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Experimental Design

CREMP’s monitoring protocols were designed to identify processes that may lead to changes in coral populations. The surveys allow CREMP to test hypotheses about how Florida’s coral reef communities are changing over time in response to periodic disturbances and/or chronic stressors. There are two components: a camera survey, which collects percent cover information, and demographic surveys that collect data on coral population abundance and condition.

Station Orientation & Setup

Two divers are facing each other on a coral reef, lining up a plastic yellow chain under a tight, straight measuring tape extending from left to right in the photo. Much of the visible reef substrate is covered by brown and purple soft corals, with bare, light tan areas of limestone in between. Blue-green water is visible in the upper left, where the spur of the reef drops off.

Each CREMP site has four stations in Southeast Florida and the Florida Keys. A few sites in the Dry Tortugas have fewer stations to account for the size and distribution of monotypic stands of Acropora. Station transects are approximately 22m (~72') in length and oriented south to north in SECREMP and offshore to inshore in CREMP in the Florida Keys and Dry Tortugas (see map and aerial photo below). Stations are permanently marked on the reef using steel stakes that were drilled and cemented into the reef. Surveyors connect the two stakes using a fiberglass transect tape and proceed from offshore to inshore (CREMP in the Florida Keys and Dry Tortugas) or south to north (SECREMP). In the Florida Keys and Dry Tortugas, after ensuring the tape is tight and straight, a plastic chain is then placed directly underneath the tape between the two stakes so it follows the contour of the substrate (see photo, right). A brass clip is attached to the chain at the 10m (~33') mark to mark the end of the demographic survey area and the tape is rolled up.

Satellite photo of a reef with four lines representing individual coral monitoring stations. A ledge is visible running southwest to northeast, with the stations oriented perpendicular to it. An inset shows a simplified black and white map with distances and bearing from each station.

An example of station set up at Alligator Shallow, an offshore forereef site in the Upper Keys. Note the offshore-to-inshore orientation of the transects. The inset is an example site map which divers use to navigate to the stations underwater.

Survey Methods

Present-day CREMP surveys include a photographic survey used to assess percent cover, and a demographic survey which includes a health assessment. Historically, CREMP performed three major surveys at each station: a video survey to estimate benthic cover along three parallel transects, a bio-eroding sponge survey, and a coral species inventory survey that quantified coral species richness, the presence or absence of disease, and long-spined sea urchin (Diadema antillarum) abundance within the station boundaries. In 2011, survey methods were modified to provide a better assessment of the benthic community and to streamline survey efficiency. The video survey was replaced with still photographs and reduced from the three parallel transects to a single centered transect. Coral species inventories were replaced by coral and octocoral demographic surveys conducted on the first 10m of the center transect. The bio-eroding sponge survey was discontinued and was replaced with a Xestospongia muta, or giant barrel sponge, demographic survey. Performing these additional surveys allows for a more comprehensive assessment of changes in coral reef community composition (especially the inclusion of octocoral and barrel sponge surveys) and improves the program’s ability to identify processes that may lead to declines or recovery in coral populations such as changes in density or size classes, juvenile coral status, prevalence of conditions that cause mortality (like disease or bleaching), and the role of chronic stressors. Collectively, these surveys continue to allow CREMP to test hypotheses about how reef communities are changing over time in response to acute disturbances or chronic stressors, or corrective actions implemented by water and resource management efforts (like the Water Quality Protection Program in the Florida Keys).

Methodology changes:

Two sets of photos on a black background. Each photo set is stitched together to create a mosaic showing a coral reef from a top-down view, with a yellow plastic chain in the middle. The top set of photos shows high coral cover, with abundant and bright golden-yellow elkhorn coral. The bottom set of photos shows mostly side and scattered small corals, octocorals, and algae.

Mosaics created from video stills from historic CREMP videography surveys. The changes between 1996 and 200 highlight the loss of elkhorn coral, Acropora palmata in Florida starting in the 1980's. The CREMP monitoring program did not start until well after the 1980's and therefore does not capture the true extent of the decline of this species from Florida's reefs. However, the data we do have still captures this drastic loss, even without true baseline values. View larger image

  • 1996
    • Original survey methods include underwater videography of three transects at each sampling station within a site accompanied by a coral species inventory in which divers recorded all coral species and long-spined sea urchin present within the boundaries of each 2 x 22 m station.
  • 2001
    • Survey added to document Clionid sponge abundance and cover.
    • Coral disease assessments expanded.
    • Juvenile coral recruits added to survey.
  • 2009
    • Clionid sponge survey changed to presence/absence.
  • 2011
    • Demographic surveys for stony coral, otctocoral, and Xestospongia muta added, replacing coral species inventory and Clionid sponge surveys.
    • Image acquisition reduced to one transect per station after statistical analysis confirmed that a single transect achieved similar results.
    • Image capture switched from using video to photographs.
  • 2018
    • Juvenile coral tally added to survey.
    • Changes in how injuries and disease are recorded on the coral colony to better describe coral conditions.
A black and white illustration shows the coral monitoring camera, demographic survey, and giant barrel sponge surveys.

CREMP Transects: Still camera transects are completed for the entire length of the station for all CREMP regions. Coral and octocoral demographic surveys are completed for the first 10x1m of the station for CREMP in the Florida Keys and CREMP in the Dry Tortugas, but coral demographic surveys are conducted the entire 22m x 1m of the transect in SECREMP. Xestospongia muta fate tracking surveys are conducted along three 22m x 1m belt transects at selected stations for CREMP in the Florida Keys, but only along the full 22m center transect in SECREMP.

A diver wearing a black wetsuit holds an underwater camera above a plastic yellow chain laid over a reef. A metal bar is attached to the camera housing.

A diver conducting a still camera survey. 

The Still Camera Survey allows for later analysis of benthic cover estimates. Images are captured using point-and-shoot cameras (currently Olympus Tough TG-4s) following the chain along the entire ~22m length of the station. An aluminum bar affixed to the camera aids in maintaining a constant height of 40cm above the substrate (see Figure 4). On flat substrate the photographs capture a roughly 0.4m wide by 0.5m tall image. To ensure minimal overlap between images, reference points are used to proceed along the transect (e.g., a clump of algae or coral). Each transect has a sampling area of ~9 m2, totaling ~36m2 for an entire site with four transects.

Images are later formatted for PointCount ‘99 image analysis software in which fifteen random points are placed on each image and benthic taxa are identified either to species, genus, higher taxonomic level, or substrate type beneath each point (see our Standard Operating Procedures on the Resources page). Using the selected number of points for each taxonomic level, the percent cover of benthic organisms is generated for each transect.

A series of panoramic photos are also taken at the offshore stake for each transect with the stake in the middle of the photo (see Figure 5). This is accomplished using the “panoramic” function on the camera and taking two overlapping pans to create a 180-degree image. For cameras without this function, a series of 5-7 overlapping photographs are taken to create a 180-degree panorama. Panoramic photos are useful in seeing long-term changes over time and used primarily for outreach purposes.

Refer to the Point Count Standard Operating Procedures and Still Camera Survey Standard Operating Procedures on the Resources page for more details.

A research diver swims towards the camera holding a clipboard and white PVC measuring stick, following a yellow plastic chain laid out on the reef in a straight line.

A diver conducting a stony coral demographic survey following the chain.

Stony coral demographic data is collected for the first 10 meters of each station transect starting at the offshore stake and working inshore for CREMP in the Florida Keys and CREMP in the Dry Tortugas, and for the entire 22m station in SECREMP. Corals 4 cm that fall within 0.5 m on either side of the chain are identified, measured, and assessed for overall health in the Florida Keys and Dry Tortugas, and corals ≥ 2 cm in Southeast Florida. This includes recording the amount of mortality on each colony as well as bleaching, disease, or predation prevalence. In 2018, the protocol was adjusted to include the enumeration of all colonies < 4 cm to collect information for juvenile coral populations. This data is used to help determine if corals are successfully recruiting to the reef which is required for long-term recovery, as well as comparing the distribution of juveniles and adult corals. CREMP demographic survey protocols are similar to those of the Atlantic and Gulf Rapid Reef Assessment (AGRRA, See the Stony Coral Demographic Survey Standard Operating Procedures on our Resources page for more detailed methodology. The presence of Millepora alcicornis (branching fire coral) and the number of long-spined sea urchin that occur within the 10x1m transect are also recorded. This survey is conducted at all CREMP sites with the exception of two sites in the Dry Tortugas. 

A research diver wearing a blue bandana and black and yellow gloves measures a sea fan with a pvc measuring stick amongst a field of purple sea fans, golden-brown sea plumes, and brown-grey sea-rods..

Diver collecting data on octocoral demographics within a CREMP site.

Octocorals (sea fans, sea rods, and sea whips) are an integral part of many Caribbean reef communities and can rival or outnumber stony corals in certain habitats. They provide food and shelter to a variety of fish and invertebrates and can increase habitat complexity of the reef. Octocorals grow extremely fast (up to several cm/year) and several species reproduce multiple times a year. The frequency at which they reproduce combined with their fast growth rates allows octocorals to recover quickly after disturbances and provides them with competitive advantages over corals. In fact, long-term CREMP findings show that octocorals have essentially replaced elkhorn and staghorn (Acropora) corals on shallow forereefs where Acroporid corals were once dominant. Due to their abundance, octocorals are useful for assessing overall reef condition. Like corals, many species are susceptible to diseases like red band disease on the sea fan Gorgonia ventalina or thermal stress which can cause tissue sloughing. By targeting octocorals, CREMP can expand its overall understanding of how reef communities are changing and determine if periodic disturbances or chronic stressors are affecting other taxonomic groups similarly to that of corals. 

Octocoral demographic surveys are completed at half (20) of the CREMP sites in the Florida Keys but at all sites in the Dry Tortugas and Southeast Florida. The surveys are completed within the same transects as the stony coral surveys. This survey quantifies the abundance of all octocoral species and collects demographic information on five species in the Florida Keys and Dry Tortugas - Antillogorgia americana, Antillogorgia bipinnata, Eunicea flexuosa, Gorgonia ventalina, and Pseudoplexaura porosa - and three species in Southeast Florida - Antillogorgia americana, Eunicea flexuosa, and Gorgonia ventalina. Colonies of any size with their base attached within the 10x1 m (Florida Keys and Dry Tortugas) or 22x1 m (Southeast Florida) belt transect boundary are recorded and their max height measured to the nearest cm. Target colonies are also visually assessed for overall health, including disease prevalence, damage, mortality, and unhealthy or abnormal areas. All non-target species are tallied separately, without being assessed for overall health. See the Octocoral Demographic Standard Operating Procedures on our Resources page for more details.

An underwater scene, with giant barrel sponge in the foreground. Octocorals and smaller sponges surround it, bent over in a strong current. Research divers and their bubbles are visible in the background.

A Xestospongia muta (giant barrel sponge) with researchers in the background.

Sponges are the most abundant sessile organisms in terms of biomass in many Caribbean reef communities and sponge species diversity can exceed that of stony corals on some reefs. Sponges play many important roles in the reef ecosystem: filtering bacteria and nutrients from the water column, binding corals to the substrate, facilitating reef regeneration, and providing a food source for spongivores. Like octocorals, sponges are also major competitors with corals in terms of reef space. Sponges historically have been neglected from monitoring projects due to the myriad of challenges they pose to researchers. Starting in 2011, CREMP began piloting a survey to track individual colonies of giant barrel sponges, Xestospongia muta, and monitor their survival, growth, and population dynamics. It is an important indicator of reef health because, similar to corals and octocorals, X. muta is susceptible to periodic episodes of bleaching and disease. Monitoring of X. muta populations tests the hypotheses that this species responds to environmental regimes similarly to stony corals, and that this species’ condition may be used as another proxy for reef health. The survey provides density and size class information of X. muta, as well as the prevalence of malignant conditions affecting the population. This survey has been conducted within Keys CREMP since 2011 and SECREMP since 2012. 

For CREMP in the Florida Keys, surveys are only conducted at the 11 deep forereef sites because that is where X. muta is most abundant. Station setup for X. muta surveys is similar to CREMP demographic surveys, but each station has three parallel transects instead of one. Each transect is 1m wide and extends the entire length of the ~22m transects for a total survey area of 66 m2. Because three transects are surveyed at a station only two stations are surveyed at each site. With the aid of underwater site maps and pictures taken from the previous year, each colony is relocated. The maximum diameter at the apex and base of sponge is measured along with maximum height. The presence of bleaching, disease, or predation is recorded for each X. muta colony, and the recent mortality associated with these conditions is estimated. After all measurements are completed, a picture of the colony is taken. See the Xestospongia muta Demographic Survey Standard Operating Procedures on the Resources page for more detailed methodology.  

For SECREMP, X. muta surveys are conducted along the same 22x1m belt transect (22 m2) as the coral demographic survey. However, only one transect is completed at each SECREMP stations (22 m2) as opposed to the 66 m2 surveyed for each CREMP station. However, X. muta surveys are conducted at all 22 SECREMP sites.