skip to main content


Title: 2D and 3D coral models imaged in Curaçao: George, Mullinix, et al PeerJ 2021
Abstract from the article associated with the dataset: George, Mullinix, et al PeerJ 2021. Reef-building corals are ecosystem engineers that compete with other benthic or- ganisms 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 Curac ̧ao were rendered using digital 3D and 2D reconstructions. The surface areas, perimeters, box-counting dimensions (as a proxy of space-filling property), 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. For the compressed files: - Reconstruction of the split file can be accomplished by issuing the command cat *.tar.bz2*part-a* > 3D_model_stl_data.tar.bz2 - Unzipping the compressed files can be accomplished by issuing the command tar -jxvf *.tar.bz2  more » « less
Award ID(s):
1951678
NSF-PAR ID:
10315263
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ; ; ; ; ; ;
Publisher / Repository:
Dryad
Date Published:
Edition / Version:
6
Subject(s) / Keyword(s):
["coral","digital rendering","fractal analysis","coral-benthic interactions","random forest","bootstrap","FOS: Biological sciences"]
Format(s):
Medium: X Size: 3115590963 bytes
Size(s):
["3115590963 bytes"]
Sponsoring Org:
National Science Foundation
More Like this
  1. 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.

     
    more » « less
  2. null (Ed.)
    Competition for limited space is an important driver of benthic community structure on coral reefs. Studies of coral-algae and coral-sponge interactions often show competitive dominance of algae and sponges over corals, but little is known about the outcomes when these groups compete in a multispecies context. Multispecies competition is increasingly common on Caribbean coral reefs as environmental degradation drives loss of reef-building corals and proliferation of alternative organisms such as algae and sponges. New methods are needed to understand multispecies competition, whose outcomes can differ widely from pairwise competition and range from coexistence to exclusion. In this study, we used 3D photogrammetry and image analyses to compare pairwise and multispecies competition on reefs in the US Virgin Islands. Sponges ( Desmapsamma anchorata, Aplysina cauliformis ) and macroalgae ( Lobophora variegata ) were attached to coral ( Porites astreoides ) and arranged to simulate multispecies (coral-sponge-algae) and pairwise (coral-sponge, coral-algae) competition. Photogrammetric 3D models were produced to measure surface area change of coral and sponges, and photographs were analyzed to measure sponge-coral, algae-coral, and algae-sponge overgrowth. Coral lost more surface area and was overgrown more rapidly by the sponge D. anchorata in multispecies treatments, when the sponge was also in contact with algae. Algae contact may confer a competitive advantage to the sponge D. anchorata, but not to A. cauliformis , underscoring the species-specificity of these interactions. This first application of photogrammetry to study competition showed meaningful losses of living coral that, combined with significant overgrowths by competitors detected from image analyses, exposed a novel outcome of multispecies competition. 
    more » « less
  3. null (Ed.)
    This protocol describes the process of phenotyping branching coral using the 3D model editing software, MeshLab. MeshLab is a free, straightforward software to analyze 3D models of corals that is especially useful in its ability to import color from Agisoft Metashape models. This protocol outlines the steps used by the Kenkel lab to noninvasively phenotype Acropora cervicornis colonies for total linear extension (TLE), surface area, volume, and volume of interstitial space. We incorporate Agisoft Metashape markers with our Tomahawk scaling system (see Image Capture Protocol) in our workflow which is useful for scaling and to improve model building. Other scaling objects can be used, however these markers provide a consistent scale that do not obstruct the coral during image capture. MeshLab measurements of TLE have been groundtruthed to field measures of TLE. 3D surface area and volume have not yet been compared to traditional methods of wax dipping, for surface area, and water displacement, for volume. However, in tests with shapes of known dimensions, i.e. cubes, MeshLab produced accurate measures of 3D surface area and volume when compared to calculated surface area and volume. For directions to photograph coral for 3D photogrammetry see our Image Capture Protocol. For a walkthrough and scripts to run Agisoft Metashape on the command line, see https://github.com/wyattmillion/Coral3DPhotogram. These protocols, while created for branching coral, can be applied to 3D models of any coral morphology or any object really. Our goal is to make easy-to-use protocols using accessible softwares in the hopes of creating a standardized method for 3D photogrammetry in coral biology. Go to http://www.meshlab.net/#download to download the appropriate software for your operating system. P. Cignoni, M. Callieri, M. Corsini, M. Dellepiane, F. Ganovelli, G. Ranzuglia MeshLab: an Open-Source Mesh Processing Tool Sixth Eurographics Italian Chapter Conference, page 129-136, 2008 DOI dx.doi.org/10.17504/protocols.io.bgbpjsmn 
    more » « less
  4. Abstract Background Predation pressure and herbivory exert cascading effects on coral reef health and stability. However, the extent of these cascading effects can vary considerably across space and time. This variability is likely a result of the complex interactions between coral reefs’ biotic and abiotic dimensions. A major biological component that has been poorly integrated into the reefs' trophic studies is the microbial community, despite its role in coral death and bleaching susceptibility. Viruses that infect bacteria can control microbial densities and may positively affect coral health by controlling microbialization. We hypothesize that viral predation of bacteria has analogous effects to the top-down pressure of macroorganisms on the trophic structure and reef health. Results Here, we investigated the relationships between live coral cover and viruses, bacteria, benthic algae, fish biomass, and water chemistry in 110 reefs spanning inhabited and uninhabited islands and atolls across the Pacific Ocean. Statistical learning showed that the abundance of turf algae, viruses, and bacteria, in that order, were the variables best predicting the variance in coral cover. While fish biomass was not a strong predictor of coral cover, the relationship between fish and corals became apparent when analyzed in the context of viral predation: high coral cover (> 50%) occurred on reefs with a combination of high predator fish biomass (sum of sharks and piscivores > 200 g m −2 ) and high virus-to-bacteria ratios (> 10), an indicator of viral predation pressure. However, these relationships were non-linear, with reefs at the higher and lower ends of the coral cover continuum displaying a narrow combination of abiotic and biotic variables, while reefs at intermediate coral cover showed a wider range of parameter combinations. Conclusions The results presented here support the hypothesis that viral predation of bacteria is associated with high coral cover and, thus, coral health and stability. We propose that combined predation pressures from fishes and viruses control energy fluxes, inhibiting the detrimental accumulation of ecosystem energy in the microbial food web. 
    more » « less
  5. Abstract. Cloud area distributions are a defining feature of Earth's radiative exchanges with outer space. Cloud perimeter distributions n(p) are also interesting because the shared interface between clouds and clear sky determines exchanges of buoyant energy and air. Here, we test using detailed model output and a wide range of satellite datasets a first-principles prediction that perimeter distributions follow a scale-invariant power law n(p) ∝ p-(1+β), where the exponent β = 1 is evaluated for perimeters within moist isentropic atmospheric layers. In model analyses, the value of β is closely reproduced. In satellite data, β is remarkably robust to latitude, season, and land–ocean contrasts, which suggests that, at least statistically speaking, cloud perimeter distributions are determined more by atmospheric stability than Coriolis forces, surface temperature, or contrasts in aerosol loading between continental and marine environments. However, the satellite-measured value of β is found to be 1.26 ± 0.06 rather than β = 1. The reason for the discrepancy is unclear, but comparison with a model reproduction of the satellite perspective suggests that it may owe to cloud overlap. Satellite observations also show that scale invariance governs cloud areas for a range at least as large as ∼ 3 to ∼ 3 × 105 km2, and notably with a corresponding power law exponent close to unity. Many prior studies observed a much smaller range for power law behavior, and we argue this difference is due to inappropriate treatments of the statistics of clouds that are truncated by the edge of the measurement domain.

     
    more » « less