Bacterial communities in Great Barrier Reef calcareous sediments: Contrasting 16S rDNA libraries from nearshore and outer shelf reefs

Estuarine, Coastal and Shelf Science

Volumn 72, Issue 1-2, 2007, Pages 188-200

  Uthicke, S ^a   McGuire, K ^a  

^a AUSTRALIAN INSTITUTE OF MARINE SCIENCE   (Australia)

Author keywords

benthic bacteria; biofilms; calcareous sediments; indicator taxa

Indexed keywords

BACTERIUM; BENTHOS; BIOFILM; CARBONATE SEDIMENT; CLUSTER ANALYSIS; COMMUNITY COMPOSITION; CORAL REEF; DNA; GENETIC ANALYSIS; MICROBIAL COMMUNITY; NEARSHORE ENVIRONMENT; SPECIES DIVERSITY; WATER QUALITY;

AUSTRALASIA; AUSTRALIA; CORAL SEA; GREAT BARRIER REEF; PACIFIC OCEAN; QUEENSLAND;

ACIDOBACTERIACEAE; ANTHOZOA; BACTERIA (MICROORGANISMS); BACTEROIDETES; CYANOBACTERIA; CYTOPHAGA; DELTAPROTEOBACTERIA; FLAVOBACTERIA; PLANCTOMYCETACEAE; PROTEOBACTERIA; VERRUCOMICROBIACEAE;

EID: 33847027667     PISSN: 02727714     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecss.2006.10.017     Document Type: Article

References (59)

1. Alongi D.M., and McKinnon A.D. The cycling and fate of terrestrially derived sediments and nutrients in the coastal zone of the Great Barrier Reef shelf. Marine Pollution Bulletin 51 (2005) 239-252
2. Amann R., Ludwig W., and Schleiffer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology Review 59 (1995) 143-169
3. Amann R., Glöckner F.O., and Neef A. Modern methods in subsurface microbiology: in situ identification of microorganisms with nucleic acid probes. FEMS Microbiology Reviews 20 (1997) 191-200
4. Ashelford K., Chuzhanova N., Fry J., Jones A., and Weightman A.J. At least one in twenty 16S rRNA sequence records currently held in public repositories estimated to contain substantial anomalies. Applied and Environmental Microbiology 71 (2005) 7724-7736
5. Baker G.C., Smith J.J., and Cowan D.A. Review and re-analysis of domain-specific 16S primers. Journal of Microbiological Methods 55 (2003) 541-555
6. Bourne D.G., and Munn C.B. Diversity of bacteria associated with the coral Pocillopora damicornis from the Great Barrier Reef. Environmental Microbiology 7 (2005) 1162-1174
7. Bowman J.P., and McCuaig R. Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. Applied and Environmental Microbiology 69 (2003) 2463-2483
8. Bowman J.P., Rea S.M., McCammon S.A., and McMeekin T.A. Diversity and community structure within anoxic sediment form marine salinity meromictic lakes and a coastal meromictic marine basin, Vestford Hills, Eastern Antarctica. Environmental Microbiology 2 (2000) 227-237
9. Braker G., Ayala-del-Río H.L., Devol A.H., Fesefeldt A., and Tiedje J.M. Community structure of dentrifiers, Bacteria, and Archaea along redox gradients in pacific northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes. Applied and Environmental Microbiology 67 (2001) 1893-1901
10. Brown M.V., Schwalbach M., Hewson I., and Fuhrman J.A. Coupling 16S-ITS rDNA clone libraries and ARISA to show marine microbial diversity; development and application to a time series. Environmental Microbiology 7 (2005) 1466-1479
11. Brunskill G., Zagorskis I., and Pfitzner J. Carbon burial rates in sediments and a carbon mass balance for the Herbert River region of the Great Barrier Reef continental shelf, north Queensland, Australia. Estuarine, Coastal and Shelf Science 54 (2002) 677-700
12. Cifuentes A., Anton J., Benllock S., Donnelly A., Herbert R.A., and Rodriguez-Valera F. Prokaryoic diversity in Zostera noltii-colonized marine sediments. Applied and Environmental Microbiology 66 (2000) 1715-1719
13. Clarke K., and Gorley R. Primer v5: User Manual/Tutorial (2001), Primer-E, Plymouth pp. 91.
14. Cottrell M., and Kirchman D. Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Applied and Environmental Microbiology 66 (2000) 5116-5122
15. Di Meo C., Wilbur A., Holben W.E., Feldman R.V.R., and Cary S.C. Genetic variation among endosymbionts of widely distributed Vestimentiferan tubeworms. Applied and Environmental Microbiology 66 (2000) 651-658
16. Dubilier N., Mulders C., Ferdelman T., de Beer D., Pernthaler A.K.M., et al. Endosymbiotic sulphate-reducing and sulphide-oxidizing bacteria in an oligochaete worm. Nature 411 (2001) 298-302
17. Dunfield K.E., and King G.M. Analysis of the distribution and diversity in recent Hawaiian volcanic deposits of a putative carbon monoxide dehydrogenase large subunit gene. Environmental Microbiology 7 (2005) 1505-1412
18. Fabricius K.E. Effects of terrestrial runoff on the ecology of corals and coral reefs: review and synthesis. Marine Pollution Bulletin 50 (2005) 125-146
19. Fabricius K.E., De'ath G., McCook L., Turak E., and Williams D.M. Changes in algal, coral and fish assemblages along water quality gradients on the inshore Great Barrier Reef. Marine Pollution Bulletin 51 (2005) 384-398
20. Felsenstein J. PHYLIP Phylogeny Inference Package version 3.5c. Distributed by the Author (1993), Department of Genetics, University of Washington, Seattle
21. Frias-Lopez J., Zerkle A., Bonheyo G., and Fouke B. Partitioning of bacterial communities between seawater and healthy, black band diseased and dead coral surfaces. Applied and Environmental Microbiology 68 (2002) 2214-2228
22. Furnas M. Catchments and Corals: Terrestrial Runoff to the Great Barrier Reef (2003), Australian Institute of Marine Science and CRC Reef, Townsville Australia
23. Guthrie J.N., Moriarty D.J.W., and Blackall L.L. DNA extraction from coral reef sediment bacteria for the polymerase chain reaction. Journal for Microbiological Methods 43 (2000) 73-80
24. Hamilton L.J. Cross-shelf colour zonation in northern Great Barrier Reef lagoon surficial sediments. Australian Journal of Earth Science 48 (2001) 193-200
25. Hentschel U., Hopke J., Horn M., Friedrich A., Wagner M., and Moore B. Molecular evidence for a uniform microbial community in sponges from different oceans. Applied and Environmental Microbiology 68 (2002) 4431-4440
26. Hentschel U., Usher K.M., and Taylor M.W. Marine sponges as microbial fermenters. FEMS Microbiology Ecology 55 (2006) 167-177
27. Hewson I., and Fuhrman J.A. Spatial and vertical biogeography of coral reef sediment bacterial and diazotroph communities. Marine Ecology Progress Series 306 (2006) 79-86
28. Holland, S.H., 1988. A Rarefactwin Program, Version 1.2. [URL Document]. http://www.uga.edu/strata/Software.html.
29. Holmes A.J., Tujula N., Holley M., Contos A., James J., Rogers P., and Gillings M.R. Phylogenetic structure of unusual aquatic microbial formations in Nullarbor Caves, Australia. Environmental Microbiology 3 (2001) 256-264
30. Huber T., Faulkner G., and Hugenholtz P. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20 (2004) 2317-2319
31. Jørgensen B. Mineralization of organic matter in the sea bed - the role of sulphate reduction. Nature 296 (1982) 643-645
32. Koenneke M., Bernhard A.E., de la Torre J.R., Walker C.B., Waterbury J.B., and Stahl D.A. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437 (2005) 543-546
33. Leuders T., and Friedrich M.W. Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Applied and Environmental Microbiology 69 (2003) 320-326
34. Li L., Guenzennec J., Nichols P., Henry P., Yanagibayashi M., and Kato C. Microbial diversity in Nankai Trough sediments at a depth of 3843 m. Journal of Oceanography 55 (1999) 635-642
35. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, et al. ARB: a software environment for sequence data. Nucleic Acid Research 32 (2004) 1363-1371
36. Madrid V.M., Aller J.Y., Aller R.C., and Chistoserdov A.Y. High prokaryote diversity and analysis of community structure in mobile mud deposits off French Guiana: identification of two new bacterial candidate divisions. FEMS Microbiology Ecology 37 (2001) 197-209
37. Maidak B., Cole J., Parker C.J., Garrity G., Larsen N., Li B., et al. A new version of the RDP Ribosomal Database Project. Nucleic Acid Research 27 (1999) 171-173
38. Marchesi J.R., Weightman A.J., Crag B.A., Parkes R.J., and Fry J.C. Methanogen and bacterial diversity and distribution in deep sea hydrate sediments from the Cascadia Margin as revealed by 16s rRNA molecular analysis. FEMS Microbiology Ecology 34 (2001) 221-228
39. Martin A.P. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Applied and Environmental Microbiology 68 (2002) 3673-3682
40. Nanba K., King G.M., and Dunfield K. Analysis of facultative lithotroph distribution and diversity on volcanic deposits by use of large subunit of Ribulose 1,5-Bisphosphat carboxylase/oxygenase. Applied and Environmental Microbiology 70 (2004) 2245-2253
41. Phelps C., Kerkhof L., and Young L.Y. Molecular characterization of a sulfate-reducing consortium which mineralizes benzene. FEMS Microbiology Ecology 27 (1998) 269-279
42. Polz M.F., and Cavanaugh C.M. Bias in template-to-product ratios in multi-template PCR. Applied and Environmental Microbiology 64 (1998) 3724-3730
43. Ravenschlag K., Sahm K., Pernthaler J., and Amann R. High bacterial diversity in permanently cold marine sediments. Applied and Environmental Microbiology 65 (1999) 3982-3989
44. Reysenbach A.-L., and Pace N. Reliable amplification of hyperthermophilic archaeal 16S rRNA genes by PCR. In: Robb F.T., and Place A.R. (Eds). Thermophiles (1995), Cold Spring Harbor Press, New York 101-106
45. Schaffelke B., Uthicke S., and Klumpp D.W. Water Quality, Sediment and Biological Parameters at Four Nearshore Reef Flats in the Herbert River Region, Central GBR (2004), Great Barrier Reef Marine Park Authority, Townsville, Australia Research Publication No. 82, p. 64
46. Schaffelke B., Mellors J., and Duke N. Water quality in the Great Barrier Reef region: responses of mangrove, seagrass and macroalgal communities. Marine Pollution Bulletin 51 (2005) 279-296
47. Schneider S., Roessli D., and Excoffier L. Arlequin ver. 2.000: a software for population genetic data analysis (2000), Genetics and Biometry Laboratory, University of Geneva, Swizerland. http://anthro.unige.ch/aelequin Available from
48. Suzuki M.T., and Giovanni S.J. Bias caused by template annealing in the amplification mixtures of 16S rRNA genes by PCR. Applied and Environmental Microbiology 62 (1996) 625-630
49. Todorov J.R., Aller J., Chistoserdov A.Y., and Aller R. Molecular microbial diversity in physically disturbed coastal sediments of southeastern Papua New Guinea. FEMS Microbiology Ecology 33 (2000) 147-155
50. Uthicke, S., 1994. Distribution Patterns and Growth of Two Reef Flat Holothurians, Holothuria atra and Stichopus chloronotus. Echinoderms Through Time, Proceedings of the 8th International Echinoderm Conference, Dijon. AA Balkema, Rotterdam, pp. 569-576.
51. Venter J., Remington K., Heidelberg J., Halpern A.L., Rusch D., Eisen J.A., et al. Environmental Genome Shotgun Sequencing of the Sargasso Sea. Science 304 (2004) 66-74
52. Vergin K.L., Urbach E., Stein J., DeLong E., Lanoil B., and Giovannoni S.J. Screening of a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of the order Planctomycetales. Applied and Environmental Microbiology 64 (1998) 3075-3078
53. Webster N.S., Wilson K.J., Blackall L.L., and Hill R.T. Phylogenetic diversity of bacteria associated with the marine sponge Rhopaloeides odorabile. Applied and Environmental Microbiology 67 (2001) 434-444
54. Webster G., Parkes R.J., Fry J.C., and Weightman A.J. Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments. Applied and Environmental Microbiology 70 (2004) 5708-5713
55. Webster N.S., Smith L.D., Heyward A.J., Watts J.E.M., Webb R.L., Blackall L.L., and Negri A.P. Metamorphosis of a scleractinian coral in response to microbial biofilms. Applied and Environmental Microbiology 70 (2004) 1213-1221
56. Wise M.G., McArthur J.V., and Shimkets L.J. Bacterial diversity of a Carolina Bay as determined by 16S rRNA gene analysis: confirmation of novel taxa. Applied and Environmental Microbiology 63 (1997) 1505-1514
57. Yanagibayashi M., Nogi Y., Li L., and Kato C. Changes in the microbial community in Japan Trench sediment from a depth of 6292 m during cultivation without decompression. FEMS Microbiology Letters 170 (1999) 271-279
58. Yi H., Bae K., and Chun J. Thalassomonas ganghwensis sp. nov., isolated from tidal flat sediment. International Journal of Systematic and Evolutionary Microbiology 54 (2004) 377-380
59. Zhang H., Sekiguchi Y., Hanada S., Hugenholtz P., Kim H., Kamagata Y., and Nakamura K. Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. International Journal of Systematic and Evolutionary Microbiology 53 (2003) 1155-1163