Graduation Year


Document Type




Degree Name

Doctor of Philosophy (Ph.D.)

Degree Granting Department

Marine Science

Major Professor

Frank E. Muller-Karger, Ph.D.

Committee Member

Pamela Hallock Muller, Ph.D.

Committee Member

Chuanmin Hu, Ph.D.

Committee Member

Joseph Torres, Ph.D.

Committee Member

C. Mark Eakin, Ph.D.


Coral Reefs, SST Variability, Water Turbidity, Coral Reef Metabolism, Photosynthetic Efficiency, Nutrients


Worldwide, coral cover has declined at rates that have often exceeded 5% per year since the 1980’s. Populations of scleractinians (stony corals) in the Florida Keys reef tract have declined as well, with some communities declining at rates > 3% per year. Decreased water quality (e.g., steady increases in the ocean water temperatures and increased pollution, nutrients, or water turbidity due to coastal runoff) are commonly attributed to this decline. But actual linkages between variability and trends in these environmental parameters, and in stony coral diversity and ecosystem functions such as net community production, have not yet been well characterized.

With this research, I examined the influence of water quality (water temperature, nutrients and turbidity) on stony coral diversity and net community productivity in shallow-water reef ecosystems of the Florida Keys between 1996 and 2010. Differences in stony coral diversity in Florida Keys patch reefs with respect to sea surface temperature (SST) variability are evaluated in Chapter Two. Habitat-specific differences in stony coral diversity with respect to changes in a suite of environmental parameters (water turbidity, nutrients, water temperature and depth) are addressed in Chapter Three. Differences in daytime net community production and light-adapted stony coral photosynthetic efficiencies among three reef sites with different turbidity levels and seasons (May and October) are presented in Chapter Four.

Environmental parameters examined to characterize the differences in stony coral diversity across the Florida Reef Tract included satellite-derived sea surface temperature [SST] and Degree Heating Weeks [DHWs], field observations of bio-optical properties of the water, and nutrient concentrations. These parameters were compared with live coral cover and species richness, net community production, and coral photo-physiological observations.

In Chapter Two, I found that stony coral cover and diversity was higher in patch reefs of the Florida Keys relative to offshore and deeper reefs. Generally, patch reefs were characterized by intermediate to high SST variability (≥7.0°C2). Intermediate SST variance (7.0–10.9°C2) was correlated with higher diversity indices for patch reefs of the Upper (Shannon Diversity: 1.2–1.5) and Middle Keys (Species Richness: 13–19), suggesting that stony coral species in these habitats are either adapted to intermediate temperature ranges or thermal acclimation has taken place for individual colonies. Additionally, I found that found that years for which cold and warm-water extremes coincided (i.e., highest SST variance), such as 1997-98 and 2009-2010, led to significant reductions in both H’ and SR. Coral bleaching and mortality were associated with exposure to cold- and warm-water temperature extremes and the combination of both extremes were associated with reductions in stony coral diversity. The highest species richness and abundance were found in patch reefs of the Middle Keys, despite exposure to the warmest water-temperature anomaly events (as indicated by DHWs exceeding the coral bleaching threshold of 4) observed during the summers of 1998 and 2010.

In Chapter Three, I found that the environmental parameters that best explained the differences in stony coral diversity (species composition and abundance) on patch reefs of the Florida Keys were water turbidity, nutrients, surface water temperature, % surface oxygen saturation and chlorophyll a concentrations averaged over a period of 24 months, along with depth (F = 4.4, R2 = 0.66, R2adj. = 0.40, p < 0.05). Surface water turbidity and depth were the most relevant environmental parameters driving the differences in stony coral diversity (R2 = 0.17, p < 0.05, R2 = 0.10, p < 0.05, respectively). The influence of these environmental parameters decreased towards offshore shallow and deep reefs. In the Florida Keys, stony coral diversity was the highest at patch reefs of the Middle and Lower Keys where exposed to higher water turbidity and nutrients than those in the Upper Keys located in clearer waters. This suggests that, at long-term scales, corals in patch reef environments exposed to higher water turbidity and water temperature variabilities (as reported in Chapter Two) might be better able to withstand thermal and light-induced stress.

Moreover, a short-term study (described in Chapter Four) indicated that the net community production (NEP) was similar among sites with different water turbidity levels (i.e., Cheeca Rocks and Crocker Reef; Upper Keys and Sugarloaf Key; Lower Keys) and seasons (May or October). However, the light-adapted photosynthetic efficiencies (F/Fm’) varied spatiotemporally. The highest F/Fm’ values (0.57–0.69) were found at the nearshore patch reef of Sugarloaf Key, Lower Keys, in October 2012. At this patch reef, high light attenuation (Kd (488) = 0.12 m-1) was associated with absorption by colored dissolved organic matter and exacerbated by particulates following thunderstorms. The lowest F/Fm’ values (

This study represents a baseline against which future observations on coral reef biodiversity and net community production in the Florida Keys reef tract may be evaluated.