isolated on Thiosulfate-Citrate-Bile-Salts-Sucrose agar (TCBS; Vibrio spp.). Three grams (g) of streambed sediment were added to 30 mL of sterile 1X phosphate buffered saline (PBS) and shaken horizontally for 45 minutes. A total of 100 µL and 1 mL of this dilution were each then spread plated on marine agar and TCBS agar. An additional 1:10 and 1:100 dilution of sediment was made in sterile deionized (DI) water and were each used with IDEXX consumables to quantify total coliforms and E. coli, and enterococci. All IDEXX and plate media were incubated according to manufacturer’s instructions. IDEXX Quanti-Tray/2000 results were identified and enumerated according to manufacturer’s instructions. Plate colony growth for all media types and dilution volumes was recorded. Final count data for dilution series was calculated and reported according to the IDEXX MPN Generator 1.4.4 (IDEXX Laboratories, 2022) and USGS National Water Quality Manual (Myers and Sylvester, 2014). IDEXX MPN Generator USGS NWQM Standard Methods 2021 Carrie E Givens USGS - MIDCONTINENT REGION Supervisory Research Microbiologist mailing and physical

MI WSC Lansing Office,WRD MI District Office

5840

Lansing MI 48911-4107 517-887-8933 cgivens@usgs.gov T1_Mudflat_Bacterial_Methods.csv Comma Separated Value (CSV) file containing data. Method parameters for microbial analyses performed by Michigan Bacteriological Research Laboratory, Lansing, Michigan, for the U.S. Geological Survey Monitoring of legacy and emerging contaminants near the discharge of a Regional Water Quality Control Plant project. Producer Defined Target_organism Bacteria type Producer Defined bacteria type Method laboratory method Producer Defined Cultivation bacteria grown on selective media Producer defined Method_type laboratory method type Producer Defined enumeration cells are counted and assigned a number of colony forming units (CFU) or most probable number (MPN) Producer defined enrichment cells are either present or absent Producer defined Growth_medium medium type of environmental sample or quality assurance sample collected Producer Defined type of media used to cultivate respective bacteria type; mL, milliliter; g, gram Temperature temperature requirements for bacteria growth Producer Defined 25 37 degrees Celsius Time incubation time required for bacteria growth Producer Defined 24 72 hours Atmosphere oxygen level required for optimal bacteria growth Producer Defined aerobic atmosphere composed primarily of oxygen (21%) and small amount of carbon dioxide (0.03%) Producer defined Units units of measurement for reported bacteria cell counts Producer Defined CFU/100 mL or 1 g Colony Forming Units (CFU) per 100 milliliters (mL) of water or 1 gram (g) of sediment Producer defined MPN/100 mL or 1 g Most Probable Number (MPN) per 100 milliliters (mL) of water or 1 gram (g) of sediment Producer defined Analyzing_Laboratory analyzing laboratory Producer Defined U.S. Geological Survey Michigan Bacteriological Research Laboratory Michigan Bacteriological Research Laboratory at 5840 Enterprise Drive; Lansing, MI 48911 Producer defined Method_Reference published reference for laboratory method Producer Defined References for laboratory method T2_Mudflat_Bacterial_Results_fin.csv Comma Separated Value (CSV) file containing data. Bacteria enumeration results from analyses performed by Michigan Bacteriological Research Laboratory, Lansing, Michigan, for the U.S. Geological Survey Monitoring of legacy and emerging contaminants near the discharge of a Regional Water Quality Control Plant project. Producer Defined Site_ID Location of site Producer Defined Location of site where samples were collected. Latitude Coordinates that specify the north to south position of a point on the surface of the Earth. Producer Defined Coordinates that specify the north to south position of a point on the surface of the Earth. Units are in decimal degrees (geodetic datum: NAD87). Longitude Coordinates that specify the east to west position of a point on the surface of the Earth. Producer Defined Coordinates that specify the east to west position of a point on the surface of the Earth. Units are in decimal degrees (geodetic datum: NAD87). Sample_Date_Time Sampling date and time Producer Defined Sampling date; format in month, date, and year (MM/DD/YYYY). Time in hour and minutes (hhmm). Lab_ID Identification number assigned to sample during receipt at the Michigan Bacteriological Research Laboratory (MIBARL; Lansing, MI). Producer Defined Series of numbers used by the laboratory for tracking purposes. Sample_Type medium type of environmental sample or quality assurance sample collected Producer Defined SW surface water Producer defined SB bed sediment Producer defined Halophilic_bacteria_dw Bacteria cell counts for halophilic bacteria. Recorded as colony forming units (CFU) per1 gram (g) sediment. Sediment enumerations were calculated based on 1 g dry weight (dw). Producer Defined n.d. No data Producer defined Bacteria cell counts for halophilic bacteria. Recorded as colony forming units (CFU) per or 1 gram (g) dry weight (dw) sediment. CFU, colony forming units Halophilic_bacteria_dw_qualifier Qualifying code or flag applied to the reported value to provide additional information about the sample result Producer Defined -- not applicable Producer defined GRL greater than reporting limit Producer defined Halophilic_bacteria_ww Bacteria cell counts for halophilic bacteria. Recorded as colony forming units (CFU) per 100 milliliters (mL) water or 1 gram (g) sediment. Sediment enumerations were calculated based on 1 g wet weight (ww). Producer Defined n.d. no data Producer defined Bacteria cell counts for halophilic bacteria. Recorded as colony forming units (CFU) per 100 milliliters (mL) water or 1 gram (g) wet weight (ww) sediment. CFU, colony forming units Halophilic_bacteria_ww_qualifier Qualifying code or flag applied to the reported value to provide additional information about the sample result Producer Defined -- not applicable Producer defined GRL greater than reporting limit Producer defined Total_coliforms_dw Total coliform cell counts reported in most probable number (MPN) per 1 gram dry weight. Sediment enumerations were calculated based on 1 g dry weight (gdw). Producer Defined n.d. no data Producer defined Recorded as Most Probable Number (MPN) per 1 gram dry weight (gdw). MPN, most probable number per 100 milliliters Total_coliforms_dw_qualifier Qualifying code or flag applied to the reported value to provide additional information about the sample result Producer Defined -- not applicable Producer defined GRL greater than reporting limit Producer defined Total_coliforms_ww Total coliform cell counts reported in most probable number (MPN) per 100 mL or 1 gram wet weight. Sediment enumerations were calculated based on 1 g wet weight (gww). Producer Defined n.d. no data Producer defined Recorded as Most Probable Number (MPN) per 100 milliliters (mL) or 1 gram dry weight (gdw). MPN, most probable number per 100 milliliters Total_coliforms_ww_qualifier Qualifying code or flag applied to the reported value to provide additional information about the sample result Producer Defined -- not applicable Producer defined GRL greater than reporting limit Producer defined Escherichia_coli_dw Escherichia coli (E. coli) cell counts reported in most probable number (MPN) per 1 gram dry weight. Sediment enumerations were calculated based on 1 g dry weight (gdw). Producer Defined n.d. no data Producer defined Recorded as Most Probable Number (MPN) per 1 gram dry weight (gdw). E. coli, Escherichia coli Escherichia_coli_dw_qualifier Qualifying code or flag applied to the reported value to provide additional information about the sample result Producer Defined -- not applicable Producer defined LRL lower than reporting limit Producer defined Escherichia_coli_ww Escherichia coli (E. coli) cell counts reported in most probable number (MPN) per 100 mL or 1 gram wet weight. Sediment enumerations were calculated based on 1 g wet weight (gww). Producer Defined n.d. no data Producer defined Recorded as Most Probable Number (MPN) per 100 milliliters (mL) or 1 gram wet weight (gww). MPN, most probable number per 100 milliliters; E. coli, Escherichia coli Escherichia_coli_ww_qualifier Qualifying code or flag applied to the reported value to provide additional information about the sample result Producer Defined -- not applicable Producer defined LRL lower than reporting limit Producer defined Enterococci_dw Enterococci cell counts reported in most probable Most Probable Number (MPN) 1 gram dry weight. Sediment enumerations were calculated based on 1 g dry weight (gdw). Producer Defined n.d. no data Producer defined Recorded as Most Probable Number (MPN) per 1 gram dry weight (gdw). MPN, most probable number per 100 milliliters Enterococci_dw_qualifier Qualifying code or flag applied to the reported value to provide additional information about the sample result Producer Defined -- not applicable Producer defined GRL greater than reporting limit Producer defined LRL lower than reporting limit Producer defined Enterococci_ww Enterococci cell counts reported in most probable number (MPN) per 100 mL or 1 gram wet weight. Sediment enumerations were calculated based on 1 g wet weight (gww). Producer Defined n.d. no data Producer defined Recorded as Most Probable Number (MPN) per 100 milliliters (mL) or 1 gram wet weight (gww). MPN, most probable number per 100 milliliters Enterococci_ww_qualifier Qualifying code or flag applied to the reported value to provide additional information about the sample result Producer Defined -- not applicable Producer defined LRL lower than reporting limit Producer defined GRL greater than reporting limit Producer defined Vibrio_spp Presence or absence of presumptive of Vibrio spp. cell growth Producer Defined n.d. no data Producer defined 1 presumptive colony present Producer defined 0 presumptive colony absent Producer defined T3_Mudflat_BacteriaQAQC.csv Comma Separated Value (CSV) file containing data. Quality control/quality assurance (QA/QC) microbial data for bacterial cultivation performed by the Michigan Bacteriological Research Laboratory, Lansing, Michigan, for the U.S. Geological Survey Monitoring of legacy and emerging contaminants near the discharge of a Regional Water Quality Control Plant project. Producer Defined Sample_ID type of quality control and quality assurance sample collected Producer Defined Lab Blank Collected in the lab following same sampling procedures of environmental processing. Sample consists of either sterile deionized water or sterile 1X phosphate buffered saline. Producer defined Media Blank Consists of prepared media incubated in tandem with environmental samples. Confirms media sterility. Producer defined Field Blank Collected in the field at sampling site in tandem with collection of environmental samples. Consists of sterile deionized water. Producer defined Sample_Date Collection date in month, date, year. Producer Defined Collection date in month, date, year (MM/DD/YYYY). Sample_Type medium type of sample Producer Defined OAQ field or laboratory blank, artificial water sample medium Producer defined OA blank, testing media sterility Producer defined Halophilic_bacteria_ww Bacteria cell counts for halophilic bacteria. Recorded as colony forming units (CFU) per 100 milliliters (mL). Producer Defined n.d. no data Producer defined Bacteria cell counts for halophilic bacteria. Recorded as colony forming units (CFU) per 100 milliliters (mL). CFU, colony forming units Halophilic_bacteria_ww_qualifier Qualifying code or flag applied to the reported value to provide additional information about the sample result Producer Defined -- not applicable Producer defined LRL lower than reporting limit Producer defined Total_coliforms_ww Total coliform cell counts reported in MPN/100 mL. Producer Defined n.d. no data Producer defined Recorded as Most Probable Number (MPN) per 100 milliliters (mL). MPN, most probable number per 100 milliliters; ww, wet weight Total_coliforms_ww_qualifier Qualifying code or flag applied to the reported value to provide additional information about the sample result Producer Defined -- not applicable Producer defined LRL lower than reporting limit Producer defined Escherichia_coli_ww Escherichia coli (E. coli) cell counts reported in MPN/100 mL. Producer Defined n.d. no data Producer defined Recorded as Most Probable Number (MPN) per 100 milliliters (mL). MPN, most probable number per 100 milliliters; ww, wet weight Escherichia_coli_ww_qualifier Qualifying code or flag applied to the reported value to provide additional information about the sample result Producer Defined -- not applicable Producer defined LRL lower than reporting limit Producer defined Enterococci_ww Enterococci cells counts reported in MPN/100 mL Producer Defined n.d. no data Producer defined Recorded as Most Probable Number (MPN) per 100 milliliters (mL). MPN, most probable number per 100 milliliters; ww, wet weight Enterococci_ww_qualifier Qualifying code or flag applied to the reported value to provide additional information about the sample result Producer Defined -- not applicable Producer defined LRL lower than reporting limit Producer defined Vibrio_spp Presence or absence of presumptive Vibrio spp. cells Producer Defined n.d. no data Producer defined 0 presumptive colony absent Producer defined U.S. Geological Survey - ScienceBase mailing address

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Denver CO 80225 1-888-275-8747 sciencebase@usgs.gov 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 for other purposes, nor on all computer systems, nor shall the act of distribution constitute any such warranty. Digital Data https://doi.org/10.5066/P18QTMPK None 20250701 Carrie E Givens USGS - MIDCONTINENT REGION Supervisory Research Microbiologist mailing and physical

Upper Midwest WSC Lansing Office

5840 Enterprise Drive

Lansing MI 48911-4107 US 517-512-9505 cgivens@usgs.gov FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata FGDC-STD-001.1-1999