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Coral Reef Bacterial Communities

  • David G. Bourne
  • Nicole S. Webster

Abstract

Tropical coral reefs form some of the richest ecosystems on Earth. Though representing less than 0.1% of the total ocean surface, coral reefs host approximately 25% of all marine species. Along with their high biodiversity, coral reefs support the livelihood of millions of people around the world through supply of food, resources, and coastal protection, plus their natural beauty attracts tourists that support associated industries. Coral reefs are complex three-dimensional structures, with an array of habitats and environmental niches. They are also one of the most vulnerable ecosystems on our planet, currently under direct threat from human activities including climate change, decreased water quality, and increased nutrient loads. The microbial community is fundamental to the functioning, health, and resilience of these coral reef ecosystems. Understanding how environmental stress affects microbial communities and their processes will allow us to better predict the resilience of coral reefs during changes in nutrient cycling and disease epidemics. This chapter explores the important role of microbial communities in keystone reef organisms such as reef-building Scleractinian corals and benthic filter-feeding sponges. These species represent the best studied systems in coral reefs for invertebrate-bacterial interactions. Diversity and function of microbial communities in the sediments and overlying seawater are also explored with microbially driven nutrient cycling in these habitats closely coupled to reef productivity.

Keywords

Microbial Community Bacterial Community Coral Reef Anaerobic Ammonium Oxidation Great Barrier Reef 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Acinas SG, Anton J, Rodriguez-Valera F (1999) Diversity of free-living and attached bacteria in offshore Western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA. Appl Environ Microbiol 65:514–522PubMedGoogle Scholar
  2. Aeby G, Work T, Fenner D, Didonato E (2008) Coral and crustose coralline algae disease on the reefs of American Samoa. In: Proceedings of the 11th international coral reef symposium, Ft. Lauderdale, FLGoogle Scholar
  3. Agostini S, Suzuki Y, Casareto BE, Nakano Y, Hidaka M, Badrun N (2009) Coral symbiotic complex: hypothesis through vitamin B12 for a new evaluation Galaxea. J Coral Reef Stud 11:1–11Google Scholar
  4. Agostini S, Suzuki Y, Higuchi T, Casareto B, Yoshinaga K, Nakano Y, Fujimura H (2011) Biological and chemical characteristics of the coral gastric cavity. Coral Reefs 31:1–10Google Scholar
  5. Ainsworth TD, Hoegh-Guldberg O (2009) Bacterial communities closely associated with coral tissues vary under experimental and natural reef conditions and thermal stress. Aquat Biol 4:289–296Google Scholar
  6. Ainsworth TD, Fine M, Blackall LL, Hoegh-Guldberg O (2006) Fluorescence in situ hybridization and spectral imaging of coral-associated bacterial communities. Appl Environ Microbiol 72:3016–3020PubMedGoogle Scholar
  7. Ainsworth TD, Hoegh-Guldberg O, Leggat W (2008) Imaging the fluorescence of marine invertebrates and their associated flora. J Micros-Oxf 232:197–199Google Scholar
  8. Angermeier H, Kamke J, Abdelmohsen UR, Krohne G, Pawlik JR, Lindquist NL, Hentschel U (2011) The pathology of sponge orange band disease affecting the Caribbean barrel sponge Xestospongia muta. FEMS Microbiol Ecol 75:218–230PubMedGoogle Scholar
  9. Anthony KRN, Maynard JA, Diaz-Pulido D, Mumby PJ, Marshall PA, Cao L, Hoegh-Guldberg O (2011) Ocean acidification and warming will lower coral reef resilience. Glob Chang Biol 17:1798–1808Google Scholar
  10. Antonius A (1973) New observations on coral destruction in reefs. In: 10th Meeting of the Association of Island Marine Laboratories of the Caribbean. University of Puerto Rico: Association of Island Marine Laboratories of the Caribbean, p. 3Google Scholar
  11. Apprill A, Rappe MS (2011) Response of the microbial community to coral spawning in lagoon and reef flat environments of Hawaii USA. Aquat Microb Ecol 62:251–266Google Scholar
  12. Aronson R, Precht WF (2001) White-band diseases and the changing face of Caribbean coral reefs. Hydrobiologia 460:25–38Google Scholar
  13. Ayukai T (1992) Picoplankton dynamics in Davies reef lagoon, the great barrier reef, Australia. J Plankton Res 14:1593–1606Google Scholar
  14. Ayukai T (1995) Retention of phytoplankton and planktonic microbes on coral reefs within the Great Barrier Reef, Australia. Coral Reefs 14:141–147Google Scholar
  15. Azam F, Malfatti F (2007) Microbial structuring of marine ecosystems. Nat Rev Microbiol 5:782–791PubMedGoogle Scholar
  16. Bally M, Garrabou J (2007) Thermodependent bacterial pathogens and mass mortalities in temperature benthic communities: a new case of emerging disease linked to climate change. Glob Chang Biol 13:2078–2088Google Scholar
  17. Banin E, Israely T, Kushmaro A, Loya Y, Orr E, Rosenberg E (2000) Penetration of the coral-bleaching bacterium Vibrio shiloi into Oculina patagonica. Appl Environ Microbiol 66:3031–3036PubMedGoogle Scholar
  18. Barneah O, Ben-Dov E, Kramarsky-Winter E, Kushmaro A (2007) Characterization of black band disease in Red Sea stony corals. Environ Microbiol 9:1995–2006PubMedGoogle Scholar
  19. Barnes RD (1987) Invertebrate zoology. Harcourt Brace Jovanovich College Publishers, Fort WorthGoogle Scholar
  20. Barnes RSK, Hughes RN (1999) An introduction to marine ecology. Blackwell Science, Oxford, UKGoogle Scholar
  21. Barott KL, Rodriguez-Brito B, Janouškovec J, Marhaver KL, Smith JE, Keeling P, Rohwer FL (2011) Microbial diversity associated with four functional groups of benthic reef algae and the reef-building coral Montastraea annularis. Environ Microbiol Rep 13:1192–1204Google Scholar
  22. Bayer K, Schmitt S, Hentschel U (2008) Physiology, phylogeny and in situ evidence for bacterial and archaeal nitrifiers in the marine sponge Aplysina aerophoba. Environ Microbiol 10:2942–2955PubMedGoogle Scholar
  23. Bell PRF, Elmetri I, Uwins P (1999) Nitrogen fixation by Trichodesmium spp. In the Central and Northern Great barrier reef lagoon: relative importance of the fixed-nitrogen load. Mar Ecol Prog Ser 186:119–126Google Scholar
  24. Ben-Haim Y, Banim E, Kushmaro A, Loya Y, Rosenberg E (1999) Inhibition of photosynthesis and bleaching of zooxanthellae by the coral pathogen Vibrio shiloi. Environ Microbiol 1:223–229PubMedGoogle Scholar
  25. Ben-Haim Y, Zicherman-Keren M, Rosenberg E (2003a) Temperature-regulated bleaching and lysis of the coral Pocillopora damicornis by the novel pathogen Vibrio coralliilyticus. Appl Environ Microbiol 69:4236–4242PubMedGoogle Scholar
  26. Ben-Haim Y, Thompson FL, Thompson CC, Cnockaert MC, Hoste B, Swings J, Rosenberg E (2003b) Vibrio coralliilyticus sp. nov., a temperature-dependent pathogen of the coral Pocillopora damicornis. Int J Syst Evol Microbiol 53:309–315PubMedGoogle Scholar
  27. Berkelmans R, De'ath G, Kininmonth S, Skirving WJ (2004) A comparison of the 1998 and 2002 coral bleaching events on the Great Barrier Reef: spatial correlation, patterns, and predictions. Coral Reefs 23:74–83Google Scholar
  28. Borouierdi AFB, Vizcaino MI, Meyers A, Pollock EC, Huynh SL, Schock TB et al (2009) NMR-based microbial metabolomics and the temperature-dependent coral pathogen Vibrio coralliilyticus. Environ Sci Technol 43:7658–7664Google Scholar
  29. Bourne DG (2005) Microbiological assessment of a disease outbreak on corals from Magnetic Island (Great Barrier Reef, Australia). Coral Reefs 24:304–312Google Scholar
  30. Bourne DG, Munn CB (2005) Diversity of bacteria associated with the coral Pocillopora damicornis from the Great Barrier Reef. Environ Microbiol 7:1162–1174PubMedGoogle Scholar
  31. Bourne DG, Høj L, Webster NS, Payne M, Skindersøe M, Givskov M, Hall MA (2007) Aspects of the microbiology of phyllosoma rearing of the ornate rock lobster Panulirus ornatus. Aquaculture 268:274–287Google Scholar
  32. Bourne DG, Iida Y, Uthicke S, Smith-Keune C (2008) Changes in coral associated microbial communities during a bleaching event. ISME J 2:350–363PubMedGoogle Scholar
  33. Bourne DG, Garren M, Work TM, Rosenberg E, Smith G, Harvell CD (2009) Microbial disease and the coral holobiont. Trends Microbiol 17:554–562PubMedGoogle Scholar
  34. Broadbent AD, Jones GB (2004) DMS and DMSP in mucus ropes, coral mucus, surface films and sediment pore waters from coral reefs in the Great Barrier Reef. Mar Freshw Res 55:849–855Google Scholar
  35. Brodie J, Mitchell A (2005) Nutrients in Australian tropical rivers changes with agricultural development and implications for receiving environments. Mar Freshw Res 56:279–302Google Scholar
  36. Brodie J, De’ath G, Devlin M, Furnas M, Wright M (2007) Spatial and temporal patterns of near-surface chlorophyll a in the Great Barrier Reef lagoon. Mar Freshw Res 58:342–353Google Scholar
  37. Bruckner AW, Bruckner RJ (2002) Coral predation by Sparisima viride and lack of relationship with coral disease. Bali 2002:1245–1249Google Scholar
  38. Bruno JF, Selig ER, Casey KS, Page CA, Willis BL, Harvell CD et al (2007) Thermal stress and coral cover as drivers of coral disease outbreaks. PLoS Biol 5:1220–1227Google Scholar
  39. Burnett WJ, McKenzie JD (1997) Subcuticular bacteria from the brittle star Ophiactis balli (Echinodermata: Ophiuroidea) represent a new lineage of extracellular marine symbionts in the alpha subdivision of the class Proteobacteria. Appl Environ Microbiol 63:1721–1724PubMedGoogle Scholar
  40. Campbell L, Nolla HA, Vaulot D (1994) The importance of Prochlorococcus to community structure in the central North Pacific Ocean. Limnol Oceanogr 39:954–961Google Scholar
  41. Capone DG (1996) Coral reef ecosystems in the context of the marine nitrogen cycle. In: Bjork M, Semesi AK, Pedersen M, Bergman B (eds) Current trends in marine botanical research in the East African region. Ord & Vetande, Uppsala, pp 61–76Google Scholar
  42. Carlton RG, Richardson LL (1995) Oxygen and sulfide dynamics in a horizontally migrating cyanobacterial mat: Black band disease of corals. FEMS Microbiol Ecol 18:155–162Google Scholar
  43. Carpenter KE, Abrar M, Aeby G, Aronson RB, Banks S, Bruckner A et al (2008) One-third of reef-building corals face elevated extinction risk from climate change and local impacts. Science 321:560–563PubMedGoogle Scholar
  44. Casareto BE, Charpy L, Blanchot J, Suzuki Y, Kurasawa K, Ishikawa Y (2006) Phototrophic prokaryotes in Bora Bay, Miyako Island, Okinawa, Japan. In: Proceedings of 10th international coral reef symposium, Okinawa, Japan, vol 1, pp 844–853Google Scholar
  45. Casareto BE, Charpy L, Langlade MJ, Suzuki T, Ohba H, Niraula M, Suzuki Y. (2008) Nitrogen fixation in coral reef environments. In: Proceedings of the 11th international coral reef symposium, Fort Lauderdale, FL, vol 2, pp 896–900Google Scholar
  46. Castillo I, Lodeiros C, Nunez M, Campos I (2001) In vitro evaluation of antibacterial substances produced by bacteria isolated from different marine organisms. Rev Biol Trop 49:1213–1222PubMedGoogle Scholar
  47. Cebrian E, Uriz MJ, Garrabou J, Ballesteros E (2011) Sponge mass mortalities in a warming Mediterranean Sea: are cyanobacteria-harboring species worse off? PLoS One 6:e20211PubMedGoogle Scholar
  48. Ceh J, van Keulen M, Bourne DG (2011) Coral-associated bacterial communities on Ningaloo Reef, Western Australia. FEMS Microbiol Ecol 75:134–144PubMedGoogle Scholar
  49. Cerrano C, Bavestrello G, Bianchi CN, Cattaneovietti R, Bava S, Morganti C et al (2000) A catstrophic mass-mortality episode of gorgonians and other organisms in the Ligurian Sea (North-Western Mediterranean), summer 1999. Ecol Lett 3:284–293Google Scholar
  50. Cervino JM, Littler MM, Littler DS, Polson S, Goreau TJ, Brooks B, Smith GW (2005) Identification of microbes associated with coralline lethal algal disease and its relationship to glacial ice melt (global warming). Phytopathology 95:120–121Google Scholar
  51. Cervino JM, Winiarski-Cervino K, Polson SW, Goreau T, Smith GW (2006) Identification of bacteria associated with a disease affecting the marine sponge Ianthella basta in New Britain, Papua New Guinea. Mar Ecol Prog Ser 324:139–150Google Scholar
  52. Charpy L (2005) Importance of photosynthetic picoplankton in coral reef ecosystems. Life Environ 55:217–223Google Scholar
  53. Charpy L, Blanchot J (1998) Photosythetic picoplankton in French Polynesian atol lagoon: estimation of taxacontribution to biomass and production by flow cytometry. Mar Ecol Prog Ser 162:57–70Google Scholar
  54. Charpy L, Blanchot J (1999) Picophytoplankton biomass, community structure and productivity in the Great Astrolabe Lagoon, Fiji. Coral Reefs 18:255–262Google Scholar
  55. Chen C-P, Tseng C-H, Chen CA, Tang S-L (2011) The dynamics of microbial partnerships in the coral Isopora palifera. ISME J 5:728–740PubMedGoogle Scholar
  56. Coles SL, Strathmann R (1973) Observations on coral mucus “flocs” and their potential trophic significance. Limnol Oceanogr 18:673–678Google Scholar
  57. Coma R, Ribes M, Gili J-M, Hughes RN (2001) The ultimate opportunists: consumers of seston. Mar Ecol Prog Ser 219:305–308Google Scholar
  58. Connell JH (1978) Diversity in tropical rain forests and coral reefs. Science 199:1302–1310PubMedGoogle Scholar
  59. Cooney RP, Pantos O, Le Tissier MD, Barer MR, O'Donnell AG, Bythell JC (2002) Characterization of the bacterial consortium associated with black band disease in coral using molecular microbiological techniques. Environ Microbiol 4:401–413PubMedGoogle Scholar
  60. Corredor JE, Wilkinson CR, Vicente VP, Morell JM, Otero E (1988) Nitrate release by Caribbean reef sponges. Limnol Oceanogr 33:114–120Google Scholar
  61. Cowart JD, Henkel TP, McMurray SE, Pawlik JR (2006) Sponge orange band (SOB): a pathogenic-like condition of the giant barrel sponge Xestospongia muta. Coral Reefs 25:513Google Scholar
  62. Crosbie ND, Furnas MJ (2001) Abundance distribution and flow-cytometric characaterization of picophytoprokaryote populations in central (17 degrees S) and southern (20 degrees S) shelf waters of the Great Barrier Reef. J Plankton Res 23:809–828Google Scholar
  63. Cullimore J, Dénarié J (2003) How legumes select their sweet talking symbionts. Science 302:575PubMedGoogle Scholar
  64. Curson ARJ, Sullivan MJ, Todd JD, Johnston AWB (2011) DddY, a periplasmic dimethysulfoniopropionate lyase found in taxonomically diverse species of Proteobacteria. ISME J 5:1191–1200PubMedGoogle Scholar
  65. Daly M, Fautin DG, Cappola VA (2003) Systematics of the Hexacorallia (Cnidaria: Anthozoa). Zoo J Linn Soc 139:419–437Google Scholar
  66. Daniels CA, Zeifman A, Heym K, Ritchie KB, Watson CA, Berzins I, Breitbart M (2011) Spatial heterogeneity of bacterial communities in the mucus of Montastraea annularis. Mar Ecol Prog Ser 426:29–40Google Scholar
  67. De Goeij JM, van Duyl FC (2007) Coral cavities are sinks of dissolved organic matter. Limnol Oceanogr 52:2608–2617Google Scholar
  68. D'Elia CF, Wiebe WJ (1990) Biogeochemical nutrient cycles in coral reef ecosystems. In: Dubinsky Z (ed) Coral reefs. Elsevier, Amsterdam, pp 49–74Google Scholar
  69. Diaz MC, Akob D, Cary CS (2004) Denaturing gradient gel electrophoresis of nitrifying microbes associated with tropical sponges. Boll Mus Ist Biol Univ Genova 68:279–289Google Scholar
  70. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM et al (2008) Functional metagenomic profiling of nine biomes. Nature 452:U628–U629Google Scholar
  71. Dubilier N, Amann R, Erséus C, Muyzer G, Park S, Giere O, Cavanaugh CM (1999) Phylogenetic diversity of bacterial endosymbionts in the gutless marine oligochete Olavius loisae (Annelida). Mar Ecol Prog Ser 178:271–280Google Scholar
  72. Ducklow HW, Mitchell R (1979) Bacterial populations and adaptations in the mucus layers on living corals. Limnol Oceanogr 24:715–725Google Scholar
  73. Ein-Gil N, Ilan M, Carmeli S, Smith GW, Pawlik JR, Yarden O (2009) Presence of Aspergillus sydowii, a pathogen of gorgonian sea fans in the marine sponge Spongia obscura. ISME J 3:752–755PubMedGoogle Scholar
  74. Fabricius KE (2005) Effects of terrestrial runoff on the ecology of corals and coral reefs: review and synthesis. Mar Pollut Bull 50:125–146PubMedGoogle Scholar
  75. Falkowski PG, Dubinsky Z, Muscatine L, McCloskey LR (1993) Population control in symbiotic corals. Bioscience 43:453–464Google Scholar
  76. Falkowski PG, Fenchel T, Delong EF (2008) The microbial engines that drive Earth’s biogeochemical cycles. Science 320:1034–1039PubMedGoogle Scholar
  77. Ferrier-Pages C, Furla P (2001) Pico- and nanoplankton biomass and production in the two largest atoll lagoons of French Polynesia. Mar Ecol Prog Ser 211:63–76Google Scholar
  78. Fieseler L, Hentschel U, Grozdanov L, Schirmer A, Wen G, Platzer M et al (2007) Widespread occurrence and genomic context of unusually small polyketide synthase genes in microbial consortia associated with marine sponges. Appl Environ Microbiol 73:2144–2155PubMedGoogle Scholar
  79. Fisher HM (1994) Genetic regulation of nitrogen fixation in rhizobia. Microbiol Rev 58:352–386Google Scholar
  80. Frias-Lopez J, Zerkle AL, Bonheyo GT, Fouke BW (2002) Partitioning of bacterial communities between seawater and healthy, black band diseased, and dead coral surfaces. Appl Environ Microbiol 68:2214–2228PubMedGoogle Scholar
  81. Frias-Lopez J, Klaus JS, Bonheyo GT, Fouke BW (2004) Bacterial community associated with black band disease in corals. Appl Environ Microbiol 70:5955–5962PubMedGoogle Scholar
  82. Fuhrman JA, Hewson I, Schwalbach MS, Steele JA, Brown MV, Naeem S (2006) Annually reoccuring bacterial communities are predicatable from ocean conditions. Proc Natl Acad Sci USA 103:13104–13109PubMedGoogle Scholar
  83. Fuhrman JA, Steele JA, Hewson I, Schwalbach MS, Brown BE, Green JL, Brown JH (2008) A latitudinal diversity gradient in planktonic marine bacteria. Proc Natl Acad Sci USA 105:7774–7778PubMedGoogle Scholar
  84. Gaidos E, Rusch A, Ilardo M (2011) Ribosomal tag pyrosequencing of DNA and RNA from benthic coral reef microbiota: community spatial structure, rare members and nitrogen-cycling guilds. Environ Microbiol 13:1138–1152PubMedGoogle Scholar
  85. Gaino E, Pronzato R, Corriero G, Buffa P (1992) Mortality of commercial sponges: incidence in two Mediterranean areas. Bolletino di Zoologia 59:79–85Google Scholar
  86. Galstoff PS (1942) Wasting disease causing mortality of sponges in the West Indies and Gulf of Mexico. In: Proceedings of the VIII American Science Congress, Washington, DC, pp 411–421Google Scholar
  87. Garnier M, Labreuche Y, Garcia C, Robert M, Nicolas JL (2007) Evidence for the involvement of pathogenic bacteria in summer mortalities of the pacific oyster Crassostrea gigas. Microbial Ecology 53:187–196PubMedGoogle Scholar
  88. Garrabou J, Coma R, Bensoussan N, Bally M, Chevaldonne P, Cigliano M et al (2009) Mass mortality in Northwestern Mediterranean rocky benthic communities: effects of the 2003 heat wave. Glob Chang Biol 15:1090–1103Google Scholar
  89. Garren M, Azam F (2010) New method for counting bacteria associated with coral mucus. Appl Environ Microbiol 76:6128–6133PubMedGoogle Scholar
  90. Garren M, Azam F (2012) New directions in coral reef microbial ecology. Environ Microbiol 14:833–844PubMedGoogle Scholar
  91. Garren M, Raymundo L, Guest J, Harvell CD, Azam F (2009) Resilience of coral-associated bacterial communities exposed to fish farm effluent. PLoS One 4:e7319PubMedGoogle Scholar
  92. Gast GJ, Jonkers PJ, van Duyl FC, Bak RPM (1999) Bacteria, flagellates and nutrients in island fringing coral reef waters: influence of the ocean, the reef and eutrophication. Bull Mar Sci 65:523–538Google Scholar
  93. Genin A, Monismith SG, Reidenbach MA, Yahel G, Koseffb JR (2009) Intense benthic grazing of phytoplankton in a coral reef. Limnol Oceanogr 54:938–951Google Scholar
  94. Giovannoni SJ, Rappe MS, Vergin KL, Adair NL (1996) 16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the green non-sulfur bacteria. Proc Natl Acad Sci USA 93:7979–7984PubMedGoogle Scholar
  95. Glas MS, Sato Y, Ulstrup KE, Bourne DG (2012) Biogeochemical conditions determine virulence of Black Band Disease in corals. ISME J 6:1526–1534PubMedGoogle Scholar
  96. Gochfeld DG, Aeby GS (2008) Antibacterial chemical defenses in Hawaiian corals provide possible protection from disease. Mar Ecol Prog Ser 362:119–128Google Scholar
  97. Gochfeld DJ, Schlöder C, Thacker RW (2007) Sponge community structure and disease prevalence on coral reefs in Bocas del Toro, Panama. In: Custódio MR, Lôbo-Hajdu G, Hajdu E, Muricy G (eds) Porifera research: biodiversity, innovation and sustainability. Museu Nacional, Rio de Janeiro, pp 335–342Google Scholar
  98. Gómez AC, Bourne DG, Hall M, Owens L, Høj L (2009) Molecular diagnosis of Vibrio harveyi in aquaculture: potential gene targets for real-time PCR detection. Aquaculture 287:1–10Google Scholar
  99. Haapkyla J, Seymour AS, Trebilco J, Smith D (2007) Coral disease prevalence and coral health in the Wakatobi Marine Park, south-east Sulawesi, Indonesia. J Mar Biol Assoc UK 87:403–414Google Scholar
  100. Harder T, Lau SCK, Dobretsov S, Fang TK, Qian P-Y (2003) A distinctive epibiotic bacterial community on the soft coral Dendronephthya sp. and antibacterial activity of coral tissue extracts suggest a chemical mechanism against bacterial epibiosis. FEMS Microbiol Ecol 43:337–347PubMedGoogle Scholar
  101. Harvell CD, Kim K, Burkholder JM, Colwell RR, Epstein PR, Grimes DJ et al (1999) Review: marine ecology - emerging marine diseases - climate links and anthropogenic factors. Science 285:1505–1510PubMedGoogle Scholar
  102. Harvell CD, Mitchell CE, Ward JR, Altizer S, Dobson AP, Ostfeld RS, Samuel MD (2002) Ecology - Climate warming and disease risks for terrestrial and marine biota. Science 296:2158–2162PubMedGoogle Scholar
  103. Hentschel U, Hopke J, Horn M, Friedrich AB, Wagner M, Hacker J, Moore BS (2002) Molecular evidence for a uniform microbial community in sponges from different oceans. Appl Environ Microbiol 68:4431–4440PubMedGoogle Scholar
  104. Hentschel U, Usher KM, Taylor MW (2006) Marine sponges as microbial fermenters FEMS Microbiol Ecol 55:167–177Google Scholar
  105. Hewson I, Fuhrman JA (2006) Spatial and vertical biogeography of coral reef sediment bacterial and diazotroph communities. Mar Ecol Prog Ser 306:79–86Google Scholar
  106. Heyward AJ, Negri AP (1999) Natural inducers for coral larval metamorphosis. Coral Reefs 18:273–279Google Scholar
  107. Hochmuth T, Piel J (2009) Polyketide synthases of bacterial symbionts in sponges – Evolution-based applications in natural products research. Phytochemistry 70:1841–1849PubMedGoogle Scholar
  108. Hoegh-Guldberg O (2004) Coral reefs and projections of future change. In: Rosenberg E, Loya Y (eds) Coral health and disease. Springer, Berlin, pp 463–484Google Scholar
  109. Hoegh-Guldberg O (2009) Climate change and coral reefs: Trojan horse or false prophecy? Coral Reefs 28:569–575Google Scholar
  110. Hoegh-Guldberg O, Mumby PJ, Hooten AJ, Steneck RS, Greenfield P, Gomez E et al (2007) Coral reefs under rapid climate change and ocean acidification. Science 318:1737–1742PubMedGoogle Scholar
  111. Hoffmann F, Larsen O, Theil V, Rapp H-T, Pape T, Michaelis W, Reitner J (2005) An anaerobic world in sponges. Geomicrobiology 22:1–10Google Scholar
  112. Hoffmann F, Radax R, Woebken D, Holtappels M, Lavik G, Rapp HT et al (2009) Complex nitrogen cycling in the sponge Geodia barretti. Environ Microbiol 11:2228–2243PubMedGoogle Scholar
  113. Hong M-J, Yu Y-T, Chen CA, Chiang P-W, Tang S-L (2009) Influence of species specificity and other factors on bacteria associated with the coral Stylophora pistillata in Taiwan. Appl Environ Microbiol 75:7797–7806PubMedGoogle Scholar
  114. Hooper JNA, Van Soest RWM (2002) Systema Porifera: a guide to the classification of sponges. Kluwer Academic / Plenum Publishers, New YorkGoogle Scholar
  115. Hovland M (2008) Deep-water coral reefs: unique Biodiversity hotspots. Praxis Publishing (Springer), ChichesterGoogle Scholar
  116. Hughes TP (1994) Catastrophies, phase shifts and large-scale degradation of a Caribbean coral reef. Science 263:1547–1551Google Scholar
  117. Hughes TP, Baird AH, Bellwood DR, Card M, Connolly SR, Folke C et al (2003) Climate change, human impacts, and the resilience of coral reefs. Science 301:929–933PubMedGoogle Scholar
  118. Jetten MSM (2008) The microbial nitrogen cycle. Environ Microbiol 10:2903–2909PubMedGoogle Scholar
  119. Jimenez E, Ribes M (2007) Sponges as a source of dissolved inorganic nitrogen: nitrification mediated by temperate sponges. Limnol Oceanogr 52:948–958Google Scholar
  120. Jones RJ, Hoegh-Guldberg O, Larkum AWD, Schreiber U (1998) Temperature-induced bleaching of corals begins with impairment of the CO2 fixation mechanism in zooxanthellae. Plant Cell Physiol 21:1219–1230Google Scholar
  121. Kamke J, Taylor MW, Schmitt S (2010) Activity profiles for marine sponge-associated bacteria obtained by 16S rRNA vs 16S rRNA gene comparisons. ISME J 4:498–508PubMedGoogle Scholar
  122. Kelman D, Kashman Y, Rosenberg E, Kushmaro A, Loya Y (2006) Antimicrobial activity of Red Sea corals. Mar Biol 149:357–363Google Scholar
  123. Kim K (1994) Antimicrobial activity in Gorgonian corals (Coelenterata, Octocorallia). Coral Reefs 13:75–80Google Scholar
  124. Kim K, Harvell CD (2004) The rise and fall of a six-year coral-fungal epizootic. Am Nat 164:S52–S63PubMedGoogle Scholar
  125. Kimes NE, Van Nostrand JD, Weil E, Zhou J, Morris PJ (2010) Microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased colonies. Environ Microbiol 12:541–556PubMedGoogle Scholar
  126. Kimes NE, Grim CJ, Johnson WR, Hasan NA, Tall BD, Kothary MH, et al (2012) Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus. ISME J 6:835–846Google Scholar
  127. Kirkwood M, Todd JD, Rypien KL, Johnston AWB (2010) The opportunistic coral pathogen Aspergillus sydowii contains dddP and makes dimethyl sulfide from dimethylsulfoniopropionate. ISME J 4:147–150PubMedGoogle Scholar
  128. Kleypas JA, Langdon CI (2006) Coral reefs and changing seawater chemistry. In: Phinney JT, Hoegh-Guldberg O, Kleypas J, Skirving W, Strong A (eds) Coral reefs and climate change: science and management. American Geophysical Union, Washington, DC, pp 73–110Google Scholar
  129. Kline DI, Kuntz NM, Breitbart M, Knowlton N, Rohwer F (2006) Role of elevated organic carbon levels and microbial activity in coral mortality. Mar Ecol Prog Ser 314:119–125Google Scholar
  130. Klussmann-Kolb A, Brodie GD (1999) Internal storage and production of symbiotic bacteria in the reproductive system of a tropical marine gastropod. Mar Biol 133:443–447Google Scholar
  131. Knowlton N, Rohwer F (2003) Multispecies microbial mutualisms on coral reefs: the host as a habitat. Am Nat 162:S51–S62PubMedGoogle Scholar
  132. Koh EGL (1997) Do Scleractinian corals engage in chemical warfare against microbes? J Chem Ecol 23:379–398Google Scholar
  133. Koren O, Rosenberg E (2006) Bacteria associated with mucus and tissues of the coral Oculina patagonica in summer and winter. Appl Environ Microbiol 72:5254–5259PubMedGoogle Scholar
  134. Krueger DM, Cavanaugh CM (1997) Phylogenetic diversity of bacterial symbionts of Solemya hosts based on comparative sequence analysis of 16S rRNA genes. Appl Environ Microbiol 63:91–98PubMedGoogle Scholar
  135. Kuta KG, Richardson LL (1997) Black band disease and the fate of diseased coral colonies in the Florida Keys. In: Proceedings of the 8th international coral reef symposium, Panama, vol 1, pp 575–578Google Scholar
  136. Kvennefors E, Roff G (2009) Evidence of cyanobacteria-like endosymbionts in Acroporid corals from the Great Barrier Reef. Coral Reefs 28:547Google Scholar
  137. Lafferty KD, Porter JW, Ford SE (2004) Are diseases increasing in the ocean? Annu Rev Ecol Evol Syst 35:31–54Google Scholar
  138. Lafi FF, Fuerst JA, Fieseler L, Hentschel U (2009) Widespread distribution of Poribacteria in Demospongiae. Appl Environ Microbiol 75:5695–5699PubMedGoogle Scholar
  139. Lalli CM, Parsons TR (1995) Biological oceanography: an introduction. Butterworth-Heinemann Ltd., Oxford, UKGoogle Scholar
  140. Lavilla-Pitogo CR, Leaño EM, Paner MG (1998) Mortalities of pond-cultured juvenile shrimp, Penaeus monodon, associated with dominance of luminescent vibrios in the rearing environment. Aquaculture 164:337–349Google Scholar
  141. Lechene CP, Luyten Y, McMahon G, Distel DL (2007) Quantitative imaging of nitrogen fixation by individual bacteria within animal cells. Science 317:1563–1566PubMedGoogle Scholar
  142. Lee OO, Wang Y, Yang J, Lafi FF, Al-Suwailem A, Qian P-Y (2011) Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea. ISME J. doi:10.1038/ismej.2010.165Google Scholar
  143. Leggat W, Hoegh-Guldberg O, Dove S, Yellowlees D (2007) Analysis of an EST library from the dinoflagellate (Symbiodinium sp.) symbiont of reef-building corals. J Phycol 43:1010–1021Google Scholar
  144. Lema KA, Willis BL, Bourne DG (2012) Coral form specific associations with diazotrophic bacteria. FEMS Microb Ecol (in press)Google Scholar
  145. Lemoine N, Buell N, Hill A, Hill M (2007) Assessing the utility of sponge microbial symbiont communities as models to study global climate change: a case study with Halichondria bowerbanki. In: Custódio MR, Lôbo-Hajdu G, Hajdu E, Muricy G (eds) Porifera research: biodiversity, innovation and sustainability. Série Livros, Museu Nacional, Rio de Janeiro, pp 419–425Google Scholar
  146. Lesser MP, Blakemore RP (1990) Description of a novel symbiotic bacterium from the brittle star, Amphipholis squamata. Appl Environ Microbiol 56:2436–2440PubMedGoogle Scholar
  147. Lesser MP, Walker CW (1992) Comparative study of the uptake of dissolved amino acids in sympatric brittle stars with and without endosymbiotic bacteria. Comp Biochem Physiol 101B:217–223Google Scholar
  148. Lesser MP, Mazel CH, Gorbunov MY, Falkowski PG (2004) Discovery of symbiotic nitrogen-fixing cyanobacteria in corals. Science 305:997–1000PubMedGoogle Scholar
  149. Lesser MP, Falcon LI, Rodriguez-Roman A, Enriquez S, Hoegh-Guldberg O, Iglesias- Prieto R (2007) Nitrogen fixation by symbiotic cyanobactieria provides a source of nitrogen for the scleractinian coral Montastraea cavernosa. Mar Ecol Prog Ser 347:143–152Google Scholar
  150. Lessios HA (1998) Mass mortality of Diadema antillarum in Teh Caribbean: what have we learned? Ann Rev Ecol Syst 19:371–393Google Scholar
  151. Lessios HA, Garrido MJ, Kessing BD (2001) Demographic history of Diadema antillarum, a keystone herbivore on Caribbean reefs. Proc Roy Soc B: Biol Sci 268:2347–2353Google Scholar
  152. Lessios HA, Cubit JD, Robertson DR, Shulman MJ, Parker MR, Garrity SD, Levings SC (1984) Mass mortality of Diadema antillarum on the Caibbean coast of Panama. Coral Reefs 3:173–182Google Scholar
  153. Levinton JS (1995) Marine biology: function, biodiversity, ecology. Oxford University Press, New YorkGoogle Scholar
  154. Linares C, Coma R, Garrabou J, Díaz D, Cabala M (2008) Size distribution, density and disturbance in two Mediterranean gorgonians: Paramuricea clavata and Eunicella singularis. J Appl Ecol 45:688–699Google Scholar
  155. Linley EAS, Koop K (1986) Significance of pelagic bacteria as a trophic resource in a coral reef lagoon, One Tree Island, Great Barrier Reef. Mar Biol 92:457–464Google Scholar
  156. Littler M, Littler D (1995) Impact of CLOD pathogen on Pacific coral reefs. Science 267:1356–1360PubMedGoogle Scholar
  157. Littler M, Littler D (1998) An undescribed fungal pathogen of reef-forming crustose coralline algae discovered in American Samoa. Coral Reefs 17:144Google Scholar
  158. Littman R, Willis BL, Bourne DG (2011) Metagenomic analysis of the coral holobiont during a natural bleaching event on the Great Barrier Reef. Environ Microbiol Rep 3:651–660Google Scholar
  159. Littman RA, Willis BL, Pfeffer C, Bourne DG (2009) Diversities of coral-associated bacteria differ with location, but not species, for three acroporid corals on the Great Barrier Reef. FEMS Microbiol Ecol 68:152–163PubMedGoogle Scholar
  160. Liu MY, Kjelleberg S, Thomas T (2010) Functional genomic analysis of an uncultured delta-proteobacterium in the sponge Cymbastela concentrica. ISME J 5:427–435PubMedGoogle Scholar
  161. López-Legentil S, Song B, McMurray SE, Pawlik JR (2008) Bleaching and stress in coral reef ecosystems: hsp70 expression by the giant barrel sponge Xestospongia muta. Mol Ecol 17:1840–1849PubMedGoogle Scholar
  162. López-Legentil S, Erwin PE, Pawlik JR, Song B (2010) Effects of sponge bleaching on ammonia-oxidizing Archaea: distribution and relative expression of ammonia monoxygenase genes associated with the giant barrel sponge Xestospongia muta. Microb Ecol 60:561–571PubMedGoogle Scholar
  163. Luter HM, Whalan S, Webster NS (2010a) Prevalence of tissue necrosis and brown spot lesions in a common marine sponge. Mar Freshw Res 61:481–484Google Scholar
  164. Luter HM, Whalan S, Webster NS (2010b) Exploring the role of microorganisms in the disease-like syndrome affecting the sponge Ianthella basta. Appl Environ Microbiol 76:5736–5744PubMedGoogle Scholar
  165. Maldonado M, Sánchez-Tocino L, Navarro C (2010) Recurrent disease outbreaks in corneous demosponges of the genus Ircinia: epidemic incidence and defense mechanisms. Mar Biol 157:1577–1590Google Scholar
  166. Mayer FW, Wild C (2010) Corl mucus release and following particle trapping contribute to rapid nutrient recycling in a Northern Red Sea fringing reef. Mar Freshw Res 61:1006–1014Google Scholar
  167. McMurray SE, Henkel TP, Pawlik JR (2010) Demographics of increasing populations of the giant barrel sponge Xestospongia muta in the Florida Keys. Ecology 91:560–570PubMedGoogle Scholar
  168. Meikle P, Richards GN, Yellowlees D (1988) Structural investigations on the mucus from 6 species of coral. Mar Biol 99:187–193Google Scholar
  169. Meron D, Atias E, Iasur Kruh L, Elifantz H, Minz D, Fine M, Banin E (2011) The impact of reduced pH on the microbial community of the coral Acropora eurystoma. ISME J 5:51–60PubMedGoogle Scholar
  170. Meyer B, Kuever J (2008) Phylogenetic diversity and spatial distribution of the microbial community associated with the Caribbean deep-water sponge Polymastia cf. corticata by 16S rRNA, aprA, and amoA gene analysis. Microbial Ecol 56:306–321Google Scholar
  171. Mohamed NM, Saito K, Tal Y, Hill RT (2010) Diversity of aerobic and anaerobic ammonia-oxidizing bacteria in marine sponges. ISME J 4:38–48PubMedGoogle Scholar
  172. Mohamed NM, Enticknap JJ, Lohr JE, McIntosh SM, Hill RT (2008) Changes in bacterial communities of the marine sponge Mycale laxissima on transfer into aquaculture. Appl Environ Microbiol 74:1209–1222PubMedGoogle Scholar
  173. Morse ANC, Iwao K, Baba M, Shimoike K, Hayashibara T, Omori M (1996) An ancient chemosensory mechanism brings new life to coral reefs. Biol Bull 191:149–154Google Scholar
  174. Mouchka ME, Hewson I, Harvell DC (2010) Coral-associated bacterial assemblages: current knowledge and the potential for climate-driven impacts. Intergr Comp Biol 50:662–674Google Scholar
  175. Mukherjee J, Webster NS, Llewellyn LE (2009) Purification and characterization of a collagenolytic enzyme from a pathogen of the Great Barrier Reef sponge Rhopaloeides odorabile. PLoS One 4:e7177PubMedGoogle Scholar
  176. Negandhi K, Blackwelder PL, Ereskovsky AV, Lopez JV (2010) Florida reef sponges harbor coral disease-associated microbes. Symbiosis 51:117–129Google Scholar
  177. Negri AP, Webster NS, Hill RT, Heyward AJ (2001) Metamorphosis of broadcast spawning corals in response to bacteria isolated from crustose algae. Mar Ecol Prog Ser 223:121–131Google Scholar
  178. Nelson CE, Alldredge AL, McCliment EA, Amaral-Zettler LA, Carlson CA (2011) Depleted dissolved organic carbon and distinct bacterial communities in the water column of a rapid-flushing coral reef ecosystem. ISME J 5:1374–1387PubMedGoogle Scholar
  179. Off S, Alawi M, Spieck E (2010) Enrichment and physiological characterization of a novel Nitrospira-like bacterium obtained from a marine sponge. Appl Environ Microbiol 76:4640–4646PubMedGoogle Scholar
  180. Olson JB, Kellogg CA (2010) Microbial ecology of corals, sponges and algae in mesophotic coral environments. FEMS Microbiol Ecol 73:17–30PubMedGoogle Scholar
  181. Olson JB, Gochfeld DJ, Slattery M (2006) Aplysina red band syndrome: a new threat to Caribbean sponges. Dis Aquat Organ 71:163–168PubMedGoogle Scholar
  182. Olson ND, Ainsworth TD, Gates RD, Takabayashi M (2009) Diazotrophic bacteria associated with Hawaiian montipora corals: diversity and abundance in correlation with symbiotic dinoflagellates. J Exper Mar Biol Ecol 371:140–146Google Scholar
  183. Pantos O, Bythell JC (2006) Bacterial community structure associated with white band disease in the elkhorn coral Acropora palmata determined using culture independent 16S rRNA techniques. Dis Aquat Organ 69:79–88PubMedGoogle Scholar
  184. Pantos O, Cooney RP, Le Tissier MDA, Barer MR, O'Donnell AG, Bythell JC (2003) The bacterial ecology of a plague-like disease affecting the Caribbean coral Montastrea annularis. Environ Microbiol 5:370–382PubMedGoogle Scholar
  185. Partensky F, Blanchot J, Vaulot D (1999) Differential distribution and ecology of Prochlorococcus and Synechococcus in oceanic waters: a review. In Charpy L, Larkum AWD (eds) Marine cyanobacteria. Bulletin de l’Institut Oce´anographique, Monaco, pp 457–475Google Scholar
  186. Patten NL, Mitchell JG, Middelboe M, Eyre BD, Seuront L, Harrison PL, Glud RN (2008) Bacterial and viral dynamics during a mass coral spawning period on the Great Barrier Reef. Aquat Microb Ecol 50:209–220Google Scholar
  187. Patterson KL, Porter JW, Ritchie KE, Polson SW, Mueller E, Peters EC et al (2002) The etiology of white pox, a lethal disease of the Caribbean elkhorn coral, Acropora palmata. Proc Natl Acad Sci U S A 99:8725–8730PubMedGoogle Scholar
  188. Pawlik JR (2011) The chemical ecology of sponges on Caribbean reefs: natural products shape natural systems. Bioscience 61:888–898Google Scholar
  189. Piel J (2009) Metabolites from symbiotic bacteria. Nat Prod Rep 26:338–362PubMedGoogle Scholar
  190. Pollock FJ, Morris PJ, Willis BL, Bourne DG (2011) The urgent need for robust coral disease diagnostics. PLoS Pathog 7:e1002183PubMedGoogle Scholar
  191. Pollock FJ, Wilson B, Johnson WR, Morris PJ, Willis BL, Bourne DG (2010) Phylogeny of the coral pathogen Vibrio coralliilyticus. Environ Microbiol Rep 2:172–178Google Scholar
  192. Porter JW, Dustan P, Jaap WC, Patterson KL, Kosmynin V, Meier OW et al (2001) Patterns of spread of coral disease in the Florida Keys. Hydrobiologia 460:1–24Google Scholar
  193. Rabus R, Fukui M, Wilkes H, Widdle F (1996) Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulfate-reducing bacteria in an anaerobic enrichment culture utilizing alkylbenzenes from crude oil. Appl Environ Microbiol 62:3605–3613PubMedGoogle Scholar
  194. Raina J-B, Tapiolas D, Willis BL, Bourne DG (2009) Coral-associated bacteria and their role in the biogeochemical cycling of sulfur. Appl Environ Microbiol 75:3492–3501PubMedGoogle Scholar
  195. Raina J-B, Dinsdale E, Willis BL, Bourne DG (2010) Do organic sulphur compounds DMSP and DMS drive coral microbial associations? Trends Microbiol 18:101–108PubMedGoogle Scholar
  196. Rath H, Schiller C, Herndl GJ (1993) Ectoenzymatic activity and bacterial dynamics along a trophic gradient in the Caribbean Sea. Mar Ecol Prog Ser 102:89–96Google Scholar
  197. Reshef L, Koren O, Loya Y, Zilber-Rosenberg I, Rosenberg E (2006) The coral probiotic hypothesis. Environ Microbiol 8:2068–2073PubMedGoogle Scholar
  198. Richardson LL (1997) Occurrence of the black band disease cyanobacterium on healthy corals of the Florida Keys. Bull Mar Sci 61:485–490Google Scholar
  199. Richardson LL (2004) Black band disease. In: Rosenberg E, Loya Y (eds) Coral health and disease. Springer, Berlin, pp 325–336Google Scholar
  200. Ritchie KB (2006) Regulation of microbial populations by coral surface mucus and mucus-associated bacteria. Mar Ecol Prog Ser 322:1–14Google Scholar
  201. Rogers AD (1999) The biology of Lophelia pertusa (Linnaeus 1758) and other deep-water reef-forming corals and impacts from human activities. Int Rev Hydrobiol 84:315–406Google Scholar
  202. Rohwer F, Seguritan V, Azam F, Knowlton N (2002) Diversity and distribution of coral-associated bacteria. Mar Ecol Prog Ser 243:1–10Google Scholar
  203. Rohwer F, Breitbart M, Jara J, Azam F, Knowlton N (2001) Diversity of bacteria associated with the Caribbean coral Montastraea franksi. Coral Reefs 20:85–91Google Scholar
  204. Rosenberg E, Kellogg CA, Rohwer F (2007a) Coral microbiology. Oceanography 20:146–154Google Scholar
  205. Rosenberg E, Koren O, Reshef L, Efrony R, Zilber-Rosenberg I (2007b) The role of microorganisms in coral health, disease and evolution. Nat Rev 5:355–362Google Scholar
  206. Rusch A, Hannides AK, Gaidos E (2009) Diverse communities of active Bacteria and Archaea along oxygen gradients in coral reef sediments. Coral Reefs 28:15–26Google Scholar
  207. Rypien KL, Ward JR, Azam F (2010) Antagonistic interactions among coral-associated bacteria. Environ Microbiol 12:28–39PubMedGoogle Scholar
  208. Sakka A, Legendre L, Gosselin M, Niquil N, Delesalle B (2002) Carbon budget of the planktonic food web in an atoll lagoon (Takapoto, French Polynesia). J Plankton Res 24:301–320Google Scholar
  209. Santos E, Alves N, Dias G, Mazotto AM, Vermelho A, Vora G et al (2011) Genomics and proteomics of the coral pathogen Vibrio coralliilyticus reveal a vast virulence repertoire. ISME J 5:1471–1483Google Scholar
  210. Sato Y, Willis BL, Bourne DG (2010) Successional changes in bacterial communities during the development of black band disease on the reef coral, Montipora hispida. ISME J 4:203–214PubMedGoogle Scholar
  211. Schläppy M-L, Schöttner S, Lavik G, Kuypers M, de Beer D, Hoffmann F (2010) Evidence of nitrification and denitrification in high and low microbial abundance sponges. Mar Biol 157:593–602Google Scholar
  212. Schmidt EW, Obraztsova AY, Davidson SK, Faulkner DJ, Haygood MG (2000) Identification of the antifungal peptide-containing symbiont of the marine sponge Theonella swinhoei as a novel delta-proteobacterium, “Candidatus Entotheonella palauensis”. Mar Biol 136:969–977Google Scholar
  213. Schmitt S, Angermeier H, Schiller R, Lindquist N, Hentschel U (2008) Molecular microbial diversity survey of sponge reproductive stages and mechanistic insights into vertical transmission of microbial symbionts. Appl Environ Microbiol 74:7694–7708PubMedGoogle Scholar
  214. Schmitt S, Tsai P, Bell J, Fromont J, Ilan M, Lindquist N et al (2011) Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges. ISME J 6:564–576PubMedGoogle Scholar
  215. Sebens K (1994) Biodiversity of coral reefs: what are we losing and why? Amer Zool 34:115–133Google Scholar
  216. Selvin J, Shanmugha Priya S, Seghal Kiran G, Thangavelu T, Sapna Bai N (2007) Sponge-associated marine bacteria as indicators of heavy metal pollution. Microbiol Res 164:352–363PubMedGoogle Scholar
  217. Seymour JR, Patten N, Bourne DG, Mitchell JG (2005) Spatial dynamics of virus-like particles and heterotrophic bacteria within a shallow coral reef system. Mar Ecol Prog Ser 288:1–8Google Scholar
  218. Shashar N, Feldstein T, Cohen Y, Loya Y (1994a) Nitrogen fixation (acetylene reduction) on a coral reef. Coral Reefs 13:171–174Google Scholar
  219. Shashar N, Cohen Y, Loya Y, Sar N (1994b) Nitrogen fixation (acetylene reduction) in stony corals: evidence for coral-bacteria interactions. Mar Ecol Prog Ser 111:259–264Google Scholar
  220. Shields JD (2011) Diseases of spiny lobsters: a review. J Invertebr Pathol 106:79–91PubMedGoogle Scholar
  221. Siboni N, Ben-Dov E, Sivan A, Kushmaro A (2008) Global distribution and diversity of coral-associated Archaea and their possible role in the coral holobiont nitrogen cycle. Environ Microbiol 10:2979–2990PubMedGoogle Scholar
  222. Siegl A, Hentschel U (2010) PKS and NRPS gene clusters from microbial symbiont cells of marine sponges by whole genome amplification. Environ Microbiol Rep 2:507–513Google Scholar
  223. Siegl A, Kamke J, Hochmuth T, Piel J, Richter M, Liang C et al (2011) Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J 5:61–70PubMedGoogle Scholar
  224. Simister RL, Deines P, Botté ES, Webster NS, Taylor MW (2012) Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms. Environ Microbiol 14:517–524PubMedGoogle Scholar
  225. Smith JE, Shaw M, Edwards RA, Obura D, Pantos O, Sala E et al (2006) Indirect effects of algae on coral: algae-mediated, microbe-induced coral mortality. Ecol Lett 9:835–845PubMedGoogle Scholar
  226. Southwell MW, Popp BN, Martens CS (2008a) Nitrification controls on fluxes and isotopic composition of nitrate from Florida Keys sponges. Mar Chem 108:96–108Google Scholar
  227. Southwell MW, Weisz J, Martens CS, Lindquist N (2008b) In situ fluxes of dissolved inorganic nitrogen from the sponge community on Conch Reef, Key Largo, Florida. Limnol Oceanogr 53:986–996Google Scholar
  228. Stambler N (2011) Zooxanthellae: the yellow symbionts inside animals. In: Dubinsky A, Stambler N (eds) Coral reefs: an ecosystem in transition Part 3. Springer, Netherlands, pp 87–106Google Scholar
  229. Steger D, Ettinger-Epstein P, Whalan S, Hentschel U, de Nys R, Wagner M, Taylor MW (2008) Diversity and mode of transmission of ammonia-oxidizing archaea in marine sponges. Environ Microbiol 10:1087–1094PubMedGoogle Scholar
  230. Stockner JG (1988) Phototrophic picoplankton: an overview from marine and freshwater ecosystems. Limnol Oceanogr 33:765–775Google Scholar
  231. Sugumar G, Nakai T, Hirata Y, Matsubara D, Muroga K (1998) Vibrio splendidus biovar II as the causative agent of bacillary necrosis of Japanese oyster Crassostrea gigas larvae. Dis Aquat Organ 33:111–118PubMedGoogle Scholar
  232. Sumich JL, Morrissey JF (2004) An introduction to the biology of marine life. Jones and Bartlett, Sudbury, MAGoogle Scholar
  233. Sunagawa S, Woodley CM, Medina M (2010) Threatened corals provide underexplored microbial habitats. PLoS One 5:e9554PubMedGoogle Scholar
  234. Sunagawa S, DeSantis TZ, Piceno YM, Brodie EL, DeSalvo MK, Voolstra CR et al (2009) Bacterial diversity and white plague disease-associated community changes in the Caribbean coral Montastraea faveolata. ISME J 3:512–521PubMedGoogle Scholar
  235. Sussman M, Willis BL, Victor S, Bourne DG (2008) Coral pathogens indentified for White Syndrome (WS) epizootics in the Indo-Pacific. PLoS One 3:e2393PubMedGoogle Scholar
  236. Sussman M, Mieog JC, Doyle J, Victor S, Willis BL, Bourne DG (2009) Vibrio zinc-metalloprotease causes photoinactivation of coral endosymbionts and coral tissue lesions. PLoS One 4:e4511PubMedGoogle Scholar
  237. Sutherland KP, Porter JW, Torres C (2004) Disease and immunity in Caribbean and Indo-Pacific zooxanthellate corals. Mar Ecol Prog Ser 266:273–302Google Scholar
  238. Sutherland KP, Shaban S, Joyner JL, Porter JW, Lipp EK (2011) Human pathogen shown to cause disease in the threatened Eklhorn coral Acropora palmata. PLoS One 6:e23468PubMedGoogle Scholar
  239. Sutherland KP, Porter JW, Turner JW, Thomas BJ, Looney EE, Luna TP et al (2010) Human sewage identified as likely source of white pox disease of the threatened Caribbean elkhorn coral, Acropora palmata. Environ Microbiol 12:1122–1131PubMedGoogle Scholar
  240. Sweatman H, Delean S, Syms C (2011) Assessing loss of coral cover on Australia’s Great Barrier Reef over two decades, with implications for longer-term trends. Coral Reefs 30:521–531Google Scholar
  241. Sweet MJ, Croquer A, Bythell JC (2011) Bacterial assemblages differ between compartments within the coral holobiont. Coral Reefs 30:39–52Google Scholar
  242. Taylor MW, Thacker RW, Hentschel U (2007a) Genetics. Evolutionary insights from sponges. Science 316:1854–1855PubMedGoogle Scholar
  243. Taylor MW, Radax R, Steger D, Wagner M (2007b) Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol Mol Biol Rev 71:295–347PubMedGoogle Scholar
  244. Thomas T, Rusch D, DeMaere MZ, Yung PY, Lewis M, Halpern A et al (2010) Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis. ISME J 4:1557–1567PubMedGoogle Scholar
  245. Todd JD, Kirkwood M, Newton-Payne S, Johnston AWB (2012) DddW, a third DMSP lyase in a model Roseobacter marine bacterium, Ruegeria pomeroyi DSS-3. ISME J 6:223–226Google Scholar
  246. Toledo-Hernandez C, Zuluaga-Montero A, Bones-Gonzalez A, Rodriguez JA, Sabat AM, Bayman P (2008) Fungi in healthy and diseased sea fans (Gorgonia ventalina): is Aspergillus sydowii always the pathogen? Coral Reefs 27:707–714Google Scholar
  247. Torréton J-P, Dufour P (1996) Temporal and spatial stability of bacterioplankton biomass and productivity in an atoll lagoon. Aquat Microb Ecol 11:251–261Google Scholar
  248. Torréton J-P, Pagès J, Talbot V (2002) Relationship between bacterioplankton and phytoplankton biomass, production and turnover rate in Tuamotu atoll lagoons. Aquat Microb Ecol 28:267–277Google Scholar
  249. Torréton J-P, Rochelle-Newall E, Jouon A, Faure V, Jacquet S, Douillet P (2007) Correspondence between the distribution of hydrodynamic time parameters and the distribution of biological and chemical variables in a semi-enclosed coral reef lagoon. Estuar Coast Shelf Sci 74:766–776Google Scholar
  250. Unson MD, Holland ND, Faulkner DJ (1994) A brominated secondary metabolite synthesized by the cyanobacterial symbiont of a marine sponge and accumulation of the crystalline metabolite in the sponge tissue. Mar Biol 119:1–11Google Scholar
  251. Uthicke S, McGuire K (2007) Bacterial communities in great barrier reef calcareous sediments: contrasting 16S rDNA libraries from nearshore and outer shelf reefs. Estuar Coast Shelf Sci 72:188–200Google Scholar
  252. Vacelet J, Fiala-Médioni A, Fisher CR, Boury-Esnault N (1996) Symbiosis between methane-oxidizing bacteria and a deep-sea carnivorous cladorhizid sponge. Mar Ecol Prog Ser 145:77–85Google Scholar
  253. Van Alstyne K, Schupp P, Slattery M (2006) The distribution of dimethylsulfoniopropionate in tropical Pacific coral reef invertebrates. Coral Reefs 25:321–327Google Scholar
  254. van Duyl F, Gast G, Steinhoff W, Kloff S, Veldhuis M, Bak R (2002) Factors influencing the short-term variation in phytoplankton composition and biomass in coral reef waters. Coral Reefs 21:293–306Google Scholar
  255. van Duyl FC, Gast GJ (2001) Linkage of small-scale spatial variations in DOC, inorganic nutrients and bacterioplankton growth with different coral reef water types. Aquat Microb Ecol 24:17–26Google Scholar
  256. Van Duyl FC, Scheffers SR, Thomas FIM, Driscoll M (2006) The effect of water exchange on bacterioplankton depletion and inorganic nutrient fluxes in coral cavities. Coral Reefs 25:23–36Google Scholar
  257. Vargas-Angel B (2010) Crustose coralline algal diseases in the U.S.-Affiliated Pacific Islands. Coral Reefs 29:943–956Google Scholar
  258. Vega Thurber RLV, Barott KL, Hall D, Liu H, Rodriguez-Mueller B, Desnues C et al (2008) Metagenomic analysis indicates that stressors induce production of herpeslike viruses in the coral Porites compressa. Proc Nat Acad Sci USA 105:18413–18418PubMedGoogle Scholar
  259. Vezzuli L, Previati M, Pruzzo C, Marchese A, Bourne DG, Cerrano C (2010) Vibrio infection triggering mass mortality events in a warming Mediterranean Sea. Environ Microbiol 12:2007–2019Google Scholar
  260. Vezzulli L, Brettar I, Pezzati E, Reid PC, Colwell RR, Höfle MG, Pruzzo C (2012) Long-term effects of ocean warming on the prokaryotic community: evidence from the vibrios. ISME J 6:21–30Google Scholar
  261. Vicente VP (1989) Regional commercial sponge extinction in the West Indies: are recent climatic changes responsible? Mar Ecol Prog Ser 10:179–191Google Scholar
  262. Vidal-Dupiol J, Ladrière O, Meistertzheim A-L, Fouré L, Adjeroud M, Mitta G (2011) Physiological responses of the scleractinian coral Pocillopora damicornis to bacterial stress from Vibrio coralliilyticus. Journal of Experimental Biology and Ecology 214:1533–1545Google Scholar
  263. Viehman S, Mills DK, Meichel GW, Richardson LL (2006) Culture and identification of Desulfovibrio spp. from corals infected by black band disease on Dominican and Florida Keys reefs. Dis Aquat Organ 69:119–127PubMedGoogle Scholar
  264. Vila-Costa M, Rinta-Kanto JM, Sun S, Sharma S, Porestsky R, Moran MA (2010) Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate. ISME J 4:1410–1420PubMedGoogle Scholar
  265. Vizcaino MI, Johnson WR, Kimes NE, Williams K, Torralba M, Nelson KE et al (2010) Antimicrobial resistance of the coral pathogen Vibrio coralliilyticus and Caribbean sister phylotypes isolated from a diseased octocoral. Microb Ecol 59:646–657PubMedGoogle Scholar
  266. Vogel G (2008) The inner lives of sponges. Science 320:1028–1030PubMedGoogle Scholar
  267. Walker CW, Lesser MP (1989) Nutrition and development of brooded embryos in the brittlestar Amphipholis squamata: do endosymbiotic bacteria play a role? Mar Biol 103:519–530Google Scholar
  268. Webster NS (2007) Sponge disease: a global threat? Environ Microbiol 9:1363–1375PubMedGoogle Scholar
  269. Webster NS, Blackall LL (2009) What do we really know about sponge- microbial symbioses? ISME J 3:1–3PubMedGoogle Scholar
  270. Webster NS, Taylor MW (2012) Marine sponges and their microbial symbionts: love and other relationships. Environ Microbiol 14:335–346PubMedGoogle Scholar
  271. Webster NS, Watts JE, Hill RT (2001a) Detection and phylogenetic analysis of novel crenarchaeote and euryarchaeote 16S ribosomal RNA gene sequences from a Great Barrier Reef sponge. Marine Biotechnol 3:600–608Google Scholar
  272. Webster NS, Cobb RE, Negri AP (2008a) Temperature thresholds for bacterial symbiosis with a sponge. ISME J 2:830–842PubMedGoogle Scholar
  273. Webster NS, Negri AP, Webb RI, Hill RT (2002) A spongin-boring alpha proteobacterium is the etiological agent of disease in the Great Barrier Reef sponge, Rhopaloeides odorabile. Mar Ecol Prog Ser 232:305–309Google Scholar
  274. Webster NS, Botté ES, Soo RM, Whalan S (2011a) The larval sponge holobiont exhibits high thermal tolerance. Environ Microbiol Rep 3:756–762Google Scholar
  275. Webster NS, Soo R, Cobb R, Negri AP (2011b) Elevated seawater temperature causes a microbial shift on crustose coralline algae with implications for the recruitment of coral larvae. ISME J 5:759–770PubMedGoogle Scholar
  276. Webster NS, Webb RI, Ridd MJ, Hill RT, Negri AP (2001b) The effects of copper on the microbial community of a coral reef sponge. Environ Microbiol 3:19–31PubMedGoogle Scholar
  277. Webster NS, Xavier JR, Freckelton M, Motti CA, Cobb R (2008b) Shifts in microbial and chemical patterns within the marine sponge Aplysina aerophoba during a disease outbreak. Environ Microbiol 10:3366–3376PubMedGoogle Scholar
  278. Webster NS, Smith LD, Heyward AJ, Watts JE, Webb RI, Blackall LL, Negri AP (2004) Metamorphosis of a scleractinian coral in response to microbial biofilms. Appl Environ Microbiol 70:1213–1221PubMedGoogle Scholar
  279. Webster NS, Taylor MW, Behnam F, Lücker S, Rattei T, Whalan S et al (2010) Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts. Environ Microbiol 12:2070–2082PubMedGoogle Scholar
  280. Wegley L, Edwards RA, Rodriguez-Brito B, Liu H, Rohwer F (2007) Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ Microbiol 9:2707–2719PubMedGoogle Scholar
  281. Weil E (2004) Coral diseases in the wider Caribbean. In: Rosenberg E, Loya Y (eds) Coral health and disease. Springer-Verlag, Berlin, pp 35–68Google Scholar
  282. Weil E, Smith G, Gil-Agudelo DL (2006) Status and progress in coral reef disease research. Dis Aquat Organ 69:1–7PubMedGoogle Scholar
  283. Weinbauer MG, Kerros ME, Motegi C, Wilhartitz IC, Rassoulzadegan F, Torréton J-P et al (2010) Bacterial community composition and potential controlling mechanisms along a trophic gradient in a barrier reef system. Aquat Microb Ecol 60:15–28Google Scholar
  284. Weisz J, Hentschel U, Lindquist N, Martens C (2007) Linking abundance and diversity of sponge-associated microbial communities to metabolic differences in host sponges. Mar Biol 152:475–483Google Scholar
  285. Wild C, Woyt H, Huettel M (2005) Influence of coral mucus on nutrient fluxes in carbonate sands. Mar Ecol Prog Ser 287:87–98Google Scholar
  286. Wild C, Laforsch C, Huettel M (2006) Detection and enumeration of microbial cells within highly porous calcareous reef sands. Mar Freshw Res 57:415–420Google Scholar
  287. Wild C, Huettel M, Klueter A, Kremb SG, Rasheed MYM, Jorgensen BB (2004a) Coral mucus functions as an energy carrier and particle trap in the reef ecosystem. Nature 428:66–70PubMedGoogle Scholar
  288. Wild C, Rasheed MYM, Werner U, Franke U, Johnstone R, Huettel M (2004b) Degradation and mineralization of coral mucus in reef environments. Mar Ecol Prog Ser 267:159–171Google Scholar
  289. Wild C, Mayr C, Wehrmann L, Schöttner S, Naumann M, Hoffmann F, Rapp HT (2008) Organic matter release by cold water corals and its implication for fauna–microbe interaction. Mar Ecol Prog Ser 372:67–75Google Scholar
  290. Wilkinson CR (1980) Cyanobacteria symbiotic in marine sponges. In: Schwemmler W, Schneck HEA (eds) Endocytobiology, endosymbiosis and cell biology. De Gruyter, Berlin, pp 553–563Google Scholar
  291. Wilkinson CR (1983) Net primary productivity in coral reef sponges. Science 219:410–412PubMedGoogle Scholar
  292. Wilkinson CR (1984) Immunological evidence for the Precambrian origin of bacterial symbioses in marine sponges. Proc Roy Soc Lond (B) 220:509–517Google Scholar
  293. Wilkinson CR (1992) Symbiotic interactions between marine sponges and algae. In: Reisser W (ed) Algae and symbioses: plants, animals, fungi, viruses, interactions explored. Biopress, Bristol, pp 112–128Google Scholar
  294. Williams WM, Viner AB, Broughton WJ (1987) Nitrogen fixation (acetylene-reduction) associated with the living coral Acropora variabilis. Mar Biol 94:531–535Google Scholar
  295. Willis BL, Page CA, Dinsdale EA (2004) Corals disease on the Great Barrier Reef. In: Rosenberg E, Loya Y (eds) Coral health and disease. Springer, Heildelberg, pp 69–104Google Scholar
  296. Work TM, Aeby GS (2006) Systematically describing gross lesions in corals. Dis Aquat Organ 70:155–160PubMedGoogle Scholar
  297. Work TM, Richardson LL, Reynolds TL, Willis BL (2008) Biomedical and veterinary science can increase our understanding of coral disease. J Exp Mar Biol Ecol 362:63–70Google Scholar
  298. Wulff JL (2007) Disease prevalence and population density over time in three common Caribbean coral reef sponge species. J Mar Biol Assoc UK 87:1715–1720Google Scholar
  299. Yahel G, Post AF, Fabricius KE, Marie D, Vaulot D, Genin A (1998) Phytoplankton distribution and grazing near coral reefs. Limnol Oceanogr 43:551–563Google Scholar
  300. Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer K-H et al (2008) The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250PubMedGoogle Scholar
  301. Yellowlees D, Rees TAV, Leggat W (2008) Metabolic interactions between algal symbionts and invertebrate hosts. Plant Cell Environ 31:679–694PubMedGoogle Scholar

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© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Australian Institute of Marine ScienceTownsvilleAustralia

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