2004 Progress Report: Consortium for Estuarine Ecoindicator Research for the Gulf of Mexico (CEER-GOM)

EPA Grant Number: R829458
Center: EAGLES - Consortium for Estuarine Ecoindicator Research for the Gulf of Mexico
Center Director: Brouwer, Marius
Title: Consortium for Estuarine Ecoindicator Research for the Gulf of Mexico (CEER-GOM)
Investigators: Brouwer, Marius , Cheek, Ann , Denslow, Nancy , Heard, Richard , Noble, Peter , Snyder, Richard , Thomas, Peter , Yang, Xiaojun
Current Investigators: Brouwer, Marius , Cheek, Ann , Denslow, Nancy , Han, Luoheng , Lepo, Joe , Noble, Peter , Rakocinski, Chet , Rose, Kenneth A. , Snyder, Richard , Thomas, Peter , Yang, Xiaojun
Institution: University of Southern Mississippi , Florida State University , Louisiana State University - Baton Rouge , Southeastern Louisiana University , The University of Texas at Austin , University of Alabama - Tuscaloosa , University of Florida
Current Institution: University of Southern Mississippi , Florida State University , Louisiana State University - Baton Rouge , The University of Texas at Austin , University of Alabama - Tuscaloosa , University of Florida , University of Washington
EPA Project Officer: Hiscock, Michael
Project Period: December 1, 2001 through November 30, 2005 (Extended to May 20, 2007)
Project Period Covered by this Report: December 1, 2003 through November 30, 2004
Project Amount: $5,906,323
RFA: Environmental Indicators in the Estuarine Environment Research Program (2000) RFA Text |  Recipients Lists
Research Category: Economics and Decision Sciences , Water , Ecosystems , Ecological Indicators/Assessment/Restoration

Objective:

The main objective of the Consortium for Estuarine Ecoindicator Research for the Gulf of Mexico (CEER-GOM) program, which works in partnership with the U.S. Environmental Protection Agency (EPA) Gulf Ecology Division (GED), is to study, develop, and validate indicators of estuarine condition at four levels of increasing biological complexity (individual, population, community and ecosystem/watershed) and integrate the suite of indicator responses into models that can be applied to assess estuarine ecosystem condition. In addition, we will develop sensitive indicators of early stages of ecological change. Our main focus will be on increased nutrient loading and concomitant hypoxic conditions, which are considered one of the major factors responsible for declines in habitat quality in the Gulf of Mexico region. During Year 3 of the program, Mobile Bay and Pensacola Bay were sampled by CEER-GOM program components in a highly coordinated design. A workshop for data analysis and integration of Year 2 data was conducted during the current year and was instrumental in identifying potential indicators and components to include in the eventual model.

Progress Summary:

Individual/Population Indicators: Reproductive Function in Estuarine Fishes

The overall long-term objective of this project is to evaluate biomarkers of reproductive function in Atlantic croaker and Fundulus grandis as early warning indicators of fish population hazards resulting from degradation of estuarine environments, using low dissolved oxygen (DO) as a stressor. The major objectives for Year 3 for croaker were to: (1) complete the measurement of these indicators in croaker collected from hypoxic and normoxic estuarine sites in Pensacola Bay and from controlled laboratory hypoxia experiments in 2003; and (2) collect croaker samples from sites in Mobile Bay for measurement and further evaluation of a subset of these reproductive indicators. Marked decreases in several reproductive indicators such as gonadal growth and circulating steroid levels were observed in croaker collected from low DO sites in East Bay, Florida, during 2003. This decline in plasma estrogen levels in females was associated with a marked decrease in estrogen signaling as assessed by measurement of liver estrogen receptor (ER) mRNA and plasma vitellogenin levels. Both indicators showed consistent and dramatic decreases at the low DO sites, suggesting they are potentially useful indicators of reproductive condition in wild croaker populations. Similar marked declines in these indicators were observed in croaker exposed to low DO in laboratory experiments. Gonadotropin secretion also was decreased in the low DO groups in the laboratory studies, suggesting that low DO impairs reproduction, at least partially, by altering reproductive neuroendocrine function. Hypoxia inducible factor (HIF) 1α and 2α, as well as their associated chaperone proteins ARNT1 and 2, have been cloned from Atlantic croaker. Preliminary results indicate both HIF1α and HIF2α mRNA levels are moderately increased in croaker exposed to low DO in the laboratory, suggesting they have potential as molecular indicators of exposure to hypoxia. A subset of indicators involved in ovarian growth and vitellogenesis were measured in female croaker collected from four sites in Mobile Bay. Although characterization of the sites is incomplete, preliminary results show decreased gonadal growth in females from two sites that experienced low DO compared to that observed in females from normoxic sites. There was a good correlation between gonadal growth and the other indicators, ER mRNA, plasma vitellogenin, and percent mature oocytes, indicating the potential utility of all of these reproductive indicators in field assessments of reproductive function.

The major goals for the second year of this project for gulf killifish, F. grandis, were to: (1) evaluate the effects of body size on reproductive parameters; and (2) compare the pattern of reproductive biomarker responses to hypoxia in wild caught fish from Terrebonne Bay, Louisiana; Pensacola Bay, Florida; and Weeks Bay, Alabama. Indicators varied with body size only during the reproductive season (April and July). Steroid hormones of both sexes increased with body size early in the spawning season. Female gonadosomatic index (GSI) increased with body size later in the season, suggesting that large females continue to produce eggs longer than small ones. The temporal sensitivity of indicators was clearly demonstrated by the response patterns observed in marshes with different durations of diel DO minima at or below 2 mg/L. Medium-term (5 weeks) diel hypoxia in a Weeks Bay marsh creek suppressed male and female GSI and steroid hormones, but condition factor and vitellogenin were unchanged. Long-term (> 3 months) diel hypoxia in a Pensacola Bay marsh creek did not alter male or female GSI and steroid hormones but did reduce condition factor and vitellogenin. These morphometric and endocrine responses are potentially useful as early warning indicators of reproductive failure, an ecologically relevant endpoint, because they correlated with declines in fecundity, gamete function, and reproductive success.

Modeling and Integration

The effort of the Louisiana State University modeling group during Year 3 centered on three objectives. These objectives were to: (1) refine and test predictive models for scaling individual-level effects of croaker to the population level; (2) use reproductive and DO stress indicator data for population and community modeling of grass shrimp, Fundulus, and sheepshead minnow; and (3) increase integration of results among the components of the CEER-GOM program. Progress toward Objective 1 consisted of continued refinement of the croaker population model and publication of a physiological model of the reproduction in an individual female croaker-like fish. We made progress in configuring a series of linked models that scale laboratory-measured indicators to croaker population responses. All three models have been developed and implemented. We completed an initial set of simulations comparing hypoxia, mercury, and PCB effects on the mid-Atlantic and Gulf of Mexico croaker populations. The physiological model simulates the reproductive process of vitellogenesis, beginning with pulse of gonadotropin and ending just before the onset of final oocyte maturation. Laboratory data, including experiments from CEER-GOM efforts, are used to configure the model, estimate model parameters, and test model predictions. The physiological model is being used to simulate hypoxia effects as documented in the Pensacola Bay sampling. We also have conducted a Monte Carlo sensitivity analysis of the physiological model to focus future measurements. Progress on Objectives 2 and 3 included the completion of an initial version of a model of a fish community inhabiting a Gulf of Mexico marsh ecosystem. The model simulates resident fish species (Fundulus, sheepshead minnow, and silversides), blue crab, bay anchovy, and grass shrimp predatory and competitive interactions on a fine-scale grid of habitat cells. The model will be used to predict the community responses to various scenarios of low DO conditions superimposed on different habitat maps. Progress towards Objective 3 focused on the development of an initial analysis of 52 indicators derived across CEER-GOM components, based on the coordinated sampling of Pensacola Bay during Year 2 of the program.

Individual/Population Indicators: Molecular Indicators of Dissolved Oxygen Stress in Crustaceans

The overall long-term objective of this component is to evaluate molecular indicators in crustacea as early warning signals of impacts of hypoxia. Occurrence of hypoxia in estuarine waters is increasing and recovery of estuaries, once impacted, is slow. Detection of early effects of hypoxia is needed for timely remedial action to be taken. The major goals of Year 3 were to: (1) identify potentially hypoxia-responsive genes in grass shrimp, Paleomonetes pugio, under controlled laboratory conditions; (2) identify potentially hypoxia-responsive genes in grass shrimp collected from hypoxia-impacted field sites; and (3) investigate the impacts of hypoxia on whole-animal metrics, such as reproduction in grass shrimp. Macroarrays were constructed using 75 potentially hypoxia-responsive genes, as determined through suppressive subtractive hybridization and direct cloning. There were no robust indicators of hypoxia found in grass shrimp exposed to chronic, moderate (2.5 ppm DO) hypoxia under controlled laboratory conditions, with the exception of strong downregulation of cytosolic manganese superoxide dismutase after 14 days. In contrast, grass shrimp exposed to chronic, severe (1.5 ppm DO) hypoxia showed significant (p < 0.05) upregulation of genes coding for hemocyanin, ATP synthase d and f chains, cytochrome b, and troponin C and I after only 3-days exposure, suggesting an attempt to increase oxygen uptake/transport (hemocyanin), ATP synthesis (ATP synthase and cytochrome b), and locomotion (troponin C and I). After 7-days exposure to chronic, severe hypoxia, ATP synthase, hemocyanin, and troponin are no longer upregulated, but there is a significant increase of transcription of genes in the mitochondrial genome (16S mitochondrial rRNA, cytochrome c oxidase 1, and cytochrome b), as well as upregulation of ferritin and heme binding protein. By day 14, a dramatic reversal of this expression pattern is seen, with a significant downregulation of transcription of genes in the mitochondrial genome (16S rRNA, cytochrome c oxidase 1 and 3, and cytochrome b), as well as ferritin. These results suggest grass shrimp respond to hypoxia in a time-dependent manner, and the up- or down-regulation of specific genes can lend insight into the hypoxia history of grass shrimp. Grass shrimp exposed to cyclic hypoxic conditions in the field showed two discernable patterns of changes in gene transcription: (1) significant downregulation of mitochondrial gene transcription indicative of long-term hypoxia exposure at some locations; and (2) downregulation of hemocyanin gene expression by late summer at nearly all locations. These expression profiles returned to “normal” in late fall, suggesting a transition from an oxygen-independent, hypometabolic state in late summer to oxidative metabolism in late fall. Furthermore, hypoxia appears to negatively impact grass shrimp reproduction, as females exposed to chronic moderate hypoxia in the laboratory had a longer interbrood-interval than normoxic females. Female grass shrimp exposed to cyclic hypoxia in the laboratory had reduced fecundity and a longer interbrood interval than normoxic females, and grass shrimp collected from the field showed a lower percentage of gravid females at cyclic hypoxic versus normoxic sites. These results suggest that both whole animal and molecular responses to hypoxia can be combined to provide diagnostic and predictive tools for the identification of effects of hypoxia on estuarine crustacea at the individual and population level.

Community Indicators: Microbial Biofilms

A primary goal of this component is to establish unequivocal linkages of environmental stressors to biofilm endpoints that also integrate well into the current framework of water quality monitoring used by EPA and state and regional regulatory agencies. Field sampling has added Mobile Bay and the Weeks Bay sub-estuary of that system in addition to the Pensacola Bay system work in 2004. Additional sampling activity was conducted in collaboration with the Pearl laboratory in the Neuse River and with State of Florida water quality sampling in the Big Bend region. Molecular analyses of biofilm microbial community diversity and richness are progressing, showing habitat fidelity and response to specific stressors such as hypoxia. Sample processing to complete the 2003 data set and building the 2004 data set have occupied most of the activity during this reporting period. Emphasis has been on developing a data set to describe the response of biofilms relative to the horizontal and vertical (stratification) gradients in the Escambia Bay estuary and to continue to develop the interannual data set of salt marsh and open water biofilm samples conducted in conjunction with the larger CEER-GOM effort. The addition of Mobile and Weeks Bay estuaries adds a cross-system dimension to these data sets. We have established assays for nitrogenase (acetylene reduction) and denitrification potential (acetylene block) in the laboratory and have measured these activities in surface and benthic biofilms collected from Weeks Bay, Mobile Bay, East Bay, and Pensacola Bay during the summer 2004 sampling season. In summary, none of the biofilms had detectable acetylene reduction activity, which was not surprising given N-loads of ambient waters, and denitrification activity was detectable in all biofilms and was noticeably higher in benthic biofilms relative to surface biofilms. Microcosms were run during August in the laboratory. Estuarine water, collected daily from Escambia Bay, was used to replenish the supply carboys. Four treatments were established: (1) control, no added nutrients; (2) added NH4Cl; (3) added NaNO3; and (4) added NO3, NH4, and PO4. Average pixel density of the resulting biofilms after 7 days for each treatment showed a clear response to nutrient amendment. Biofilms from microcosms had no detectable acetylene reduction activity in any of the treatments. Denitrification activities were lowest in control biofilms and the same in all three nutrient-amended treatments. Phosphatase activities are markedly depressed in biofilms exposed to added phosphate. Many observations of biofilm community structure, biomass, and activities support that microbial biofilms can signal biological responses that may be logically and experimentally linked to specific stressors, (e.g., nutrient-loading, hypoxia, and possibly other factors). Biofilms indicators seem to meet the requirements of critical balance between an unstable or hyperreactive indicator system and an unresponsive or insensitive indicator system.

Community Indicators: Macrobenthic Indicators

Macrobenthic process indicators hypothetically reflect ecosystem function and thus can be used to assess the effects of eutrophication, hypoxia, and other anthropogenic stressors. The benthic environment plays a pivotal role in the regeneration of nutrients and macrobenthic communities mediate trophic function by affecting rates, directions, and pathways of exchange and transformation between the water column and sediments. Thus, macrobenthos should provide effective specific indicators of excessive nutrient loading and hypoxia, but macrobenthic functional metrics are seldom used as ecological indicators. There is a pressing need to develop practical indicators of macrobenthic processes related to ecosystem function. Seven specific objectives were pursued by the macrobenthic indicator component of CEER-GOM in Year 3 of the project: (1) conduct integrated field sampling along with other CEER-GOM components; (2) process CEER-GOM macrobenthic samples; (3) provide macrobenthic process indicator data files through 2003; (4) devise an instrument to obtain the Environmental Modeling and Assessment Program for Estuaries Benthic Index from CEER-GOM macrobenthic data; (5) examine and compare relationships between the Benthic Index, Process Indicators, and selected functional variables using the 2002 Grand Bay National Estuarine Research Reserve (NERR) trial data set; (6) begin interpretation and integration of CEER-GOM macrobenthic data; (7) disseminate CEER-GOM macrobenthic component findings. Field sampling efforts continued in the 11 established stations within the East Bay system and were expanded to include 6 stations in the Weeks Bay/Mobile Bay system. During the 2004 study period, a total of 114 macrofaunal grabs were obtained from 38 stations along with accompanying sediment samples. Processing is complete for 108 macrofaunal samples from 36 stations obtained from East Bay between May and November 2003. In addition, all of the 114 macrofaunal samples from 2004 have been sorted, 80 percent have been size fractionated, 70 percent have undergone taxonomic identification, and 60 percent have had biomass determination. Post-processing of raw macrofaunal data and calculation of macrobenthic process indicators has been completed for all pooled collections through 2003. Process indicators still must be determined for individual grabs for the most of the 2003 collections. A computer program was written to calculate the Benthic Index using input data produced by the macrobenthic component of CEER-GOM; this program was checked using macrofaunal samples taken during the 2002 pilot study in the Grand Bay NERR. Relationships were compared between the Benthic Index, process indicators, and selected functional variables within the 2002 Grand Bay NERR trial data set. Bivariate relationships between the Benthic Index and parameters for the macrobenthic process indicators illustrated that there was general agreement among all the indicators; however, relationships involving the Benthic Index were weaker than relationships among the process indicators, and they were weakest between the Benthic Index and log macrobenthic production potential. Furthermore, relationships between the Benthic Index and functional environmental variables including pore water ammonia and phosphorous, as well as surface chlorophyll and bottom DO, were consistent but fairly weak. In contrast, strong bivariate relationships were evident between log macrobenthic production potential and all four of the selected environmental variables. Although none of the process indicators were significantly related with total organic carbon (TOC), the Benthic Index was strongly related with TOC. Four macrobenthic process indicators were plotted onto a map of integrated sites sampled in August 2003 that was generated by the biofilm component of CEER-GOM. Spatial patterns in the process indicators were consistent with other landscape-scale patterns, and joint behavior of the macrobenthic indicators was informative. High production coincided with a long community turnover as well as a shallow biomass-size spectrum slope and low spectrum intercept and characterized larger organisms within the Marsh Creek; as opposed to relatively lower production, shorter turnover, a steeper slope, and higher intercept characteristic of smaller organisms in the Marsh Pond. Intermediate production in conjunction with short turnovers and steep slopes along with high intercepts associated with smaller organisms likely reflected organically enriched sediments at P12 and P13. This interpretation is also consistent with the spatial pattern in surface chlorophyll. In contrast, intermediate production occurred in connection with longer community turnover, a shallower slope, and a lower intercept characteristic of larger organisms at P5, located away from high surface chlorophyll. Markedly low production occurred, however, in connection with an intermediate turnover as well as shallow slope and low intercept at P14, located within the area of low DO, high surface chlorophyll, and moderately deep water in lower East Bay. The lowest observed production was associated with a short turnover, a shallow slope, and low intercept at SRS1, the site located nearest to a sewage outflow.

Ecosystem/Watershed Indicators: Remote Sensing of Water Quality

During Year 3 of the CEER-GOM project, the remote sensing of water quality component added the Mobile Bay system to their analysis. The primary goals for this year were to: (1) continue the hyperspectral characterization of the Gulf of Mexico; (2) compare regression (band ratioing) and artificial neural networks (ANN) models in estimating and mapping chlorophyll concentration using Landsat Thematic Mapper/Enhanced Thematic Mapper (TM/ETM+) Data; and (3) map the sea surface temperature using Landsat TM/ETM+ data. Spectral reflectances collected over Pensacola Bay and Mobile Bay in July 2004 clearly indicate differences in water quality between the two systems, with low chlorophyll a concentrations in Pensacola Bay at almost all GED sampling sites, whereas the spectral curves of Mobile Bay indicate much higher chlorophyll concentration and dissolved organic matter. During periods of low chlorophyll a concentration, ANN provides a useful alternative to regression analysis to predict phytoplankton distribution. An operational model was created for retrieving sea-surface temperature (SST) with delineation of water body. A well-developed algorithm was applied to calculate SST using Landsat TM band 6 (thermal band).

Ecosystem/Watershed Indicators: GIS and Terrestrial Remote Sensing

The primary goal of the GIS and terrestrial remote sensing component is to develop a suite of large-scale indicators that can be integrated to quantify the anthropogenic impacts upon the estuarine ecosystems. We spent the first 2 years primarily on database construction. Some preliminary data analysis also was done during the second year. During the period of April 2004-April 2005, we focused on data analysis and modeling that aimed to understand the causal relationship among upstream watershed landscape metrics, socioeconomic conditions, and downstream watershed water quality indicators. Specifically, we conducted two major studies. First, we extended the preliminary research done during the second year beyond a single water quality indicator. We considered a suite of critical water quality indicators and used both qualitative and quantitative approaches for mining information contained in the data set. We targeted water quality because it is considered to be a significant factor determining the estuarine ecosystem health. Our second study was on nonpoint pollution modeling and simulation. We conducted pilot research to simulate the generation and transport of pollutants in overland flow to waterways (and finally the receiving basin) by using the Agricultural Nonpoint Source Pollution Model over a study area of 610 km 2 in size.

Data Analysis and Integration

Progress by the data analysis component during Year 3 of the project can be divided into four areas; (1) manuscripts and presentations; (2) collaboration with other CEER-GOM participants; (3) Web site developments; and (4) participation in the Estuarine and Great Lakes (EaGLe) Project Data Management Committee. A methods paper describing Neuroet, an easy-to-use artificial neural network for ecological and biological modeling, has been accepted for publication in the journal Ecological Modelling. So far, more than 125 scientists have downloaded the Neuroet package from the Web site. Seven articles have been published and two presentations given that have been funded (or partially funded) through the EPA Science To Achieve Results program. Dr. Peter Noble has analyzed microarray data (Brouwer), fish data (Thomas), and biofilm image and phytoplankton pigment data (Snyder/Morris) produced for this project and has worked with Karen J. Jordon (a graduate student of Dr. Han at the University of Alabama), teaching her the fundamentals of neural networks and how to extract equations from neural networks. Dr. Noble has collaborated with Dr. Rose in integrating the CEER-GOM data, which involved converting all data into SAS format. The Web site that contains “Tools for data analysis” is complete. Participation in the EaGLe Data Management Committee as a representative of the CEER-GOM group has included assisting researchers in depositing their data and metadata to the EPA Web Site by providing researchers with the metadata requirements, helping researchers assemble their data and metadata, uploading their data to an intermediate Web site where the contents and organization of the metadata and data will be validated, and sending the completed package to the centralized database.

Joint Studies/Experiments

Microbial Biofilms—GED Collaboration

  • Co-locating biofilm samplers with monthly water quality monitoring stations to compare biofilm response to phytoplankton response and nutrients in the water column in 16 of their Pensacola Bay open water stations during April, June, July and August (EPA collaborators: Greene, Hagy, Murrell).
  • Stable isotope analysis on biofilm material (EPA collaborator: Chapman).

Macrobenthic Ecoindicators—GED Collaboration. A computer program was written to calculate the Benthic Index using input data from the Macrobenthic Component of CEER-GOM, and checked using macrofaunal samples taken during the 2002 pilot study in the Grand Bay NERR. Up-to-date DFA parameters provided by EPA-GED were integral to development of this computer program (EPA collaborator: Engle).

Remote Sensing—GED Collaboration. Dr. Han (University of Alabama-CEER) collected hyperspectral data over the Pensacola Bay in collaboration with researchers of the EPA-GED on July 6, 2004. The GED provided water sampling data including chlorophyll α

Future Activities:

Analysis of the multiyear and multisystem data set will be the primary focus of Year 4 activity. We plan on expanding the analysis approach to include this year’s sampling of Pensacola Bay and the coordinated sampling of Mobile Bay.


Journal Articles: 48 Displayed | Download in RIS Format

Other center views: All 171 publications 54 publications in selected types All 48 journal articles
Type Citation Sub Project Document Sources
Journal Article Breitburg DL, Adamack A, Rose KA, Kolesar SE, Decker MB, Purcell JE, Keister JE, Cowan JH. The pattern and influence of low dissolved oxygen in the Patuxent River, a seasonally hypoxic estuary. Estuaries 2003;26(2A):280-297. R829458C009 (2003)
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Journal Article Brouwer M, Larkin P, Brown-Peterson N, King C, et al. Effects of hypoxia on gene and protein expression in the blue crab, Callinectes sapidus. Marine Environmental Research 2004;58(2-5):787-792. R829458C003 (2003)
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Journal Article Brouwer M, Brown-Peterson NJ, Larkin P, Patel V, Denslow N, Manning S, Brouwer TH. Molecular and whole animal responses of grass shrimp, Palaemonetes pugio, exposed to chronic hypoxia. Journal of Experimental Marine Biology and Ecology 2007;341(1):16-31. R829458C003 (2005)
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  • Journal Article Brown-Peterson NJ, Larkin P, Denslow N, King C, Manning S, Brouwer M. Molecular indicators of hypoxia in the blue crab Callinectes sapidus. Marine Ecology Progress Series 2005;286:203-215. R829458C003 (2004)
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  • Journal Article Popular article featuring Cheek & Thomas projects: Janet Raloff. Choked Up: How dead zones affect fish reproduction. Science News 2004;166(20):309. R829458C005 (2004)
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    Journal Article El Fantroussi S, Urakawa H, Bernhard AE, Kelly JJ, Noble PA, Smidt H, Yershov GM, Stahl DA. Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays. Applied and Environmental Microbiology 2003;69(4):2377-2382. R829458 (2005)
    R829458C004 (2003)
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  • Journal Article Ferguson HJ, Rakocinski CF. Tracking marsh restoration using macrobenthic metrics: implementing a functional approach. Wetlands Ecology and Management 2008;16(4):277-289. R829458 (2005)
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  • Journal Article Fuiman LA, Rose KA, Cowan Jr. JH, Smith EP. Survival skills required for predator evasion by fish larvae and their relation to laboratory measures of performance. Animal Behaviour 2006;71(6):1389-1399. R829458C009 (2005)
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  • Journal Article Gough HL, Dahl AL, Tribou E, Noble PA, Gaillard J-F, Stahl DA. Elevated sulfate reduction in metal-contaminated freshwater lake sediments. Journal of Geophysical Research: Biogeosciences 2008;113(G4):G04037, doi:10.1029/2008JG000738. R829458 (2005)
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  • Journal Article Han LH, Jordan KJ. Estimating and mapping chlorophyll-a concentration in Pensacola Bay, Florida using Landsat ETM+ data. International Journal of Remote Sensing 2005;26(23):5245-5254. R829458C001 (2004)
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    Journal Article Han LH. Estimating chlorophyll-a concentration using first-derivative spectra in coastal water. International Journal of Remote Sensing 2005;26(23):5235-5244 R829458C001 (2004)
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    Journal Article Kelly JJ, Siripong S, McCormack J, Janus LR, Urakawa H, El Fantroussi S, Noble PA, Sappelsa L, Rittmann BE, Stahl DA. DNA microarray detection of nitrifying bacterial 16S rRNA in wastewater treatment plant samples. Water Research 2005;39(14):3229-3238. R829458 (2005)
    R829458C004 (2005)
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  • Journal Article Landry CA, Steele SL, Manning S, Cheek AO. Long term hypoxia suppresses reproductive capacity in the estuarine fish, Fundulus grandis. Comparative Biochemistry and Physiology-Part A: Molecular & Integrative Physiology 2007;148(2):317-323. R829458 (2005)
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  • Journal Article Lewitus AJ, White DL, Tymowski RG, Geesey ME, Hymel SN, Noble PA. Adapting the CHEMTAX method for assessing phytoplankton taxonomic composition in Southeastern U.S. estuaries. Estuaries 2005;28(1):160-172. R829458 (2005)
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  • Journal Article Martinez ML, Landry C, Boehm R, Manning S, Cheek AO, Rees BB. Effects of long-term hypoxia on enzymes of carbohydrate metabolism in the Gulf killifish, Fundulus grandis. Journal of Experimental Biology 2006;209(19):3851-3861. R829458C005 (2005)
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  • Journal Article Morris JT, Porter D, Neet M, Noble PA, Schmidt L, Lapine LA, Jensen JR. Integrating LIDAR elevation data, multi-spectral imagery and neural network modelling for marsh characterization. International Journal of Remote Sensing 2005;26(23):5221-5234. R829458 (2005)
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  • Journal Article Moss JA, Nocker A, Lepo JE, Snyder RA. Stability and change in estuarine biofilm bacterial community diversity. Applied and Environmental Microbiology 2006;72(9):5679-5688. R829458 (2005)
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  • Journal Article Murphy CA, Rose KA, Thomas P. Modeling vitellogenesis in female fish exposed to environmental stressors: predicting the effects of endocrine disturbance due to exposure to a PCB mixture and cadmium. Reproductive Toxicology 2005;19(3):395-409. R829458C005 (2003)
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    Journal Article Murphy CA, Rose KA, Alvarez MC, Fuiman LA. Modeling larval fish behavior:scaling the sublethal effects of methylmercury to population-relevant endpoints. Aquatic Toxicology 2008;86(4):470-484. R829458 (2005)
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  • Journal Article Niemi G, Wardrop D, Brooks R, Anderson S, Brady V, Paerl H , Rakocinski C, Brouwer M, Levinson B, McDonald M. Rationale for a new generation of indicators for coastal waters. Environmental Health Perspectives 2004;112(9):979-986. R829458C003 (2003)
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  • Journal Article Noble PA, Tymowski RG, Fletcher M, Morris JT, Lewitus AJ. Contrasting patterns of phytoplankton community pigment composition in two salt marsh estuaries in southeastern United States. Applied and Environmental Microbiology 2003;69(7):4129-4143. R829458 (2005)
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  • Journal Article Noble PA, Tribou EH. Neuroet: an easy-to-use artificial neural network for ecological and biological modeling. Ecological Modelling 2007;203(1-2):87-98. R829458 (2005)
    R829458C004 (2004)
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  • Journal Article Nocker A, Lepo JE, Snyder RA. Influence of an oyster reef on development of the microbial heterotrophic community of an estuarine biofilm. Applied and Environmental Microbiology 2004;70(11):6834-6845. R829458 (2005)
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  • Abstract: Applied and Environmental Microbiology-Abstract
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  • Other: Applied and Environmental Microbiology-Full Text PDF
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  • Journal Article Nocker A, Lepo JE, Martin LL, Snyder RA. Response of estuarine biofilm microbial community development to changes in dissolved oxygen and nutrient concentrations. Microbial Ecology 2007;54(3):532-542. R829458 (2005)
    R829458C002 (2004)
  • Abstract from PubMed
  • Abstract:
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  • Journal Article Pozhitkov AE, Bailey KD, Noble PA. Development of a statistically robust quantification method for microorganisms in mixtures using oligonucleotide microarrays. Journal of Microbiological Methods 2007;70(2):292-300. R829458 (2005)
  • Abstract from PubMed
  • Full-text: Science Direct
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  • Other: Science Direct PDF
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  • Journal Article Pozhitkov AE, Tautz D, Noble PA. Oligonucleotide microarrays: widely applied—poorly understood. Briefings in Functional Genomics and Proteomics 2007;6(2):141-148. R829458 (2005)
  • Abstract from PubMed
  • Full-text: Oxford Journals
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  • Other: Oxford Journals
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  • Journal Article Pozhitkov AE, Stedtfeld RD, Hashsham SA, Noble PA. Revision of the nonequilibrium thermal dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarrays. Nucleic Acids Research 2007;35(9):e70. R829458 (2005)
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  • Full-text: Oxford Journals
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  • Journal Article Pozhitkov A, Chernov B, Yershov G, Noble PA. Evaluation of gel-pad oligonucleotide microarray technology by using artificial neural networks. Applied and Environmental Microbiology 2005;71(12):8663-8676. R829458 (2005)
    R829458C004 (2004)
    R829458C004 (2005)
  • Full-text from PubMed
  • Abstract from PubMed
  • Associated PubMed link
  • Full-text: Applied and Environmental Microbiology-Full Text HTML
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  • Abstract: Applied and Environmental Microbiology-Abstract
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  • Other: Applied and Environmental Microbiology-Full Text PDF
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  • Journal Article Pozhitkov A, Noble PA, Domazet-Loso T, Nolte AW, Sonnenberg R, Staehler P, Beier M, Tautz D. Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Research 2006;34(9):e66. R829458 (2005)
    R829458C004 (2005)
  • Full-text from PubMed
  • Abstract from PubMed
  • Associated PubMed link
  • Full-text: Oxford Journals-Full Text HTML
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  • Abstract: Oxford Journals-Abstract
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  • Other: Oxford Journals-Full Text PDF
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  • Journal Article Rahman MS, Thomas P. Molecular cloning, characterization and expression of two hypoxia-inducible factor alpha subunits, HIF-1α and HIF-2α, in a hypoxia-tolerant marine teleost, Atlantic croaker (Micropogonias undulatus). Gene 2007;396(2):273-282. R829458 (2005)
  • Abstract from PubMed
  • Full-text: Science Direct
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  • Journal Article Rakocinski CF. Linking allometric macrobenthic processes to hypoxia using the Peters mass balance model. Journal of Experimental Marine Biology and Ecology 2009;381(Suppl 1):S13-S20. R829458 (2005)
  • Full-text: Science Direct
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  • Abstract: Science Direct
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  • Journal Article Richmond CE, Breitburg DL, Rose KA. The role of environmental generalist species in ecosystem function. Ecological Modelling 2005;188(2-4):279-295. R829458 (2005)
  • Full-text: Science Direct
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  • Abstract: Science Direct
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  • Journal Article Richmond CE, Breitburg DL, Rose KA. The effect of stress tolerance on the relationship between species richness and system function. Ecological Modelling. R829458C009 (2004)
    not available
    Journal Article Rose KA, Murphy CA, Diamond SL, Fuiman LA, Thomas P. Using nested models and laboratory data for predicting population effects of contaminants on fish: a step towards a bottom-up approach for establishing causality in field studies. Human and Ecological Risk Assessment 2003;9(1):231-257. R829458C009 (2003)
    not available
    Journal Article Rose KA. Lack of relationship between simulated fish population responses and their life history traits: inadequate models, incorrect analysis, or site-specific factors?. Canadian Journal of Fisheries and Aquatic Sciences 2005;62(4):886-902 R829458C009 (2003)
    R829458C009 (2004)
    not available
    Journal Article Thomas P, Rahman MS, Kummer JA, Lawson S. Reproductive endocrine dysfunction in Atlantic croaker exposed to hypoxia. Marine Environmental Research 2006;62(Suppl 1):S249-S252. R829458C005 (2005)
    R826130 (1999)
  • Abstract from PubMed
  • Full-text: Science Direct - Full Text HTML
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  • Abstract: Science Direct
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  • Other: Science Direct - Full Text PDF
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  • Journal Article Thomas P, Rahman MS, Khan IA, Kummer JA. Widespread endocrine disruption and reproductive impairment in an estuarine fish population exposed to seasonal hypoxia. Proceedings of The Royal Society B: Biological Sciences 2007;274(1626):2693-2701. R829458 (2005)
  • Abstract from PubMed
  • Full-text: Royal Society Publishing
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  • Other: Royal Society Publishing PDF
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  • Journal Article Thomas P, Rahman MS. Biomarkers of hypoxia exposure and reproductive function in Atlantic croaker: a review with some preliminary findings from the northern Gulf of Mexico hypoxic zone. Journal of Experimental Marine Biology and Ecology 2009;381(Suppl 1):S38-S50. R829458 (2005)
  • Full-text: Science Direct
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  • Abstract: Science Direct
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  • Journal Article Thomas P, Rahman MS. Chronic hypoxia impairs gamete maturation in Atlantic croaker induced by progestins through nongenomic mechanisms resulting in reduced reproductive success. Environmental Science & Technology 2009;43(11):4175-4180. R829458 (2005)
  • Abstract from PubMed
  • Abstract: ES&T
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  • Journal Article Urakawa H, El Fantroussi S, Smidt H, Smoot JC, Tribou EH, Kelly JJ, Noble PA, Stahl DA. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Applied and Environmental Microbiology 2003;69(5):2848-2856. R829458 (2005)
    R829458C004 (2003)
    R829458C004 (2005)
  • Full-text from PubMed
  • Abstract from PubMed
  • Associated PubMed link
  • Full-text: Applied and Environmental Microbiology-Full Text HTML
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  • Abstract: Applied and Environmental Microbiology-Abstract
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  • Other: Applied and Environmental Microbiology-Full Text PDF
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  • Journal Article Yang X, Liu Z. Quantifying landscape pattern and its change in an estuarine watershed using satellite imagery and landscape metrics. International Journal of Remote Sensing 2005;26(23):5297-5323. R829458C007 (2004)
    R829458C007 (2005)
  • Abstract: Informa World Abstract
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  • Journal Article Yang XJ. Remote sensing and GIS applications for estuarine ecosystem analysis:an overview. International Journal of Remote Sensing 2005;26(23):5347-5356. R829458C007 (2004)
    R829458C007 (2005)
  • Abstract: Ingenta Connect Abstract
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  • Journal Article Yang X. Estimating landscape imperviousness with remotely sensed imagery. IEEE Geoscience and Remote Sensing Letters 2006;3(1):6-9. R829458C007 (2004)
    R829458C007 (2005)
  • Abstract: IEEE Abstract
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  • Journal Article Yang X, Lo CP. Using a time series of satellite imagery to detect land use and land cover changes in the Atlanta, Georgia metropolitan area. International Journal of Remote Sensing 2002;23(9):1775-1798 R829458C007 (2003)
    not available
    Journal Article Yang X. Geospatial technologies for coastal and estuarine ecosystem analysis: status and research priorities. Journal of Coastal Research R829458C007 (2004)
    not available
    Journal Article Yang X, Liu Z. Use of satellite-derived landscape imperviousness index to characterize urban spatial growth. Computers, Environment and Urban Systems 2005; 29(5):524-540. R829458C007 (2003)
    R829458C007 (2004)
    R829458C007 (2005)
  • Abstract: Science Direct Abstract
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  • Journal Article Yang X, Liu Z. Using satellite imagery and GIS for land-use and land-cover change mapping in an estuarine watershed. International Journal of Remote Sensing 2005;26(23):5275-5296. R829458C007 (2005)
  • Abstract: Informa World Abstract
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  • Journal Article Yang X, Liu Z. Use of remote sensing and landscape metrics to analyze estuarine landscape changing dynamics. International Journal of Remote Sensing . R829458C007 (2003)
    R829458C007 (2004)
    not available

    Supplemental Keywords:

    population, community, ecosystem, watersheds, estuary, estuaries, Gulf of Mexico, nutrients, hypoxia, innovative technology, biomarkers, water quality, remote sensing, geographic information system, GIS, integrated assessment, risk assessment, fisheries, conservation, restoration, monitoring/modeling, benthic indicators, ecological exposure, ecosystem monitoring, environmental indicators, environmental stress, estuarine ecoindicator, estuarine integrity,, RFA, Scientific Discipline, Geographic Area, Ecosystem Protection/Environmental Exposure & Risk, Aquatic Ecosystems & Estuarine Research, Ecosystem/Assessment/Indicators, Aquatic Ecosystem, Monitoring/Modeling, Environmental Monitoring, Ecological Risk Assessment, Ecology and Ecosystems, Biology, Ecological Indicators, Gulf of Mexico, ecological exposure, monitoring, ecoindicator, ecosystem monitoring, estuaries, estuarine integrity, Mobile Bay, Galveston Bay, benthic indicators, Apalachicola Bay, estuarine ecoindicator, environmental indicators, environmental stress, water quality

    Relevant Websites:

    http://www.usm.edu/gcrl/ceer_gom/index.php Exit

    Progress and Final Reports:

    Original Abstract
  • 2002 Progress Report
  • 2003 Progress Report
  • 2005 Progress Report
  • 2006
  • Final
  • Subprojects under this Center: (EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
    R829458C001 Remote Sensing of Water Quality
    R829458C002 Microbial Biofilms as Indicators of Estuarine Ecosystem Condition
    R829458C003 Individual Level Indicators: Molecular Indicators of Dissolved Oxygen Stress in Crustaceans
    R829458C004 Data Management and Analysis
    R829458C005 Individual Level Indicators: Reproductive Function in Estuarine Fishes
    R829458C006 Collaborative Efforts Between CEER-GOM and U.S. Environmental Protection Agency (EPA)-Gulf Ecology Division (GED)
    R829458C007 GIS and Terrestrial Remote Sensing
    R829458C008 Macrobenthic Process Indicators of Estuarine Condition for the Northern Gulf of Mexico
    R829458C009 Modeling and Integration