Fungi in healthy and diseased sea fans (<Emphasis Type="Italic">Gorgonia ventalina)</Emphasis>: is <Emphasis Type="Italic">Aspergillus sydowii</Emphasis> always the pathogen?

Caribbean corals, including sea fans (Gorgonia spp.), are being affected by severe and apparently new diseases. In the case of sea fans, the pathogen is reported to be the fungus Aspergillus sydowii, and the disease is named aspergillosis. In order to understand coral diseases and pathogens, knowledge of the microbes associated with healthy corals is also necessary. In this study the fungal community of healthy Gorgonia ventalina colonies was contrasted with that of diseased colonies. In addition, the fungal community of healthy and diseased tissue within colonies with aspergillosis was contrasted. Fungi were isolated from healthy and diseased fans from 15 reefs around Puerto Rico, and identified by sequencing the nuclear ribosomal ITS region and by morphology. Thirty fungal species belonging to 15 genera were isolated from 203 G. ventalina colonies. Penicillum and Aspergillus were the most common genera isolated from both healthy and diseased fans. However, the fungal community of healthy fans was distinct and more diverse than that of diseased ones. Within diseased fans, fungal communities from diseased tissues were distinct and more diverse than from healthy tissue. The reduction of fungi in diseased colonies may occur prior to infection due to environmental changes affecting the host, or after infection due to increase in dominance of the pathogen, or because of host responses to infection. Data also indicate that the fungal community of an entire sea fan colony is affected even when only a small portion of the colony suffers from aspergillosis. An unexpected result was that A. sydowii was found in healthy sea fans but never in diseased ones. This result suggests that A. sydowii is not the pathogen causing aspergillosis in the studied colonies, and suggests several fungi common to healthy and diseased colonies as opportunistic pathogens. Given that it is not clear that Aspergillus is the sole pathogen, calling this disease aspergillosis is an oversimplification at best. Communicated by Biology Editor Dr Michael Lesser     

Regeneration of artificial injuries on scleractinian corals and coral/algal competition for newly formed substrate

Porites cylindrica and Porites lutea fragments of colonies were inflicted with five different injury types: chisel, file, Water Pik, osmotic and cement injuries. The fragments were maintained in outdoor aquaria for a period of 240 days under light intensities varying from 2-5% to 70-90% of incident surface photosynthetic active radiation (PAR₀). During the exposure, changes in weight of the fragments, the rates of regeneration of the injuries, abundance of algae and animals settled onto injured areas were monitored. The regeneration rate of the injuries depended on interspecific differences in corals, injury types, number and composition of algae and animals settled onto the lesions, and light and temperature conditions. Competitive interactions between polyps and settlers occurred after colonizers settled onto the damaged surface or the live tissue. It is noteworthy that recovered coral tissue generally overgrew about 100 algal species with or without inhibition of coral growth by algae. In the summer period, the cyanobacterium Lyngbya majuscula covered some lesions (osmotic and cement) by 100%, thus reducing dramatically the regeneration rate of the inflicted injuries and also caused coral bleaching when in direct contact.     

<Emphasis Type="Italic">Symbiodinium</Emphasis> associations with diseased and healthy scleractinian corals

Despite recent advances in identifying the causative agents of disease in corals and understanding the impact of epizootics on reef communities, little is known regarding the interactions among diseases, corals, and their dinoflagellate endosymbionts (Symbiodinium spp.). Since the genotypes of both corals and their resident Symbiodinium contribute to colony-level phenotypes, such as thermotolerance, symbiont genotypes might also contribute to the resistance or susceptibility of coral colonies to disease. To explore this, Symbiodinium were identified using the internal transcribed spacer-2 region of ribosomal DNA from diseased and healthy tissues within individual coral colonies infected with black band disease (BB), dark spot syndrome (DSS), white plague disease (WP), or yellow blotch disease (YB) in the Florida Keys (USA) and the US Virgin Islands. Most of the diseased colonies sampled contained B1, B5a, or C1 (depending on host species), while apparently healthy colonies of the same coral species frequently hosted these types and/or additional symbiont diversity. No potentially “parasitic” Symbiodinium types, uniquely associated with diseased coral tissue, were detected. Within most individual colonies, the same dominant Symbiodinium type was detected in diseased and visually healthy tissues. These data indicate that specific Symbiodinium types are not correlated with the infected tissues of diseased colonies and that DSS and WP onset do not trigger symbiont shuffling within infected tissues. However, few diseased colonies contained clade D symbionts suggesting a negative correlation between hosting Symbiodinium clade D and disease incidence in scleractinian corals. Understanding the influence of Symbiodinium diversity on colony phenotypes may play a critical role in predicting disease resistance and susceptibility in scleractinian corals.     

Gene expression associated with white syndromes in a reef building coral,Acropora hyacinthus

Background

Corals are capable of launching diverse immune defenses at the site of direct contact with pathogens, but the molecular mechanisms of this activity and the colony-wide effects of such stressors remain poorly understood. Here we compared gene expression profiles in eight healthy Acropora hyacinthus colonies against eight colonies exhibiting tissue loss commonly associated with white syndromes, all collected from a natural reef environment near Palau. Two types of tissues were sampled from diseased corals: visibly affected and apparently healthy.

Results

Tag-based RNA-Seq followed by weighted gene co-expression network analysis identified groups of co-regulated differentially expressed genes between all health states (disease lesion, apparently healthy tissues of diseased colonies, and fully healthy). Differences between healthy and diseased tissues indicate activation of several innate immunity and tissue repair pathways accompanied by reduced calcification and the switch towards metabolic reliance on stored lipids. Unaffected parts of diseased colonies, although displaying a trend towards these changes, were not significantly different from fully healthy samples. Still, network analysis identified a group of genes, suggestive of altered immunity state, that were specifically up-regulated in unaffected parts of diseased colonies.

Conclusions

Similarity of fully healthy samples to apparently healthy parts of diseased colonies indicates that systemic effects of white syndromes on A. hyacinthus are weak, which implies that the coral colony is largely able to sustain its physiological performance despite disease. The genes specifically up-regulated in unaffected parts of diseased colonies, instead of being the consequence of disease, might be related to the originally higher susceptibility of these colonies to naturally occurring white syndromes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1540-2) contains supplementary material, which is available to authorized users.     

Within-colony variation in inducibility of coral disease resistance

The abiotic environment influences a variety of ecological processes, including the emergence, transmission, and distribution of disease. In the oceans, increased temperatures associated with climate change are hypothesized to decrease host resistance and/or increase pathogen growth, virulence, or infectivity. Colonial organisms, such as corals, could face a unique challenge with respect to temperature and disease stress: heterogeneous within-colony distribution of constitutive and temperature-induced resistance to infection. This could facilitate disease if warming temperatures promote pathogen growth while decreasing resistance of some areas of the coral colony. Here, an experiment was used to test the hypothesis that temperature-induced disease resistance is heterogeneous within colonies of the sea fan coral, Gorgonia ventalina. Resistance, measured as activity of antifungal metabolites, increased (approx. 30%) with temperature only in young edge tissue, not in older center tissue, consistent with patterns of infection in older, larger sea fan colonies on Caribbean reefs.     

Gibberellins in shoots and developing capsules of Populus species

Extracts of stems of growing shoots of Populus deltoides and P. trichocarpa, and developing capsules of P. deltoides were analysed for gibberellins (GAs) by gas chromatography-mass spectrometry. The following known GAs were identified by comparison of their Kovats retention indices (KRIs) and mass spectra with those of standards: GA1, GA8, GA9, GA19, GA20, 16 beta,17-dihydro-17-hydroxy GA20, GA23, GA28, GA29, GA34, GA44, and GA97. Several of these have not been previously reported from Populus. In addition, two new GAs were identified as 12 beta-hydroxy GA53 (GA127) and 16 beta,17-dihydro-17-hydroxy GA53 and their structures were confirmed by partial synthesis. Evidence was found of 16,17-dihydro-16,17-dihydroxy GA9, 16,17-dihydro-16,17-dihydroxy GA12, 12-hydroxy GA14, and GA34-catabolite by comparison of mass spectra and KRIs with published data. Several putative GAs (hydroxy- and dihydroxy-GA12-like) were also found. The catabolites of active GAs or of key precursors, hydroxylated at C-2 in stems and either C-2, C-12, C-17, or C-16,17 in capsules, were the major proportion of the GAs.     

Skeletal structure and progression of growth anomalies in Porites australiensis in Okinawa, Japan

Growth anomalies (GAs), one of the diseases recently reported for scleractinian corals, are characterized by an abnormal skeletal structure and reduced zooxanthella density. The pathological characteristics of GAs were studied in colonies of Porites australiensis on a reef in Kayo, Okinawa, Japan. Corallites in the GA region lost the skeletal architecture characteristic of P. australiensis, and polyp density had decreased in the GAs due to enlargement of both calices and the coenosteum. The gross productivity of isolated GA samples was lower than in healthy samples and decreased to almost 0 within 11 d after isolation. However, when GA samples were brought into contact with healthy-looking samples from the same colony, they fused and both the GA and healthy regions grew. Healthy samples fused with GA samples grew more slowly than those fused with healthy samples. For in situ GAs surrounded by healthy tissue, tissue death usually started at the center of the GA, probably due to a deficiency in the translocated energy supply from the surrounding tissue. The total area of the GA region and the dead area increased at a rate of 5.3 ± 2.9 cm2 yr-1. These results suggest that GA regions are maintained by energy supplies from surrounding healthy tissues and that GAs may have a negative impact on host corals.     

Ecological characterization of coral growth anomalies on Porites compressa in Hawai��i

Bulbous skeletal structures with associated aberrant corallites have been abundant on Porites compressa in Kāne‘ohe Bay, O‘ahu, Hawai‘i, for at least the last 19 years. These growth anomalies (GA) appear in the summer in shallow (<3 m) water on some, but not on all colonies. GA-free branches, collected from colonies with GAs, produced GAs when cultured in outdoor flow-thru aquaria. Normal branches, whose tissues were continuous with those of GAs, grew in length much more slowly than normal branches from the same colony that were not connected with a GA, suggesting that there is a translocation of materials from normal tissue to GAs. Small experimental colonies that were either exposed to, or protected from, UV radiation did not differ in their rate of GA formation. GAs had a lower probability of survival than normal branches. This characteristic, in combination with their effect on the growth of normal branches and other reported deficiencies in the tissues of growth anomalies (e.g., reduced or failed reproduction), suggests that GA-bearing colonies of this species have reduced fitness.     

Engineering of coral reef larval supply through transplantation of nursery-farmed gravid colonies

The continuous worldwide degradation of coral reefs raises an urgent need for novel active restoration techniques as traditional conservation practices have failed to impede the incessant reefs' decline. While applying the “gardening coral reefs” methodology in Eilat (Red Sea, Israel), we examined reproductive outputs of naturally-grown and outplanted, nursery-farmed Stylophora pistillata colonies from three coral-transplantation trials (November 2005, May 2007, and September 2008), along three reproductive seasons. Surprisingly, transplanted colonies showed better reproductive capacities than the natal Stylophora colonies during > 4 post-transplantation years. A higher percentage of nursery-farmed colonies released planula larvae as compared to naturally-grown colonies. Gravid transplants also shed more planulae per colony, yielding significantly augmented numbers of total planulae over naturally developed S. pistillata colonies. Our results indicate that nursery-grown corals may be used to enhance reef resilience by contributing to the larval pool, forming an engineered larval dispersal instrument for reef rehabilitation.     

Bacterial profiling of White Plague Disease in a comparative coral species framework

Coral reefs are threatened throughout the world. A major factor contributing to their decline is outbreaks and propagation of coral diseases. Due to the complexity of coral-associated microbe communities, little is understood in terms of disease agents, hosts and vectors. It is known that compromised health in corals is correlated with shifts in bacterial assemblages colonizing coral mucus and tissue. However, general disease patterns remain, to a large extent, ambiguous as comparative studies over species, regions, or diseases are scarce. Here, we compare bacterial assemblages of samples from healthy (HH) colonies and such displaying signs of White Plague Disease (WPD) of two different coral species (Pavona duerdeni and Porites lutea) from the same reef in Koh Tao, Thailand, using 16S rRNA gene microarrays. In line with other studies, we found an increase of bacterial diversity in diseased (DD) corals, and a higher abundance of taxa from the families that include known coral pathogens (Alteromonadaceae, Rhodobacteraceae, Vibrionaceae). In our comparative framework analysis, we found differences in microbial assemblages between coral species and coral health states. Notably, patterns of bacterial community structures from HH and DD corals were maintained over species boundaries. Moreover, microbes that differentiated the two coral species did not overlap with microbes that were indicative of HH and DD corals. This suggests that while corals harbor distinct species-specific microbial assemblages, disease-specific bacterial abundance patterns exist that are maintained over coral species boundaries.     

Resilience and acclimation to bleaching stressors in the scleractinian coral Porites cylindrica

‘Resilience’, the capacity of the coral symbiosis with dinoflagellate algal symbionts (‘zooxanthellae’) to recover after bleaching, is a little-studied but crucial aspect of coral responses to bleaching stressors. This study investigated the response of the zooxanthella population in the coral Porites cylindrica after bleaching either naturally on a shallow subtidal reef or experimentally in response to elevated temperature and darkness. Coral resilience was influenced by the nature and duration of the stressor. Corals strongly bleached by natural stressors were less resilient than those that had been partially bleached; and a similar recovery profile was obtained for corals experimentally bleached by exposure to elevated temperature, in which recovery was slower for corals thermally-stressed 96 h than for 72 h. The opposite trend was evident for corals exposed to darkness, indicating that the bleaching trigger had a strong impact on coral resilience. When P. cylindrica recently recovered from bleaching was subjected to a repetition of bleaching stressors, it did not display acclimation, i.e. experience-mediated acquisition of resistance to bleaching stressors. The zooxanthella populations in all corals tested throughout the experiments were typed by PCR-RFLP as clade C, indicating that coral responses were not accompanied by any substantial change in zooxanthella composition at the cladal level.     

The physiological response of reef corals to diel fluctuations in seawater temperature

An opportunity to explore the effects of fluctuating temperatures on tropical scleractinian corals arose when diurnal warming (as large as 4.7 °C) was detected over the rich coral communities found within the back reef of Moorea, French Polynesia. In April and May 2007, experiments were completed to determine the effects of fluctuating temperature on Pocillopora meandrina and Porites rus, and consecutive trials were used to expose them for 13 days to 26 °C, 28 °C (ambient conditions), 30 °C, or a fluctuating treatment ranging from 26 to 30 °C over 24 h. The multivariate response was assessed using maximum dark-adapted quantum yield of PSII (F_V/F_M), Symbiodinium density, chlorophyll-a content, and calcification. In trial 1, multivariate physiology of both species was significantly affected by treatments, with the fluctuating temperature resulting in a 17-45% decline in Symbiodinium density (relative to the ambient) matching that occurring at a constant 30 °C; F_V/F_M, chlorophyll-a content, and calcification, did not differ between the fluctuating and the steady treatments. In contrast, in trial 2 that utilized corals collected two weeks after those used in trial 1, the corals were unaffected by the treatments, likely due to an environment × trial interaction caused by seasonal declines in Symbiodinium density. Together, these results demonstrate that short transgressions to ecologically relevant high and low temperatures can elicit a potentially detrimental response equivalent to that occurring upon exposure to a constant high temperature. The dissimilar responses among dependent variables and consecutive trials underscore the importance of temporal replication and multivariate approaches in coral ecophysiology. It is likely that recent history has a stronger effect on the response of corals to treatments than is currently recognized.     

PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology

Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease.     

Bacteria associated with the rapid tissue necrosis of stony corals

The rapid tissue necrosis (RTN) is a common disease of both wild and captive stony corals, which causes a fast tissue degradation (peeling) and death of the colony. Here we report the results of an investigation carried out on the stony coral Pocillopora damicornis, affected by an RTN-like disease. Total abundance of prokaryotes in tissue samples, determined by epifluorescence microscopy, was significantly higher in diseased than in healthy corals, as well as bacterial counts on MB2216 agar plates. Further experiments performed by fluorescent in situ hybridization using a 16S rDNA Vibrio-specific probe showed that vibrios were significantly more abundant in diseased than in healthy corals. Accordingly, bacterial counts on TCBS agar plates were higher in diseased than in healthy tissues. 16S rDNA sequencing identified as Vibrio colonies from diseased tissues only. Cultivated vibrios were dominated by a single ribotype, which displayed 99% of similarity with Vibrio harveyi strain LB4. Bacterial ribotype richness, assessed by terminal-restriction fragment length polymorphism analysis of the 16S rDNA, was significantly higher in diseased than in healthy corals. Using an in silico software, we estimated that a single terminal restriction fragment, putatively assigned to a Vibrio sp., accounted for > 15% and < 5% of the total bacterial assemblage, in diseased and healthy corals respectively. These results let us hypothesize that the RTN in stony corals can be an infectious disease associated to the presence of Vibrio harveyi. However, further studies are needed to validate the microbial origin of this pathology.     

High potential for formation and persistence of chimeras following aggregated larval settlement in the broadcast spawning coral, Acropora millepora

In sessile modular marine invertebrates, chimeras can originate from fusions of closely settling larvae or of colonies that come into contact through growth or movement. While it has been shown that juveniles of brooding corals fuse under experimental conditions, chimera formation in broadcast spawning corals, the most abundant group of reef corals, has not been examined. This study explores the capacity of the broadcast spawning coral Acropora millepora to form chimeras under experimental conditions and to persist as chimeras in the field. Under experimental conditions, 1.5-fold more larvae settled in aggregations than solitarily, and analyses of nine microsatellite loci revealed that 50 per cent of juveniles tested harboured different genotypes within the same colony. Significantly, some chimeric colonies persisted for 23 months post-settlement, when the study ended. Genotypes within persisting chimeric colonies all showed a high level of relatedness, whereas rejecting colonies displayed variable levels of relatedness. The nearly threefold greater sizes of chimeras compared with solitary juveniles, from settlement through to at least three months, suggest that chimerism is likely to be an important strategy for maximizing survival of vulnerable early life-history stages of corals, although longer-term studies are required to more fully explore the potential benefits of chimerism.     

Nosema bombi: A pollinator parasite with detrimental fitness effects

Nosema bombi is an obligate intracellular parasite that infects different bumblebee species at a substantial, though variable, rate. To date its pathology and impact on host fitness are not well understood. We performed a laboratory experiment investigating the pathology and fitness effects of this parasite on the bumblebee Bombus terrestris. We experimentally infected one group of colonies with N. bombi spores at the start of the worker production, while a second uninfected group of colonies served as controls. During colony development we collected live workers for dissections to measure infection intensities. In parallel, we measured several life history traits, to investigate costs to the host. We succeeded in infecting 11 of 16 experimental colonies. When infection occurred at an early stage of colony development, virtually all individuals were infected, with spores being found in a number of tissues, and the functional fitness of males and young queens was reduced to zero. Further, the survival of workers from infected colonies and infected males were reduced. With such severe effects, N. bombi appears to decrease its opportunities for transmission to the next host generation.     

A comparison of culture-dependent and culture-independent techniques used to characterize bacterial communities on healthy and white plague-diseased corals of the Montastraea annularis species complex

Diseases of hermatypic corals pose a global threat to coral reefs, and investigations of bacterial communities associated with healthy corals and those exhibiting signs of disease are necessary for proper diagnosis. One disease, commonly called white plague (WP), is characterized by acute tissue loss. This investigation compared the bacterial communities associated with healthy coral tissue (N = 15), apparently healthy tissue on WP-diseased colonies (N = 15), and WP-diseased tissues (N = 15) from Montastraea annularis (species complex) colonies inhabiting a Bahamian reef. Aliquots of sediment (N = 15) and water (N = 15) were also obtained from the proximity of each coral colony sampled. Samples for culture-dependent analyses were inoculated onto one-half strength Marine Agar (½ MA) and Thiosulfate Citrate Bile Salts Sucrose Agar to quantify the culturable communities. Length heterogeneity PCR (LH-PCR) of the 16S rRNA gene characterized the bacterial operational taxonomic units (OTU) associated with lesions on corals exhibiting signs of a white plague-like disease as well as apparently healthy tissue from diseased and non-diseased conspecifics. Analysis of Similarity was conducted on the LH-PCR fingerprints, which indicated no significant difference in the composition of bacterial communities associated with apparently healthy and diseased corals. Comparisons of the 16S rRNA gene amplicons from cultured bacterial colonies (½ MA; N = 21) with all amplicons obtained from the whole coral-associated bacterial community indicated ≥39 % of coral-associated bacterial taxa could be cultured. Amplicons from these bacterial cultures matched amplicons from the whole coral-associated bacterial community that, when combined, accounted for >70 % total bacterial abundance. An OTU with the same amplicon length as Aurantimonas coralicida (313.1 bp), the reported etiological agent of WPII, was detected in relatively low abundance (<0.1 %) on all tissue types. These findings suggest a coral disease resembling WP may result from multiple etiologies.     

Effects of the fish anesthetic, clove oil (eugenol), on coral health and growth

Ecological research within coral reefs often requires the use of anesthetics to immobilize organisms. It is therefore important to consider the effect of these chemicals on the surrounding flora and fauna, particularly to the corals themselves. We quantified the effects of clove oil, a commonly used fish anesthetic, on the growth and occurrence of bleaching in three species of corals: Acropora striata, Pocillopora verrucosa, and Porites australiensis. We compared coral responses to five treatments: a gradient of four clove oil concentrations (0-28%) in seawater, and one concentration of clove oil (14%) in ethanol. Each week, we assessed the presence of bleaching, and then applied the treatment. We measured growth over the duration of the 6-week experiment using the buoyant weight technique. Growth and bleaching showed a dose response to clove oil exposure, and the use of ethanol as a solvent had an additional deleterious effect, as also suggested by observed changes in concentrations of eugenol following field application. Overall, growth was reduced by 37.6% at the highest concentration (28% clove oil in seawater) relative to the control (0% clove oil). The reduction in growth was nearly as great (35.3% of the control) at half the concentration of clove oil (14%) when dissolved in ethanol. These results suggest the repeated use of clove oil (even without a solvent) can deleteriously affect corals.     

Does Dark-Spot Syndrome Experimentally Transmit among Caribbean Corals?

Over the last half-century, coral diseases have contributed to the rapid decline of coral populations throughout the Caribbean region. Some coral diseases appear to be potentially infectious, yet little is known about their modes of transmission. This study experimentally tested whether dark-spot syndrome on Siderastrea siderea was directly or indirectly transmissible to neighboring coral colonies. We also tested whether open wounds were necessary to facilitate disease transmission. At the completion of the experiments, we sampled bacterial communities on diseased, exposed, and healthy coral colonies to determine whether bacterial pathogens had transmitted to the susceptible colonies. We saw no evidence of either direct or waterborne transmission of dark-spot syndrome, and corals that received lesions by direct contact with diseased tissue, healed and showed no signs of infection. There were no significant differences among bacterial communities on healthy, exposed, and diseased colonies, although nine individual ribotypes were significantly higher in diseased corals compared with healthy and exposed corals, indicating a lack of transmission. Although our experiments do not fully refute the possibility that dark-spot syndrome is infectious and transmissible, our results suggest that in situ macroscopic signs of dark-spot syndrome are not always contagious.     

Visibly healthy corals exhibit variable pigment concentrations and symbiont phenotypes

Understanding the natural variability of photosynthetic pigment ranges and distributions in healthy corals is central to evaluating how useful these measurements are for assessing the health and bleaching status of endosymbiotic reef-building corals. This study examined the photosynthetic pigment variability in visibly healthy Porites lobata and Porites lutea corals from Kaneohe Bay, Hawaii and explored whether pigment variability was related to the genetic identity or phenotypic characteristics of the symbionts. Concentrations of the photosynthetic pigments chlorophyll a, peridinin, chlorophyll c ₂ , diadinoxanthin, diatoxanthin, β,β-carotene and dinoxanthin were quantified using high-performance liquid chromatography (HPLC). Pigment concentrations were found to range 1.5–10 fold in colonies of each species at similar depths (0–2, 2–4, 10–15 and 19–21 m). Despite the high pigment variability, pigment ratios for each species were relatively conserved over the 0–21 m depth gradient. The genetic identity of the symbiont communities was examined for each colony using 18S nuclear ribosomal DNA (nrDNA) restriction fragment length polymorphisms. All colonies contained symbionts belonging to clade C. The density and phenotypic characteristics of the symbionts were explored using flow cytometry, and fluorescence and side scatter (cell size) properties revealed phenotypically distinct symbiont subpopulations in every colony. The symbiont subpopulations displayed pigment trends that may be driven by acclimatization to irradiance microenvironments within the host. These results highlight the biological complexity of healthy coral–symbiont associations and the need for future research on pigments and symbiont subpopulation dynamics.