A small, yellow boat-like device floating on the water's surface
Autonomous devices like this one utilize a computer program, underwater cameras, and GPS precision to collect visual imagery of benthic habitat. Photo: NOAA

Innovations in science and data collection technologies provide a more efficient and accurate way for scientists to obtain more comprehensive information about the ecosystems of the Florida Keys. This includes new information on species that inhabit these ecosystems and their behaviors, ecosystem services provided to humans, and how human activities impact these important ecosystems.

Sensor Arrays

a yellow object on the seafloor
A strategic array of instruments measured wave height, currents, and temperature at Eastern Dry Rocks during Category 4 Hurricane Ian. Photo: NOAA

Even though coral reefs occupy less than 0.1% of the world's ocean area, they are one of the most diverse ecosystems on the planet and they provide numerous ecosystem services to humans worldwide. In addition to the habitat they provide for numerous organisms, the reef building corals that occur on these reefs produce massive, wave resistant structures that act as a barrier to the effects of major storms and waves. This barrier is one of an island's main defenses against the effects of hurricanes.

The extent to which reefs protect the island from storm waves and how this changes as corals are returned to the reef is being monitored by the Mission: Iconic Reefs team in partnership with researchers from Duke University at Eastern Dry Rocks. To do this, scientists use an array of pressure and temperature sensors and current meters that track the direction, height and force of the waves hitting the reef, and the effect of the reef and restored corals in reducing these waves forces. During Hurricane Ian, these sensors recorded over an 80% decrease in wave height between the front of the reef to the back of the reef. This means that coral reefs provide protection to the homes and people who live behind these reef structures.

These sensor arrays may help researchers determine how much coral restoration efforts under Mission: Iconic Reefs are enhancing the reef's ability to protect coastlines from storms over time. As the elkhorn corals planted here increase in size, it may be possible to measure changes in wave activity.


3D model of a coral reef with red lines in the shape of a box that indicate transects
A 3D mosaic of a section of Looe Key Reef was created by aggregating thousands of individuals images. Photo: NOAA.

Photogrammetry is a powerful addition to Florida Keys National Marine Sanctuary's monitoring toolbox. Field teams use specially-rigged high resolution digital SLR cameras to collect thousands of overlapping images of the seafloor and then use computer programs to stitch these images together to create one large image, much like making a quilt. These photomosaics can then be analyzed to track species composition, abundance and cover, coral growth, and the structural complexity of the site, and provide a record of what the reef looked like when first imaged and how it changes over time. Scientists are working to perfect and train an artificial intelligence (A.I.) program to identify and measure the corals and other benthic organisms within these photomosaics. The goal of switching from manual (human) analysis to A.I. is to reduce the time needed to analyze the imagery and improve the accuracy of the assessment.

Photogrammetry is also useful for looking at changes at archaeological sites over time.

Environmental DNA

A yellow, white and black-striped porkfish inspects a white cylinder on the seafloor.
A sub-surface, automated device samples eDNA in the water column. Photo: NOAA.

As much as they would like to, scuba divers can't be under the water all day and night observing the animals in a coral reef area. Environmental DNA, or eDNA, is a way for scientists to collect information about the life that's present in a reef area. Scientists use a sensor to collect water samples that contain small pieces of nuclear or mitochondrial DNA that creatures shed when they're present in the water. This eDNA is filtered out of the water sample and analyzed.

The eDNA that is present could be from large animals like sharks or turtles, or tiny microscopic creatures like bacteria and microbes which could tell scientists a lot of information about the diversity of a reef site or what may be causing coral diseases in an area. eDNA will be an important monitoring component of reef restoration efforts like Mission: Iconic Reefs, where scientists will be looking to eDNA to discover differences within and among these seven iconic reef areas as restoration progresses.

Aquaculture of Crabs and Urchins

Fingers hold open a compartment under a king crab that contains thousands of eggs that look like tiny red dots
A clutch of eggs in a Caribbean king crab can produce thousands of offspring. Photo: Scott Atwell/NOAA

Another area of growing research inside Florida Keys National Marine Sanctuary is examining the best way to raise important herbivorous animals like the Caribbean king crab (Maguimithrax spinosissimus) and the long-spined sea urchin (Diadema antillarum). As part of Mission: Iconic Reefs, these herbivores have an important job to do to remove algae from the reef structure so new corals can grow. Scientists are studying the best places to raise these important animals, whether that be in a lab, quarry, or even in cages near reef ecosystems. Scientists are also looking at how different aspects of the environment like temperature may affect the growth and mortality rates of these animals when they're raised in human care. Understanding and scaling up these aquaculture operations will help coral restoration in the future by allowing more herbivores to make their way onto the reef.