Characterizing coral condition using estimates of three-dimensional colony surface area

Reef structure of the Florida Reef Tract for the period 2005-2020

Shallow-water coral reefs of the Florida Reef Tract compose the third largest reef in the world, but during the last several decades, scleractinian (stony) corals have suffered unprecedented declines from global and local stressors. A program to evaluate the effects of high-temperature bleaching events was initiated by The Nature Conservancy's Florida Reef Resilience Program in 2005 and surveys have been completed across at least some portion of the entire region every year since. The program adopted a demographic (colony-based) assessment approach, which records colony species, size (height and maximum diameter), and estimated partial mortality (percent barren skeleton). Because reef structure is critical to ecosystem functioning and services, data from 2005 to 2020 were analyzed to describe the abundance, size, and morphological complexity of stony coral colonies forming the biogenic reef. Colony height, footprint, surface area, and volume summed for 6016 transects were used to describe reef structure and averages were used to characterize the components that contributed to the structure. Nearly 150,000 colonies representing 49 species were reported during this period and results demonstrated both spatial and temporal changes for the region and for geographic subregions. Some subregions showed increasing colony density, especially for three small, hemispheric species, and declining average colony size.

Skeletal growth capacity as a measure of coral species and community resilience

Accretion and erosion of scleractinian (stony coral) carbonate skeletons determine whether a colony will increase or decrease in size with potential consequences for ecosystem processes, functions and services. The capacity for skeletal growth can be estimated by comparing a colony's rate of calcification with its rate of erosion. Calcification depends on the species-specific metabolic activity of living tissue, and erosion depends primarily on the availability and density of barren skeleton, those areas on the colony where polyps have died. Assessment of skeletal growth capacity requires data on calcification rates, erosion rates and both live and barren colony surface area. Rates of calcification and erosion are documented for many Caribbean species and others can be estimated from existing data. Three-dimensional surface area of colonies can be determined from data collected during demographic surveys, which identify species, measure dimensions, and estimate the proportion of live tissue on a colony. Data from demographic surveys conducted in the U.S. Virgin Islands are used to calculate the skeletal growth capacity (GC) as an indicator of coral species and community resilience. Scleractinia are the primary architects of coral reefs, and the gain or loss of skeletal framework is vitally important to reef ecosystem processes that lead to valued goods and services. Estimates of GC reflect stony coral resilience, which is the capacity to recover from disturbances by returning to previous physical and functional levels. GC can also provide insight to the effects of stressors such as ocean acidification, and can inform several management decisions, including restoration site selection and threatened species designation.

A biological condition gradient for coral reefs in the US Caribbean Territories: Part I. Coral narrative rules

As coral reef condition and sustainability continue to decline worldwide, losses of critical habitat and their ecosystem services have generated an urgency to understand and communicate reef response to management actions, environmental contamination, and natural disasters. Increasingly, coral reef protection and restoration programs emphasize the need for robust assessment tools for protecting high-quality waters and establishing conservation goals. Of equal importance is the need to communicate assessment results to stakeholders, beneficiaries, and the public so that environmental consequences of decisions are understood. The Biological Condition (BCG) model provides a structure to evaluate the condition of a coral reef in increments of change along a gradient of human disturbance. Communication of incremental change, regardless of direction, is important for decision makers and the public to better understand what is gained or lost depending on what actions are taken. We developed a narrative (qualitative) Biological Condition Gradient (BCG) from the consensus of a diverse expert panel to provide a framework for coral reefs in US Caribbean Territories. The model uses narrative descriptions of biological attributes for benthic organisms to evaluate reefs relative to undisturbed or minimally disturbed conditions. Using expert elicitation, narrative decision rules were proposed and deliberated to discriminate among six levels of change along a gradient of increasing anthropogenic stress. Narrative rules for each of the BCG levels are presented to facilitate the evaluation of benthic communities in coral reefs and provide specific narrative features to detect changes in coral reef condition and biological integrity. The BCG model can be used in the absence of numeric, or quantitative metrics, to evaluate actions that may encroach on coral reef ecosystems, manage endangered species habitat, and develop and implement management plans for marine protected areas, watersheds, and coastal zones. The narrative BCG model is a defensible model and communication tool that translates scientific results so the nontechnical person can understand and support both regulatory and non-regulatory water quality and natural resource programs.

Development of a reef fish biological condition gradient model with quantitative decision rules for the protection and restoration of coral reef ecosystems

Coral reef ecosystems are declining due to multiple interacting stressors. A bioassessment framework focused on stressor-response associations was developed to help organize and communicate complex ecological information to support coral reef conservation. This study applied the Biological Condition Gradient (BCG), initially developed for freshwater ecosystems, to fish assemblages of U.S. Caribbean coral reef ecosystems. The reef fish BCG describes how biological conditions changed incrementally along a gradient of increasing anthropogenic stress. Coupled with physical and chemical water quality data, the BGC forms a scientifically defensible basis to prioritize, protect and restore water bodies containing coral reefs. Through an iterative process, scientists from across the U.S. Caribbean used fishery-independent survey data and expert knowledge to develop quantitative decision rules to describe six levels of coral reef ecosystem condition. The resultant reef fish BCG provides an effective tool for identifying healthy and degraded coral reef ecosystems and has potential for global application.

New approaches to high-resolution mapping of marine vertical structures

Vertical walls in marine environments can harbour high biodiversity and provide natural protection from bottom-trawling activities. However, traditional mapping techniques are usually restricted to down-looking approaches which cannot adequately replicate their 3D structure. We combined sideways-looking multibeam echosounder (MBES) data from an AUV, forward-looking MBES data from ROVs and ROV-acquired videos to examine walls from Rockall Bank and Whittard Canyon, Northeast Atlantic. High-resolution 3D point clouds were extracted from each sonar dataset and structure from motion photogrammetry (SfM) was applied to recreate 3D representations of video transects along the walls. With these reconstructions, it was possible to interact with extensive sections of video footage and precisely position individuals. Terrain variables were derived on scales comparable to those experienced by megabenthic individuals. These were used to show differences in environmental conditions between observed and background locations as well as explain spatial patterns in ecological characteristics. In addition, since the SfM 3D reconstructions retained colours, they were employed to separate and quantify live coral colonies versus dead framework. The combination of these new technologies allows us, for the first time, to map the physical 3D structure of previously inaccessible habitats and demonstrates the complexity and importance of vertical structures.

End to End Digitisation and Analysis of Three-Dimensional Coral Models, from Communities to Corallites

Coral reefs hosts nearly 25% of all marine species and provide food sources for half a billion people worldwide while only a very small percentage have been surveyed. Advances in technology and processing along with affordable underwater cameras and Internet availability gives us the possibility to provide tools and softwares to survey entire coral reefs. Holistic ecological analyses of corals require not only the community view (10s to 100s of meters), but also the single colony analysis as well as corallite identification. As corals are three-dimensional, classical approaches to determine percent cover and structural complexity across spatial scales are inefficient, time-consuming and limited to experts. Here we propose an end-to-end approach to estimate these parameters using low-cost equipment (GoPro, Canon) and freeware (123D Catch, Meshmixer and Netfabb), allowing every community to participate in surveys and monitoring of their coral ecosystem. We demonstrate our approach on 9 species of underwater colonies in ranging size and morphology. 3D models of underwater colonies, fresh samples and bleached skeletons with high quality texture mapping and detailed topographic morphology were produced, and Surface Area and Volume measurements (parameters widely used for ecological and coral health studies) were calculated and analysed. Moreover, we integrated collected sample models with micro-photogrammetry models of individual corallites to aid identification and colony and polyp scale analysis.

Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs

The structural complexity of coral reefs plays a major role in the biodiversity, productivity, and overall functionality of reef ecosystems. Conventional metrics with 2-dimensional properties are inadequate for characterization of reef structural complexity. A 3-dimensional (3D) approach can better quantify topography, rugosity and other structural characteristics that play an important role in the ecology of coral reef communities. Structure-from-Motion (SfM) is an emerging low-cost photogrammetric method for high-resolution 3D topographic reconstruction. This study utilized SfM 3D reconstruction software tools to create textured mesh models of a reef at French Frigate Shoals, an atoll in the Northwestern Hawaiian Islands. The reconstructed orthophoto and digital elevation model were then integrated with geospatial software in order to quantify metrics pertaining to 3D complexity. The resulting data provided high-resolution physical properties of coral colonies that were then combined with live cover to accurately characterize the reef as a living structure. The 3D reconstruction of reef structure and complexity can be integrated with other physiological and ecological parameters in future research to develop reliable ecosystem models and improve capacity to monitor changes in the health and function of coral reef ecosystems.

Regional status assessment of stony corals in the US Virgin Islands

States may protect coral reefs using biological water quality standards outlined by the Clean Water Act. This requires biological assessments with indicators sensitive to human disturbance and regional, probability-based survey designs. Stony coral condition was characterized on a regional scale for the first time in the nearshore waters of the US Virgin Islands (USVI). Coral composition, abundance, size, and health were assessed at 66 stations in the St. Croix region in fall 2007 and at 63 stations in the St. Thomas and St. John region in winter 2009. Indicators were chosen for their sensitivity to human disturbance. Both surveys were probability-based (random) designs with station locations preselected from areas covered by hardbottom and coral reef substrate. Taxa richness was as high as 21 species but more than half the area of both regions exhibited taxa richness of <10 species in the 25 m(2) transect area. Coral density was as high as 5 colonies m(-2) but more than half the area of both regions had <2 colonies m(-2). Both regions showed similar dominant species based on frequency of occurrence and relative abundance. Because of large colony sizes, Montastrea annularis provided more total surface area and live surface area than more abundant species. The surveys establish baseline regional conditions and provide a foundation for long-term regional monitoring envisioned by the USVI Department of Planning and Natural Resources. The probabilistic sampling design assures the data can be used in Clean Water Act reporting.

Development and implementation of coral reef biocriteria in U.S. jurisdictions

Coral reefs worldwide are declining at an alarming rate and are under continuous threat from both natural and anthropogenic environmental stressors. Warmer sea temperatures attributed to global climate change and numerous human activities at local scales place these valuable ecosystems at risk. Reefs provide numerous services, including shoreline protection, fishing, tourism and biological diversity, which are lost through physical damage, overfishing, and pollution. Pollution can be controlled under provisions of the Clean Water Act, but these options have not been fully employed to protect coral reefs. No U.S. jurisdiction has implemented coral reef biocriteria, which are narrative or quantitative water quality standards based on the condition of a biological resource or assemblage. The President's Ocean Action Plan directs the U.S. Environmental Protection Agency (EPA) to develop biological assessment methods and biological criteria for evaluating and maintaining the health of coral reef ecosystems. EPA has formed the Coral Reef Biocriteria Working Group (CRBWG) to foster development of coral reef biocriteria through focused research, evaluation and communication among Agency partners and U.S. jurisdictions. Ongoing CRBWG activities include development and evaluation of a rapid bioassessment protocol for application in biocriteria programs; development of a survey design and monitoring strategy for the U.S. Virgin Islands; comprehensive reviews of biocriteria approaches proposed by states and territories; and assembly of data from a variety of monitoring programs for additional metrics. Guidance documents are being prepared to assist U.S. jurisdictions in reaching protective and defensible biocriteria.

Evaluation of stony coral indicators for coral reef management

Colonies of reef-building stony corals at 57 stations around St. Croix, US Virgin Islands were characterized by species, size and percentage of living tissue. Taxonomic, biological and physical indicators of coral condition were derived from these measurements and assessed for their response to gradients of human disturbance-a requirement for indicators used in regulatory assessments under authority of the Clean Water Act. At the most intensely disturbed location, five of eight primary indicators were highly correlated with distance from the source of disturbance: Coral taxa richness, average colony size, the coefficient of variation of colony size, total topographic coral surface area, and live coral surface area. An additional set of exploratory indicators related to rarity, reproductive and spawning mode and taxonomic identity were also screened. The primary indicators demonstrated sufficient precision to detect levels of change that would be applicable in a regional-scale regulatory program.