Coral reef ecology

Reefs off the coast of Florida face threats from stressors associated with climate change which leads to phase shifts. Under rapid climate change, a clear understanding of how reefs and their benthic organisms respond is still lacking and needs to be investigated. Using in situ imagery, a sponge cell model, and long-term benthic biota surveys, the effects of climate change on reef dynamics were explored in this dissertation project. Results from the in situ imagery found that differences in spectral signatures are found between functional groups (i.e., corals, sponges, and algae) and different species from substrate. Results based on a sponge cell model and transcriptomics data have found a resilience of these sponges to the predicted thermal extremes. Results from benthic biota surveys suggested that depth and light attenuation have the largest influence on the predicted distribution of corals, sponges, and algae at Pulley Ridge. Climate change has been impacting reef benthic biota starting at the organismal scale up to the reef scale. This research demonstrates the importance of monitoring reefs at a finer scale and determining the thresholds and limits of benthic biota to projected thermal extremes to better inform resource managers to preserve these irreplaceable ecosystems.

Climate change has intensified thermal anomalies in coral reef ecosystems, contributing to coral bleaching and decline. As corals die, reef fragmentation increases, and species interactions in the benthos change. However, it is unclear which competitive interactions may prevail and structure future reef ecosystems. The aim of this thesis was to evaluate the effect of thermal anomalies on coral reef benthic competitive interactions. Photoquadrats in southeast Florida reef sites were assessed over 15-years to generate interaction metrics and determine effects on hard coral survivorship. A state-transition model was created to predict the resultant community across 100 years with thermal scenarios concordant with the IPCC RCP 4.5 and 8.5. Interaction doubled across three thermal anomaly events and ended up mainly composed of pairwise examples between Dictyota, Halimeda, Niphates erecta, and Erythropodium caribaeorum. Century projections confirm that soft coral and sponge interactions will increase through thermal anomalies. The survival of hard corals was more successful when colonies were in permanent or intermittent interactions than when colonies were solitary (indirect interactions). Living hard corals were mostly found interacting with the macroalgae, Dictyota, and sponge Aplysina cauliformis, while corals that died were mainly in interactions with the soft coral E. caribaeorum, and sponges N. erecta, C. delitrix, D. anchorata, and Ircinia campana. Future reefs will be composed of more interactions between soft corals and sponges as thermal anomalies intensify, which will result in a patchier and flatter community.

This thesis is encompasses the design, construction, control and testing of an improvement upon the novel soft robotic Jennifish platform. The advancement of this platform includes the addition of light and depth sensors as well increasing the separation of tentacle groups from two to three sets. The final vehicle model consists nine PneuNetstyle actuators divided into three groups of three, molded around a machined Delrin pressure vessel. With a 12V submersible impellor pump connected to each actuator grouping, propulsion is created by the filling and emptying of these tentacles with surrounding ambient water. The Jellyfish2.0 is capable of omnidirectional lateral movement as well as upward driven motion. The vehicle also has a temperature sensor and IMU as did the previous of this platform. Qualitative free-swimming testing was conducted, recorded and analyzed as well as quantitative inline load cell testing, to create a benchmark for comparison with other jellyfish like robots.

The overall goal of this research was to isolate key genes involved in the
diterpene biosynthesis from Euniceafusca and Erythropodium caribaeorum using
molecular biology techniques. The initial goal was to use fuscol induced cell
cultures of Symbiodinium sp. isolated from E. fusca and to develop an approach
based on differential display of mRNA-reverse transcription-PeR. Together with
inverse PCR, these techniques ultimately provided a full-length farnesyl
diphosphate synthase sequence. Functional expression of this enzyme was
demonstrated with the addition of appropriate substrates and confirmed by
chromatography. From this data, degenerate primer based PCR was used to
isolate putative geranylgeranyl diphosphate biosynthetic genes from E.
caribaeorum. Both chemical and genetic examinations of Pseudopterogorgia
elisabethae eggs and their associated Symbiodinium sp. were employed to identify
the biosynthetic origin of their diterpenes. Terpene content and biosynthetic
capabilities of azooxanthellae eggs demonstrated the presence of pseudopterosins
but also indicated that the eggs were not capable of producing these compounds.
Likewise, no correlation could be observed for the phylogenetic relationships
inferred for the Symbiodinium sp., with that of the terpene chemistry present in P.
elisabethae. This finding leads us to speculate about an additional source of
terpene production within this coral.
Based on these and other recent findings suggesting symbiotic bacteria as
the source of secondary metabolites from marine invertebrates, bacterial
assemblages from E. caribaeorum were examined. This study revealed
considerable phylogenetic bacterial diversity within this coral and the
identification of several bacteria known to produce terpenes in other organisms.

The marine environment is a prolific source of novel compounds for therapeutic
use due to the complex biological and chemical diversity. Throughout the past 30-40
years, over 15,000 natural products have been discovered from the oceans, many of
which display a broad range of potential clinical and commercial applications. Many
marine invertebrates are sessile organisms that lack physical protection, and which
chemical defense may be a possible explanation for these secondary metabolites. Despite
the promise marine natural products have as potent pharmaceutical agents, one of the
major factors delaying clinical use is the supply issue. These bioactive compounds are
often found in trace amounts in the host organism, which makes harvesting from the reefs
unfeasible. A general goal in our lab was to investigate the biosynthesis of secondary
metabolite terpenes to ultimately provide a production method of these potent marine
derived compounds. Eleutherobin and desmethyleleutherobin are diterpenes isolated from the
Caribbean soft coral Erythropodium caribaeorum. These extremely valuable anticancer
agents disrupt cell division by polymerizing and stabilizing microtubules, and have
demonstrated tumor tissue selectivity toward selected breast, renal, ovarian and lung
cancer cell lines. Determining the first intermediate in terpene biosynthesis is the initial
step in developing a biotechnological production method of these cytotoxic agents. We
investigated the complex chemistry of this coral using a radioactivity-guided isolation
procedure, and isolated and partially characterized a diterpene hydrocarbon from E.
caribaeorum.
The close association between marine invertebrates, zooxanthellae and numerous
bacteria gives rise to the question of the identity of the producer of secondary metabolites
in marine organisms. If the symbiont produces these therapeutic agents, cell culture
methods could be employed to supply the compounds rather than obtaining them from
coral reefs. Sesquiterpenes have been isolated from the gorgonian Plexaurella spp.,
however, no investigations concerning host/symbiont contribution of the sesquiterpenes
have been reported. We investigated the biosynthetic source of terpenes in this coral, and
experimental evidence indicates that bacteria are responsible for sesquiterpene
production. We also examined sesquiterpene variation of Plexaurella spp. from various
locations, and found sesquiterpene content to vary within and between species,
identifying Plexaurella as a chemically indistinguishable genus.

Crustose coralline algae (CCA) are important reef stabilizers and their susceptibility to anthropogenic climate change and ocean acidification (OA) is of concern. Ocean acidification effects on benthic algal communities were determined by the response of CCA, fleshy macroalgae and microalgae to the interaction of pCO2 and light. I examined if elevated pCO2 and light influences CCA dominance by assessing their growth, recruitment and calcification. Elevated pCO2 under natural reef diurnal CO2 cycles did not significantly affect CCA percent cover, calcification rates or survival of adult CCA lobes. No significant community pCO2 effects were observed, rather light controlled dominance. The percent cover of microalgae increased in highlight, while CCA increased in the shade. My results indicate that algal response to irradiance is a more significant driver of reef benthic algal change than pCO2 levels predicted for 2100; however, this conclusion should be corroborated in longer-term and in field experiments.

The sea anemone Aiptasia pallida is a biological model for anthozoan research.
Like all cnidarians, A. pallida possesses nematocysts for food capture and defense.
Studies have shown that anthozoans, such as corals, can rapidly increase nematocyst
concentration when faced with competition or predation, suggesting that nematocyst
production may be an induced trait. The potential effects of two types of tissue damage,
predator induced (Lysmata wurdemanni) and artificial (forceps), on nematocyst
concentration was assessed. Nematocysts were identified by type and size to examine the
potential plasticity associated with nematocyst production. While no significant
differences were found in defensive nematocyst concentration between shrimp predation
treatments versus controls, there was a significant difference in small-sized nematocyst in
anemones damaged with forceps. The proportions of the different types of nematocysts between treatment types were also found to be different suggesting that nematocyst
production in A. pallida is a plastic trait.