Characterization of geographically distinct bacterial communities associated with coral mucus produced by Acropora spp. and Porites spp.

Applied and Environmental Microbiology

Volumn 78, Issue 15, 2012, Pages 5229-5237

  McKew, B A ^a   Dumbrell, A J ^a   Daud, S D ^a   Hepburn, L ^a   Thorpe, E ^a   Mogensen, L ^a   Whitby, C ^a  

^a UNIVERSITY OF ESSEX   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACROPORA; BACTERIAL COMMUNITY; FIRMICUTES; GAMMAPROTEOBACTERIA; HALOMONAS; INDONESIA; ME-XICO; PORITES; PYROSEQUENCING; RELATIVE ABUNDANCE;

BODY FLUIDS; LIBRARIES; REEFS; SEAWATER;

BACTERIA;

RNA 16S;

BACTERIUM; COMMUNITY STRUCTURE; CORAL REEF; CYANOBACTERIUM; HOST-PARASITE INTERACTION; TAXONOMY;

ANALYSIS OF VARIANCE; ANIMAL; ANTHOZOA; ARTICLE; BACTERIUM; BIOTA; CLUSTER ANALYSIS; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA SEQUENCE; GENETICS; GEOGRAPHY; INDONESIA; METABOLISM; MEXICO; MICROBIOLOGY; MOLECULAR GENETICS; MUCUS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPECIES DIFFERENCE;

ANALYSIS OF VARIANCE; ANIMALS; ANTHOZOA; BACTERIA; BASE SEQUENCE; BIOTA; CLUSTER ANALYSIS; DENATURING GRADIENT GEL ELECTROPHORESIS; GEOGRAPHY; INDONESIA; MEXICO; MOLECULAR SEQUENCE DATA; MUCUS; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

ATLANTIC OCEAN; CARIBBEAN SEA; INDIAN OCEAN; INDONESIA; PACIFIC OCEAN;

ACROPORA; ALPHAPROTEOBACTERIA; ANTHOZOA; BACTERIA (MICROORGANISMS); CLOSTRIDIALES; CYANOBACTERIA; FIRMICUTES; GAMMAPROTEOBACTERIA; HALOMONAS; PORITES; PSYCHROBACTER;

EID: 84866173362     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.07764-11     Document Type: Article

References (50)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Alvarez LA, Exton DA, Timmis K.N, Suggett DJ, McGenity TJ. 2009. Characterization of marine isoprene-degrading communities. Environ. Microbiol. 11:3280-3291.
3. Bell JJ, Smith DJ. 2004. Ecology of sponge assemblages (Porifera) in the Wakatobi region, southeast Sulawesi, Indonesia: richness and abundance. J. Mar. Biol. Assoc. UK 84:581-591.
4. Bourne DG, Munn CB. 2005. Diversity of bacteria associated with the coral Pocillopora damicornis from the Great Barrier Reef. Environ. Microbiol. 7:1162-1174.
5. Boyett HV, Bourne DG, Willis BL. 2007. Elevated temperature and light enhance progression and spread of black band disease on staghorn corals of the Great Barrier Reef. Mar. Biol. 151:1711-1720.
6. Breitbart M, Bhagooli R, Griffin S, Johnston I, Rohwer F. 2005. Microbial communities associated with skeletal tumors on Porites compressa. FEMS Microbiol. Lett. 243:431-436.
7. Brown BE, Bythell JC. 2005. Perspectives on mucus secretion in reef corals. Mar. Ecol. Prog. Ser. 296:291-309.
8. Caporaso JG, et al. 2010. QIIME allows analysis of high-throughput community sequence data. Nat. Methods 7:335-336.
9. Clarke KR, Gorley RN. 2006. PRIMER v6: user manual/tutorial. PRIMER-E, Plymouth, MA.
10. Crabbe MJC, Smith DJ. 2002. Comparison of two reef sites in the Wakatobi Marine National Park (SE Sulawesi, Indonesia). Using digital image analysis. Coral Reefs 24:437-441.
11. Crabbe MJC, Karaviotis S, Smith DJ. 2004. Preliminary comparison of three coral reef sites in the Wakatobi Marine National Park (S.E. Sulawesi, Indonesia): estimated recruitment dates compared with Discovery Bay, Jamaica. Bull. Mar. Sci. 74:469-476.
12. Ducklow HW, Mitchell R. 1979. Bacterial populations and adaptations in the mucus layers on living corals. Limnol. Oceanogr. 24:715-725.
13. Dumbrell AJ, Nelson M, Dytham C, Helgason T, Fitter AH. 2010. Relative roles of niche and neutral processes in structuring a soil microbial community. ISME J. 4:337-345.
14. Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460-2461.
15. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC. 1989. Isolation and direct complete nucleotide determination of entire genes: characterization of a gene coding for 16S-ribosomal RNA. Nucleic Acids Res. 17: 7843-7853.
16. Felsenstein J. 1989. PHYLIP: Phylogeny Inference package (version 3.2). Cladistics 5:164-166.
17. 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.
18. Glynn PW. 1993. Coral reef bleaching: ecological perspectives. Coral Reefs 12:1-17.
19. Haapkylä J, Seymour AS, Trebilco J, Smith DJ. 2007. Coral disease prevalence and coral health in the Wakatobi Marine Park, southeast Sulawesi, Indonesia. J. Mar. Biol. Assoc. UK 87:1-12.
20. Haapkyla et al. 2009. Spatio-temporal coral disease dynamics in the Wakatobi Marine National Park, South-East Sulawesi. Indones. Dis. Aquat. Organ. 87:105-115.
21. Jukes TH, Cantor CR. 1969. Evolution of protein molecules, p 21-132. In Munro HN (ed), Mammalian protein metabolism. Academic Press, New York, NY.
22. Lampert Y, Kelman D, Dubinsky Z, Nitzan Y, Hill RT. 2006. Diversity of culturable bacteria in the mucus of the Red Sea coral Fungia scutaria. FEMS Microbiol. Ecol. 58:99-108.
23. Lampert Y, et al. 2008. Phylogenetic diversity of bacteria associated with the mucus of Red Sea corals. FEMS Microbiol. Ecol. 64:187-198.
24. Lozupone C, Hamady M, Knight R. 2006. UniFrac: an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7:371.
25. 2 springs. Appl. Environ. Microbiol. 77:4770-4777.
26. McKew BA, Coulon F, Osborn AM, Timmis KN, McGenity TJ. 2007. Determining the identity and roles of oil-metabolizing marine bacteria from the Thames estuary UK. Environ. Microbiol. 9:165-176.
27. Meikle P, Richards GN, Yellowlees D. 1988. Structural investigations on the mucus from six species of coral. Mar. Biol. 99:187-193.
28. Muyzer G, de Waal EC, Uitterlinden AG. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
29. Nawrocki EP, Eddy SR. 2007. Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput. Biol. 3:e56. doi:10.1371/ journal.pcbi.0030056.
30. Nicol G, Tscherko D, Embley TM, Prosser JI. 2005. Primary succession of soil Crenarchaeota across a receding glacier foreland. Environ. Microbiol. 7:337-347.
31. Page RDM. 1996. TreeView: an application to display phylogenetic trees on personal computers. Bioinformatics 12:357-358.
32. Pantos O, et al. 2003. The bacterial ecology of a plague-like disease affecting the Caribbean coral Montastrea annularis. Environ. Microbiol. 5:370-382.
33. Parameswaran P, et al. 2007. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res. 35:e130.
34. Remily ER, Richardson LL. 2006. Ecological physiology of a coral pathogen and the coral reef environment. Microb. Ecol. 51:345-352.
35. 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.
36. Ritchie KB. 2006. Regulation of microbial populations by coral surface mucus and mucus-associated bacteria. Mar. Ecol. Progr. Ser. 322:1-14.
37. Ritchie KB, Smith GW. 1997. Physiological comparison of bacterial communities from various species of scleractinian corals, p 521-526. Proc. 8th Int. Coral Reef Symp. Smithsonian Tropical Research Institute, Balboa, Panama.
38. Rohwer F, Breitbart M, Jara J, Azam F, Knowlton N. 2001. Diversity of bacteria associated with the Caribbean coral Montastraea franksi. Coral Reefs 20:85-91.
39. Rohwer F, Seguritan V, Azam F, Knowlton N. 2002. Diversity and distribution of coral-associated bacteria. Mar. Ecol. Progr. Ser. 243:1-10.
40. 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.
41. Ruìz-Renterìa F, van Tussenbroek BI, Jordán-Dahlgren E. 1998. Puerto Morelos, Quintana Roo, Mexico, p 57-66. In Kjerfve B (ed), CARICOMP: Caribbean coral reef, seagrass and mangrove sites. UNESCO, Paris, France.
42. Saitou N, Nei M. 1987. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
43. Shashar N, Cohen Y, Loya Y, Sar N. 1994. Nitrogen-fixation (acetylene reduction) in stony corals: evidence for coral-bacteria interactions. Mar. Ecol. Progr. Ser. 111:259-264.
44. Smith DJ, Pilgrim S, Cullen L. 2007. Coral reefs and people, p 1081-1117. In Pretty J, et al (ed), Sage handbook on environment and society. Sage Publications, London, England.
45. Sogin ML, et al. 2006. Microbial diversity in the deep sea and the underexplored rare biosphere.' Proc. Natl. Acad. Sci. U. S. A. 103:12115-12120.
46. Solow AR. 1993. A simple test for change in community structure. J. Anim. Ecol. 62:191-193.
47. Sunagawa S, Woodley CM, Medina M. 2010. Threatened corals provide underexplored microbial habitats. PLoS One 5:1-6. doi:10.1371/ journal.pone.0009554.
48. Wallace CC, Chen CA, Fukami H, Muir PR. 2007. Recognition of separate genera within Acropora based on new morphological, reproductive and genetic evidence from Acropora togianensis, and elevation of the subgenus Iso pora Studer, 1878 to genus (Scleractinia: Astrocoeniidae; Acroporidae). Coral Reefs 26:231-239.
49. Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73:5261-5267.
50. Wild C, et al. 2004. Degradation and mineralization of coral mucus in reef environments. Mar. Ecol. Progr. Ser. 267:159-171.