Final Report: Environmental Indicators in the Estuarine Environment: Seagrass Photosynthetic Efficiency as an Indicator of Coastal Ecosystem Health

EPA Grant Number: R828677C004
Subproject: this is subproject number 004 , established and managed by the Center Director under grant R828677
(EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).

Center: EAGLES - Atlantic Coast Environmental Indicators Consortium
Center Director: Paerl, Hans
Title: Environmental Indicators in the Estuarine Environment: Seagrass Photosynthetic Efficiency as an Indicator of Coastal Ecosystem Health
Investigators: Fonseca, Mark , Biber, Patrick , Field, Donald , Gallegos, Charles L. , Kenworthy, Judson , Thursby, G.
Institution: National Oceanic and Atmospheric Administration (NOAA) , University of North Carolina at Chapel Hill
EPA Project Officer: Hiscock, Michael
Project Period: March 1, 2001 through February 28, 2003
RFA: Environmental Indicators in the Estuarine Environment Research Program (2000) RFA Text |  Recipients Lists
Research Category: Ecological Indicators/Assessment/Restoration , Water , Ecosystems


The objectives of this research project were to:  (1) create an indicator of estuarine health based on seagrasses; (2) examine the physiological state of seagrass in response to environmental conditions and correlate the plant’s physiological state with ambient conditions based on both in situ and remote sensed data sources; and (3) evaluate the feasibility of scaling field assessments to remote sensed data sources.

In only 2 years the Atlantic Coast Environmental Indicators Consortium (ACE INC) Seagrass Indicators (SI) project has developed indicators at a range of temporal and spatial scales that are metrics of the status of seagrass and other submerged aquatic vegetation (SAV).  Seagrass bioindicators were developed in the Neuse-Pamlico site, in conjunction with commonly used physical and chemical (i.e., light, temperature, and salinity) and biological (plant morphology) indicators of seagrass community health, to provide a link between field observations, mesocosm experiments, remote sensing, and modeling.

Water quality measurements and a bio-optical model were used to predict maximum depth of seagrasses in North River, North Carolina.  Validation of the bio-optical model results were done using state-of-the-art differential global positioning system (DGPS) technology to provide bathymetry of existing seagrass beds to within 10 cm resolution.  The modeling approach since has been expanded to include mapping of water quality protective of seagrasses and development of software to make this approach readily available to nonexperts.

Controlled experiments (Press vs. Pulse) were used to determine minimum light levels for plant survival and the importance of recovery intervals of high light availability between low-light attenuation events for natural populations.  A minimum of a 1:1 stress:recovery time interval is recommended to mitigate against SAV losses.

Summary/Accomplishments (Outputs/Outcomes):

Water Quality Indicators and the Bio-Optical Model

A healthy community of underwater plants known as seagrasses is essential for healthy estuarine ecosystems like Pamlico Sound, North Carolina.  These marine plant communities provide food for waterfowl and shelter for numerous important shellfish, invertebrates, and fish.  Ecosystem services provided by seagrasses abound.  Microscopic algae living on the grass blades are the base of a food chain that cascades up to shrimp, blue crabs, red drum, croaker, flounder, menhaden, and a myriad of other valuable fish species.  Seagrass meadows help stabilize bottom sediments, provide a protective nursery for many aquatic organisms, and are a key food source for migratory waterfowl.

Seagrasses need relatively high amounts of light.  Decreased light penetration limits the growth and distribution of seagrasses.  Turbidity, chlorophyll, and color are natural contributors to reduced light penetration with increasing depth.  Increases in sediment from development on the land and increases in nutrients (eutrophication) in the water, however, lead to epiphytes on the seagrass leaves and to algal blooms, which both block light and ultimately can kill the plants.

As part of ACE INC, researchers at the University of North Carolina at Chapel Hill and the National Oceanic and Atmospheric Administration (NOAA) Beaufort Laboratory, in collaboration with the Smithsonian Environmental Research Center (Atlantic Slope Consortium [ASC]), have tested and applied the bio-optical model for monitoring seagrass-habitat condition in North River, North Carolina.  To parameterize the bio-optical model, monthly water quality samples were collected along a strong optical and Population Attributable Risk (PAR) gradient from September 2002 to September 2004.


  • Optical characteristics of the North River, North Carolina, are different from the Rhode River, Maryland, likely because of greater tidal energetics.
  • Water quality parameters are supportive of presence of seagrasses based on the bio-optical model.  A total of 180 water samples were collected from 9 sites in the North River around beds of eelgrass, Zostera marina, for the purpose of generalizing the bio-optical model.  Another 108 samples were collected from 9 stations in Pamlico Sound for comparison purposes.  Cooperative efforts between the ASC and the ACE INC Estuarine and Great Lakes (EaGLes) projects were undertaken to develop a regionally extensive atlas of optical properties for broad geographic application of the bio-optical indicator (Massachusetts, Chesapeake Bay, Pamlico Sound, Indian River Lagoon Florida, and Mississippi Sound).
  • Predictions of the bio-optical model were confirmed by measuring the deep-edges of Z. marina beds that have been stable for three decades in North River in September 2004.  The depth measurements were made using the DGPS Phase-Carrier technique.  This technique used a Trimble base-station at Harkers Island on a geodetic benchmark and two roving Trimble GPS units in the field.  Vertical precision was better than 5cm.  Depth of the deep-edges of the seagrass beds agreed to within 10 cm of the model predictions.


These water-quality based procedures have produced a diagnostic tool (the bio-optical model) for setting water-quality targets for seagrass protection in North Carolina.  In addition, this research has suggested new ideas on the mechanisms by which increasing eutrophication may be altering water column optical properties to the detriment of large and long-lived aquatic organisms.
State and federal watershed managers in North Carolina are using this tool to make management decisions on reducing suspended solids and chlorophyll as part of the new Coastal Habitat Protection Plan designed, in part, to protect seagrasses in North Carolina estuaries.  Ongoing development and implementation of real-time operational indicators of water quality with relevance to seagrasses will further create tools for management agencies.

Software implementation of the bio-optical model into a graphical user interface-based program running under Microsoft Excel was tested in 2004 as proof-of-concept.  The initial product was received favorably at both ACE INC and EaGLes Annual Meetings, as well as the 2004 U.S. Environmental Protection Agency Environmental Monitoring and Assessment Program conference.

We conclude that further development of this product is required.  A contract has been awarded to Seagrass CriteriaBase by NOAA’s Center for Coastal Fisheries and Habitat Research for this effort.  An estimated 200 man-hours of programming and development will be required to create a stand-alone package that runs under Windows.

Light Limitation and Seagrass Responses

Seagrasses require relatively high amounts of light.  Decreased light penetration limits the growth and distribution of seagrasses.  Natural light-limitation events occur as spatially and temporally sporadic and often unpredictable events (phytoplankton blooms, turbidity plumes). Better understanding of the tolerance of seagrass species to these events, including duration and return frequency of light-limitation, are important in linking water-quality stressors to seagrass population responses.

Controlled light-limitation experiments were conducted as Press (2003) versus Pulse (2004) stressors on Z. marina and Halodule wrightii (shoalgrass) and were successful in illuminating mechanisms by which light-limitation causes plant mortality.  In 2003, we undertook two experiments (Press) designed to determine minimum light requirements for these two species and to evaluate potential indicator measurements.  In 2004, two additional experiments (Pulse) were conducted to determine the importance of timing and duration of light attenuation events (e.g., turbidity plumes/extreme phytoplankton blooms) on seagrass survival.  These experiments compared the responses of Z. marina seedlings (2-3 months old) against adults of the same species (> 1 year) in spring and against H. wrightii, a second ubiquitous seagrass species.  Results indicated that stress-recovery time needs to be no less than 1:1 for seagrass survival of both species.  These results are broadly applicable to seagrass habitats along the entire Atlantic seaboard of the United States.

Conclusions of the seagrass Press and Pulse experiments can be summarized:  

  • Mortality processes occur at a range of time-scales from minutes to months.
  • Chlorophyll fluorescence using Fv/Fm is useful only for measuring stress-recovery phases over a few hours or days.
  • Leaf and root tissue-nutrient and nonstructural carbohydrate contents follow plant stress closely over days to weeks.
  • Leaf chlorophyll pigment concentration is needed to explain both Fv/Fm and leaf reflectance spectrum information, and it is time-consuming.
  • Plant morphology:  number of shoots, leaves, leaf length, and area are all good measures of integrated stress occurring over weeks.
  • Population mortality is an integrated response to the previous five variables and is the metric of concern for maintaining viable seagrass habitat.  Unfortunately, it is almost impossible to measure in the field.

PAR monitoring, using LI-COR underwater sensors and dataloggers, can be used to measure daily light levels at selected stations in the field.  From the information gained on seagrass light requirements in the Press and Pulse experiments, managers now can predict when light levels are limiting for survival.  Increasing numbers of red and yellow days will indicate increasing plant stress and higher mortality probabilities.

Outreach Activities

Dr. Kenworthy gave a presentation to the Water Quality Subcommittee of the North Carolina Marine Fisheries Commission on development of an optical water quality model for the conservation of seagrasses in North Carolina for consideration in development of a Coastal Habitat Protection Plan in North Carolina.

Dr. Kenworthy served as a reviewer for the Chesapeake Bay Program’s development of water quality criteria for SAV management in the Bay.

Dr. Biber led 1-day field training courses for the Carolina Environmental Program on seagrass field techniques in October 2003 and October 2004.

Dr. Biber reviewed the North Carolina Department of Environment and Natural Resources Coastal Habitat Protection Plan for SAV and provided guidance on water quality criteria.

Dr. Biber was awarded a contract to monitor the impact to and recovery of SAV in a local coastal construction project at Carteret Community College.  He commenced the monitoring of SAV before the construction in April 2004.  This included a subcontract to a local minority-owned small business (Geodynamics, Inc.) for high-resolution mapping of bathymetry at the site using multibeam sonar.  In October 2004 seagrasses were transplanted to a protected nursery location on site.  He assessed the success of transplanting in April 2005, successful establishment was found at both transplant locations.

Dr. Kenworthy and Dr. Biber successfully obtained a Memorandum of Agreement between the NOAA Beaufort Laboratory and Massachusetts Department of Environmental Protection (DEP) to undertake an assessment of water-quality issues causing declines of seagrasses in Massachusetts.  This project made extensive use of the bio-optical modeling framework developed under ACE INC and applied the results to making management recommendations to Massachusetts DEP on how to best proceed with protecting their seagrass inventory.  A workshop was held March 30-31 in Falmouth, Massachusetts, with about 30 participants from DEP and 6 invited guest speakers.

Contributions to State of Knowledge

The two groups of SI that we developed provided new tools for evaluating the condition of intertidal and subtidal seagrass and SAV communities along the Atlantic Seaboard of the United States.  The products include indicators that are based on water quality and seagrass measurements made in the field.  All the indicators investigated, however, have significant potential for being developed as applications that can be calibrated using either limited field samples or remotely sensed data.  To date, three products have been produced from the ACE INC SI component:  (1) Bio-optical Modeling Pamphlet:  distributed at numerous State Agency and National meetings; (2) Seagrass CriteriaBase software v1.0, which runs as an add-in under Microsoft Windows; and (3) Massachusetts-DEP workshop report, Kenworthy and Costello, 2005, Evaluating the Feasibility of Using a Bio-Optical Model for the Conservation and Restoration of Seagrasses in Massachusetts Embayments (MDEP and NOAA).

Journal Articles on this Report : 2 Displayed | Download in RIS Format

Other subproject views: All 37 publications 7 publications in selected types All 6 journal articles
Other center views: All 383 publications 99 publications in selected types All 88 journal articles
Type Citation Sub Project Document Sources
Journal Article Biber PD, Irlandi EA. Temporal and spatial dynamics of macroalgal communities along an anthropogenic salinity gradient in Biscayne Bay. Aquatic Botany 2006;85(1):65-77. R828677C004 (Final)
not available
Journal Article Irlandi EA, Orlando BA, Biber PD. Drift algae-epiphyte-seagrass interactions in a subtropical Thalassia testudinum meadow. Marine Ecology-Progress Series 2004;279:81-91. R828677C004 (2004)
R828677C004 (Final)
not available

Supplemental Keywords:

seagrass, bio-optics, nutrients, bioindicators, conservation, environmental assets, scaling, aquatic, habitat, estuary, coastal, regionalization, integrated assessment, restoration, water quality and habitat management, remote sensing,, RFA, Scientific Discipline, Water, ECOSYSTEMS, Ecosystem Protection/Environmental Exposure & Risk, RESEARCH, estuarine research, Ecosystem/Assessment/Indicators, Ecosystem Protection, Ecological Effects - Environmental Exposure & Risk, Monitoring, Environmental Monitoring, Ecological Monitoring, Ecological Risk Assessment, Ecology and Ecosystems, Ecological Indicators, bioassessment, bioindicator, ecoindicator, remote sensing, aquatic biota , indicator plants, diagnostic indicators, ecosystem indicators, estuarine ecoindicator, estuarine ecosystems, aquatic ecosystems, environmental indicators, estuarine waters, seagrass photosynthesis, water quality, biogeochemistry, bio-optics, environmental stress indicators

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Progress and Final Reports:

Original Abstract
  • 2001

  • Main Center Abstract and Reports:

    R828677    EAGLES - Atlantic Coast Environmental Indicators Consortium

    Subprojects under this Center: (EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
    R828677C001 Phytoplankton Community Structure as an Indicator of Coastal Ecosystem Health
    R828677C002 Trophic Indicators of Ecosystem Health in Chesapeake Bay
    R828677C003 Coastal Wetland Indicators
    R828677C004 Environmental Indicators in the Estuarine Environment: Seagrass Photosynthetic Efficiency as an Indicator of Coastal Ecosystem Health