Workshop Ab
Coastal Intensive
Site Network (CISNet)
Final Pro
September 4-5,2002
Edgewater, Maryland

                              CISNet Final Progress Review Workshop
                                  Table of Contents
Introduction	in

Indicators of UV Exposure in Coral: Relevance to Global Climate Change and Coral Bleaching	1
     Susan Anderson, Richard Zepp, Jana Machula, William Fisher, Leah Oliver,
     Debbie Santavy, Lara Hansen, Gary Cherr, Erich Mueller

In Situ and Remote Monitoring of Productivity and Nutrient Cycles in Puget Sound	2
     Steven Emerson, Allan Devol, Wendi Ruef

Rhode River CISNet: Estuarine Optical Properties as an Integrative Response to Natural and
Anthropogenic Stressors	4
     Charles L. Gallegos, Thomas E. Jordan, Patrick J. Neale

CISNet for the Neuse River Estuary, NC: A Program for Evaluating Nitrogen-Driven Eutrophication
Associated With Changing Land Use in a Coastal Watershed	6
     Rick Luettich, Hans Paerl, Jay Pinckney

The Choptank River: A Mid-Chesapeake Bay Index Site for Evaluating Ecosystems Responses
to Nutrient Management	8
     Thomas C. Malone, Jeffrey C. Cornwell, William C. Boicourt, Lawrence W. Harding, Jr.,
     J. Court Stevenson

CISNet: Molecular to Landscape-Scale Monitoring of Estuarine Eutrophication	10
     James T. Morris, Madilyn Fletcher, John Jensen, Alan Lewitits, Peter Noble, Dwayne Porter

CISNet San Pablo Bay Network of Environmental Stress Indicators	12
     S. Geoffrey Schladow, Thomas M. Young, Inge Werner, Bruce Thompson, Jay Davis, Nadav Nur,
     David Schoellhamer

CISNet: Nutrient Inputs as a Stressor and Net Nutrient  Flux as an Indicator of Stress Response
in Delaware's Inland Bays Ecosystem	14
     William J. Ullman, Kiio-Chuin Wong, Joseph R. Scudlark, John M. Madsen, David E. Krantz,
     A. Scott Andres, Thomas E. McKenna

Index of Authors	15
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                                  CISNet Final Progress Review Workshop
In Fiscal Year (FY) 1998, the U.S. Environmental Protection Agency (EPA), in partnership with the National Oceanic
and Atmospheric Administration (NOAA) and the National Aeronautics and Space Administration (NASA), funded a
set of research grants through a competitive solicitation. The goal of the solicitation was to establish a network of
pilot sites along the U.S. Marine and Great Lakes coasts known as the Coastal Intensive Site Network (CISNet).
CISNet research topics focused on using ecological indicators and investigating the ecological effects of environ-
mental stressors.

CISNet had three main objectives, which included:

•  Developing a scientific basis for understanding ecological responses to anthropogenic stresses in coastal environ-
   ments, including the interactions of exposure, environment/climate, and ecological factors, as well as the spatial
   and temporal nature of these interactions.

•  Demonstrating the usefulness of intensively monitored sites for examining short-term variability and long-term
   trends in the relationships between natural and anthropogenic stressors and ecological responses.

•  Evaluating indicators of change in coastal systems at particular intensively monitored sites.

In 2000, as a follow-on and expansion of the 1998 CISNet Research Program, EPA and NASA funded an additional
set of larger, longer term grants, collectively referred to as the Estuarine and Great Lakes (EaGLe) Program. There
currently are five EaGLe Programs focusing on ecological indicators, with two in the Atlantic, one in the Pacific, one
in the Great Lakes region, and one in the Gulf of Mexico. Additional information about these programs and an open
solicitation for a sixth EaGLe research program can be found at:

The Coastal Intensive Site Netvcork (CISNet) Workshop Abstracts publication was developed in support of the Final
CISNet Progress Review Workshop in Edgewater, MD, on September 4-5, 2002.  This document contains abstracts
outlining results and accomplishments for the eight CISNet grants funded by EPA in FY 1998 through the National
Center for Environmental Research's (NCER) Science to Achieve Results (STAR) Program. EPA's STAR Program
funds research grants in numerous environmental science and engineering disciplines through a competitive process
and independent peer review.

This Final Progress Review Workshop provides a forum for EPA's STAR CISNet award recipients to discuss their
results and lessons learned. EPA representatives and other interested parties also have been invited to attend to
stimulate a discussion of research needs between government and private-sector researchers.

Any opinions, findings, conclusions, or recommendations expressed in this report  are those of the investigators who
participated hi the research.  For questions on the EPA CISNet grants, please contact the EPA CISNet Program
Manager, Gina Perovich, by telephone at 202-564-2248 or by e-mail at For further informa-
tion about  the EaGLe Program, please  contact Barbara Levinson by telephone  at 202-564-6911  or by e-mail at

To learn more about EPA's STAR Program, visit NCER's Web Site at:
               The Office of Research and Development's National Center for Environmental Research         iii

                                 CISNet Final Progress Review Workshop
        Indicators of UV Exposure in Coral:  Relevance to Global
                      Climate Change and Coral Bleaching

           Susan Anderson', Richard Zepp2, Jana Machula',  William Fisher3, Leah Oliver3,
                  Debbie Santavy3, Lara Hansen3, Gary Cherr1, and Erich Mueller4
  'Bodega Marine Laboratory,  University of California-Davis, Bodega Bay, CA; 2USEPA NERL/ERD,
  Athens, GA; 3USEPA NHEERL/GED, Gulf Breeze, FL; 4Mote Marine Laboratory, Suntmerland Key, FL
   The overarching goal of this project has been to evalu-
ate the potential contribution of interactions between
climate change and ultraviolet (UV) radiation in coral
bleaching. To provide additional tools for evaluating the
role of UV radiation, UV-specific stresses on corals have
been examined and factors that alter the penetration of
UV radiation over coral reefs have been characterized at
sites located in the Florida Keys.
   The first objective of this project was to develop im-
munofluorescence techniques to examine UV-specific
lesions in DNA (thymine dimers) of coral and zooxan-
thellae. A 96-well  enzyme-linked immunosorbent-type
assay for evaluating thymine dimers in coral and zoox-
anthellae has been developed.  Methods for immuno-
localization of thymine dimer and coral tissue also have
been finalized.
   The second objective was to determine whether UV-
induced DNA damage and indices of coral bleaching are
correlated, including laboratory and field assessments of
photoprotective pigment concentrations. To date, this
research group has complete laboratory and field expo-
sures to address this relationship. Both  laboratories
(Bodega Marine Laboratory and EPA's Gulf Ecology
Division, Gulf Breeze, FL) are completing analysis of
the tissues from these experiments.
   The third objective was to further examine the rela-
tionships between temperature, UV, and coral bleaching
in controlled experiments. During the 2001 field season,
an outdoor  exposure test was conducted at the Mote
Marine Laboratory for UV and temperature. Early in the
course of this 8-day exposure, coral polyps demonstrated
altered behavior based on  level  of exposure. Those in
high UV/high temperature treatments spent more time
retracted and were showing early stages of bleaching.
   The fourth objective was to measure underwater so-
lar UV irradiance and attenuation coefficients as well as
to develop continuous observations of chromophoric dis-
solved organic matter (CDOM) concentrations and
algorithms that relate CDOM concentrations to UV ex-
posure of coral assemblages. Research has focused on
factors that affect UV exposure of coral assemblages in
the Florida Keys. The location of the sites used for these
studies ranged from Sand Key near Key West, FL, to
Sombrero Tower near Marathon, FL.
   Activities included the following:
•  Measurements of underwater solar UV radiation and
   optical properties of water samples at various sites
   located in the Lower Keys
•  Development of algorithms that describe the penetra-
   tion of UV radiation into the Florida Keys water
•  Use of fluorometers for the measurement of UV-
   protective CDOM at SEAKEYS CMAN towers lo-
   cated at Sombrero Tower (near Marathon,  FL) sites
•  Comparisons of fluorescence and UV attenuation
   along transects from land out to the coral reefs
•  Research on thermal stratification effects on UV pen-
   etration and initial studies in the field and under con-
   trolled conditions on UV attenuation by CDOM de-
   rived from Florida Bay sea grasses and mangroves
•  Experiments on  the rates of UV absorbance loss
   (photobleaching) to CDOM in water samples col-
   lected near the coral reefs  when they were exposed
   to simulated solar radiation.
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                                  CISNet Final Progress Review Workshop
                In Situ and Remote Monitoring of Productivity
                        and Nutrient  Cycles in Puget Sound

                             Steven Emerson, Allan Devol, and Wendi Ruef
                    School of Oceanography, University of Washington, Seattle, WA
    The Ocean Remote Chemical Analyzer (ORCA) is
 an autonomous, moored profiler developed to sense a
 variety of chemical and optical properties in the upper
 ocean. Since deployment in May 2000, ORCA has been
 used to monitor water quality parameters in South Puget
 Sound, a largely undeveloped area subject to extensive
 future urbanization that also is potentially sensitive to
 impacts from eutrophication. The goal of the ORCA
 Project was to use the long-term, high-resolution dataset
 collected with the profiler to monitor tidal, diel, seasonal,
 and interannual cycles and trends in stratification, dis-
 solved oxygen (DO) concentrations, nutrients, and phy-
 toplankton abundance.
    ORCA has three main components: (1) a three-point
 moored autonomous temperature line acquisition system
 toroidal float; (2) a housed platform equipped with a com-
 puter, winch,  cellular system, meteorological sensors
 (wind, temperature, humidity, irradiance), solar panels,
 and batteries; and (3) an underwater sensor package con-
 sisting of a Seabird conductivity, temperature, and depth
 (CTD) profiler, DO electrode, Wetlabs transmissometer,
 Wetlabs chlorophyll fluorometer, and a recently added
 WS Ocean EcoLab nutrient sensor. ORCA profiles the
 water column at regular sampling intervals,  using the
 pressure information from the CTD to run the winch.
 The data are recorded on the computer and transmitted
 back to the laboratory automatically via cellular commu-
    The dataset that ORCA  has collected in the last 2
 years reveals a covariation in temperature, salinity, oxy-
 gen, and chlorophyll, indicating a tight coupling between
physical and biological processes. As seen in the 2002
data (see Figure 1), the water column was well mixed
during the winter and early spring, with low DO and chloro-
phyll concentrations both at the surface and at depth.
Variability in wind, rainfall, and sunlight forced changes
in surface temperature and salinity, producing intermit-
tent periods of either strong stratification or deep mixing
throughout the summer.
   At depth, temperature and salinity steadily increased
during the summer. Chlorophyll and oxygen covaried,
with a maximum chlorophyll concentration of 12.113 mg
nr3,  observed at the  surface during a spring bloom in
April, resulting in an oxygen concentration of 440.45
(imol kg'1 (154.15% saturation).
   Following the bloom, the chlorophyll maximum
moved subsurface, varying between 5 and 10 meters. At
depth, chlorophyll concentrations remained low through-
out the year, while oxygen, undersaturated in the winter,
increased steadily during the spring to near saturation in
   A box model calculation of the 2000 data suggests
that oxygen variation primarily is a result of gas exchange
and net biological oxygen production, and that oxygen
production is largely  dominated by photosynthesis. Net
biological oxygen production in the summer of 2000 had
a mean value of 0.2 mol m~2d~'. This value is nearly equal
to I4C uptake productivity measured over the same time
period, indicating that there is very little respiration oc-
curring in the euphotic zone during the summer months.
   ORCA will continue to gather data through 2002,
which will be combined with the existing data to further
refine the box model terms and calculations as well as
provide a better understanding of oxygen variability and
other processes in the South Sound.
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                                  CISNet Final Progress Review Workshop
                                          Temperature (°C)
                                   Mar          Apr
                                         Time (month in 2002)
Figure 1.   Maps of temperature (°C), salinity, density (c). oxygen (U.M kg"1), oxygen saturation (%). and
           chlorophyll fluorometry (mg m~3) versus pressure (decibars) and time (yearday) from Carr Inlet, Puget
           Sound (January 1, 2002-July 22, 2002).
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                                  CISNet Final Progress Review Workshop
 Rhode River CISNet:  Estuarine Optical Properties as an Integrative
              Response  to Natural and Anthropogenic Stressors

                     Charles L. Gallegos,  Thomas E. Jordan, and Patrick J. Neale
                     Smithsonian Environmental Research Center, Edgewater, MD
    The primary objective of the Rhode River CISNet
 was to develop monitoring of estuarine spectral optical
 properties as an integrated measure of estuarine response
 to perturbations.  Research to interpret continuously
 monitored optical properties focused on: (1) determina-
 tion of the concentrations of suspended particulate
 matter (SPM), phytoplankton chlorophyll, and colored
 dissolved organic matter (CDOM); (2) quantification of
 nutrient inputs and their effects on concentrations of chlo-
 rophyll, SPM, and CDOM; and (3) research to examine
 the effects of solar ultraviolet (UV) radiation on near-
 shore plankton communities, as influenced by potential
 changes in estuarine optical properties.
   The approach  combined automated monitoring to
 measure salinity as a surrogate for nutrient inputs and
 inherent optical properties to gauge system responses, in
 situ measurements of nutrient concentrations and benthic
 nutrient fluxes, and experimental measurements of bio-
 logical weighting function (BWF) of phytoplankton re-
 sponse to UV radiation. Optical data and BWF were used
 to model phytoplankton photosynthetic response to UV
   Almost 2  full years of data on  continuously moni-
 tored inherent optical properties  were obtained. The
 seasonal pattern in absorption coefficient  appeared
 remarkably similar in the 2 years (see Figure 1), although
 differences in magnitudes of spring and fall blooms be-
 tween the 2 years were apparent. Salinity monitors docu-
mented that the onset of the spring blooms was initiated
by the spring freshet of the Susquehanna River. Together,
the 2 years of hourly data on inherent optical properties
gave an unprecedented picture of the optical variability
in a shallow coastal system.
   Measurements of sediment nutrient release rates re-
vealed a high degree of spatial and temporal variability.
Rates of ammonium release appeared to largely follow
the temperature cycle, with peak rates occurring in June
to July. Phosphate release rates peaked later than ammo-
nium release. The nitrogemphosphorous (N:P) ratio for
benthic nutrient release rates appeared to average approxi-
mately 4, which is similar to the average N:P ratio of
sediment discharged from the local watershed.
   Variations in  irradiance-dependent BWFs showed
considerable variation in BWFs within each season. The
average, absolute spectral weightings for inhibition of
photosynthesis in phytoplankton assemblages from the
Rhode River was similar to an average BWF for Antarc-
tic assemblages.
   The monitored inherent optical properties and esti-
mates of diffuse attenuation coefficients derived from
them documented the effect of eutrophication on degra-
dation of the underwater light climate for supporting sub-
merged aquatic vegetation in this system. Both remote
(i.e., Susquehanna River) and local (i.e., benthic release)
sources of nutrients were shown to be important in fuel-
ing eutrophication. The models of phytoplankton photo-
synthetic response showed that UV radiation contributed
to wide daily swings  in inhibition, ranging  between a
maximum of 35 percent and a minimum of 5 percent of
daily water column production.
   Ongoing work will extend the geographical extent of
the inventory of inherent optical properties. This will be
used in radiative transfer modeling to develop indicators
of habitat suitability for submerged aquatic  vegetation
using data available from government-sponsored wa-
ter quality monitoring networks  throughout the Mid-
Atlantic States.
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                                CISNet Final Progress Review Workshop
          0    30    60    90    120   150    180   210   240   270   300   330   360

                                           Day of Year

Figure 1.  Time-series of hourly monitored absorption coefficient at 440 nm [total less that due to water,
          at H.(440)] in the Rhode River, MD. The seasonal pattern is driven by the spring phytoplankton bloom
          (approximately day 100-145), and a gradual increase in absorption by nonalgal particulates during the
               The Office of Research and Development's National Center for Environmental Research

                                 CISNet Final Progress Review Workshop
 CISNet for the Neuse River Estuary, NC:  A Program for Evaluating
       Nitrogen-Driven  Eutrophication Associated With Changing
                          Land Use  in a Coastal Watershed

                            Rick Luettich, Hans Paerl, and Jay Pinckney
             University of North Carolina Institute of Marine Sciences, Morehead City, NC
    During the past 2 decades, the Neuse River Estuary
 (NRE) has been plagued with nuisance algal blooms,
 hypoxia, toxicity, and fish kills associated with declining
 water quality. Increased nitrogen (N) loading has been
    In 1997, the State of North Carolina legislated a 30
 percent reduction in external N loading to the NRE by
 2003. hi 1999,  Hurricane Fran caused 100-500 year
 flooding in the Neuse River Basin and generated an ex-
 treme loading event to the NRE. Both the longer term
 load reduction and the extreme, episodic loading repre-
 sent large-scale manipulations to the NRE and provide
 the opportunity to examine the effects of nutrients on the
    In 1998, a suit brought by the Neuse River Founda-
 tion against the U.S. Environmental Protection Agency
 (EPA) was settled, resulting in an agreement by the State
 of North Carolina to set a formal total maximum daily
 load (TMDL) for total N for the NRE. This CISNetproject
 has contributed substantially to the development of this
    The approach has  included field-based studies of:
 (1) hydrography, nutrients, dissolved oxygen (DO), and
 light and phytoplankton dynamics; (2) atmospheric N in-
 puts; and (3) circulation in the NRE-Pamlico Sound sys-
 tem. The project has focused on DO and the planktonic
 microalgal community as easy-to-measure indicators of
 biotic response of this ecosystem to external stressors. DO
 depletion restricts benthic habitat and plays a causal role
 in fish kills. Phytoplankton dominate primary production
 and nutrient fluxes. A natural attribute of the phytoplank-
 ton—photopigments (determined by high-performance
 liquid chromatography coupled to spectrophotometry)—
have been utilized to rapidly and effectively distinguish
major phytoplankton functional groups.
   This research has  provided quantitative data on:
(1) the role of atmospheric loading  in the delivery of N
to the NRE; (2) circulation patterns in the NRE, includ-
ing wind-driven upwelling of low-oxygen bottom water
in the near-shore regions (a causal mechanism for fish
kills); and (3) the response of microalgal communities
to several years of N loading. The most dramatic re-
sponse occurred following Hurricane Floyd, when the
organic and inorganic nutrient load caused extensive
bottom-water hypoxia and the development of an algal
bloom (chlorophyll-a levels above 20 pg/L compared
to typical values of approximately 3-6 Hg/L) at  the
mouth of the NRE. Diagnostic pigment analysis indi-
cated a shift toward mainly freshwater species with low
diversity. Physical, microalgal, and DO conditions in
the NRE appeared to return to near normal during the
summer of 2000.
    The NRE may be expected to respond very differ-
ently to long-term chronic stress and short-term episodic
stress. This grant has allowed the research group to build
toward time-series that are capable of separating long-
term trends from interannual variability in the NRE. It
also has provided the unprecedented opportunity to  ob-
serve the ecological consequences of an extreme event
in the NRE. Understanding the relative roles of chronic
and event-based stressors is critical for determining the
effectiveness of nutrient reduction in the NRE, given the
forecast of enhanced hurricane activity for the next 20
    To meet the State of North Carolina's responsibility
to establish a TMDL for total N, three water quality mod-
els were developed for the NRE from 1999-2001. Data
collected in the NRE as part of this grant were crucial for
calibrating and verifying these water quality models (see
Figure  1). The State of North Carolina submitted the N
TMDL to the U.S. Environmental Protection Agency
(EPA) for review in December 2001.
   The CISNet research efforts have been expanded to
include the response of Pamlico Sound (which lies down-
stream of the NRE), aircraft remote sensing of algal pig-
ments, and comparative studies in other East Coast estu-
aries. Funding for this work is being provided in part by
an EPA grant from the Esruarine and Great Lake Ecosys-
tems Program.
               The Office of Research and Development's National Center for Environmental Research

                                   CISNet Final Progress Review Workshop
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Figure 1.  Comparison between 3 years of observed data and model output from the Neuse Estuary
           Eutrophication Model at upstream (Station 30) and downstream (Station 120) stations in the NRE.
           Results from this and two other water quality models were used to determine a TMDL on total N for
           the NRE.
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                                  CISNet Final Progress Review Workshop
         The  Choptank River:  A Mid-Chesapeake Bay Index Site
                      for Evaluating Ecosystems Responses
                               to  Nutrient Management

                     Thomas C. Malone, Jeffrey C. Cornwell,  William  C. Boicourt,
                          Lawrence W. Harding, Jr., and J. Court Stevenson
   Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD
    The primary goal of this research project was to de-
 velop and examine methods for detecting responses to
 anthropogenic stresses in the Choptank River Index Site
 and to establish the Site as a sentinel of change for a
 broader domain of coastal plain ecosystems. Of particu-
 lar interest are the impacts of meteorological fluctuations
 and nutrient management in the Choptank drainage ba-
 sin on water quality and living resources in the estuary.
 The intent is to: (1) resolve responses caused by human
 activities from the variability imposed by nature, (2) de-
 velop key indices of ecosystem change, and (3) predict trends
 and their consequences. The strategy has been to use
 modem, high-intensity, high-resolution sampling and ana-
 lytical tools in conjunction with the historical record to
 understand these changes.
    The use of high temporal resolution nutrient and
 physical measurements at few sites was contrasted to simi-
 lar measurements taken at the monthly time scale over
 large spatial scales.  The use of buoys, airborne remote
 sensing equipment,  and research vessels provided dif-
 ferent views of estuarine processes. Nutrient retention
 within the tidal wetlands in the Choptank River Estuary
 was assessed using  210Pb-dated cores at a large number
 of sites. Small-scale (tens of meters) variability in sedi-
 ment and nitrogen (N) and phosphorus (P) burial have
 been compared to that observed over a larger (tens  of
 kilometers) scale, with a goal of optimizing the extrapo-
 lation of nutrient burial rates to the whole system.
   Highlights from within the Choptank CISNet Site
 Program were the construction of nutrient burial esti-
mates from core analyses, the successful measurement
of high-resolution time-series observations, and the pro-
duction of an interactive geographic information sys-
tem-based data structure for delivery to a wide variety
of users. The expansion of the time-series observations
occurred not only through internal CISNet efforts, but
also through linking and collaboration with related pro-
   Core analysis from the Choptank River CISNet Site
indicated that sedimentation rates varied from less than
1 kg m~2 y' to more than 5 kg nr2 y1. Estimates of N and
P burial were 8-43 g nr2 y1 and 0.5-3.7 g nr2 y1 (n =
23), respectively, clearly indicating that these tidal marsh
sediments are important sinks for N and P in this system.
Trends in water column N and P over the 3-year CISNet
Program were dishearteningly upward throughout the up-
per Choptank River (see Figures 1 and 2).
   The results of this program have  shown  how:
(1) different scales of observation provide similar ideas
of estuarine processes; (2) the inclusion of marsh pro-
cesses, particularly in a system with relatively high rates
of sea level of rise, is  important for understanding estua-
rine nutrient balances; and (3) cooperative data catalog-
ing efforts involving citizen monitoring can provide im-
portant information needed for local decisionmaking.
   The award of the STAR Grant to the ACE INC EaGLe
Program provides a mechanism to continue a portion of the
CISNet Program, and thereby allow a longer term assessment
of the effects of land use on ecosystem health. Sea Grant-
funded efforts on understanding oyster restoration have ben-
efited from this improved understanding of the estuary.
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                                 CISNet Final Progress Review Workshop
                                    CISNET 1999-2001
Figure 1.   Contour plot of CISNet total nitrogen (TN) data. The vertical axis is distance from the mouth of the
           river. The horizontal axis is time, with all sampling dates indicated. The contours are of total nitrogen.
           with the spatial trends driven mainly by changes in nitrate concentration. The high TN concentrations
           at the freshwater end of the estuary have increased in the last decade. Nitrogen inputs are largely from
           diffuse sources.
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Figure 2.   Contour plot of total phosphorus data. The highest concentrations are located in the part of the upper
           river receiving inputs from a sewage treatment plant.
                The Office of Research and Development's National Center for Environmental Research

                                 CISNet Final Progress Review Workshop
             CISNet:  Molecular to Landscape-Scale Monitoring
                              of Estuarine Eutrophication

    James T. Morris, Madilyn Fletcher, John Jensen, Alan Lewitus, Peter Noble, and Dwayne Porter
                  Belle W. Baruch Institute for Marine Biology and Coastal Research,
                             University of South Carolina, Columbia, SC
    This research group investigated: (1) molecular ap-
proaches (polymerase chain reaction/denaturing gradi-
ent gel electrophoresis,  pigments) for quantifying
changes in the composition and abundance of bacterial
andphytoplankton communities among South Carolina
estuaries; (2) the dependence of plankton community
composition on water quality; (3) spatial and temporal
variation in canopy chlorophyll density in salt marshes;
(4) technologies for remotely sensing canopy chloro-
phyll density; and (5) neural net technologies for clas-
sifying remote images and microbial communities.
   High-performance liquid chromatography (HPLC)
pigments have been analyzed from taxonomically diverse
algal species acclimated to growth at saturating or limit-
ing light, and harvested from exponential or stationary
growth phase. The CHEMTAX algorithm has been cali-
brated to predict community composition. Neural net-
works successfully have been trained to HPLC pigment
profiles and environmental data, and correlative relation-
ships between pigments and physicochemical properties
have been found. Seasonal differences in community
composition and differences among estuaries will be dis-
   In situ radiometric and biophysical (chlorophyll, bio-
mass) data were obtained seasonally at approximately
                                     50 locations within each of the Spartina alterniflora-
                                     dominated study areas in the North Inlet Estuary and the
                                     Ashepoo-Combabee-Edisto (ACE) Basin. The biophysi-
                                     cal data were correlated to leaf radiance data collected
                                     using the field spectrometer and with remotely sensed
                                        Spectrophotometer scans of plant leaves from experi-
                                     mentally fertilized plots have demonstrated that signifi-
                                     cant differences exist between  treatments in reflected
                                     light. Significant differences in canopy chlorophyll den-
                                     sity were found between the North Inlet and ACE Basin
                                     Estuaries, and it was shown that the chlorophylhbiomass
                                     ratio varies seasonally.
                                        Existing regression models (e.g., Normalized Differ-
                                     ence Vegetation Index) were used to fit chlorophyll den-
                                     sity to brightness values  from Airborne Data Acquisition
                                     and Registration (ADAR) imagery. In addition, a neural
                                     net was trained to classify ADAR imagery (see Figure 1)
                                     and predict canopy chlorophyll  density. The neural net
                                     model was significantly better at predicting chlorophyll
                                     than traditional regression approaches. A neural network
                                     is proving to be an excellent tool for classifying coastal
                                     landscapes. Excellent resolution of wetland areas, open
                                     water, and uplands has been found using this approach
                                     (see Figures 1 and 2).
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                                  CISNet Final Progress Review Workshop
                                                            North Inlet
                                H water
B                                   marsh
                                  no data
Figure 1.  Neural network classification of North Inlet intertidal marshland and open water based on an ADAR
           image with a 60 cm spatial resolution.
1.2 -,

w 1.0-
0 0.8 -
re 0.6 -
ID a4 -

J~~ 0.2 -

O 0.0-


Water, n=35

Other. n=81
•••^•••••^M* •• •
stated Marstr n=383


                                  -0.2  0.0   0.2   0.4   0.6   0.8   1.0   1.2   1.4
                                             Predicted Categories

Figure 2.  Observed and neural net predicted classification categories from North Inlet Estuary. Results show
           perfect separation between water and other classes. The overlap between marsh and other categories
           was 8 percent of the total number of samples, 466, in those two classes. The overlap represents
           transition area.
                The Office of Research and Development's National Center for Environmental Research

                                   CISNet Final Progress Review Workshop
  CISNet San Pablo  Bay Network  of Environmental  Stress Indicators

                S. Geoffrey Schladow1, Thomas M.  Young1, Inge Werner2, Bruce Thompson3,
                           Jay Davis3, Nadav Nur4, and David Schoellhamer5
  'Department of Civil and Environmental Engineering, University of California, Davis, CA; Department
          of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine,  University
      of California, Davis,  CA; 3San Francisco Estuary Institute, Richmond, CA; 4Point Reyes Bird
               Observatory, Stinson Beach,  CA; 5U.S.  Geological Survey, Sacramento, CA
    San Pablo Bay and its surrounding rivers, sloughs,
 and marshlands, is a highly complex and energetic es-
 ruarine system that is subject to the influence of several
 major environmental stressors. These include sediment
 loads; heavy metal and pesticide residues from Cal-
 ifornia's Central Valley, the Sierra Nevada, and the coastal
 range; the impact of a population of more than 7,000,000
 people; and industrial waste from the San Francisco Bay
 Area (including several oil refineries). The objective of
 this project was to assess the adequacy of conventional
 monitoring protocols, test potential indicators, and de-
 sign a monitoring network that is temporally and spa-
 tially compatible with the system's inherent complexity.
    The approach was based on investigating linkages
 between waterbome and sediment-borne contaminant
 fluxes and toxicity. A network of intensive and interme-
 diate measurement stations was established. Measure-
 ments included the continuous acquisition of current, tem-
 perature, salinity, and suspended sediment concentration
 data, as well as monthly water and sediment sampling.
    Biochemical, cellular, and histological indicators  of
 ecological stress in resident clams (Macoma spec.,
 Potamocorbula amurensis) and amphipods (Ampelisca
 abdita) were analyzed to foretell subtler and possibly
 longer term consequences of exposure to chemicals  in
 the environment. Ecological stress indicators considered
 included number and diversity of species within benthic
 assemblages, contaminant bioaccumulation in fish tis-
 sue, and reproductive success for two bird species,
 double-crested cormorants (Phalacrocorax auritus) and
 song sparrows  (Melospiza melodid).
    From the standpoint of hydrodynamic and sediment
 transport processes, the system presents tremendous com-
 plexity, in both a spatial and temporal sense. Of the areas
 studied in greatest detail, the Napa River and the Petaluma
 River, both have a unique and somewhat singular set of
 controlling factors. In the Napa River, there is baroclinic
 flow convergence arising due to a phase mismatch at the
junction  of two  tidal channels. By contrast, in the
                                      Petaluma River there is the formation of a transitional
                                      sediment storage zone, driven by the interaction of the
                                      semidiurnal tides with the river-estuary interface.
                                         Both mechanisms lead to the concentration of sus-
                                      pended sediment in a relatively small geographic zone.
                                      For sediment-borne contaminants—both organic and in-
                                      organic—this has led to local "hot spots" in both areas.
                                      Benthic assemblage sampling at the Petaluma River Site
                                      showed unusually high species diversity and high abun-
                                      dances coupled with the presence of many opportunistic
                                      and contamination-tolerant species, suggesting that this
                                      station may be impacted. In addition, seasonal "first flush"
                                      phenomena have been responsible for observations of
                                      organic contaminants several orders of magnitude above
                                      observations from regional monitoring efforts.
                                         Indicator species, such as P. amurensis, showed mark-
                                      edly reduced survival when exposed to sediments from
                                      the Napa and Petaluma Rivers (see Figure 1). Tidal marsh
                                      song sparrow nest success is low both in San Pablo Bay
                                      and the adjoining Suisun Bay, although further analysis
                                      is required to ascertain whether the population viability
                                      is at risk, and the role (if any) that aquatic contaminants
                                         The results suggest that spatial and temporal varia-
                                      tions in the study system are discontinuous, and that char-
                                      acterizing such a system requires a priori knowledge of
                                      where and when to conduct sampling. Whereas many of
                                      the sampling locations yielded information similar  to a
                                      parallel regional monitoring program, the greater inten-
                                      sity of observations allowed for a vastly different picture
                                      of contaminant transport and flux to emerge.
                                         Future research is centered on better characterization
                                      of the hydrodynamic flows to identify those areas most
                                      likely to harbor conditions of contaminant accrual. Sen-
                                      sor development, to provide more continuous chemical
                                      data in remote and hostile conditions, is a further  key
                                      area of research. This approach is being carried forward
                                      in several parallel research efforts.
The Office of Research and Development's National Center for Environmental Research

                                CISNet Final Progress Review Workshop
                               Percent Survival of Potamocorbula amurensis
                                            (February 2001)


 80 -


 40 -

                        Control    M14     M19     MIC     PET

                                            Sediment Source
Figure 1.  Survival (%) of Potamocorbula amurensis exposed for 10 days to sediments from sampling sites in
          San Pablo Bay and adjacent marshes (mean and standard error). Sediments were collected in February
          2001. Sites MIC and PET were from the Napa and Petaluma Rivers, respectively.
               The Office of Research and Development's National Center for Environmental Research

                                  CISNet Final Progress Review Workshop
      CISNet:  Nutrient Inputs as a Stressor and Net Nutrient Flux
              as  an Indicator of Stress  Response  in  Delaware's
                                  Inland Bays  Ecosystem

           William J. Ullman'-2, Kuo-Chuin Wong', Joseph R. Scudlark1, John M. Madsen'2,
                   David E. Krantz'-2-4, A. Scott Andres3, and Thomas E. McKenna3
         'College of Marine Studies, Department of Geology, and 3Delaware Geological Survey,
        University  of Delaware, Lewes, DE, and Newark, DE; Department of Earth, Ecological,
                     and Environmental Sciences, University of Toledo, Toledo, OH
    This project focused on the input and cycling of
 nutrient elements (nitrogen [N], phosphorus [P], car-
 bon, and silicon) in the Delaware Inland Bays, a mem-
 ber of a common but understudied class of shallow
 coastal plain estuaries. Subprojects encompassing sur-
 face and groundwater discharge, atmospheric deposition,
 water-salt-nutrient exchanges with the ocean, and inter-
 nal cycling within the Bays have been pursued during
 the last 4 years.
    Surface water discharges and nutrient loads were
 measured at sites  representing the range of land uses
 and land cover common in this system. For the agri-
 cultural subwatersheds, the total dissolved nitrogen
 (TON) loading ranged from 21  to 23 kg/ha/yr. TON
 loading for a forested subwatershed was substantially
 lower (4 kg/ha/yr). TDN loading for the most  urban-
 ized subwatershed was only 2 kg/ha/yr. Total phos-
 phorus loading ranged from 0.008 to 0.35 kg/ha/yr,
 with both  agricultural and urbanized watersheds sig-
 nificantly contributing. The CISNet Water Quality
 Database (
 DATA/) currently is being used by the State of Dela-
 ware to establish total maximum daily load targets for
 the watershed.
   The areal distribution of groundwater discharges
 to the Bays was determined by thermal infrared imag-
 ery of the Bay margins. In addition, seismic, resistiv-
 ity, hydrogeological, and stratigraphic surveys were
 conducted along the margins and across the Bays to
determine  the extent to which groundwater transport
and discharge were focused by the underlying geol-
ogy. At some sites, discharge was measured directly;
at other sites, techniques  to determine discharge are
still under investigation.
                                        Atmospheric deposition to the watershed was estimated
                                     from preexisting and new data. Atmospheric ammonia
                                     (NH3g) concentrations varied from 0.1 to 14 ug/m3, with
                                     the highest values measured in poultry production areas.
                                     Highest NH3 a concentrations were found in the spring and
                                     summer when fertilizer application is greatest and poultry
                                     production facilities are most intensively ventilated. A study
                                     of NH3 e concentrations around poultry production facili-
                                     ties is being used to estimate the extent to which local ver-
                                     sus distant sources of atmospheric N contribute to load-
                                     ings to the watershed.
                                        The distribution of nutrients in the Bays, at tributary
                                     discharges, and at ocean discharges has been monitored.
                                     Patterns of nutrient distribution reflect both seasonal pat-
                                     terns of biogeochemical cycling within the Bays and hy-
                                     drological forcing. Generally, dissolved N concentrations
                                     reflect inputs from the watershed, and dissolved P concen-
                                     trations reflect patterns of internal cycling of particles and
                                     inputs from wastewater discharges and the ocean. N/P ra-
                                     tios of waters and of plankton vary seasonally and spatially,
                                     and reflect changing patterns of nutrient limitation.
                                        Temperature, salinity, and current surveys were con-
                                     ducted at the principal hydrographic boundaries in the Bays.
                                     These data have been used to determine the tidal and
                                     nontidal contributions to discharge,  and the intra- and
                                     interannual variability in these contributions. Both local
                                     and remote wind effects contribute to subtidal exchange
                                     within the Bays. These results currently are being used to-
                                     gether with nutrient data to estimate the role of tidal and
                                     nontidal flows on the exchange of nutrients between the
                                     Inland Bays and the coastal ocean. In addition, these data
                                     were used to develop a new hydrodynamic/water quality
                                     model for the Inland Bays that already is being used by
                                     State of Delaware managers.
The Office of Research and Development's National Center for Environmental Research

               CSINet Final Progress Review Workshop
                  Index of Authors

                      Anderson, S., 1
                      Emerson, S., 2
                      Gallegos, C.L., 4
                      Luettich, R., 6
                      Malone, T.C., 8
                      Morris, J.T., 10
                      Schladow, S.G, 12
                      Ullman, W.J., 14
The Office of Research and Development's National Center for Environmental Research        15