Date of Award
2025
Degree Type
Dissertation
Degree Name
Doctor of Philosophy in Biological and Environmental Sciences
Department
Biological Sciences
First Advisor
Carlos Prada
Abstract
Coral reefs are one of the most biodiverse and productive ecosystems on the planet. In recent decades, however, climate change and other global threats have caused severe declines in live coral cover worldwide. Coral propagation, or “gardening,” is a popular strategy to attempt to restore healthy corals to degraded reefs. Slow-growing boulder corals are often restored using microfragmentation, where cutting coral colonies into roughly 1 cm2 fragments can increase their growth rates up to 5x. However, extreme early mortality of fragments has been observed in the field, which has been at least partially attributed to predation. It has been hypothesized that corals may be producing secondary metabolites to deter predators, similar to terrestrial plants.
In this dissertation, I present three manuscripts examining the mechanisms at play during microfragment acclimation and how they affect survivorship. First, we acclimated groups of 100 microfragments from ten different source colonies of the Caribbean boulder coral Orbicella faveolata for 24, 38, 112, or 126 d, with a control group of 0 d spent in the acclimation cage. We then planted half of these fragments on the reef in La Parguera, Puerto Rico and preserved the other half for later omics analysis. In Chapter 1, we tracked survivorship, growth, and evidence of predation of these fragments for three months. We found that fragments experienced almost no mortality in the acclimation cage, and fragments acclimated for longer than two months experienced higher survival in the field than fragments acclimated for less than two months. Additionally, we found fragments that showed evidence of predation experienced significantly lower overall survivorship. In Chapter 2, we used a novel sample processing method based in forestry analysis and liquid chromatography-mass spectrometry combined with Global Natural Product Social Molecular Networking (GNPS) to analyze metabolic patterns and identify any that could affect predation. We found that trends in the coral metabolome indicated a stress response in fragments as they were moved to the cage and then acclimated to the field environment. We identified a key metabolite, betaine, that significantly decreased with acclimation time and was associated with higher mortality rates in the field. In terrestrial plants, betaine is often produced when organisms experience environmental stress, but it can also make these same plants more vulnerable to predation. Our results showed preliminary evidence of a similar dynamic in corals. In Chapter 3, we used 16S rRNA sequencing to analyze the microbiome community of these corals and used neural network modeling to examine connections between the metabolome and the microbiome to investigate dynamics within the coral holobiont. We found that multiple bacterial families previously associated with stress in corals, including Vibrionaceae, Flavobacteriaceae, and Nostocaceae, were also associated with shorter acclimation times. These bacteria significantly co-occurred with betaine. This co-occurrence pattern has been previously recognized as a bioindicator to identify corals under stress, supporting the use of metabolomics as an alternate strategy to identify “hearty” corals to prioritize during restoration.
The results of this project produced preliminary findings on the ability of corals to resist predation. It has also demonstrated the benefits of caging microfragments as part of restoration efforts and the potential for using metabolites as bioindicators for future success. Microfragments survived well in the acclimation cage, and after two months, contained significantly lower abundances of metabolites and microbes that indicate stress and make them more attractive to predators. Acclimated corals then experienced higher survival rates in the field.
Recommended Citation
Raker, Catherine E., "THE CHEMICAL ECOLOGY OF A CARIBBEAN BOULDER CORAL DURING RESTORATION AND THE INTERPLAY BETWEEN FISH PREDATION AND MICROBIOME VARIATION" (2025). Open Access Dissertations. Paper 4490.
https://digitalcommons.uri.edu/oa_diss/4490