2003 Progress Report: Phytoplankton Community Structure as an Indicator of Coastal Ecosystem Health

EPA Grant Number: R828677C001
Subproject: this is subproject number 001 , established and managed by the Center Director under grant R828677
(EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).

Center: EAGLES - Atlantic Coast Environmental Indicators Consortium
Center Director: Paerl, Hans
Title: Phytoplankton Community Structure as an Indicator of Coastal Ecosystem Health
Investigators: Paerl, Hans , Blackwood, Denene , Fear, John M. , Fulcher, Crystal , Gallo, Thomas , Gregory, Jason , Hall, Nathan , Luettich Jr., Richard A. , Noble, Rachel T. , Peierls, Benjamin , Pinckney, James L. , Reynolds-Fleming, Janelle V. , Rosignol, Karen , Valdes, Lexia M. , Waggener, Amy , Weaver, Richard , Whipple, Anthony , Wyrick, Pamela
Current Investigators: Paerl, Hans , Fries, Steven , Luettich Jr., Richard A. , Noble, Rachel T. , Pinckney, James L. , Valdes, Lexia M. , Wyrick, Pamela
Institution: University of North Carolina at Chapel Hill , Texas A & M University
Current Institution: University of North Carolina at Chapel Hill
EPA Project Officer: Hiscock, Michael
Project Period: March 1, 2001 through February 28, 2003
Project Period Covered by this Report: March 1, 2002 through February 28, 2003
RFA: Environmental Indicators in the Estuarine Environment Research Program (2000) RFA Text |  Recipients Lists
Research Category: Ecological Indicators/Assessment/Restoration , Water , Ecosystems


The objective of this research project are to: (1)develop broadly-applicable, phytoplankton- and other microbial (bacterial viral) based indicators of estuarine and coastal ecological condition; (2) link these to nutrient and physical-chemical forcing features and remote sensing analyses of water column optical properties; (3) incorporate these indicators in state and federal (U.S. Environmental Protection Agency [EPA]) water quality/habitat assessment and compliance programs, including total maximum daily load (TMDL) formulations for the Neuse River Estuary and other regional/national estuarine systems.

Progress Summary:

The Atlantic Coast Environmental Indicators Consortium (ACE INC), “Phytoplankton Community Structure as an Indicator of Coastal Ecosystem Condition” component has been operational since April 2001. All aspects of the proposed work plan are in place and coordinated with ongoing water quality and habitat monitoring programs on the Neuse River Estuary (NRE), and a ferry-based water quality monitoring program for the NRE and Pamlico Sound (PS). These programs (ModMon and FerryMon) have served as the backbone for the collection of nutrient, photopigment (chlorophylls and carotenoids), productivity, water optical property turbidity and physical data needed to characterize the structure, function and environmental controls of indicator phytoplankton communities comprising the base of the estuarine food Web. We have been collecting comprehensive diagnostic (of phytoplankton community composition) photopigment samples that will serve to establish a baseline of phytoplankton community composition against which we will be able to gauge trophic state and ecological change in response to a wide variety of environmental forcing features, including; nutrient inputs, salinity (reflecting freshwater inputs and residence time), water clarity and other optical properties, zooplankton, grazing and toxic substances. We also have been collecting in situ hydrographic, dissolved oxygen, and water velocity data to allow calculation of the residence time in the system. Lastly, during the summer of 2003, we initiated boat and ferry-based sampling for bacterial pathogens as indicators of human and other waste pollution sources to the NRE and Pamlico Sound.

Using Phytoplankton Photopigments to Assess Estuarine Ecological Condition and Change

Photopigment indicators have proven to be highly-sensitive, diagnostic indicators of seasonal and interannual changes in hydrologic and nutrient inputs to these systems (Pinckney et al., 2001, 2002; Paerl et al., 2001; Paerl et al., 2002, Paerl et al., 2003). Our long-term vision of the regional deployment and interpretive use of photopigment indicators is shown in Figure 1. Note the strategic location of these indicators in the context of estuarine and coastal ecosystem function and resource value.

Roles of Diagnostic Photopigments as Indicators of Ecosystem Productivity and Plant Community Composition in Response to Physical-Chemical Stressors in Estuarine and Coastal Waters

Figure 1. Roles of Diagnostic Photopigments as Indicators of Ecosystem Productivity and Plant Community Composition in Response to Physical-Chemical Stressors in Estuarine and Coastal Waters

Specific chlorophyll and carotenoid photopigments are diagnostic for certain phytoplankton taxonomic groups (chlorophytes, cryptophytes, cyanobacteria, diatoms, dinoflagellates). Concentrations of these photopigments have been determined from HPLC analysis of bi-weekly surface and bottom water samples collected since 1994 in the NRE and since October 1999 in PS. We recently have been able to generate annual, seasonal, and spatial trends in the relative and absolute abundances of these phytoplankton taxonomic groups using ChemTax analysis of the long-term photopigment data (see Figure 2). These trends have allowed us to determine the response of phytoplankton communities to the combined stresses of anthropogenic nutrient enrichment, droughts (reduced flushing combined with minimal nutrient inputs), and increased hurricane frequency (high flushing accompanied by elevated nutrient inputs) that have influenced these systems since 1994. Figure 2 shows how these distinct perturbations have affected mean annual total chlorophyll a concentrations and mean annual phytoplankton community structure within specific geographic regions of the NRE/PS. Trends in mean annual total chlorophyll a concentrations were found to vary between regions of the NRE/PS. For example, the Upper Neuse River showed greater mean annual total chlorophyll a concentrations in years characterized by reduced river flushing rates (1994, 1997, 2000-2002), whereas mean annual total chlorophyll a concentrations in the other regions of the Neuse River did not seem to be as significantly affected by these changes in hydrology (see Figure 2). Changes in flushing rates and thus water residence time appear to control mean annual total phytoplankton abundance (as chlorophyll a concentration) in the Upper Neuse River. These hydrologic changes also had a dramatic effect on the historic phytoplankton composition of the Upper Neuse River (see Figure 2). During years characterized by increased river flushing rates (1995, 1996, 1998, and 1999), dinoflagellates demonstrated significantly reduced abundance when compared to their abundance during dry years. Slower-growing dinoflagellates are thus sensitive and ecologically-relevant indicators of changes in hydrology in the Upper Neuse River, as they appear to be more abundant during periods of long residence time, when flushing rates are minimal.

Mean Annual Surface Concentrations of Chlorophyll

Figure 2. Mean Annual Surface Concentrations of Chlorophyll a Contributed by Chlorophytes, Cryptophytes, Cyanobacteria, Diatoms, and Dinoflagellates in the Upper, Middle, and Lower Portions of the NRE and in the Southwest and Southeast Regions of PS. Data were collected in the upper and middle portions of the NRE since 1994; data from the lower NRE and PS were collected since 1997 and October 1999, respectively. Values were derived from ChemTax analysis of bi-weekly diagnostic photopigment concentrations.

The Southwest and Southeast regions of PS demonstrated very similar trends in mean annual phytoplankton abundance and composition, with the exception that dinoflagellates were more abundant in the region closest to the NRE (Southwest region) (see Figure 2). Spatially, these long-term data have shown that the highest mean annual total chlorophyll a concentrations in the NRE/PS generally occurred in the Middle Neuse River region. Spatial trends in mean annual phytoplankton composition demonstrated that dinoflagellates were less abundant in the two PS regions when compared to the three Neuse River regions. In the NRE/PS, mean annual abundance of dinoflagellates was generally greater in the Middle and Lower portions of the Neuse River.

The three sequential fall 1999 hurricanes (Dennis, Floyd, and Irene) had an effect on total phytoplankton abundance and composition in the NRE/PS (see Figure 2). These hurricanes delivered a large amount of rainfall and increased nitrogen loads to the NRE/PS system. As a result, mean annual total chlorophyll a concentrations in the Middle Neuse River peaked in 2000, the year immediately following the hurricanes. In addition, all phytoplankton taxonomic groups increased in mean annual abundance in 2000 in both the Upper and Middle regions of the Neuse River. In the two PS regions, mean annual total chlorophyll a concentrations were significantly greater immediately following the hurricanes than in the more recent years. Gradual decreases in total chlorophyll a concentrations were evident in both regions of PS with each successive year following the 1999 hurricanes, indicating that this system may have still been recovering from the effects of these hurricanes through 2001. Phytoplankton community structure in the two regions of PS has changed since the period immediately following the hurricanes from a community dominated by chlorophytes, cryptophytes, cyanobacteria, and diatoms to one primarily dominated by cyanobacteria and diatoms in 2001 and 2002.

These trends have demonstrated how phytoplankton taxonomic groups are remarkably sensitive to environmental perturbations. Differences in seasonal total abundance and community structure between years also are being examined to identify the impacts of these environmental perturbations on a finer scale.

The reconstructed phytoplankton taxonomic composition for Chesapeake Bay (see Figure 3) also shows strong contrasting responses between dominant phytoplankton groups during the spring and summer due to the variability of freshwater flow and nutrient loading. This pattern is strongest in the spring-early summer wherein high flow alleviates N limitation of the mid to lower estuary and supports diatom blooms in the spring, and sometimes in the summer. Low flow produces improved photic conditions but causes an expanded zone of N limitation in the main stem of the bay during the summer, thereby changing phytoplankton dominance to those groups that can grow efficiently under these conditions.

Mean Annual Surface Concentrations of Chlorophyll

Figure 3. Regional Means ± s.e. (1995 – 2000) for Chlorophyll (mg m-3) and the Relative Abundance (fraction chl-ataxa) of Phytoplankton Groups Determined by ChemTax. One approach to developing indicators from measurements of phytoplankton biomass and composition is to define the ‘average’ conditions, as shown above, and then conduct analyses of deviations (seasonal, regionally, inter-annually) in relation to differences in environmental forcing functions and patterns of primary production.

H. Paerl and L. Valdes of the Neuse River Estuary/Pamlico Sound component of ACE INC and L. Harding and J. Adolf of the Chesapeake Bay component of ACE INC have conducted a comparative analysis of phytoplankton taxonomic group responses to nutrient and climatic (freshwater discharge) perturbations in the context of estuarine eutrophication in the NRE and Chesapeake Bay. The results from this analysis and its implications for assessing human versus climatic alteration of water quality and ecological condition in these estuaries are in a manuscript submitted to Limnology and Oceanography (Paerl et al., March 2004) for inclusion in a Special Issue on Eutrophication edited by M. Joye, R. Howarth and V. Smith.

Post doctoral researchers L. Valdes, has made considerable progress on the seasonal, annual, and spatial analysis of the long-term dataset on diagnostic phytoplankton photopigments concentrations and associated ChemTax results for the NRE and PS. She is in the process of preparing two manuscripts. One of these manuscripts focuses on the effects of hydrologic variability, resulting specifically from droughts and hurricanes, on phytoplankton community structure in these systems. This manuscript compares and contrasts several of these hydrologic events of varying magnitude to determine whether specific hurricanes and/or droughts caused particular responses in phytoplankton community structure or whether the responses were similar following all hurricane or drought events. This paper also addresses the question of whether phytoplankton communities are pushed downstream with the increased river flow rates during the heavy rainfall events associated with hurricanes, or whether the resulting reduced salinity conditions and increased nutrient loading control phytoplankton composition immediately following these events. The other manuscript has an ecological focus and discusses historic annual, seasonal, and spatial trends in the absolute concentration of phytoplankton taxonomic groups (chlorophytes, cryptophytes, cyanobacteria, diatoms, and dinoflagellates (see Figure 2) throughout the length of the NRE and in the southern portion of PS during 1994 through 2002. This paper will determine whether phytoplankton composition has changed during this time in response to anthropogenic and climatic effects that have affected these systems both simultaneously and discretely over the years.

Ecosystem diversity is an important property for assessing the environmental condition of estuaries. Phytoplankton are major primary producers in these systems and the diversity of this component affects ecosystem structure and function. Diversity indices (e.g., Simpsons Index, Shannon-Weiner function, Brillouin Index) can be easily calculated and compared within and among different ecosystems to provide an indirect bioindicator for ecosystem health. The absolute value of the index is less important than how the index changes over time. For example, an increasing diversity index value over time would indicate an increase in phytoplankton diversity-a characteristic of stable ecosystems. Alternatively, a decrease in the diversity index would signal an increasing frequency and magnitude of monospecific phytoplankton blooms- one of the consequences of eutrophication and declining ecosystem health. A combined HPLC-ChemTax approach was used to estimate the relative abundance of different algal groups in the Neuse River Estuary. Group diversity indices (see Figure 4) were calculated for biweekly samples to examine changes in phytoplankton diversity over time (years). We are currently attempting to relate these changes to variations in relevant environmental conditions such as hurricanes, nutrient concentrations, salinity, and so forth.

Bacteria-Phytoplankton Relationships

Benjamin Peierls (a graduate student) is examining the spatiotemporal relationships between the phytoplankton (autotrophic) and bacterioplankton (heterotrophic) communities in the estuary. The microbial community mediates carbon, nutrient, and oxygen (i.e., hypoxia/anoxia) cycling in these waters and determines the net trophic status for the system. Understanding microbial loop dynamics is critical to understanding overall ecosystem structure and function.

Long Term Measurements of Phytoplankton Group Diversity in the Neuse River Estuary

Figure 5. Long Term Measurements of Phytoplankton Group Diversity in the Neuse River Estuary. The green line is a 3-point FFT showing cycles in diversity. The vertical magenta lines indicate the dates of major hurricanes that passed over the area. The dashed blue line shows the long-term trend in group diversity at this location. The slope of the line is positive and significantly different from 0 (p < 0.01), suggesting that group diversity may be increasing in this region of the Neuse River estuary.

Bacterioplankton productivity exhibited a strong seasonal trend with temperature as a driving factor (see Figure 5, top). The difference between the 2 years appeared to be driven by the variable hydrologic conditions, with less spatial variability in the spring of 2003 when flow rates were high (see Figure 5, top). The passage of Hurricane Isabel in September 2003 caused a peak in bacterial productivity, presumably through organic matter and nutrient loading. Primary productivity did not show similar seasonality nor did the hurricane produce a noticeable signal (see Figure 5, bottom). Phytoplankton and bacterioplankton did correlate on a broad spatial scale. Both communities showed highest productivity in the oligohaline portion of the estuary and lowest productivity at the salinity extremes of the system (see Figure 6).

Land-Use as an Indicator of Primary Productivity and Trophic State in Estuarine Creeks

Graduate student Tom Gallo is examining proximate landuse influence as an indicator of microalgal primary productivity and trophic state in the oligo-meso-haline creeks along the estuary margins. These sub-estuaries of the Neuse-Pamlico system are cited as critical nursery area for diverse fisheries and harbor rich microbial communities that mediate terrestrial-to-marine material transfer with possible effect on system wide nutrient budgets. He is conducting controlled seasonal manipulative experiments and regular in situ sampling in four spatially analogous creeks with watersheds that represent the lower Neuse River and Pamlico Estuary drainage landuse and land cover as delineated by analysis of remote sensing data. The sampling objectives are (1) quantify the contrasting amounts and forms of biologically available nitrogen derived from representative watersheds; and (2) establish spatial and temporal patterns in nutrient attenuation and phytoplankton production along the creek axis. Three of four planned seasonal microcosm experiments have been conducted to determine phytoplankton primary productivity rates and community compositional responses to nutrient amendments mimicing observations from monitoring and remote sampling systems deployed at the creek headwaters. Preliminary results from the first two experiments indicate N limitation in all creeks but few statistically significant differences in biomass and productivity to varied the forms of N (NO3, NH3, DON) within each creek. Increases in productivity and chlorophyll a within the agricultural creek, however, occurred a full day before similar responses in treatments of other creeks and water from the main stem of the estuary. Further analysis of diagnostic indicator pigments aims to elucidate a possible shift in the phytoplankton community in agricultural creeks in response to episodic nutrients pulses not observed below forested and undisturbed drainages. Tom’s work is augmented by a contemporaneous project developing robust nutrient budgets in the creek watersheds.

Box and Whisker Plots of Bacterioplankton (top, BP) and Phytoplankton (bottom, PP) Productivity in the Neuse River/Pamlico Sound Estuary Over Time

Figure 5. Box and Whisker Plots of Bacterioplankton (top, BP) and Phytoplankton (bottom, PP) Productivity in the Neuse River/Pamlico Sound Estuary Over Time. The blue line is daily mean stream flow measured by the USGS at Kinston, NC, about 60 km from the head of the estuary.

Box and Whisker Plots of Bacterioplankton (top, BP) and Phytoplankton (bottom, PP) Productivity in the Neuse River/Pamlico Sound Estuary Across the Salinity Gradient

Figure 6. Box and Whisker Plots of Bacterioplankton (top, BP) and Phytoplankton (bottom, PP) Productivity in the Neuse River/Pamlico Sound Estuary Across the Salinity Gradient. Stations are ordered approximately by salinity with lowest to the left and highest to the right.

Developing Bacterial and Viral Indicators of Estuarine Ecological Condition

In the Fall of 2003, we were awarded supplemental funds for the laboratory of Dr. Rachel Noble to conduct research supporting the development of microbial indicators as part of the NRE-PS component of the ACE INC project. Her supplemental research is specifically entitled “Developing bacterial and viral indicators of estuarine ecological condition”. Through a series of discussions, it was identified that the prokaryotic and viral components of this estuarine system may offer insight to development of suitable microbial indicators. Dr. Noble’s laboratory is conducting a two-pronged supplemental research effort in conjunction with the ACE INC project; it will contribute to the development of ecologically meaningful indicators of coastal water quality and ecosystem health that can assess present status and long-term trends and will assist in the differentiation between anthropogenic and natural stress on ecosystem function, water quality, and habitability. This supplemental research will yield a matrix of related bio-indicators, some of them related to estuarine water quality, that will permit a more complete understanding of ecosystem condition. It is our hope that this matrix based approach may be more broadly applicable to other systems, in particular other estuaries that face heavy inputs from agricultural, livestock, and human sources. Other STAR EaGLe research programs involve microbiological bio-indicators, and this supplemental research program will facilitate the formation of direct links between the ACE INC project and the other STAR EaGLe projects.

The Noble lab is examining the potential of specific bacterial species as bio-indicators, to be used as *sentinels* of anthropogenic inputs to estuarine systems. In addition, this specific approach will help the ACE INC project to accomplish the goal of being able to differentiate between anthropogenic and natural stress to the estuarine system. Eutrophication is a key factor in supporting the growth, survival, and proliferation of human pathogens in estuarine waters, and presents a potential risk to both ecosystem and human health. Growth of heterotrophic bacteria is commonly limited by the availability of nutrients and bioavailable organic substrates. We speculate that the growth of heterotrophic pathogenic bacteria, coming from the variety of anthropogenic sources mentioned above, is subject to the same types of controls in natural waters.

Sampling is being conducted in conjunction with the Paerl Laboratory to quantify viral and bacterial abundance in NRE samples and to identify key bacterial species, allochtonous and autochthonous, that co-exist in estuarine environments with key phytoplankton species. Molecular methods are being used to characterize key bacterial pathogens/species present in the NRE-PS, and their quantitative relationships to other biotic and abiotic factors. This approach is important that these key species can be used as bio-indicators in and of themselves (and they have been in the field of water quality), but their responses to eutrophication provide a tremendous bridge to understanding ecosystem condition. To accomplish this, quantitative polymerase chain reaction (QPCR) is being used, in conjunction with traditional culture-based methods, for identifying and enumerating “sentinel” bacterial species as indicators of anthropogenic inputs. There are a large number of potential pathogens that could be transmitted through the waters of the NRE-PS due to its extensive contamination from swine pollution, agriculture, and other anthropogenic activities. The Noble lab is focusing on several species that are likely to have ecological importance. The most important of these is Vibrio species, that can represent potential significant disease agents and/or indicate poor water quality, and that also are found naturally in estuarine and coastal waters. QPCR is being used in the lab to detect and quantify both the general Vibrio group, and pathogenic species of Vibrios. Research also is being conducted on Salmonella spp., and Campylobacter species, using a suite of traditional and newly developed molecular methods.

Preliminary mesocosm experiments also have been done, to begin to partition the importance of the native viral and bacterial assemblages, and their roles in controlling or contributing to phytoplankton community succession. The Noble Lab will participate in the design of future mesocosm experiments to determine the ability of specific microbial indicators to survive and grow during transport through the estuary and to assess the role that these bacteria have in nutrient metabolism. This work will yield important predictive information (input to models) for the understanding the fate and transport of anthropogenic inputs into the system.

The Noble lab also is attempting to develop virus probes of key estuarine phytoplankton species, notable bloom forming species in the NRE. Viruses are species specific and have the capability to be used as both tracers of specific types of organisms (use fluorescently labeled viruses as probes). Work on these viral tracers is an important departure from the current ACE INC efforts because viral tracers will hopefully permit further resolution by examination of the phytoplankton at the species level (HPLC provides group level information). This will be important during the mesocosm experiments for understanding multi-scalar changes in phytoplankton community composition. Once developed, these virus probes will be tested in real-time experiments in conjunction with the ModMon and FerryMon sampling programs. In the laboratory, we have been creating viral, bacterial, and phytoplankton concentrates from samples from the NRE, and we have been challenging bacterial and phytoplankton species with the virus concentrates, attempting to develop successful virus-host systems. The process involves ultraconcentration of seawater and is difficult and time-consuming, but we will continue to attempt this approach for several key months during times of bloom formation of specific phytoplankton species, such as Heterocapsa. Our hope is to isolate viruses specific for key phytoplankton species and fluorescently label the virus for use as probes in natural samples, for species level identification of phytoplankton. Because the diagnostic pigment work (being conducted as an integral part of the existing ACE-INC project) will only provide a group level discrimination between phytoplankton types, this may be a key factor in resolving the smaller scale dynamics of key phytoplankton species that are likely to be important both on an ecosystem level (bloom-forming species) or on a mesocosm level (virus tracer will help us to understand patterns of phytoplankton from nutrient inputs and reductions.)

Coupled Physical-Biological Studies: Neuse River Estuary/Pamlico Sound Component

Turbulent mixing in the lower NRE has been measured (by technician, Tony Whipple) using an Acoustic Doppler Current Profiler (ADCP) deployed beside the profiling platform on two occasions. The devices were configured with high ping rates to measure water column mixing parameters. Combined with data from the profiler, we were able to generate profiles of Reynolds stress and gradient Richardson number (see Figure 7). These data will help us to establish physical conditions under which aggregations of phytoplankton can occur as well as physical conditions under which chlorophyll distributions would be vertically uniform. Figure 7 shows an example from November 2003 where a regular vertical migration was disrupted by a high wind event and was subsequently re-established. By understanding the timing of aggregation in response to waning surface wind stress and turbulence, it may be possible to predict windows of opportunity when remotely sensed chlorophyll concentrations will more accurately assess average water column chlorophyll. Also, the use of aircraft for the remote sensing of biological pigments requires assumptions or knowledge concerning the vertical structure of biological populations/pigments in the water column. The vertical profiles of water column hydrography (salinity, temperature, turbidity) and in situchl-a fluorescence reveal strong diurnal vertical migration of the chl-a source as well as close correspondence between chl-a levels and mixing events. These data will be important for interpreting the remotely sensed pigments.

Janelle Reynolds-Fleming received her Ph.D. degree in Marine Sciences (UNC-CH) in 2003. Her dissertation included utilizing a 3-dimensional, finite difference Environmental Fluid Dynamics Code (EFDC) model to simulate hydrodynamic conditions in the NRE. The model was calibrated with ModMon/CISNet data from 1998-2000 by EPA region 4 to provide assistance to the State of North Carolina in its efforts to develop a nutrient Total Maximum Daily Load (TMDL) for the NRE. We have completed an independent validation study with the model and found that it compares well with salinity and velocity data from two bottom mounted CTDs and ADCPs moored on opposite shores of the upper NRE during 1999-2000. Regressions between model data and field data suggest that the model explains 78 percent of the variability seen in the field data. The model is presently being used to study transit time and flushing rates over a variety of discharge scenarios in the system.

Climatological studies of the physical/nutrient characteristics of the NRE are being conducted using the along channel profile data from 1994-2003. Mean conditions for each month of the year have been constructed and are being used as initial conditions for the modeling effort as well as to drive simple salt and dissolved oxygen models of the system. This climatological analysis provides a baseline for assessing short term perturbations as well as longer term shifts in the system.

Technician Tony Whipple, has continued development of the autonomous vertical profiler (AVP). The profiler deployed at the mouth of the NRE has been working reliably for the majority of the past year. Profiles of salinity, temperature, dissolved oxygen, in vivo fluorescence, and turbidity are taken every half hour, stored on-board, and transmitted back to the lab each night. Figures are then automatically generated and made available on the Internet via a link on the ACE INC Web pages.

Graduate student Nathan Hall is analyzing the vertical phytoplankton distribution documented by in vivo fluorescence profiles from the AVP (see Figure 7). In the Year 1 of the project, (when the platform was at Mod-Mon site 120), there were two seasonally dominant aggregation patterns to the vertical distribution of phytoplankton. In the late spring through late fall, diel vertical migration dominated the variance in the depth distribution of the phytoplankton. During the winter through early spring, aggregation at the pycnocline was the dominant pattern. For the past year, the platform has been moored at Mod Mon site 180 at the mouth of the NRE. This region of the NRE is more oligotrophic and often less stratified than the previous site (Mod Mon 120) making it a very different environment. Interestingly, the two seasonally dominant patterns of vertical distribution observed at the upstream site have again been recorded at the mouth of the Neuse, diel vertical migration during the warmer months and aggregation at the pycnocline during the colder months. These patterns in the vertical distribution of phytoplankton may be indicative of shifts in the nature of light/nutrient/temperature limitation regimes of the phytoplankton community. Heterogeneous vertical distributions of phytoplankton affect our ability to assess standing crops of phytoplankton biomass through traditional (e.g., surface grabs) and remotely sensed sampling strategies. These data provide information on the measurement error of average water column chlorophyll from discrete samples/ remote sensing and are being used to develop more effective sampling strategies.

Ten Day Time Series of Wind Speed, Turbulent Reynolds Stress, Gradient Richardson Number, Water Column Density , and Chlorophyll From the Observation Buoy at the Mouth of the Neuse River Estuary (station 180) During November 2003

Figure 7. Ten Day Time Series of Wind Speed, Turbulent Reynolds Stress, Gradient Richardson Number, Water Column Density , and Chlorophyll From the Observation Buoy at the Mouth of the Neuse River Estuary (station 180) During November 2003. Wind speed was collected from the Cape Lookout C-MAN station. Turbulent Reynolds stress was calculated from a bottom mounted ADCP. The gradient Richardson number was derived from both ADCP and profiler data. Density was calculated from the temperature and salinity profiles. Chlorophyll concentration was derived from invivo fluorescence measured by the profiler. The x-axis tick marks are centered at midnight.

Contributions to the State of Knowledge

The mirobiological, phytoplankton and associated physical-chemical indicators that are being developed and applied in this component project have already proven useful and applicable for evaluating ecosystem and regional responses to a variety of environmental stressors, including nutrient loads, changes in hydrologic characteristics (salinity, circulation), large-scale frontal passages (i.e., “noreasters”), and major storms, including hurricanes (Paerl et al., 2001; Paerl et al, 2002, in preparation). In addition, they offer great promise as a data source for development, verification, and modification of remote-sensing of plankton production and community structure of a range of estuarine and coastal water bodies regionally and nationally. Lastly, these indicators have been adapted to unattended water quality monitoring of large estuaries and coastal sounds, as illustrated below for the Ferry-Based Water Quality Monitoring Program (FerryMon) for North Carolina’s Pamlico Sound System. Most recently, we were able to use the ferries for large-scale assessment of the impacts of Hurricane Isabel (September, 2003) on this system.

Using FerryMon as a Water Quality Tool: Hydrologic Impacts of a Transient Inlet to the Pamlico Sound Opened by Hurricane Isabel: A study by J. Ramus, Duke Marine Lab, Beaufort, NC, and H.W. Paerl, UNC-Institute of Marine Sciences, Morehead City, NC

Hurricane Isabel, a long-lived Cape Verde tropical cyclone, made landfall near Drum Inlet on the Outer Banks of North Carolina on September 18, 2003. Even as a low Category 2 (90-100 mph), Isabel is considered to be one of the most significant hurricanes to affect portions of northeastern North Carolina and east-central Virginia since Hurricanes Dennis and Floyd in 1999 (Paerl, et al., 1991), Hazel in 1954, and the Chesapeake-Potomac Hurricane of 1933 (National Hurricane Center). Isabel is the latest of a recent spate of hurricanes that have struck the U.S. East Coast, and appears indicative of a projected increase in Atlantic hurricane frequency (Goldenberg, et al., 2001). Isabel’s most notable effects were storm surges on the Outer Banks and inland estuaries. Overwash breached Hatteras Island between Hatteras Village and Frisco, creating an inlet which measured about 1,700 feet across with depths ranging to 20 feet. It was the site of a 1963 breach that had been repaired. Within a week the North Carolina Department of Transportation and US Army Corps of Engineers began filling the breach with sand to restore NC 12 to the cut-off Hatteras Village. By November 18, the breach had been filled and NC 12 repaired.

A large, albeit temporary inlet, should affect the hydrography of the Pamlico Sound, as do the three permanent inlets (Pietrafesa et al. 1996). The FerryMon automated water quality monitoring program was fully operational before and after the passage of Hurricane Isabel. The ferries on the Cedar Island—Ocracoke and Swan Quarter—Ocracoke routes stopped regular service for only 36 hours around the passage of the hurricane. Thus it is reasonable to assume that FerryMon data could be used to detect the opening and closing of the new inlet, a 2-month event. For this purpose an important hydrographic and water quality property, salinity, was examined.

The Pamlico Sound is separated into two basins by Bluff Shoal which is positioned north-south at approximately 076.07 degrees West longitude. We hypothesized that the Bluff Shoal restricted exchanges of water between the two basins, and the basins exchange water with the coastal ocean somewhat independently of each other. The northeast basin receives fresh water mostly from the Chowan and Roanoke River watersheds via the Albemarle Sound, whereas the southwest basin receives fresh water mostly from the Tar-Pamlico and Neuse River watersheds.

We expect the new inlet to affect primarily the northeast basin because it connects that basin directly with the coastal ocean. On their Pamlico Sound routes, the ferries pass between the two basins by traversing the Bluff Shoal over roughly the same course (c.f. Buzzelli, et al., 2003). We delineated 4 km2 areas, now called the east focal region (EFR) and west focal regions (WFR), on either side of the Bluff Shoal, which the ferries transect. Salinity data were collected by each ferry every three minutes en route. Salinity data from the 4 months preceding and following Hurricane Isabel are included in the analysis. The differences in salinity between the EFR and WFR are highly significant (p < 0.002), and depict the sudden opening of the new inlet and its gradual closing (see Figure 8).

Differences in Average Weekly Salinity Between the East and West Focal Regions

Figure 8. Differences in Average Weekly Salinity Between the East and West Focal Regions

For the months preceding Hurricane Isabel, the salinity differences between the EFR and the WFR declined, the EFR became fresher relative to the WFR. This can be explained as follows. The Chowan and Roanoke Rivers drainage basins account for 48 percent of the Albemarle-Pamlico Sounds Estuarine System watersheds, whereas the Tar-Pamlico and Neuse account for 32 percent. The east basin receives fresh water mostly from the Chowan and Roanoke River watersheds, and the west basin receives fresh water mostly from the Tar-Pamlico and Neuse River watersheds. Since the Fall of 2002, precipitation on eastern North Carolina has been far above normal, as has river discharge into the Pamlico Sound (USGS-Raleigh, NC). The increased discharge has been greatest for the Chowan and Roanoke Rivers. Thus the east basin has been freshening at a comparatively greater rate than the west basin, hence a steady decline in basin salinity differences, until Hurricane Isabel impacted the system. The freshening trend in the east basin relative to the west basin is dramatically reversed upon the opening of the new inlet (see Figure 8). The reversed trend continued until the inlet was closed, around November 18, and then the freshening began again.

We offer this data as an example of the utility of the FerryMon Program as a water quality monitoring and assessment tool. Hurricane Isabel produced considerable human suffering, but the impact on the Pamlico Sound system was small. Nevertheless, with the robust data stream produced by the FerryMon program, we are able to demonstrate that the sudden inlet opening and slow closure could be detected as a signal in water quality. No other monitoring program was in place to detect that signal. Perhaps most importantly, the water quality baseline, storm-related and human (i.e. nutrient) perturbations that FerryMon are documenting will prove invaluable in determining long-term trends in water quality and identifying potential needs for environmental management of the Nation’s second largest estuarine complex and its most important fisheries nursery.


Buzzelli CP, Ramus JR, Paerl HW. Ferry-based monitoring of surface water quality in North Carolina estuaries. Estuaries 2003;26:975-984.

Goldenberg SB, Landsea CW, Mestas-Nuzes AM, Gray WM. The recent increase in Atlantic hurricane activity: causes and implications. Science 2001;293:474-479.

Paerl HW, Bales JD, Ausley LW, Buzzelli CP, Crowder LB, Eby LA, Fear JM, Go M, Peierls BL, Richardson TL, Ramus JR . Ecosystem impacts of 3 sequential hurricanes (Dennis, Floyd and Irene) on the US’s largest lagoonal estuary, Pamlico Sound, NC. Proceedings of the National Academy of Sciences USA 2001;98(10):5655-5660.

Pietrafesa LJ, Janowitz GS, Chao T-Y, Weisberg RH, Askari F, Noble E. The physical oceanography of Pamlico Sound. UNC Sea Grant Publication UNC-WP-86-5, 1996, 125pp.

Future Activities:

Analyses and interpretation of the long-term data are being performed to develop qualitative and quantitative relationships between the abundance of specific phytoplankton functional groups and various estuarine chemical and physical variables. These analyses will yield information that will link the abundance of each phytoplankton functional group with a particular set of environmental conditions. This way, specific phytoplankton functional groups can be used as bio-indicators of estuarine condition far beyond the ACE INC systems. Recent correlative statistical analyses revealed that phytoplankton functional groups in the NRE differed in their relationship to these variables. In addition, the extent of these associations varied with season. As a result of the non-linear and complex associations between these biological, chemical, and physical variables, we will be using more robust data analysis procedures, including neural network analysis, to establish quantitative associations between these variables.

Journal Articles on this Report : 7 Displayed | Download in RIS Format

Other subproject views: All 135 publications 32 publications in selected types All 28 journal articles
Other center views: All 383 publications 99 publications in selected types All 88 journal articles
Type Citation Sub Project Document Sources
Journal Article Luettich RA, Carr SD, Reynolds-Fleming JV, Fulcher CW, McNinch JE. Semi-diurnal seiching in a shallow, micro-tidal lagoonal estuary. Continental Shelf Research 2002;22(11-13):1669-1681. R828677C001 (2002)
R828677C001 (2003)
R826938 (2000)
R826938 (2001)
R826938 (Final)
not available
Journal Article Paerl HW. Connecting atmospheric nitrogen deposition to coastal eutrophication. Environmental Science & Technology 2002;36(15):323A-326A. R828677C001 (2002)
R828677C001 (2003)
R828677C001 (Final)
R826938 (Final)
not available
Journal Article Paerl HW, Dyble J, Twomey L, Pinckney JL, Nelson J, Kerkhof L. Characterizing man-made and natural modifications of microbial diversity and activity in coastal ecosystems. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology 2002;81(1-4):487-507. R828677 (2001)
R828677 (Final)
R828677C001 (2002)
R828677C001 (2003)
  • Abstract from PubMed
  • Abstract: SpringerLink-Abstract
  • Journal Article Paerl HW, Valdes LM, Joyner AB, Piehler MF. Solving problems resulting from solutions: Evolution of a dual nutrient management strategy for the eutrophying Neuse River Estuary, North Carolina. Environmental Science & Technology 2004;38(11):3068-3073. R828677C001 (2003)
    R828677C001 (2004)
    not available
    Journal Article Piehler MF, Twomey LJ, Hall NS, Paerl HW. Impacts of inorganic nutrient enrichment on phytoplankton community structure and function in Pamlico Sound, NC, USA. Estuarine, Coastal and Shelf Science 2004;61(2):197-209. R828677C001 (2003)
    R828677C001 (2004)
    R830652 (2004)
  • Full-text: EPA(only)
  • Abstract:
  • Other: EPA(only)
  • Journal Article Reynolds-Fleming JV, Luettich Jr. RA. Wind-driven lateral variability in a partially mixed estuary. Estuarine, Coastal and Shelf Science 2004;60(3):395-407. R828677C001 (2003)
    R826938 (Final)
    R827957 (Final)
  • Full-text: ScienceDirect-Full Text HTML
  • Abstract: ScienceDirect-Abstract
  • Other: ScienceDirect-Full Text PDF
  • Journal Article Reynolds-Fleming JV, Luettich RA. Simulation of lateral salinity variability in a shallow, wind-driven estuary affected by fish kills. Ocean Dynamics (in preparation, 2004). R828677C001 (2003)
    not available

    Supplemental Keywords:

    phytoplankton, estuarine and coastal indicators, photopigments, nutrients, hydrology, water quality, habitat, ecosystem and regional scale, management, physical factors, climatology, hurricanes, nutrient management, TMDLs, modeling, remote sensing, ferry-based monitoring,, RFA, Scientific Discipline, Air, Ecosystem Protection/Environmental Exposure & Risk, Ecosystem/Assessment/Indicators, Ecosystem Protection, Chemistry, climate change, Air Pollution Effects, Monitoring/Modeling, Ecological Effects - Environmental Exposure & Risk, Environmental Engineering, Atmosphere, Ecological Indicators, environmental monitoring, remote sensing, coastal ecosystem, aquatic ecosystem, atmospheric dispersion models, ecoindicator, fish habitats, climate change effects, assessment models, environmental measurement, nutrient loading, climate, Choptank River, trophic effects, estuarine ecosystems, estuarine ecoindicator, environmental stress, water quality, climate model, ecological models, atmospheric chemistry, zooplankton

    Relevant Websites:

    http://www.aceinc.org Exit

    http://www.ferrymon.org Exit

    http://www.marine.unc.edu/neuse/modmon/ Exit

    Progress and Final Reports:

    Original Abstract
  • 2001
  • Final Report

  • Main Center Abstract and Reports:

    R828677    EAGLES - Atlantic Coast Environmental Indicators Consortium

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