National marine sanctuary offices and visitor centers closed to the public; waters remain open

NOAA's national marine sanctuary offices and visitor centers are currently closed to the public, and in accordance with Executive Order 13991 - Protecting the Federal Workforce and Requiring Mask Wearing, all individuals in NOAA-managed areas are required to follow Centers for Disease Control and Prevention (CDC) guidance on mask-wearing and maintaining social distances. Sanctuary waters remain open for responsible use in accordance with CDC guidance, U.S. Coast Guard requirements, and local regulations. More information on the response from NOAA's Office of National Marine Sanctuaries can be found on

Skip to main content
Monterey Bay National Marine Sanctuary National Marine Sanctuaries Home Page National Oceanic and Atmospheric Administration Home Page

Research Technical Report

Flow Cytometric Analysis of Phytoplankton Viability in Elkhorn Slough, California

Smith, Sarah Rose (December 2009)

M.S. Thesis, Moss Landing Marine Laboratories and San Jose State University, 69pp.


The phytoplankton community structure of Elkhorn Slough was characterized flow cytometrically and found to be dominated in the upper reaches by small cryptophytes (<5um) and picoeukaryotic phytoplankton (<3um). Cell-specific viability of the small cryptophyte population was quantified along a 5 km transect from the mouth to the shallow upper reaches of Elkhorn Slough using fluorescein diacetate (FDA). Corroborative viability techniques, including SYTOX Green stain and cell digestion assay, were determined to be inappropriate for use in Elkhorn Slough due to indiscriminate staining of suspended particulates and incompatibility with cell target material. Viability analysis with FDA revealed a higher fraction of active cryptophyte cells in the upper reaches, the area of their dominance, and a lower fraction of active cells in the lower slough. It was concluded that cell death (as defined by a lack of FDA-linked esterase enzyme activity) is an important force structuring the phytoplankton community of Elkhorn Slough.