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

Atsuko Fukunaga,Randall Kosaki,Brianna Craig,John Burns

doi:10.3390/jmse7020027

Abstract

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.

Highlights

Long-term ecological monitoring of reef fish populations generally aims to evaluate the current status of the ecosystem and to detect any trend or sudden changes in the ecosystem due to natural and/or anthropogenic disturbances
Fractal dimension remains the same across different spatial scales as the relationship between log(δ) and logS(δ) is linear [34]. (i.e., The slope of log(δ) and logS(δ) is a constant.) In our case where we investigate habitat metrics within a limited spatial area, working from small to large scales, the 3D surface area starts approaching an asymptote as it approaches the 2D planar area because the 3D surface area cannot be smaller than the 2D planar area
Ground sampling distances of the 3D models generated in Agisoft Photoscan ranged from 0.00026 to 0.00084 m/pixel, with errors of 0.5–2.3 pixels, confirming that the designated resolution of 0.01 m (1 cm) for digital elevation models (DEMs) was within the range of model accuracy

Summary

Introduction

Long-term ecological monitoring of reef fish populations generally aims to evaluate the current status of the ecosystem and to detect any trend or sudden changes in the ecosystem due to natural and/or anthropogenic disturbances. Measures of a habitat’s structural complexity, such as numbers and sizes of holes and topographic relief, affect the diversity and abundance of fish assemblages by altering the amount of available refuge space, capacity for niche specialization and the encounter rate between competitors [3,4,5,6,7]. Disturbances such as tropical storms [8], bleaching events [9,10] and the decline of herbivores [11] all have the potential to alter benthic cover and structural complexity, which in turn affect the structure of fish assemblages. Variations in the structure of fish assemblages explained by these variables need to be considered when assessing temporal changes in the fish assemblages [12]

Objectives

Methods

Results