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Interagency Ecological Program: Phytoplankton monitoring in the Sacramento-San Joaquin Bay-Delta, collected by the Environmental Monitoring Program, 2008-2022

General Information
Data Package:
Local Identifier:edi.1320.6
Title:Interagency Ecological Program: Phytoplankton monitoring in the Sacramento-San Joaquin Bay-Delta, collected by the Environmental Monitoring Program, 2008-2022
Alternate Identifier:DOI PLACE HOLDER
Abstract:

The State Water Resources Control Board (SWRCB) sets water quality objectives to protect beneficial uses of water in the Sacramento-San Joaquin Delta and Suisun Bay. These objectives are met by establishing standards mandated in water right permits issued to the Department of Water Resources and U.S. Bureau of Reclamation by the SWRCB. The standards include minimum Delta outflows, limits to Delta water export by the State Water Project (SWP) and the Central Valley Project (CVP), and maximum allowable salinity levels.

In 1971, the State Water Resources Control Board (SWRCB) established Water Right Decision 1379 (D-1379). This Decision contained new water quality requirements for the San Francisco Bay-Delta Estuary. D-1379 was also the first water right decision to provide terms and conditions for a comprehensive monitoring program to routinely determine water quality conditions and changes in environmental conditions within the estuary. The monitoring program described in D-1379 was developed by the Stanford Research Institute through a contract with the SWRCB. Implementation of the monitoring program began in 1972, as SWRCB, DWR, and USBR met to define their individual responsibilities for various elements of the monitoring program. In 1978, amendments to water quality standards were implemented and resulted in Water Right Decision 1485 (D-1485). More recently these standards were again amended under the 1995 Water Quality Control Plan and Water Right Decision 1641 (D-1641) established in 1999. The SWP and CVP are currently operated to comply with the monitoring and reporting requirements described in D-1641. D-1641 requires DWR and USBR to conduct a comprehensive environmental monitoring program to determine compliance with the water quality standards and also to submit an annual report to SWRCB discussing data collected.

The phytoplankton monitoring program is one element of DWR’s and USBR’s Environmental Monitoring Program (EMP) conducted under the Interagency Ecological Program (IEP) umbrella. The EMP also includes monitoring of water quality, zooplankton, and benthic organisms. The overall objective of the phytoplankton monitoring program is to determine the impacts of water project operations on the estuary. These impacts are interpreted by changes in phytoplankton diversity, abundance, and distribution associated with physical and other biological factors in the estuary.

Links to other EMP datasets can be found [here](https://emp-des.github.io/emp-reports/data-links.html).

Publication Date:2023-10-05
For more information:
Visit: DOI PLACE HOLDER

Time Period
Begin:
2008-01-14
End:
2021-12-04

People and Organizations
Contact:Brown, Tiffany (CA Department of Water Resources) [  email ]
Creator:Perry, Sarah E (CA Department of Water Resources)
Creator:Brown, Tiffany (CA Department of Water Resources)
Creator:Klotz, Vivian (CA Department of Water Resources)

Data Entities
Data Table Name:
EMP_Phyto_Data_2008-2022
Description:
EMP phytoplankton data from 2008 to 2022
Data Table Name:
EMP_Phyto_Stations_2008-2022
Description:
Stations where EMP collects/collected phytoplankton samples.
Data Table Name:
EMP_Phyto_QC_Codes
Description:
quality control codes and explanations corresponding to the "QualityCheck" column
Detailed Metadata

Data Entities

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1320/6/67b9d4ee30d5eee6e74b2300426471f9
Name:EMP_Phyto_Data_2008-2022
Description:EMP phytoplankton data from 2008 to 2022
Number of Records:36647
Number of Columns:20

Table Structure
Object Name:EMP_Phyto_Data_2008-2022.csv
Size:5810893 byte
Authentication:01772a6cc83e81ba756530af9f143dec Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited:
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 LabSampleDateSampleTimeStationCodeOrigTaxonTaxonKingdomPhylumClassAlgalGroupGenusSpeciesUnits_per_mLCells_per_mLAverageBiovolume_per_mLGALDPhytoFormQualityCheckWestLong
Column Name:Lab  
Date  
Time  
Station  
OrigTaxon  
Taxon  
Kingdom  
Phylum  
Class  
AlgalGroup  
Genus  
Species  
Units_per_mL  
Cells_per_mL  
AverageBiovolume_per_mL  
GALD  
PhytoForm  
QualityCheck  
Latitude  
Longitude  
Definition:which lab the data was analyzed atdate of sampling eventtime of sampling eventname of station sampledthe originally recorded taxon of the specimenstandardized taxon name for the specimenthe kingdom of the specimenthe kingdom of the specimenthe class of the specimenthe algal group of the specimenthe genus of the specimenthe species of the specimenunit (organism) densitycell densityaverage biovolume densitythe greatest axial linear dimensionthe phytoplankton form codenotes any quality control issues (see EDI csv for code explanations)latitude of non-fixed stationlongitude of non-fixed station
Storage Type:string  
dateTime  
string  
string  
string  
string  
string  
string  
string  
string  
string  
string  
float  
float  
float  
float  
string  
string  
float  
float  
Measurement Type:nominaldateTimenominalnominalnominalnominalnominalnominalnominalnominalnominalnominalratioratioratiorationominalnominalratioratio
Measurement Values Domain:
Definitiontext
FormatYYYY-MM-DD
Precision
Definitiontext
Definitiontext
Definitiontext
Definitiontext
Definitiontext
Definitiontext
Definitiontext
Definitiontext
Definitiontext
Definitiontext
Unitunits_per_mililiter
Typereal
Unitcells_per_mililiter
Typereal
Unitcubic_microns_per_mililiter
Typereal
Unitmicron
Typereal
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Codec
Definitioncolony
Source
Code Definition
Codef
Definitionfilament
Source
Code Definition
Codei
Definitionindividual cell
Source
Definitiontext
UnitdecimalDegree
Typereal
UnitdecimalDegree
Typereal
Missing Value Code:    
CodeNA
ExplNA
  
CodeNA
ExplNA
                
CodeNA
ExplNA
CodeNA
ExplNA
CodeNA
ExplNA
    
CodeNA
ExplNA
CodeNA
ExplNA
Accuracy Report:                                        
Accuracy Assessment:                                        
Coverage:                                        
Methods:                                        

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1320/6/857fb9a315cd6bc47f2090f74fd1c938
Name:EMP_Phyto_Stations_2008-2022
Description:Stations where EMP collects/collected phytoplankton samples.
Number of Records:26
Number of Columns:4

Table Structure
Object Name:EMP_Phyto_Stations_2008-2021.csv
Size:1647 byte
Authentication:5fcd8dfb39c4c19e115693fe1bf792e9 Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited:
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 StationLocationLatitudeLongitude
Column Name:StationCode  
Location  
Latitude  
Longitude  
Definition:station ID for EMP's phytoplankton stationslocation of EMP's phytoplankton stationslatitude of EMP's phytoplankton stationslongitude of EMP's phytoplankton stations
Storage Type:string  
string  
float  
float  
Measurement Type:nominalnominalratioratio
Measurement Values Domain:
Definitiontext
Definitiontext
UnitdecimalDegree
Typereal
UnitdecimalDegree
Typereal
Missing Value Code:        
Accuracy Report:        
Accuracy Assessment:        
Coverage:        
Methods:        

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1320/6/c9d20460e3479409a05f5c7b8233970f
Name:EMP_Phyto_QC_Codes
Description:quality control codes and explanations corresponding to the "QualityCheck" column
Number of Records:5
Number of Columns:2

Table Structure
Object Name:EMP_Phyto_QC_Codes.csv
Size:248 byte
Authentication:0a17321f8f401cdfaf8b66fec6da1003 Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited:
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 QC_CodeExplanation
Column Name:QualityCheck  
Explanation  
Definition:quality control code used in "QualityCheck" columnexplanation for the quality control code
Storage Type:string  
string  
Measurement Type:nominalnominal
Measurement Values Domain:
Definitiontext
Definitiontext
Missing Value Code:    
Accuracy Report:    
Accuracy Assessment:    
Coverage:    
Methods:    

Data Package Usage Rights

This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.

Keywords

By Thesaurus:
(No thesaurus)environmental, San Francisco Estuary
LTER Controlled Vocabularyestuaries, phytoplankton, water, water quality, monitoring

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package
Description:

Field Methods

Phytoplankton samples are collected with a submersible pump or a Van Dorn sampler from a water depth of one meter (approximately three feet) below the water surface.

Samples are stored in 60-milliliter glass bottles. Two mL of Lugol's solution are added to each sample as a stain and preservative. All samples are kept at room temperature and away from direct sunlight until analyzed.

Description:

Laboratory Methods: EcoAnalysts, Inc.

Phytoplankton are identified to the lowest taxonomic level possible using the Utermöhl method and APHA standard methods (Utermöhl 1958, APHA 2012). An aliquot is allowed to settle onto a counting chamber for a minimum of 12 hours. The aliquot volume is adjusted according to the algal population density and turbidity of the sample. For the Estuary, the aliquot volume is usually about 10 ml. Aliquots are enumerated at a magnification of 630X using a Leica DMIL inverted microscope. For each settled aliquot, phytoplankton in randomly chosen transects are counted and photos are taken of the specimen, first encounter; measurements are made with an ocular micrometer. Taxa are enumerated as they appear along the transects. A minimum of 400 total algal units are counted, and a minimum of 100 algal units of the dominant taxon. For taxa that are in filaments or colonies, the number of cells per filament or colony is recorded. Length measurements are performed on 10 to 25 algal units of the dominant taxon, and up to 5 units of each minor taxon. The measurements taken are 1st greatest axial length, 2nd greatest axial length, and 3rd greatest axial length. From these measurements, biovolume is calculated for each cell measured. Biovolume equations are considered proprietary by the contractor but are based on the equations found in Hillebrand et. al. 1999. EcoAnalysts, Inc. processed data from 2008 to 2013, except for September 2013 and November 2013, which were contracted out to BSA Environmental, Inc.

Description:

Laboratory Methods: BSA Environmental, Inc.

Phytoplankton are identified to the lowest taxonomic level possible using the Utermöhl method and APHA standard methods (Utermöhl 1958, APHA 2012). An aliquot is allowed to settle onto a counting chamber for a minimum of 12 hours. The aliquot volume is adjusted according to the algal population density and turbidity of the sample. For the Estuary, the aliquot volume is usually about 10 ml. Aliquots are enumerated at a magnification of 1200X using a Leica DMIL inverted microscope. For each settled aliquot, phytoplankton in randomly chosen transects are counted and photos are taken of the specimen, first encounter; measurements are made with an ocular micrometer. Taxa are enumerated as they appear along the transects. A minimum of 400 total algal units are counted, and a minimum of 100 algal units of the dominant taxon. For taxa that are in filaments or colonies, the total number of cells counted is recorded. Length measurements are performed on 10 algal units of the dominant taxon, and up to 5 units of each minor taxon. The measurements taken are 1st greatest axial length, 2nd greatest axial length, and 3rd greatest axial length. From these measurements, biovolume is calculated for each cell measured. Biovolume equations are considered proprietary by the contractor but are based on the equations found in Hillebrand et. al. 1999. BSA Environmental, Inc. processed samples from September 2013, November 2013, and from 2014 to present.

Description:

Natural Unit Density Calculations (Organisms per mL)

Both contractors calculate natural unit density per unit volume of water using the same equation. Organism counts for each sample can be converted to organisms/ml using the following formula:

Organisms/ml = (C x Ac) / (V x Af x F)

where:

C = count obtained

Ac = Area of cell bottom (mm2)

Af = Area of each grid field (mm2)

F = Number of fields examined

V = volume settled, in ml

This simplifies to:

Organisms/ml = C / cV

where:

C = count obtained

cV = counted volume, in ml (cV = Ac /(V x Af x F))

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@edirepository.org
Web Address:
https://edirepository.org
Id:https://ror.org/0330j0z60
Creators:
Individual: Sarah E Perry
Organization:CA Department of Water Resources
Email Address:
sarah.perry@water.ca.gov
Id:https://orcid.org/0000-0002-2561-8195
Individual: Tiffany Brown
Organization:CA Department of Water Resources
Email Address:
tiffany.brown@water.ca.gov
Individual: Vivian Klotz
Organization:CA Department of Water Resources
Email Address:
vivian.klotz@water.ca.gov
Contacts:
Individual: Tiffany Brown
Organization:CA Department of Water Resources
Email Address:
tiffany.brown@water.ca.gov

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period
Begin:
2008-01-14
End:
2021-12-04
Geographic Region:
Description:From the western boundaries of San Pablo Bay to the eastern boundaries of the Sacramento-San Joaquin Delta.
Bounding Coordinates:
Northern:  38.369Southern:  37.678
Western:  -122.393Eastern:  -121.262
Taxonomic Range:
Classification:
Rank Name:Phylum
Rank Value:cyanobacteria
Common Name:blue-green algae
Identifer:National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 1117 (cyanobacteria)
Taxonomic Range:
Classification:
Rank Name:Kingdom
Rank Value:Viridiplantae
Common Name:green plants
Identifer:National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 33090 (Viridiplantae)
Classification:
Rank Name:Phylum
Rank Value:Chlorophyta
Common Name:green algae
Identifer:National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 3041 (Chlorophyta)
Taxonomic Range:
Classification:
Rank Name:Phylum
Rank Value:centric diatoms
Taxonomic Range:
Classification:
Rank Name:Phylum
Rank Value:pennate diatoms
Taxonomic Range:
Classification:
Rank Name:Phylum
Rank Value:Chrysophyte flagellates
Taxonomic Range:
Classification:
Rank Name:Phylum
Rank Value:Cryptophyte flagellates
Taxonomic Range:
Classification:
Rank Name:Phylum
Rank Value:dinoflagellate
Taxonomic Range:
Classification:
Rank Name:Phylum
Rank Value:Euglenoid flagellates
Taxonomic Range:
Classification:
Rank Name:Phylum
Rank Value:Haptophyte flagellates
Taxonomic Range:
Classification:
Rank Name:Phylum
Rank Value:Nanoflagellates
Taxonomic Range:
Classification:
Rank Name:Phylum
Rank Value:Synurophyte flagellates
Taxonomic Range:
Classification:
Rank Name:Phylum
Rank Value:Xanthophyte flagellates

Project

Parent Project Information:

Title:Interagency Ecological Program: Phytoplankton monitoring in the Sacramento-San Joaquin Bay-Delta, collected by the Environmental Monitoring Program, 2008-2021
Personnel:
Individual: Sarah E Perry
Organization:CA Department of Water Resources
Id:https://orcid.org/0000-0002-2561-8195
Role:publication lead
Individual: Tiffany Brown
Organization:CA Department of Water Resources
Role:subject matter expert

Maintenance

Maintenance:
Description:

This dataset will be updated annually with new phytoplankton data.

Frequency:annually
Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n    '
        |___element 'metadata'
        |     |___text '\n      '
        |     |___element 'unitList'
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'decimalDegree'
        |     |     |     |  \___attribute 'name' = 'decimalDegree'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'cubic_microns_per_mililiter'
        |     |     |     |  \___attribute 'name' = 'cubic_microns_per_mililiter'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'units_per_mililiter'
        |     |     |     |  \___attribute 'name' = 'units_per_mililiter'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'cells_per_mililiter'
        |     |     |     |  \___attribute 'name' = 'cells_per_mililiter'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'micron'
        |     |     |     |  \___attribute 'name' = 'micron'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n        '
        |     |     |___text '\n      '
        |     |___text '\n    '
        |___text '\n  '

Additional Metadata

additionalMetadata
        |___text '\n    '
        |___element 'metadata'
        |     |___text '\n      '
        |     |___element 'emlEditor'
        |     |        \___attribute 'app' = 'ezEML'
        |     |        \___attribute 'release' = '2023.08.30'
        |     |___text '\n    '
        |___text '\n  '

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