Supporting Scientific Discovery and Science-Based 

Guidance for Restoration and Management 

through the Mississippi Based RESTORE Act 

Center of Excellence (MBRACE) 

Kelly Darnell

Director, MBRACE

Kelly.Darnell@usm.edu
• All adhere to RESTORE Act policies and execute a grant program

• Each State receives $26M+ over 15 years

• Each Center is structured differently, has different scientific focus

AL COE

Centers of Excellence Research Grants Program
• MBRACE is a consortium of Mississippi’s four main research universities

• Designated by the State of Mississippi as the Center of Excellence in August 2016

• Mississippi Departmental of Environmental Quality is the state entity for MBRACE
Organizational Structure
Organizational Structure

ESC: Works with the Directorate to ensure success of the program, reviews 

and approves the Science Plan and Requests for Proposals, and makes final 

funding decisions
Organizational Structure

Bill Benson, US EPA 

(retired)

Jane Caffrey, UWF

David Rudnick, NPS 

(retired)

Bill Fisher, EPA (retired)

Jennifer Pollack, 

TAMU-CC / HRI

EAG: Technical and scientific experts in relevant fields, advise on long-term direction, conduct

annual programmatic evaluations 
Organizational Structure

Mississippi-Alabama Sea Grant Consortium: Coordinates proposal review 

process and assists with science communication
Organizational Structure

Participation 

by all four 

consortium 

universities

PI must be 

from 

a consortium 

university
• Seek sound comprehensive science-and technology-based understanding of 

the chronic and acute stressors on the dynamic and productive waters 

and ecosystems of the northern Gulf of Mexico, and to facilitate 

sustainable use of the Gulf’s important resources

• Serve as a focal point for new, long-term research and socioeconomic 

initiatives along the northern Gulf with relevance to Mississippi’s resources

• Serve the people of Mississippi and the northern Gulf region with a 

scientifically based understanding of ecosystem status and trends with 

special emphasis on improved forecasting abilities to ensure sustainable 

coastal and ocean ecosystems of the Gulf

MBRACE Mission
Oyster reef sustainability and water quality

MDMR

• Responsive to State 

management needs

• >$7M to support research

• Focus on MS Sound

Mississippi oyster landings over time
Core Research Program

Four integrated projects that together focus on oyster reef 

sustainability and restoration, as well as the environmental 

factors that support healthy oyster reefs

• Focused on needs 

identified by State 

management agencies

• Oyster biology, 

ecology, and 

response to stressors

• Suitable locations for 

oyster restoration

• Field and lab studies, high 

tech remote sensing, 

monitoring, experiments, 

modelling

• Western MS Sound
Competitive Grants Program

• Projects compliment Core 

Research Program

• Oyster response to 

stressors

• Influence of submarine 

groundwater discharge

• Oyster food availability 

and quality
• Encourage collaboration across projects to facilitate 

integration and synthesis of data 

• Fund projects under same themes

• Annual All Hands Meeting, research seminars

• Sessions at scientific conferences

• Historical perspective paper

• Conceptual model

• Close partnership with MDMR and MDEQ to ensure 

projects address needs and to leverage resources

Coordination and Collaboration
Impact of MBRACE-funded Research

55

Graduate Students Supported

30

Undergraduates Supported

81

Conference Presentations

5

Dissertations/Theses Supported

65+

Datasets Available at GRIIDC

Visit mbrace.usm.edu

for more information

15

Peer-Reviewed Publications

This project was paid for with federal funding from the Department of the Treasury under the Resources and Ecosystems Sustainability, Tourist Opportunities, and Revived Economies of the Gulf Coast 

States Act of 2012 (RESTORE Act). The statements, findings, conclusions, and recommendations are those of the author(s) and do not necessarily reflect the views of the Department of the Treasury.
Featured Speakers

Dr. Adam Skarke

Mississippi State University

Dr. Kristine Willett

University of Mississippi
MSU Core Research Program:

Integrated River and Estuary Water 

Quality Monitoring and Modeling in 

the Northern Gulf of Mexico

PI Adam Skarke, MSU (July 2021- February 2023)

PI Anna Linhoss, MSU (January 2020-July 2021)

Co-PI Robert Moorhead, MSU

Co-PI Padmanava Dash, MSU

Co-PI Prem Parajuli, MSU
Project Motivation

Water quality is one of the most important factors affecting the ecological benefits and ecosystem services 

provided by a water body.

Water quality in coastal ecosystems can be particularly impacted by the dynamics of freshwater inflow due to

the high amounts of organic matter, nutrients, pathogens, and sediments it introduces. 

Oyster Reef

Bay Saint Louis
Project Motivation

In the Mississippi Sound, spatiotemporal variability in water quality associated with 

freshwater inflow can lead to altered salinity regimes, harmful algal blooms, and hypoxia 

which can imperil marine species, particularly oysters. 
Project Goals and Objectives

Development of Jourdan 

and Wolf River SWAT 

watershed models

Application of models to 

evaluate impact of potential 

watershed management 

practices on MS Sound

Development of UAS 

remote sensing water 

quality monitoring 

approach in western MS 

Sound

Primary Goal: Development of watershed, 

riverine, and estuarine water quality models as 

well as remote sensing water quality monitoring 

approaches for the western Mississippi Sound.

Objectives:

• Develop of Soil and Water Assessment Tool 

(SWAT) models for Jourdan and Wolf Rivers. 

• Evaluation of variation in total suspended 

solids and phosphorus yield to MS Sounds 

from Wolf and Jourdan Rivers resulting from 

implementation of different watershed best 

management practices.

• Development of unmanned aerial system 

(UAS) remote sensing algorithms for water 

quality monitoring in the western Mississippi 

Sound. 
Methods

Objectives:

• Develop of Soil and Water Assessment Tool (SWAT) 

models for Jourdan and Wolf Rivers. 

• Calibration and validation of SWAT models with in 

situ hydrology and water quality data from 

Jourdan and Wolf Rivers.

• Evaluation of variation in total suspended solids 

and phosphorus yield to MS Sounds from Wolf 

and Jourdan Rivers resulting from implementation 

of different watershed best management practices

Methods:

• Tools: ArcGIS, SWAT (Arnold, J.G et. al., 1998), 

SWATCUP-Sufi2 (Abbaspour, 2013)

• Data: 

• USGS: Surface Elevation, Discharge, Water 

Quality Observed Data (TSS and Min P)

• NOAA: Climate Data

• USDA: Land Use Data

Objectives:

• Develop remote sensing algorithms for Unmanned Arial 

Systems imagery (UAS) so that the results can be used with 

satellite data to map the water quality and display the 

spatiotemporal distribution of a suite of water quality 

parameters..

Methods:

• Manned Vessel

• CTD Profiles

• Water Samples (3-depths)

• Radiometer Data

• Autonomous Surface Vessel

• Water Quality Observations

• Unmanned Aerial Systems

• MicaSense RedEdge MX

• Visible Light and Infrared Camera 
SWAT Model Development

Soil and Water Assessment Tool (SWAT) models 

were developed for the Wolf and Jourdan Rivers 

based on a robust set of observed environmental 

data parameters. (USDA-ARS).

The Soil & Water Assessment Tool is a small 

watershed to river basin-scale model used to 

simulate the quality and quantity of surface and 

ground water and predict the environmental 

impact of land use, land management practices, 

and climate change. SWAT is widely used in 

assessing soil erosion prevention and control, 

non-point source pollution control and regional 

management in watersheds.
SWAT Model Validation

TSS Calibration and Validation of Wolf River Watershed

TSS Calibration and Validation of Jourdan River Watershed

Phosphorus Calibration and Validation of Wolf River Watershed

Phosphorus Calibration and Validation of Jourdan River Watershed
SWAT Model Validation
SWAT Evaluation of Watershed Management Practices for 

Mississippi Sound Water Quality

SWAT model used to assess the impact of three watershed scale 

structural best management practices on water quality entering MS 

Sound

• Pond Creation

• Wetland Creation

• Streamside Management Zone Implementation 
Evaluation of Watershed Management Practices

Effectiveness of Best Management Practices in Wolf River 

Watershed

Effectiveness of Best Management Practices in Jourdan 

River Watershed
UAS Remote Sensing Water Quality Monitoring

Remote Sensing Algorithms 

Developed:

• Suspended Particulate Matter (SPM)

• Turbidity

• Chlorophyll a

• Colored Dissolved Organic Matter (CDOM)

• Phycocyanin

• Total Alkalinity (TA)

• Partial Pressure of CO2(pCO2) 

• Salinity
Remote Sensing Data Collection

Field Data Collection

• November 12, 2020 (12 sites)

• March 18, 2021 (1 site)

• June 2, 2021 (12 sites & ASV)

• July 26-29, 2021 (41 sites, ASV, & 

UAS)

• September 29, 2021 (ASV)

• April 1, 2022 (12 sites)

• September 12-16, 2022 (27 sites 

ASV & UAS)
Remote Sensing Algorithm for Turbidity

Remote Sensing Algorithm for Chlorophyll a

Remote Sensing Algorithm for pCO2

Remote Sensing Algorithm for Salinity

Remote Sensing Algorithm Development 
Remote Sensing Algorithm Predictive Capacity: 

Remote Sensing Algorithm Development 
Water Quality Monitoring

Time Series of SPM Over Henderson Point Reef SPM Trends Over Henderson Point Reef
SWAT Modeling Key Results

• SWAT watershed models were developed for the Wolf and Jourdan Rivers.

• Resulting models demonstrate the influence of the Wolf and Jourdan Rivers on 

water quality in the western Mississippi Sound. 

• Models evaluate the effectiveness of implementing best management practices 

in the Wolf and Jourdan River watersheds on reducing total suspended solids 

and phosphorus loading in waters entering the western Mississippi Sound. 

• Greatest effect in reducing TSS and phosphorus loading:

• Ponds

• Wetlands

• Ponds + Wetlands + Streamside Management Zone (30m)
Water Quality Monitoring Key Results

• Field data was collected through 7 sampling trips from 105 sites

• ASV data was collected through 4 field campaigns from thousands of sites

• UAS data was collected through 2 week-long trips by 68 flights

• Remote sensing algorithms were developed that can quantifying suspended 

particulate matter, turbidity, CDOM, chlorophyll a, phycocyanin, total alkalinity, 

pCO2, and salinity in the western Mississippi Sound.

• Remote sensing algorithms yield time series of water quality parameters over 

oyster reefs. 

• All the algorithms look promising with reasonably high R2 and low RMSE
How Results Can Inform Restoration/Management

• Results demonstrate which watershed management practices are most effective 

at reducing total suspended solid and phosphorus in Mississippi Sound waters.

• Scenarios of low flow from the Wolf and Jordan Rivers during summer months 

will be run to understand the resulting dissolved oxygen, temperature, and 

salinity in oyster reef areas and how these scenarios may affect oyster 

populations. 

• SWAT watershed modeling creates capacity to better understand and predict the 

dynamics of freshwater inflow from the Wolf and Jordan Rivers into the 

Mississippi Sound including alteration of temperature, DO, and salinity regimes 

as well as water quality parameters including nutrient loading.

• Remote sensing results will indicate the spatiotemporal distribution of a suite of 

water quality parameters in WMS and causal mechanisms, which may inform 

management of water quality and oyster fisheries. 
Project Outputs

• Theses & Dissertations:

• Shreeya Bhattarai, Mississippi State University Ph.D. Dissertation. 2023

• Conference Presentations:

• Dash, P., Moorhead, R. J., Herman, J., Sankar, M. S., Moorhead, J., Beshah, W., Chesser, D., Lowe, W., Simmerman, J., and Turnage, G. 2021. Evaluation of Water Quality Data Collected using a Novel Autonomous Surface Vessel, Global 

Oceans 2021 Conference and Exposition, San Diego, CA, September 20-23, 2021.

• Bhattarai Shreeya, and Prem B. Parajuli. 2022. Assessment of BMP practices on water quality of coastal watersheds in Mississippi. ASABE Annual International Virtual Meeting, July 17 to 20, 2022; Marriott Marquis Houston, Texas.

• Bhattarai Shreeya, Prem B. Parajuli, and Filip To. 2022. Evaluation of terrestrial flow into coastal water by anticipating the sediment yield and nutrient loss. 2022 Mississippi Water Resources Conference, April 12-14, The Mills in 

Starkville, MS.

• Peer-Reviewed Publications:

• Dash, P., Moorhead, R. J., Herman, J., Sankar, M. S., Moorhead, J., Beshah, W., Chesser, D., Lowe, W., Simmerman, J., and Turnage, G. 2021. Evaluation of Water Quality Data Collected using a Novel Autonomous Surface Vessel, 

Proceedings of Global Oceans 2021 Conference and Exposition, San Diego, CA, September 20-23, 2021.

• Sankar, M.S., Dash, P., Lu, Y. et al. 2023. Seasonal changes of trace elements, nutrients, dissolved organic matter, and 

coastal acidification over the largest oyster reef in the Western Mississippi Sound, USA. Environ. Monit. Assess., 195, 

175

• Shreeya Bhattarai, Prem B. Parajuli, and S. D. Filip To. 2023. Comparison of flood frequency at different climatic 

scenarios in coastal forested watersheds. Climate.

• Shreeya Bhattarai and Prem B. Parajuli. 2023. Water quality assessment with best management practices in coastal watersheds. Sustainability.
Mississippi Based RESTORE Act Center of Excellence

Mississippi State University Department of Geosciences

Northern Gulf Institute

Field Assistance: Jonathan Harris, Gray Turnage

Data Processing: Lee Hathcock

UAS Crew: David Young, Sean Meacham, Logan Renz, Cary Daniel McCraine, and Jessica Wolfe

ASV Crew: Jessica Wolfe & Daniel Chesser

This project was paid for with federal funding from the Department of the Treasury under the 

Resources and Ecosystems Sustainability, Tourist Opportunities, and Revived Economies of the 

Gulf Coast States Act of 2012 (RESTORE Act). The statements, findings, conclusions, and 

recommendations are those of the author(s) and do not necessarily reflect the views of the 

Department of the Treasury.

Acknowledgements
Impacts of water quality on oyster 

development to inform oyster reef restoration 

and sustainability on the Mississippi Gulf Coast

Deborah Gochfeld

Lead PI

Kristie Willett

Co-PI

Stephanie Otts

Co-PI

Jessica Pruett

Postdoctoral Fellow

Ann Fairly Pandelides

Associate R&D Biologist
What has Happened to Mississippi’s Oysters?

Source: MSU Extension Center

Source: MS Dept. of Archives & History
21st Century Declines in MS Oyster Populations

Source: MDMR Shellfish Bureau
Area II "G"

Area III

Area II

Area II "G"

Area II "B"

Area II

Area II "F"

Area II "E"

Area II "A"

Area II "I" Area II "I"

Area IV

Area III

Area II "D"

Area II

Area II

Area II

De Lisle

Pass Christian

Bay Saint Louis

2019 Environmental Toxicology Study Sites

 ̄

Explanation

City and Town Points

Spring/Summer 2019 Sites

Public Oyster Reefs

2017 Harvest Zones

0 1 2 4

Miles

#

#

#

#

#

#

No live oysters at any sites 2 months after BCS closure

U.S. Army Corp of Engineers 
NOAA Chesapeake Bay Office 

Oyster reef restoration success 

depends on early life stages

Source: NOAA Gulf Spill Restoration

Source: NOAA Chesapeake Bay Office 
Increases

stormwater 

runoff Increases 

freshwater into

estuaries

Increases 

nutrients

Die and decay

Decreases oxygen

Increases CO2/

Reduces pH 

How do early oyster life 

stages respond to floodassociated stressors?

Heavy

rainfall

Algal Blooms

Adult oyster reef

Veliger larvae Pediveliger larvae

Juvenile spat

Low 

Salinity

= water quality stressor

Oyster Life 

Stages

Images from the Integration and Application Network 

(ian.umces.edu/media-library)

Coastal 

Acidification Hypoxia
Project Goals and Objectives

Goal: Integrate field, laboratory and policy research on impacts of abiotic and biotic stressors 

on early life stages of oysters to inform sustainable oyster reef restoration efforts in MS coastal 

waters

Objective 1:

• Collect data on levels of water quality stressors across the MS Sound
Salinity conditions near priority sites for oyster 

restoration in Mississippi (May-September 2021) 

HS
Project Objectives

Objectives 2 & 3:

• Characterize effects of single and multiple stressors on early life stages of oysters in the lab

• Assess growth and survival of juvenile oysters deployed in the MS Sound
Pediveliger larvae 

(14+ days old)

Post-settlement juvenile 

(1-day post-set)

Early juvenile 

(~4 weeks old)

Veliger larvae 

(48 hours old)

Stressor Treatments

• Low dissolved oxygen (< 2 mg/L O2)

• Low pH (7.3-7.6)

• Low salinity (15 ppt 6 ppt)

• Two-way combinations of stressors

• All three stressors

How do early oyster life stages respond to 

flood-associated stressors?
Reduced veliger growth in hypoxic and low salinity conditions 

*Different letters denote means that are significantly different (P < 0.05)

Control treatment

All stressors treatment
Reduced settlement in flood-associated stressors

*Different letters denote means that are significantly different (P < 0.05)

Settlement = Larvae attached 

to substrate 
Increased post-settlement mortality in lower 

salinity 

7-day old spat

*Different letters denote means that are significantly different (P < 0.05)
Increased juvenile mortality only in the 

presence of all three water quality stressors 

*Different letters denote means that are significantly different (P < 0.05)
Negative growth in the presence of all three stressors

Control End

All Stressors End

*Different letters denote means that are significantly different (P < 0.05)
Adult spawning?

Veliger larvae 

(48 hours old) Pediveliger larvae 

(14+ days old)

Post-settlement 

spat

Early juvenile 

Reduced 

growth Reduced 

settlement

Longer time

in water column

Decreased 

survival

Reduced

recruitment

Reduced

recruitment

Reduced 

growth

Delayed sexual maturity/

Reduced resilience 

Eastern Oyster 

Life Cycle

Flood-associated 

stressors
Objective 4. 

Policy Brief 

• Flood-associated stressors have 

negative impacts on early oyster life 

stages

• Salinity is an important indicator of 

oyster recruitment at a potential 

restoration site

• Hypoxia and acidification stressors 

can add to already damaging 

effects of low salinity 

Project website: http://nsglc.olemiss.edu/projects/oysterreefrestoration/index.html
Next Steps 

• Incorporation of early life stage tolerance thresholds into decisionmaking tools

• Enhancement of restoration aquaculture practices 

• Leveraging existing environmental datasets to better understand the 

issues and challenges that affect oyster reef resilience 

• Establishment of continuous monitoring stations at priority oyster 

reef locations throughout the Gulf of Mexico 
Increases

stormwater 

runoff Increases 

freshwater into

estuaries

Increases 

nutrients

Die and decay

Decreases oxygen

Increases CO2/

Reduces pH 

Questions?

Project Webpage: 

http://nsglc.olemiss.edu/projects/oyster

reefrestoration/index.html

Heavy

rainfall

Algal Blooms

Adult oyster reef

Low 

Salinity

= water quality stressor

Oyster Life 

Stages

Coastal 

Acidification Hypoxia

Slower

development

Veliger larvae Pediveliger larvae

Juvenile spat
Acknowledgements

This project was paid for with federal funding from the U.S. Department of the 

Treasury, the Mississippi Department of Environmental Quality, and the 

Mississippi Based RESTORE Act Center of Excellence under the Resources 

and Ecosystems Sustainability, Tourist Opportunities, and Revived Economies of 

the Gulf Coast States Act of 2012 (RESTORE Act). The statements, findings, 

conclusions, and recommendations are those of the author(s) and do not 

necessarily reflect the views of the Department of the Treasury, the Mississippi 

Department of Environmental Quality, or the Mississippi Based RESTORE Act 

Center of Excellence.

• UM MBRACE Core Research Team

• Greg Easson, Marc Slattery, Luke Campbell, 

Allison Woolsey

• MBRACE Directorate

• Kelly Darnell, Luke Fairbanks

• Letha Boudreaux & the St. Stanislaus High School 

Marine Science Interns

• Scott Rikard at Auburn University Shellfish Laboratory

• Megan Gima at Thad Cochran Marine Aquaculture 

Center