Fluorescence functional groups.

<p>These 15 spectra denote the most common fluorescent emissions we have measured on Caribbean reefs. Note: All of the stony coral functional groups (1–7) also include a chlorophyll component. Fluorescence intensities are plotted in arbitrary units, and the spectra indicate typical peak-to-peak ratios. The spectra also illustrate actual inter-functional-group differences. For example, corals with pigments 486 and 515 (group 4) tend to fluorescence ‘brighter’ than the other groups, and chlorophyll fluorescence in soft corals (group 8) is approximately 4 times more intense than that in green or brown algae (group 9). The spectra used in the classification comparisons included the effects of water-column attenuation and observed peak shifts, as described in the text.</p

Classification results for <i>MAHAL</i>.

<p>Highlighted values indicate the minimum score for each band configuration.</p

Water-column attenuation of fluorescence.

<p>The wavelength dependence of the diffuse attenuation coefficient (black) differentially attenuates the emission spectra of the pigments designated 486, 515, 575, and 685 (gray).</p

Classification results for <i>SAM</i>.

<p>Highlighted values indicate the minimum score for each band configuration.</p

Functional groups and the pigment-mixing formulations used in the fluorescence model.

<p>Numbers indicate relative fluorescence-peak intensities. A value within the specified range was randomly chosen for each of the 10,000 synthesized spectra for each functional group.</p

Fluorescence endmember library.

<p>Based on our measurements, most fluorescent signals observed on Caribbean reefs are attributable to one or more of these spectra.</p

Different spectral band sets used in the classification tests.

<p>Each band is designated by a center wavelength and half bandwidth, both in nm.</p

Classification results for empirically-measured, fluorescence spectra.

<p>Water-column attenuation effects were applied for distances of 1 m and 3 m. Different numbers of example field spectra were used for each functional group. Example spectra from multiple genera were used for each group when possible. Erroneous classifications are indicated by the corresponding functional-group number. Asterisks denote groups for which classification success changed with increasing attenuation effects.</p

Comparing Bacterial Community Composition between Healthy and White Plague-Like Disease States in <i>Orbicella annularis</i> Using PhyloChip™ G3 Microarrays

<div><p>Coral disease is a global problem. Diseases are typically named or described based on macroscopic changes, but broad signs of coral distress such as tissue loss or discoloration are unlikely to be specific to a particular pathogen. For example, there appear to be multiple diseases that manifest the rapid tissue loss that characterizes ‘white plague.’ PhyloChip™ G3 microarrays were used to compare the bacterial community composition of both healthy and white plague-like diseased corals. Samples of lobed star coral (<i>Orbicella annularis</i>, formerly of the genus <i>Montastraea</i> <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079801#pone.0079801-Budd1" target="_blank">[1]</a>) were collected from two geographically distinct areas, Dry Tortugas National Park and Virgin Islands National Park, to determine if there were biogeographic differences between the diseases. In fact, all diseased samples clustered together, however there was no consistent link to <i>Aurantimonas coralicida</i>, which has been described as the causative agent of white plague type II. The microarrays revealed a large amount of bacterial heterogeneity within the healthy corals and less diversity in the diseased corals. Gram-positive bacterial groups (Actinobacteria, Firmicutes) comprised a greater proportion of the operational taxonomic units (OTUs) unique to healthy samples. Diseased samples were enriched in OTUs from the families Corynebacteriaceae, Lachnospiraceae, Rhodobacteraceae, and Streptococcaceae. Much previous coral disease work has used clone libraries, which seem to be methodologically biased toward recovery of Gram-negative bacterial sequences and may therefore have missed the importance of Gram-positive groups. The PhyloChip™data presented here provide a broader characterization of the bacterial community changes that occur within <i>Orbicella annularis</i> during the shift from a healthy to diseased state.</p></div

Enumeration of taxonomic rank members detected across replicate PhyloChips™ from healthy and diseased coral samples (after Sunagawa et al, 2009).

<p>Enumeration of taxonomic rank members detected across replicate PhyloChips™ from healthy and diseased coral samples (after Sunagawa et al, 2009).</p