Data Package Metadata   View Summary

Methods to derive ‘WQdata_smscg_2018-2020.csv’

Water Quality data were collected by the Department of Water Resources (DWR) Suisun Marsh Branch and Environmental Monitoring Program via stationary water quality probes deployed at Collinsville, Montezuma Slough at Roaring River, National Steel, Hunter Cut, Tule Red Breach, Grizzly Bay, and Grizzly Bay Buoy.

Continuous water quality measurements were taken using Yellow Springs International (YSI) EXO2 multi-parameter water quality probes. The probes were used to measure temperature, turbidity, specific conductivity, and chlorophyll fluorescence at 15-minute intervals from January 1, 2018 – December 31, 2020, in accordance with DWR’s QAQC protocols. These data are telemetered to DWR’s California Data Exchange Center (CDEC). To derive the dataset, we downloaded the data from CDEC (https://cdec.water.ca.gov/) and performed outlier detections.

Methods to derive SMSCG_phytoplankton_EDI_2020.csv

Phytoplankton community composition was monitored every two weeks from mid-July to late October at nine locations in the Lower Sacramento River and Suisun Marsh. Samples were collected via boat from the top one meter of the water column of large channels. 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 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_CBNet_2018to2020CPUE_12July2021.csv

Zooplankton 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, 2020) (Bashevkin et al. 2020). The Interagency Ecological Program’s Environmental Monitoring Program (EMP) (http://www.water.ca.gov/iep/activities/emp.cfm), 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 zooplankton 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.

==================== Data Sources =========================

Title: Interagency Ecological Program: Zooplankton abundance in the Upper San Francisco Estuary from 1972-2020, an integration of 5 long-term monitoring programs

DOI: https://doi.org/10.6073/pasta/e67851d690088a1244f69fb38d6659d6

Creator: Bashevkin, S.M.

Contact: Bashevkin, S.M.

===========================================================

Methods to derive SMSCG_clam_EDI_2020_corrected_dates.csv

Clam data were collected at 28 sites in and near Suisun Marsh between 2018 and 2020, 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.

Data for this analysis came from sampling 28 different sites at two sampling events a year (May or July and October) in 2018-2020. 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 (see stations_SMSCG.csv). 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. 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, and were used as continuous variables in analysis. Water depth (meters) at each site visit was also recorded and was used as used as a continuous variable for analysis. 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. The estimated percent of organic matter in each sediment visit was used as a continuous variable. Sediment was categorized as "Fines", "Sand", "Gravel", or "Organic", depending on majority composition. If the composition was estimated at 50:50, the coarser fraction was used for categorization (Gravel>Organic>Sand>Fines). 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 in as 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 ‘EDSMsmelt_summer_2018.csv”:

Since 2016, the US Fish and Wildlife Service’s Enhanced Delta Smelt Monitoring Program (EDSM) (https://doi.org/10.6073/pasta/98bce400502fae3a6b77b3e96f6d51e7), conducts Kodiak trawls to monitor Delta Smelt throughout the upper San Francisco Estuary (United States Fish and Wildlife Service et al. 2019). 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.

==================== Data Sources =========================

Title: Interagency Ecological Program and US Fish and Wildlife Service: San Francisco Estuary Enhanced Delta Smelt Monitoring Program data, 2016-2021

DOI: https://doi.org/10.6073/pasta/be90161581213fdae9f308327c436d8e

Creator: United States Fish and Wildlife Service

===========================================================

This method step describes provenance-based metadata as specified in the LTER EML Best Practices.

This provenance metadata does not contain entity specific information.

This method step describes provenance-based metadata as specified in the LTER EML Best Practices.

This provenance metadata does not contain entity specific information.