2004 Progress Report: Great Lakes Diatom and Water Quality Indicators

EPA Grant Number: R828675C001
Subproject: this is subproject number 001 , established and managed by the Center Director under grant R828675
(EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).

Center: EAGLES - Great Lakes Environmental Indicators Project
Center Director: Niemi, Gerald J.
Title: Great Lakes Diatom and Water Quality Indicators
Investigators: Reavie, Euan D. , Axler, Richard , Johansen, Jeffrey R. , Kelly, John R. , Kingston, John C. , Kireta, Amy R. , Kreis, Jr., Russell G. , Morrice, John , Sgro, Gerald V. , Stoermer, Eugene F. , Thompson, Jo , Yurista, Peder
Current Investigators: Reavie, Euan D. , Andresen, Norman A. , Axler, Richard , Ferguson, Michael J. , Johansen, Jeffrey R. , Kingston, John C. , Kireta, Amy R. , Sgro, Gerald V. , Stoermer, Eugene F.
Institution: John Carroll University , Center for Water and the Environment, Natural Resources Research Institute , Ely Field Station, Center for Water and the Environment, Natural Resources Research Institute , U.S. EPA Mid-Continent Ecology Division-Duluth , University of Michigan
Current Institution: University of Minnesota , John Carroll University , University of Michigan
EPA Project Officer: Packard, Benjamin H
Project Period: January 10, 2001 through January 9, 2005
Project Period Covered by this Report: January 10, 2003 through January 9, 2004
RFA: Environmental Indicators in the Estuarine Environment Research Program (2000) RFA Text |  Recipients Lists
Research Category: Ecological Indicators/Assessment/Restoration , Water , Ecosystems


The objective of this research project is to quantify the extent to which pressure indicators influence diatom community structure in nearshore wetlands, estuaries, and reaches of the Laurentian Great Lakes including the following approaches:

  • Develop predictive models through multivariate analyses of communities and ecosystems to infer ecological status at local and regional scales and describe pre-disturbance to recent baselines, trends, and magnitudes of change in restricted river-influenced and other wetlands
  • Evaluate and modify existing diatom metrics and devise and validate new diatom metrics so that a number of state indicators for nutrient loading, siltation, and salinity in nearshore waters of the Great Lakes will be available to federal and state agencies
  • Construct multimetric diatom indices from the best of these state or condition metrics
  • Develop integrated indices of biotic integrity based on a combination of selected metrics developed in the diatom subprogram and by other teams in the larger program
  • Develop a QA/QC infrastructure for the diatom subprogram and future assessment efforts
  • Conduct a limited water quality survey (field and laboratory measurements) of nearshore sites contemporaneously with diatom sampling to: (1) calibrate diatom indices; (2) further characterize sampling sites for all Great Lakes Environmental Indicators (GLEI) subprojects and related U.S. Environmental Protection Agency/Mid-Continent Ecology Division (EPA-MED) Great Lakes coastal wetlands projects; and (3) evaluate the efficacy of several relatively inexpensive, field-friendly measurements as surrogates for more expensive analytes typically used to characterize water quality

Progress Summary:

Our efforts in the past year have centered on three major tasks.

  • The assessment of all diatom samples was completed and data have been entered into a temporary Excel database for data analysis and formatting for eventual incorporation into the master GLEI database.
  • Several preliminary statistical evaluations of the diatom and environmental data were performed to provide guidance on upcoming indicator development. Initial diatom-environmental investigations show that the diatom indicators will yield robust models and multimetric indices for assessing environmental stress in coastal environments.
  • We completed the analysis, quality assurance, and GLEI database entry for all field data documenting site characterization and condition. Several exploratory analyses have been completed relating water quality to segment shed stressors and, for the development of surrogate, cost-effective water quality parameters.

Expected Results

The research will develop and evaluate indicators by local habitat, by lake, by ecoregion, and by stressor activity/intensity. The diatom project will provide linkages from ecosystem function to water quality and to pressure indicators documented by other subproposals. We are confident that a suite of powerful diatom indicators can be developed for key pressure indicators for use throughout the Great Lakes basin.


The PI of the diatom component of GLEI has transitioned to Euan Reavie. As a result of John Kingston’s illness and eventual passing away in June 2004, analytical effort was delayed on the diatom work, and Dr. Reavie’s primary goal for the year was to catch up and meet predefined goals in the GLEI agenda. For this reason, about 75 percent of our GLEI effort in 2004 was allocated to the identification and enumeration of remaining diatom samples. Despite setbacks, significant progress has been made in the last year.

Field Work . All field work was completed in Year 3 of the project. Diatom and water quality samples were collected from approximately 240 segment sheds of shoreline distributed across the U.S. shoreline of all 5 Great Lakes and 5 geomorphic units from 2001 to 2003. The sampling effort generated more than 500 discrete water samples that were analyzed in the laboratory for nutrients, chlorophyll, suspended solids, dissolved organic carbon (DOC), chloride, and several other parameters. At least four times that number of samples was also analyzed in the field for additional water quality characteristics.

Sample Assessment . Diatom samples from the upper lakes were processed at Natural Resources Research Institute (NRRI) Ely Field Station, and the lower lakes samples were analyzed at John Carroll University. Water quality analyses were performed at the NRRI University of Minnesota–Duluth (UMD) Central Analytical Laboratory in Duluth, Minnesota, with the exception of DOC (which was graciously analyzed by EPA-MED) and certain field measurements. Database activities were coordinated at NRRI-UMD, and data entry via the Web has been developed to provide unified methods for entry and suitable quality control of the procedures.

As of March 2005, all diatom samples have been assessed for species composition and abundance, and data have been entered into a temporary Excel database for data analysis, formatting, and eventual incorporation into the master GLEI database. Taxonomic collaborations have been ongoing to ensure taxonomic harmony between researchers enumerating diatoms at the three universities.

All water samples have now been analyzed, quality assured, and entered into the GLEI database. Field profiles of temperature, dissolved oxygen (DO), specific electrical conductivity (EC25), secchi and transparency tube depth, pH, turbidity, and soluble and particulate chlorophyll-fluorescence were also entered into the database. Metadata are being created for all parameters along with a set of queries to expedite retrieval of appropriate data sets for various statistical analyses. Field data (mostly temperature, DO, and EC25) collected by the Fish-Invertebrate subproject were added to the larger Diatom subproject dataset as well as EPA-MED field and laboratory water chemistry data from their 2002-2003 wetland and high energy sites. Because a common experimental unit, the segment-shed, and similar methodology and QA/QC protocols were used for all four subgroup studies, combining the data should provide us with better estimates of interannual and seasonal variation. Additional field and laboratory physical and chemical data is now being processed from the deepwater surveys collected in collaboration with EPA Great Lakes cruises in 2002 and 2003.

Diatom–Stressor Relationships . Significant relationships between surficial taxa and water chemistry (total phosphorus concentration) were found from the diatom samples analyzed as of September 2004. These preliminary results (see Figures 1-3) reflect the strong indicator potential for the diatoms. At this time, these methods are being expanded to develop the diatoms as a more general indicator of pollution (i.e., an index providing a more holistic integration of stressors, including nutrients, salinity, and water clarity). The same approach will also be evaluated using the diatom general to test the feasibility of an indicator-based tool that would provide more rapid and user-friendly assessments when a detailed, species-based approach is not feasible. These diatom-based tools will be developed and tested for the entire Great Lakes system and for particular habitats (wetlands, high energy shorelines, bays) so that the most appropriate model may be selected.

Water Chemistry–Stressor Relationships . Exploratory analyses have begun to examine the relationship between GLEI-measured coastal zone water quality and segment shed stressors computed from the statistical analysis of 207 GIS data layers for the Great Lakes coastal zone (see Figure 4). This analysis was conducted for determining the stressor gradients used for establishing the GLEI sampling design and is being used for preliminary analyses until the final segment shed-specific stressors are calculated. Over the next few months results using the stressor value–water quality relationships computed from the segment shed analysis for the purpose of site selection will be compared to the final stressor values that are being computed based on hydrology/watershed analyses.

Surrogate Water Quality Indicators . Laboratory water chemistry analyses are expensive and the coastal zones are extremely variable. The GLEI diatom water quality group is evaluating the efficacy of relatively inexpensive, field-friendly measurements as surrogates for more expensive analytes typically used to characterize coastal zone water quality. These include a new field-instrument for algal-fluorescence and turbidity, specific conductivity, optical color, and transparency tube clarity. All can be used in existing agency monitoring programs but also could easily be adapted to existing models for stream and lake volunteer monitoring programs. Such data should also be useful for ground-truthing (calibration) of satellite or aircraft remote sensing data.

Figure 1. A Multivariate Analysis (Canonical Correspondence Analysis [CCA] Using Forward Selection and Monte Carlo Permutation Tests) Was Employed To Determine Which Environmental Variables Explained Variance in the Diatom Assemblages. Diatom assemblage composition exhibited strong responses across the gradients of eight of the measured variables. Selected environmental variables that can reflect stress, such as nutrients, are suited to diatom-based indicator approaches. The CCA biplot above illustrates the forward-selected variables that had strong relationships to patterns in the diatom assemblages. A reconstructive model was developed for total phosphorus to evaluate this approach.

Figure 2. Diatom Responses to Total Phosphorus (TP). Weighted average regression was used to determine diatom species relationships to TP. The weighted average method assumes a unimodal response of the diatoms along the environmental gradient, so each species is assigned an optimum and a tolerance for TP. Subsequently, these weighted average optima and tolerances could be used to infer TP concentrations for a study site with weighted average calibration.

Figure 3. Diatom-TP Model Testing. By comparing measured to diatom-inferred TP concentrations, the power of the model can be tested. The root mean square error (RMSE) provides a measure of the model’s predictive ability. These results indicate a strong relationship between diatoms and stressor-related variables in Great Lakes coastlines and that diatom assemblages may be used to infer environmental conditions. Although this evaluation focuses on TP, additional proxies of ecological stress also are being evaluated.

Figure 4. Statistically Significant Relationships for Great Lakes Coastal Wetlands Between Four Water Quality Parameters and the First Principal Component of the Agricultural Variables. Increasing values on PC1 indicate increasing agriculture, especially nitrogen and phosphorous applications.

Future Activities:

We will:

  1. develop diatom-based models and multimetric indices;
  2. assess diatom sampling and taxonomic methods;
  3. integrate all available water quality data into the GLEI database (diatom, fish-invert, and EPA-MED collaborators) for all subprojects' use;
  4. analyze surrogate measures of water quality such as EC25, turbidity, color, and particulate and filtrate fluorescence;
  5. analyze relationships between landscape-scale stressors and coastal zone water quality;
  6. and draft manuscripts based on results.

Journal Articles on this Report : 3 Displayed | Download in RIS Format

Other subproject views: All 35 publications 19 publications in selected types All 16 journal articles
Other center views: All 268 publications 54 publications in selected types All 45 journal articles
Type Citation Sub Project Document Sources
Journal Article Brazner JC, Danz NP, Niemi GJ, Regal RR, Trebitz AS, Howe RW, Hanowski JM, Johnson LB, Ciborowski JJH, Johnston CA, Reavie ED, Brady VJ, Sgro GV. Evaluation of geographic, geomorphic and human influences on Great Lakes wetland indicators:a multi-assemblage approach. Ecological Indicators 2007;7(3):610-635. R828675 (Final)
R828675C001 (2004)
  • Full-text: Science Direct Full Text
  • Abstract: Science Direct Abstract
  • Other: Science Direct Full Text pdf
  • Journal Article Danz NP, Regal RR, Niemi GJ, Brady VJ, Hollenhorst T, Johnson LB, Host GE, Hanowski JM, Johnston CA, Brown T, Kingston J, Kelly JR. Environmentally stratified sampling design for the development of Great Lakes environmental indicators. Environmental Monitoring and Assessment 2005;102(1-3):41-65. R828675 (Final)
    R828675C001 (2003)
    R828675C001 (2004)
    R828675C001 (Final)
    R828675C002 (2003)
  • Abstract from PubMed
  • Full-text: Springer - Full Text PDF
  • Abstract: Springer
  • Journal Article Sgro GV, Ketterer ME, Johansen JR. Ecology and assessment of the benthic diatom communities of four Lake Erie estuaries using Lange-Bertalot tolerance values. Hydrobiologia 2006;561(1):239-249. R828675 (Final)
    R828675C001 (2004)
    R828675C001 (Final)
  • Full-text: Springer - Full Text PDF
  • Abstract: Springer
  • Other: University of Minnesota PDF
  • Supplemental Keywords:

    diatoms, algae, water quality, metrics, multimetric indices, nutrients, salinity, siltation, Great Lakes, coastal wetlands, environmental indicators, ecological indicators, pollutant loads, aquatic ecosystem, monitoring, toxics,, RFA, Scientific Discipline, ENVIRONMENTAL MANAGEMENT, Geographic Area, Water, ECOSYSTEMS, Ecosystem Protection/Environmental Exposure & Risk, Nutrients, Ecosystem/Assessment/Indicators, Ecosystem Protection, Ecological Effects - Environmental Exposure & Risk, Air Deposition, Ecological Monitoring, Ecological Risk Assessment, Ecology and Ecosystems, Great Lakes, Ecological Indicators, Risk Assessment, coastal ecosystem, diatoms, ecological condition, aquatic ecosystem, hydrological stability, nutrient supply, nutrient transport, ecosystem assessment, hierarchically structured indicators, wetland vegetation, environmental stressor, hydrological, coastal environments, environmental consequences, ecological assessment, ecosystem indicators, estuarine ecosystems, nutrient stress, aquatic ecosystems, toxic environmental contaminants, water quality, ecosystem stress, ecological response

    Relevant Websites:

    http://glei.nrri.umn.edu Exit

    Progress and Final Reports:

    Original Abstract
  • 2001
  • 2002 Progress Report
  • 2003 Progress Report
  • Final Report

  • Main Center Abstract and Reports:

    R828675    EAGLES - Great Lakes Environmental Indicators Project

    Subprojects under this Center: (EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
    R828675C001 Great Lakes Diatom and Water Quality Indicators
    R828675C002 Vegetative Indicators of Condition, Integrity, and Sustainability of Great Lakes Coastal Wetlands
    R828675C003 Testing Indicators of Coastal Ecosystem Integrity Using Fish and Macroinvertebrates
    R828675C004 Development and Assessment of Environmental Indicators Based on Birds and Amphibians in the Great Lakes Basin
    R828675C005 Development and Evaluation of Chemical Indicators for Monitoring Ecological Risk