Understanding coral disease dynamics within the heterogeneous populations in which they act is critical for predicting how the structure of reefs may change as a result of enzootic or epizootic levels of these important sources of mortality. This work focused on combining field studies and the development and testing of a spatially-explicit, individual-based epizootiological computer model with the aim of gaining a greater understanding of the dynamics and impact of white plague, a significant source of mortality on reef-building corals in the Caribbean region. Field studies focused on the incidence and distribution of all sources of coral mortality, including suspect white plague in situ, at two locations; the Florida Keys (United States of America) and Little Cayman Island (Cayman Islands, British West Indies). Results indicated that in both regions disease was the most significant source of mortality during the monitoring time periods, and that suspect white plague type II in Cayman is likely contributing to major structural changes. In Florida, observations made during a mass bleaching event indicated that a significant relationship exists between bleaching severity and disease incidence, and that mortality during the event was largely the result of disease and not bleaching. The simulation model was developed using a long-term data set from Little Cayman, and results of calibration indicated that suspect white plague type II on these reefs is transmissible between colonies within a limited field and require a yearly input from an outside source, and that host susceptibility to infection is low and likely not variable among species. Parameters describing the distribution and composition of the coral population were varied, and results indicated a significant effect of colony density, aggregation, and mean size on the impact of disease. Scenario testing of various disease management strategies indicated that should local prevention measures be developed in the future, it is they, and not treatment, that will likely be the most effective in limiting the impact of disease.

The encrusting sponge Terpios hoshinota is a cyanobacteriosponge with symbiotic photosynthetic cyanobacteria. It covers live corals causing their death. Corals at Green Island were suspected to be infected by Terpios hoshinota in 2006, and field investigations indicated there was massive propagation of the species in both Green Island (Lyudao) and Orchid Island (Lanyu) in 2008 to 2010. We propose two hypotheses, either by Self-Seeding or by Long-Range Dispersal, that explain the fast propagation of Terpios hoshinota in the islands offshore of southeastern of Taiwan. We use ribosomal DNA and mitochondria DNA as molecular markers to investigate how the sponge disperses locally and in a greater geographic scale. A total of 110 samples, from Taiwan: Green Island, Orchid Island, and Kenting (Wanlitong). Japan: Okinawa, Nakijin, Miyako, Bise, Shiraho, Arahama Kumeshima, Yakomo (Okinoerabu), San (Takunoshima), and Xisha Island of China, were collected. Internal Transcribed Spacer 2 (ITS2) from ribosomal DNA and cytochrome oxidase I (COI) from mitochondria DNA are used as markers to infer population structure of Terpios hoshinota. No genetic variation within COI sequence over all sponges from Taiwan to Japan and China was found, although the only sponge sample from Wanlitong in Kenting had three variable sites, which suggest different species of Terpios hoshinota. Based on ITS2 analysis, haplotype diversity (h) is commonly high among most populations, but with different single haplotype found at Green Island and Arahama (Japan). Pairwise population differentiations (FST) are usually high and significant among populations supporting self-seeding, although Bise, Shiraho and Lanyu populations showed no significant differentiation that supports long-range dispersal. Analysis of Molecular Variance (AMOVA) shows no population subdivision; however, genetic differentiations among populations are significantly greater than within populations. TCS analysis indicates that single haplotype in Green Island is originated from Lanyu, and populations in Bise are widely dispersed over other sponge populations in Taiwan and Japan regions. By evidence of TCS analysis with nucleotide diversity, haplotype diversity and field investigation, Bise is the origin of Terpios hoshinota among populations within this study. Frequency of sequence haplotypes indicates one dominant haplotype is shared among most of the sponge populations, and the dominated sponge haplotype takes highest proportions of local populations. The existence of dominant haplotype may result from better dispersal or reproduction ability than other haplotype in populations. Nested clade analysis shows that populations mainly have restricted gene flow with some clade have contiguous range expansion. We suggest that populations of Terpios hoshinota propagate mainly by self-seeding method with occasional long-range dispersal event that leading to genetic connection among populations and obscuring evidence of isolation by distance in these populations. In Green Island, we consider local populations as undergoing explosion within past several years and propagate by self-seeding method coming from single lineage of Lanyu. Populations in Lanyu may come from Bise, Shiraho, and Yakomo, yet may still in status of population explosion. Populations in Japan may underwent founder effect with rapid population growth, while most populations are rarely interact with each other showing deep genetic differentiation among islands, and Bise is the origin of Terpios hoshinota in this study. Not all of the sponge individuals have ability to dominate local populations, expect for one special haplotype of Terpios hoshinota is capable of dominating local population in both range and quantity, which also has capability of spreading across islands as larger distances than its habitats range in Taiwan and Japan.

The coral holobiont contains diverse communities of bacteria that play a role in the maintenance of coral ecosystems, however little is known about the structure and conservation of the host-bacterial relationship. Declines in coral ecosystems have been partly attributed to outbreaks of disease in tropical and sub-tropical regions, which have been linked to increasing temperatures. Bacteria are thought to play a role in some of these diseases, however little is understood about the mechanisms behind disease progression or the series of events involved in the shifts of coral-associated bacteria from conserved, potentially beneficial communities to those including potential pathogens. Investigations into a cold-water gorgonian coral, Eunicella verrucosa, have shown similar bacterial communities to those present in tropical and sub-tropical regions, with high proportions of Spongiobacter and Endozoicomonas genera, suggesting an important role for these associates in the coral holobiont irrespective of location or the presence of zooxanthellae. A shift in bacterial community with disease was also shown, with suggestions that sedimentation and depth may affect the extent of bacterial community alteration. With the increasing knowledge that bacteria exhibit elaborate systems of intercellular communication (quorum sensing; QS) to allow a population response and to control the expression of genes for pathogenesis, antibiotic production and biofilm formation, the present study showed the presence, stability and species-specific nature of N-acyl-homoserine lactones (AHLs; most prevalent type of QS) in situ in a number of coral species. This finding and a high proportion of coral-associated bacteria found producing AHLs suggests an important role for QS in the coral holobiont. Further, AHL signals have been shown to break down in Stylophora pistillata kept at 30 °C, which coincided with a drop in bacterial numbers and a changing bacterial community which included more quorum quenching (QQ; AHL-degrading) bacteria. Temperature was shown to affect AHL-QS in a strain-dependent manner in E. verrucosa isolates, suggesting that the decline seen in S. pistillata is not primarily an effect of temperature. Further experiments with three species of soft coral (Sinularia sp., Discosoma sp. and a gorgonian) showed no such decline in AHLs at 30 °C and instead show a coral-specific response to temperature, including the ability of coral extracts to inhibit putative pathogens. A decline in the ability of crude coral extract to degrade AHLs in the Discosoma sp. and the high QQ activity in crude extract from all three species suggests a role for QQ in the coral holobiont, confirmed by the high percentage of QQ found in coral-associated bacterial isolates; again suggesting a role in the maintenance of bacterial communities. Further investigations attempted to link QS and QQ to antagonism and susceptibility in coral associated bacteria; however these results were inconclusive. The thesis concludes that priority should be given to further research of QS and QQ in the coral holobiont, which will reveal important knowledge that may lead to future mitigation of some forms of coral disease.

Coral diseases were unknown in the scientific community fifty years ago. Since the discovery of a coral disease in 1965, there has been an exponential increase in the number of known coral diseases, as the abundance, prevalence, distribution, and number of host species affected has also significantly increased. Coral diseases are recognized as contributing significantly to the dramatic losses of coral cover on a global basis, particularly in the Caribbean. The apparent sudden emergence of coral diseases suggests that they may be a symptom of an overall trend associated with changing environmental conditions. However, not much evidence has been gathered to address this question. The following studies were designed to build a comprehensive argument to support this hypothesis for one important coral disease – black band disease (BBD). A meta-analysis of clone libraries identifying the microbial communities associated with BBD reveal important information including that a single cyanobacterial operational taxonomic unit (OTU) was by far the most prevalent OTU in diseased samples, and that the alphaproteobacteria, which include some of the most common bacteria in marine waters, were the most diversely represented. The analysis also showed that samples exhibited regional similarities. An fine and ultrastructural characterization of the disease revealed that the cyanobacteria are prolific borers through the coral skeleton, and that the cyanobacteria penetrate coral tissue, leading to their presence ahead of the main migrating disease band. It was further found that apparently healthy corals exposed to toxins found in BBD, exhibited similar tissue degradation to those infected with BBD. Comparing the disease progression to biofilm formation, it was determined that scouting cyanobacteria may contribute to the migration of the disease through progressive biofilm development over intact coral tissue. Together, these studies provide significant evidence for the hypothesis that BBD is an opportunistic disease, caused by common environmental bacteria, facilitated by the changing environmental conditions associated with climate change.

The pillar coral, Dendrogyra cylindrus, has been commonly described as widely distributed, but rare throughout its geographical range in the Caribbean. Having recently been listed as Threatened under the US Endangered Species Act, an understanding of population status is needed to promote species conservation and population recovery. Previous to this study the status of the pillar coral population in the state waters of Florida, U.S.A, was relatively unknown primarily due to few colonies being recorded and no comprehensive summary of population abundance, distribution or health being completed. Along with various environmental and anthropogenic factors affecting the pillar coral population on the Florida Reef Tract (FRT), it appears that reproductive limitations may also be contributing to species decline and limiting population recovery as evidenced by the lack of reported juvenile D. cylindrus colonies reported on the Florida Reef Tract (FRT) in the past 17 years. The factors contributing to this phenomenon are currently unknown, however are suspected to be derived from the pillar corals reproductive biology. Being described as a gonochoric, broadcast spawner, sexual reproduction relies on the synchronous release of gametes from colonies of separate sexes, and with low adult colony densities reported for the pillar coral on the FRT, gamete concentrations from both sexes may be too low for fertilization to occur. In 2014 submissions of pillar coral locations from the scientific and lay community were compiled and 610 D. cylindrus colonies along Florida Reef Tract were identified (Lunz et al. 2016). In my study, I describe the population structure of D. cylindrus for the southeast Florida region of the FRT which includes 65 of the total 610 colonies. For each of the 65 colonies, colony depth, demographic, and condition data were recorded including size (length, width, and height), percent of recent mortality, and presence and severity of disease and bleaching. Out of all locations identified in this region, about 50% contained only a single colony of D. cylindrus and the maximum number of colonies per site was 14. Throughout the duration of the study, devastating losses of live tissue were observed following the bleaching and disease events impacting the Florida Reef Tract in 2014, 2015, and 2016 and the status of the southeast Florida population of pillar coral is at serious risk of local extinction. To investigate the ability of colonies of D. cylindrus to sexually reproduce (referred to as sexual reproduction potential) tissue samples were collected from 95 colonies within 15 sites along the FRT and were prepared for histological analysis. The sex of each colony, sizes of gametes in mature developmental stages, the abundance of gametes per cm2 of tissue, and sex ratios for locations on the FRT were reported. All tissue samples from male and female colonies contained gametes that were ≥90% mature; however sex ratios were found to be skewed in all locations, deviating significantly from the 1:1 ratio expected for typical resource allocation in random mating. Hermaphroditic colonies of D. cylindrus are described for the first time throughout its geographical range in this study and comparisons to gonochoristic colonies confirmed that these hermaphrodites are sexually reproductive individuals. Results from this effort provide a more thorough understanding of the reproductive biology of D. cylindrus and essential data for the support of future conservation management and restoration strategies for this FRT population and comparative data for other Caribbean populations.

Coral diseases have become more prevalent and destructive over the past 20 years, possibly due to an increase in stressful environmental factors that may weaken corals defenses against disease. Aspergillosis is a disease caused by the fungus Aspergillus sydowii, which apparently infects only two species of gorgonian corals in the Caribbean Ocean (Gorgonia ventalina and G. flabellum). We hypothesized that the differential resistance to infection is caused by differences in chemical defenses among gorgonians. Freeze-dried gorgonian powders and extracts deterred fungal growth, but potencies varied among gorgonian species and among fungi. Extracts and powders generated from G. ventalina all strongly inhibited fungal growth. Since G. ventalina was predicted to have weak antifungal chemical defenses compared to gorgonians not known to suffer from aspergillosis, we concluded that gorgonian susceptibility to fungal infection is determined by factors other than, or in addition to, chemical defenses. In order to investigate specific gorgonian antifungal strategies, we attempted to use bioassay-guided fractionation to isolate antifungal compounds from four gorgonians: Gorgonia ventalina, Briareum asbestinum, Eunicea succinea, and Pseudopterogorgia americana. We succeeded in isolating two antifungal compounds, diastereomers of 9,11-seco-24-hydroxydinosterol, from the gorgonian Pseudopterogorgia americana. This compound was previously identified by other groups, but this study is the first to establish its antifungal activity. At natural concentration, one diastereomer of 9,11-seco-24-hydroxydinosterol inhibited the growth of three different fungi, suggesting that at least this diastereomer may possess broad-spectrum antifungal activity. The results from our survey of gorgonian chemical defenses indicate that susceptibility to aspergillosis cannot be explained by chemical growth inhibition alone. Further areas of investigation include induction of gorgonian chemical defenses, examination of growth-inhibiting mechanisms of antifungal metabolites, and identification of non-chemical factors affecting gorgonians vulnerability to fungal infection.

Coral disease represents one of the many challenges facing coral reefs, and is a contributing factor to the overall decline in coral reef health worldwide. An increase in disease frequency, outbreaks and the emergence of new diseases has fuelled much concern over the impact of coral diseases and subsequently prompted research into their possible causes. Our understanding of putative coral pathogens has lagged behind the emergence of coral disease as a major threat to the health of coral reefs. The Great Barrier Reef (GBR) is the largest contiguous reef in the world, and is still regarded as one the healthiest and best managed coral reef ecosystems in existence today. Despite this, the frequency of coral disease has begun to increase sharply over the past decade, prompting researchers to focus on the aetiology, causal factors and ecological impact of coral disease within the Great Barrier Reef Marine Park (GBRMP). This PhD thesis focused on two distinct disease elements: brown band (BrB) and white syndrome (WS). These two diseases affect corals within the GBRMP, yet their microbiology and ecology is largely unknown. The research project investigated the microbiology and ecology of WS and BrB affecting acroporids, using culture-dependent and independent methods to characterise the microbial community associated with healthy and diseased corals and identify putative coral pathogens. The lifecycle and diurnal cycles of BrB ciliates were also explored to gain a greater understanding of the effect of these ciliates on coral health. Ecological surveys were carried out at Heron Island sites commonly used for the collection of corals to ascertain the prevalence and significance of these diseases in the context of laboratory results. Surveys at five sites revealed a mean prevalence of 8.11% of tabular acroporids affected by WS, which is consistent with previous studies. BrB revealed a much lower prevalence of less than 0.04%. Bacterial 16S rRNA gene clone libraries were constructed from Acropora hyacinthus samples derived from a healthy control colony, and a healthy section and lesion border of a WS affected colony. Distinct shifts in the microbial community and partitioning between the lesion border and healthy section of the diseased colony were observed. In addition, the healthy section of the diseased colony displayed a different microbial community to the control colony, supporting previous data that a microbial shift occurs preceding visible signs of infection. A number of bacteria from the healthy section of diseased coral shared close sequence affiliations to a number of Vibrio spp., including potentially pathogenic Vibrio species. Sequences retrieved from the lesion border of WS affected Acropora hyacinthus were dominated by Pseudoalteromonas spp., although these species have not been previously implicated in coral disease. The coral disease BrB is characterised by the presence of a brown ciliate band and these ciliates have been identified as a new species belonging to the class Oligohymenophorea, subclass Scuticociliatia. Within BrB-affected Acropora muricata, numerous filamentous, coccoid and rod bacteria were observed to be closely associated with the ciliate band, but absent in coral tissue adjacent to the typical brown band. It is unknown whether the bacteria associated with the mass of ciliates are the primary pathogens, a food source for the ciliates or simply opportunistic pathogens. Several isolates retrieved from BrB corals were tested for their pathogenicity in controlled infection trials using Acropora muricata. The preliminary results identified at least two isolates of interest (CC1 and HB-8). However, the results of a replicated infection trial failed to conclusively identify the bacteria as the causative agents of this disease. The findings from the cross-infection trials and ecological surveys suggest that BrB is an infectious but not highly contagious coral disease. This study revealed important aspects of both WS and BrB that were previously unknown. The research carried out has built a greater understanding, and a platform for future research directed at understanding key processes involved in these coral diseases. This research has highlighted the need for ongoing infection trials in diseases, even when a pathogen has been identified. The discovery of possible key bacterial species involved in WS and BrB warrants further research aimed at understanding the mechanisms in which bacteria may affect the coral holobiont. In conclusion, this research has further supported the notion that corals are a complex community with bacterial, animal and protistan partners, which when disturbed may see one or several of the previous benign partners becoming pathogenic. In a rapidly changing climate, this conclusion is consistent with the idea that coral diseases are on the rise due to changing environmental circumstances disturbing the balance between these interdependent partners.

Previous studies have shown that bacteria associated with coral diseases are not found in the surrounding water column at detectable levels, yet at the same time, coral diseases are becoming more prominent. Sponges are coral reef residents, which expel filtered seawater that is practically sterile of microbes. Therefore sponges harbor very diverse and abundant microbial communities. This leads to the possibility that coral disease associated bacteria (CDAB) may be present within reef sponge microcosms. In order to identify internal microbes, nonculturable techniques including fluorescent in situ hybridization (FISH), electron microscopy (EM) and 16S small subunit (SSU) rRNA gene cloning and sequencing were applied to local Florida reef sponges Agelas tubulata, Amphimedon compressa and Aplysina fistularis. This study targeted potential coral bacterial pathogens with FISH including Aurantimonas coralicida, Cytophaga sp., Desulfvibrio spp., Firmicutes, Serrattia marcescans, and Vibrio shiloni AK-1. All of the targeted coral disease associated bacteria were found within A. compressa and A. tubulata with FISH, but not in every individual. Differences in the spatial arrangement of targeted microbes were also seen within these sponge hosts. For instance, the two anaerobic bacteria Desulfovibrio spp. and S. marcescans were found in aggragates. In addition, electron microscopy revealed a higher abundance of bacteria in Applysina fistularis choanosome compared to the ectosome.

Coral colonies, from a reef near Abu Dhabi, United Arab Emirates (UAE), were counted and assessed for condition using photo-transects. An epidemic model, used to track how a communicable disease moves through a population, was constructed to help predict the future condition of this coral reef. In situ data from a disease outbreak that occurred in September 2011 provided a baseline for the model. Coral Populations of Porites, Platygyra, Acropora and Dipsastrea were modelled using condition categories that included Healthy, Black Band Disease Infected, Cyanobacteria Infected, Recovered, Recruits or Dead. Results from the modelling indicate that populations of Platygyra and Dipsastrea are healthy and growing, even with continued presence of diseases, due to the high rates of recovery (chance for host colony to overcome infection; high recovery rate = high chance of colony recovering from the infection) and low mortality rates (chance of dying from an infection; low mortality rate = low chance of a infected colony dying from the infection) in the genus. Porites showed no signs of population growth, but stabilized near its initial population size, despite having a high infection rate because population growth (recruitment) and recovery rate were canceled by a high mortality rate. Acropora showed a loss in population numbers over time, losing 25% of its population before the disease was eliminated. Diseases may have been eliminated from the Acropora population because population density was low and coral died quickly after becoming infected with a disease, due to the high mortality rate of this genus, before infecting other colonies. Acropora was the only genus to display what seems to be a density dependent infection rate, since chance of infection was reduced and then eliminated by the rapid mortality of infected colonies, if the population was higher disease spread may have been higher. In addition to results obtained using in situ data, higher modified infection rates were used to assess how they might impact these coral populations. Results suggest that all four genera seem to be resilient, shown by in situ modeling and parameters extracted from the phototransects, and able to withstand acute (rapid increase of infection rate which was then again quickly brought back to normal infection rate, an infection “spike”) increases of disease infection, which is shown by either a high recovery rate (Dipsastrea and Platygyra), a high recruitment/low mortality rate (Porites), or a high mortality rate (Acropora) that may not allow for the diseases to spread. However, all four genera would be slowly driven to extinction by a sustained (chronic) increase of disease infection rate brought on by growing stressors such as an increase in average water temperature or pollutants within the Gulf. These results demonstrate fragility of Gulf coral genera when exposed to chronic episodes of disease, which over time causes total collapse of the coral populations.

Visible lesions on coral colonies are potential indicators that environmental stressors are influencing a reef. To test this hypothesis, pairs of near-shore reefs on Taiwan were surveyed along an anthropogenically influenced gradient that included locations near the cities of Taipei and Taitung, and more remote reefs off Green Island. Two fringing reefs at Sanya, Hainan Island, a popular Chinese resort area, were also assessed. Field surveys were undertaken to detect, quantify and visually describe the occurrence of lesions at each site. Coral mucus samples were collected from both normal-appearing polyps and lesion-afflicted areas of colonies to assess carbon requirements of associated microbes. Tissue samples were also collected to identify bacterial communities inhabiting healthy tissue for comparison with those associated with lesions; denaturing gradient gel electrophoresis and 16S rRNA sequencing for bacterial identification were utilized in these analyses. In addition, tissue samples were collected in the vicinity of lesions and prepared for histological examination. At sites in Taiwan, lesions were encountered twice as often at the sites near Taipei and Taitung than at Green Island. The fewest (15/72 sightings) lesions were encountered at the reefs near Sanya, primarily because there has been nearly an 80% loss of coral cover at Sanya in recent decades. Overall, tissue loss was the most common lesion recorded (52%), followed by pink discoloration (27%) and color loss (i.e., bleaching, 15%). Porites was the taxon most commonly observed with one or more lesions (45% of sightings). Microbes within mucus from lesioned areas utilized similar carbon sources as microbes from mucus from healthy polyps, but utilized those sources more than twice as often. Examples of carbon sources utilized by microbes in >50% of the lesion samples were D-cellobiose, D-mannitol, N-acetyl-D-glucosamine, alpha-cyclodextrin, and glycogen. Bacterial assemblages on corals were significantly different between Taiwan and China, among sites, and between water samples and coral samples, but not between healthy samples and lesions. Bacterial sequences identified in tissue samples from lesions revealed the presence of well-known disease-related genera, such as Clostridium and Vibrio. Microbes specifically indicating anthropogenic sources, included Bacillus sp. (sewage sludge) and Geobacillus thermolevorans (irritable bowel syndrome). Histological examination of tissue samples, particularly those from lesions characterized as tissue loss, revealed fragmentation and detachment from the mesoglea of gastrodermis and epidermis, as well as brown granular material, and the presence of ciliates and small crustaceans. Corals are susceptible to a variety of diseases. For reefs in the western Atlantic and Caribbean, occurrences of lesions and characterization of coral diseases have been relatively well documented. In contrast, many areas in the vast Indo-Pacific, including the reefs of Taiwan and China, have received much less attention. This study of lesions and associated microbiomes on nearshore reefs of Taiwan and Hainan Island supports previous research that has revealed higher incidences of coral lesions and disease in reefs near extensive human populations. The results also support the hypothesis that many of the microbes associated with coral lesions are part of the natural coral microbiome and that some microbes can become opportunistic when the host corals are stressed.