Sanctuary Integrated Monitoring Network
Monitoring Project

Characterization of the Benthic and Planktonic Communities of Elkhorn Slough

Principal Investigator(s)

  • RIchard Zimmerman
    Old Dominion University
  • Rikk Kvitek
    California State University, Monterey Bay
  • Nick Welschmeyer
    Moss Landing Marine Laboratories, California State University
  • Stacy Kim
    Moss Landing Marine Laboratories, California State University
  • John Oliver
    Moss Landing Marine Laboratories, California State University
  • Mike Foster
    Moss Landing Marine Laboratories, California State University
  • Gregor Cailliet
    Moss Landing Marine Laboratories, California State University
  • Jim Harvey
    Moss Landing Marine Laboratories, California State University


  • SIMoN
Start Date: December 01, 2002
End Date: December 01, 2007

Our goal is an ecosystem description of Elkhorn Slough that will serve as a baseline for assessments of the rapid change in this coastal habitat. Available historical data will be gathered to evaluate past changes and guide predictions of future ecological shifts. Research, including published studies, theses, gray literature, and unpublished data from our 25-plus years of research in the slough, will be compiled into a computer database. We propose new studies, focusing on benthic and planktonic ecosystem components, to provide a well-defined foundation for future comparative and experimental work. We will work closely with the Sanctuary Integrated Monitoring Network (SIMoN) to make the historical and new data easily and rapidly accessible to any interested parties. In the future, check the SIMoN website for this data.

Historically, Elkhorn Slough was a shallow freshwater marsh with extensive tidal flats. The establishment of a permanent entrance for Moss Landing Harbor in 1947 initiated increased seawater flux that began altering the ecosystem. A deep marine lagoon was well-developed by the time of the first quantitative community surveys in the early 1970ís; nevertheless, sampling sites that were intertidal are now completely subtidal. Erosion has led to habitat loss and is continuing in the slough system as flow speeds increase due to enhanced tidal flux in the deepening channels, a positive feedback process. With the good descriptions of benthic invertebrates and zooplankton that were made in the 1970ís and the changes in the habitat that have occurred since then, an expanded resurvey of benthic invertebrates and zooplankton will allow analysis of decadal changes and community response to enhanced marine influence. Elkhorn Slough is an example of a low coastal region invaded by the tidal flow of seawater.

Though the invading tidal flow was engineered by establishing a permanent harbor mouth, this mimics increased tidal flow that will follow sea level rise. Sea level is predicted to rise 0.6 m in the next century in response to global increases in temperature. The changes that have occurred in Elkhorn Slough may be predictive of ecosystem response to global changes. Though good data for some taxa allow comparative studies, early descriptions were incomplete, with little information available on phytoplankton and macrophytes in particular. We propose to establish a baseline for these community components, and to further utilize this data to compare the relative importance of planktonic versus benthic primary production in Elkhorn Slough. This will require close coordination with studies on the hydrography of the slough, and we will work jointly with researchers funded by SIMoN to develop a circulation model for Elkhorn Slough. Increases in the mean volume of the slough alone suggest that changes may be occurring in the relative proportions of planktonic versus benthic metabolism in the ecosystem as a whole. Those changes may influence the tendency of the slough to act as a source or sink of nutrients to local Monterey Bay waters, and may influence its function in retaining or passing watershed pollutants. The baseline ecosystem function of Elkhorn Slough has yet to be established.

We will produce several products that are highly relevant and valuable to science and to the managers of Elkhorn Slough and the Monterey Bay National Marine Sanctuary. First will be a comprehensive database for Elkhorn Slough, that will include information on fishes, birds and mammals, and macrophytes, as well as benthic invertebrates, zooplankton, and phytoplankton. Part of this database will be a bathymetric map at cm scale resolution that will allow erosional rates to be calculated, with overlying habitat mosaics to determine habitat loss or gain. The extensive dataset will be available to track invasions by exotic species as well as shifts in resource utilization by animals that transiently use the slough for feeding or reproduction, and may be enhanced by a matching dataset produced by researchers examining the offshore thermal effects of the power plant outfall. In addition to storing data, we will archive samples for future processing and provide continuity for past through future studies. We will expand sampling areas to encompass the variety of marine habitats in the slough, and thus create a comprehensive description. The research efforts will be synthesized to analyze the contributions of primary producers in the slough, and to examine potential impacts of sea-level rise on low coastal environments. Finally, this work will emphasize educational opportunities, by providing support and training for graduate and undergraduate students in the California State University (CSU) system. The decadal comparisons will stimulate further research, especially experiments, to better understand how the Elkhorn Slough functions as an ecosystem.

Summary to Date

In 2005, the invertebrate team completed the seasonal sampling of the 7 intertidal and 7 subtidal stations that were selected from our initial sampling of over 70 benthic stations slough wide. We sampled in January, April, and September 2005, which was also our annual sampling of these stations. Two of the intertidal stations will be subtidal very soon. One of the original intertidal stations from the slough-wide sampling, in the north harbor nearest to Bennett Slough, has already retreated into the subtidal environment. The benthic invertebrate and habitat data show the overwhelming impacts of erosion too well. All the benthic community samples have been fully processed through January 2005. The last two sampling efforts are still in the processing stage. Those from April are with the taxonomists. September samples are being sorted.

We have completed all of the statistical analyses on the slough-wide data set, including comparisons with the infaunal data from the 1970ís. All that is missing is the description of the sediments, which depends on the analysis of samples already collected (see below). We will complete a quantitative assessment of prey availability to include in a paper focused on fluctuations in sea otter populations and their relation to prey in the slough. We are still hoping to sample the major peripheral wetland systems around the slough next summer. Finally, we will help in the production of potentially several geological papers that are mentioned below.

This fall we sampled the sediments at all stations where we previously collected infaunal samples. We took a standard sample of the top 2 cm of deposit, which are being analyzed with the marine labís new particle counter to document the distribution of grain sizes. The particle counter is a Beckman-Coulter LS 13 320 laser particle size analyzer with aqueous module equipped with a pump and a built-in ultrasound unit. The measured size distributions range from 0.04 ?m to 2 mm. The particle sizer is composed of two units: a laser beam for conventional (Fraunhofer) diffraction (from 0.4 ?m to 2 mm) and a polarized intensity differential scatter (PIDS) unit, which measures particles based on the Mie theory of light scattering (0.04 ?m). This technology separates the silt and clay fractions into many discrete size categories, which may permit separating the poorly consolidated deposits in the back slough from those in other relatively quiet water areas like Parsons Slough. More likely, we might see a distinction between these soft deposits and the hard clays being eroded into throughout the slough. The soft deposits may be dominated by fines, which eroded from the more local watershed since statehood. The hard clays should be much older and probably originated from local as well as much larger regional sources, including floods from the Pajaro River. If we see these differences, analysis of sample mineralogy may reveal even more about potential differences in source material.

At each station, we also collected a vertical core at least 10 cm deep to document vertical structure in the zone where most of the infauna live. The cores were examined visually in the lab, and are frozen for potential future analyses depending on the results from the former work. We expect to use them to measure pore water content and bulk sediment density at least. We also tested a one-meter long, larger-area plastic core, which must be dug out by divers. Before the end of the project, we hope to collect one of these cores from each major benthic community in the slough for an analysis of deep vertical structure. The clear plastic walls permit excellent photo-documentation of vertical structure, including close up views of the bottom surface and the top cm of deposit, where most small infauna live. These images provide an excellent view of different benthic communities and habitats. The photos will be done in the laboratory. We have good video footage of the slough bottom in those regions of the slough where in situ water clarity permits video work (primarily below Kirby Park). But the laboratory images provide a much more detailed view of the sediment surface, as well as details of vertical structure.

This year Sea Engineering compiled the first, comprehensive geological description of the erosion process in Elkhorn Slough. This was made possible by the SIMoN grant. Their description relies heavily on the multibeam and sub-bottom sonar surveys competed by Rikk Kvitek and his team with SIMoN support. Their report displays the sonar images from different sections of the slough and then interprets them. The three-dimensional cross sections they show are highly revealing. The report includes a quantitative evaluation of the inlet stability at the slough mouth, which turns out to be uniquely unstable. The slough occupies parts of the stability curve where no other system has yet been seen.

Study Parameters

  • Historical changes and baseline for fut
  • Habitat association
  • Diversity
  • Habitat
  • Abundance
  • Distribution
  • Optical properties
  • Erosion
  • Maps

Figures and Images

Sample locations in the Elkhorn Slough.

Figure 2. Map showing the locations of subtidal and intertidal stations for invertebrate sampling in Elkhorn Slough.

Figure 3. The Benthic Lab crew transfers samples that have been fixed in formaldehyde to ethanol, a preservative that can be used for safer storage and handling of specimens and samples.

Figure 4. Dr. John Oliver collects an intertidal core. The mud will be sieved away, and the invertebrate animals left behind will be preserved, counted and identified to distinguish community changes at different locations in the slough and over seasons and years.

Figure 5. Kamille Hammerstrom demonstrates the latest in sloughwear while using the GPS to relocate an intertidal station in the North Harbor.

Figure 6. Ulva mats covering a large area within Elkhorn Slough. October 2004.

Figure 7. Sampling quadrat shown before the alga was collected. All Ulva within the PVC frame was collected. April 2004.

Figure 8. Tim Schaadt slogging through the calf deep mud in search of Ulva mats. March 2004. Photo credit: Max Overstrom-Coleman.