Renee K. Takesue
20230725
Geochemistry of fine sediment from San Francisco Bay shoals (2012) and tributaries (2010, 2012, 2013)
comma-delimited text
data release
DOI:10.5066/P9CH2ZWD
Pacific Coastal and Marine Science Center, Santa Cruz, California
U.S. Geological Survey
Suggested Citation: Takesue, R.K., 2023, Geochemistry of fine sediment from San Francisco Bay shoals (2012) and tributaries (2010, 2012, 2013): U.S. Geological Survey data release, https://doi.org/10.5066/P9CH2ZWD
https://doi.org/10.5066/P9CH2ZWD
Elemental chemistry and weight percent of the less than 0.063 mm fine sediment fraction are reported for surface sediments from shoals, the ebb tide delta, local tributaries, and inland rivers that carry sediment to San Francisco Bay, California.
A sediment geochemical sourcing study was carried out in San Francisco Bay, its local tributaries, and inland rivers to explore the relative importance of fine sediment inputs from local versus inland watersheds. The availability of sediment from local watersheds is an important consideration for wetland habitat restoration and coastal resilience planning because sediment loads from inland watersheds are decreasing and relative water levels are increasing.
Surface sediment from San Francisco Bay was collected by the San Francisco Estuary Institute Regional Monitoring Program (RMP) in August 2011 (14 sites with Sample_ID beginning in RMP). Additional information about USGS field activities from which data were derived is available online at:
http://cmgds.marine.usgs.gov/fan_info.php?fan=S710SF
http://cmgds.marine.usgs.gov/fan_info.php?fan=S0112SF
Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
20100307
20130611
Bay sediment was collected in August 2011 (RMP) and January 2012 (USGS). River and stream sediments were collected in March and April 2010, March 2012 (Petaluma River), and February 2013 (additional sites on the Sacramento and San Joaquin Rivers).
None planned
-122.67853
-121.22921
38.56064
37.33939
ISO 19115 Topic Category
environment
geoscientificInformation
Data Categories for Marine Planning
Substrate
USGS Thesaurus
geochemistry
rare earth elements
mass spectroscopy
grab sampling
Marine Realms Information Bank (MRIB) keywords
Sediment geochemistry
None
U.S. Geological Survey
USGS
Coastal and Marine Hazards and Resources Program
CMHRP
Pacific Coastal and Marine Science Center
PCMSC
USGS Metadata Identifier
USGS:63387bfcd34e900e86cdd8c8
Geographic Names Information System (GNIS)
San Francisco Bay
Suisun Bay
San Pablo Bay
South Bay
Sacramento River
San Joaquin River
Napa River
Sonoma Creek
Petaluma River
Corte Madera Creek
San Francisquito Creek
Guadelupe River
Alameda Creek
Wildcat Creek
Fort Funston
None
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 originator(s) 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
https://www.sciencebase.gov/catalog/file/get/63387bfcd34e900e86cdd8c8?name=pic_BenthicSampler.JPG&allowOpen=true
USGS scientists prepare to collect mud from a benthic sampler.
JPEG
Don Woodrow collected single hand-grab samples from stream banks or stream beds of local and inland tributaries in March and April 2010. Angela Tan analyzed sediment grain size distributions at the USGS Pacific Coastal and Marine Science Center Sediment Laboratory. Elemental chemistry analyses were performed by AGAT Laboratories under contract to the Analytical Chemistry Project of the USGS Geology, Geophysics, and Geochemistry Science Center (GGGSC). GGGSC staff performed QA/QC checks.
Geochemical data are tabulated in comma separated variable (CSV) format.
For sediment grain size analyses (GSA), the laser particle counter was calibrated with three manufacturer-provided standards every day. Process duplicates for GSA were analyzed every 20 samples and were within 15 percent. For elemental chemistry determinations, long-term internal reference materials were used to standardize the data. The percent recovery for all elements was within 15 percent of reference values for concentrations that were not less than five times the limit of detection.
No formal logical consistency tests were conducted.
Sample collection depths were not determined for 14 samples collected by RMP. Grain size distribution (percent fines) was not analyzed in CB_598 or tributary samples collected in 2012 and 2013. Thirty size sandy samples out of 143 total had insufficient fine material for multi-acid analysis of elements: potassium (K), sodium (Na), arsenic (As), beryllium (Be), bismuth (Bi), cadmium (Cd), indium (In), lithium (Li), manganese (Mn), molybdenum (Mo), niobium (Nb), phosphorus (P), scandium (Sc), thallium (Tl), tungsten (W), and zinc (Zn).
A Garmin handheld GPS reported a horizontal accuracy of +/- 3 meters.
SEDIMENT COLLECTION. Single hand-grab samples were collected from local streams and inland rivers in March and April 2010. Surface sediment from the shoals and ebb tide delta of San Francisco Bay was collected in January 2012 using a benthic grab sampler deployed from the USGS research vessel Parke Snavely. Single hand-grab samples were collected from Petaluma River in March 2012 and inland rivers in February 2013.
20130209
SEDIMENT GRAIN SIZE ANALYSIS. Sediment grain size distributions were determined at the USGS Pacific Coastal and Marine Science Center Sediment Laboratory. To remove organic material, 10 milliliters of 35 percent hydrogen peroxide were added to 20 grams of sediment. The sample was heated to 250 degrees Celsius to remove any remaining hydrogen peroxide and was placed in an ultrasonic bath to liberate the less than 0.063 millimeter-diameter fine fraction. The sample was centrifuged for 1.5 hours in deionized water to remove soluble salts. Samples were funneled through 2 millimeter- and 0.063 millimeter-diameter mesh sieves to separate gravel-sized (greater than 2 millimeter), sand-sized (0.063 to 2 millimeter), and mud-sized (less than 0.063 millimeter) particles. The sand and gravel fractions were dried at 80 degrees Celsius and weighed. Five milliliters of sodium hexametaphosphate were added to the mud fraction and a 20-milliliter aliquot was taken from a 1-liter graduated cylinder to determine the weight of the mud. The particle-size distribution of the mud and sand fraction was analyzed separately using a Beckman Coulter LS 13 320, and the gravel, sand, and mud results were integrated into a single grain-size distribution for each sample.
20120427
Angela Tan
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Physical Scientist
mailing and physical
2885 Mission Street
Santa Cruz
CA
95060
831-460-7409
atan@usgs.gov
ELEMENTAL CHEMISTRY. Bulk sediment was oven-dried at 60 degrees Celsius and disaggregated gently with a mortar and pestle to avoid changing grain sizes. Disaggregated sediment was dry-sieved through stainless steel sieves to obtain 2 grams of the less than 0.063 millimeter fine fraction. Fine sediments were sent to the Analytical Chemistry Project of the USGS Geology, Geophysics, and Geochemistry Science Center (GGGSC), which contracted SGS Inc. Laboratory for analyses of major, minor, and trace element contents using two methods: a near-total four-acid digestion (labeled multi-acid in the table of data) and a total digestion with a sodium peroxide fusion (labeled fusion in the table of data) for elements hosted in acid-resistant minerals. Quantification was performed by inductively coupled plasma atomic emission spectroscopy (ICP-OES) for major and some minor elements and by inductively coupled plasma mass spectroscopy (ICP-MS) for some minor and all trace elements.
20130611
Jaime Azain
USGS Geology, Geophysics, and Geochemistry Science Center
Research Geologist
mailing
Denver Federal Center, Bldg 20
Denver
CO
80225
303-236-9376
jsazain@usgs.gov
Point
Point
143
0.00001
0.00001
Decimal degrees
D_WGS_1984
WGS84
6378137.0000
298.2572
SanFranciscoBayandTributaryGeochemistry.csv
Table of data. -9999 indicates not determined, -1111 indicates the sample was below the analytical detection limit.
Producer defined
Job_ID
Unique laboratory identifier assigned to a batch of samples by the GGGSC Analytical Chemistry Laboratory
producer defined
Unique alphanumeric batch identifier
Lab_ID
Unique laboratory identifier assigned to each sample by the GGGSC Analytical Chemistry Laboratory
producer defined
Unique alphanumeric lab sample identifier
Sample_ID
Unique sample identifier assigned during field collection based on location and order of collection
producer defined
Unique alphanumeric field sample identifier
Latitude
Latitude where the sample was collected
producer defined
37.33939
38.56064
decimal degrees
0.00001
Longitude
Longitude where the sample was collected
producer defined
-122.67853
-121.22921
decimal degrees
0.00001
Collection_date
Date the sample was collected, in mm/dd/yy
producer defined
03/07/2010
02/09/2013
mm/dd/yyyy
1
Depth
Water depth at which the sample was collected; -9999=not determined
producer defined
0.0
29.9
meters
0.1
Site_description
Location where the sample was collected
producer defined
Text describing the sample collection site
Percent_fines
Percentage of the less than 0.063 mm sediment size fraction; -9999=not determined
producer defined
0
99
weight percent
1
Al_by_fusion
Aluminum (Al) content of fused, digested sediment
Producer defined
5.26
9.04
weight percent
0.01
Ca_by_fusion
Calcium (Ca) content of fused, digested sediment
Producer defined
0.8
6.0
weight percent
0.1
Fe_by_fusion
Iron (Fe) content of fused, digested sediment
Producer defined
2.39
8.38
weight percent
0.01
K_by_multi-acid
Potassium (K) content of multi-acid digested sediment; -9999=not determined
Producer defined
0.98
2.29
weight percent
0.01
Mg_by_fusion
Magnesium (Mg) content of fused, digested sediment
Producer defined
0.73
2.51
weight percent
0.01
Na_by_multi-acid
Sodium (Na) content of multi-acid digested sediment; -9999=not determined
producer defined
0.51
2.93
weight percent
0.01
Ti_by_fusion
Titanium (Ti) content of fused, digested sediment
producer defined
0.32
1.05
weight percent
0.01
As_by_multi-acid
Arsenic (As) content of multi-acid digested sediment; -9999=not determined
producer defined
5
21
milligrams per kilogram (mg per kg)
1
Ba_by_fusion
Barium (Ba) content of fused, digested sediment
producer defined
344
1280
milligrams per kilogram (mg per kg)
1
Be_by_multi-acid
Beryllium (Be) content of multi-acid digested sediment; -9999=not determined
producer defined
0.7
1.8
milligrams per kilogram (mg per kg)
0.1
Bi_by_multi-acid
Bismuth (Bi) content of multi-acid digested sediment; -9999=not determined
producer defined
0.06
0.60
milligrams per kilogram (mg per kg)
0.01
Cd_by_multi-acid
Cadmium (Cd) content of multi-acid digested sediment; -9999=not determined
producer defined
0.1
0.9
milligrams per kilogram (mg per kg)
0.1
Ce_by_fusion
Cerium (Ce) content of fused, digested sediment
producer defined
32.2
138.0
milligrams per kilogram (mg per kg)
0.1
Co_by_fusion
Cobalt (Co) content of fused, digested sediment
producer defined
7.7
39.7
milligrams per kilogram (mg per kg)
0.1
Cr_by_fusion
Chromium (Cr) content of fused, digested sediment
producer defined
120
2050
milligrams per kilogram (mg per kg)
1
Cs_by_fusion
Cesium (Cs) content of fused, digested sediment
producer defined
1.4
10.7
milligrams per kilogram (mg per kg)
0.1
Cu_by_fusion
Copper (Cu) content of fused, digested sediment
producer defined
7
93
milligrams per kilogram (mg per kg)
1
Dy_by_fusion
Dysprosium (Dy) content of fused, digested sediment
producer defined
2.81
8.79
milligrams per kilogram (mg per kg)
0.01
Er_by_fusion
Erbium (Er) content of fused, digested sediment
producer defined
1.59
6.64
milligrams per kilogram (mg per kg)
0.01
Eu_by_fusion
Europium (Eu) content of fused, digested sediment
producer defined
0.72
1.61
milligrams per kilogram (mg per kg)
0.01
Ga_by_fusion
Gallium (Ga) content of fused, digested sediment
producer defined
11
20
milligrams per kilogram (mg per kg)
1
Gd_by_fusion
Gadolinium (Gd) content of fused, digested sediment
producer defined
3.03
8.83
milligrams per kilogram (mg per kg)
0.01
Hf_by_fusion
Hafnium (Hf) content of fused, digested sediment
producer defined
3
120
milligrams per kilogram (mg per kg)
1
Ho_by_fusion
Holmium (Ho) content of fused, digested sediment
producer defined
0.55
1.89
milligrams per kilogram (mg per kg)
0.01
In_by_multi-acid
Indium (In) content of multi-acid digested sediment; -9999=not determined
producer defined
0.03
0.09
milligrams per kilogram (mg per kg)
0.01
La_by_fusion
Lanthanum (La) content of fused, digested sediment
producer defined
15.2
69.0
milligrams per kilogram (mg per kg)
0.1
Li_by_multi-acid
Lithium (Li) content of multi-acid digested sediment; -9999=not determined
producer defined
18
59
milligrams per kilogram (mg per kg)
1
Lu_by_fusion
Lutetium (Lu) content of fused, digested sediment
Producer defined
0.22
1.49
milligrams per kilogram (mg per kg)
0.01
Mn_by_multi-acid
Manganese (Mn) content of multi-acid digested sediment; -9999=not determined
producer defined
311
2000
milligrams per kilogram (mg per kg)
1
Mo_by_multi-acid
Molybdenum (Mo) content of multi-acid digested sediment; -9999=not determined
producer defined
0.48
1.96
milligrams per kilogram (mg per kg)
0.01
Nb_by_multi-acid
Niobium (Nb) content of multi-acid digested sediment; -9999=not determined
producer defined
6.4
18.3
milligrams per kilogram (mg per kg)
0.1
Nd_by_fusion
Neodymium (Nd) content of fused, digested sediment
producer defined
14.3
54.1
milligrams per kilogram (mg per kg)
0.1
Ni_by_fusion
Nickel (Ni) content of fused, digested sediment
producer defined
41
125
milligrams per kilogram (mg per kg)
1
P_by_multi-acid
Phosphorus (P) content of multi-acid digested sediment; -9999=not determined
producer defined
480
1430
milligrams per kilogram (mg per kg)
1
Pb_by_fusion
Lead (Pb) content of fused, digested sediment
producer defined
6
99
milligrams per kilogram (mg per kg)
1
Pr_by_fusion
Praseodymium (Pr) content of fused, digested sediment
producer defined
3.78
15.20
milligrams per kilogram (mg per kg)
0.01
Rb_by_fusion
Rubidium (Rb) content of multi-acid digested sediment
producer defined
26.5
95.0
milligrams per kilogram (mg per kg)
0.1
Sb_by_fusion
Antimony (Sb) content of fused, digested sediment
producer defined
0.3
3.2
milligrams per kilogram (mg per kg)
0.1
Sc_by_multi-acid
Scandium (Sc) content of multi-acid digested sediment; -9999=not determined
producer defined
9.2
22.8
milligrams per kilogram (mg per kg)
0.1
Sm_by_fusion
Samarium (Sm) content of fused, digested sediment
Producer defined
3.1
10.5
milligrams per kilogram (mg per kg)
0.1
Sn_by_fusion
Tin (Sn) content of fused, digested sediment; -1111 indicates the sample was below the analytical detection limit of 0.5 mg per kg
Producer defined
1
18
milligrams per kilogram (mg per kg)
1
Sr_by_fusion
Strontium (Sr) content of fused, digested sediment
producer defined
116
370
milligrams per kilogram (mg per kg)
1
Tb_by_fusion
Terbium (Tb) content of fused, digested sediment
producer defined
0.45
1.37
milligrams per kilogram (mg per kg)
0.01
Th_by_fusion
Thorium (Th) content of fused, digested sediment
producer defined
3.9
29.2
milligrams per kilogram (mg per kg)
0.1
Tl_by_multi-acid
Thallium (Tl) content of multi-acid digested sediment; -9999=not determined
producer defined
0.2
0.5
milligrams per kilogram (mg per kg)
0.1
Tm_by_fusion
Thulium (Tm) content of fused, digested sediment
producer defined
0.20
1.10
milligrams per kilogram (mg per kg)
0.01
U_by_fusion
Uranium (U) content of fused, digested sediment
producer defined
1.85
13.00
milligrams per kilogram (mg per kg)
0.01
V_by_fusion
Vanadium (V) content of fused, digested sediment
producer defined
83
242
milligrams per kilogram (mg per kg)
1
W_by_multi-acid
Tungsten (W) content of multi-acid digested sediment; -9999=not determined
producer defined
0.7
3.2
milligrams per kilogram (mg per kg)
0.1
Y_by_fusion
Yttrium (Y) content of fused digested sediment
producer defined
15.7
58.9
milligrams per kilogram (mg per kg)
0.1
Yb_by_fusion
Ytterbium (Yb) content of fused digested sediment
producer defined
1.6
8.5
milligrams per kilogram (mg per kg)
0.1
Zn_by_multi-acid
Zinc (Zn) content of multi-acid digested sediment; -9999=not determined
producer defined
55
216
milligrams per kilogram (mg per kg)
1
Zr_by_fusion
Zirconium (Zr) content of the fused, digested sediment
producer defined
109
4280
milligrams per kilogram (mg per kg)
1
The first line of the csv 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 csv format (SanFranciscoBayandTributaryGeochemistry.csv) contained in a single zip file, which also includes CSDGM FGDC-compliant metadata.
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
File contains the csv table and the associated metadata.
No compression applied
0.046
https://www.sciencebase.gov/catalog/file/get/63387bfcd34e900e86cdd8c8
https://doi.org/10.5066/P9CH2ZWD
Data can be downloaded using the Network_Resource_Name links. The first link is a direct link to download the zipped file of data and metadata. The second link points to a landing page with metadata and data.
None.
These data can be viewed with any text reader.
20230725
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