Graduation Year


Document Type




Degree Name

Doctor of Philosophy (Ph.D.)

Degree Granting Department

Biology (Integrative Biology)

Major Professor

Susan S. Bell, Ph.D.

Committee Member

Lori D. Collins, Ph.D.

Committee Member

David Lewis, Ph.D.

Committee Member

Philip Motta, Ph.D.

Committee Member

C. Edward Proffitt, Ph.D.


3D Scanning, 3D Technology, Habitat Complexity, Reef Ecology


Understanding how organisms utilize and interact with habitat features may improve predictions of habitat preferences and species interactions, and may assist in the development of conservation and management strategies. The architecture of a habitat provides a complex array of structural features that influences interactions between the abiotic and biotic factors, and impact the biodiversity and species abundance through altering recruitment patterns and the survival of associated fauna. Characterizing potential refugia however has been challenging with minimal attempts to measure interstitial space size and abundance in reef systems. Here, I present novel methodology utilizing 3D technology to characterize interstitial spaces within oyster habitats and compared the effects of interstices and standard measures of habitat complexity on the macroinvertebrates residing in the oyster habitat.

Natural oyster clusters (~225 cm2 each) were collected from the field and three-dimensionally (3D) recorded with both computed tomography (CT) and surface laser scanners. Resultant 3D models were rendered in Geomagic® Studio software. The abundance and size of interstitial spaces were determined within each cluster from models of the two 3D capture techniques. Both 3D scanning techniques had strong agreement of volume measurements for the same space between scan types (r = 0.974; p < 0.0001) and precision of at least 90%. Slight variation in the abundance of interstitial spaces was noted between scanning approaches, as CT 3D imaging better captured larger interstitial spaces.

To determine the relative contribution of different structural components as descriptors of oyster habitat complexity, the 3D models of oyster clusters (above) were examined to collected vii metrics of 1) interstitial space size: mean, maximum, and total interstitial space volume, and interstitial space abundance and 2) commonly utilized metrics of complexity: rugosity, fractal dimensions, surface area, and abundance of structural components of the oyster clusters. Comparison of the interstitial space metrics to those of surface area for the set of oyster clusters revealed a strong contribution of interstices to the overall complexity of oyster architectural structure. When the both space and surface area metrics were considered together in a principal components analysis they collectively explained ~ 73% of the variation of the data. All macroinvertebrates were collected from the oyster clusters to examine the potential relationship between the complexity metrics and the mobile (decapod and gastropod) or sessile (bivalve) macrofaunal abundance collected from the clusters with interstitial space and surface area metrics were inconsistent. Significant negative associations based on Pearson correlations were noted between decapod abundance and the number of oyster shells and total interstitial space volume were observed. These negative relationships do not support an expected strong positive effect of interstitial space volume on the abundance of decapods nor measures of surface area having a strong positive effect on sessile bivalve species and more extensive surveys were necessary.

To further explore the relationships between macroinvertebrates and habitat complexity, a manipulative field experiment using artificial oyster habitats was conducted. Specifically, how measures of habitat complexity change over time and the effects of those changes on the associated macroinvertebrate fauna in oyster habitats were examined. The incorporation of 3D technology and the manipulative field experiment enabled the detection of an increase in artificial oyster habitat surface area by 60 – 71 % within an 8 month period. During that time interstitial space volume decreased between 3 – 34%. Three invertebrate taxa: barnacle, oysters, viii and decapods were examined to determine the effects of habitat complexity on their abundances. Barnacle, oyster, and decapod abundances all had positive relationships with surface area. Barnacles and decapods had a positive relationship to interstitial space volume, though their responses varied with time. A positive relationship was noted between barnacles and interstitial space volume within a 4 month period although after 8 months that relationship was no longer significant. The relationship between interstitial space volume and decapod abundance was only significant after 8 months. No significant effect of interstitial space volume on oyster abundances was detected. While surface area metrics remain important features of a habitat, this study demonstrates in detail how interstitial space size and abundance add to the architectural complexity of habitats and suggest that such metric should be incorporated into future studies.

Combining 3D methodology workflow presented here with existing metrics of habitat complexity may provide additional insights into specific habitat architectural features that influence community development, composition, and species interactions. Our estimations of interstitial spaces enhance the currently utilized procedures for measuring habitat complexity and because the generation of 3D models is nondestructive, use of these approaches present an opportunity to quantify habitat structural changes over time. Measures of interstitial space volume and abundance expand the list of metrics describing habitat architecture and may represent potential refuge availability within a habitat. These findings highlight the importance of the interstitial spaces formed by varying structure components, and the response of the dominant invertebrate taxa to these spaces within an oyster reef system. Specifically, this is the first study to document the change in interstitial space volume through the colonization of sessile species. The use of oyster clusters and 3D modeling and analyses provide a pathway by which interstitial space volume can be assessed. Evaluating the effects of complexity, primarily the effects of interstitial spaces in reef habitats, may provide insight into more effective ways of maintaining existing reefs and restoring or rehabilitating damaged reef systems.