Phytoplankton Species Composition, Abundance and Cell Size in San Francisco Bay: Microscopic Analyses of USGS Samples Collected 1992-2014

Sampling event
Latest version published by United States Geological Survey on Dec 14, 2017 United States Geological Survey

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This Data Release makes available measurements of phytoplankton species composition, abundance and cell size made on samples collected in San Francisco Bay (CA) from April 1992 through March 2014. Phytoplankton samples were collected at 31 stations along a 145-km transect where the variability of salinity, temperature, turbidity and nutrient concentrations reflected a broad range of environmental factors that regulate phytoplankton growth and abundance (map of sampling locations is available on the project website at: Whole water samples were preserved with acid Lugol’s solution, and 2 to 50 ml aliquots were settled in chambers for 6 to 24 hours (Utermöhl 1958). Phytoplankton cells were then counted and identified using a phase-contrast inverted microscope at 125x magnification, all cells greater than 30 μm diameter were enumerated. Cells smaller than 30 μm were counted at 1250x magnification; following the APHA (1989) strip count method, at least 100 cells of the most numerous taxon were counted. Cell volumes were estimated from measured linear dimensions and geometric formulas that varied with cell shapes. Phytoplankton samples representing 923 distinct date, station and depths were included. The 16,442 entries in this dataset include 609 different taxa within 11 functional groups. Diatoms dominated the total biovolume contributed by each functional group (77%) followed by dinoflagellates (14%) and cryptophytes (4.5%). The top 5 species contributing to the summed biovolume in all samples were: Thalassiosira punctigera, Chaetoceros socialis, Ditylum brightwellii, Thalassiosira rotula and Noctiluca scintillans. By frequency of occurrence, the top 5 species were: Teleaulax amphioxeia, Nannochloropsis spp., Plagioselmis prolonga var. nordica, Skeletonema costatum and Thalassiosira eccentrica.

Data Records

The data in this sampling event resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 932 records.

2 extension data tables also exist. An extension record supplies extra information about a core record. The number of records in each extension data table is illustrated below.

Event (core)

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How to cite

Researchers should cite this work as follows:

Nejad, E.S., Schraga, T.S., and Cloern, J.E., 2017, Phytoplankton Species Composition, Abundance and Cell Size in San Francisco Bay: Microscopic Analyses of USGS Samples Collected 1992-2014: U.S. Geological Survey data release


Researchers should respect the following rights statement:

The publisher and rights holder of this work is United States Geological Survey. To the extent possible under law, the publisher has waived all rights to these data and has dedicated them to the Public Domain (CC0 1.0). Users may copy, modify, distribute and use the work, including for commercial purposes, without restriction.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 3c89212d-104e-43ef-913a-bc71592551ff.  United States Geological Survey publishes this resource, and is itself registered in GBIF as a data publisher endorsed by U.S. Geological Survey.




James Cloern
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  • Point Of Contact
Senior (ST) Scientist
U.S. Geological Survey
Mail Stop 496, 345 Middlefield Road
94025 Menlo Park
Abigail Benson
  • Metadata Provider
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U.S. Geological Survey

Geographic Coverage

San Francisco Bay, California

Bounding Coordinates South West [37.472, -122.472], North East [38.152, -121.688]

Bibliographic Citations

  1. Utermöhl, H. 1958. Zur Vervollkommnung der quantitativen Phytoplankton-Methodik. Mitt Int Verh Theor Angew Limnology 9:1-38. Not electronically available
  2. APHA. 1989. Standard methods for the examination of water and wastewater. 17th edn. American Public Health Association, Washington, DC. Not electronically available
  3. Hillebrand H, Durselen C, Kirschtel D, Pollingher U, Zohary T. 1999. Biovolume calculation for pelagic and benthic microalgae. Journal of Phycology 35:403–424.
  4. Wetzel RG, Likens GE. 1991. Limnological Analyses. 2nd edn. Springer-Verlag, New York.

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