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Name of study: ENTRAPMENT ZONE STUDY

Program manager
  Name:   Wim Kimmerer
  Agency:     Romberg Tiburon Center,
              San Francisco State University
  Address:   PO Box 855, Tiburon CA 94920
  Phone:     (415) 435-7118
  Fax:       (415) 435-7120
  Email:     kimmerer@sfsu.edu

Purpose/Objective:
  The main objective of this study was to determine the relationship
  between vertical and longitudinal positions of common entrapment zone
  species and the velocity field under various conditions of tide and
  outflow.  Entrapment zone species examined included phytoplankton,
  bacteria, microzooplankton, Eurytemora, Neomysis, and larval fish that
  are sufficiently abundant in the entrapment zone, including striped bass,
  longfin smelt, and gobies.
  Additional objectives were:
       To determine the importance of particle-bound bacteria to bacterial
       community metabolism in and out of the entrapment zone.
       To assess the importance of losses from populations through exchange
       and advection.
       To obtain information on small-scale spatial (particularly vertical)
       distribution of larval fish and zooplankton.
       
Geographic range of field work:
  The estuarine entrapment zone or the salinity range of 0.5 to 6,
  generally ranging from the western delta to San Pablo Bay.

Number of sites:
  Variable.  In 1994 samples were taken at 3 stations based on surface
  specific conductance: 1, 3, and 6 mS/cm. .  In 1995 samples were taken at
  approximately 2 psu (practical salinity units) at the bottom and at a
  location 1-5 km downstream from that.  These stations varied with the
  tide.

Period of record (Start year): 1994

Size for complete data base for program element in KB (MB): To be determined

Number of individual files: To be determined

Sample frequency per time unit (second, week, month):
       1994: Once on each flood and ebb tide at 1, 3, and 6 mS/cm, and once
       on each high and low slack at 3 mS/cm for up to 30 hours

       1995: Hourly for up to 30 hours

General category of data collected:
  CTD data (temperature, specific conductance, salinity, optical
  backscatter intensity), current velocities and backscatter intensity from
  acoustical backscatter current profilers,  chlorophyll (whole and 
  size-fractionated), and abundance of zooplankton (adult and juvenile 
  copepods, mysids, amphipods) and larval fish.

Comments about element:
  This is a special study designed with specific questions in mind each
  year.  Sampling methods differed greatly between the years.   1994 was a
  dry year in which the sampling region was in eastern Suisun Bay and the
  western delta.  1995 was a very wet year in which samples were taken from
  western Suisun Bay through Carquinez Strait to eastern San Pablo Bay.

Field Sampling
  Gear type or field instrument used:
       1994:   Continuous flow-through system for surface specific conductance
             Global positioning satellite (GPS) receiver
             Seabird SBE-19 CTD with optical backscatter
             Shipboard 1200 kHz broadband Acoustic Doppler Current Profiler
             (ADCP), and bottom-mounted narrow-band ADCP at Chipps Island
             Tareq opening-closing Bongo nets, 60 cm diameter with 0.5 mm
             mesh
             Submersible pump: 100 liters/min, discharged into 35 æm mesh net
             for zooplankton or bottles for phytoplankton
       1995: As above, except plankton samples were taken with high-volume
             submersible pumps discharged into 335 and 53 æm mesh nets (San
             Carlos) or 53 æm mesh nets (Turning Tide).

  Brief description of sampling procedure:
       1994: Data were taken during 3 cruises of Research Vessel San Carlos
       in April-May 1994.  During each cruise the vessel cycled among three
       stations defined by a surface specific conductance of approximately 1,
       3, and 6 mS/cm.  Each station was visited once per tidal cycle
       starting at station 6, with the timing set to arrive at station 3 (the
       "EZ" station) near the maximum flood and ebb. Station 3 was also
       visited as close as possible to predicted slack water on most tides. 

       At each station the ADCP, mounted on a swing arm, was lowered into
       the water, then turned on to record at approximately 5-second
       intervals and 25-cm depth bins.  The ADCP was used to provide on-board
       readouts of velocity profiles and also to attempt to detect scattering
       layers of organisms.  At each station the position was recorded on
       disk and on data sheets.  Two casts were taken with the CTD. 

       Bongo nets were fished for 10 minutes near the surface, near the
       bottom, and (except on cruise C) at about the middle of the water
       column.   At least one of each pair of nets was equipped with a flow
       meter so that volume filtered could be calculated.  Nets were rinsed
       with surface water after fishing, and samples were concentrated and
       fixed in 5% formaldehyde in surface water.  

       Samples were taken for small zooplankton with a 100 liter/minute (30
       gpm) submersible pump equipped with a non-collapsible hose at the
       intake, and discharging into a 30-cm diameter, 35 æm mesh net.  Volume
       sampled and flow rate were determined using a flow meter calibrated by
       timing the filling of a bucket.  Zooplankton samples were preserved in
       2-5% formaldehyde in surface water.  Whole water samples were taken
       for chlorophyll and either filtered whole or size fractionated using
       various mesh sizes before filtration.  Glass-fiber filters (GF/C) were
       folded, placed in small envelopes, and frozen for transport and
       storage.  Water samples were preserved with Lugol's solution for
       identification of phytoplankton.

       Samples for bacterial abundance and metabolic rates were taken
       separately on R/V Questuary by dipping with a bucket or using a 5-liter
       Niskin sampler.  Organic aggregates were sampled carefully to
       prevent disruption.      

       1995: Samples were taken more or less continuously, with the pump
       intake cycled between the surface and the bottom.  Samples were taken
       at 3 depths for larval fish and large zooplankton on San Carlos (15
       minutes), and at 3-5 depths for smaller zooplankton.  CTD casts were
       taken every 10 minutes and ADCP data were taken continuously.  Other
       sampling was as in 1994.


  Reference to any written protocols and how to obtain a copy:
       Contact project leader.  Details of the 1994 study are in Report of
       the 1994 Entrapment Zone Study, under review for publication as an
       IEP Technical Report.

  Changes in gear or procedures which affected the data over time:
       See above description

Laboratory analysis - Chemical
  Name and address of laboratory(s) running analysis:
       Romberg Tiburon Center, PO Box 855, Tiburon CA 94920
  Current since (date):
       1993
  Analytical methodology for each parameter or group of  parameters:
        Particulate C and N were analyzed on a Carlo Erba CHN analyzer.
  Quality assurance/control (QA/QC) protocols (if brief) or one-line
  qualifier:
       Standards and blanks were run with each batch of samples.

Laboratory analysis - Biological
  Name and address of laboratory(s) running analysis:
       Most macrozooplankton samples were analyzed by  project staff at the
          California Dept of Fish and Game Bay-Delta office in Stockton (J.
          Orsi; 4001 N. Wilson Way, Stockton, Ca. 95205).     
       Mesozooplankton and some macrozooplankton were analyzed at the Romberg
          Tiburon Center (W. Kimmerer; PO Box 855, Tiburon CA 94920)
       Bacteria, chlorophyll, and particulate C and N  were analyzed at the
          Romberg Tiburon Center (J.T. Hollibaugh)
       Larval fish were analyzed at the Bodega Marine Laboratory (W. Bennett)
       Data from ADCPs and CTDs was prepared at the US Geological Survey (J.
          Burau)

  Current since (date):

  Methods for each analysis:

       Chlorophyll samples were placed in darkened tubes and extracted using
       a mixture of acetone, DMSO (dimethylsulfonate), and water in a ratio
       9:9:2.  This mixture completely extracts chlorophyll without the need
       for grinding (K. Webb, Virginia Institute of Marine).  Samples were
       then read on a Turner Designs Model 10 fluorometer calibrated with
       pure chlorophyll.  Phytoplankton species and size composition were
       determined on settled preserved samples.

       Bacterial abundance was determined by direct counts of DAPI-stained
       cells (Porter and Feig 1980) and converted to biomass at 20 fgC/cell
       (Lee and Fuhrman 1986).  Bacterial production was measured by
       incorporation of tritiated leucine (Hollibaugh and Wong 1993).

       Pump samples for mesozooplankton were subsampled as necessary using a
       splitter or a piston pipette, and copepods were counted and identified
       to life stage under a dissecting microscope.  Life stages comprised
       males, females, and early (stages 1-3) and late (4-5) copepodites. 
       Mesozooplankton in these cruises consisted mostly of three species of
       copepod: the native (or naturalized) Eurytemora affinis, and the
       introduced Sinocalanus doerrii and Pseudodiaptomus forbesi. 
       Macrozooplankton samples were subsampled if necessary, and amphipods
       and mysids (Neomysis mercedis  and Acanthomysis sp.) were counted
       under a dissecting microscope. 

       All fish (eggs, larvae, juveniles) were sorted from the samples,
       identified (Wang 1986) and measured with a dissecting microscope
       fitted with an ocular micrometer (standard length +-0.1mm). As a
       quality control measure, all larval smelt (<15mm), larval cyprinid,
       and fish egg identifications were subsequently verified by J.C.S.
       Wang.

  Historical procedures (if known) or reference to other documentation:

  References used for identification of organisms:
       Phytoplankton: 
       Bacteria:
          Lee, S. And J.A. Fuhrman.  1986.  Relationships between biovolume
          and biomass of naturally derived marine bacterioplankton.  Appl.
          Environ. Microbiol. 53: 1298-1303.
          Porter, K.G. and Y.S. Feig.  1980.  The use of DAPI for identifying
          and counting aquatic microflora.  Limnol. Oceanogr. 25:943-948
       Zooplankton: See Neomysis-Zooplankton monitoring study
       Fish: 
          Wang, J. 1986.  Fishes of the Sacramento - San Joaquin Estuary And
          Adjacent Waters, California: A Guide to The Early Life Histories.  
          Interagency Ecological Studies Program for the Sacramento - San
          Joaquin Estuary.
  Location of reference collection (if one exists):
          California Dept. of Fish and Game, Bay-Delta Division Stockton, Ca.

  Reference to table listing scientific name, common name (if any), and
  code used:
          See data file format tables listed in the FMT file.