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Two teams from the St. Petersburg Coastal and Marine Science Center (SPCMSC) traveled to the Florida Keys this summer, collaborating to better understand and predict seafloor erosion at Looe Key Reef.

Scientists working on the Processes Impacting Seafloor Change & Ecosystem Services (PISCES) project spent 10 days in the Keys this summer, collecting essential data for understanding important marine processes such as seafloor change and coral growth.

Some areas along the Florida Keys Reef Tract have lost as much as 10 feet of elevation in the last few decades due to seafloor erosion. Not only does this cause a loss of habitat for fish and other marine life, but also increases coastal vulnerability to sea-level rise and storms. Although conservation groups in the Keys have already started working to restore the lost coral reefs, more information about seafloor change is needed to help guide their efforts. To understand just how much the reef has eroded and where erosion is most severe, USGS staff had to develop innovative methods to collect high-resolution measurements of seafloor change.


Seafloor Mapping Technology

The SQUID-5 camera system sits on the deck of the R/V Sallenger at dock
The SQUID-5 system sits on the deck of the R/V Sallenger USGS research vessel. It is being used to image the seafloor off of Looe Key, FL.

The first half of the PISCES field work team included Gerry Hatcher of the Pacific Coastal and Marine Science Center (PCMSC) and Dr. Dave Zawada of the SPCMSC, two of the lead scientists behind the creation of the Structure-from-Motion Quantitative Underwater Imaging Device with 5 Cameras (SQUID-5) system. The SQUID-5 is the product of a cross-center partnership, with the Remote Sensing Coastal Change team at the PCMSC in charge of engineering the device, and the PISCES team at the SPCMSC tasked with its deployment and data collection.

Essentially the SQUID-5 is a floating platform that has five cameras which are situated at different angles accompanied by an onboard GPS system. When you tow it over the reef, it takes pictures very rapidly from all five cameras. And because the positions of those cameras are slightly different, the pictures can be used to build 3D imagery of that reef,

explained Dr. Kimberly Yates, Project Chief of the PISCES project and SPCMSC Research Oceanographer.

The PISCES team towed the SQUID-5 system over the hundreds of feet of seafloor encompassing Looe Key to gather the pictures required to construct high-resolution 3-dimensional models of seafloor structures. The final products will include full-color 3D maps, sharp enough to see individual corals on the ocean floor, and digital elevation models of both the seafloor and the reefs.


Informing Coral Reef Restoration

These models will be utilized by USGS partner organizations including the National Oceanic and Atmospheric Administration (NOAA), Mote Marine Laboratory, and the Florida Fish and Wildlife Conservation Commission (FWC) Florida Fish and Wildlife Research Institute, who use the elevation change and seafloor stability data as guidance for their own research projects. Most notably, the models will help NOAA and its partners gauge the success of reef restoration site efforts through the Mission: Iconic Reefs project throughout its 20-year timeline.


How Much Reef Erosion is From Organisms?

The second half of the PISCES team spent their time in the Keys collecting diver-based surveys of reef ecosystems. At dozens of Mote Marine Laboratory’s coral restoration sites across various reefs, divers surveyed transects, or gridded areas, where they counted fish, sponges, and urchins, and collected images of the reef. The numbers of each species that contribute to reef growth (corals and coralline algae) and to reef bioerosion (fish, sponges, and urchin) will be put into a carbonate budget equation to determine the effect ongoing restoration efforts are having on the balance between these processes. This data is helpful to determine which factors are most beneficial to reef growth at restoration sites. It also helps partners such as Mote Marine Laboratory, who will use the data to make decisions such as which types of coral to plant at future restoration sites.

Two divers float near coral reef with measuring tools to survey marine life
Two divers from the CREST research team float underwater near Looe Key, FL to survey fish, urchins, and sponges. 

The instantaneous monitoring of reef growth is really hard to measure because reef growth really is a long-term process. We use what is called a carbonate budget to measure reef growth in real time. We count all the organisms out on the reef building up the structure (e.g., coral) and count all the organisms that are eating away at that structure (e.g., parrotfish, urchins, sponges) to get a net budget of reef growth,

said Dr. Lauren Toth, a SPCMSC Research Oceanographer and one of the principal investigators of the study.



Painting a Full Picture

Much like the SQUID-5 images, these underwater images collected at the reefs will be made into 3D models and serve as a reference for what the reefs looked like at present. Future models will be compared to this year’s model to visualize changes in the reef over time. The SQUID-5 imagery can also be used to supplement diver-based imagery if both are collected at the same sites. Yates said,

The SQUID-5 data provide highly accurate locational information for collected imagery. Divers can collect repeat imagery where we have already collected SQUID-5 data, then use our georeferenced data to apply accurate positioning to their data. This means they can go back year after year to the same site and accurately measure change over time.


Working with Local Partners

In order to successfully complete their field work, both teams worked with several collaborators who assisted with field operations. The reef areas being imaged must be closed to the public to minimize image interference for collection of the most accurate data from the SQUID-5. The Florida Keys National Marine Sanctuary assisted in communicating to the public that USGS field work teams would be in the area and that large parts of Looe Key reef would be shut down. Teams from the U.S. Coast Guard, NOAA, FWC, and the National Weather Service all assisted in regulating the waters around the reefs and supporting the USGS field work teams. Yates praised these partners saying,

A scientist on the back of the R/V Sallenger tows the SQUID-5 system behind the boat.
The SQUID-5 system is pulled behind the USGS research vessel the R/V Sallenger near Looe Key. The SQUID-5 is taking images of the seafloor which will be made into 3-dimensional models.

We appreciate the local community so much. Their understanding with [these projects] has been pretty great. Their livelihoods and businesses depend on healthy reefs and the work that we're doing is helping keep those reefs healthy and they understand it. They're very respectful and supportive of the work.

The PISCES team has plans to conduct seafloor surveys and carbonate budget studies through 2025 and anticipates a further continuation of the project beyond then. Toth concluded,

This is the start of what I’m hoping to be a several year project where we can look at several different sites throughout the Keys where restoration activities are happening. We can look at different types of corals, different types of reefs that are being restored, and hopefully get an idea of where restoration is most successful and what we might expect as restoration is scaled up in the future.

The field crew this summer included Andy Farmer, Ben Galbraith, Selena Johnson, Ben Klein, Christine Kranenburg, Erin Lyons, Anastasios Stathakopoulos, and Lauren Toth of the St. Petersburg Coastal and Marine Science Center.


Video Transcript
Coral reefs are important for supporting biodiversity, fisheries, tourism, and coastal protection, but are in decline worldwide, primarily due to extreme heat waves and subsequent coral bleaching, in addition to other stressors. By combining data and knowledge on seafloor elevation and coral reef carbonate budgets, USGS scientists are collaborating to better understand the current state, and predict the future of, the Florida Keys Reef Tract. The data being collected by USGS can also help inform partners working on coral reef restoration efforts such as the National Oceanic and Atmospheric Administration (NOAA).  Learn more about this research.

Listen to the audio-described version.

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