Southeast Science Surveys and Research

Coral Reef Science

Mesophotic Reef Fish Surveys

Description: We conduct deep-water fish surveys to collect fish size and composition data on species of high ecological/management importance that cannot be landed (e.g., Nassau grouper) and economically valuable species targeted by the fishery (e.g., groupers, snappers, parrotfishes). Reliable fishery-independent reef fish monitoring data is only collected in shallower waters of less than 30 meters and is presently missing up to half of the shelf from 30 to 60 meters near important management areas. This is particularly problematic since declines in shallow water catches have resulted in fishermen regularly targeting economically valuable species over the deep mesophotic or low light reef habitat, where light penetration drops off sharply. The expansion of fishery-independent surveys to encompass the entire reef tract from 0 to 60 meters provides accurate and unbiased information needed for island-based management. This study is funded by NOAA’s Coral Reef Conservation Program.

National Coral Reef Monitoring Program in U.S. Atlantic

Description:The program surveys the reef's benthic community including corals, algae, and fish in the U.S. Atlantic coral reefs. Reef Visual Census fish surveys, coral demographic, and benthic assessment SCUBA surveys are conducted annually in shallow waters  between zero and 30 meters. The data collected are used to describe population status and trends, inform coral and fish population management strategies, document threatened and endangered species, track coral disease, and assist with local monitoring efforts. NOAA Fisheries samples both fish and corals for the program however, the Southeast Fisheries Science Center is the lead for the fish data and our National Centers for Coastal Ocean Science partners are the lead for the benthic data in all regions. This study is funded by NOAA’s Coral Reef Conservation Program.  

Learn more about the national coral reef monitoring program

Calibration of Historical Coral Reef Fish Datasets

Description: In the U.S. Caribbean and Flower Garden Banks, fish survey data was historically collected using the belt-transect method. In 2016, the National Coral Reef Monitoring Program made the change to collect fish samples using the same Reef Visual Census method in all U.S. Atlantic jurisdictions. Presently, these two datasets cannot be combined. Each year this calibration study samples sites in targeted regions using both the belt-transect and reef visual survey methods. Following thorough data collection, an analyst will complete a method calibration to ensure that the existing historical data can be combined with newer reef visual census data. This calibration is important because it ensures the preservation and use of a long-time series reef fish dataset for the public, scientific, and management communities in these regions. Funded through multiple sources including NOAA's Coral Reef Conservation Program and Marine Fisheries Initiative grants.

Acroporid Coral Mapping

Description: We document long-term, reef-scale trends of local acroporid coral populations and the effect of population enhancement efforts (i.e. coral outplanting) via periodic, broad-scale census of elkhorn coral (Acropora palmata) and staghorn coral (Acropora cervicornis). The upper Florida Keys populations have experienced multiple disturbance events since this census began in 2005, including multiple tropical storms, severe cold thermal events and severe warm thermal bleaching events. This sustained effort provides a novel opportunity to evaluate potential reef-scale effects of acroporid population enhancement against a backdrop of ongoing chronic and acute disturbances in the reef environment.

Coral Spawning

Description: Since 2002, this project has documented spawning activity among two Caribbean coral species Elkhorn coral  (Acropora palmata) and Mountainous star coral (Orbicella faveolata) in the upper Florida Keys. Both of these species are listed as Threatened under the U.S. Endangered Species Act. Our observations have advanced the understanding of the timing of spawning in these broadcast spawning species. Additionally, our collection of coral gametes and larval propagation has provided opportunities to examine and better understand factors that may influence larval success (i.e. settlement and survivorship) under future climate regimes including ocean warming and acidification. This work has contributed to the new and rapidly expanding field of larval propagation to support reef restoration. In addition to improving techniques, we have been the primary source for coral larvae (particularly elkhorn coral larvae) for Florida restoration efforts as well as laboratory research collaborators. Recently, our monitoring and spawn-collection efforts have expanded to include other species with less known spawning information (i.e. grooved brain coral) as well as outplanted colonies of elkhorn and staghorn coral.

Elkhorn Coral Status & Conservation

Description: This project is centered on long-term demographic monitoring of the endangered coral, Acropora palmata (elkhorn coral) in the upper Florida Keys. We collect basic population metrics such as the numbers and sizes of individual colonies, recruitment (birth rates), mortality (death rates) and various health parameters (disease, bleaching, predation, etc.) along with genotypic identification for individual colonies. These surveys have been conducted in fixed monitoring plots since 2004, and are necessary to determine changes to the population, estimate future population trajectories and identify factors that hinder recovery. These data allow us to understand the relative impacts of stressors so managers can prioritize conservation efforts and resources. In particular, the genotypic analysis has allowed NOAA managers and restoration practitioners to establish an organized gene banking effort for remaining genotypes on Florida Keys reefs, and is supporting the effort to identify ‘donor’ colonies for nursery propagation. A detailed protocol was released in 2006 describing our fixed-plot survey methodology that has been used by several research agencies throughout the Caribbean resulting in region-wide data that can be easily compared.

Coral Restoration Science

Description: Propagating and raising coral fragments in a nursery for transplantation to the reef has become an increasingly popular tool to promote reef restoration. We evaluate various methodologies in coral outplanting to determine best practices promoting coral growth and survivorship. Beginning in 2013, our team has examined the effect of habitat, fragment size and fragment genotype on outplant success for elkhorn coral. In 2016, a follow-up study was implemented to evaluate the effect of genotypic diversity and spatial design on coral outplant success and ecosystem function (i.e. fish habitat). As coral restoration science is still in its infancy, it is crucial to understand factors that may influence outplant success, particularly for elkhorn coral, a foundational reef building species with complex morphology providing critical habitat for reef organisms.

Coral Disease Resistance Monitoring

Description: This project aims to identify disease-resistant genotypes of Atlantic corals. We use standardized field protocol based on replicated direct-graft challenge assays along with a strategic long-term monitoring design of outplanted acroporid coral fragments. Additionally, in collaboration with the NOAA Atlantic Oceanic and Meteorological Laboratory's Omics Project, our team collected coral tissue samples, environmental data (ocean current and temperature data), and observations of various coral health indicators to evaluate the relationship between a coral’s microbiome and the coral’s susceptibility to disease. Disease mortality is a primary driver of coral population declines. Understanding genetic resistance to disease can aid in the development of effective diagnostic tests and disease treatments, and can inform coral restoration practitioners and managers in developmental strategies for population enhancement efforts.

Fish Research

Red Snapper Movements on Natural Reefs

Description: This field-based study in the Gulf of Mexico aims to quantify the home range and site fidelity of red snapper on natural reefs using underwater listening devices, i.e. acoustic telemetry (Vemco VPS), and underwater camera systems. The goal is to provide critical and currently lacking data to inform upon the implications that localized removals of red snapper on artificial structures may have upon adjacent natural areas. The project focuses on an extremely high-profile need to provide much-needed management alternatives for the recreational fishery. This study is a partnership with the Florida Fish and Wildlife Conservation Commission. Field sites and tagging are completed with the assistance of Cooperative Research Program anglers. This study is funded by NOAA's Marine Fisheries Initiative and Coral Reef Conservation Program grants.

SEAMAP Groundfish Survey

Description: We collect data concerning the distribution and abundance of bottom dwelling fish (also called "groundfish") and invertebrate populations to aid in stock assessments. In addition, we collect morphological measurements (the size and shape of organisms) and biological samples to facilitate life history studies. Survey data are used in ecosystem models for the Gulf of Mexico and provide critical shrimp bycatch estimates that have been used in multiple assessments (SEDAR) across several species groups. The Southeast Area Monitoring and Assessment Program (SEAMAP) Fall Groundfish Survey has been conducted in the northern Gulf of Mexico since 1972. The SEAMAP Summer Groundfish Survey has been conducted in the northern Gulf of Mexico since 1982. They represent a partnership between NOAA Fisheries and Gulf state partners (Florida Fish and Wildlife Conservation Commission, Alabama Department of Conservation and Natural Resources, Louisiana Department of Wildlife and Fisheries, and the University of Southern Mississippi).

Learn more about the Summer and Fall Groundfish Surveys

Southeast Fishery-Independent Survey

Description: We use fish traps with attached video cameras to index the abundance of various economically important reef fish species like red snapper, gag grouper, gray triggerfish, and red porgy. The Southeast Fishery-Independent Survey (SEFIS) was created in 2010 to increase scientific fish sampling in the Southeast region, in collaboration with the South Carolina Department of Natural Resources. The survey provides key data inputs for various reef fish stock assessments.

Southeast Region Headboat Survey

Description: We collect catch and effort information, along with dockside biological samples, from the headboat fishery in the southeast United States where groups of fishermen pay to fish together. This fishery-dependent survey provides data to support stock assessments and annual quota monitoring for a suite of bottom-dwelling (demersal) and coastal migratory species in the South Atlantic and Gulf of Mexico waters. Resulting data is used by the South Atlantic Fishery Management Council and the Gulf of Mexico Fishery Management Council Assessment and Review (SEDAR) process, NOAA Fisheries' Southeast Regional Office, the Gulf States Marine Fisheries Commission, and the Atlantic States Marine Fisheries Commission.

Menhaden Ecological Reference Points

Description: Center scientists collaborate with the Atlantic States Marine Fisheries Commission, academic scientists, state agency scientists, and others to provide tools for use in an ecosystem-based approach to fisheries management of Atlantic menhaden. The Atlantic menhaden population supports the largest fishery by volume on the U.S. East Coast and is an important forage species for predators.

Shark/Snapper/Grouper Bottom Longline Survey

Description: We provide data for indices of abundance for sharks, snapper, grouper, and tilefish in the western North Atlantic Ocean. Operations are conducted from Cape Hatteras, North Carolina to approximately West Palm Beach, Florida off the east coast and throughout the northern Gulf of Mexico, from the Dry Tortugas to Brownsville, Texas. We also collect biological materials (fin clips, otoliths, gonads, and more), conduct life history studies, and tag species of interest to monitor movement patterns and growth in the wild.

Marine Mammal Science

Marine Mammal Health and Stranding Response Program

Description: As a part of the National Marine Mammal Health and Stranding Response Program, we coordinate emergency responses to sick, injured, distressed, or dead marine mammals (cetaceans and pinnipeds) in the Southeast U.S. Our role is to investigate stranding events and health trends, provide oversight and guidance to the Southeast Marine Mammal Stranding Network, and manage data collected from stranded marine mammals. Information collected from stranded marine mammals can provide a better understanding of basic marine mammal biology, mortality trends, and human impacts on marine mammal populations. The valuable biological information collected during stranding responses helps us make better management decisions for marine mammal conservation.

To report dead, debilitated, or distressed live marine mammals (i.e., whales, dolphins) on land or in the water, including either oiled or non-oiled animals, call 1-877-WHALE HELP (1-877-942-5343).  

Learn more about how to help a stranded marine mammal

Learn more about our Marine Mammal Health and Stranding Response Program 

Marine Mammal Population Assessments

Description: Our teams conduct vessel and aerial surveys in the coastal and offshore waters of the U.S. to collect the necessary data to monitor several marine mammal species and stocks. In the bay, sound, and estuaries we use photo-identification techniques to determine the population size, habitat use, and health condition of different stocks of bottlenose dolphin. In the offshore waters of the Atlantic Ocean and Gulf of Mexico, through the AMAPPS and GoMMAPPS programs respectively, we collect data on the distribution and abundance of whales, dolphins, and sea turtles. Using the visual sighting and acoustic detection data from these offshore surveys, we develop models and tools that incorporate environmental habitat characteristics to provide seasonal density estimates for these protected species. Coastal and offshore stocks are determined by the sampling of tissue for genetic studies. All these data allow for the production of Stock Assessment Reports and provide enhanced data to managers to properly monitor different marine mammal populations and mitigate potential impacts of human activities, including those related to energy development.

Learn more about southeast marine mammal research surveys

Trophic Interactions and Habitat Requirements of Gulf of Mexico Rice’s Whales

Location / Timing: Gulf of Mexico / 2017-2020

Description: We conducted 3 research cruises in the primary habitat of Rice's whales to develop a comprehensive ecological understanding of the physical, oceanographic, and biological features that potentially affect this population. We collected data on the distribution of the whales and their potential prey, deployed tags to study their foraging and acoustic behaviors, sampled whale tissue for genetic studies and performed net trawls to characterize their prey species, among other data. The Deepwater Horizon Oil Spill impacted half of the Rice's whale's main habitat and these whales have an estimated population of less than 40 individuals. Analyzing the data from these research cruises combined with other environmental habitat characteristics will provide critical information to managers for recovery and restoration activities.

Learn more about the research to understand the Rice's whale's trophic interactions and habitat requirements

Learn more about this Restore Science Program

Passive Acoustic Monitoring Program

Location / Timing: U.S. Atlantic and Gulf of Mexico waters / Year-round

Description: We use underwater recording instruments to listen to and detect sounds in the ocean, including the sounds produced by whales and dolphins. As part of our ship-based offshore population assessments, we deploy towed hydrophone (underwater microphone) arrays and sonobuoys (small expendable listening devices released from planes or ships) to detect and localize calling marine mammals. This data is used in spatial density and abundance modeling, and to improve our understanding of calling behavior. Additionally, we deploy moored instruments that remain at the bottom of the ocean for long periods and continuously record ocean sounds including calling marine mammals if present in the area. These data are vital to determine seasonal, annual, and decadal trends in marine mammal distribution to understand movement patterns and habitat use.

Assessing Trends and Variability in Cetacean Density throughout the Gulf of Mexico

Location / Timing: U.S. and Mexican waters of the Gulf of Mexico / 2020-2024

Description: We are implementing a comprehensive, long-term, multi-scale moored passive acoustic monitoring program throughout the U.S. and Mexican Gulf of Mexico waters. It will provide data to develop predictive habitat models to assess the processes that drive seasonal, interannual, and decadal trends in spatial distribution, density, and abundance of oceanic cetaceans (whales, dolphins). This project will integrate long-term sampling to identify temporal trends and variability at reference sites over the study period. It will include short-term sampling over a broad area of the Gulf of Mexico to capture spatial trends and variability in cetacean density and environmental processes. It will also include targeted sampling using arrays to obtain acoustic behavior data for density estimation. 

Learn more about this Restore Act science project 

Marine Mammal Genetics Program

Description: At the Marine Mammal Molecular Genetics Lab, scientists collect and study the DNA of cetaceans (whales, dolphins and porpoises) to detect new species, investigate how species are related to one another, determine how many populations there are for each species, and identify where different species and populations occur. DNA is extracted from marine mammal soft tissue (e.g., skin, muscle) and bones collected from field biopsies, live captures, bycatch and stranding events. Information gathered from genetic data helps to improve our understanding of how marine mammals partition themselves within their environment and how they may be affected by natural and anthropogenic (man-made) impacts. Using this information we collaborate with others to develop management plans to conserve the diversity of the marine mammals inhabiting U.S. waters.   

Assessing Species Occurrence and Diversity Using Environmental DNA (eDNA)

Description: Scientists at the Marine Mammal Molecular Genetics Lab are developing collection and analysis protocols to study environmental DNA, commonly referred to as eDNA, from fish and marine mammal species. Water samples have been collected from Rice's whale habitat during research cruises and are being analyzed to determine how well we can detect the presence of these endangered whales through non-invasive sampling of the water they are swimming through. We are also developing techniques using eDNA to identify what fish species are present when Rice's whales are feeding to better characterize their prey preference and habitat use.

Assessing Risk of Mortality and Serious Injury to Cetaceans from Commercial Fisheries

Location / Timing: U.S. Atlantic and Gulf of Mexico waters / Year-round

Description: Our scientists assess risk of incidental death and serious injury from commercial fisheries for different species of cetaceans and provide data for developing effective management measures for these species. For example, we provide information on incidental mortality and serious injury of common bottlenose dolphins in western North Atlantic coastal and estuarine waters for the Bottlenose Dolphin Take Reduction Team. The team then makes recommendations on how to reduce this bycatch in gillnet, pound net, and trap pot fisheries in the region. We additionally provide information on incidental mortality and serious injury of common bottlenose dolphins and Atlantic spotted dolphins in the Gulf of Mexico shrimp otter trawl fishery. We work with NOAA Fisheries’ Southeast Regional Office and other partners to develop gear modifications to reduce bycatch in this fishery. Long-finned and short-finned pilot whales also have teams of scientists assessing mortality and serious injury. These two species are subject to interactions with the Atlantic pelagic longline fishery and the main goal of the Pelagic Longline Take Reduction Team is to reduce bycatch of pilot whales in this fishery.

Observers/Samplers

Platform Removal Observer Program

Description: We protect sea turtles and marine mammals from impacts of underwater explosives associated with the salvage and removal of offshore oil and gas structures in the U.S. Gulf of Mexico. Observers perform surface and aerial monitoring of the area around the platforms to detect the presence of sea turtles and marine mammals. When protected animals are within the blast impact zone around the platform, detonation of explosives is delayed, and surveys are repeated until the animals have either moved outside the impact zone or are no longer observed. Observers document sightings of sea turtles and marine mammals both before and after detonations. They record data on the condition of observed animals, assess impacts on these protected species, and coordinate retrieval of impacted animals for medical examination, rehabilitation, and necropsy (an autopsy on a dead animal).  

Learn more about the Platform Removal Observer Program

Trip Interview Program

Description: We collect detailed commercial fisheries information including the catch, effort, and biological data collected at the individual trip level by shore-based samplers. Our trained field biologists visit docks and fish houses to interview fishermen and take length, weight, and biological samples from their catch. These samples, which include otoliths, spines, and occasional tissue samples, are sent to one of two laboratories for biologists to analyze and determine the fish’s age and other biological information. These data contribute to the Atlantic Coastal Cooperative Statistics Program in the Southeastern Atlantic coastal region and the commercial Fisheries Information Network in the Gulf of Mexico coastal region. 

Learn more about the Trip Interview Program

Plankton Research

Southeast Area Monitoring and Assessment Program (SEAMAP) Ichthyoplankton Surveys

Description: Our SEAMAP surveys provide a time series of standardized, fisheries-independent data on the occurrence, abundance, geographical distribution and pelagic habitat of the early life stages of fish. Plankton nets collect samples of larval fish (ichthyoplankton) and invertebrate zooplankton such as crab, shrimp, and squid. Instruments collect environmental data such conductivity, temperature, depth, dissolved oxygen, fluorescence, and turbidity. Data are used to generate fishery-independent indices of relative abundance used in the assessment for a number of important species in the Gulf of Mexico. There are a number of non-fisheries applications of the survey data as well. These SEAMAP surveys have been conducted in the Gulf of Mexico since 1982.

Effects of Nitrogen Sources and Plankton Food-Web Dynamics on Habitat Quality for the Larvae of Atlantic Bluefin Tuna in the Gulf of Mexico

Description: This NOAA RESTORE Science Program project focuses on the iconic Atlantic bluefin tuna in the Gulf of Mexico. These fish are highly migratory and spawn in the Gulf of Mexico, but as adults they are distributed throughout the Atlantic Ocean. This migratory behavior, as well as year to year changes in environmental conditions at sites where Atlantic bluefin tuna spawn, makes management of the species complex and difficult to predict. Being able to track how changes in nutrient availability, particularly nitrogen, impact tuna food webs and larval survival is essential to managing open ocean ecosystems. Our goal is to improve stock assessments of bluefin tuna by filling in data gaps to forecast the feeding, growth, and survival of Atlantic bluefin tuna larvae based on the ocean conditions in the Gulf of Mexico. This project has a large research team including researchers from NOAA’s Southeast Fisheries Science Center, University of Miami, Florida State University, Scripps Inst. of Oceanography, University of California at San Diego, and University of Hawaii at Manoa. 

Sea Turtle Science

Sea Turtle Age and Growth Studies

Description: We refine and apply analytical techniques to investigate sea turtle age and growth through analysis of bone growth marks. All sea turtle populations in U.S. waters are listed as threatened or endangered under the U.S. Endangered Species Act. To conserve these populations, it is necessary to collect age and growth data to help understand how long they spend in different habitats where they are exposed to habitat-specific threats to their survival, as well as how long it takes them to become adults.

Learn more about the scientists who do this work

Sea Turtle Stranding and Salvage Network

Description: The Network is a cooperative effort of federal, state, and permitted private partners working to inform causes of morbidity and mortality in sea turtles. This is done by responding to and documenting sea turtles, found either dead or alive (but sick or injured) to inform conservation management and recovery. Typical strandings data collected include date, species, location, condition and disposition, and specifics describing anomalies (e.g.propeller damage, entanglement, illness). The Network may also collect samples (e.g. humeri for aging, tissue for genetics / stable isotope study) or salvage an entire carcass for necropsy. All sea turtles that occur in U.S. waters are listed as either threatened or endangered under the Endangered Species Act. While NOAA Fisheries coordinates the Network, it is the participating local organizations that respond to stranded turtles, collect scientific data, transport sick and injured turtles to rehabilitation facilities, and help educate the public about sea turtle conservation.

Learn more about how to help or report a stranded sea turtle 

Learn more about the sea turtle stranding and salvage network

Use of Drift Studies to Understand Seasonal Variability in Sea Turtle Stranding Patterns

Description: Sea turtle stranding data are important to identify areas of concern and in some cases likely cause of death. The majority of strandings are only reported when carcasses reach the beach, which varies depending on the time of year and oceanographic conditions. Wooden effigies (models) and sea turtle carcasses with GPS satellite tags attached were used to investigate how weather and wind patterns influence drifting behavior. This study found that the probability of a carcass beaching greatly decreases in the summer months due to increased scavenging and shifting wind patterns, which blow carcasses offshore. Information from this study has helped sea turtle mortality investigators understand patterns in stranding data. This research was funded by the Deepwater Horizon Sea Turtle Early Restoration Project.