Oxygen production and consumption were measured in five species of benthic foraminifers using a "Clark-type" oxygen electrode. Net photosynthesis and respiration were calculated and normalized to both μg Chl a and mm² upper surface area for the chlorophyte-bearing soritid foraminifers, Archaias angulatus and Cyclorbiculina compressa, and the diatom-bearing amphisteginids, Amphistegina gibbosa, A. lessonii and A. radiata. Photosynthesis/Irradiance curves were generated by fitting data to the hyperbolic tangent equation P = Pmax tanh (α I/ Pmax). Derived photosynthetic parameters, Pmax, α, Ik were found to correspond to the general responses of the endosymbiont taxa. Chlorophyll concentration was found to be significantly lower in Cyclorbiculina compressa than in the other four species. Maximum O2 production (Pmax) when normalized to Chl a was 3-4 times higher in soritid species than in amphisteginids. Photosynthetic efficiency (α) was significantly higher in Amphistegina gibbosa and A. lessonii than in the soritids. Mean Ik, which indicates approaching light saturation, was 13 and 26 μmol photon m-2sec-1 respectively for A. gibbosa and A. lessonii compared with 95 and 119 μmol photon m-2sec-1 respectively for Archaias and Cyclorbiculina. Calculated P/I data were to variable for Amphistegina radiata to estimate reliable α and Ik values. Factorial metabolic scope, which indicates potential for activity was only 2-6 for amphisteginids versus 9-16 for soritids. Annual primary production was estimated to be 285 mmoles O2 m-2 of habitat for A. angulatus, 9.3 mmoles O2 m-2 of habitat for C. compressa and 15.3 mmoles O2 m-2 of habitat for Amphistegina lessonii. Pmax values for Amphistegina gibbosa fluctuated at the compensation point and did not indicate significant oxygen production. Pmax values for Amphistegina radiata failed to reach the compensation point and net oxygen production was not recorded.

Studies of larger symbiont-bearing foraminifers on reefs have revealed their potential as indicators of environmental stress because of their physiological analogies to corals (dependence on algal symbionts for growth and calcification) and relatively short life cycle (a few months to 2 years or more). The purpose of this study is to report distribution patterns and population densities of larger benthic foraminifers (LBF) of the Florida reef tract, specifically reporting abundance data collected from offshore (1995-2000, 2006, 2007) and patch reefs (1996, 2006, 2007). Six years of quarterly data collected from two offshore reefs, Conch (10, 18 and 30m) and Tennessee (8 and 20m), revealed that LBF assemblages primarily varied with habitat depth, in turn reflecting available light and water motion.These assemblages were dominated by Amphistegina gibbosa d'Orbigny and Laevipeneroplis proteus d'Orbigny, which tended to occur together, making up ~40-50% of the assemblages and up to 80% at the Tennessee 20m site. Both overall abundance and evenness of the LBF assemblage structure exhibited the greatest variability at shallower depths. Evenness was inversely related to densities of A. gibbosa, which were typically higher at depth keeping evenness below 0.5. Across the Keys, region (location along the reef tract), reef type (offshore shallow, deep or patch reefs) and symbiont type strongly influenced LBF assemblage dynamics. Upper Keys sites shared the highest degree of inter-region similarity among assemblages (73%), while Biscayne National Park (BNP) and lower Keys sites had the lowest similarity (~60%). This likely reflects the greater variability of habitats found in the latter areas, mainly patch reefs.Chlorophyte-bearers were typically more abundant in shallower turbid waters, with diatom-bearers more abundant at depth. Additionally, I observed a significant two-fold decrease in the proportion of chlorophyte-bearers in the middle Keys likely due to light-limitation by turbid Florida Bay outflow. Finally, data comparisons revealed an inverse relationship between LBF abundances and percent coral cover. Coral cover (2005) was staggeringly low on offshore reefs (5%), but was significantly higher on nearshore patch reefs (12%). Contrastingly, LBF species showed either no difference in abundance between reef types or a greater abundance on offshore reefs.

Marine microbiome research is a rapidly expanding field of study, as scientists investigate the functions of microbial associations in eukaryotic organisms. Foraminifera are among the most abundant shelled organisms in the oceans, yet little is known of their associated microbiomes. This study investigated microbes associated with four species of Foraminifera that host three kinds of algal endosymbionts. The Order Miliolida, Family Soritidae, was represented by three species: Archaias angulatus and Cyclorbiculina compressa, which both host chlorophyte symbionts, and Sorites orbiculus, which hosts dinoflagellate symbionts. The fourth species, Amphistegina gibbosa, belongs to the Order Rotaliida and hosts diatom endosymbionts. Bacterial DNA extraction was attempted from 5−8 specimens per species followed by amplification and amplicon sequencing of the V4 variable region of the 16S rRNA gene. Three Ar. angulatus specimens shared 177 Operational Taxonomic Units (OTUs), and six C. compressa specimens shared 58 OTUs, of which 31 OTUs were found in all specimens of both species. Four S. orbiculus specimens shared 717 OTUs dominated by Proteobacteria, notably Amoebophilaceae. The three soritid species shared 26 OTUs, predominantly representing the bacterial families Rhodobacteraceae and Flavobacteriaceae. Since S. orbiculus shared 84% of the OTUs shared by Ar. angulatus and C. compressa, which host similar endosymbionts, phylogenetic relatedness of host taxa clearly had more influence on core microbiomes than the algal-symbiont taxon. The microbiomes of three normal-appearing and five partly-bleached specimens of Am. gibbosa varied widely, sharing only six OTUs, four of which represented Proteobacteria. All four species shared only four OTUs, three of which may have been contaminants. As the first known microbiome study to include western Atlantic/Caribbean benthic foraminifers that host algal endosymbionts, the results for Am. gibbosa revealed quite similar results to a recent study of the microbiome of Am. lobifera, a closely related Indo-Pacific taxon.

Photo-oxidative stress is one of the key factors that can induce bleaching in reef organisms. With the decline of coral reefs and recurrent bleaching events, many studies have focused on understanding the mechanism behind this phenomenon. Two of the hypotheses that explain how the photosynthetic performance of the symbiont is affected and influences bleaching are: (1) disruption of the photosynthetic pathway by direct damage to the photosystem II (PSII), and (2) by inhibition of the Calvin-Benson cycle. In this dissertation I examine different aspects of photosynthetic performance in symbiont-bearing reef organisms and how this is influenced by symbiont loss and changes in photic stress as a result of different levels of irradiance modulated by time of the year (e.g., season) and depth; and take a closer look into primary productivity by symbionts with controlled laboratory experiments. Field experiments during 2012–2013 at Tennessee Reef, FL, assessed the photosynthetic performance of PSII in the diatom-bearing foraminifer, Amphistegina gibbosa, and the anthozoans: Palythoa cariabeorum, Siderastrea siderea, and Montastraea cavernosa. Data collected for the bleaching trends of A. gibbosa revealed that bleaching rates are higher in the summer months than in winter. Photochemical efficiencies of PSII in A. gibbosa, as measured with PAM fluorometry on the day of collection, were more variable in the shallow site (6 m) than in the deeper site (18 m). Also, photochemical efficiencies at the shallow site were lower during the summer months than during winter months. At the 18 m site, photochemical efficiencies did not exhibit a clear seasonal trend. Depth also had an effect on the measured photochemical efficiencies of the anthozoans. Photochemical efficiencies were lower and more variable in colonies at 6 m compared to colonies from 18 m. Although previous studies have reported seasonal effects on the photochemical efficiency of some coral colonies, that trend was not apparent in this study. Photoacclimation and productivity were assessed for A. gibbosa using rapid light curves (RLC) and photosynthesis vs. irradiance curves (P-E). Maximum relative electron transport rate (rETRmax) as described by RLCs was significantly different between A. gibbosa without visual signs of bleaching and those with severe bleaching. Individuals with partial bleaching had a rETRmax that was intermediate between the other two categories. The P-E curves showed a similar trend. In this case individuals that were non- or partly bleached had significantly higher photosynthesis maxima than those with severe bleaching. The onsets of photosynthesis and saturation irradiance were not significantly different among the categories of bleaching analyzed. Results from this dissertation suggest that A. gibbosa has the capability to detect and digest damaged symbionts, that the symbionts even in the deeper chambers react in a similar way to irradiance, but that in severe cases of bleaching the symbionts may not produce enough energy to sustain the requirements of the host, even in non-stressful conditions.