NCRMP has developed consistent and comparable methods and standard operating procedures (SOPs), which detail specific field, laboratory, and/or analytical procedures and best practices for all indicators (with periodic updates to reflect new technologies or logistical considerations). Some methodological differences exist for benthic and environmental surveys between the Atlantic and Pacific states and territories. Please email ncrmp.questions@noaa.gov with any inquiries about methodologies.
Benthic: Atlantic
Corals and benthic communities are monitored using a Benthic Community Assessment survey and a Coral Demographics survey. The Benthic Community Assessment survey includes: (1) benthic cover (%) measurements along a 15-m line-point intercept (LPI) transect, and (2) macroalgae cover (%). In Coral Demographics surveys, within a 10 x 1 m belt-transect area, all coral colonies ≧ 4 cm are counted, identified to species, measured to the nearest cm (length, width, height), and estimates are made of the proportion per colony of any present mortality (recent or old), disease (present, slow, fast), and/or bleaching (total, partial, paling). Only live coral colonies are included in the survey; dead colonies with 100% mortality are not surveyed (e.g., colonies killed by coral disease).
Benthic community assessment data (coral and macroalgae) are collected adjacent to coral demographics data, but not in the exact same area. Because the same set of corals are not sampled, this can lead to data values for density, bleaching and disease (i.e., from the Coral Demographics survey), while coral cover remains 0% (from the Benthic Community Assessment survey). NCRMP benthic community assessment data also includes CCA, sponges, gorgonians, and other broad categories.
Access Atlantic benthic survey protocol documents:
Benthic: Pacific
Coral abundance metrics are typically heterogeneous and vary in space according to environmental covariates such as depth, topographic complexity, and patchiness of reef habitats. To account for such variation, a stratified random sampling design is applied to more effectively and efficiently sample coral populations across defined strata.
Corals and benthic communities are monitored using a Benthic Photo-quadrat survey and a Coral Demographics survey. Surveys at each site are conducted within replicate segments (1 m × 2.5 m) spaced along one 30 m belt transect and include the following suite of observations:
- Adult coral colony (≥5 cm) abundance, size, partial mortality, and disease/condition
- Juvenile coral colony (<5 cm) abundance and size
- Benthic cover
Estimates of benthic cover are generated from benthic substrate photographs, which are taken along the same 30 m transect at the demographic surveys at each site. Photo-quadrats are collected at 1 m intervals along one side of the transect line, starting at the 1 m mark, for a total of 30 photo-quadrats per site. The benthic photoquadrat imagery is analyzed using the web-based annotation tool CoralNet, which places 10 random points per photo. The benthic elements falling directly underneath each point are identified at different functional group levels: Tier 1 (e.g., hard coral, soft coral, macroalgae, turf algae), or Tier 2 (hard coral by morphology: massive, branching, foliose, encrusting, etc.).
NCRMP uses image-based surveys to collect benthic observations. Divers collect both photogrammetry models, stitching together thousands of images of a site, as well as photoquadrat imagery, relying on “unstitched” single images of a site. Using photogrammetry we can build 3D models of the coral reef and extract data, including coral demographic data (measured by divers in situ before 2024). The photoquadrat imagery is annotated with the AI tool CoralNet to provide estimates of benthic cover. We conduct surveys at both fixed and random sites; random sites allow us to provide geographically comprehensive estimates of data for an island or region, whereas fixed sites allow us to compare changes in the benthos over time at the same site, such as growth of specific coral colonies.
Fish
The stationary point count (SPC) protocol consists of a pair of divers conducting simultaneous counts in adjacent, visually-estimated 15-m-diameter cylindrical plots extending from the substrate to the limits of vertical visibility. Each count consists of two components. The first of these is a 5-minute species enumeration period in which the diver records the taxa of all species observed within their cylinder. At the end of the 5-minute period, divers begin the tallying portion of the count, in which they systematically work through their species list and record the number and estimated size (total length (TL) to the nearest cm) of each individual fish. The tallying portion is conducted as a series of rapid visual sweeps of the plot, with one species-grouping counted per sweep.
Using the fish count and size data collected per observer in each replicate survey, the bodyweight of individual fish is calculated using length-to-weight conversion parameters. Biomass per fish is calculated using the standard length-weight equation. Herein, the term “biomass” refers to the aggregate body weight of a group of fishes per unit area. Total counts per fish species are used to calculate fish density, and further turned into presence-absence per species to calculate occurrence per species. Response metrics are calculated for individual species, consumer groups, and all fishes combined.
Environmental
NCRMP monitors changes in ocean conditions and how they impact coral reef ecosystems such as investigating how thermal stress impacts coral bleaching, how water temperature changes with depth on coral reefs, how seawater chemistry is changing, and whether coral reef habitat is growing or eroding.
Carbonate chemistry data are collected at fixed and stratified random sites in U.S. coral reef jurisdictions to assess spatial and temporal variation in the seawater carbonate systems of coral reef ecosystems. These samples are collected by hand at the surface, either from the boat or by SCUBA divers and depending upon the location may be paired with Conductivity-Temperature-Depth (CTD) casts. Samples are analyzed for total alkalinity (TA) and dissolved inorganic carbon (DIC). Carbonate chemistry system parameters (including pH, pCO2, and aragonite saturation state) are then calculated from TA, DIC, temperature, and salinity using the seacarb package in R.
Surface water samples for carbonate chemistry analysis are collected from small boats using Niskin Bottles and stored in borosilicate glass bottles. The sample bottle is rinsed three times and allowed to overflow for at least twice the sample volume. Samples are fixed with 200 µl of mercuric chloride (HgCl2), and the bottle is greased and sealed for transportation to the lab for analysis. Temperature and salinity values are derived from co-located CTD profiles.
NCRMP deploys stand-alone instruments on the reef for several years such as STRs (subsurface-temperature-recorders), CAUs (calcium-accretion-units), and BMUs (bioerosion-monitoring-units). Carbonate budgets estimate whether a reef is growing, eroding, or at a tipping point.
Socioeconomic
The socioeconomic component of NCRMP collects and monitors socioeconomic information, including human use of coral reef resources, knowledge, attitudes, and perceptions of coral reefs and coral reef management. Socioeconomic data are collected in each of the seven inhabited U.S. coral reef jurisdictions every 5-7 years. The potential respondent universe in each of the jurisdictions are adult household residents aged 18 years or older. A stratified sampling methodology is used for all seven inhabited jurisdictions, and sample sizes will be selected proportionately across strata/sub-strata to allow for the estimation of jurisdiction-level parameters.
A standard survey instrument uses a core set of survey questions that is consistent across all locations, but also includes a set of jurisdiction-specific questions to assess local management needs. All NCRMP surveys must be cleared through the Federal Office of Management and Budget’s Paperwork Reduction Act process.
Two final sampling weights are developed to meet the analytic objectives of this study: a person-level weight and a household-level weight. The weighting plan must include any necessary procedures to produce weights at each stage of sample design. An analysis of weight variability is required, as is the potential for trimming. Final weights must sum to the population total.
Access the Socioeconomic Survey Sampling Protocols, and the specific survey questionnaires for each jurisdiction below.