Properties of sediment collected from two marshes and adjacent shallows in Northern San Francisco Bay, California, 2022-2023

SEDIMENT COLLECTION. Sediment samples were collected from a small vessel near pre-established USGS instrument moorings using a either a Gomex box corer that was then subsampled with three push cores (38 mm in diameter) when a sufficient amount of sediment was recovered, or via a ship-side push core (59 mm in diameter) with triplicates collected in succession. At the Corte Madera tidal creek sites, accessible on foot, push cores were collected by pressing the core liner directly into the sediment. At each site, six or more subsamples were collected from the upper 5 (cm) of each push core. Several longer cores had additional subsamples collected (up to 18 cm from the top). For each core, the two uppermost subsamples were collected at 0.5 cm intervals. The rest of the core was sampled at 1 cm intervals, except for some longer cores where 2 cm intervals were sampled below 6 cm depth in the core. Sediment samples were carefully extracted from cores by siding core on top of an extruder, which pushed the sediment in the core upward, allowing us to section precise sample depths starting with the surface sample. Subsamples were placed into pre-weighed Whirl-pak bags. Subsamples of sediment deposited upon ceramic tiles placed on the marsh top were collected and processed for grain size.

GRAIN-SIZE ANALYSIS: A total of 205 samples (including occasional duplicates) were analyzed for grain size. Grain-size analysis was conducted by the USGS Pacific Coastal and Marine Science Center (PCMSC) sediment lab using a Beckman Coulter LS 13 320 grain size analyzer with an aqueous liquid module attachment. PCMSC procedures are modified from those described in Carver (1971) and Folk (1974, 1980). 5-50 grams of sediment was sub-sampled and at least 10 milliliters of 30 percent hydrogen peroxide was added and left for approximately 12 hours to remove organics. The samples were then heated to 250 degrees Celsius to remove excess hydrogen peroxide. Next, samples were placed in an ultrasonic bath to help disperse silt and clay (mud) from sand and larger-sized particles. Samples were then rinsed twice in deionized water with centrifugation to remove soluble ions. Subsequently, the samples were wet sieved with 1 millimeter and 0.063 millimeter sieves to segregate the combined gravel and coarse sand fraction (greater than 1 millimeter), sand (1 millimeter to 0.063 millimeter), and mud (less than 0.063 millimeter). The coarse sand + gravel fractions were then dried, dry sieved at 1/4phi intervals and weighed (Carver, 1971). The sand fraction was dried and weighed. The mud fraction was collected in a 1 liter graduated cylinder, 5 milliliters of at least 10 percent sodium hexametaphosphate (dispersant) was added, and deionized water was added to bring the total the volume to 1 liter. The mud + dispersant solution sat overnight to ensure complete dispersion and to observe if flocculation occurred. Subsequently, a 20 milliliter aliquot was extracted from the graduated cylinder and dried to obtain the mud fraction weight normalized to a 1-liter basis. The mud and sand fractions were analyzed separately via the Beckman Coulter LS 13 320 with the aqueous liquid module attachment. All size fraction data were compiled and converted by the PCMSC sediment lab pcSDSZ program (Penscil, 2015) to a grain-size distribution at 1/4phi size intervals on a weight percent basis. pcSDSZ also calculated interpolated sizes and graphical statistics on a percent coarser basis (Folk and Ward, 1957; Folk, 1966; Folk, 1974, 1980; Inman, 1952; Trask, 1930, 1932) and moment measures (Collias and others, 1963; Jaquet and Vernet, 1976; Folk, 1980).

INTERPOLATED SIZES: Grain sizes at select cumulative percentage values (D) were calculated by the PCMSC Sediment Lab software pcSDSZ version 1.71 on a percent coarser basis, which summed from coarse to fine bins. D values were interpolated between phi bins bracketing the specified D value. Grain sizes were converted into units of millimeters (mm) using the formula mm=reciprocal of 2(exponent)phi or (phi=-log2(mm)). Interpolated grain sizes at D50 are reported in phi and millimeter units.

A total of 495 samples were analyzed for bulk density by the USGS Pacific Coastal and Marine Science Center sediment lab. Bulk density was calculated with the formula: bulk density = (dry sediment mass + water mass) /((dry sediment mass/sediment density) + (water mass/water density)), where water density is 1 g/cm3 and sediment density is 2.65 g/cm3. Local salinity readings were used to calculate salt mass, which was removed from dry sediment mass prior to this calculation. Salinity data are available in the time-series section of this data release.

CARBON ANALYSIS: A total of 64 samples were analyzed for percent carbon. Carbon analysis was performed by the PCMSC carbon lab employing a coulometric titration technique described in Engleman and others (1985) and UIC operating manuals for the UIC CM5200 autosampler furnace, the UIC CM5230 acidification module, and the UIC CM5017 coulometer. Total carbon (TC), total inorganic carbon (TIC), total organic carbon (TOC) and percent calcium carbonate (CaCO3) are reported as percent dry weight. Approximately 5 grams of sediment were dried in an 80 degrees Celsius oven. Samples were then pulverized, redried, and placed in a desiccator. For TC analysis, approximately 20 milligrams of the pulverized sample were weighed and wrapped in an aluminum capsule then combusted at 950 degrees Celsius in an UIC CM5200 autosampler furnace attached to an UIC CM5017 coulometer. The carbon dioxide (CO2) produced by combusting the sample was then converted to TC by the UIC CM5017 coulometer. For TIC, approximately 20 milligrams of sample were weighed and loaded into an UIC CM5230 acidification module attached to an UIC CM5017 coulometer. The samples were then digested in a perchloric acid solution, and the CO2 generated was measured and converted to TIC. Two analyses per sample were run and the results were averaged. TOC was calculated by subtracting TIC from TC. The TIC value was then multiplied by 8.333 (the molar stochiometric ratio of CaCO3 to C) to convert TIC to percent CaCO3.

LOSS ON IGNITION ANALYSIS: A total of 77 samples were analyzed for Loss on Ignition (LOI). LOI was performed by the PCMSC sediment lab employing using method "Solids, volatile-on-ignition, total-in-bottom-material, gravimetric" from Fishman and Friedman (1989). Samples were placed in oven at 103 deg C for 2 hours, then weighted. Dried samples were placed in a furnace at 550 deg C for 2 hours, then weighted. Loss was calculated as oven dried weights minus the after furnace ignition weights. Percent loss was calculated from the fraction of after furnace ignition weights to oven dried weights.