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Phytoplankton Meta Data - Tiffany Brown
IEP Bay-Delta Monitoring and Analysis Section
Phytoplankton Meta Data

Last updated: July 26, 2016
I. Contact Information

Program Manager: Shaun Philippart

Lead Contact: Tiffany Brown
Department of Water Resources
Division of Environmental Services
3500 Industrial Blvd, West Sacramento, CA 95691
(916) 376-9723
email Tiffany Brown

Mailing Address:
Tiffany Brown
Department of Water Resources
Division of Environmental Services
P.O. Box 942836
Sacramento, CA 95814

II. Study Mandate and Objectives

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 and San Pablo Bays. 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 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 Bay-Delta Monitoring and Analysis Section (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.

III. Study Area and Sample Sites

A. General Information

Geographic coverage of the sampling sites ranges from San Pablo Bay east through the upper Estuary to the mouths of the Sacramento, Mokelumne, and San Joaquin rivers. The study area currently consists of 15 sites that are sampled monthly (see Table 1 for site specific information). These sites represent a variety of aquatic habitats from narrow, freshwater channels in the Delta to broad, estuarine bays. Two are "floating" stations located where bottom electrical conductance (EC) was 2,000 µS/cm and 6,000 µS/cm, +/-10% (station ID's EZ2 and EZ6; these were added in 2007). The mixing of river water with tidal water creates a wide range of water quality conditions. For example, salinity ranges from freshwater to around 30,000 µS/cm in the most western sites. Salinity and other water quality variables are monitored at all phytoplankton sites.

B. Name and Location Information for Phytoplankton Sampling Sites

Note: Coordinates are in decimal degrees, geographic coordinate system, North American Datum 1983 and have been verified to be accurate for 1:24,000 scale mapping.

IV. Period of Record

Phytoplankton data are available for 1975 - present. The data and associated meta-data are updated regularly.

V. Sampling Frequency

Historically, phytoplankton samples have been collected once or twice per month. Currently they are collected once per month.

VI. Field Methods

Phytoplankton samples are collected with a submersible pump from a water depth of one meter (approximately three feet) below the water surface. Samples are stored in 50-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. There are no required holding times but the samples are sent to the lab within two weeks of collection. After about one year the samples begin degrading and they are discarded after two years.

VII. Laboratory Methods

Prior to 2008, phytoplankton identification and enumeration were performed at DWR’s Bryte Laboratory according to the Utermöhl microscopic method (Utermöhl 1958) and modified Standard Methods (APHA 1998). An aliquot was placed into a counting chamber and allowed to settle for a minimum of 15 hours. The aliquot volume, normally 10 mL, was adjusted according to the algal population density and turbidity of the sample. Phytoplankton were enumerated in twenty randomly chosen fields of a Whipple ocular micrometer grid for each settled aliquot. Sample analysis was conducted at a magnification of 800X using a Wilde M-40 inverted microscope.  From 2008 on, samples are counted for a minimum number of organisms instead of a minimum number of fields.

Currently, phytoplankton samples are analyzed by BSA Environmental, Inc.  Phytoplankton are identified to the lowest taxonomic level possible using the Utermöhl method and APHA standard methods (Utermöhl 1958, APHA 1998).  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 Delta, 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 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.

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)
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
C = count obtained
cV = counted volume, in ml (cV = Ac /(V x Af x F))
Algal biovolume can be calculated from the dimensions using for example the formulas given for different algal shapes by Kellar et al. (1980).
Shapes and biovolume formulas used in EMP’s phytoplankton database

VIII. Data Management

When phytoplankton data are received from BSA Environmental, Inc., they are entered into a Microsoft Access database at DES's main office in West Sacramento, CA where they are quality assured and then they are made available online here.

IX. Phytoplankton Types

Phytoplankton collected by the EMP fall into four broad categories: cyanobacteria, diatoms, green algae (including green algal flagellates), and various flagellate groups (excluding green algal flagellates). These categories are further subdivided as follows (definitions of specific types and a mini-glossary of terms used are below):

1. Cyanobacteria

2. Diatoms
3. Green Algae
Green Algal Flagellates
Non-motile Coccoid/Colonial
4. Flagellate Groups*

*Note: Some groups contain non-flagellated species; however, the taxa collected by the EMP have all been flagellated taxa.


Definitions of Algal Types:

Araphid Pennate Diatom: diatom with bilaterally symmetrical valves (symmetry about a line) and no raphe system on either valve.
Biraphid Pennate Diatom: diatom with bilaterally symmetrical valves (symmetry about a line) and a raphe system on both valves.
Centric Diatom: diatom with radially symmetrical valves (symmetry about a point).
Chrysophyte Flagellate: unicellular biflagellate with an external covering (if present) of scales or a lorica.
Coccoid/Colonial Cyanobacterium: prokaryotic alga with a coccoid unicellular or colonial growth habit.
Cryptomonad Flagellate: unicellular biflagellate with a unique furrow/gullet system.
Desmid Green Alga: green alga that gives rise to non-flagellated amoeboid gametes that conjugate. Growth habit may be unicellular or filamentous.
Dinoflagellate: unicellular biflagellate with a theca as the external covering.
Euglenoid Flagellate: unicellular protist with 1 or 2 flagella. External covering is a pellicle (within the plasma membrane). Not all euglenoids are photosynthetic.
Filamentous Cyanobacterium: prokaryotic alga with a filamentous growth habit. Cells are arranged in trichomes; trichomes with a sheath are termed filaments.
Filamentous Green Alga: green alga which is filamentous, parenchymatous, or possesses a macroscopic plant-like thallus. Usually attached to a substrate.
Green Algal Flagellate: green alga that possesses one or more flagella in the vegetative state.
Haptophyte Flagellate: unicellular biflagellate covered by non-siliceous scales and possessing a haptonema.
Monoraphid Pennate Diatom: diatom with bilaterally symmetrical valves (symmetry about a line) and a raphe system on only one valve.
Nanoflagellates: very small flagellates (<10?m) that are of unknown taxonomic origin. May or may not be photosynthetic.
Non-motile Coccoid/Colonial Green Alga: green alga that is non-motile in the vegetative state. Growth habit is solitary coccoid cells or colonial.
Synurophyte Flagellate: unicellular biflagellate covered in siliceous scales. May form colonies.
Xanthophyte Flagellate: solitary unicellular alga with 1 or 2 flagella.
(For a list of individual genera and species of phytoplankton collected by the EMP please see the Phytoplankton Dictionary.)

Mini-Glossary of Algal Terms:

The following is a mini-glossary of terms used in the above definitions:
1. Amoeboid: type of cell organization that lacks a cell wall and is capable of frequent, flexible changes in shape.
2. Biflagellate: cell having two flagella.
3. Coccoid: simple cell type that is spherical, sub-spherical, or rod-shaped.
4. Conjugate: a sexual reproduction process in which non-flagellated gametes join by means of a specialized tube or papillae.
5. Filamentous: thallus that is growing as a filament (cells are arranged in a linear series where adjacent cells share a common cross wall).
6. Furrow/Gullet: a depression in the anterior region of the cell where the flagellum (or flagella) emerge.
7. Haptonema: flagellum-like organelle, the base of which is linked to the basal bodies of the flagella.
8. Lorica: protective investment or envelope that surrounds the protoplast (naked, non-walled cell).
9. Parenchymatous: type of thallus with true tissues, formed from cell division in three planes.
10. Pellicle: in euglenoids, the outer proteinaceous surface layer.
11. Prokaryotic: cell type that lacks membrane-bound organelles and true flagella.
12. Raphe: structure in monoraphid and biraphid diatoms that consists of a slit through the valve face, and associated cytoplasmic structures; usually situated along the apical axis or within a marginal keel; composed of (usually) two branches per valve. The raphe enables a diatom cell to move over substrata.
13. Siliceous: composed primarily of silicon.
14. Thallus: general form or body of an alga.
15. Theca: in dinoflagellates, cellulose plate covering.
16. Trichome: in cyanobacteria, a term referring to a filament without its sheath.

X. Reference

A. Methodological and Taxonomic Texts

  1. Abbott, I.A., & C.J. Hollengerg, 1976, Marine Algae of California, Stanford Univ. Press, 827 pp.
  2. Bourrelly, P. 1968, Les Algues d'eau Douce, vols. I, II & III, Editions N. Boubee & Cie, vol. I - 570 pp., vol. II - 438 pp., vol. III - 512 pp.
  3. Hustedt, F., 1930, Die - Susswasser - flora Mittel - Europas, Verlag von Gustav Fischer, 466 pp.
  4. Kellar, P.E., S.A. Paulson, and L.J. Paulson. 1980. Methods for biological, chemical, and physical analyses in reservoirs. Tech. Report 5, Lake Mead Limnological Research Center, University of Nevada, Las Vegas, 234 pages.
  5. Palmer, C.M., 1962, Algae in Water Supplies, U.S. Public Health Service, 88 pp.
  6. Patrick, R., 1966, The Diatoms of the United States, vol. I, The Academy of Natural Sciences of Philadelphia, Monograph No. 13, 688 pp.
  7. Patrick, R., 1975, The Diatoms of the United States, vol. II - part 1, The Academy of Natural Sciences of Philadelphia, No. 13, 213 pp.
  8. Prescott, G.W., 1962, Algae of the Western Great Lakes Area, Wm. C. Brown Co., 977 pp.
  9. Smith, B.M., 1950, Freshwater Algae of the United States, McGraw - Hill, 719 pp.
  10. Standard Methods, 20th Edition, 1998. Prepared and published jointly by the American Public Health Association, American Water Works Association and Water Environment Federation
  11. Tiffany, L.H., 1952, The Algae of Illinois, Univ. of Chicago Press, 407 pp.
  12. Uterm´┐Żhl, H. 1958. Zur Vervollkommnung der quantitativen Phytoplankton-Methodik. Mitt. Int. Verh. Limnol. 9: 38.
  13. Vinyard, Wm. C., 1974, Key to the Genera of Diatoms of the Inland Waters of Temperate North America, Mad River Press, 19 pp.
  14. Weber, C.I., 1966, A Guide to the Common Diatoms at Water Pollution Surveillance System Stations, Federal Water Pollution Control Administration, U.S. Department of the Interior, 101 pp.
  15. Wehr, J.D. & R.G. Smith, 2003, Freshwater Algae of North America, Academic Press, 918 pp.
  16. Whitford, L.A., 1973, A Manual of Fresh-Water Algae, Sparks Press, 323 pp.

B. DWR Reports, Publications, and Other Pertinent Literature.

  1. California Department of Water Resources. 1975-1995. Annual Reports, Fiscal Years 1975-1995, Water Quality Conditions in the Sacramento-San Joaquin Delta. Sacramento, California. Sacramento (CA): California Department of Water Resources. Reports prepared for the State Water Resources Control Board.
  2. California Department of Water Resources. 1995. Sacramento-San Joaquin Delta Atlas. State of California, Department of Water Resources, Sacramento, California. 121 pp.
  3. California Department of Water Resources. 1996. Water quality conditions in the Sacramento-San Joaquin Delta, 1970-1993, California Department of Water Resources, Sacramento, CA