Threatened corals provide underexplored microbial habitats

PLoS ONE

Volumn 5, Issue 3, 2010, Pages

  Sunagawa, Shinichi ^a   Woodley, Cheryl M ^b   Medina, Mónica ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b CENTER FOR COASTAL ENVIRONMENTAL HEALTH AND BIOMOLECULAR RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; SEA WATER;

ARTICLE; BIOSPHERE; CENTRAL AMERICA; CONTROLLED STUDY; CORAL REEF; ECOLOGICAL NICHE; ECOSYSTEM; GENE SEQUENCE; MARINE ENVIRONMENT; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; ANIMAL; ANTHOZOA; BACTERIUM; BIOLOGY; CLUSTER ANALYSIS; ENDANGERED SPECIES; GENETIC VARIABILITY; GENETICS; METHODOLOGY; MICROBIOLOGY; PHYSIOLOGY;

ANIMALIA; ANTHOZOA; BACTERIA (MICROORGANISMS); OTUS;

ANIMALS; ANTHOZOA; BACTERIA; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; CORAL REEFS; ECOSYSTEM; ENDANGERED SPECIES; GENETIC VARIATION; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEAWATER;

EID: 77949674527     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0009554     Document Type: Article

References (56)

1. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95: 6578-6583.
2. Pedros-Alio C (2006) Marine microbial diversity: can it be determined? Trends Microbiol 14: 257-263.
3. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A 103: 12115-12120.
4. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 5: e16.
5. Pedros-Alio C (2007) Ecology. Dipping into the rare biosphere. Science 315: 192-193.
6. Baas Becking LGM (1934) Geobiologie of inleiding tot de milieukunde. W.P. Van Stockum & Zoon N.V., Den Haag, Netherlands.
7. Carpenter KE, Abrar M, Aeby G, Aronson RB, Banks S, et al. (2008) One-third of reef-building corals face elevated extinction risk from climate change and local impacts. Science 321: 560-563.
8. 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.
9. 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.
10. Geffen Y, Ron EZ, Rosenberg E (2009) Regulation of release of antibacterials from stressed scleractinian corals. FEMS Microbiol Lett 295: 103-109.
11. Ritchie KB (2006) Regulation of microbial populations by coral surface mucus and mucus-associated bacteria. Mar Ecol Prog Ser 322: 1-14.
12. Wild C, Huettel M, Klueter A, Kremb SG, Rasheed MY, et al. (2004) Coral mucus functions as an energy carrier and particle trap in the reef ecosystem. Nature 428: 66-70.
13. Reshef L, Koren O, Loya Y, Zilber-Rosenberg I, Rosenberg E (2006) The coral probiotic hypothesis. Environ Microbiol 8: 2068-2073.
14. 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: 2214-2228.
15. Rohwer F, Seguritan V, Azam F, Knowlton N (2002) Diversity and distribution of coral-associated bacteria. Mar Ecol Prog Ser 243: 1-10.
16. Bourne DG, Munn CB (2005) Diversity of bacteria associated with the coral Pocillopora damicornis from the Great Barrier Reef. Environmental Microbiology 7: 1162-1174.
17. Dunbar J, Barns SM, Ticknor LO, Kuske CR (2002) Empirical and Theoretical Bacterial Diversity in Four Arizona Soils. Appl Environ Microbiol 68: 3035-3045.
18. 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.
19. DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, et al. (2007) High-Density Universal 16S rRNA Microarray Analysis Reveals Broader Diversity than Typical Clone Library When Sampling the Environment. Microb Ecol 53: 371-383.
20. Bent SJ, Forney LJ (2008) The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. ISME J 2: 689-695.
21. Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, et al. (2007) Microbial population structures in the deep marine biosphere. Science 318: 97-100.
22. Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6: 639-641.
23. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P (2009) Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates. Environ Microbiol: doi: 10.1111/j.1462-2920.2009.02051.x.
24. Gilbert JA, Field D, Swift P, Newbold L, Oliver A, et al. (2009) The seasonal structure of microbial communities in the Western English Channel. Environ Microbiol 11: 3132-3139.
25. Webster NS, Taylor MW, Behnam F, Lucker S, Rattei T, et al. (2009) Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts. Environ Microbiol: doi: 10.1111/j.1462-2920.2009.02065.x.
26. Apprill A, Marlow HQ, Martindale MQ, Rappe MS (2009) The onset of microbial associations in the coral Pocillopora meandrina. ISME J 3: 685-699.
27. Medina M, Collins AG, Takaoka TL, Kuehl JV, Boore JL (2006) Naked corals: skeleton loss in Scleractinia. Proc Natl Acad Sci U S A 103: 9096-9100.
28. Romano SL, Palumbi SR (1996) Evolution of scleractinian corals inferred from molecular systematics. Science 271: 640-642.
29. 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: 152-163.
30. Koren O, Rosenberg E (2006) Bacteria associated with mucus and tissues of the coral Oculina patagonica in summer and winter. Appl Environ Microbiol 72: 5254-5259.
31. Ritchie KB, Smith GW (2004) Microbial Communities of Coral Surface Mucopolysaccharide Layers. In: Rosenberg E, Loya Y, eds. Coral Health and Disease. Berlin: Springer-Verlag. pp 259-263.
32. Dethlefsen L, McFall-Ngai M, Relman DA (2007) An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449: 811-818.
33. Fraune S, Bosch TC (2007) Long-term maintenance of species-specific bacterial microbiota in the basal metazoan Hydra. Proc Natl Acad Sci U S A 104: 13146-13151.
34. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, et al. (2008) Evolution of mammals and their gut microbes. Science 320: 1647-1651.
35. Moran NA (2006) Symbiosis. Curr Biol 16: R866-871.
36. Taylor MW, Schupp PJ, Dahllof I, Kjelleberg S, Steinberg PD (2004) Host specificity in marine sponge-associated bacteria, and potential implications for marine microbial diversity. Environ Microbiol 6: 121-130.
37. Kuramitsu HK, He X, Lux R, Anderson MH, Shi W (2007) Interspecies interactions within oral microbial communities. Microbiol Mol Biol Rev 71: 653-670.
38. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI (2008) Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6: 776-788.
39. Kühl M, Cohen Y, Dalsgaard T, Jorgensen BB, Revsbech NP (1995) Microenvironment and Photosynthesis of Zooxanthellae in Scleractinian Corals Studied with Microsensors for O2, pH and Light. Mar Ecol Prog Ser 117: 159-172.
40. Shashar N, Cohen Y, Loya Y (1993) Extreme Diel Fluctuations of Oxygen in Diffusive Boundary-Layers Surrounding Stony Corals. Biol Bull 185: 455-461.
41. Vega Thurber RL, Barott KL, Hall D, Liu H, Rodriguez-Mueller B, et al. (2008) Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. Proc Natl Acad Sci U S A 105: 18413-18418.
42. 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.
43. Bourne DG, Garren M, Work TM, Rosenberg E, Smith GW, et al. (2009) Microbial disease and the coral holobiont. Trends Microbiol 17: 554-562.
44. Costanza R, dArge R, deGroot R, Farber S, Grasso M, et al. (1997) The value of the world's ecosystem services and natural capital. Nature 387: 253-260.
45. Wu D, Hartman A, Ward N, Eisen JA (2008) An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS One 3: e2566.
46. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
47. Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113.
48. Howe K, Bateman A, Durbin R (2002) QuickTree: building huge Neighbour-Joining trees of protein sequences. Bioinformatics 18: 1546-1547.
49. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-1506.
50. Hamady M, Lozupone C, Knight R (2009) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4: 17-27.
51. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072.
52. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
53. Felsenstein J (1989) PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
54. Letunic I, Bork P (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23: 127-128.
55. DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, et al. (2006) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394-399.
56. Ihaka R, Gentleman R (1996) R: A language for data analysis and graphics. Journal of Computational and Graphical Statistics 5: 299-314.