Project

New quantitative tools using 3D modeling by photogrammetry to describe coral reef environments

Goal: Develop new quantitative tools of 3D models by photogrammetry, of coral colonies and coral reefs landscape, aiming to understand the correlation between habitat complexity and associated biodiversity of these ecosystems.

The project involves:
- photogrammetry underwater protocols and 3D models analyses
- assessments and monitoring of benthic communities and fish assemblage in South West Indian Ocean.

This project is conducted as a PhD project started in Octobre 2017, implying the environment & oceanography company Creocean OI, engineering company Geolab and UMR 9220 ENTROPIE laboratory in Reunion Island, France.

Date: 1 October 2017 - 30 September 2020

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Project log

Isabel Urbina-Barreto
added a research item
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 R 2) 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 Isabel Urbina-Barreto and Simon Elise contributed equally to this study. and the increasing availability of world-reef photogrammetric surveys, this new technology should be key to bringing solutions to 21st-century conservation issues.
Isabel Urbina-Barreto
added a research item
Habitat structural complexity plays a key role in the dynamics and resilience of coral reef communities. The critical situation of coral reef ecosystems beseeches a rapid improvement of monitoring tools to assist in the implementation of efficient conservation measures. Today, new reef assessment technologies support researchers and managers to collect information safer, faster, and with greater accuracy. Among them, photogrammetry by Structure-from-Motion (SfM) creates three-dimensional models and reef zone maps from overlapping images to conduct quantitative surveys of benthic communities. This thesis addressed four objectives: 1) define underwater photogrammetry protocols to create 3D models of coral colonies and reefscapes, in order to conduct physical and ecological assessments, 2) develop new quantitative reef habitat descriptors, 3) determine the links between these descriptors and the key functional processes ensured by associated fish assemblages, 4) compare photogrammetric methods with a traditional monitoring method, the Line Intercept Transect (LIT). Overall, 120 coral colonies, 24 reefscapes, and two artificial structures (breakwaters) were 3D modeled in two biogeographic provinces: New Caledonia (Pacific Ocean), Europa Island, and Reunion Island (Indian Ocean). Two photogrammetric protocols were defined corresponding to the study scales: the coral colony (≤ 2 m3) and the reefscapes and breakwaters (> 100 m2). Analyzing the 3D models of coral colonies provided 2D and 3D metrics to estimate their shelter volume. Predictive models were then built and fitted to estimate shelter capacity at the reefscape scale. Mapped reefscapes provided the necessary information to calculate 22 new quantitative descriptors. Among them, seven were the most complementary: surface complexity, shelter capacity, diversity of shelter - Shannon Shelter Index, the abundance of branching, massive and tabular, and total coral cover. They explained 63% and 70% of the distribution of reef fish biomass and abundance, respectively. Multifactorial analyses demonstrated the importance of these habitat descriptors in supporting five key functions of reef ecosystems that are ensured by groups of fishes (herbivory-bioerosion, secondary production, plankton assimilation, predation, and coral feeding). Comparisons between photogrammetric methods and the LIT method showed that the surface analysis on the orthomosaics is the most efficient method considering the quantity and quality of data that can be gathered and the time expenditure. The LIT method is less time- consuming and more efficient for specific taxonomic identifications, though it is the most limited method in terms of descriptors and the representativeness of the ecosystem. In addition to the four principle objectives, the 3D models and other photogrammetric outputs served as communication tools in different awareness actions.To sum up, this thesis demonstrated the relevance of underwater SfM photogrammetry applications for coral reef studies, management, and awareness actions. The collected data and their analyses also contribute to establishing a baseline for monitoring the state of reef ecosystems and their functions. In doing so, it provides new scientific information to enhance future management measures and confront the ambitious twenty-first-century conservation targets.
Isabel Urbina-Barreto
added a research item
Structural complexity plays a key role in the functioning of coral reef ecosystems. Reef-building corals are major contributors to this complexity, providing shelter and food for numerous invertebrates and fish species. Both structural complexity and shelter capacity of reefscapes are determined by several components such as spurs and grooves, slope, caves and holes, vegetation and coral colonies. Quantifying the shelter capacity from coral colonies to reefscapes is a fundamental step to estimating ecosystem potential to support biodiversity. Here, we applied underwater photogrammetry to quantify shelter volumes provided by individual coral colonies. Overall, 120 3D models of coral colonies from branching, massive, columnar and tabular growth forms were studied. Three reefscapes were also 3D modeled. The study encompasses three Indo-Pacific Islands: Reunion, Europa and New Caledonia. At the colony level, measurements of diameter, planar area, surface and shelter volume were computed. At the reefscape, the diameter and planar area of each colony were extracted from orthomosaics and then used to estimate shelter capacity. Linear models had high accuracy for predicting shelter volume (a 3D metric) from 2D metrics: the diameter= 83.1%, R 2 = 0.95; the planar area= 87.5%, R 2 = 0.95 and the colony surface= 87.3%, R 2 = 0.96. The surface complexity and the shelter volume of the colonies allowed inferring the size of shelters provided by coral growth forms. Quantitative descriptors (i.e. relative percentage of shelter by growth form, the abundance of coral colonies, "Shannon-Shelter Index") revealed reefscape-scale shelter differences. Our major finding is that planar area and diameter of coral colonies are satisfactory proxies for estimating shelter volume. These new proxies allow 2D metrics to quantify 3D shelter provision, which can support scientists and managers in conservation actions since such metrics are widely used in monitoring programs. Future investigations on the relationships between shelter provision and reef biodiversity will improve the understanding of these complex ecosystems.
Isabel Urbina-Barreto
added an update
3D printing for awareness actions !
 
Isabel Urbina-Barreto
added a research item
The functioning of tropical coral reefs is imperilled by climate change, overfishing, and decreasing water quality. Maintaining their capacity to provide goods and services will critically depend on our ability to monitor their functioning at appropriate spatial and temporal scales. Given the constraints of traditional methods to respond to those needs, the potential of complementary tools such as Passive Acoustic Monitoring (PAM) is emerging. Coral reef soundscapes (i.e. ambient sound) encompass sounds produced by numerous organisms. Soundscape characteristics quantified by ecoacoustic indices have been found to reflect general ecosystem properties, such as diversity and abundance of fishes, and coral cover. The present study tested, on the virtually pristine coral reefs around Europa Island, SouthWest Indian Ocean, the capacity of acoustic indices to assess key ecosystem functions. Soundscapes were recorded during 2 h, and ecosystem functions were evaluated using video footage of the fish assemblages and underwater photogrammetry of the benthic landscapes. We found significant and strong correlations between six ecoacoustic indices and six key ecosystem functions, including habitat features and fish assemblage characteristics. The six ecoacoustic indices were representative of several combinations of frequency, amplitude and time analysis domains, highlighting the diversity of the functional information conveyed by soundscapes. Our findings reveal that a 2 h daytime recording on a coral reef could provide sufficient acoustic information to characterise major ecosystem functions of a site. This should facilitate the detection of functional disturbances at temporal and spatial scales adapted to the rapidity of upcoming climate changes. Our results also highlight the potential of ecoacoustics to bring novel and relevant insights in the functioning of ecosystems.
Isabel Urbina-Barreto
added an update
Participation - oral presentation - in 11 WIOMSA symposium (1-6 July 2019). https://symposium.wiomsa.org
Authors: Urbina-Barreto, I.* ; Pinel, R.; Mahamadaly, V.; Elise, S.; Facon, M.; Bureau, S.; Garnier, R.; Penin, L.; Adjeroud, M.
*presenting author
Abstract:
The critical situation of coral reef ecosystems claims towards a rapid improvement of techniques to better characterize their structure and dynamics, in order to implement efficient conservation measures. This implies a better understanding of the relationships between ecosystem function and associated biodiversity. Structural complexity of habitat has become a main focus in coral reef studies, as habitat structure plays a key role in the dynamics of reef communities. Indeed, biodiversity and biomass are strongly linked to this important feature. Since the early 60’s, reef ecology has used two-dimensional tools to assess the structure and function of coral reef communities and habitats. Thanks to new technologies and advances in computer performances in the last decade, a new generation of tools emerged, like Structure-from-Motion (SfM-photogrammetric technique), allowing innovating three-dimensional (3D) assessments. This technique allows a fine quantification of structural complexity and the accurate temporal monitoring of its potential changes. In this talk, we present the results of the first study using underwater SfM applications on coral reefs of the South West Indian Ocean (SWIO) to examine the relationships between fish assemblages and habitat structure among contrasting sites in terms of human impacts and substrate types.The major question addressed is: Can differences in habitat structural complexity explain the variability of associated fish biodiversity? The present study also contributes to establish a baseline for monitoring ecosystem state and function. Simultaneously, 3D models are used as a powerfully and effective communication tool, in order to increase popularity of underwater SfM applications in coral reefs’ studies, management and/or awareness programs.
The study was carried from February to December 2018 on two French islands in the SWIO, which represent two contrasted environments in terms of human impact: (i) Europa Island (French Scattered Islands in the Mozambique channel) is a nearly pristine coral reef ecosystem, (ii) Reunion Island represents a highly impacted coral reefs and offers other substrate types like basaltic spur at underwater lava flows, and coastal installations (e.g. breakwater structures). Eighteen sites were sampled on outer coral reef slopes (5 sites in western Reunion Island / 9 sites at Europa Island), on basaltic spurs (2 sites in eastern Reunion Island), and on coastal installations (2 sites – port and highway breakwater in northern Reunion Island).
Underwater photogrammetry protocols were deployed for data acquisition and were adapted at each site (250-500m2), all models were geo-referenced. Fish surveys were conducted using underwater visual census methods (UVC) at Reunion Island, and video census methods ( stereo camera) at Europa Island. All detected individuals were counted and their size evaluated. Benthic surveys were conducted using LIT (line intercept transect) protocol in Reunion Island.
We used Pix4Dmapper to build 3D models and generate Digital Elevation Models (DEM) and orthomosaics - orthophotos. Global Mapper and QGIS were used to analyse and quantify: physical attributes, surface complexity (3D/2D surface), slope and profiles on DEM and benthic descriptors, mineral substrates and life coral %-m2(classified by growth forms: massive, columnar, branching, foliaceous, helmet shaped, encrusting, tabular, and free-living forms) on the orthophotos.
Diversity, abundance, and biomass of fish assemblages were estimated for each site. Life history traits (diet, size class, schooling, home range, position in the water column, activity) were compiled for each encountered species. Traits were combined to define functional entities.
We looked for correlations between physical attributes and benthic descriptors and functional characteristics of associated reef fish assemblages.
The first results of this study highlighted strong correlations between specific features of fish assemblages and surface complexity at Europa Island. Some types of coral growth forms or other mineral substrates were linked with life history traits and functional entities of fishes.
At Reunion Island, preliminary results showed remarkable differences of fish assemblage response to variations among substrates.
- Habitat structural complexity seem to strongly influence reef fish assemblages.
- Underwater photogrammetry is an economic affordable technique that opens new exciting and pertinent approach to coral reefs studies and management.
- 3D model, DEM and orthophotos are powerful tools to better describe and improve knowledge of coastal and coral reefs ecosystems.
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more information :
- PHOTOGRAMMÉTRIE SOUS-MARINE à la Réunion : https://www.youtube.com/watch?v=73kOjif8pHE
- Underwater photogrammetry : https://vimeo.com/204849386
 
Isabel Urbina-Barreto
added a project goal
Develop new quantitative tools of 3D models by photogrammetry, of coral colonies and coral reefs landscape, aiming to understand the correlation between habitat complexity and associated biodiversity of these ecosystems.
The project involves:
- photogrammetry underwater protocols and 3D models analyses
- assessments and monitoring of benthic communities and fish assemblage in South West Indian Ocean.
This project is conducted as a PhD project started in Octobre 2017, implying the environment & oceanography company Creocean OI, engineering company Geolab and UMR 9220 ENTROPIE laboratory in Reunion Island, France.