MORPHOLOGY: CNIDARIANS
CORALS
Fabri M. C., Vinha B., Allais A. G., Bouhier M. E., Dugornay O., Gaillot A., Arnaubec A. (2019): Evaluating the ecological status of cold-water coral habitats using non-invasive methods: An example from Cassidaigne canyon, northwestern Mediterranean Sea. Progress in Oceanography 178: 102172.
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Cold-water coral ecosystems have been identified as vulnerable, but quantitative data on their conservation status is very limited. The Marine Strategy Framework Directive (MSFD) is the tool implemented by the European Union’s Integrated Maritime Policy to achieve Good Environmental Status (GES) of marine waters by 2020. In this context, the aim of this study was to evaluate the Ecological Status of benthic habitats in Cassidaigne canyon, focusing in particular on cold-water coral habitats dominated by Madrepora oculata. Data were collected during the Videocor1 cruise (2017). Videos and photos collected during eight dives of the H-ROV Ariane were used to reconstruct, in 3-dimensions, the areas where cnidarians have settled in the canyon. A total of 33 3D models were built, which allowed measuring the spatial and vertical distribution, surface, density and size structure of cnidarian populations at four different sites. When 3D reconstructions were not possible, GIS tools were used. The seven cnidarian species considered were the scleractinian M. oculata; three antipatharians: Leiopathes glaberrima, Antipathella subpinnata, Antipathes dichotoma; and three aclyonaceans: the precious red coral Corallium rubrum and the gorgonians Callogorgia verticllata and Viminella flagellum. Using photogrammetry, we were able to reveal the size structure of the dense population of M. oculata in the canyon, as well as to obtain knowledge on a complex site (Cassis-200) composed of 15 knolls, and to quantify the surface occupied by M. oculata at a separate site (Cassis-500) influenced by industrial discharges. At the southern flank of the canyon we found a highly diverse site (SW Flank) dominated by antipatharians and gorgonians composing large forests, and finally a reservoir of M. oculata was identified under overhangs at a site called the Wall. The diversity of accompanying species is also reported and marine litter quantified. Images collected before 2017 were compared to the 3D models to precisely locate them on the sites, and assess temporal changes in M. oculata colony sizes at Cassis-200 site. We also report on the ground-truthing of predicted habitat maps produced previously, and confirm their good representation of the distribution of cold-water coral habitats. Finally, we quantified the criteria defined by the MSFD, aimed at evaluating the GES of benthic habitats for M. oculata ecosystems, at the scale of the Cassidaigne canyon. Measurements showed that the extent of loss of the observed M. oculata habitat reached 56% according to the MFSD definition.
Bayley D. T., Mogg A. O. (2020): A protocol for the large‐scale analysis of reefs using Structure from Motion photogrammetry. Methods in Ecology and Evolution 11: 1410-1420.
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Substrate complexity is an essential metric of reef health and a strong predictor of several ecological processes connected to the reef, including disturbance, resilience, and associated community abundance and diversity. Underwater Structure from Motion (SfM) photogrammetry has been growing rapidly in use over the last 5 years due to advances in computing power, reduced costs of underwater digital cameras and a push for reproducible data. This has led to the adaptation of an originally terrestrial survey technique into the marine realm, which can now be applied at the habitat scale. This technique allows researchers to make detailed 3D reconstructions of reef surfaces for morphometric analysis of reef physical structure and perform large-scale image-mosaic mapping. SfM is useful for both reef-scale and colony-scale assessments, where visual or acoustic methods are impractical or not sufficiently detailed. Here we provide a protocol for the collection, analysis and display of 3D reef data, focussing on large-scale habitat assessments of coral reefs using primarily open-source software. We further suggest applications for other underwater environments and scales of assessment, and hope this standardized protocol will help researchers apply this technology and inspire new avenues of ecological research.
Lange, I. D., & Perry, C. T. (2020). A quick, easy and non‐invasive method to quantify coral growth rates using photogrammetry and 3D model comparisons. Methods in Ecology and Evolution 11: 714-726.
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Coral growth rates vary significantly with environmental conditions and are thus important indicators of coral health and reef carbonate production. Despite the importance of this metric, data are sparse for most coral genera and species globally, including for many key reef-building species. Traditional methods to obtain growth rates, such as coral coring or staining with Alizarin are destructive and only work for a limited number of species and morphological growth forms. Emerging approaches, using underwater photogrammetry to create digital models of coral colonies, are providing novel and non-invasive ways to explore colony-scale growth patterns and to address existing knowledge gaps. We developed an easy-to-follow workflow to construct three-dimensional (3D) models from overlapping photographs and to measure linear, radial and vertical extension rates of branching, massive and encrusting corals after aligning colony models from subsequent years. The method presented here was applied to measure extension rates for 46 colonies of nine coral species in the remote Chagos Archipelago, Indian Ocean. Proposed image acquisition and software settings produced 3D models of consistently high resolution and detail (precision ≤ 0.2 mm) and variability in growth measurements was small despite manual alignment, clipping and ruler placement (SD ≤ 0.9 mm). Measured extension rates for the Chagos Archipelago are similar to published rates in the Indo-Pacific where comparable data are available, and provide the first published rates for several species. For encrusting corals, the results emphasize the importance of differentiating between radial and vertical growth. Photogrammetry and 3D model comparisons provide a fast, easy, inexpensive and non-invasive method to quantify coral growth rates for a range of species and morphological growth forms. The simplicity of the presented workflow encourages its repeatability and permits non-specialists to learn photogrammetry with the goal of obtaining linear coral growth rates. Coral growth rates are essential metrics to quantify functional consequences of ongoing community changes on coral reefs and expanded datasets for key coral taxa will aid predictions of geographic variations in coral reef response to increasing global stressors.
Chimienti G., Aguilar R., Maiorca M., Mastrototaro F. (2021): A newly discovered forest of the whip coral Viminella flagellum (Anthozoa, Alcyonacea) in the Mediterranean Sea: a non-invasive method to assess its population structure. Biology 11: 39.
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Coral forests are vulnerable marine ecosystems formed by arborescent corals (e.g., Anthozoa of the orders Alcyonacea and Antipatharia). The population structure of the habitat-forming corals can inform on the status of the habitat, representing an essential aspect to monitor. Most Mediterranean corals live in the mesophotic and aphotic zones, and their population structures can be assessed by analyzing images collected by underwater vehicles. This is still not possible in whip-like corals, whose colony lengths and flexibilities impede the taking of direct length measurements from images. This study reports on the occurrence of a monospecific forest, of the whip coral Viminella flagellum in the Aeolian Archipelago (Southern Tyrrhenian Sea; 149 m depth), and the assessment of its population structure through an ad-hoc, non-invasive method to estimate a colony height based on its width. The forest of V. flagellum showed a mean density of 19.4 ± 0.2 colonies m−2 (up to 44.8 colonies m−2) and no signs of anthropogenic impacts. The population was dominated by young colonies, with the presence of large adults and active recruitment. The new model proved to be effective for non-invasive monitoring of this near threatened species, representing a needed step towards appropriate conservation actions.
Koch H. R., Wallace B., DeMerlis A., Clark A. S., Nowicki R. J. (2021): 3D scanning as a tool to measure growth rates of live coral microfragments used for coral reef restoration. Frontiers in Marine Science 8: 623645.
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Rapid and widespread declines in coral health and abundance have driven increased investments in coral reef restoration interventions to jumpstart population recovery. Microfragmentation, an asexual propagation technique, is used to produce large numbers of corals for research and restoration. As part of resilience-based restoration, coral microfragments of different genotypes and species are exposed to various stressors to identify candidates for propagation. Growth rate is one of several important fitness-related traits commonly used in candidate selection, and being able to rapidly and accurately quantify growth rates of different genotypes is ideal for high-throughput stress tests. Additionally, it is crucial, as coral restoration becomes more commonplace, to establish practical guidelines and standardized methods of data collection that can be used across independent groups. Herein, we developed a streamlined workflow for growth rate quantification of live microfragmented corals using a structured-light 3D scanner to assess surface area (SA) measurements of live tissue over time. We then compared novel 3D and traditional 2D approaches to quantifying microfragment growth rates and assessed factors such as accuracy and speed. Compared to a more conventional 2D approach based on photography and ImageJ analysis, the 3D approach had comparable reliability, greater accuracy regarding absolute SA quantification, high repeatability, and low variability between scans. However, the 2D approach accurately measured growth and proved to be faster and cheaper, factors not trivial when attempting to upscale for restoration efforts. Nevertheless, the 3D approach has greater capacity for standardization across dissimilar studies, making it a better tool for restoration practitioners striving for consistent and comparable data across users, as well as for those conducting networked experiments, meta-analyses, and syntheses. Furthermore, 3D scanning has the capacity to provide more accurate surface area (SA) measurements for rugose, mounding, or complex colony shapes. This is the first protocol developed for using structured-light 3D scanning as a tool to measure growth rates of live microfragments. While each method has its advantages and disadvantages, disadvantages to a 3D approach based on speed and cost may diminish with time as interest and usage increase. As a resource for coral restoration practitioners and researchers, we provide a detailed 3D scanning protocol herein and discuss its potential limitations, applications, and future directions.
Jaffe J. S., Schull S., Kühl M., Wangpraseurt D. (2022): Non-invasive estimation of coral polyp volume and surface area using optical coherence tomography. Frontiers in Marine Science 9: 2434.
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The surface area (SA) and three-dimensional (3D) morphology of reef-building corals are central to their physiology. A challenge for the estimation of coral SA has been to meet the required spatial resolution as well as the capability to preserve the soft tissue in its native state during measurements. Optical Coherence Tomography (OCT) has been used to quantify the 3D microstructure of coral tissues and skeletons with nearly micron-scale resolution. Here, we develop a non-invasive method to quantify surface area and volume of single coral polyps. A coral fragment with several coral polyps as well as calibration targets of known areal extent are scanned with an OCT system. This produces a 3D matrix of optical backscatter that is analyzed with computer algorithms to detect refractive index mismatches between physical boundaries between the coral and the immersed water. The algorithms make use of a normalization of the depth dependent scatter intensity and signal attenuation as well as region filling to depict the interface between the coral soft tissue and the water. Feasibility of results is judged by inspection as well as by applying algorithms to hard spheres and fish eggs whose volume and SA can be estimated analytically. The method produces surface area estimates in calibrated targets that are consistent with analytic estimates within 93%. The appearance of the coral polyp surfaces is consistent with visual inspection that permits standard programs to visualize both point clouds and 3-D meshes. The method produces the 3-D definition of coral tissue and skeleton at a resolution close to 10 µm, enabling robust quantification of polyp volume to surface area ratios.
Urbina‐Barreto I., Elise S., Guilhaumon F., Bruggemann J. H., Pinel R., Kulbicki M., Vigliola L., Mou‐Tham G., Mahamadaly V., Facon M., Bureau S., Peignon C., Dutrieux E., Garnier R., Penin L., Adjeroud M. (2022): Underwater photogrammetry reveals new links between coral reefscape traits and fishes that ensure key functions. Ecosphere 13: e3934.
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Maintaining key functions of coral reefs is vital for the persistence of these ecosystems as well as for securing the goods and services that they provide in the Anthropocene. Underwater photogrammetry by Structure from Motion (SfM) allows the quantification of novel habitat descriptors that may be particularly relevant in assessing key reefscape traits, that is, physical and ecological characteristics of coral reef habitats. Here, we combined this new technology with fish surveys to explore how reefscape traits shape the functional structure of reef fish assemblages around three environmentally contrasted islands of the Indo-Pacific (Europa Island, Reunion Island, and New Caledonia). At 24 sites, habitat descriptors were computed from digital elevation models (DEM) and orthomosaics, while reef fish assemblages were assessed by visual census and video footage. Four habitat descriptors were marginally correlated and presented low variance inflation factor (VIF) values, thus being the most complementary descriptors: surface complexity, total shelter capacity, Shannon Shelter Index, and total coral cover. Linear mixed models (LMM) were used to explore the relationships between these habitat descriptors and four key fish functional entities: prey, planktivores, grazers, and predators. For each model, the variance explained (i.e., marginal R2) was significantly higher when considering multiple predictors, including the novel three-dimensional descriptors (i.e., total shelter capacity and Shannon Shelter Index). The habitat descriptors quantified from underwater photogrammetry outputs (i.e., DEM and orthomosaics) provide easily available data to assess key reefscape traits and predict fish assemblage structure in coral reef ecosystems. This trait-based functional approach allows consistent assessment of the links between these descriptors from local to regional scales. Considering the global coral reef crisis and the increasing availability of world-reef photogrammetric surveys, this new technology should be key to bringing solutions to 21st-century conservation issues.
Irawan D., Mukti A. T., Andriyono S., Muhsoni F. F. (2023): Three-dimensional (3D) modelling to determine the weight of massive corals in Gili Labak Island, Sumenep, Madura, East Java, Indonesia. Biodiversity 24: 24-33.
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This study aimed to non-destructively measure the weight of massive (live) corals through three-dimensional (3D) modelling. The 3D models were constructed using the volumes and weight of massive (dead) corals. The study was conducted through photographs, 3D analysis, and weighing 32 massive (dead) coral samples. Volume and weight were modelled using linear and non-linear regressions, and their accuracy was tested using root mean square error (RMSE) and mean absolute percentage error (MAPE). This study showed that the weight of massive (live) corals could be measured using a 3D model of the massive (dead) coral’s volume and the weight mainly through regression, polynomial, and geometric equations. The power/geometric equation is a more suitable approach for determining the actual value of coral weight. Linear regression obtained an average weight of 6.13 kg per plot. Three-dimensional modelling can be widely applied to measure the massive corals in the deep sea.