Data Package Metadata View Summary

Interagency Ecological Program: Phytoplankton monitoring in the Sacramento-San Joaquin Bay-Delta, collected by the Environmental Monitoring Program, 2008-2021

General Information

Data Package:

Local Identifier:

edi.1320.4

Title:

Interagency Ecological Program: Phytoplankton monitoring in the Sacramento-San Joaquin Bay-Delta, collected by the Environmental Monitoring Program, 2008-2021

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.

Complimentary EMP Datasets:

Water Quality: https://portal.edirepository.org/nis/mapbrowse?scope=edi&identifier=458&revision=7

Benthic: https://portal.edirepository.org/nis/mapbrowse?packageid=edi.1036.2

Publication Date:

2023-03-06

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_2008-2021
Description:	EMP phytoplankton data from 2008 to 2021
Data Table Name:	EMP_Phyto_Stations_2008-2021
Description:	Stations that EMP collects/collected phytoplankton samples at
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/1320/4/1eee2c2a562a5b856398082c487dc1a7
Name:	EMP_Phyto_Data_2008-2021
Description:	EMP phytoplankton data from 2008 to 2021
Number of Records:	34299
Number of Columns:	19

Table Structure

Object Name:

EMP_Phyto_Data_2008-2021.csv

Size:

5353274 byte

Authentication:

b753cfdc537150ba40e8db9a26ee3936 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Lab

SampleDate

SampleTime

StationCode

OrigName

Name

Kingdom

Phylum

Class

AlgalGroup

Genus

Species

Organisms_per_mL

AverageBiovolume

AverageBiovolume_per_mL

GALD

Colony_or_FilamentGroupCode

Shape

QualityCheck

Column Name:

Lab

SampleDate

SampleTime

StationCode

OrigName

Name

Kingdom

Phylum

Class

AlgalGroup

Genus

Species

Organisms_per_mL

AverageBiovolume

AverageBiovolume_per_mL

GALD

Colony_or_FilamentGroupCode

Shape

QualityCheck

Definition:

which lab the data was analyzed at

date of sampling event

time of sampling event

name of station sampled at

the originally recorded name of the specimen

currently accepted name of the specimen

the kingdom of the specimen

the phylum of the specimen

the class of the specimen

the algal group of the specimen

the genus of the specimen

the species of the specimen

organisms (in natural units) per mL

average biovolume of the specimen

average biovolume per mL

the greatest axial linear dimension

the colony or filament group code

the shape of the specimen

notes any quality control issues

Storage Type:

string

dateTime

string

float

string

Measurement Type:

nominal

dateTime

nominal

ratio

nominal

Measurement Values Domain:

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	BSA
Definition	BSA Labs
Source

Code Definition

Code	EcoAnalysts
Definition	EcoAnalysts Labs
Source

Format	YYYY-MM-DD
Precision

Definition

time of sampling event

Definition

name of station sampled at

Definition

the originally recorded name of the specimen

Definition

currently accepted name of the specimen

Definition

the kingdom of the specimen

Definition

the phylum of the specimen

Definition

the class of the specimen

Definition

the algal group of the specimen

Definition

the genus of the specimen

Definition

the species of the specimen

Unit	organismsPerMilliLiter
Type	real

Unit	cubicMicrons
Type	real

Unit	cubicMicronsPerMilliLiter
Type	real

Unit	microns
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	c
Definition	colony
Source

Code Definition

Code	f
Definition	filament
Source

Code Definition

Code	i
Definition	individual cell
Source

Definition

the shape of the specimen

Definition

notes any quality control issues

Missing Value Code:

Code	NA
Expl	no time recorded

Code	NA
Expl	current name and original name are the same

Code	NA
Expl	no kingdom recorded

Code	NA
Expl	no phylum recorded

Code	NA
Expl	no class recorded

Code	NA
Expl	no algal group recorded

Code	NA
Expl	organisms per mL not recorded

Code	NA
Expl	average biovolume not recorded

Code	NA
Expl	average biolvolume per mL not recorded

Code	NA
Expl	no GALD recorded

Code	NA
Expl	colony/filament code not recorded

Code	NA
Expl	no shape defined

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1320/4/00b61678378071f779f1135be223fe0a
Name:	EMP_Phyto_Stations_2008-2021
Description:	Stations that EMP collects/collected phytoplankton samples at
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:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Station

Location

Latitude

Longitude

Column Name:

StationCode

Location

Latitude

Longitude

Definition:

station ID for EMP's phytoplankton stations

location of EMP's phytoplankton stations

latitude of EMP's phytoplankton stations

longitude of EMP's phytoplankton stations

Storage Type:

string

float

Measurement Type:

nominal

ratio

Measurement Values Domain:

Definition

station ID for EMP's phytoplankton stations

Definition

location of EMP's phytoplankton stations

Unit	decimalDegree
Type	real

Unit	decimalDegree
Type	real

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1320/4/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:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

QC_Code

Explanation

Column Name:

QualityCheck

Explanation

Definition:

quality control code used in "QualityCheck" column

explanation for the quality control code

Storage Type:

string

Measurement Type:

nominal

Measurement Values Domain:

Definition

quality control code used in "QualityCheck" column

Definition

explanation for the quality control code

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 Vocabulary	estuaries, 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:	38.369	Southern:	37.678
Western:	-122.393	Eastern:	-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' = 'organismsPerMilliLiter'
        |     |     |     |  \___attribute 'name' = 'organismsPerMilliLiter'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'organisms (in natural units) per mL'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = ' cubicMicrons'
        |     |     |     |  \___attribute 'name' = ' cubicMicrons'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = ' cubicMicronsPerMilliLiter'
        |     |     |     |  \___attribute 'name' = ' cubicMicronsPerMilliLiter'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'microns'
        |     |     |     |  \___attribute 'name' = 'microns'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'decimalDegree'
        |     |     |     |  \___attribute 'name' = 'decimalDegree'
        |     |     |     |___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' = '2023.02.19'
        |     |___text '\n    '
        |___text '\n  '

Copyright 2024 Environmental Data Initiative. This material is based upon work supported by the National Science Foundation under grants #2223103 and #2223104. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. Please contact us with questions, comments, or for technical assistance regarding this web site or the Environmental Data Initiative. Please read our privacy policy to know what information we collect about you and to understand your privacy rights.

EDI is a collaboration between the University of New Mexico and the University of Wisconsin – Madison, Center for Limnology:

Data Package Metadata View Summary

Interagency Ecological Program: Phytoplankton monitoring in the Sacramento-San Joaquin Bay-Delta, collected by the Environmental Monitoring Program, 2008-2021

Data Entities

Data Table

Data Table

Data Table

Data Package Usage Rights

Keywords

Methods and Protocols

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

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Parent Project Information:

Maintenance

Additional Metadata

Additional Metadata

Recently Added

Recently Updated

Data Package Metadata View Summary

Interagency Ecological Program: Phytoplankton monitoring in the Sacramento-San Joaquin Bay-Delta, collected by the Environmental Monitoring Program, 2008-2021

+/- Data Entities

Data Table

Data Table

Data Table

+/- Data Package Usage Rights

+/- Keywords

+/- Methods and Protocols

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

+/- People and Organizations

+/- Temporal, Geographic and Taxonomic Coverage

+/- Project

Parent Project Information:

+/- Maintenance

+/- Additional Metadata

+/- Additional Metadata

Data Entities

Data Package Usage Rights

Keywords

Methods and Protocols

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Maintenance

Additional Metadata

Additional Metadata