Microbial diversity within the water column of a larval rearing system for the ornate rock lobster (Panulirus ornatus)

Aquaculture

Volumn 258, Issue 1-4, 2006, Pages 80-90

  Payne, Matthew S ^a,b   Hall, Mike R ^a   Bannister, Raymond ^a,c   Sly, Lindsay ^b   Bourne, David G ^a  

^a AUSTRALIAN INSTITUTE OF MARINE SCIENCE   (Australia)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c JAMES COOK UNIVERSITY   (Australia)

Author keywords

16S rRNA; Bacterial diversity; Clone library; DGGE; Flow cytometry; Panulirus ornatus phyllosoma

Indexed keywords

FLOW CYTOMETRY; LARVA; LOBSTER; MICROBIAL COMMUNITY; REARING; STATISTICAL ANALYSIS; WATER COLUMN;

ALPHAPROTEOBACTERIA; ANIMALIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; CHLAMYDIACEAE; CHLAMYDIALES; EPSILONPROTEOBACTERIA; PANULIRUS ORNATUS; SPHINGOBACTERIALES; VIBRIO;

EID: 33747193007     PISSN: 00448486     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.aquaculture.2006.04.001     Document Type: Article

References (60)

1. ABARE. Australian Fisheries Statistics 2002 (2003), Canberra, Australian Bureau of Agricultural and Resource Economics
2. Acinas S.G., Klepac-Ceraj V., Hunt D.E., Pharino C., Ceraj I., Distel D.L., and Polz M.F. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430 6999 (2004) 551-554
3. Altschul S.F., Madden T.L., Schaeffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25 (1997) 3389-3402
4. Amann R.I., Ludwig W., and Schleifer K.-H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews 59 1 (1995) 143-169
5. Benlloch S., Lopez-Lopez A., Casamayor E.O., Ovreas L., Goddard V., Daae F.L., Smerdon G., Massana R., Joint I., Thingstad F., Pedros-Alio C., and Rodriguez-Valera F. Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern. Environmental Microbiology 4 6 (2002) 349-360
6. Bourne D.G., Young N., Webster N., Payne M., Salmon M., Demel S., and Hall M. Microbial community dynamics in a larval aquaculture system of the tropical rock lobster, Panulirus ornatus. Aquaculture 242 (2004) 31-51
7. Chao A. Non-parametric estimation of the number of classes in a population. Scandinavian Journal of Statistics 11 (1984) 265-270
8. Chao A. Estimating the population-size for capture recapture data with unequal catchability. Biometrics 43 (1987) 783-791
9. Colwell R.K. EstimateS: Statistical Estimation of Species Richness and Shared Species From Samples. Version 7.5. User's Guide and Application (2005)
10. Dennis D.M., Skewes T.D., and Pitcher C.R. Habitat use and growth of juvenile ornate rock lobsters, Panulirus ornatus (Fabricius, 1798), in Torres Strait, Australia. Marine and Freshwater Research 48 (1997) 663-670
11. Diggles B.K., Moss G.A., Carson J., and Anderson C.D. Luminous vibriosis in rock lobster Jasus verreauxi (Decapoda: Palinuridae) phyllosoma larvae associated with infection by Vibrio harveyi. Diseases of Aquatic Organisms 43 (2000) 127-137
12. Ferris M.J., Muyzer G., and Ward D.M. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Applied and Environmental Microbiology 62 (1996) 340-346
13. Fisher R.A., Corber A.S., and Williams C.B. The relation between the number of species and the number of individuals in a random sample of an animal population. Journal of Animal Ecology 12 (1943) 42-58
14. Foggo A., Rundle S.D., and Bilton D.T. The net result: evaluating species richness extrapolation techniques for littoral pond invertebrates. Freshwater Biology 48 (2003) 1756-1764
15. Gelsomino A., Keijzer-Wolters A.C., Cacco G., and Van Elsas J.D. Assessment of bacterial community structure in soil by polymerase chain reaction and denaturing gradient gel electrophoresis. Journal of Microbiological Methods 38 1-2 (1999) 1-15
16. Giovannoni S., and Rappé M. Evolution, diversity and molecular ecology of marine prokaryotes. In: Kirchman D. (Ed). Microbial Ecology of the Oceans (2000), Wiley-Liss, New York 47-84
17. Gonzalez J.M., and Moran M.A. Numerical dominance of a group of marine bacteria in the alpha-subclass of the class Proteobacteria in coastal seawater. Applied and Environmental Microbiology 63 11 (1997) 4237-4242
18. Good I.J. The population frequencies of species and the estimation to the population parameters. Biometrika 40 (1953) 237-264
19. Handlinger J., Carson J., Ritar A.J., Crear B.J., Taylor D.P., and Johnston D. Disease conditions of cultured phyllosoma larvae and juveniles of the southern rock lobster (Jasus edwardsii, Decapoda; Palinuridae). International Symposium on Lobster Health Management (1999) 75-87
20. Handlinger J., Carson J., Ritar A., and Crear B. A study of diseases in cultured phyllosoma larvae and juveniles of southern rock lobster (Jasus edwardsii). Journal of Shellfish Research 19 (2000) 676
21. Heck K.L.J., Van Belle G., and Simberloff D. Explicit calculation of the rarefaction diversity measurements and the determination of sufficient sample size. Ecology 56 (1975) 1459-1461
22. Holland S.H. A Rarefactwin Program, Version 1.2 (1988). http://www.uga.edu/strata/Software.html [URL Document]. http://www.uga.edu/strata/Software.html
23. Hurlbert S.H. The non-concept of species diversity: a critique and alternative parameters. Ecology 52 (1971) 577-586
24. Janvier M., Regnault B., and Grimont P. Development and use of fluorescent 16S rRNA-targeted probes for the specific detection of Methylophaga species by in situ hybridization in marine sediments. Research in Microbiology 154 (2003) 483-490
25. Juinio-Menezm M.A., and Ruinata J. Survival, growth and food conversion efficiency of Panulirus ornatus following eyestalk ablation. Aquaculture 146 (1996) 225-235
26. Khan S.T., Horiba Y., Yamamoto M., and Hiraishi A. Members of the family Comamonadaceae as primary Poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate)-degrading denitrifiers in activated sludge as revealed by a polyphasic approach. Applied and Environmental Microbiology 68 (2002) 3206-3214
27. Lane D.J. 16S/23S rRNA sequencing. In: Goodfellow E.S.M. (Ed). Nucleic Acid Techniques in Bacterial Systematics (1991), Wiley, Chichester 115-175
28. Lavilla-Pitogo C.R., Baticados M.C.L., Cruz-Lacierda E.R., and De la Pena L.D. Occurrence of luminous bacterial disease of Penaeus monodon larvae in the Philippines. Aquaculture 91 (1990) 1-13
29. Lavilla-Pitogo C.R., Leano E.M., and Paner M.G. Mortalities of pond-cultured juvenile shrimp, Penaeus monodon, associated with the dominance of luminescent Vibrios in the rearing environment. Aquaculture 164 (1998) 337-349
30. Lee K.K., Yu S.R., Chen F.R., Yang T.I., and Liu P.C. Virulence of Vibrio alginolyticus isolated from diseased tiger prawn, Penaeus monodon. Current Microbiology 32 (1996) 229-231
31. Lellis W.A., and Russell J.A. Effect of temperature on survival, growth and feed intake of postlarval spiny lobsters, Panulirus argus. Aquaculture 90 (1990) 1-9
32. Liu P.C., Lee K.K., and Chen S.N. Pathogenicity of different isolates of Vibrio harveyi in tiger prawn, Penaeus monodon. Letters in Applied Microbiology 22 (1996) 413-416
33. Ludwig W., Strunk O., Klugbauer S., Klugbauer N., Weizenegger M., Neumaier J., Bachleitner M., and Schleifer K.H. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19 4 (1998) 554-568
34. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S., Jobb G., Förster W., Brettske I., Gerber S., Ginhart A.W., Gross O., Grumann S., Hermann S., Jost R., König A., Liss T., Lüβmann R., May M., Nonhoff B., Reichel B., Strehlow R., Stamatakis A., Struckmann N., Vilbig A., Lenke M., Ludwig T., Bode A., and Schleifer K.-H. ARB: a software environment for sequence data. Nucleic Acids Research 32 4 (2004) 1363-1371
35. Maarit Niemi R., Heiskanen I., Wallenius K., and Lindstrom K. Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia. Journal of Microbiological Methods 45 3 (2001) 155-165
36. Magurran A.E. Ecological Diversity and Its Measurement (1988), Princeton University Press, Princeton, NJ
37. Maidak B.L., Olsen G.J., Larsen N., Overbeek R., McCaughey M.J., and Woese C.R. The Ribosomal Database Project (RDP). Nucleic Acids Research 24 (1996) 82-85
38. Marie D., Brussaard C.P.D., Thyrhaug R., Bratbak G., and Vaulot D. Enumeration of marine viruses in culture and natural samples by flow cytometry. Applied and Environmental Microbiology 65 1 (1999) 45-52
39. Mergaert J., Boley A., Cnockaert M.C., Müller W.R., and Swings J. Identity and potential functions of heterotrophic bacterial isolates from a continuous-upflow fixed-bed reactor for denitrification of drinking water with bacterial polyester as source of carbon and electron donor. Systematic and Applied Microbiology 24 (2001) 303-310
40. Moyer C.B., Dobbs F., and Karl D. Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Applied and Environmental Microbiology 60 (1994) 871-879
41. Muyzer G., and Smalla K. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek 73 1 (1998) 127-141
42. Muyzer G., de Waal E.C., and Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology 59 3 (1993) 695-700
43. Nikolausz M., Sipos R., Revesz S., Szekely A., and Marialigeti K. Observation of bias associated with re-amplification of DNA isolated from denaturing gradient gels. FEMS Microbiology Letters 244 2 (2005) 385-390
44. Owens L., Muir P., Sutton D., and Wingfield M. The pathology of microbial diseases in tropical Australian crustacea. In: Shariff M., Subasinghe R.P., and Arthur J.R. (Eds). Diseases in Asian Aquaculture I (1992), Fish Health Section, Asian Fisheries Society, Manila, Philippines
45. Pukall R., Buntefuss D., Fruhling A., Rohde M., Kroppenstedt R.M., Burghardt J., Lebaron P., Bernard L., and Stackebrandt E. Sulfitobacter mediterraneus sp. nov., a new sulfite-oxidizing member of the alpha-Proteobacteria. International Journal of Systematic Bacteriology 49 2 (1999) 513-519
46. Retief J.D. Phylogenetic analysis using PHYLIP. Methods in Molecular Biology 132 (2000) 243-258
47. Rosemark R., and Fisher W.S. Vibriosis of lobster. In: Sindermann C.J., and Lightner D.V. (Eds). Disease Diagnosis and Control in North American Marine Aquaculture, 2nd rev. (1988), Elsevier Science Publishers, B.V., Amsterdam 240-243
48. Ruangpan L., and Kitao T. Vibrio bacteria isolated from black tiger shrimp, Penaeus monodon Fabricius. Journal of Fish Diseases 14 (1991) 383-388
49. Schauer M., Massana R., and Pedros-Alio C. Spatial differences in bacterioplankton along the Catalan coast (NW Mediterranean) assessed by molecular fingerprinting. FEMS Microbiology Letters 33 (2000) 51-59
50. Schafer H., Servais P., and Muyzer G. Successional changes in the genetic diversity of a marine bacterial assemblage during confinement. Archives of Microbiology 173 2 (2000) 138-145
51. Schloe K., Gillis M., Hoste B., Pot B., Vancanneyt M., Mergaert J., Swings J., Biedermann J., and Süssmuth R. Polyphasic characterization of poly-3-hydroxybutyrate-co-3-hydroxyvalerate (P(HB-co-HV)) metabolizing and denitrifying Acidovorax sp. strains. Systematic and Applied Microbiology 23 (2000) 364-372
52. Shannon C.E., and Weaver W. The Mathematical Theory of Communication (1963), University of Illinois Press, Urbana, IL
53. Sieburth J.M. Chemolithotrophs. In: Sieburth J.M. (Ed). Sea Microbes (1979), Oxford University Press, New York 165-176
54. Simberloff D. Use of rarefaction and related methods in ecology. In: Dickson K.L., Cairns J.J., and Livingston R.J. (Eds). Biological Data in Water Pollution Assessment: Quantitative and Statistical Analyses (1978), American Society for Testing and Materials, Philadelphia, PA 150-165
55. Sudheesh P.S., and Xu H.S. Pathogenicity of Vibrio parahaemolyticus in tiger prawn Penaeus monodon Fabricius: possible role of extracellular proteases. Aquaculture 196 (2001) 37-46
56. Suzuki M.T., and Giovannoni S.J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Applied and Environmental Microbiology 62 2 (1996) 625-630
57. Suzuki M., Rappe M.S., and Giovannoni S.J. Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Applied and Environmental Microbiology 64 11 (1998) 4522-4529
58. Takahashi Y., Itami T., and Kondo M. Immunodefense system of crustacea. Fish Pathology/Gyobyo Kenkyu 30 (1995) 141-150
59. Venter J.C., Remington K., Heidelberg J.F., Halpern A.L., Rusch D., Eisen J.A., Wu D., Paulsen I., Nelson K.E., Nelson W., Fouts D.E., Levy S., Knap A.H., Lomas M.W., Nealson K., White O., Peterson J., Hoffman J., Parsons R., Baden-Tillson H., Pfannkoch C., Rogers Y.-H., and Smith H.O. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304 (2004) 66-74
60. Webster, N.S., Bourne, D.G., Hall, M., in press. Vibrio infection in phyllosomas of the tropical rock lobster Panulirus ornatus as detected by fluorescence in situ hybridisation. Aquaculture.