Data Package Metadata   View Summary

1.) Data Collection methods:

Both the Summer Townet (STN) and Fall Midwater Trawl (FMWT) surveys are conducted by the California Department of Fish and Wildlife. STN samples biweekly from June through August and Fall Midwater Trawl (FMWT) samples monthly from September through December. Both projects use a modified Clarke-Bumpus (CB) net made of 160 μm knotless nylon mesh with a cod-end jar attached to target mesozooplankton (i.e. copepods and cladocerans). STN has the CB net mounted on top of the townet sled used for fish sampling. FMWT utilizes a sled with a 500 μm nylon mesh mysid net attached to target macrozooplankton (i.e. mysid shrimp and amphipods), as well as the CB net to target mesozooplankton, with cod-end jars attached to each net. More details on the fish sampling gear and specifications can be found on the STN and FMWT project websites: https://wildlife.ca.gov/Conservation/Delta. Both projects tow the sled for ten minutes in a stepwise oblique pattern, according to a tow schedule based on station depth to sample the entire water column. Environmental variables collected at the start of each tow include the tide level, surface and bottom water temperature, surface and bottom electrical conductivity, secchi, and surface turbidity. This information comes from the FMWT and STN field project databases. Refer to the STN and FMWT survey websites here: https://wildlife.ca.gov/Conservation/Delta for equipment details and methods specifications on the collection of environmental variables. General Oceanics flowmeters are used to measure the volume of water sampled to later calculate catch per unit effort (CPUE). For the CB net, a flowmeter is fixed inside a plexiglass housing at the opening of the net. For the mysid net, the flowmeter is attached with line to hang in the middle of the mouth of the net. Start flowmeter readings are recorded before the tow begins and end flowmeter readings are recorded immediately upon sled retrieval. Before bottling the sample, nets are rinsed with ambient water sprayed along the outside of the net and any net seams to flush organisms possibly stuck in the net down to the cod-end jar. After the sample is thoroughly rinsed into the cod-end, the cod-end jar is unscrewed from the net. The sample is then swirled to suspend all organisms and poured into a 946 ml glass jar labeled with the project, station, date, survey number, and sample type (i.e. CB or mysid). A sample tag with the same information is also placed into the sample jar. Each jar contains formaldehyde dyed with Rose-Bengal dye so that the end concentration, when combined with the collected sample and ambient water, is 10% formalin. The Rose Bengal dye helps to later distinguish organisms from debris and vegetation during processing. Once the sample is poured into the preservation jar, the cod-end jar is dipped halfway into a bucket with ambient water, so any organisms stuck in the cod end mesh are not left behind. The mouth of cod-end jar is not submerged during this process so as not to contaminate the sample. The cod-end jar is again swirled gently, and the contents are poured into the sample jar. This is repeated until the sample is fully deposited into the sample jar and the sample jar is full. After field collection, samples are transferred to and stored at the CDFW Stockton labs until processed. Each type of sample is sorted or sieved to separate the target organisms from debris or vegetation, and then processed in the laboratory. Before processing, macro-zooplankton samples are concentrated in the laboratory by pouring them through a 0.5 mm sieve. Mysids and amphipods are identified to the lowest possible taxonomic level, enumerated, measured, sexed, and number of eggs counted and staged if present under a dissecting microscope. Other organisms not targeted or effectively caught by the mysid net (e.g. copepods) are not counted in macrozooplankton samples. Presence of jellyfish and fish are noted, but not counted, with the exception of endangered fish species such as Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys). Samples are then placed into a square sorting tray equipped with removable partitions and carefully stirred to allow for equal distribution and random sampling of organisms. Subsampling is conducted if a sample appears to contain more than 400 organisms. If subsampling is required, then samples are divided into 4, 16, or 64 equal subsamples using partitions placed in the sorting tray. The fraction of the sample that is processed is recorded and later used to estimate the total counts for the sample. When processing mesozooplankton, CB samples are first concentrated in the laboratory by pouring them through a sieve screened with 0.154 mm mesh wire. The concentrated sample is rinsed from the sieve into a beaker where the sample is reconstituted to an organism density of 200-400 per milliliter; this volume is recorded as the dilution volume. The sample is stirred to distribute organisms homogeneously and a 1 mL subsample is extracted with an automatic pipette and placed in a Sedgewick-Rafter cell (slide) for identification and enumeration under a compound microscope. A minimum of 5 and a maximum of 20 cells are processed for each sample depending on the dilution and the count of organisms. Organisms not targeted by the CB net (e.g. mysids and amphipods) are not enumerated. Presence of jellyfish and fish are noted, but not counted, with the exception of endangered fish species such as Delta Smelt and Longfin Smelt. Sample data for both types of processed samples is entered directly into a processing database.

2.) Link to blank datasheet:

Field collection datasheet available upon request. Sample processing data is entered directly into a database and therefore does not have a datasheet.

3.) Instrument and Equipment Specifications, including QAQC methods and frequency:

Meso-zooplankton sampling during Summer Townet (STN) is conducted using a modified Clarke-Bumpus (CB) net with a plexiglass housing attached to the top of the D-frame that is 1.2 m tall and to which the fish net is lashed. The fish D-frame is attached to a sled (Refer to the Summer Townet protocol and metadata here: https://wildlife.ca.gov/Conservation/Delta/Townet-Survey for full descriptions of the fish sampling gear). The CB housing is an acrylic tube measuring 19.05 cm long with a 12.7 cm inner diameter of the CB housing. A General Oceanics model 2030R flow meter is mounted in the center of the plexiglass CB housing with metal brackets so that the meter does not come loose, and the propeller can spin freely. The CB net is lashed to the rear of the CB housing, is 78 cm long, constructed of 160 μm knotless nylon mesh, and has an inner mouth diameter of 13 cm tapering to 5 cm where it attaches to a 250 mL polyethylene cod end jar. The cod end jar has a rectangular hole cut in the side measuring 6.99 cm x 5.08 cm covered with a 7.94 cm x 6.35 cm 140 μm nylon mesh. Fall Midwater Trawl (FMWT) conducts both meso (CB) and macrozooplankton sampling using a metal sled that measures 91.5 cm x 63.5 cm x 47 cm with a 1.75 cm welded steel pipe and with both a CB and mysid net attached. The CB net, cod end, and housing measurements are the same as those described above for STN. A 0.48 cm stainless steel wire rope and swivel connects the sled frame to the tow cable. The mysid net is a 1.48 m long net constructed from 0.50 mm nylon mesh. The mouth of the net measures 30 cm in outer diameter with a 28 cm inner diameter. Around the mouth of the net are 8 evenly spaced grommets, for lashing to the frame of the sled, on a 12 cm cylindrical section of bolting cloth. The net tapers down to a final 12 cm long cylindrical cod-end with a 76 mm opening. Attached to the cod-end is a modified 1000 mL polyethylene jar to collect the contents. The jar has a 10.8 cm x 7.62 cm hole cut into the side. 500 μm wire mesh, cut to 12.7 cm x 10.16 cm, is placed over the hole. The mesh left overlapping the hole is melted into place. To estimate the water volume filtered by the net, General Oceanics model 2030 flow meters are mounted at three locations on the sled. One in the middle of the mouth of the mysid net. One is mounted in the acrylic housing at the mouth of the CB net, and one on the frame of the sled adjacent to the mouth of the net which allows for comparisons and as a QC to the mysid net meter. Temperature and electrical conductivity are measured using a YFI Pro 30 that is calibrated monthly. Turbidity is measured using a Hach 2100Q Portable Turbidimeter which is also calculated monthly.

4.) Analysis Methods and SOPs:

Abundance of each taxon is reported as catch-per-unit-effort (CPUE). CPUE for organisms collected by the CB net is calculated by CPUE = ((C/S) L)/ V. Where CPUE is the number of an organism per cubic meter of water filtered. C is the cumulative number of a taxon counted in the sample. L is the reconstituted sample volume (dilution volume) in milliliters. S is the number of Sedgewick-Rafter cells examined (1 ml each). V is the volume of water filtered through the net (m3) where volume filtered is calculated by (end meter value – start meter value) * k * a. k is the factory flowmeter correction value of 0.026873. The mouth area of the CB net is 0.0113m ² . CPUE for organisms collected by the mysid net is calculated by CPUE = ((C/S)/V). Where C is the cumulative number of a taxon counted in tray segment(s) (sub-samples) examined. S is the fraction of total sample examined (1/number of tray segment(s) examined). V is the volume of water filtered through the net (m3) where volume filtered is calculated by (end meter value – start meter value) * k * a. k is the factory flowmeter correction value of 0.026873. The mouth area of mysid net= 0.062 m ² . Salinity in parts per thousand (PPT) for surface and bottom water is calculated from specific conductance (SP) using the formula: PPT=((0.36966/(((SP*0.001)^-1.07)-0.00074))*1.28156).

5.) Project History:

2005 – STN began collecting mesozooplankton samples at 32 stations to determine the amount of food available to young pelagic fishes by concurrently collecting fish and zooplankton during the same tow.

2005 – Mesozooplankton samples collected at a subset of FMWT stations in September.

2006 – FMWT collected mesozooplankton samples in September and October at 28 stations.

2007 – FMWT added macrozooplankton sampling and collected both CB and mysid samples at 10 stations from the lower Sacramento River through Suisun Bay in September and October.

2008 – Amphipods identified in FMWT mysid net samples.

2009 – No zooplankton samples were collected during FMWT.

2010 – Surface water turbidity (NTU) added using Hach turbidity meters.

2010 – Zooplankton tows in FMWT standardized to 31 stations, however only 10 were completed due to loss of the sled and lack of replacement.

2011 – The number of routinely sampled zooplankton stations increased to 40 for STN and 32 for FMWT extending sampling further up the Sacramento River, Cache Slough, and the Deep Water Ship Channel. Started measuring bottom water temperature (Celsius).

2013 – Amphipods identified and enumerated in samples collected by the mysid net.

2019 – Added Grandierella japonica to the list of identified amphipods in macrozooplankton samples. Previously this taxa was counted under the unidentified amphipod taxa category. Counts under the G. japonica category are reported as N/A before 2019.

2020 – The taxon category Acanthocyclops vernalis was changed to Acanthocyclops spp. due to the confirmed presence of a cryptic species complex consisting of three morphologically similar species (i.e. A. vernalis, A. robustus, A. americanus). It is unknown whether organisms identified as A. vernalis over the project history are truly A. vernalis or other members of the complex therefore all “A. vernalis” counts in the past are assumed to be Acanthocyclops spp.

2021 – Station 722 was added to both STN and FMWT zooplankton sampling to replace sampling at station 721 due to continued difficulties with vegetation at 721.

6.) QA/QC

Field Collection: After each tow, the field lead verifies that the tow was conducted without errors, and the sample was collected correctly (e.g. no holes in the nets, no flowmeter error, sled and net positioned correctly). If any of these situations occur, then a re-tow is conducted. Any errors or retows are recorded in the datasheet and database comments. Once the sample is collected, the field lead verifies that the net and cod end were positioned correctly (e.g. cod end screwed on all the way, net not wrapped around the frame), the nets are rinsed completely so all of the sample is retained, and the sample jars and tags are labeled correctly. Sample, tow, and environmental data are entered into the field project’s database from field datasheets and a QC is done on the data entry.

Sample Processing: A portion of the samples processed by each processor are subject to QC checks. 5% to 10% of samples are randomly selected following processing for a second round of identification by a different processor. The identification, enumeration, and length measurements in a sample are verified.

Processed sample data: Sample data is entered directly into a database during processing. Once samples are processed, a QC is done on the organism counts, taxa found in the sample for any outliers or incorrectly coded species identification, CPUE, and that all samples were processed correctly. Outliers are verified by comparing sample data and CPUE from surrounding stations, surveys, or data from other projects that monitor zooplankton in the same area. A sample is processed again to confirm outliers if needed. Any outliers, the QC checks done, possible reasons for outliers, or invalidation are noted in the zooplankton database.