We thank Donna Epps, histologist at Institute for Genomic Biology, University of Illinois Urbana-Champaign (UIUC), for her capable technical assistance in sample preparation and sectioning. This work was supported by a research grant to B.W. Fouke from the Office of Naval Research (N00014-00-1-0609). In addition, C.A.H. Miller received grants from the UIUC Department of Geology Wanless Fellowship, UIUC Department of Geology Leighton fund and UIUC Department of Geology Roscoe Jackson fieldwork fund. Interpretations presented in this manuscript are those of the authors and may not necessarily represent those of the granting institutions. We also thank the Caribbean Research and Management of Biodiversity (Carmabi) laboratory on Cura&#231;ao for their support and collaboration in collecting the coral tissue biopsy samples. We thank Claudia Lutz, IGB Media Communication Specialist for her able language correction.

NOTE: Reagents to be prepared for Serial Block Face Imaging of Coral Samples
1. Preinfiltration Wax
<ol>
	<li>Melt 3.6 g of STEARIN flakes in a glass beaker. Mix well on a hot plate (60-70 &#176;C).</li>
	<li>Add 400 mg of Sudan IV (to minimize wax background fluorescence). Mix well and wait until a red translucent solution is achieved.</li>
	<li>Add 96 ml&#160;hot molten paraffin (100%) and mix well.</li>
</ol>
1.2) Embedding Wax
<ol>
	<li>Melt 7.2 g of STEARIN flakes in a glass beaker and mix well on a hot plate (60-70 &#176;C).</li>
	<li>Add 0.8 g of Sudan IV. Mix well and wait until a red translucent solution is achieved.</li>
	<li>Add paraffin granules (162 g) and mix until paraffin melts completely.</li>
	<li>Add 30 g of white granular Vybar and melt completely in the same beaker; once melted, mix.</li>
	<li>Loosely close the glass bottle with a lid. Place the glass bottle in a 60 &#176;C convection oven to keep the ingredients in a liquid state. Carry out all infiltrations in this oven.</li>
	<li>Split the total volume of the 200 ml&#160;red wax in to two glass bottles of 100 ml&#160;each. Use one aliquot for infiltration and the other for final embedding.</li>
</ol>
1.3) Embedding Coral Tissues for Serial Block Face Imaging
<ol>
	<li>Wash the coral polyps collected in the field (SI Video 1) and stored (3-6 months at 4-5 &#176;C in paraformaldehyde) in phosphate buffered saline (3x 5 min) and decalcify when ready to be imaged. Decalcify the polyps in ExCal solution&#160;for 24 hr or until as the polyps are totally devoid of CaCO3. Incubate several decalcified coral polyps as a single block in a 25, 50, 75, and 100% ethanol series, followed by 1x xylene substitute&#160;to dehydrate the samples.</li>
	<li>Place the processed polyps in a preheated 65 &#176;C oven containing 100% xylene substitute. Incubate for 30 min twice by changing to fresh solution. Orient the polyps in such a way that the top of the polyps faces down and the top surface is as flat as possible.</li>
	<li>Make solutions of 2:1, 1:1, and 1:2 xylene substitute and preinfiltration wax (step 1.1) in 50 ml Falcon tubes.</li>
	<li>Incubate coral polyps with these three increasing concentrations of preinfiltration wax, followed by 3x&#160;incubation in 100% preinfiltration wax for 30-60 min&#160;each time.</li>
	<li>Note: Depending on the thickness of the samples, steps 1.3.1-1.3.5 could be increased with longer periods of time.</li>
	<li>Move the samples to embedding wax (see step 1.2.6) after 3x incubation in 100% preinfiltration wax.</li>
	<li>Remove the embedding wax after 30 min. Replace with fresh embedding wax and continue incubation for a minimum of 4 hr at 65 &#176;C.</li>
</ol>
1.4) Embedding in Red Wax
<ol>
	<li>Photograph the block (the stainless steel tray where the white wax is placed and on top of which the sample is placed). This is necessary because once embedded in the wax, the location of the sample will become invisible as the embedding red wax is opaque.</li>
	<li>Place small drops of high melting point wax around the new preheated stainless steel embedding mold and allow it to cool. Pour a small volume of freshly melted embedding wax from second container as stated in step 1.2.6.</li>
	<li>Position the coral polyp facing down quickly over the white wax dot, then place a plastic sample holder on the stainless steel tray and pour more embedding wax so that the wax comes up to the surface of the plastic mold.</li>
	<li>Take the entire setup out of 65 &#176;C oven and allow it to cool on a bench or a cool surface until the wax completely hardens.</li>
	<li>This may take 6 hr up to day or two. Place the block desiccated in a refrigerator at 4 &#176;C, protected from light, for long term storage.</li>
</ol>
1.5) Sectioning at the Serial Block Face Setup
<ol>
	<li>Trim the block and cut 1 &#956;m sections using a microtome. Do not collect the sections as they will become like powder. Remember, we are imaging only the block face.&#160;The sample appears when the white wax begins to disappear.</li>
	<li>Capture images of the smooth block face which contains the sample every time a section is removed. Continue until the coral polyp disappears as in SI Video 2.</li>
	<li>Record/Capture the images with a monochrome camera using a FITC fluorescent filter to pick up the auto-fluorescence of the chromatophores/coral polyp. Image 3-4 decalcified cores from each species.</li>
</ol>
2. Imaging Corals Under Two-photon Fluorescence Microscopy
<ol>
	<li>Fix coral polyp cores, each containing around 10-12 polyps about an inch in diameter, in 4% paraformaldehyde at the site of collection (sea shore) as soon as they are harvested under water.</li>
	<li>Keep samples at 4 &#176;C until imaging. Washed cores are placed in the same solution upside down in a cover glass bottom dish (0.17 mm thick).</li>
	<li>Using a two photon laser at 780 nm excitation, image 3-4 polyps at two different magnifications (digital zoom) using a 10X&#160;(0.3 NA) objective. The coral polyp shape and height varies between samples (usually 1-2 mm) and the imaging depth is also limited by the imaging objective&#8217;s working distance.</li>
	<li>Use the tile scan mode to collect approximately 25-100 (5 x 5 or 10 x 10 tiles) images per focal plane in xy&#160;and 50-100 images through the z&#160;axis at 10 or 20 &#181;m interval, totaling around 5,000-10,000 images/coral polyp.</li>
	<li>Image three to four polyp areas to represent a core and coral species. NOTE: Image acquisition time varies between 2-5 hr/polyp area.</li>
	<li>Store all images in raw data format in the system&#8217;s hard disk as LSM 5. Render 3D in a 3D image analysis and rendering software.</li>
</ol>
3. 3D Volume Rendering and Visualization of SBFI and Two-photon Spectral Fluorescence Data
<ol>
	<li>Crop the 2D data to reduce the file size by focusing on a single polyp using the square cropping tool in the program and compile as a single tiff file (reduce the file size also by saving the file in 8 bit format) in the acquisition software.</li>
	<li>Open the assembled files of the SBFI data (collected in step 1.5.1) or the tiled multiple z-stacks of two photon optical sections (collected in step 2.1.4) in the program Imaris Surpass module under volume algorithm.</li>
	<li>Project the SBFI data rendered in 3D using a shadow projection. Create an isosurface mode where the voxels are thresholded to create a solid surface pattern (SI Video 3).</li>
	<li>Visualize the 3D projections using a clipping plane algorithm at xy, xz, and yz&#160;orthogonal modes to reveal 3D structure and shape of corals.</li>
	<li>Animate the projections using a key frame animation module in the same Imaris program (SI Videos 3-7).</li>
	<li>Generate video files at 5% compression and generate a movie clips in avi format using volume (SI Videos 4 and 6), 3D and Isosurface modalities (SI Videos 5 and 7).</li>
</ol>

<ol>
	<li>Stocker, T. F., Qin, D., Plattner, G. -. K., Tignor, M., Allen, S. K., Boschung, J., Nauels, A., Xia, Y., Bex, V., Midgley, P. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. , 1535 (2013).</li><li>Buddemeir, R. W., Kleypas, J. A., Aronson, R. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Coral Reefs &amp; Global Climate Change: Potential Contributions of Climate Change to Stresses on Coral Reef Ecosystems). 46, (2004).</li><li>Wilkinson, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Status of coral reefs of the world. , 1-2 (2004).</li><li>Lough, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Climate+records+from+corals.">Climate records from corals.</a> WIREs Clim. Chang. 1, 318-331 (2010).</li><li>Harvell, C. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tropical+Archaea:+diversity+associated+with+the+surface+microlayer+of+corals.">Tropical Archaea: diversity associated with the surface microlayer of corals.</a> Mar. Ecol. Prog. Ser. 273, 81-88 (2004).</li><li>Rosenberg, E., Loya, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Coral Health and Disease. , (2004).</li><li>Rohwer, F., Breitbart, M., Jara, J., Azam, F., Knowlton, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Diversity+of+bacteria+associated+with+the+Caribbean+coral+Montastrea+franksi.">Diversity of bacteria associated with the Caribbean coral Montastrea franksi.</a> Coral Reefs. 20, 85-91 (2001).</li><li>Frias-Lopez, J., Zerkle, A. L., Bonheyo, G. T., Fouke, B. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Partitioning+of+bacterial+communities+between+seawater+and+healthy,+black+band+diseased,+and+dead+coral+surfaces.">Partitioning of bacterial communities between seawater and healthy, black band diseased, and dead coral surfaces.</a> Appl. Environ. Microbiol. 68, 2214-2228 (2002).</li><li>Stanley, G. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+evolution+of+modern+corals+and+their+early+history.">The evolution of modern corals and their early history.</a> Earth Sci. Rev. 60, 195-225 (2003).</li><li>Piggot, A. M., Fouke, B. W., Sivaguru, M., Sanford, R., Gaskins, H. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Change+in+zooxanthellae+and+mucocyte+tissue+density+as+an+adaptive+response+to+environmental+stress+by+the+coral+Montastraea+annularis.">Change in zooxanthellae and mucocyte tissue density as an adaptive response to environmental stress by the coral Montastraea annularis.</a> Mar. Biol. 156, 2379-2389 (2009).</li><li>Stanley, G. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Photosymbiosis+and+the+evolution+of+modern+coral+reefs.">Photosymbiosis and the evolution of modern coral reefs.</a> Evolution. 1, 3 (2006).</li><li>Gordon, B. R., Leggat, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Symbiodinium&#8212;Invertebrate+Symbioses+and+the+Role+of+Metabolomics.">Symbiodinium&#8212;Invertebrate Symbioses and the Role of Metabolomics.</a> Mar. Drugs. 8, 2546-2568 (2010).</li><li>Schlichter, D., Weber, W., Fricke, H. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+chromatophore+system+in+the+hermatypic,+deep-water+coral+Leptoseris+fragilis+(Anthozoa:+Hexacorallia).">A chromatophore system in the hermatypic, deep-water coral Leptoseris fragilis (Anthozoa: Hexacorallia).</a> Marine Biology. 89, 143-147 (1994).</li><li>Fouke, B. W., Meyers, W. J., Hanson, G. N., Beets, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chronostratigraphy+and+dolomitization+of+the+Seroe+Domi+Formation,+Curacao,+Netherlands+Antilles.">Chronostratigraphy and dolomitization of the Seroe Domi Formation, Curacao, Netherlands Antilles.</a> Facies. 35, 293-320 (1996).</li><li>Frias-Lopez, J., Bonheyo, G. T., Jin, Q., Fouke, B. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cyanobacteria+associated+with+coral+black+band+disease+in+Caribbean+and+Indo-Pacific+reefs.">Cyanobacteria associated with coral black band disease in Caribbean and Indo-Pacific reefs.</a> Appl. Environ. Microbiol. 69, 2409-2413 (2003).</li><li>Frias-Lopez, J., Klaus, J., Bonheyo, G. T., Fouke, B. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+bacterial+community+associated+with+black+band+disease+in+corals.">The bacterial community associated with black band disease in corals.</a> Appl. Environ. Microbiol. 70, 5055-5062 (2004).</li><li>Frias-Lopez, J., Bonheyo, G. T., Fouke, B. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+differential+gene+expression+in+bacteria+associated+with+coral+black+band+disease+using+RNA-arbitrarily+primed+PCR.">Identification of differential gene expression in bacteria associated with coral black band disease using RNA-arbitrarily primed PCR.</a> Appl. Environ. Microbiol. 70, 3687-3694 (2004).</li><li>Klaus, J. S., Frias-Lopez, J., Bonheyo, G. T., Heikoop, J. M., Fouke, B. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bacterial+communities+inhabiting+the+healthy+tissues+of+two+Caribbean+reef+corals:+interspecific+and+spatial+variation.">Bacterial communities inhabiting the healthy tissues of two Caribbean reef corals: interspecific and spatial variation.</a> Coral Reefs. 24, 129-137 (2005).</li><li>Klaus, J., Janse, I., Sandford, R., Fouke, B. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coral+microbial+communities,+zooxanthellae,+and+mucus+along+gradients+of+seawater+depth+and+coastal+pollution.">Coral microbial communities, zooxanthellae, and mucus along gradients of seawater depth and coastal pollution.</a> Environ. Microbiol. 9, 1291-1305 (2007).</li><li>van Duyl, F. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Atlas of the living reefs of Curacao and Bonaire (Netherlands Antilles). , (1985).</li><li>Carricart-Ganivet, J. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sea+surface+temperature+and+the+growth+of+the+West+Atlantic+reef+building+coral+Montastraea+annularis.">Sea surface temperature and the growth of the West Atlantic reef building coral Montastraea annularis.</a> J. Exp. Mar. Biol. Ecol. 302, 249-260 (2004).</li><li>Barnes, D. J., Lough, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coral+skeletons:+Storage+and+recovery+of+environmental+information.">Coral skeletons: Storage and recovery of environmental information.</a> Global Chang. Biol. 2, 569-582 (1996).</li><li>Mohun, T. J., Weninger, W. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Generation+of+volume+data+by+episcopic+three-dimensional+imaging+of+embryos.">Generation of volume data by episcopic three-dimensional imaging of embryos.</a> Cold Spring Harbor Protocols. 6, 069591 (2012).</li><li>Mohun, T. J., Weninger, W. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+heart+development+using+high-resolution+episcopic+microscopy.">Imaging heart development using high-resolution episcopic microscopy.</a> Curr. Opin. Genet. Dev. 21, 573-578 (2011).</li><li>Mohun, T. J., Weninger, W. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Embedding+embryos+for+episcopic+fluorescence+image+capturing+(EFIC).">Embedding embryos for episcopic fluorescence image capturing (EFIC).</a> Cold Spring Harb. Protoc. 6, 069575 (2012).</li><li>Rosenthal, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+high+resolution+three+dimensional+reconstruction+of+embryos+with+episcopic+fluorescence+image+capture.">Rapid high resolution three dimensional reconstruction of embryos with episcopic fluorescence image capture.</a> Birth Defects Res. C: Embryo Today: Rev. 72, 213-223 (2004).</li><li>Slyfield, C. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Three-dimensional+surface+texture+visualization+of+bone+tissue+through+epifluorescence-based+serial+block+face+imaging.">Three-dimensional surface texture visualization of bone tissue through epifluorescence-based serial block face imaging.</a> J. Microsc. 236, 52-59 (2009).</li><li>Weninger, W., Mohun, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phenotyping+transgenic+embryos:+a+rapid+3-D+screening+method+based+on+episcopic+fluorescence+image+capturing.">Phenotyping transgenic embryos: a rapid 3-D screening method based on episcopic fluorescence image capturing.</a> Nat. Genet. 30, 59-65 (2001).</li><li>Weninger, W., Mohun, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Three-dimensional analysis of molecular signals with episcopic imaging techniques. Reporter Genes. , 35-46 (2007).</li><li>Gerneke, D. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Surface+imaging+microscopy+using+an+ultramiller+for+large+volume+3D+reconstruction+of+wax-and+resin-embedded+tissues.">Surface imaging microscopy using an ultramiller for large volume 3D reconstruction of wax-and resin-embedded tissues.</a> Microsc. Res. Tech. 70, 886-894 (2007).</li><li>Denk, W., Horstmann, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Serial+block-face+scanning+electron+microscopy+to+reconstruct+three-dimensional+tissue+nanostructure.">Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure.</a> PLoS Biol. 2, e329 (2004).</li><li>Salih, A., Larkum, A., Cox, G., K&#252;hl, M., Hoegh-Guldberg, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorescent+pigments+in+corals+are+photoprotective.">Fluorescent pigments in corals are photoprotective.</a> Nature. 408, 850-853 (2000).</li><li>Sivaguru, M., Mander, L., Fried, G., Punyasena, S. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Capturing+the+surface+texture+and+shape+of+pollen:+A+comparison+of+microscopy+techniques.">Capturing the surface texture and shape of pollen: A comparison of microscopy techniques.</a> PloS one. 7 (6), (2012).</li><li>Helmchen, F., Denk, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Deep+tissue+two-photon+microscopy.">Deep tissue two-photon microscopy.</a> Nat. Methods. 2, 932-940 (2005).</li></ol>

The authors declare no conflict of interests.

Coral reef research is a highly interdisciplinary research effort, involving analysis of the simultaneous physical, chemical, and biological phenomena that operate in the marine environment. The study of complex coral reef ecosystems is therefore best completed within a &#8216;Powers of Ten&#8217; contextual framework (Figure&#160;10). This graphic compilation illustrates that the coral ecosystem covers a wide range of spatial dimensions (10-9 to 105 m). Furthermore, this exercise i...

Global warming and accompanying environmental change are directly affecting the health and distribution of tropical marine corals1-4. Multiple impacts are being observed, including coral bleaching and the emergence of infectious diseases5-6. However, more accurate prediction of future coral response to these environmental threats will require that a histological &#8220;baseline&#8221; be established, which defines tissue morphology and cell composition and distribution for &#8220;apparently healthy&#8221; corals. In turn, &#8220;impacted&#8221; corals can then be quantitatively compared. Furthermore, this baseline should be established for apparently healthy corals under a variety of environmental conditions, so that &#8220;healthy response&#8221; can also be gauged across environmental gradients. As an initial step toward establishing this baseline, a high-resolution 3D study has been undertaken of how apparently healthy coral polyp tissue morphology and cellular composition responds to increases in water depth (WD) and accompanying decreases in sunlight irradiance. Results can then be used to establish a more comprehensive mechanistic understanding of coral adaptation, as well as to gain insight into coral-symbiont evolution and the enhancement of light harvesting.
Stony corals (Scleractinia) are colonial marine invertebrate animals that play host to a complex assemblage of other microorganisms, collectively referred to as the coral holobiont7-10. The research undertaken in the present study seeks to use a suite of cutting-edge imaging technologies to simultaneously track changes with increasing water depth in the tissue pigments and symbiotic zooxanthellae of apparently healthy host corals. This will establish the required comparative tissue cell &#8220;baseline&#8221; across a bathymetric gradient for apparently healthy corals and act as indicators of coral health10. Coral pigments, called chromatophores, act to absorb, reflect, scatter, refract, diffract, or otherwise interfere with incident solar radiation11. The zooxanthellae-chromatophore endosymbiotic relationship has enabled the coevolution of strategically advantageous light-harvesting optimization and skeletal growth strategies, as well as trophic plasticity (shifting feeding strategies back-and-forth from autotrophy to heterotrophy) for the coral animal12.
The southern Caribbean island nation of Cura&#231;ao (formerly part of the Netherlands Antilles) lies approximately 65 km north of Venezuela within the east-west trending Aruba-La Blanquilla archipelago (Figure 1A). The 70 km long southern coast of Cura&#231;ao contains a continuous modern and Miocene-Pliocene-Pleistocene-Holocene ancient fringing coral reef tract13,14. Mean annual SST on Cura&#231;ao varies approximately 3 &#176;C annually, ranging from a minimum of 26 &#176;C in late January to a maximum of 29 &#176;C in early September, with a mean annual temperature of 27.5&#177;0.5 &#186;C (NOAA SST Data Sets, 2000-2010). The coral reef at Playa Kalki (12&#176;22&#8217;31.63&#8221;N, 69&#176;09&#8217;29.62&#8221;W), lying near the northwestern tip of Cura&#231;ao (Figure 1A), was chosen for sampling because it has been previously well-studied and the marine ecosystem at this location is bathed in fresh nonpolluted seawater7,15-19. Two closely related scleractinian coral species, M. annularis and M. faveolata, were chosen for experimentation and analysis in this study because each species: (1) exhibits distinctly different and nonoverlapping bathymetric distributions on the reef tract with respect to the shelf break and the associated carbonate sedimentary depositional environments (M. annularis range = 0-10 m WD; M. faveolata range = 10-20 m WD20; Figures 1B, 2A, and 2B); (2) is a common coral reef framework builder throughout the Caribbean Sea21; and (3) has well-studied ecological, physiological, and evolutionary relationships22.
Field sampling for the present study was conducted using standard SCUBA diving techniques offshore of Playa Kalki on Cura&#231;ao. A shallow-to-deep water bathymetric transect was established that ran across the shelf, over the shelf break, and into the deep water fore reef environments. Apparently healthy coral heads were then identified for sampling along this bathymetric transect, including: (1) three individual ~ 1 m diameter coral heads of M. annularis, all of which were at 5 m water depth (WD); and (2) three individual ~ 1 m diameter coral heads of M. faveolata, all of which were at 12 m WD. Photosynthetically active radiation (PAR) was measured as 33-36% PAR at 5 m WD and 18-22% PAR at 10 m WD. Sampling was conducted in January when the SST was 26 &#176;C at the water depths of both the 5 m and 12 m. Each of these six coral heads was sampled in triplicate at equivalent spatial positions (i.e., approximately 45&#176; N latitude on each of the six hemispherical coral heads). Each individual sample consisted of a 2.5 cm diameter coral tissue-skeleton core biopsy that was collected with a cleaned arch punch. Three coral tissue-skeleton biopsies were sampled on standard SCUBA with gloved hands from each of the coral heads (9 from M. annularis colonies at 5 m WD and 9 from M. faveolata at 12 m WD). Immediately upon collection at depth, each biopsy core sample was placed in a sterile 50 ml polypropylene centrifuge tube, screw-top sealed, and returned to the surface. The seawater was decanted from each centrifuge tube and each core biopsy was then immersed, stored, and transported in 4% paraformaldehyde.
SBFI imaging has previously been performed on a wide range of biological samples, including whole-brain and whole-heart human tissues, intact mouse embryos, zebra fish embryos, and multiple types of animal samples with intact bones23-30. Most of these studies utilized optical/light microscopy with either fluorescence or bright field techniques. However, studies have been conducted at ultra-high magnifications using scanning electron serial block face imaging in the past31. In the present study, a modified SBFI protocol has been developed for and applied to corals for the first time. Because M. annularis and M. faveolata coral polyps are 1-2 mm in thickness, none of the routine light microscopy techniques would be capable of penetrating the entire thickness of coral polyp tissue. Therefore, we have SBFI sample preparation protocol specifically designed for coral samples. In addition, we have custom designed a stereomicroscope holder, which is motorized to move in both x and y directions. This apparatus takes images of the block face of the sample rather than collecting the sections using a regular microtome in front of the microscope. We also introduced another nonlinear optical two-photon microscopic technique to image the same coral polyps across the entire thickness of the coral tissues. This overcomes the limitations imposed by SBFI in terms of decalcification and the possibility of changes in tissue morphology and volume (shrinking) that may be induced by sample preparation (dehydration) and processing protocols. Furthermore, the emission profiles from the corals were spectrally resolved to identify their peak emissions and variations between the chromatophores and the photosynthetic zooxanthellae. These results were evaluated in the context of the method used and their individual advantages regarding acquisition time, analysis time, and the ability to resolve fine structural details without compromising structural integrity of the coral tissue.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Coral Tissue Skeleton</td>
			<td>None</td>
			<td>None</td>
			<td>2.5 cm Biopsy from natural habitat</td>
		</tr>
		<tr>
			<td>Arch Punch Coring Device</td>
			<td>C.S. Osborne and Company</td>
			<td>No. 149</td>
			<td>For Coral biopsy collection</td>
		</tr>
		<tr>
			<td>Paraformaldehyde</td>
			<td>Electron Microscopy Sciences</td>
			<td>RT 15700</td>
			<td>16% Pre-diluted</td>
		</tr>
		<tr>
			<td>Histoclear/Safeclear II</td>
			<td>Electron Microscopy Sciences</td>
			<td>RT 64111-04</td>
			<td>Non-Toxic alternate to Xylene, Dehydration and Deparafinization</td>
		</tr>
		<tr>
			<td>Xylene and Ethanol</td>
			<td>Fisher Scientific</td>
			<td>Fisher Scientific</td>
			<td>Dehydration</td>
		</tr>
		<tr>
			<td>Paraffin Wax</td>
			<td>Richard Allen Scientific</td>
			<td>Type H REF 8338</td>
			<td>Infiltration solution</td>
		</tr>
		<tr>
			<td>Vybar</td>
			<td>The Candle Maker</td>
			<td>None</td>
			<td>Component of Red Wax</td>
		</tr>
		<tr>
			<td>Stearin</td>
			<td>The Candle Maker</td>
			<td>None</td>
			<td>Component of Red Wax</td>
		</tr>
		<tr>
			<td>Sudan IV</td>
			<td>Fisher Chemical</td>
			<td>S667-25</td>
			<td>Red Wax-Opaque background</td>
		</tr>
		<tr>
			<td>Wheat Germ Agglutinin (WGA)</td>
			<td>Life Technologies</td>
			<td>W32466</td>
			<td>For labeling&#160; Coral Mucus</td>
		</tr>
		<tr>
			<td>Prolong Gold</td>
			<td>Life Technologies</td>
			<td>P36095</td>
			<td>Anti-fade mounting media</td>
		</tr>
		<tr>
			<td>Fluoro Dish</td>
			<td>World Precision Instruments</td>
			<td>FD-35-100</td>
			<td>For two-photon imaging</td>
		</tr>
		<tr>
			<td>XY Motor, Driver and Controller</td>
			<td>Lin Engineering</td>
			<td>211-13-01R0, R325, R256-RO</td>
			<td>XY Translational Movement</td>
		</tr>
		<tr>
			<td>Hot Plate</td>
			<td>Corning</td>
			<td>DC-220</td>
			<td>Melting all wax</td>
		</tr>
		<tr>
			<td>Convection Oven</td>
			<td>Yamato</td>
			<td>DX-600</td>
			<td>Infiltration and Embedding</td>
		</tr>
		<tr>
			<td>Tissue Processor</td>
			<td>Leica</td>
			<td>ASP 300</td>
			<td>Dehydration, Infiltration</td>
		</tr>
		<tr>
			<td>Microtome</td>
			<td>Leica</td>
			<td>RM2055</td>
			<td>Disposable knifes</td>
		</tr>
		<tr>
			<td>Stereo Microscope</td>
			<td>Carl Zeiss</td>
			<td>Stereolumar V 12</td>
			<td>1.5x (30 mm WD) Objective</td>
		</tr>
		<tr>
			<td>Fluorescence Microscope with ApoTome</td>
			<td>Carl Zeiss</td>
			<td>Axiovert M 200, ApoTome I System</td>
			<td>Imaging thin section of a polyp: Zooxanthellae</td>
		</tr>
		<tr>
			<td>Axiocam camera</td>
			<td>Carl Zeiss</td>
			<td>MRm</td>
			<td>Monochrome camera 1388x1040 pixels</td>
		</tr>
		<tr>
			<td>Axiovision Software</td>
			<td>Carl Zeiss</td>
			<td>Version 4.8</td>
			<td>Image acquisition program</td>
		</tr>
		<tr>
			<td>Two-Photon Laser</td>
			<td>Spectraphysics</td>
			<td>Maitai eHP, pulsed laser (70 fs)</td>
			<td>With DeepSee module</td>
		</tr>
		<tr>
			<td>Laser Scanning Microscope</td>
			<td>Carl Zeiss</td>
			<td>LSM 710 with Spectral Detector</td>
			<td>34 channel PMT detection</td>
		</tr>
		<tr>
			<td>Zen Software</td>
			<td>Carl Zeiss</td>
			<td>2010 or above</td>
			<td>for two-photon and spectral image acquisition</td>
		</tr>
		<tr>
			<td>Imaris Suite Software</td>
			<td>Bitplane, Inc.,</td>
			<td>Version 7.0 or above</td>
			<td>3D Volume, Iso-surface Rendering, Visualization</td>
		</tr>
	</tbody>
</table>

multimodal optical microscopy methods reveal polyp tissue morphology and structure in caribbean reef building corals

An integrated suite of imaging techniques has been applied to determine the three-dimensional (3D) morphology and cellular structure of polyp tissues comprising the Caribbean reef building corals Montastraeaannularis and M. faveolata. These approaches include fluorescence microscopy (FM), serial block face imaging (SBFI), and two-photon confocal laser scanning microscopy (TPLSM). SBFI provides deep tissue imaging after physical sectioning; it details the tissue surface texture and 3D visualization to tissue depths of more than 2 mm. Complementary FM and TPLSM yield ultra-high resolution images of tissue cellular structure. Results have: (1) identified previously unreported lobate tissue morphologies on the outer wall of individual coral polyps&#160;and (2) created the first surface maps of the 3D distribution and tissue density of chromatophores and algae-like dinoflagellate zooxanthellae endosymbionts. Spectral absorption peaks of 500 nm and 675 nm, respectively, suggest that M. annularis and M. faveolata contain similar types of chlorophyll and chromatophores. However, M. annularis and M. faveolata exhibit significant differences in the tissue density and 3D distribution of these key cellular components. This study focusing on imaging methods indicates that SBFI is extremely useful for analysis of large mm-scale samples of decalcified coral tissues. Complimentary FM and TPLSM reveal subtle submillimeter&#160;scale changes in cellular distribution and density in nondecalcified coral tissue samples. The TPLSM technique affords: (1) minimally invasive sample preparation,&#160;(2) superior optical sectioning ability,&#160;and (3) minimal light absorption and scattering, while still permitting deep tissue imaging.

A custom designed SBFI apparatus (manufactured specifically for the present study; Figure 3) produced the first detailed 3D digital elevation maps (DEMs) of the outer surface texture and morphology of the M. annularis and M. faveolature coral polyps (Figure 4 and SI Videos 1-2). This yielded images of previously undescribed stacked lobes of coral tissue concentrically radiating outward from the center of each polyp (Figures 4B, 4D, and ...

Watch this Scientific Journal Video about Multimodal Optical Microscopy Methods Reveal Polyp Tissue Morphology and Structure in Caribbean Reef Building Corals at JoVE.com

Multimodal Optical Microscopy Methods Reveal Polyp Tissue Morphology and Structure in Caribbean Reef Building Corals

An integrated suite of imaging techniques has been applied to determine polyp morphology and tissue structure in the Caribbean corals Montastraeaannularis and M. faveolata. Fluorescence, serial block face,&#160;and two-photon confocal laser scanning microscopy have identified lobate structure, polyp walls, and estimated chromatophore and zooxanthellae densities and distributions.

An integrated suite of imaging techniques has been applied to determine the three-dimensional (3D) morphology and cellular structure of polyp tissues ...

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12.2K Views.  University of Illinois at Urbana-Champaign. An integrated suite of imaging techniques has been applied to determine polyp morphology and tissue structure in the Caribbean corals Montastraeaannularis and M. faveolata. Fluorescence, serial block face, and two-photon confocal laser scanning microscopy have identified lobate structure, polyp walls, and estimated chromatophore and zooxanthellae densities and distributions.