Effect of freezing on PCR amplification of 16S rRNA genes from microbes associated with black band disease of corals

Applied and Environmental Microbiology

Volumn 75, Issue 8, 2009, Pages 2581-2584

  Sekar, Raju ^a,b   Kaczmarsky, Longin T ^a   Richardson, Laurie L ^a  

^a FLORIDA INTERNATIONAL UNIVERSITY   (United States)

^b UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA GENES; 16S RRNA SEQUENCES; MOLECULAR ANALYSIS; PCR AMPLIFICATIONS;

SULFUR;

AMPLIFICATION;

RNA 16S;

BACTERIAL DISEASE; CORAL; FREEZING; MOLECULAR ANALYSIS; POLYMERASE CHAIN REACTION; RNA;

ALPHAPROTEOBACTERIA; ARTICLE; BACTEROIDETES; CONTROLLED STUDY; CORAL; CYANOBACTERIUM; DELTAPROTEOBACTERIA; EPSILONPROTEOBACTERIA; FREEZING; GAMMAPROTEOBACTERIA; GENE AMPLIFICATION; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; RNA SEQUENCE; SULFUR OXIDIZING BACTERIUM; UNINDEXED SEQUENCE;

ANIMALS; ANTHOZOA; BACTERIA; BACTERIAL INFECTIONS; BIODIVERSITY; DNA, BACTERIAL; DNA, RIBOSOMAL; FREEZING; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPECIMEN HANDLING;

ANTHOZOA; BACTERIA (MICROORGANISMS); CYANOBACTERIA; PROTEOBACTERIA;

EID: 64749085263     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01500-08     Document Type: Article

References (24)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Meyers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Barneah, O., E. Ben-Dov, E. Kramarsky-Winter, and A. Kushmaro. 2007. Characterization of black band disease in Red Sea stony corals. Environ. Microbiol. 9:1995-2006.
3. Bissett, A., J. Bowman, and C. Burke. 2006. Bacterial diversity in organically enriched fish farm sediments. FEMS Microbiol. Ecol. 55:48-56.
4. Cooney, R. P., O. Pantos, M. D. A. L. Tissier, M. R. Barer, A. G. O'Donnell, and J. C. Bythell. 2002. Characterization of the bacterial consortium asso- ciated with black band disease in coral using molecular microbiological techniques. Environ. Microbiol. 4:401-413.
5. Day, J. G. 2007. Cryopreservation of microalgae and cyanobacteria. Methods Mol. Biol. 368:141-151.
6. Ducklow, H. W., and R. Mitchell. 1979. Observations on naturally and arti- ficially diseased tropical corals: a scanning electron microscopy study. Mi- crob. Ecol. 5:215-223.
7. Frias-Lopez, J., G. T. Bonheyo, Q. S. Jin, and B. W. Fouke. 2003. Cyanobac- teria associated with coral black band disease in Caribbean and Indo-Pacific Reefs. Appl. Environ. Microbiol. 69:2409-2413.
8. Frias-Lopez, J., J. S. Klaus, G. T. Bonheyo, and B. W. Fouke. 2004. Bacterial community associated with black band disease in corals. Appl. Environ. Microbiol. 70:5955-5962.
9. Frias-Lopez, J., A. L. Zerkle, G. T. Bonheyo, and B. W. Fouke. 2002. Parti- tioning of bacterial communities between seawater and healthy, black band diseased, and dead coral surfaces. Appl. Environ. Microbiol. 68:2214-2228.
10. Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Forster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. Konig, T. Liss, R. Lussmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K. H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
11. Messing, J. 1983. New M13 vectors for cloning. Methods Enzymol. 101:20-78.
12. Mills, D. K., K. Fitzgerald, C. D. Litchfield, and P. M. Gillevet. 2003. A comparison of DNA profiling techniques for monitoring nutrient impact on microbial community composition during bioremediation of petroleum-con- taminated soils. J. Microbiol. Methods 54:57-74.
13. Muyzer, G., E. C. de Waal, and A. G. Uitterlinden. 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.
14. Muyzer, G., A. Teske, C. O. Wirsen, and H. W. Jannasch. 1995. Phylogenetic relationship of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch. Microbiol. 164:165-172.
15. Nübel, U., F. Garcia-Pichel, and G. Muyzer. 1997. PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl. Environ. Microbiol. 63:3327-3332.
16. Richardson, L. L. 2004. Black band disease, p. 325-349. In E. Rosenberg and Y. Loya (ed.), Coral health and disease. Springer-Verlag, Berlin, Germany.
17. Rützler, K., and D. Santavy. 1983. The black band disease of Atlantic reef corals. I. Description of the cyanophyte pathogen. PSZNI Mar. Ecol. 4:301-319.
18. Rützler, K., D. L. Santavy, and A. Antonius. 1983. The black band disease of Atlantic reef corals. III. Distribution, ecology and development. PSZNI Mar. Ecol. 4:329-358.
19. Sekar, R., L. T. Kaczmarsky, and L. L. Richardson. 2008. Microbial com- munity composition of black band disease on the coral host Siderastrea siderea from three regions of the wider Caribbean. Mar. Ecol. Prog. Ser. 362:85-98.
20. Sekar, R., D. K. Mills, E. R. Remily, J. D. Voss, and L. L. Richardson. 2006. Microbial communities in the surface mucopolysaccharide layer and the black band microbial mat of black band-diseased Siderastrea siderea. Appl. Environ. Microbiol. 72:5963-5973.
21. Sievert, S. M., E. B. A. Wieringa, C. O. Wirsen, and C. D. Taylor. 2007. Growth and mechanism of filamentous-sulfur formation by Candidatus Ar- cobacter sulfidicus in opposing oxygen-sulfide gradients. Environ. Microbiol. 9:271-276.
22. Suomalainen, L.-R., H. Reunanen, R. Ijas, E. T. Valtonen, and M. Tiirola. 2006. Freezing induces biased results in the molecular detection of Flavobac- terium columnare. Appl. Environ. Microbiol. 72:1702-1704.
23. Sussman, M., D. G. Bourne, and B. L. Willis. 2006. A single cyanobacterial ribotype is associated with both red and black bands on diseased corals from Palau. Dis. Aquat. Org. 69:111-118.
24. Wirsen, C. O., S. M. Sievert, C. M. Cavanaugh, S. J. Molyneaux, A. Ahmad, L. T. Taylor, E. F. DeLong, and C. D. Taylor. 2002. Characterization of an autotrophic sulfide-oxidizing marine Arcobacter sp. that produces filamen- tous sulfur. Appl. Environ. Microbiol. 68:316-325.