Workshop Ab
Coastal Intensive
Site Network (CISNet)
Final Pro
Workshop
September 4-5,2002
Edgewater, Maryland
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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
Introduction
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: http://www.epa.gov/ncer/centers/eagles/.
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 perovich.gina@epa.gov. For further informa-
tion about the EaGLe Program, please contact Barbara Levinson by telephone at 202-564-6911 or by e-mail at
levinson.barbara@epa.gov.
To learn more about EPA's STAR Program, visit NCER's Web Site at: http://www.epa.gov/ncer.
The Office of Research and Development's National Center for Environmental Research iii
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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-
nications.
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
mid-summer.
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
OI—T
Temperature (°C)
Jan
Mar Apr
Time (month in 2002)
Jui
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
radiation.
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
summer.
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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
implicated.
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
ecosystem.
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
TMDL.
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
years.
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.
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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-
grams.
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
TN
Cambridge
STP
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2000
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
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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-
cussed.
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
data.
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).
10
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CISNet Final Progress Review Workshop
North Inlet
Classification
Key
H water
B marsh
transition
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Figure 1. Neural network classification of North Inlet intertidal marshland and open water based on an ADAR
image with a 60 cm spatial resolution.
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Veg<
Water, n=35
Max=0.39
Other. n=81
•••^•••••^M* •• •
Win
=0.611
!
t
stated Marstr n=383
Min
=0.46
Max
=0.77
-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
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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
play.
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.
12
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CISNet Final Progress Review Workshop
Percent Survival of Potamocorbula amurensis
(February 2001)
120
100
80 -
60
40 -
20
T
Control M14 M19 MIC PET
Sediment Source
SOCR
CAN
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.
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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 (http://www.udel.edu/dgs/ftp/cisnet/CHEM-
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.
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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
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