3D photogrammetry quantifies growth and external erosion of individual coral colonies and skeletons

Precision and accuracy of common coral reef sampling protocols revisited with photogrammetry

The rapid decline of coral reefs calls for cost-effective benthic cover data to improve reef health forecasts, policy building, management responses and evaluation. Reef monitoring has been largely based on divers' observations along transects, and secondarily on quadrat-based protocols, video and photographic records. However, the accuracy and precision of the most common sampling approaches are not yet fully understood. Here, we compared benthic cover estimates from three common sampling protocols: Reef Check (RC), Atlantic and Gulf Rapid Reef Assessment (AGRRA) and photoquadrats (PQ). The reef cover of two contrasting sites was reconstructed with ∼450 m2 orthomosaics built with high resolution Structure-from-Motion (SfM) photogrammetry, which were used as references for comparisons among protocols. In addition, we explored sample size requirements for each protocol and provided cost-effectiveness comparisons. Our results evidenced between-reef differences in the accuracy and precision of estimates with the different protocols. The three protocols performed similarly in the reef with low macroalgal cover (<0.5%), but PQ were more accurate and precise in the reef with relatively high (∼20%) macroalgal cover. The sample size for estimating coral cover with a 20% error margin and a 0.05 significance level was lower for PQ, followed by AGRRA and RC. Considering performance, cost surrogates and equipment needs, cost-effectiveness was higher for PQ. We also discuss costs, limitations and advantages/disadvantages of SfM photogrammetry as a sampling approach for coral reef monitoring.

Vulnerability of six cold-water corals to sediment resuspension from bottom trawling fishing

Bottom trawling can significantly affect benthic communities, directly through immediate removal of sessile organisms and indirectly through sediment resuspension. Submarine canyons, often surrounded by fishing grounds, are important habitats for cold-water corals (CWC). Vulnerability of CWCs to increased suspended sediment concentration (SSC) is key to understanding the severity of bottom trawling effects on those communities. Here we show survival, growth, and physiological response of six CWCs from a Mediterranean submarine canyon (Dendrophyllia cornigera, Desmophyllum dianthus, Desmophyllum pertusum, Madrepora oculata, Leiopathes glaberrima and Muriceides lepida), exposed to a long-term, aquarium-based sedimentary disturbance experiment. Compared to cup coral and octocoral, which did not exhibit symptoms of distress, our data indicate that colonial scleractinian corals and black coral, which experienced substantial polyp mortality in enhanced SSC treatments, are more vulnerable. Indirect impact of bottom trawling could thus contribute to structural simplification of CWC communities posing an additional stressor alongside with global climate change.

Dead but not forgotten: complexity of Acropora palmata colonies increases with greater composition of dead coral

Coral reefs are highly biodiverse ecosystems that have declined due to natural and anthropogenic stressors. Researchers often attribute reef ecological processes to corals' complex structure, but effective conservation requires disentangling the contributions of coral versus reef structures. Many studies assessing the relationships between reef structure and ecological dynamics commonly use live coral as a proxy for reef complexity, disregarding the contribution of dead coral skeletons to reef habitat provision or other biogeochemical reef dynamics. This study aimed to assess the contribution of dead coral to reef complexity by examining structural variations in live and dead Acropora palmata colonies. We used photogrammetry to reconstruct digital elevation models (DEMs) and orthomosaics of the benthic region immediately surrounding 10 A. palmata colonies. These reconstructions were used to quantify structural metrics, including surface rugosity, fractal dimension, slope, planform curvature, and profile curvature, as a function of benthic composition (i.e., live A. palmata, dead A. palmata, or non-A. palmata substrate). The results revealed that dead coral maintained more varied profile curvatures and higher fractal dimensions than live or non-coral substrate. Conversely, A. palmata colonies with a higher proportion of live coral displayed more uniform structure, with lower fractal dimensions and less variability in profile curvature measures. Other metrics showed no significant difference among substrate types. These findings provide novel insights into the structural differences between live and dead coral, and an alternative perspective on the mechanisms driving the observed structural complexity on reefs. Overall, our results highlight the overlooked potential contributions of dead coral to reef habitat provision, ecological processes, and other biogeochemical reef dynamics, and could have important implications for coral reef conservation.

Three-dimensional species distribution modelling reveals the realized spatial niche for coral recruitment on contemporary Caribbean reefs

The three-dimensional structure of habitats is a critical component of species' niches driving coexistence in species-rich ecosystems. However, its influence on structuring and partitioning recruitment niches has not been widely addressed. We developed a new method to combine species distribution modelling and structure from motion, and characterized three-dimensional recruitment niches of two ecosystem engineers on Caribbean coral reefs, scleractinian corals and gorgonians. Fine-scale roughness was the most important predictor of suitable habitat for both taxa, and their niches largely overlapped, primarily due to scleractinians' broader niche breadth. Crevices and holes at mm scales on calcareous rock with low coral cover were more suitable for octocorals than for scleractinian recruits, suggesting that the decline in scleractinian corals is facilitating the recruitment of octocorals on contemporary Caribbean reefs. However, the relative abundances of the taxa were independent of the amount of suitable habitat on the reef, emphasizing that niche processes alone do not predict recruitment rates.

No apparent trade-offs associated with heat tolerance in a reef-building coral

As marine species adapt to climate change, their heat tolerance will likely be under strong selection. Yet trade-offs between heat tolerance and other life history traits could compromise natural adaptation or assisted evolution. This is particularly important for ecosystem engineers, such as reef-building corals, which support biodiversity yet are vulnerable to heatwave-induced mass bleaching and mortality. Here, we exposed 70 colonies of the reef-building coral Acropora digitifera to a long-term marine heatwave emulation experiment. We tested for trade-offs between heat tolerance and three traits measured from the colonies in situ - colony growth, fecundity, and symbiont community composition. Despite observing remarkable within-population variability in heat tolerance, all colonies were dominated by Cladocopium C40 symbionts. We found no evidence for trade-offs between heat tolerance and fecundity or growth. Contrary to expectations, positive associations emerged with growth, such that faster-growing colonies tended to bleach and die at higher levels of heat stress. Collectively, our results suggest that these corals exist on an energetic continuum where some high-performing individuals excel across multiple traits. Within populations, trade-offs between heat tolerance and growth or fecundity may not be major barriers to natural adaptation or the success of assisted evolution interventions.

Design, Analysis, and 3D Printing of a Patient-Specific Polyetheretherketone Implant for the Reconstruction of Zygomatic Deformities

The reconstruction of craniomaxillofacial deformities, especially zygomatic bone repair, can be exigent due to the complex anatomical structure and the sensitivity of the crucial organs involved. The need to reconstruct the zygomatic bone in the most precise way is of crucial importance for enhancing the patient outcomes and health care-related quality of life (HRQL). Autogenous bone grafts, despite being the gold standard, do not match bone forms, have limited donor sites and bone volume, and can induce substantial surgical site morbidity, which may lead to adverse outcomes. The goal of this study is to provide an integrated approach that includes various processes, from patient scanning to implant manufacture, for the restoration of zygomatic bone abnormalities utilizing Polyetheretherketone (PEEK) material, while retaining adequate aesthetic and facial symmetry. This study takes an integrated approach, including computer-aided implant design using the mirror reconstruction technique, investigating the biomechanical behavior of the implant under loading conditions, and carrying out a fitting accuracy analysis of the PEEK implant fabricated using state-of-the-art additive manufacturing technology. The findings of the biomechanical analysis results reveal the largest stress of approximately 0.89 MPa, which is relatively low in contrast to the material's yield strength and tensile strength. A high degree of sturdiness in the implant design is provided by the maximum value of strain and deformation, which is also relatively low at roughly 2.2 × 10^-4 and 14 µm. This emphasizes the implant's capability for load resistance and safety under heavy loading. The 3D-printed PEEK implant observed a maximum deviation of 0.4810 mm in the outside direction, suggesting that the aesthetic result or the fitting precision is adequate. The 3D-printed PEEK implant has the potential to supplant the zygoma bone in cases of severe zygomatic reconstructive deformities, while improving the fit, stability, and strength of the implant.

Structure-from-motion photogrammetry demonstrates variability in coral growth within colonies and across habitats

Coral growth is an important metric of coral health and underpins reef-scale functional attributes such as structural complexity and calcium carbonate production. There persists, however, a paucity of growth data for most reef-building regions, especially for coral species whose skeletal architecture prevents the use of traditional methods such as coring and Alizarin staining. We used structure-from-motion photogrammetry to quantify a range of colony-scale growth metrics for six coral species in the Mexican Caribbean and present a newly developed workflow to measure colony volume change over time. Our results provide the first growth metrics for two species that are now major space occupiers on Caribbean reefs, Agaricia agaricites and Agaricia tenuifolia. We also document higher linear extension, volume increase and calcification rates within back reef compared to fore reef environments for four other common species: Orbicella faveolata, Porites astreoides, Siderastrea siderea and Pseudodiploria strigosa. Linear extension rates in our study were lower than those obtained via computed tomography (CT) scans of coral cores from the same sites, as the photogrammetry method averages growth in all dimensions, while the CT method depicts growth only along the main growth axis (upwards). The comparison of direct volume change versus potential volume increase calculated from linear extension emphasizes the importance of assessing whole colony growth to improve calcification estimates. The method presented here provides an approach that can generate accurate calcification estimates alongside a range of other whole-colony growth metrics in a non-invasive way.

Emerging 3D technologies for future reformation of coral reefs: Enhancing biodiversity using biomimetic structures based on designs by nature

The rapid decline of vulnerable coral reefs has increased the necessity of exploring interdisciplinary methods for reef restoration. Examining how to upgrade these tools may uncover options to better support or increase biodiversity of coral reefs. As many of the issues facing reef restoration today deal with the scalability and effectiveness of restoration efforts, there is an urgency to invest in technology that can help reach ecosystem-scale. Here, we provide an overview on the evolution to current state of artificial reefs as a reef reformation tool and discuss a blueprint with which to guide the next generation of biomimetic artificial habitats for ecosystem support. Currently, existing artificial structures have difficulty replicating the 3D complexity of coral habitats and scaling them to larger areas can be problematic in terms of production and design. We introduce a novel customizable 3D interface for producing scalable, biomimetic artificial structures, utilizing real data collected from coral ecosystems. This interface employs 3D technologies, 3D imaging and 3D printing, to extract core reef characteristics, which can be translated and digitized into a 3D printed artificial reef. The advantages of 3D printing lie in providing customized tools by which to integrate the vital details of natural reefs, such as rugosity and complexity, into a sustainable manufacturing process. This methodology can offer economic solutions for developing both small and large-scale biomimetic structures for a variety of restoration situations, that closely resemble the coral reefs they intend to support.

A 3D perspective on sediment turnover and feeding selectivity in blennies

Sediments in algal turfs can modify a wide variety of key ecological processes on coral reefs. While some larger reef fishes can remove these turf-bound sediments, the role of small, yet abundant, cryptobenthic fishes is currently unclear. To address this knowledge gap, we explored the extent to which the blenny, Ecsenius stictus, can shape sediment dynamics on coral reefs by quantifying their sediment ingestion and space use. Per unit body mass, E. stictus process sediments at comparable rates to key parrotfish and surgeonfish species. However, in absolute terms, E. stictus has a negligible influence on net sediment dynamics, despite their abundance. Behavioural observations and 3D photogrammetry reveal that E. stictus preferentially feed and rest on elevated surfaces; potentially because of low sediment loads on these surfaces. Overall, E. stictus may be responding to sediment loads rather than manipulating them; it is a passenger rather than a driver in reef processes.

Automated 2D, 2.5D, and 3D Segmentation of Coral Reef Pointclouds and Orthoprojections

Enabled by advancing technology, coral reef researchers increasingly prefer use of image-based surveys over approaches depending solely upon in situ observations, interpretations, and recordings of divers. The images collected, and derivative products such as orthographic projections and 3D models, allow researchers to study a comprehensive digital twin of their field sites. Spatio-temporally located twins can be compared and annotated, enabling researchers to virtually return to sites long after they have left them. While these new data expand the variety and specificity of biological investigation that can be pursued, they have introduced the much-discussed Big Data Problem: research labs lack the human and computational resources required to process and analyze imagery at the rate it can be collected. The rapid development of unmanned underwater vehicles suggests researchers will soon have access to an even greater volume of imagery and other sensor measurements than can be collected by diver-piloted platforms, further exacerbating data handling limitations. Thoroughly segmenting (tracing the extent of and taxonomically identifying) organisms enables researchers to extract the information image products contain, but is very time-consuming. Analytic techniques driven by neural networks offer the possibility that the segmentation process can be greatly accelerated through automation. In this study, we examine the efficacy of automated segmentation on three different image-derived data products: 3D models, and 2D and 2.5D orthographic projections thereof; we also contrast their relative accessibility and utility to different avenues of biological inquiry. The variety of network architectures and parameters tested performed similarly, ∼80% IoU for the genus Porites, suggesting that the primary limitations to an automated workflow are 1) the current capabilities of neural network technology, and 2) consistency and quality control in image product collection and human training/testing dataset generation.

Modified horseshoe crab peptides target and kill bacteria inside host cells

Bacteria that occupy an intracellular niche can evade extracellular host immune responses and antimicrobial molecules. In addition to classic intracellular pathogens, other bacteria including uropathogenic Escherichia coli (UPEC) can adopt both extracellular and intracellular lifestyles. UPEC intracellular survival and replication complicates treatment, as many therapeutic molecules do not effectively reach all components of the infection cycle. In this study, we explored cell-penetrating antimicrobial peptides from distinct structural classes as alternative molecules for targeting bacteria. We identified two β-hairpin peptides from the horseshoe crab, tachyplesin I and polyphemusin I, with broad antimicrobial activity toward a panel of pathogenic and non-pathogenic bacteria in planktonic form. Peptide analogs [I11A]tachyplesin I and [I11S]tachyplesin I maintained activity toward bacteria, but were less toxic to mammalian cells than native tachyplesin I. This important increase in therapeutic window allowed treatment with higher concentrations of [I11A]tachyplesin I and [I11S]tachyplesin I, to significantly reduce intramacrophage survival of UPEC in an in vitro infection model. Mechanistic studies using bacterial cells, model membranes and cell membrane extracts, suggest that tachyplesin I and polyphemusin I peptides kill UPEC by selectively binding and disrupting bacterial cell membranes. Moreover, treatment of UPEC with sublethal peptide concentrations increased zinc toxicity and enhanced innate macrophage antimicrobial pathways. In summary, our combined data show that cell-penetrating peptides are attractive alternatives to traditional small molecule antibiotics for treating UPEC infection, and that optimization of native peptide sequences can deliver effective antimicrobials for targeting bacteria in extracellular and intracellular environments.

Photogrammetry as a tool to improve ecosystem restoration

Ecosystem restoration has been practiced for over a century and is increasingly supported by the emergent applied science of restoration ecology. A prerequisite for successful ecosystem restoration is determining meaningful and measurable goals. This requires tools to monitor success in a standardized way. Photogrammetry uses images to reconstruct landscapes and organisms in three dimensions, enabling non-invasive measurement of key success indicators with unprecedented accuracy. We propose photogrammetry can improve restoration success by: (i) facilitating measurable goals; (ii) innovating and standardizing indicators of success; and (iii) standardizing monitoring. While the case we present is specific to coral reefs, photogrammetry has enormous potential to improve restoration practice in a wide range of ecosystems.

Space-filling and benthic competition on coral reefs

Reef-building corals are ecosystem engineers that compete with other benthic organisms for space and resources. Corals harvest energy through their surface by photosynthesis and heterotrophic feeding, and they divert part of this energy to defend their outer colony perimeter against competitors. Here, we hypothesized that corals with a larger space-filling surface and smaller perimeters increase energy gain while reducing the exposure to competitors. This predicted an association between these two geometric properties of corals and the competitive outcome against other benthic organisms. To test the prediction, fifty coral colonies from the Caribbean island of Curaçao were rendered using digital 3D and 2D reconstructions. The surface areas, perimeters, box-counting dimensions (as a proxy of surface and perimeter space-filling), and other geometric properties were extracted and analyzed with respect to the percentage of the perimeter losing or winning against competitors based on the coral tissue apparent growth or damage. The increase in surface space-filling dimension was the only significant single indicator of coral winning outcomes, but the combination of surface space-filling dimension with perimeter length increased the statistical prediction of coral competition outcomes. Corals with larger surface space-filling dimensions (Ds > 2) and smaller perimeters displayed more winning outcomes, confirming the initial hypothesis. We propose that the space-filling property of coral surfaces complemented with other proxies of coral competitiveness, such as life history traits, will provide a more accurate quantitative characterization of coral competition outcomes on coral reefs. This framework also applies to other organisms or ecological systems that rely on complex surfaces to obtain energy for competition.

Quantifying impacts of stony coral tissue loss disease on corals in Southeast Florida through surveys and 3D photogrammetry

Since 2014, stony coral tissue loss disease (SCTLD) has contributed to substantial declines of reef-building corals in Florida. The emergence of this disease, which impacts over 20 scleractinian coral species, has generated a need for widespread reef monitoring and the implementation of novel survey and disease mitigation strategies. This study paired SCTLD prevalence assessments with colony-level monitoring to help improve understanding of disease dynamics on both individual coral colonies and at reef-wide scales. Benthic surveys were conducted throughout the northern Florida Reef Tract to monitor the presence/absence of disease, disease prevalence, and coral species affected by SCTLD. Observed SCTLD prevalence was lower in Jupiter and Palm Beach than in Lauderdale-by-the-Sea or St. Lucie Reef, but there were no significant changes in prevalence over time. To assess colony-level impacts of the disease, we optimized a low-cost, rapid 3D photogrammetry technique to fate-track infected Montastraea cavernosa coral colonies over four time points spanning nearly four months. Total colony area and healthy tissue area on fate-tracked colonies decreased significantly over time. However disease lesion area did not decrease over time and was not correlated with total colony area. Taken together these results suggest that targeted intervention efforts on larger colonies may maximize preservation of coral cover. Traditional coral surveys combined with 3D photogrammetry can provide greater insights into the spatiotemporal dynamics and impacts of coral diseases on individual colonies and coral communities than surveys or visual estimates of disease progression alone.

Among-genotype responses of the coral Pocillopora acuta to emersion: implications for the ecological engineering of artificial coastal defences

Stony corals are promising transplant candidates for the ecological engineering of artificial coastal defences such as seawalls as they attract and host numerous other organisms. However, seawalls are exposed to a wide range of environmental stressors associated with periods of emersion during low tide such as desiccation and changes in salinity, temperature, and solar irradiance. All of these variables have known deleterious effects on coral physiology, growth, and fitness. In this study, we performed parallel experiments (in situ and ex situ) to examine among-genotype responses of Pocillopora acuta to emersion by quantifying growth, photophysiological metrics (F_v/F_m, non-photochemical quenching [NPQ], endosymbiont density, and chlorophyll [chl] a concentration) and survival, following different emersion periods. Results showed that coral fragments emersed for longer durations (>2 h) exhibited reduced growth and survival. Endosymbiont density and NPQ, but not F_v/F_m and chl a concentration, varied significantly among genotypes across different durations of emersion. Overall, the ability of P. acuta to tolerate emersion for up to 2 h suggests its potential to serve as a 'starter species' for transplantation efforts on seawalls. Further, careful characterisation and selection of genotypes with a high capacity to withstand emersion can help maximise the efficacy of ecological engineering using coral transplants.

Repeatable Semantic Reef-Mapping through Photogrammetry and Label-Augmentation

In an endeavor to study natural systems at multiple spatial and taxonomic resolutions, there is an urgent need for automated, high-throughput frameworks that can handle plethora of information. The coalescence of remote-sensing, computer-vision, and deep-learning elicits a new era in ecological research. However, in complex systems, such as marine-benthic habitats, key ecological processes still remain enigmatic due to the lack of cross-scale automated approaches (mms to kms) for community structure analysis. We address this gap by working towards scalable and comprehensive photogrammetric surveys, tackling the profound challenges of full semantic segmentation and 3D grid definition. Full semantic segmentation (where every pixel is classified) is extremely labour-intensive and difficult to achieve using manual labeling. We propose using label-augmentation, i.e., propagation of sparse manual labels, to accelerate the task of full segmentation of photomosaics. Photomosaics are synthetic images generated from a projected point-of-view of a 3D model. In the lack of navigation sensors (e.g., a diver-held camera), it is difficult to repeatably determine the slope-angle of a 3D map. We show this is especially important in complex topographical settings, prevalent in coral-reefs. Specifically, we evaluate our approach on benthic habitats, in three different environments in the challenging underwater domain. Our approach for label-augmentation shows human-level accuracy in full segmentation of photomosaics using labeling as sparse as 0.1%, evaluated on several ecological measures. Moreover, we found that grid definition using a leveler improves the consistency in community-metrics obtained due to occlusions and topology (angle and distance between objects), and that we were able to standardise the 3D transformation with two percent error in size measurements. By significantly easing the annotation process for full segmentation and standardizing the 3D grid definition we present a semantic mapping methodology enabling change-detection, which is practical, swift, and cost-effective. Our workflow enables repeatable surveys without permanent markers and specialized mapping gear, useful for research and monitoring, and our code is available online. Additionally, we release the Benthos data-set, fully manually labeled photomosaics from three oceanic environments with over 4500 segmented objects useful for research in computer-vision and marine ecology.

Projected shifts in coral size structure in the Anthropocene

Changes in the size structure of coral populations have major consequences for population dynamics and community function, yet many coral reef monitoring projects do not record this critical feature. Consequently, our understanding of current and future trajectories in coral size structure, and the demographic processes underlying these changes, is still emerging. Here, we provide a conceptual summary of the benefits to be gained from more comprehensive attention to the size of coral colonies in reef monitoring projects, and we support our argument through the use of case-history examples and a simplified ecological model. We neither seek to review the available empirical data, or to rigorously explore causes and implications of changes in coral size, we seek to reveal the advantages to modifying ongoing programs to embrace the information inherent in changing coral colony size. Within this framework, we evaluate and forecast the mechanics and implications of changes in the population structure of corals that are transitioning from high to low abundance, and from large to small colonies, sometimes without striking effects on planar coral cover. Using two coral reef locations that have been sampled for coral size, we use demographic data to underscore the limitations of coral cover in understanding the causes and consequences of long-term declining coral size, and abundance. A stage-structured matrix model is used to evaluate the demographic causes of declining coral colony size and abundance, particularly with respect to the risks of extinction. The model revealed differential effects of mortality, growth and fecundity on coral size distributions. It also suggested that colony rarity and declining colony size in association with partial tissue mortality and chronic declines in fecundity, can lead to a demographic bottleneck with the potential to prolong the existence of coral populations when they are characterized by mostly very small colonies. Such bottlenecks could have ecological importance if they can delay extinction and provide time for human intervention to alleviate the environmental degradation driving reductions in coral abundance.

Metrics of Coral Reef Structural Complexity Extracted from 3D Mesh Models and Digital Elevation Models

Underwater photogrammetry has been increasingly used in coral-reef research in recent years. Habitat metrics extracted from resulting three-dimensional (3D) reconstructions can be used to examine associations between the structural complexity of the reef habitats and the distribution of reef organisms. We created simulated 3D models of bare surface structures and 3D reconstructions of coral morphologies to investigate the behavior of various habitat metrics that were extracted from both Digital Elevation Models (DEMs) and 3D mesh models. Analyzing the resulting values provided us with important insights into how these metrics would compare with one another in the characterization of coral-reef habitats. Surface complexity (i.e., reef rugosity), fractal dimension extracted from DEMs and vector dispersion obtained from 3D mesh models exhibited consistent patterns in the ranking of structural complexity among the simulated bare surfaces and coral morphologies. The vector ruggedness measure obtained from DEMs at three different resolutions of 1, 2, and 4 cm effectively captured differences in the structural complexity among different coral morphologies. Profile curvature and planform curvature, on the other hand, were better suited to capture the structural complexity derived from surface topography such as walls and overhanging ledges. Our results indicate that habitat metrics extracted from DEMs are generally suitable when characterizing a relatively large plot of a coral reef captured from an overhead planar angle, while the 3D metric of vector dispersion is suitable when characterizing a coral colony or a relatively small plot methodically captured from various angles.

Multi-Temporal UAV Data and Object-Based Image Analysis (OBIA) for Estimation of Substrate Changes in a Post-Bleaching Scenario on a Maldivian Reef

Coral reefs are declining worldwide as a result of the effects of multiple natural and anthropogenic stressors, including regional-scale temperature-induced coral bleaching. Such events have caused significant coral mortality, leading to an evident structural collapse of reefs and shifts in associated benthic communities. In this scenario, reasonable mapping techniques and best practices are critical to improving data collection to describe spatial and temporal patterns of coral reefs after a significant bleaching impact. Our study employed the potential of a consumer-grade drone, coupled with structure from motion and object-based image analysis to investigate for the first time a tool to monitor changes in substrate composition and the associated deterioration in reef environments in a Maldivian shallow-water coral reef. Three key substrate types (hard coral, coral rubble and sand) were detected with high accuracy on high-resolution orthomosaics collected from four sub-areas. Multi-temporal acquisition of UAV data allowed us to compare the classified maps over time (February 2017, November 2018) and obtain evidence of the relevant deterioration in structural complexity of flat reef environments that occurred after the 2016 mass bleaching event. We believe that our proposed methodology offers a cost-effective procedure that is well suited to generate maps for the long-term monitoring of changes in substrate type and reef complexity in shallow water.

Quantifying Coral Reef Composition of Recreational Diving Sites: A Structure from Motion Approach at Seascape Scale

Recreational diving is known to have both direct and indirect impacts on coral habitats. Direct impacts include increasing sedimentation, breaks and diseases that lead to a decrease in the richness and abundances of hard corals. Indirect impacts include urban development, land management and sewage disposal. The ecological effects of scuba diving on the spatial composition metrics of reef benthic communities are less well studied, and they have not been investigated at seascape scale. In this study, we combine orthomosaics derived from Structure from Motion (SfM) photogrammetry and data-mining techniques to study the spatial composition of reef benthic communities of recreational diving sites at seascape scale (>25 m 2 ). The study focuses on the case study area of Ponta do Ouro Partial Marine Reserve (Mozambique). Results showed that scuba-diving resistant taxa (i.e., sponges and algae) were abundant at small (>850 m 2 ) and highly dived sites (>3000 dives yr − 1 ), characterized by low diversity and density, and big organisms with complex shapes. Fragile taxa (i.e., Acropora spp.) were abundant at low (365 dives yr − 1 ) and moderately dived sites (1000–3000 dives yr − 1 ) where the greater depth and wider coral reef surfaces attenuate the abrasive effect of waves and re-suspended sediments. Highest taxa diversity and density, and lowest abundance of resistant taxa were recorded at large (>2000 m 2 ) and rarely dived sites. This study highlights the potential applications for a photogrammetric approach to support monitoring programs at Ponta do Ouro Partial Marine Reserve (Mozambique), and provides some insight to understand the influence of scuba diving on benthic communities.

Growth estimates of Caribbean reef sponges on a shipwreck using 3D photogrammetry

The growth rates and ages of many benthic marine organisms are poorly understood, complicating our understanding of ecosystem change. This is particularly true for sponges, which are morphologically diverse and lack indicators of annual growth. In this study, we used emerging technologies to measure volume, surface area, and approximate age of 16 sponge species on the Tibbetts shipwreck off Cayman Brac, Caribbean Sea. Photogrammetry was used to determine the volume of individual sponges on the wreck surface, and a time series of YouTube videos was amassed in order to approximate the greatest possible age of the sponges as 8.74 y. Applying the volume measurements to an existing growth equation for the Caribbean sponge Aiolochroia crassa yielded age estimates of 5.2–10.4 y for the largest individuals of the 16 species. Specific growth rates were then calculated for 7 species from the Tibbetts and 8 species from a second shipwreck (Spiegel Grove, Key Largo, FL). Subsequent growth forecasts from these 15 species corroborate a resource trade-off between growth and the production of chemical defenses. Shipwrecks and other anthropogenic structures can be an important source of demographic information for benthic organisms, provided that certain assumptions about their provenance and history can be met.

Reef Rover: A Low-Cost Small Autonomous Unmanned Surface Vehicle (USV) for Mapping and Monitoring Coral Reefs

In the effort to design a more repeatable and consistent platform to collect data for Structure from Motion (SfM) monitoring of coral reefs and other benthic habitats, we explore the use of recent advances in open source Global Positioning System (GPS)-guided drone technology to design and test a low-cost and transportable small unmanned surface vehicle (sUSV). The vehicle operates using Ardupilot open source software and can be used by local scientists and marine managers to map and monitor marine environments in shallow areas (<20 m) with commensurate visibility. The imaging system uses two Sony a6300 mirrorless cameras to collect stereo photos that can be later processed using photogrammetry software to create underwater high-resolution orthophoto mosaics and digital surface models. The propulsion system consists of two small brushless motors powered by lithium batteries that follow pre-programmed survey transects and are operated by a GPS-guided autopilot control board. Results from our project suggest the sUSV provides a repeatable, viable, and low-cost (<$3000 USD) solution for acquiring images of benthic environments on a frequent basis from directly below the water surface. These images can be used to create SfM models that provide very detailed images and measurements that can be used to monitor changes in biodiversity, reef erosion/accretion, and assessing health conditions.

Plasticity in Three-Dimensional Geometry of Branching Corals Along a Cross-Shelf Gradient

Scleractinian corals often exhibit high levels of morphological plasticity, which is potentially important in enabling individual species to occupy benthic spaces across a wide range of environmental gradients. This study tested for differences in the three-dimensional (3D) geometry of three branching corals, Acropora nasuta, Pocillopora spp. and Stylophora pistillata among inner-, mid- and outer-shelf reefs in the central Great Barrier Reef, Australia. Important attributes of coral morphology (e.g., surface area to volume ratio) were expected to vary linearly across the shelf in accordance with marked gradients in environmental conditions, but instead, we detected non-linear trends in the colony structure of A. nasuta and Pocillopora spp. The surface area to volume ratio of both A. nasuta and Pocillopora spp. was highest at mid-shelf locations, (reflecting higher colony complexity) and was significantly lower at both inner-shelf and outer-shelf reefs. The branching structure of these corals was also far more tightly packed at inner-shelf and outer-shelf reefs, compared to mid-shelf reefs. Apparent declines in complexity and inter-branch spacing at inner and outer-shelf reefs (compared to conspecifics from mid-shelf reefs) may reflect changes driven by gradients of sedimentation and hydrodynamics. The generality and explanations of observed patterns warrant further investigation, which is very feasible using the 3D-photogrammetry techniques used in this study.

Effects of bleaching-associated mass coral mortality on reef structural complexity across a gradient of local disturbance

Structural complexity underpins the ecological functioning of coral reefs. However, rising ocean temperatures and associated coral bleaching threaten the structural integrity of these important ecosystems. Despite the increased frequency of coral bleaching events, few studies to date have examined changes in three-dimensional (3D) reef structural complexity following severe bleaching. The influence of local stressors on reef complexity also remains poorly understood. In the wake of the 2015-2016 El Niño-induced mass coral bleaching event, we quantified the effects of severe heat stress on 3D reef structural complexity across a gradient of local human disturbance. Using Structure-from-Motion photogrammetry we created 3D reconstructions of permanent reef plots and observed substantial declines in reef structural complexity, measured as surface rugosity and terrain ruggedness, and a detectable loss of habitat volume one year after the bleaching event. 3D reef complexity also declined with increasing levels of human disturbance, and with decreasing densities of branching and massive corals. These findings improve our understanding of the effects of local and global stressors on the structural foundation of coral reef ecosystems. In the face of accelerating climate change, mitigating local stressors may increase reef structural complexity, thereby heightening reef resilience to future bleaching events.

Integrating Three-Dimensional Benthic Habitat Characterization Techniques into Ecological Monitoring of Coral Reefs

Long-term ecological monitoring of reef fish populations often requires the simultaneous collection of data on benthic habitats in order to account for the effects of these variables on fish assemblage structure. Here, we described an approach to benthic surveys that uses photogrammetric techniques to facilitate the extraction of quantitative metrics for characterization of benthic habitats from the resulting three-dimensional (3D) reconstruction of coral reefs. Out of 92 sites surveyed in the Northwestern Hawaiian Islands, photographs from 85 sites achieved complete alignment and successfully produced 3D reconstructions and digital elevation models (DEMs). Habitat metrics extracted from the DEMs were generally correlated with one another, with the exception of curvature measures, indicating that complexity and curvature measures should be treated separately when quantifying the habitat structure. Fractal dimension D64, calculated by changing resolutions of the DEMs from 1 cm to 64 cm, had the best correlations with other habitat metrics. Fractal dimension was also less affected by changes in orientations of the models compared to surface complexity or slope. These results showed that fractal dimension can be used as a single measure of complexity for the characterization of coral reef habitats. Further investigations into metrics for 3D characterization of habitats should consider relevant spatial scales and focus on obtaining variables that can complement fractal dimension in the characterization of reef habitats.

Limited Cross-Shelf Variation in the Growth of Three Branching Corals on Australia’s Great Barrier Reef

Pronounced differences exist in the biodiversity and structure of coral reef assemblages with increasing distance from shore, which may be expected given marked cross-shelf gradients in environmental conditions. Cross-shelf variation in the abundance of coral reef organisms is likely to be caused, at least in part, by differences in demography (e.g., growth and survival), though this has rarely been tested. This study quantified growth of three distinct branching coral taxa (Acropora nasuta, Pocillopora spp. and Stylophora pistillata) at six locations on Australia’s Great Barrier Reef (GBR), encompassing inshore, mid-shelf and outer-shelf reefs. Replicate colonies (0–15 colonies per species, per reef) were stained using Alizarin Red in December 2015 and retrieved one year later to quantify linear extension on replicate branches for each colony. Annual linear extension varied within and among coral taxa, with pronounced differences among reefs. For A. nasuta. and S. pistillata, growth rates were highest at one of the inshore reefs, Orpheus Island. However, inter-reef differences in linear extension were not explained by shelf position. Based on differences in skeletal density, which did vary according to shelf position, branching corals at the inshore sites may actually have higher rates of calcification compared to conspecifics on mid-and outer-shelf reefs. This study shows that growth of branching corals is not lower at inshore sites (and perhaps even higher) compared to sites at mid-shelf and outer reefs, despite generally higher levels of sedimentation and turbidity.

Repeated cyclone events reveal potential causes of sociality in coral-dwelling Gobiodon fishes

Social organization is a key factor influencing a species' foraging and reproduction, which may ultimately affect their survival and ability to recover from catastrophic disturbance. Severe weather events such as cyclones can have devastating impacts to the physical structure of coral reefs and on the abundance and distribution of its faunal communities. Despite the importance of social organization to a species' survival, relatively little is known about how major disturbances such as tropical cyclones may affect social structures or how different social strategies affect a species' ability to cope with disturbance. We sampled group sizes and coral sizes of group-forming and pair-forming species of the Gobiid genus Gobiodon at Lizard Island, Great Barrier Reef, Australia, before and after two successive category 4 tropical cyclones. Group sizes of group-forming species decreased after each cyclone, but showed signs of recovery four months after the first cyclone. A similar increase in group sizes was not evident in group-forming species after the second cyclone. There was no change in mean pair-forming group size after either cyclone. Coral sizes inhabited by both group- and pair-forming species decreased throughout the study, meaning that group-forming species were forced to occupy smaller corals on average than before cyclone activity. This may reduce their capacity to maintain larger group sizes through multiple processes. We discuss these patterns in light of two non-exclusive hypotheses regarding the drivers of sociality in Gobiodon, suggesting that benefits of philopatry with regards to habitat quality may underpin the formation of social groups in this genus.

SfM-Based Method to Assess Gorgonian Forests (Paramuricea clavata (Cnidaria, Octocorallia))

Animal forests promote marine habitats morphological complexity and functioning. The red gorgonian, Paramuricea clavata, is a key structuring species of the Mediterranean coralligenous habitat and an indicator species of climate effects on habitat functioning. P. clavata metrics such as population structure, morphology and biomass inform on the overall health of coralligenous habitats, but the estimation of these metrics is time and cost consuming, and often requires destructive sampling. As a consequence, the implementation of long-term and wide-area monitoring programmes is limited. This study proposes a novel and transferable Structure from Motion (SfM) based method for the estimation of gorgonian population structure (i.e., maximal height, density, abundance), morphometries (i.e., maximal width, fan surface) and biomass (i.e., coenenchymal Dry Weight, Ash Free Dried Weight). The method includes the estimation of a novel metric (3D canopy surface) describing the gorgonian forest as a mosaic of planes generated by fitting multiple 5 cm × 5 cm facets to a SfM generated point cloud. The performance of the method is assessed for two different cameras (GoPro Hero4 and Sony NEX7). Results showed that for highly dense populations (17 colonies/m2), the SfM-method had lower accuracies in estimating the gorgonians density for both cameras (60% to 89%) than for medium to low density populations (14 and 7 colonies/m2) (71% to 100%). Results for the validation of the method showed that the correlation between ground truth and SfM estimates for maximal height, maximal width and fan surface were between R2 = 0.63 and R2 = 0.9, and R2 = 0.99 for coenenchymal surface estimation. The methodological approach was used to estimate the biomass of the gorgonian population within the study area and across the coralligenous habitat between −25 to −40 m depth in the Portofino Marine Protected Area. For that purpose, the coenenchymal surface of sampled colonies was obtained and used for the calculations. Results showed biomass values of dry weight and ash free dry weight of 220 g and 32 g for the studied area and to 365 kg and 55 Kg for the coralligenous habitat in the Marine Protected Area. This study highlighted the feasibility of the methodology for the quantification of P. clavata metrics as well as the potential of the SfM-method to improve current predictions of the status of the coralligenous habitat in the Mediterranean sea and overall management of threatened ecosystems.