Methods to derive ‘smscg_data_water_quality.csv’

NOTE: Previous versions of this water quality data set have significant amounts of missing and incorrect data and should not be used.

Water Quality data were collected separately by the Department of Water Resources’ (DWR) Water Quality Assessment unit, Continuous Environmental Monitoring Program unit, and the Tidal Habitat Restoration section via a network of stationary water quality probes deployed in and around Suisun Marsh. Continuous water quality measurements were collected using Yellow Springs International (YSI) multi-parameter water quality probes. The probes were used to measure water temperature, turbidity, pH, dissolved oxygen, specific conductance, and chlorophyll fluorescence at 15-minute intervals. These data are telemetered to DWR’s California Data Exchange Center (CDEC).

To create this data set, data was gathered from various repositories (existing EDI data and internal databases) and compiled into a single format. Cutoff values were established for each parameter to deal with the outliers detected. Since negative values are impossible to occur naturally for all parameters included in this data set, all data below 0 were replaced with “N/A”. Chlorophyll fluorescence data above 500, turbidity data above 300, water temperature data above 100, pH data above 14, and specific conductance data above 30,000 were replaced with “N/A”. The specific conductance cutoff was determined based on the most western stations with the highest marine influence.

Codes of “X” and “B” indicate data of poor quality. Data with these codes were marked as “N/A”, while the code itself is unchanged to show when this occurred. Much of the data currently in this data set are unchecked (code = "U"), meaning that QAQC protocols have not yet been applied. Please contact the package authors prior to using these data.

YSI EXO2 or YSI 6600 sonde

Methods to derive 'smscg_phytoplankton_samples.csv'

NOTE: In February 2022, an error in the original biovolume calculation was discovered and a corrected version was uploaded. This error affected the first two versions of the data package (edi.876.1-edi.876.2).

Phytoplankton community composition was monitored every two weeks from mid-July to late October at a network of stations in and around Suisun Marsh. Samples were collected via boat from the top one meter of the water column of large channels. EMP samples are collected at a consistent tidal stage (high slack), but DFW samples are not. The 60-mL samples were fixed on site with Lugol’s solution and stored in amber glass bottles until analyzed. BSA Environmental Services, Inc. (https://www.bsaenv.com/) conducted identification and enumeration using the Utermöhl microscopic method (Utermöhl 1958) and modified Standard Methods (American Public Health Association 2012). In brief, an aliquot (10-20 mL) was placed into a counting chamber and allowed to settle for a minimum of 12 h. Within an aliquot, phytoplankton were enumerated in randomly chosen transects at a magnification of 800x using a Leica DMIL inverted microscope. A minimum of 400 total phytoplankton units were counted, and a minimum of 100 units of the dominant taxon were counted. For taxa that were in filaments or colonies, number of cells per filament or colony was recorded. Phytoplankton were identified to the lowest taxonomic level possible (usually genus). Photosynthetic biovolume was estimated for up to ten individuals per taxon per sample. All samples were analyzed in less than a year from time of collection. Counts were converted to organisms per mL and cells per mL and estimated photosynthetic biovolumes were used to estimate biovolume per mL.

American Public Health Association. 2012. Standard Methods for the Examination of Water and Wastewater. 22nd ed. American Public Health Association, Washington, D.C.

Utermöhl H. 1958. Zur Vervollkommnung der quantitativen Phytoplankton Methodik. Mitt Int Ver Theor Angew Limnol 9:1–38.

Methods to derive ‘smscg_mesozooplankton_samples.csv’

Mesozooplankton and Microcystis sampling relied on data from several long-term boat-based sampling programs, all of which are available as in integrated data set on EDI (Bashevkin et al. 2022). The Interagency Ecological Program’s Environmental Monitoring Program (EMP) (https://wildlife.ca.gov/Conservation/Delta/Zooplankton-Study), which collects zooplankton samples on a monthly basis at fixed sites throughout the upper SFE (Hennessy 2019); California Department of Fish and Wildlife’s Summer Townet Survey (STN) (https://www.wildlife.ca.gov/Conservation/Delta/Townet-Survey), which collects zooplankton and fish samples at fixed sites on a biweekly basis in July and August; and the Fall Midwater Trawl (FMWT) (https://www.wildlife.ca.gov/Conservation/Delta/Fall-Midwater-Trawl), which operates on a monthly basis in September-December and also collects zooplankton samples in addition to fish sampling at fixed sites in the study area. Additional sampling was conducted by STN and FMWT in September and October as part of this monitoring. Sampling methods were similar between surveys. For each mesozooplankton sample, an 85 cm long, 12.5 cm diameter zooplankton net made of 0.16 mm nylon mesh was attached to a steel sampling sled and towed through the water in a stepwise oblique manner for ten minutes to sample the entire water column. A General Oceanics model 2030 flowmeter was fixed in the mouth of the net to calculate water volume sampled. Samples were preserved in 10% formalin and subsamples were identified by taxonomists at CDFW’s laboratory in Stockton, CA. Catch per cubic meter of water sampled (CPUE) was calculated based on volume of water passing through the net as measured by the flowmeter. CPUE was converted to biomass per cubic meter (BPUE) by using published conversion factors (Dumont et al. 1975, Rian and Stephen 2004, Kimmerer et al. 2011).

Methods to derive ‘smscg_macrozooplankton_samples.csv’

Macrozooplankton (i.e., mysid) sampling relied on data from two long-term boat-based sampling programs. The California Department of Fish and Wildlife’s Summer Townet Survey (STN) (https://www.wildlife.ca.gov/Conservation/Delta/Townet-Survey), which collects zooplankton and fish samples at fixed sites on a biweekly basis in July and August and Fall Midwater Trawl (FMWT) (https://www.wildlife.ca.gov/Conservation/Delta/Fall-Midwater-Trawl), which operates on a monthly basis in September-December and also collects zooplankton samples in addition to fish sampling at fixed sites in the study area. Additional sampling was conducted by STN and FMWT as part of this monitoring during 2018 and 2019 but subsequently discontinued. Sampling methods were similar between surveys. For each macrozooplankton sample, a net made of 0.505-mm nylon mesh (1.4 m long, 30 cm diameter) was attached to a steel sampling sled and towed through the water in a stepwise oblique manner for ten minutes to sample the entire water column. A General Oceanics model 2030 flowmeter was fixed in the mouth of the net to calculate water volume sampled. Samples were preserved in 10% formalin and subsamples were identified by taxonomists at CDFW’s laboratory in Stockton, CA. Catch per cubic meter of water sampled (CPUE) was calculated based on volume of water passing through the net as measured by the flowmeter.

Methods to derive ‘smscg_clams.csv’

NOTE1: In September 2022, an error was found in the calculations of mass, which resulted in slightly inaccurate values for ash free dry mass (AFDM), filtration rate, and grazing rate. Error affected the first three versions of the data package (edi.876.1-edi.876.3). Values have been corrected for all years.

NOTE2: In November 2022, an error was found in the calculation of grazing rates for both clam species caused by the inclusion of a unit conversion twice, resulting in units of kilo-cubic meters per meter squared per day instead of cubic meters per meter squared per day. Error only affected one version of the data package (edi.876.4). All values have been corrected.

Clam data were collected at 28 sites in and near Suisun Marsh between 2018 and 2021, visited in July and September each year. The sites we used extended from Grizzly Bay, up into Suisun and Montezuma Sloughs and the smaller sloughs that branch off of them, and eastward into Suisun Bay at Sherman Lake. Fourteen of the 28 sites were either part of the Interagency Ecological Program’s (IEP) long-term Ecological Monitoring Program (EMP), had been visited as part of an EMP benthic special study, or had previously hosted water quality sondes as part of other Department of Water Resources (DWR) monitoring efforts. The remaining 14 sites were chosen to expand the sampling up into the smaller and shallower sloughs, and to fill in geographic gaps along the length of Suisun and Montezuma Sloughs.

Sites were sorted by decreasing stream order into three categories: River, Channel, and Slough. Environmental data was taken during the sampling runs at each of the sites, including water temperature (C), electrical conductivity as a proxy for salinity (uS/cm), turbidity (Nephelometric Turbidity Unit, or NTU), fluorescence as a proxy for chlorophyll-a (milligrams/liter), and dissolved oxygen (milligrams/liter) were measured using a YSI 6600 V2 or YSI EXO multi-parameter sonde. Water depth (meters) at each site visit was also recorded. Sediment composition at each site visit was described by visually estimating the percentage volume of silt/clay, sand, gravel, and organic material in each grab. Sediment was categorized as "Fines", "Sand", "Gravel", or "Organic", depending on majority composition. Any missing sediment category data points were filled post-hoc in with the predominant sediment type for that site from other visits.

All samples were collected using a Ponar dredge with a sample area of 0.052 m2, to a depth that varied from 4-10 cm with sediment type. Four Ponar grabs were taken at each of the two long-term monitoring sites and one grab sample was taken at the other 26 sites. Each sample was sieved on 595 µm mesh and preserved with 70% ethyl alcohol for subsequent identification, enumeration, and measuring to the nearest millimeter.

Density was calculated as the number of individual clams per square meter. A shell-length:ash free dry mass (AFDM) log-log regression was constructed for each species and each sampling event at a reference site (EMP monitoring sites D4-L for Corbicula fluminea and D7-C for Potamocorbula amurensis). Total ash-free dry mass for each sample was estimated using the appropriate shell length:AFDM regression and converted to AFDM/m2. Grazing rates (GR) for each sample were calculated following the method outlined in Kimmerer and Thompson 2014, which incorporates biomass, filtration rates, and an estimated refiltration proportion (see Equation 1) to account for boundary layers of water that are re-grazed. Grazing rate turnover (GRTO) is the grazing rate divided by the depth of the water at the sample site, and is in units of m3/day. For EMP monitoring sites, where more than one replicate sample was taken at each sampling event, replicate samples were averaged.

Equation 1:

GR = AFDM * FR * 1 - nmax

where:

GR = grazing rate, in (m3 water)/(m2 benthic surface)/day

AFDM = ash-free dry mass, in g/m2 benthic surface

FR = filtration rate, temperature-corrected and species-specific, in (m3 water)/(g AFDM)/day

nmax = refiltration proportion = 3.0/(s/do)

s = clam spacing factor, calculated as 100/√(density in individuals/m2)

do = mean clam siphon diameter, estimated from mean clam shell size, in mm

Methods to derive ‘smscg_edsm_delta_smelt.csv’

Since 2016, the US Fish and Wildlife Service’s Enhanced Delta Smelt Monitoring Program (EDSM), has conducted Kodiak trawls to monitor Delta Smelt throughout the upper San Francisco Estuary (United States Fish and Wildlife Service et al. 2022). The Kodiak trawl had maximum mouth dimensions of 1.83 m x 7.62 m, with a body consisting of five panels of mesh starting with 5.1-cm stretch near the net mouth and decreasing to 0.3 cm stretch before the cod end, which was attached to a live box. Over the course of a week, field crews sample between 18 and 37 random sites, stratified by region of the estuary. During each weekly survey period a Kodiak trawl crew sampled 3-4 sites per day with a minimum of 2 tows per site. If no Delta Smelt were captured in the first two tows, up to four additional samples were taken. For each tow, the total number of Delta Smelt was counted, measured, and individuals were saved for future research. The results for each weekly sampling period and region were summarized based on catch per tow (CPUE) for each sampling region. Fish that could not be assigned to a particular tow (gilled in the net), and tows which were not completed (GearCondition Codes 4 and 9) were not included.

Formatting of data sets for publication on EDI was often completed using R scripts. The input data files and scripts are located in a GitHub repository: https://github.com/InteragencyEcologicalProgram/SMSCG/tree/master/EDI