Microbes in the coral holobiont: Partners through evolution, development, and ecological interactions

Frontiers in Cellular and Infection Microbiology

Volumn 4, Issue DEC, 2014, Pages

  Thompson, Janelle R ^a   Rivera, Hanny E ^a   Closek, Collin J ^b   Medina, Mónica ^b  

^a Massachusetts Institute of Technology Cambridge   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; ELECTROPHILE;

ALGA; ANTHOZOA; ANTIBIOSIS; ARTICLE; BLEACHING; COLONY FORMATION; CORAL REEF; CORAL-MICROBIAL INTERACTION; EVOLUTION; GAMETOGENESIS; HOLOBIONT; HOMEOSTASIS; IMMUNE RESPONSE; INTERSTITIUM; METAMORPHOSIS; MICROBIAL COMMUNITY; MUCUS; NITROGEN FIXATION; NONHUMAN; NUTRIENT SUPPLY; ORGANISMAL INTERACTION; PHOTOTROPH; PLANULA; PREDATION; REPRODUCTION; RESOURCE PARTITIONING; SEXUAL MATURATION; SYMBIODINIUM; SYMBIONT;

EID: 84990976005     PISSN: None     EISSN: 22352988     Source Type: Journal    
DOI: 10.3389/fcimb.2014.00176     Document Type: Article

References (217)

1. Agostini, S., Y. Suzuki, T. Higuchi, B. E. Casareto, K. Yoshinaga, Y. Nakano, and H. Fujimura. 2012. Biological and chemical characteristics of the coral gastric cavity. Coral Reefs 31:147-156.
2. Ainsworth, T. D., K. Wasmund, L. Ukani, F. Seneca, D. Yellowlees, D. Miller, and W. Leggat. 2011. Defining the tipping point: a complex cellular life/death balance in corals in response to stress. Sci Rep 1:160.
3. Al-Moghrabi, S., D. Allemand, and J. Jaubert. 1993. Valine uptake by the sleractinian coral Galaxea fascicularis: characterization and effect of light and nutritional stress. Journal of Comparitive Physiology B 163:365-362.
4. Aloisi, G., A. Gloter, M. KrOger, K. Wallmann, F. Guyot, and P. Zuddas. 2006. Nucleation of calcium carbonate on bacterial nanoglobules. Geology 34:1017-1020.
5. Amend, A. S., D. J. Barshis, and T. A. Oliver. 2012. Coral-associated marine fungi form novel lineages and heterogeneous assemblages. ISME J 6:1291-1301.
6. Antonius, A. and D. Lipscomb. 2000. First protozoan coral-kliller in the Indo-Pacific. Atoll. Res. Bull. 481:1-21.
7. Apprill, A., H. Q. Marlow, M. Q. Martindale, and M. S. Rappe. 2009. The onset of microbial associations in the coral Pocillopora meandrina. ISME J 3:685-699.
8. Apprill, A. and M. S. Rappe. 2011. Response of the microbial community to coral spawning in lagoon and reef flat environments of Hawaii, USA. Aquatic Microbial Ecology 62:251-266.
9. Augustin, R. and T. C. Bosch. 2010. Cnidarian Immunity: A Tale of Two Barriers. Pages 1-16 in K. Soderhall, editor. Invertebrate Immunity. Landes Biosciences and Springer Science.
10. Augustin, R., S. Fraune, and T. C. G. Bosch. 2010. How Hydra senses and destroys microbes. Seminars in Immunology 22:54-58.
11. Augustin, R., S. Siebert, and T. C. Bosch. 2009. Identification of a kazal-type serine protease inhibitor with potent anti-staphylococcal activity as part of Hydras innate immune system. Dev Comp Immunol 33:830-837.
12. Azam, F. and B. Cho. 1987. Bacterial utilization of orgainic matter in the sea.in M. Fletcher, T. R. G. Gray, and J. G. Jones, editors. Ecology of Microbial Communities. General Society for Microbiology.
13. Azam, F., T. Fenchel, J. G. Field, J. S. Gray, L. A. Meyerreil, and F. Thingstad. 1983. The Ecological Role of Water-Column Microbes in the Sea. Marine Ecology- Progress Series 10:257-263.
14. Babcock, R. C., G. D. Bull, P. L. Harrison, A. J. Heyward, J. K. Oliver, C. C. Wallace, and B. L. Willis. 1986. Synchronous spawnings of 105 scleractinian coral species on the Great Barrier Reef. Marine Biology 90:379-394.
15. Baker, A. C. 2003. Flexibility and specificity in coral-algal symbiosis: diversity, ecology, and biogeography of Symbiodinium. Annual Review of Ecology, Evolution and Systematics 34:661-689.
16. Banaszak, A., T. C. LaJeunesse, and R. K. Trench. 2000. The synthesis of mycosporinelike amino acids (MAAs) by cultured, symbiotic dinoflagellates. Journal of Experimental Marine Biology and Ecology 249:219-233.
17. Banin, E., T. Israely, A. Kushmaro, Y. Loya, E. Orr, and E. Rosenberg. 2000. Penetration of the Coral-Bleaching Bacterium Vibrio shiloi into Oculina patagonica. Appl Environ Microbiol 66:3031-3036.
18. Banin, E., D. Vassilakos, E. Orr, R. J. Martinez, and E. Rosenberg. 2003. Superoxide dismutase is a virulence factor produced by the coral bleaching pathogen Vibrio shiloi. Curr Microbiol 46:418-422.
19. Barr, J. J., R. Auro, M. Furlan, K. L. Whiteson, M. L. Erb, J. Pogliano, A. Stotland, R. Wolkowicz, A. S. Cutting, K. S. Doran, P. Salamon, M. Youle, and F. Rohwer. 2013. Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci U S A 110:10771-10776.
20. Bayer, T., C. Arif, C. Ferrier-Pages, D. Zoccola, M. Aranda, and C. R. Voolstra. 2013a. Bacteria of the genus Endozoicomonas dominate the microbiome of the Mediterranean gorgonian coral Eunicella cavolini. Marine Ecology Progress Series 479:75-+.
21. Bayer, T., M. J. Neave, A. Alsheikh-Hussain, M. Aranda, L. K. Yum, T. Mincer, K. Hughen, A. Apprill, and C. R. Voolstra. 2013b. The microbiome of the Red Sea coral Stylophora pistillata is dominated by tissue-associated Endozoicomonas bacteria. Appl Environ Microbiol 79:4759-4762.
22. Bell, P. R., B. E. Lapointe, and I. Elmetri. 2007. Reevaluation of ENCORE: support for the eutrophication threshold model for coral reefs. Ambio 36:416-424.
23. Ben-Haim, Y., E. Banim, A. Kushmaro, Y. Loya, and E. Rosenberg. 1999. Inhibition of photosynthesis and bleaching of zooxanthellae by coral pathogen Vibrio shiloi. Environ Microbiol 1:223-229.
24. Ben-Haim, Y., F. L. Thompson, C. C. Thompson, M. C. Cnockaert, B. Hoste, J. Swings, and E. Rosenberg. 2003a. Vibrio coralliilyticus sp nov., a temperaturedependent pathogen of the coral Pocillopora damicornis. Int. J. of Syst. Evol. Microbiol. 53:309-315.
25. Ben-Haim, Y., M. Zicherman-Keren, and E. Rosenberg. 2003b. Temperature- Regulated Bleaching and Lysis of the Coral Pocillopora damicornis by the Novel Pathogen Vibrio coralliilyticus. Applied and Environmental Microbiology 69:4236-4242.
26. Bentis, C. J., L. Kaufman, and S. Golubic. 2000. Endolithic fungi in reef-building corals (Order: Scleractinia) are common, cosmopolitan, and potentially pathogenic. Biology Bulletin 198:254-260.
27. Bondarev, V., M. Richter, S. Romano, J. Piel, A. Schwedt, and H. N. Schulz-Vogt. 2013. The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis. Environmental Microbiology 15:2095-2113.
28. Bosch, T. C. and M. J. McFall-Ngai. 2011. Metaorganisms as the new frontier. Zoology (Jena) 114:185-190.
29. Bourne, D. G., H. V. Boyett, M. E. Henderson, A. Muirhead, and B. L. Willis. 2008. Identification of a ciliate (Oligohymenophorea: Scuticociliatia) associated w i th brown band disease on corals of the Great Barrier Reef. Appl Environ Microbiol 74:883-888.
30. Bourne, D. G., M. Garren, T. M. Work, E. Rosenberg, G. W. Smith, and C. D. Harvell. 2009. Microbial disease and the coral holobiont Trends in Microbiology 17:554-562.
31. Bourne, D. G., A. Muirhead, and Y. Sato. 2011. Changes in sulfate-reducing bacterial populations during the onset of black band disease. Isme Journal 5:559-564.
32. Bourne, D. G. and C. B. Munn. 2005. Diversity of bacteria associated w i t h the coral Pocillopora damicornis from the Great Barrier Reef. Environ Microbiol 7:1162-1174.
33. Brandt, M. and J. McManus. 2009. Disease incidence is related to bleaching extent in reef-building corals. Ecology 90:2859-2867.
34. Brown, B. E. 1997. Coral bleaching: causes and consequences. Coral Reefs 16:S129- S138.
35. Brown, B. E. and J. C. Bythell. 2005. Perspectives on mucus secretion in reef corals. Mar Ecol Prog Ser 296:291-309.
36. Burris, R. H. 1983. Uptake and assimilation of 15NH4+ by a variety of corals. Marine Biology 75:151-155.
37. Carilli, J. E., J. Godfrey, R. D. Norris, S. A. Sandin, and J. E. Smith. 2010. Periodic Endolithic Algal Blooms in Montastraea Faveolata Corals May Represent Periods of Low-Level Stress. Bulletin of Marine Science 86:709-718.
38. Carlton, R. G. and L. L. Richardson. 1995. Oxygen and sulfide dynamics in a horizontally migrating cyanobacterial mat: Black band disease of corals. Microb Ecol 18:155-162.
39. Carreiro-Silva, M., W. E. Kiene, S. Golubic, and T. R. McClanahan. 2012. Phosphorus and nitrogen effects on microbial euendolithic communities and their bioerosion rates. Mar Pollut Bull 64:602-613.
40. Ceh, J., J. B. Raina, R. M. Soo, M. van Keulen, and D. G. Bourne. 2012. Coral-Bacterial Communities before and after a Coral Mass Spawning Event on Ningaloo Reef. PLoS One 7.
41. Ceh, J., M. van Keulen, and D. G. Bourne. 2013. Intergenerational Transfer of Specific Bacteria in Corals and Possible Implications for Offspring Fitness. Microbial Ecology 65:227-231.
42. Cervino, J. M., R. L. Hayes, S. W. Polson, S. C. Polson, T. J. Goreau, R. J. Martinez, and G. W. Smith. 2004. Relationship of Vibrio species infection and elevated temperatures to yellow blotch/band disease in Caribbean corals. Appl Environ Microbiol 70:6855-6864.
43. Chapman, J. A., E. F. Kirkness, O. Simakov, S. E. Hampson, T. Mitros, T. Weinmaier, T. Rattei, P. G. Balasubramanian, J. Borman, D. Busam, K. Disbennett, C. Pfannkoch, N. Sumin, G. G. Sutton, L. D. Viswanathan, B. Walenz, D. M. Goodstein, U. Hellsten, T. Kawashima, S. E. Prochnik, N. H. Putnam, S. Shu, B. Blumberg, C. E. Dana, L. Gee, D. F. Kibler, L. Law, D. Lindgens, D. E. Martinez, J. Peng, P. A. Wigge, B. Bertulat, C. Guder, Y. Nakamura, S. Ozbek, H. Watanabe, K. Khalturin, G. Hemmrich, A. Franke, R. Augustin, S. Fraune, E. Hayakawa, S. Hayakawa, M. Hirose, J. S. Hwang, K. Ikeo, C. Nishimiya-Fujisawa, A. Ogura, T. Takahashi, P. R. Steinmetz, X. Zhang, R. Aufschnaiter, M. K. Eder, A. K. Gorny, W. Salvenmoser, A. M. Heimberg, B. M. Wheeler, K. J. Peterson, A. Bottger, P. Tischler, A. Wolf, T. Gojobori, K. A. Remington, R. L. Strausberg, J. C. Venter, U. Technau, B. Hobmayer, T. C. Bosch, T. W. Holstein, T. Fujisawa, H. R. Bode, C. N. David, D. S. Rokhsar, and R. E. Steele. 2010. The dynamic genome of Hydra. Nature 464:592-596.
44. Chimetto, L. A., M. Brocchi, C. C. Thompson, R. C. Martins, H. R. Ramos, and F. L. Thompson. 2008. Vibrios dominate as culturable nitrogen-fixing bacteria of the Brazilian coral Mussismilia hispida. Syst Appl Microbiol 31:312-319.
45. Closek, C. J., S. Sunagawa, M. K. DeSalvo, Y. M. Piceno, T. Z. DeSantis, E. L. Brodie, M. Weber, C. R. Voolstra, G. L. Andersen, and M. Medina. 2014. Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata. Isme Journal.
46. Coleman-Derr, D. and S. G. Tringe. 2014. Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance. Front. Microbiol. 5.
47. Coles, S. L. and R. Strathman. 1973. Observations on coral mucus "floc" and their potential trophic significance. Limnology and Oceanography 18:673-678.
48. Correa, A. M., R. M. Welsh, and R. L. Vega Thurber. 2012. Unique nucleocytoplasmic dsDNA and +ssRNA viruses are associated with the dinoflagellate endosymbionts of corals. ISME J.
49. Croquer, A., C. Bastidas, D. Lipscomp, R. Rodriguez-Martinez, E. Jordan-Dahlgren, and H. Guzman. 2006. First report of folliculinid ciliates affecting Caribbean scleractinian corals. Coral Reefs 25:187-191.
50. Daniels, C., A. Zeifman, K. Heym, K. B. Ritchie, C. A. Watson, I. Berzins, and M. Breitbart. 2011. Spatial heterogeneity of bacterial communities in the mucus of Montastraea annularis. Mar Ecol Prog Ser 426:29-40.
51. de Castro, A. P., S. D. Araujo, Jr., A. M. Reis, R. L. Moura, R. B. Francini-Filho, G. Pappas, Jr., T. B. Rodrigues, F. L. Thompson, and R. H. Kruger. 2010. Bacterial community associated with healthy and diseased reef coral Mussismilia hispida from eastern Brazil. Microb Ecol 59:658-667.
52. de Goeij, J. M., D. van Oevelen, M. J. Vermeij, R. Osinga, J. J. Middelburg, A. F. de Goeij, and W. Admiraal. 2013. Surviving in a marine desert: the sponge loop retains resources within coral reefs. Science 342:108-110.
53. de Lima, L. A., L. Migliolo, C. Barreiro e Castro, O. Pires Dde, C. Lopez-Abarrategui, E. F. Goncalves, I. M. Vasconcelos, J. T. de Oliveira, J. Otero-Gonzalez Ade, O. L. Franco, and S. C. Dias. 2013. Identification of a novel antimicrobial peptide from Brazilian coast coral Phyllogorgia dilatata. Protein Pept Lett 20:1153-1158.
54. Dinsdale, E. A., O. Pantos, S. Smriga, R. A. Edwards, F. Angly, L. Wegley, M. Hatay, D. Hall, E. Brown, M. Haynes, L. Krause, E. Sala, S. A. Sandin, R. V. Thurber, B. L. Willis, F. Azam, N. Knowlton, and F. Rohwer. 2008. Microbial ecology of four coral atolls in the Northern Line Islands. PLoS One 3:e1584.
55. Dobretsov, S., R. M. M. Abed, and M. Teplitski. 2013. Mini-review: Inhibition of biofouling by marine microorganisms. Biofouling 29:423-441.
56. Dobretsov, S. and P.-Y. Qian. 2004. The role of epibotic bacteria from the surface of the soft coral Dendronephthya sp. in the inhibition of larval settlement. Journal of Experimental Marine Biology and Ecology 299:35-50.
57. Downs, C. A., J. E. Fauth, J. C. Halas, P. Dustan, J. Bemiss, and C. M. Woodley. 2002. Oxidative stress and seasonal coral bleaching. Free Radical Biology and Medicine 33:533-543.
58. Drew Ferrier, M. 1991. Net uptake of dissolved free amino acids by four scleractinian corals. Coral Reefs 10:183-187.
59. Dunlap, W. C., A. Starcevic, D. Baranasic, J. Diminic, J. Zucko, R. Gacesa, M. J. van Oppen, D. Hranueli, J. Cullum, and P. F. Long. 2013. KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome. BMC Genomics 14:509.
60. Fabricius, K. E. 2005. Effects of terrestrial runoff on the ecology of corals and coral reefs: review and synthesis. Mar Pollut Bull 50:125-146.
61. Fernando, S. C., J. Wang, K. Sparling, G. Garcia, R. B. Francini-Filho, R. L. deMoura, R. Paranhos, F. Thompson, and J. R. Thompson. 2014. Microbiota of the major South Atlantic reef building coral Mussismilia. Microb Ecol September.
62. Fine, M. and Y. Loya. 2002. Endolithic algae: an alternative source of photoassimilates during coral bleaching. Proc Biol Sci 269:1205-1210.
63. Fine, M., G. Roff, T. D. Ainsworth, and O. Hoegh-Guldberg. 2006. Phototrophic microendoliths bloom during coral "white syndrome". Coral Reefs 25:577-581.
64. Franzenburg, S., J. Walter, S. Kunzel, J. Wang, J. F. Baines, T. C. Bosch, and S. Fraune. 2013. Distinct antimicrobial peptide expression determines host speciesspecific bacterial associations. Proc Natl Acad Sci U S A 110:E3730-3738.
65. Fraune, S., Y. Abe, and T. C. Bosch. 2009. Disturbing epithelial homeostasis in the metazoan Hydra leads to drastic changes in associated microbiota. Environ Microbiol 11:2361-2369.
66. Fraune, S. and T. C. Bosch. 2007. Long-term maintenance of species-specific bacterial microbiota in the basal metazoan Hydra. Proc Natl Acad Sci U S A 104:13146-13151.
67. Frias-Lopez, J., J. S. Klaus, G. T. Bonheyo, and B. W. Fouke. 2004. Bacterial community associated with black band disease in corals. Appl Environ Microbiol 70:5955-5962.
68. Frias-Lopez, J., A. L. Zerkle, G. T. Bonheyo, and B. W. Fouke. 2002. Partitioning of bacterial communities between seawater and healthy, black band diseased, and dead coral surfaces. Appl Environ Microbiol 68:2214-2228.
69. Garren, M. and F. Azam. 2012. Corals shed bacteria as a potential mechanism of resilience to organic matter enrichment. Isme Journal 6:1159-1165.
70. Garren, M., K. Son, J. B. Raina, R. Rusconi, F. Menolascina, O. H. Shapiro, J. Tout, D. G. Bourne, J. R. Seymour, and R. Stocker. 2014. A bacterial pathogen uses dimethylsulfoniopropionate as a cue to target heat-stressed corals. Isme Journal 8:999-1007.
71. Geffen, Y. and E. Rosenberg. 2005. Stress-induced rapid release of antibacterials by scleractinian corals. Marine Biology 146:931-935.
72. Gerardo, N. M. 2013. The give and take of host-microbe symbioses. Cell host& microbe 14:1-3.
73. Glynn, P. W. 1991. Coral reef bleaching in the 1980s and possible connections with global warming. Trends in Ecology & Evolution 6:175-179.
74. Glynn, P. W. 1993. Coral reef bleaching: ecological perspectives. Coral Reefs 12:1-17.
75. Grover, R., J. F. Maguer, D. Allemand, and C. Ferrier-Pages. 2008. Uptake of dissolved free amino acids by the scleractinian coral Stylophora pistillata. J Exp Biol 211:860-865.
76. Gutner-Hoch, E. and M. Fine. 2011. Genotypic diversity and distribution of Ostreobium quekettii within scleractinian corals. Coral Reefs 30:643-650.
77. Hadfield, M. G. 2011. Biofilms and marine invertebrate larvae: what bacteria produce that larvae use to choose settlement sites. Ann Rev Mar Sci 3:453-470.
78. Hamada, M., E. Shoguchi, C. Shinzato, T. Kawashima, D. J. Miller, and N. Satoh. 2013. The complex NOD-like receptor repertoire of the coral Acropora digitifera includes novel domain combinations. Mol Biol Evol 30:167-176.
79. Harel, M., E. Ben-Dov, D. Rasoulouniriana, N. Siboni, E. Kramarsky-Winter, Y. Loya, Z. Barak, Z. Wiesman, and A. Kushmaro. 2008. A new Thraustochytrid, strain Fng1, isolated from the surface mucus of the hermatypic coral Fungia granulosa. FEMS Microbiol Ecol 64:378-387.
80. Harke, M. J. and C. J. Gobler. 2013. Global transcriptional responses of the toxic cyanobacterium, Microcystis aeruginosa, to nitrogen stress, phosphorus stress, and growth on organic matter. PLoS One 8:e69834.
81. Harrison, P. L. 2011. Coral Reefs: An Ecosystem in Transition. Pages 59-85 in Z. Dubinsky and N. Stambler, editors. Sexual Reproduction of Scleractinian Corals. Springer Science and Business Media.
82. Hoegh-Guldberg, O.1999. Climate change, coral bleaching and the future of the worlds coral reefs. Marine and Freshwater Research 50:839-866.
83. Hoegh-Guldberg, O., P. J. Mumby, A. J. Hooten, R. S. Steneck, P. Greenfield, E. Gomez, C. D. Harvell, P. F. Sale, A. J. Edwards, K. Caldeira, N. Knowlton, C. M. Eakin, R. Iglesias-Prieto, N. Muthiga, R. H. Bradbury, A. Dubi, and M. E. Hatziolos. 2007. Coral reefs under rapid climate change and ocean acidification. Science 318:1737-1742.
84. Huang, Y., S. Callahan, and M. G. Hadfield. 2012. Recruitment in the sea: bacterial genes required for inducing larval settlement in a polychaete worm. Sci Rep 2:228.
85. Husnik, F., N. Nikoh, R. Koga, L. Ross, R. P. Duncan, M. Fujie, M. Tanaka, N. Satoh, D. Bachtrog, A. C. Wilson, C. D. von Dohlen, T. Fukatsu, and J. P. McCutcheon. 2013. Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis. Cell 153:1567-1578.
86. Jackson, D. J., L. Macis, J. Reitner, and G. Wörheide. 2011. A horizontal gene transfer supported the evolution of an early metazoan biomineralization strategy. BMC Evolutionary Biology 11:238.
87. Jatkar, A., B. Brown, J. Bythell, R. Guppy, N. Morris, and J. Pearson. 2010. Measuring mucus thickness in reef corals using a technique devised for vertebrate applications. Marine Biol 2:261-267.
88. Johnston, I. S. and F. Rohwer. 2007. Microbial landscapes on the outer tissue surfaces of the reef-building coral Porites compressa. Coral Reefs 26:375-383.
89. Jung, S. 2009. Hydramacin-1: Structure and antibacterial activity of a protein from the basal metazoan Hydra. Journal of Biological Chemistry 284:1896.
90. Kellogg, C. A. 2004. Tropical Archaea: diversity associated with the surface microlayer of corals. Marine Ecology Progress Series 273:81-88.
91. Kelly, L. W., K. L. Barott, E. Dinsdale, A. M. Friedlander, B. Nosrat, D. Obura, E. Sala, S. A. Sandin, J. E. Smith, M. J. A. Vermeij, G. J. Williams, D. Willner, and F. Rohwer. 2012. Black reefs: iron-induced phase shifts on coral reefs. ISME J 6:638-649.
92. Kimes, N. E., C. J. Grim, W. R. Johnson, N. A. Hasan, B. D. Tall, M. H. Kothary, H. Kiss, A. C. Munk, R. Tapia, L. Green, C. Detter, D. C. Bruce, T. S. Brettin, R. R. Colwell, and P. J. Morris. 2012. Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus. ISME J 6:835-846.
93. Kline, D. I., N. M. Kuntz, M. Breitbart, N. Knowlton, and F. Rohwer. 2006. Role of elavated organic carbon levels and microbial activity in coral mortality. Marine Ecology Progress Series 314:119-125.
94. Koop, K., D. Booth, A. Broadbent, J. Brodie, D. Bucher, D. Capone, J. Coll, W. Dennison, M. Erdmann, P. Harrison, O. Hoegh-Guldberg, P. Hutchings, G. B. Jones, A. W. Larkum, J. O'Neil, A. Steven, E. Tentori, S. Ward, J. Williamson, and D. Yellowlees. 2001. ENCORE: the effect of nutrient enrichment on coral reefs. Synthesis of results and conclusions. Mar Pollut Bull 42:91-120.
95. Koren, O. and E. Rosenberg. 2006. Bacteria associated with mucus and tissues of the coral Oculina patagonica in summer and winter. Appl Environ Microbiol 72:5254-5259.
96. Krediet, C. J., K. B. Ritchie, A. Alagely, and M. Teplitski. 2013. Members of native coral microbiota inhibit glycosidases and thwart colonization of coral mucus by an opportunistic pathogen. ISME J 7:980-990.
97. Kuffner, I., L. Walters, M. Becerro, V. Paul, R. Ritson-Williams, and K. Beach. 2006. Inhibition of coral recruitment by macroalgae and cyanobacteria. Marine Ecology Progress Series 323:107-117.
98. Kuhl, M., Y. Cohen, T. Dalsgaard, B. B. Jorgense, and N. P. Revsbech. 1995. Microenvironment and photosynthesis of zooxanthellae in scleractinian corals studied with microsensors for O2, pH, and light. Marine Ecology Progress Series 117:159-172.
99. Kuhl, M., G. Holst, A. W. Larkum, and P. J. Ralph. 2008. Imaging of oxygen dynamics within the endolithic algal community of the massive coral Porites lobata. J. Phycol 44:541-550.
100. Le Campion-Alsumard, T., S. Golubic, and P. Hutchings. 1995a. Microbial endoliths in skeletons of live and dead corals: Porites lobata(Moorea, French Polynesia). Marine ecology progress series. Oldendorf 117:149-157.
101. Le Campion-Alsumard, T., S. Golubic, and K. Priess. 1995b. Fungi in corals: symbiosis or disease? Interaction between polyps and fungi causes pearl-like skeleton biomineralization. Marine Ecology Progress Series 117:137-147.
102. Lema, K. A., B. L. Willis, and D. G. Bourne. 2012. Corals form characteristic associations with symbiotic nitrogen-fixing bacteria. Appl Environ Microbiol 78:3136-3144.
103. Lesser, M. P. 1996. Elevated temperatures and ultraviolet radiation cause oxidative stress and inhibit photosynthesis in symbiotic dinoflagellates. Limnol. Oceanogr. 41:271-283.
104. Lesser, M. P., L. I. Falcón, A. Rodríguez-Román, S. Enríquez, O. Hoegh-Guldberg, and R. Iglesias-Prieto. 2007. Nitrogen fixation by symbiotic cyanobacteria provides a source of nitrogen for the scleractinian coral Montastraea cavernosa. Marine Ecology Progress Series 346:143-152.
105. Lesser, M. P. and J. H. Farrell. 2004. Exposure to solar radiation increases damage to both host tissues and algal symbionts of corals during thermal stress. Coral Reefs 23:367-377.
106. Lesser, M. P., C. H. Mazel, M. Y. Gorbunov, and P. G. Falkowski. 2004. Discovery of symbiotic nitrogen-fixing cyanobacteria in corals. Science 305:997-1000.
107. Littman, R., B. L. Willis, and D. G. Bourne. 2011. Metagenomic analysis of the coral holobiont during a natural bleaching event on the Great Barrier Reef. Environmental Microbiology Reports 3:651-660.
108. Littman, R. A., D. G. Bourne, and B. L. Willis. 2010. Responses of coral-associated bacterial communities to heat stress differ with Symbiodinium type on the same coral host. Molecular Ecology 19:1978-1990.
109. Littman, R. A., B. L. Willis, and D. G. Bourne. 2009. Bacterial communities of juvenile corals infected with different Symbiodinium (dinoflagellate) clades. Marine Ecology-Progress Series 389:45-59.
110. Loya, Y., H. Lubinevsky, M. Rosenfeld, and E. Kramarsky-Winter. 2004. Nutrient enrichment caused by in situ fish farms at Eilat, Red Sea is detrimental to coral reproduction. Mar Pollut Bull 49:344-353.
111. Lukas, K. J. 1974. 2 Species of Chlorophyte Genus Ostreobium from Skeletons of Atlantic and Caribbean Reef Corals. Journal of Phycology 10:331-335.
112. Magnusson, S., M. Fine, and M. Kuhl. 2007. Light microclimate of endolithic phototrophs in the scleractinian corals Montipora monasteriata and Porites cylindrica. Mar Ecol Prog Ser 332:119-128.
113. Marhaver, K. L., R. A. Edwards, and F. Rohwer. 2008. Viral communities associated with healthy and bleaching corals. Environ Microbiol 10:2277-2286.
114. Marhaver, K. L., M. J. Vermeij, F. Rohwer, and S. A. Sandin. 2013. Janzen-Connell effects in a broadcast-spawning Caribbean coral: distance-dependent survival of larvae and settlers. Ecology 94:146-160.
115. Marquis, C. P., A. H. Baird, R. de Nys, C. Holmström, and N. Koziumi. 2005. An evaluation of the antimicrobial properties of the eggs of 11 species of scleractinian corals. Coral Reefs 24:248-253.
116. Martinez-Garcia, M., D. M. Brazel, B. K. Swan, C. Arnosti, P. S. Chain, K. G. Reitenga, G. Xie, N. J. Poulton, M. Lluesma Gomez, D. E. Masland, B. Thompson, W. K. Bellows, K. Ziervogel, C. C. Lo, S. Ahmed, C. D. Gleasner, C. J. Detter, and R. Stepanauskas. 2012. Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. PLoS One 7:e35314.
117. Marubini, F. and P. S. Davies. 1996. Nitrate increases zooxanthellae population density and reduces skeletogenesis in corals Marine Biol 127:319-328.
118. Mass, T., A. Genin, U. Shavit, M. Grinstein, and D. Tchernov. 2010. Flow enhances photosynthesis in marine benthic autotrophs by increasing the efflux of oxygen from the organism to the water. Proc Natl Acad Sci U S A 107:2527-2531.
119. Mavromatis, K., B. Abt, E. Brambilla, A. Lapidus, A. Copeland, S. Deshpande, M. Nolan, S. Lucas, H. Tice, J. F. Cheng, C. Han, J. C. Detter, T. Woyke, L. Goodwin, S. Pitluck, B. Held, T. Brettin, R. Tapia, N. Ivanova, N. Mikhailova, A. Pati, K. Liolios, A. Chen, K. Palaniappan, M. Land, L. Hauser, Y. J. Chang, C. D. Jeffries, M. Rohde, M. Goker, J. Bristow, J. A. Eisen, V. Markowitz, P. Hugenholtz, H. P. Klenk, and N. C. Kyrpides. 2010. Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24). Standards in genomic sciences 2:290-299.
120. McCutcheon, J. P. and N. A. Moran. 2012. Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol 10:13-26.
121. McDole, T., J. Nulton, K. L. Barott, B. Felts, C. Hand, M. Hatay, H. Lee, M. O. Nadon, B. Nosrat, P. Salamon, B. Bailey, S. A. Sandin, B. Vargas-Angel, M. Youle, B. J. Zgliczynski, R. E. Brainard, and F. Rohwer. 2012. Assessing Coral Reefs on a Pacific-Wide Scale Using the Microbialization Score. PLoS One 7.
122. McFall-Ngai, M., M. G. Hadfield, T. C. Bosch, H. V. Carey, T. Domazet-Loso, A. E. Douglas, N. Dubilier, G. Eberl, T. Fukami, S. F. Gilbert, U. Hentschel, N. King, S. Kjelleberg, A. H. Knoll, N. Kremer, S. K. Mazmanian, J. L. Metcalf, K. Nealson, N. E. Pierce, J. F. Rawls, A. Reid, E. G. Ruby, M. Rumpho, J. G. Sanders, D. Tautz, and J. J. Wernegreen. 2013. Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci U S A 110:3229-3236.
123. Meron, D., E. Atias, L. Iasur Kruh, H. Elifantz, D. Minz, M. Fine, and E. Banin. 2011. The impact of reduced pH on the microbial community of the coral Acropora eurystoma. ISME J 5:51-60.
124. Meron, D., R. Rodolfo-Metalpa, R. Cunning, A. C. Baker, M. Fine, and E. Banin. 2012. Changes in coral microbial communities in response to a natural pH gradient. ISME J 6:1775-1785.
125. Mills, M. and K. Sebens. 2004. Ingestion and assimilation of nitrogen from benthic sediments by three species of coral. Mar. Biol. 145:1097-1106.
126. Mora, C. 2008. A clear human footprint in the coral reefs of the Caribbean. Proceedings of the Royal Society B: Biological Sciences 275:767-773.
127. Moran, N. A., J. P. McCutcheon, and A. Nakabachi. 2008. Genomics and evolution of heritable bacterial symbionts. Annual review of genetics 42:165-190.
128. Morrow, K. M., D. G. Bourne, C. Humphrey, E. S. Botte, P. Laffy, J. Zaneveld, S. Uthicke, K. E. Fabricius, and N. S. Webster. 2014. Natural volcanic CO2 seeps reveal future trajectories for host-microbial associations in corals and sponges. ISME J advance online publication doi:10.1038/ismej.2014.188.
129. Morrow, K. M., A. G. Moss, N. E. Chadwick, and M. R. Liles. 2012. Bacterial associates of two Caribbean coral species reveal species-specific distribution and geographic variability. Appl Environ Microbiol 78:6438-6449.
130. Morse, D., N. Hooker, A. Morse, and R. Jensen. 1988. Control of larval metamorphosis and recruitment in sympatric agariciid corals Journal of Experimental Marine Biology and Ecology 116:193-217.
131. Mullen, K. M., E. C. Peters, and C. D. Harvell. 2003. Coral Resistance to Disease.in E. Rosenberg and Y. Loya, editors. Coral Health and Disease. Springer.
132. Muscatine, L. 1973. Nutrition of corals. Pages 77-115 in O. A. Jones and R. Endean, editors. Biology and Geology of coral reefs. Academic Press, New York.
133. Muscatine, L. 1990. The role of symbiotic algae in carbon and energy flux in reef corals. Pages 75-88 in Z. Dubinsky, editor. Ecosystems of the World: Coral Reefs. Elsevier, Amsterdam.
134. Muscatine, L., P. G. Falkowski, Z. Dubinsky, P. A. Cook, and L. R. McCloskey. 1989. The effect of external nutrient resources on the population dynamics of zooxanthellae in a reef coral. Proc R Soc Lond B 236:311-324.
135. Muscatine, L. and J. W. Porter. 1977. Reef corals: Mutualistic symbioses adapted to nutrient-poor environments. BioScience 27:454-460.
136. Nakajima, R., T. Yoshida, B. A. R. Azman, K. Zaleha, B. H. R. Othman, and T. Toda. 2009. In situ release of coral mucus by Acropora and its influence on the heterotrophic bacteria. Aquatic Ecology 43:815-823.
137. Naumann, M., C. Mayr, U. Struck, and C. Wild. 2010. Coral mucus stable isotope composition and labeling: experimental evidence for mucus uptake by epizoic acoelomorph worms. Marine Biology 157:2521.
138. Neave, M., C. Michell, A. Apprill, and C. R. Voolstra. 2014. Whole-Genome Sequences of Three Symbiotic Endozoicomonas Bacteria. Genome Announc 2:e00802-00814.
139. Negri, A. P., N. S. Webster, R. T. Hill, and A. J. Heyward. 2001. Metamorphosis of broadcast spawning corals in response to bacteria isolated from crustose algae. Marine Ecology Progress Series 223.
140. Nelson, C. E., S. J. Goldberg, L. Wegley Kelly, A. F. Haas, J. E. Smith, F. Rohwer, and C. A. Carlson. 2013. Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages. ISME J 7:962-979.
141. Olson, N. D., T. D. Ainsworth, R. D. Gates, and M. Takabayashi. 2009. Diazotrophic bacteria associated with Hawaiian Montipora corals: Diversity and abundance in correlation with symbiotic dinoflagellates. Journal of Experimental Marine Biology and Ecology 371:140-146.
142. Olson, N. D. and M. P. Lesser. 2013. Diazotrophic diversity in the Caribbean coral, Montastraea cavernosa. Archives of microbiology 195:853-859.
143. Ovchinnikova, T. V., S. V. Balandin, G. M. Aleshina, A. A. Tagaev, Y. F. Leonova, E. D. Krasnodembsky, A. V. Menshenin, and V. N. Kokryakov. 2006. Aurelin, a novel antimicrobial peptide from jellyfish Aurelia aurita with structural features of defensins and channel-blocking toxins. Biochem Biophys Res Commun 348:514-523.
144. Padilla-Gamino, J. L., X. Pochon, C. Bird, G. T. Concepcion, and R. D. Gates. 2012. From parent to gamete: vertical transmission of Symbiodinium (Dinophyceae) ITS2 sequence assemblages in the reef building coral Montipora capitata. PLoS One 7:e38440.
145. Palmer, C. V. and N. Traylor-Knowles. 2012. Towards an integrated network of coral immune mechanisms. Proc Biol Sci 279:4106-4114.
146. Pandolfi, J. M., R. H. Bradbury, E. Sala, T. P. Hughes, K. A. Bjorndal, R. G. Cooke, D. McArdle, L. McClenachan, M. J. Newman, G. Paredes, R. R. Warner, and J. B. Jackson. 2003. Global trajectories of the long-term decline of coral reef ecosystems. Science 301:955-958.
147. Patten, N. L., P. L. Harrison, and J. G. Mitchell. 2008. Prevalence of virus-like particles within a staghorn scleractinian coral (Acropora muricata) from the Great Barrier Reef. Coral Reefs 27:569-580.
148. Pernice, M., A. Meibom, A. Van Den Heuvel, C. Kopp, I. Domart-Coulon, O. Hoegh- Guldberg, and S. Dove. 2012. A single-cell view of ammonium assimilation in coral-dinoflagellate symbiosis. ISME J.
149. Pike, R. E., B. Haltli, and R. G. Kerr. 2013. Description of Endozoicomonas euniceicola sp nov and Endozoicomonas gorgoniicola sp nov., bacteria isolated from the octocorals Eunicea fusca and Plexaura sp., and an emended description of the genus Endozoicomonas. Int J Syst Evol Microbiol 63:4294-4302.
150. Raghukumar, S. 1991. Occurence of thraustochytrid fungi in corals and coral mucus. Indian Journal of Marine Sciences 20:176-181.
151. Raina, J. B., D. Tapiolas, B. L. Willis, and D. G. Bourne. 2009. Coral-associated bacteria and their role in the biogeochemical cycling of sulfur. Appl Environ Microbiol 75:3492-3501.
152. Reshef, L., O. Koren, Y. Loya, I. Zilber-Rosenberg, and E. Rosenberg. 2006. The coral probiotic hypothesis. Environmental Microbiology 8:2068-2073.
153. Reshef, L., E. Ron, and E. Rosenberg. 2008. Genome analysis of the coral bleaching pathogen Vibrio shiloi. Archives of microbiology 190:185-194.
154. Richardson, L. L., A. W. Miller, E. Broderick, L. Kaczmarsky, M. Gantar, D. Stanic, and R. Sekar. 2009. Sulfide, microcystin, and the etiology of black band disease. Dis Aquat Organ 87:79-90.
155. Ritchie, K. B. 2006. Regulation of microbial populations by coral surface mucus and mucus-associated bacteria. Marine Ecology Progress Series 322:1-14.
156. Ritchie, K. B. 2011. Bacterial symbionts of corals and Symbiodinium. Springer Berlin Heidelberg:139-150.
157. Rivera, H. and G. Goodbody-Gringley. 2014. Aggregation and cnidae development as early defensive strategies in Favia fragum and Porites astreoides. Coral Reefs, in press.
158. Rogers, C. S. 1990. Responses of Coral Reefs and Reef Organisms to Sedimentation. Marine Ecology Progress Series 62:185-202.
159. Rohwer, F., M. Breitbart, J. Jara, F. Azam, and N. Knowlton. 2001. Diversity of bacteria associated with the Caribbean coral Montastraea franksi. Coral Reefs 20:85-91.
160. Rohwer, F., V. Seguritan, F. Azam, and N. Knowlton. 2002. Diversity and distribution of coral-associated bacteria. Marine Ecology Progress Series 243:1-10.
161. Rosenberg, E., O. Koren, L. Reshef, R. Efrony, and I. Zilber-Rosenberg. 2007. The role of microorganisms in coral health, disease and evolution. Nat Rev Microbiol 5:355-362.
162. Rypien, K. L., J. R. Ward, and F. Azam. 2010. Antagonistic interactions among coralassociated bacteria. Environ Microbiol 12:28-39.
163. Ryu, J. H., S. H. Kim, H. Y. Lee, J. Y. Bai, Y. D. Nam, J. W. Bae, D. G. Lee, S. C. Shin, E. M. Ha, and W. J. Lee. 2008. Innate immune homeostasis by the homeobox gene caudal and commensal-gut mutualism in Drosophila. Science 319:777-782.
164. Santos, E. O., N. Alves, Jr., G. M. Dias, A. M. Mazotto, A. Vermelho, G. J. Vora, B. Wilson, V. H. Beltran, D. G. Bourne, F. Le Roux, and F. L. Thompson. 2011. Genomic and proteomic analyses of the coral pathogen Vibrio coralliilyticus reveal a diverse virulence repertoire. ISME J.
165. Sato, Y., B. L. Willis, and D. G. Bourne. 2011. Successional changes in bacterial communities during the development of black band disease on the reef coral, Montipora hispida. ISME J 4:203-214.
166. Schleheck, D., M. Weiss, S. Pitluck, D. Bruce, M. L. Land, S. Han, E. Saunders, R. Tapia, C. Detter, T. Brettin, J. Han, T. Woyke, L. Goodwin, L. Pennacchio, M. Nolan, A. M. Cook, S. Kjelleberg, and T. Thomas. 2011. Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T)). Standards in genomic sciences 5:298-310.
167. Sharp, K. H., D. Distel, and V. J. Paul. 2012. Diversity and dynamics of bacterial communities in early life stages of the Caribbean coral Porites astreoides. ISME J 6:790-801.
168. Sharp, K. H., K. B. Ritchie, P. J. Schupp, R. Ritson-Williams, and V. J. Paul. 2010. Bacterial acquisition in juveniles of several broadcast spawning coral species. PLoSOne5:e10898.
169. Shashar, N., A. T. Banaszak, M. P. Lesser, and D. Amrami. 1997. Coral endolithic algae: Life in a protected environment. Pacific Science 51:167-173.
170. Shashar, N., N. Cohen, and Y. Loya. 1993. Extreme Diel Fluctuations of Oxygen in Diffusive Boundary Layers Surrounding Stony Corals. Biol. Bull. Mar. Biol. Lab Woods Hole 185:455-461.
171. Shashar, N., T. Feldstein, Y. Cohen, and Y. Loya. 1994. Nitrogen fixation (acetylene reduction) on a coral reef. Coral Reefs 13:171-174.
172. Shashar, N. and N. Stambler. 1992. Endolithic Algae w i t h in Corals - Life in an Extreme Environment. Journal of Experimental Marine Biology and Ecology 163:277-286.
173. Shibata, K. and F. Haxo. 1969. Light transmission and spectral distribution through epi- and endozoic algal layers in the brain coral (Favia). Biol. Bull. Mar. Biol. Lab Woods Hole 136:461-468.
174. Shikuma, N. J., M. Pilhofer, G. L. Weiss, M. G. Hadfield, G. J. Jensen, and D. K. Newman. 2014. Marine tubeworm metamorphosis induced by arrays of bacterial phage tail-like structures. Science 343:529-533.
175. Shinzato, C., M. Hamada, E. Shoguchi, T. Kawashima, and N. Satoh. 2012. The repertoire of chemical defense genes in the coral Acropora digitifera genome. ZoologSci 29:510-517.
176. Shinzato, C., E. Shoguchi, T. Kawashima, M. Hamada, K. Hisata, M. Tanaka, M. Fujie, M. Fujiwara, R. Koyanagi, T. Ikuta, A. Fujiyama, D. J. Miller, and N. Satoh. 2011. Using the Acropora digitifera genome to understand coral responses to environmental change. Nature 476:320-323.
177. Shoguchi, E., C. Shinzato, T. Kawashima, F. Gyoja, S. Mungpakdee, R. Koyanagi, T. Takeuchi, K. Hisata, M. Tanaka, M. Fujiwara, M. Hamada, A. Seidi, M. Fujie, T. Usami, H. Goto, S. Yamasaki, N. Arakaki, Y. Suzuki, S. Sugano, A. Toyoda, Y. Kuroki, A. Fujiyama, M. Medina, M. A. Coffroth, D. Bhattacharya, and N. Satoh. 2013. Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure. Current biology: CB 23:1399-1408.
178. Simpson, C. J., J. L. Cary, and R. J. Masini. 1992. Destruction of corals and other reef animals by coral spawn slicks on Ningaloo Reef, Western Australia. Coral Reefs 12:185-191.
179. Smillie, C. S., M. B. Smith, J. Friedman, O. X. Cordero, L. A. David, and E. J. Alm. 2011. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480:241-244.
180. Smith, J. E., M. Shaw, R. A. Edwards, D. Obura, O. Pantos, E. Sala, S. A. Sandin, S. Smriga, M. Hatay, and F. L. Rohwer. 2006. Indirect effects of algae on coral: algae-mediated, microbe-induced coral mortality. Ecol Lett 9:835-845.
181. Sneed, J. M., K. H. Sharp, K. B. Ritchie, and V. J. Paul. 2014. The chemical cue tetrabromopyrrole from a biofilm bacterium induces settlement of multiple Caribbean corals. Proc Biol Sci 281.
182. Sorokin, Y. I.1973. On the feeding of some scleractinian coral with bacteria and dissolved organic matter. Limnology and Oceanography 18:380-385.
183. Starcevic, A., S. Akthar, W. C. Dunlap, J. M. Shick, D. Hranueli, J. Cullum, and P. F. Long. 2008. Enzymes of the shikimic acid pathway encoded in the genome of a basal metazoan, Nematostella vectensis, have microbial origins. Proc Natl Acad Sci U S A 105:2533-2537.
184. Sunagawa, S., C. M. Woodley, and M. n. Medina. 2010. Threatened corals provide underexplored microbial habitats. PLoS One 5:e9554.
185. Sweet, M. J., A. Cróquer, and J. C. Bythell. 2011. Bacterial assemblages differ between compartments within the coral holobiont. Coral Reefs 30:39-52.
186. Tanaka, Y., A. Iguchi, M. Inoue, C. Mori, K. Sakai, A. Suzuki, H. Kawahata, and T. Nakamura. 2013. Microscopic observation of symbiotic and aposymbiotic juvenile corals in nutrient-enriched seawater. Mar Pollut Bull 68:93-98.
187. Tanner, J. E. 1996. Seasonality and lunar periodicity in the reproduction of Pocilloporid corals. Coral Reefs 15:59-66.
188. Tebben, J., D. M. Tapiolas, C. A. Motti, D. Abrego, A. P. Negri, L. L. Blackall, P. D. Steinber, and T. Harder. 2011. Induction of larval metamorphosis of the coral Acropora millepora by tetrabromopyrrole isolated from a Pseudoalteromonas bacterium. PLoS One 6:e19082.
189. Tremblay, P., M. S. Naumann, S. Sikorski, R. Grover, and C. Ferrier-Pagès. 2012. Experimental assessment of organic carbon fluxes in the scleractinian coral Stylophora pistillata during a thermal and photo stress event. Marine Ecology Progress Series 453:63-77.
190. Tremblay, P., M. G. Weinbauer, C. Rottier, Y. Guérardel, C. Nozais, and C. Ferrier- Pagès. 2011. Mucus composition and bacterial communities associated with the tissue and skeleton of three scleractinian corals maintained under culture conditions. Journal of the Marine Biological Association of the United Kingdom 91:649-657.
191. Trench, R. K. 1970. Synthesis of a mucous cuticle by a zoanthid. Nature 227:1155-1156.
192. Trench, R. K. 1983. Dinoflagellates in non-parasitic symbioses.in F. J. R. Taylor, editor. The Dinoflagellates. Blackwell Publications, London.
193. Trench, R. K. 1993. Microalgal-invertebrate symbioses - a review. Endocytobiosis and Cell Research 9:135-175.
194. Vega Thurber, R. and A. Correa. 2011. Viruses of reef-building scleractinian corals. Journal of Experimental Marine Biology and Ecology 408:102-113.
195. Vega Thurber, R., D. Willner-Hall, B. Rodriguez-Mueller, C. Desnues, R. A. Edwards, F. Angly, E. Dinsdale, L. Kelly, and F. Rohwer. 2009. Metagenomic analysis of stressed coral holobionts. Environ Microbiol 11:2148-2163.
196. Vega Thurber, R. L., K. L. Barott, D. Hall, H. Liu, B. Rodriguez-Mueller, C. Desnues, R. A. Edwards, M. Haynes, F. E. Angly, L. Wegley, and F. L. Rohwer. 2008. Metagenomic analysis indicates that stressors induce production of herpeslike viruses in the coral Porites compressa. Proc Natl Acad Sci U S A 105:18413-18418.
197. Vega Thurber, R. L., D. E. Burkepile, C. Fuchs, A. A. Shantz, R. McMinds, and J. R. Zaneveld. 2014. Chronic nutrient enrichment increases prevalence and severity of coral disease and bleaching. Glob Chang Biol 20:544-554.
198. Venn, A. A., E. Tambutte, S. Lotto, D. Zoccola, D. Allemand, and S. Tambutte. 2009. Imaging intracellular pH in a reef coral and symbiotic anemone. Proc Natl Acad Sci U S A 106:16574-16579.
199. Vermeij, M. J., J. E. Smith, C. M. Smith, R. Vega Thurber, and S. A. Sandin. 2009. Survival and settlement success of coral planulae: independent and synergistic effects of macroalgae and microbes. Oecologia 159:325-336.
200. Vidal-Dupiol, J., O. Ladriere, D. Destoumieux-Garzon, P. E. Sautiere, A. L. Meistertzheim, E. Tambutte, S. Tambutte, D. Duval, L. Foure, M. Adjeroud, and G. Mitta. 2011. Innate immune responses of a scleractinian coral to vibriosis. J Biol Chem 286:22688-22698.
201. Vizcaino, M. I., W. R. Johnson, N. E. Kimes, K. Williams, M. Torralba, K. E. Nelson, G. W. Smith, E. Weil, P. D. Moeller, and P. J. Morris. 2010. Antimicrobial resistance of the coral pathogen Vibrio coralliilyticus and Caribbean sister phylotypes isolated from a diseased octocoral. Microb Ecol 59:646-657.
202. Ward, S. and P. Harrison. 2000. Changes in gametogenesis and fecundity of acroporid corals that were exposed to elevated nitrogen and phosphorus during the ENCORE experiment. J Exp Mar Bio Ecol 246:179-221.
203. Weber, M., D. de Beer, C. Lott, L. Polerecky, K. Kohls, R. M. Abed, T. G. Ferdelman, and K. E. Fabricius. 2012. Mechanisms of damage to corals exposed to sedimentation. Proc Natl Acad Sci U S A 109:E1558-1567.
204. Weber, M. and M. Medina. 2012. The role of microalgal symbionts (Symbiodinium) in holobiont physiology. Pages 119-140 in G. Piganeau, editor. Genomic Insights into the Biology of Algae. Elsevier.
205. Webster, N. S., L. D. Smith, A. J. Heyward, J. E. M. Watts, R. I. Webb, L. L. Blackall, and A. P. Negri. 2004. Metamorphosis of a Scleractinian Coral in Response to Microbial Biofilms. Applied and Environmental Microbiology 70:1213-1221.
206. Webster, N. S., R. Soo, R. Cobb, and A. P. Negri. 2011. Elevated seawater temperature causes a microbial shift on crustose coralline algae with implications for the recruitment of coral larvae. ISME J 5:759-770.
207. Webster, N. S., S. Uthicke, E. S. Botte, F. Flores, and A. P. Negri. 2013. Ocean acidification reduces induction of coral settlement by crustose coralline algae. Glob Chang Biol 19:303-315.
208. Wegley, L., R. Edwards, B. Rodriguez-Brito, H. Liu, and F. Rohwer. 2007. Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ Microbiol 9:2707-2719.
209. Wild, C., M. Huettel, A. Klueter, S. G. Kremb, M. Y. Rasheed, and B. B. Jorgensen. 2004. Coral mucus functions as an energy carrier and particle trap in the reef ecosystem. Nature 428:66-70.
210. Williams, W. M., A. B. Viner, and W. J. Broughton. 1987. Nitrogen fixagtion (acetylene reduction) associated with the living coral Acropora variabilis. Marine Biology 94:531-535.
211. Work, T. and G. Aeby. 2014. Microbial aggregates within tissues infect a diversity of corals throughout the Indo-Pacific. Mar Ecol Prog Ser 500:1-9.
212. Work, T. M., R. Russell, and G. S. Aeby. 2012. Tissue loss (white syndrome) in the coral Montipora capitata is a dynamic disease with multiple host responses and potential causes. Proc Biol Sci 279:4334-4341.
213. Yakovleva, I., R. Bhagooli, A. Takemura, and M. Hidaka. 2004. Differential susceptibility to oxidative stress of two scleractinian corals: antioxidant functioning of mycosporine-glycine. Comparative Biochemistry and Physiology B-Biochemistry & Molecular Biology 139:721-730.
214. Yang, C. S., M. H. Chen, A. B. Arun, C. A. Chen, J. T. Wang, and W. M. Chen. 2010. Endozoicomonas montiporae sp. nov., isolated from the encrusting pore coral Montipora aequituberculata. Int J Syst Evol Microbiol 60:1158-1162.
215. Yarden, O. 2014. Fungal association with sessile marine invertebrates. Front. Microbiol. 5:228.
216. Yokouchi, H., Y. Fukuoka, D. Mukoyama, R. Calugay, H. Takeyama, and T. Matsunaga. 2006. Whole-metagenome amplification of a microbial community associated with scleractinian coral by multiple displacement amplification using phi29 polymerase. Environ Microbiol 8:1155-1163.
217. Zasloff, M. 2002. Antimicrobial peptides of multicellular organisms. Nature 415:389-395.