Community shifts in the surface microbiomes of the coral Porites astreoides with unusual lesions

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Meyer, Julie L ^a   Paul, Valerie J ^b   Teplitski, Max ^a,b  

^a UNIVERSITY OF FLORIDA   (United States)

^b SMITHSONIAN MARINE STATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ACHROMOBACTER; ALTERNARIA; ARTICLE; BACTERIAL INFECTION; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; CORAL; ENDOZOICOMONAS; MARINE BACTERIUM; MICROBIAL COMMUNITY; MICROBIOME; NONHUMAN; POPULATION ABUNDANCE; PORITES ASTREOIDES; SPECIES COMPOSITION; SPECIES DOMINANCE; STENOTROPHOMONAS; ANIMAL; ANTHOZOA; BACTERIUM; CLASSIFICATION; CORAL REEF; DEMOGRAPHY; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; MICROBIOLOGY; MICROFLORA;

ANIMALS; ANTHOZOA; BACTERIA; CORAL REEFS; MICROBIOTA; RESIDENCE CHARACTERISTICS; RNA, RIBOSOMAL, 16S;

EID: 84903288635     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0100316     Document Type: Article

References (76)

1. Riegl B, Bruckner A, Coles SL, Renaud P, Dodge RE (2009) Coral reefs: threats and conservation in an era of global change. Ann N Y Acad Sci 1162: 136-186.
2. Loya Y, Sakai K, Yamazato K, Nakano Y, Sambali H, et al. (2001) Coral bleaching: the winners and the losers. Ecol Lett 4: 122-131. (Pubitemid 32228508)
3. Hughes TP, Baird AH, Bellwood DR, Card M, Connolly SR, et al. (2003) Climate change, human impacts, and the resilience of coral reefs. Science 301: 929-933. (Pubitemid 36994796)
4. Hoegh-Guldberg O, Mumby PJ, Hooten AJ, Steneck RS, Greenfield P, et al. (2007) Coral reefs under rapid climate change and ocean acidification. Science 318: 1737-1742.
5. Bruckner AW, Hill RL (2009) Ten years of change to coral communities off Mona and Desecheo Islands, Puerto Rico, from disease and bleaching. Dis Aquat Org 87: 19-31.
6. Edmunds PJ (2010) Population biology of Porites astreoides and Diploria strigosa on a shallow Caribbean reef. Mar Ecol Prog Ser 418: 87-U508.
7. van Woesik R, Sakai K, Ganase A, Loya Y (2011) Revisiting the winners and the losers a decade after coral bleaching. Mar Ecol Prog Ser 434: 67-76.
8. Green DH, Edmunds PJ, Carpenter RC (2008) Increasing relative abundance of Porites astreoides on Caribbean reefs mediated by an overall decline in coral cover. Mar Ecol Prog Ser 359: 1-10. (Pubitemid 351798225)
9. Levas SJ, Grottoli AG, Hughes A, Osburn CL, Matsui Y (2013) Physiological and biogeochemical traits of bleaching and recovery in the mounding species of coral Porites lobata: implications for resilience in mouding corals. Plos One 8: e63267.
10. Burge CA, Eakin CM, Friedman CS, Froelich B, Hershberger PK, et al. (2014) Climate change influences on marine infectious diseases: implications for management and society. Ann Rev Mar Sci, Vol 6 6: 249-277.
11. Rosenberg E, Koren O, Reshef L, Efrony R, Zilber-Rosenberg I (2007) The role of microorganisms in coral health, disease and evolution. Nat Rev Microbiol 5: 355-362. (Pubitemid 46605489)
12. Bourne DG, Garren M, Work TM, Rosenberg E, Smith GW, et al. (2009) Microbial disease and the coral holobiont. Trends Microbiol 17: 554-562.
13. Arboleda MDM, Reichardt WT (2010) Vibrio sp causing Porites ulcerative white spot disease. Dis Aquat Org 90: 93-104.
14. Aeby GS, Williams GJ, Franklin EC, Kenyon J, Cox EF, et al. (2011) Patterns of coral disease across the Hawaiian Archipelago: relating disease to environment. Plos One 6: e20370.
15. Pollock FJ, Morris PJ, Willis BL, Bourne DG (2011) The urgent need for robust coral disease diagnostics. PLoS Pathog 7: e1002183.
16. Weil E, Irikawa A, Casareto B, Suzuki Y (2012) Extended geographic distribution of several Indo-Pacific coral reef diseases. Dis Aquat Organ 98: 163-170.
17. Dixon P (2003) VEGAN, a package of R functions for community ecology. Jo Veget Sci 14: 927-930.
18. Efrony R, Loya Y, Bacharach E, Rosenberg E (2007) Phage therapy of coral disease. Coral Reefs 26: 7-13. (Pubitemid 46491131)
19. Efrony R, Atad I, Rosenberg E (2009) Phage therapy of coral white plague disease: properties of phage BA3. Curr Microbiol 58: 139-145.
20. Cohen Y, Joseph Pollock F, Rosenberg E, Bourne DG (2012) Phage therapy treatment of the coral pathogen Vibrio coralliilyticus. Microbiologyopen 2:64-74.
21. Atad I, Zvuloni A, Loya Y, Rosenberg E (2012) Phage therapy of the white plague-like disease of Favia favus in the Red Sea. Coral Reefs 31: 665-670.
22. Muller EM, van Woesik R (2012) Caribbean coral diseases: primary transmission or secondary infection? Global Change Biol 18: 3529-3535.
23. Lesser MP, Bythell JC, Gates RD, Johnstone RW, Hoegh-Guldberg O (2007) Are infectious diseases really killing corals? Alternative interpretations of the experimental and ecological data. J Exp Mar Biol Ecol 346: 36-44. (Pubitemid 46726366)
24. Bourne D, Iida Y, Uthicke S, Smith-Keune C (2008) Changes in coral-associated microbial communities during a bleaching event. ISME J 2: 350-363. (Pubitemid 351518395)
25. Sunagawa S, DeSantis TZ, Piceno YM, Brodie EL, DeSalvo MK, et al. (2009) Bacterial diversity and white plague disease-associated community changes in the Caribbean coral Montastraea faveolata. ISME J 3: 512-521.
26. Kimes NE, Johnson WR, Torralba M, Nelson KE, Weil E, et al. (2013) The Montastraea faveolata microbiome: ecological and temporal influences on a Caribbean reef-building coral in decline. Environ Microbiol 15: 2082-2094.
27. Krediet CJ, Ritchie KB, Paul VJ, Teplitski M (2013) Coral-associated microorganisms and their roles in promoting coral health and thwarting diseases. Proc Royal Soc B 280: 20122328.
28. Apprill A, Hughen K, Mincer T (2013) Major similarities in the bacterial communities associated with lesioned and healthy Fungiidae corals. Environ Microbiol 15: 2063-2072.
29. Wegley L, Edwards R, Rodriguez-Brito B, Liu H, Rohwer F (2007) Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ Microbiol 9: 2707-2719. (Pubitemid 47547539)
30. Sharp KH, Distel D, Paul VJ (2012) Diversity and dynamics of bacterial communities in early life stages of the Caribbean coral Porites astreoides. ISME J 6: 790-801.
31. Morrow KM, Moss AG, Chadwick NE, Liles MR (2012) Bacterial associates of two Caribbean coral species reveal species-specific distribution and geographic variability. Appl Environ Microbiol 78: 6438-6449.
32. Rodriguez-Lanetty M, Granados-Cifuentes C, Barberan A, Bellantuono AJ, Bastidas C (2013) Ecological inferences from a deep screening of the complex bacterial consortia associated with the coral, Porites astreoides. Mol Ecol 22: 4349-4362.
33. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7: 335-336.
34. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
35. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic Local Alignment Search Tool. J Mol Biol 215: 403-410.
36. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, et al. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41: D590-D596.
37. Mizrachi I (2002) GenBank: The Nucleotide Sequence Database. In: McEntyre J, Ostell J, editors. The NCBI Handbook [Internet], updated 2007 Aug 22. Bethesda, MD: National Center for Biotechnology Information.
38. Horn HS (1966) Measurement of overlap in comparative ecological studies. Am Natural 100: 419-&.
39. Aitchison J (2003) A concise guide to compositional data analysis. Compositional Data Analysis Workshop, Girona.
40. Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, et al. (2012) Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol 8: e1002606.
41. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504. (Pubitemid 37428274)
42. Work TM, Aeby GS (2006) Systematically describing gross lesions in corals. Dis Aquat Organ70: 155-160. (Pubitemid 44073884)
43. Miller J, Muller E, Rogers C, Waara R, Atkinson A, et al. (2009) Coral disease following massive bleaching in 2005 causes 60% decline in coral cover on reefs in the US Virgin Islands. Coral Reefs 28: 925-937.
44. Richardson LL, Goldberg WM, Carlton RG, Halas JC (1998) Coral disease outbreak in the Florida Keys: Plague Type II. Rev Biol Tropic 46: 187-198.
45. Sere MG, Tortosa P, Chabanet P, Turquet J, Quod JP, et al. (2013) Bacterial communities associated with Porites White Patch Syndrome (PWPS) on three Western Indian Ocean (WIO) coral reefs. Plos One 8: e83746.
46. Croquer A, Weil E (2009) Spatial variability in distribution and prevalence of Caribbean scleractinian coral and octocoral diseases. II. Genera-level analysis. Dis Aquat Organ 83: 209-222.
47. Sunagawa S, Woodley CM, Medina M (2010) Threatened corals provide underexplored microbial habitats. PLoS ONE 5: e9554.
48. Rohwer F, Seguritan V, Azam F, Knowlton N (2002) Diversity and distribution of coral-associated bacteria. Mar Ecol Prog Ser 243: 1-10. (Pubitemid 35436643)
49. Bayer T, Neave MJ, Alsheikh-Hussain A, Aranda M, Yum LK, et al. (2013) The microbiome of the Red Sea coral Stylophora pistillata Is dominated by tissue-associated Endozoicomonas bacteria. Appl Environ Microbiol 79: 4759-4762.
50. Pike RE, Haltli B, Kerr RG (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. Intl J System Evol Microbiol 63: 4294-4302.
51. Yang CS, Chen MH, Arun AB, Chen CA, Wang JT, et al. (2010) Endozoicomonas montiporae sp nov., isolated from the encrusting pore coral Montipora aequituberculata. Intl J System Evol Microbiol 60: 1158-1162.
52. Kurahashi M, Yokota A (2007) Endozoicomonas elysicola gen. nov., sp nov., a gamma-proteobacterium isolated from the sea slug Elysia ornata. System Appl Microbiol 30: 202-206. (Pubitemid 46428508)
53. Vezzulli L, Pezzati E, Huete-Stauffer C, Pruzzo C, Cerrano C (2013) 16SrDNA Pyrosequencing of the Mediterranean Gorgonian Paramuricea clavata reveals a link among alterations in bacterial holobiont members, anthropogenic influence and disease outbreaks. Plos One 8: e67745.
54. Mouchka ME, Hewson I, Harvell CD (2010) Coral-associated bacterial assemblages: current knowledge and the potential for climate-driven impacts. Integr Comp Biol 50: 662-674.
55. Jessen C, Lizcano JFV, Bayer T, Roder C, Aranda M, et al. (2013) In-situ effects of eutrophication and overfishing on physiology and bacterial diversity of the Red Sea coral Acropora hemprichii. Plos One 8: e62091.
56. Kellogg CA, Piceno YM, Tom LM, DeSantis TZ, Gray MA, et al. (2013) Comparing bacterial community composition between healthy and White Plague-Like Disease states in Orbicella annularis using PhyloChip (TM) G3 microarrays. Plos One 8: e79801.
57. Kellogg CA, Piceno YM, Tom LM, DeSantis TZ, Zawada DG, et al. (2012) PhyloChip (TM) microarray comparison of sampling methods used for coral microbial ecology. J Microbiol Method 88: 103-109.
58. Cardenas A, Rodriguez RL, Pizarro V, Cadavid LF, Arevalo-Ferro C (2012) Shifts in bacterial communities of two Caribbean reef-building coral species affected by white plague disease. ISME J 6: 502-512.
59. Roder C, Arif C, Bayer T, Aranda M, Daniels C, et al. (2014) Bacterial profiling of White Plague Disease in a comparative coral species framework. ISME J 8: 31-39.
60. Roder C, Arif C, Daniels C, Weil E, Voolstra CR (2014) Bacterial profiling of White Plague Disease across corals and oceans indicates a conserved and distinct disease microbiome. Mol Ecol 23: 965-974.
61. Croquer A, Bastidas C, Elliott A, Sweet M (2013) Bacterial assemblages shifts from healthy to yellow band disease states in the dominant reef coral Montastraea faveolata . Environ Microbiol Report 5: 90-96.
62. Kimes NE, Van Nostrand JD, Weil E, Zhou JZ, 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: 541-556.
63. Sweet MJ, Croquer A, Bythell JC (2011) Bacterial assemblages differ between compartments within the coral holobiont. Coral Reefs 30: 39-52.
64. Thomma BPHJ (2003) Alternaria spp.: from general saprophyte to specific parasite. Mol Plant Path 4: 225-236.
65. Morrison-Gardiner S (2002) Dominant fungi from Australian coral reefs. Fung Divers 9: 105-121.
66. Yu ZS, Zhang BH, Sun W, Zhang FL, Li ZY (2013) Phylogenetically diverse endozoic fungi in the South China Sea sponges and their potential in synthesizing bioactive natural products suggested by PKS gene and cytotoxic activity analysis. Fung Divers 58: 127-141.
67. Zheng CJ, Shao CL, Guo ZY, Chen JF, Deng DS, et al. (2012) Bioactive hydroanthraquinones and anthraquinone dimers from a soft coral-derived Alternaria sp fungus. J Nat Prod 75: 189-197.
68. Le Campion-Alsumard T, Golubic S, Priess K (1995) Fungi in corals - symbiosis or disease - interaction between polyps and fungi causes pearl-like skeleton biomineralization. Mar Ecol Prog Ser 117: 137-147. (Pubitemid 26446599)
69. Zhang Y, Mu J, Feng Y, Kang Y, Zhang J, et al. (2009) Broad-spectrum antimicrobial epiphytic and endophytic fungi from marine organisms: isolation, bioassay and taxonomy. Marine Drugs 7: 97-112.
70. Kim MY, Sohn JH, Ahn JS, Oh H (2009) Alternaramide, a cyclic depsipeptide from the marine-derived fungus Alternaria sp SF-5016. J Natur Prod 72: 2065-2068.
71. Garrity GM, Brenner DJ, Krieg NR, Staley JT (2005) The Proteobacteria, Part B: The Gammaproteobacteria. Bergey's Manual of Systematic Bacteriology. New York: Springer.
72. Brooke JS (2012) Stenotrophomonas maltophilia: an emerging global opportunistic pathogen. Clin Microbiol Rev 25: 2-41.
73. Lee OO, Yang JK, Bougouffa S, Wang Y, Batang Z, et al. (2012) Spatial and species variations in bacterial communities associated with corals from the Red Sea as revealed by pyrosequencing. Appl Environ Microbiol 78: 7173-7184.
74. Li XY, Hu Y, Gong J, Zhang LS, Wang GJ (2013) Comparative genome characterization of Achromobacter members reveals potential genetic determinants facilitating the adaptation to a pathogenic lifestyle. Appl Microbiol Biotechnol 97: 6413-6425.
75. Vega Thurber R, Willner-Hall D, Rodriguez-Mueller B, Desnues C, Edwards RA, et al. (2009) Metagenomic analysis of stressed coral holobionts. Environ Microbiol 11: 2148-2163.
76. Ruiz-Moreno D, Willis BL, Page AC, Weil E, Croquer A, et al. (2012) Global coral disease prevalence associated with sea temperature anomalies and local factors. Dis Aquat Org 100: 249-261.