Phylogenetic analysis of bacterial communities associated with larvae of the atlantic halibut propose succession from a uniform normal flora

Systematic and Applied Microbiology

Volumn 27, Issue 6, 2004, Pages 728-736

  Jensen, Sigmund ^a   Øvreås, Lise ^b   Bergh, Øivind ^a   Torsvik, Vigdis ^b  

^a INSTITUTE OF MARINE RESEARCH   (Norway)

^b UNIVERSITY OF BERGEN   (Norway)

Author keywords

16S rRNA; Aquaculture; Atlantic halibut; Bacterial community; DGGE; Normal flora; Phylogeny

Indexed keywords

PRIMER RNA;

ARTICLE; BACTERIAL FLORA; BACTERIUM COLONY; BIOFILM; CANADA; COMMUNITY SUCCESSION; COMPARATIVE STUDY; CONTROLLED STUDY; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA EXTRACTION; EUBACTERIUM; FERMENTATION; FISH; GEOGRAPHY; HATCHING; ICELAND; LARVAL DEVELOPMENT; MICROBIAL ACTIVITY; NONHUMAN; NORWAY; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PSEUDOMONAS; RNA SEQUENCE; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE; UNITED KINGDOM; VIBRIO;

BACTERIA (MICROORGANISMS); HIPPOGLOSSUS HIPPOGLOSSUS; JANTHINOBACTERIUM; MARINOMONAS; PLEURONECTIFORMES; PSEUDOMONAS; SILO; VIBRIO;

EID: 9944256168     PISSN: 07232020     EISSN: None     Source Type: Journal    
DOI: 10.1078/0723202042369929     Document Type: Article

References (44)

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., Lipman D. J.: Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
2. Bergh, Ø.: Bacteria associated with early life stages of halibut, Hippoglossus hippoglossus L., inhibit growth of a pathogenic Vibrio sp. J. Fish Dis. 18, 31-40 (1995).
3. Bergh, Ø., Naas, K. E., Harboe T.: Shift in the intestinal microflora of Atlantic halibut (Hippoglossus hippoglossus) larvae during first feeding. Can. J. Fish. Aquat. Sci. 51, 1899-1903 (1994).
4. Bergh, Ø., Nilsen, F., Samuelsen, O. B.: Diseases, prophylaxis and treatment of the Atlantic halibut, Hippoglossus hippoglossus: a review. Dis. Aquatic. Org. 48, 57-74 (2001).
5. Bidle, K. D., Azam, F.: Bacterial control of silicon regeneration from diatom detritus: significance of bacterial ectohydrolases and species identity. Limnol. Oceanogr. 46, 1606-1623 (2001).
6. Bolinches, J., Egidius, E.: Heterotrophic bacterial communities associated with the rearing of halibut Hippoglossus hippoglossus with special reference to Vibrio spp. J. Appl. Ichthyol. 3, 165-173 (1987).
7. Eilers, H., Pernthaler, J., Glöckner, F. O., Amann R.: Culturability and in situ abundance of pelagic bacteria from the North sea. Appl. Environ. Microbiol. 66, 3044-3051 (2000).
8. Felsenstein, J.: Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 22, 521-565 (1988).
9. Gatesoupe, F. J.: The use of probiotics in aquaculture. Aquaculture 180, 147-165 (1999).
10. Gram, L., Melchiorsen, J., Spanggaard, B., Huber, I., Nielsen, T. F.: Inhibition of Vibrio anguillarum by Pseudomonas fluorescens AH2, a possible probiotic treatment of fish. Appl. Environ. Microbiol. 65, 969-973 (1999).
11. Griffiths, S., Melville, K., Cook, M., Vincent, S., Pierre, M. St., Lanteigne, C.: Profiling of bacterial species associated with haddock larviculture by PCR amplification of 16S rDNA and denaturing gradient gel electrophoresis. J. Aquat. Anim. Health. 13, 355-363 (2001).
12. Gutell, R. R., Larsen, N., Woese, C. R.: Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev. 58, 10-26 (1994).
13. Hansen, G. H., Olafsen, J. A.: Bacterial interactions in early life stages of marine cold water fish. Microb. Ecol. 38, 1-26 (1999).
14. Hentschel, U., Hopke, J., Horn, M., Friedrich, A. B., Wagner, M., Hacker, J., Moore, B. S.: Molecular evidence for a uniform microbial community in sponges from different oceans. Appl. Environ. Microbiol. 68, 4431-4440 (2002).
15. Higgins, D., Thompson, J., Gibson, T., Thompson, J. D., Higgins, D. G., Gibson, T. J.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680 (1994).
16. Holben, W. E., Williams, P., Saarinen, M., Sarkilahti, L. K., Apajalahti, J. H. A.: Phylogenetic analysis of intestinal microflora indicates a novel Mycoplasma phylotype in farmed and wild salmon. Microbiol. Ecol. 44, 175-185 (2002).
17. Holmström, C., Kjelleberg, S.: Marine Pseudoalteromonas species are associated with higher organisms and produce biologically active extracellular agents. FEMS Microbiol. Ecol. 30, 285-293 (1999).
18. Jensen, S., Bergh, Ø., Enger, Ø., Hjeltnes, B.: Use of PCR-RFLP for genotyping 16S rRNA and characterizing bacteria cultured from halibut fry. Can. J. Microbiol. 48, 379-386 (2002).
19. Lau, W. W., Jumars, P. A., Armbrust, E. V.: Genetic diversity of attached bacteria in the hindgut of the deposit-feeding shrimp Neotrypaea (formerly Callianassa) californiensis (decapoda: thalassinidae). Microb. Ecol. 43, 455-466 (2002).
20. Liston, J.: The occurrence and distribution of bacterial types on flatfish. J. Gen. Microbiol. 16, 205-216 (1957).
21. Long, R. A., Azam, F.: Antagonistic interactions among marine pelagic bacteria. Appl. Environ. Microbiol. 67, 4975-4983 (2001).
22. Mangor-Jensen, A., Harboe, T., Shields, R. J., Gara, B., Naas, K. E.: Atlantic halibut, Hippoglossus hippoglossus L., larvae cultivation literature, including a bibliography. Aquaculture Res. 29, 857-886 (1998).
23. McFall-Ngai, M. J.: Unseen forces: the influence of bacteria on animal development. Dev. Biol. 242, 1-14 (2002).
24. Muyzer, G., DeWaal, E. C., Uitterlinden, A. G.: 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 (1993).
25. Neefs, J. M., Peer, Y. V., Rijk, P., Chapelle, S., Wachter, R.: Compilation of small ribosomal subunit RNA structures. Nucleic Acid Res. 21, 3025-3049 (1993).
26. Onarheim, A. M., Raa, J.: Characteristics and possible biological significance of an autochthonous flora in the intestinal mucosa of sea-water fish, pp. 197-201. In: Microbiology in poecilotherms (R. Lésel., ed.) Elsevier Science Publishers, B.V. The Netherlands 1990.
27. Øvreås, L., Bourne, D., Sandaa, R. A., Casamayor, E. O., Benlloch, S., Goddard, V., Smerdon, G., Heldal, M., Thingstad, T. F.: Response of bacterial and viral communities to nutrient manipulations in seawater mesocosms. Aquat. Microb. Ecol. 31, 109-121 (2003).
28. Øvreås, L., Forney, L., Daae, F. L., Torsvik, V.: Distribution of bacterioplankton in meromictic lake Sælenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 63, 3367-3373 (1997).
29. Porter, K. G., Feig Y. S.: The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25, 943-948 (1980).
30. Ringø, E., Birkbeck, T. H.: Intestinal microflora of fish larvae and fry. Aquaculture Research 30, 73-93 (1999).
31. Sambrook, J., Fritsch, E. F., Maniatis T.: Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, New York (1989).
32. Sandaa, R. A., Magnesen, T., Torkildsen, L., Bergh, Ø.: Characterisation of the bacterial community associated with early stages of great scallop (Pecten maximus), using denaturing gradient gel electrophoresis (DGGE). System. Appl. Microbiol. 26, 202-311 (2003).
33. Schabereiter-Gurtner, C., Lubitz, W., Rölleke, S.: Application of broad-range 16S rRNA PCR amplification and DGGE fingerprinting for detection of tick-infecting bacteria. J. Microbiol. Methods. 52, 251-260 (2003).
34. Schäfer, H., Abbas, B., Witte, H., Muyzer, G.: Genetic diversity of 'satellite' bacteria present in cultures of marine diatoms. FEMS Microbiol. Ecol. 42, 25-35 (2002).
35. Shields, R. J., Gara, B., Gillespie, M. J. S.: A UK perspective on intensive hatchery rearing methods for Atlantic halibut (Hippoglossus hippoglossus L.). Aquaculture 176, 15-25 (1999).
36. Sieburth, J. M.: Sea microbes. Oxford University Press, New York (1979).
37. Simidu, U., Tsukamoto, K.: Habitat segregation and biochemical activities of marine members of the family Vibrionaceae. Appl. Environ. Microbiol. 50, 781-790 (1985).
38. Skjermo, J., Vadstein, O.: Techniques for microbial control in the intensive rearing of marine larvae. Aquaculture. 177, 333-343 (1999).
39. Snel, J.: Symbiosis between the mouse and segmented filamentous bacteria: a gnotobiotic study. Thesis University of Nijmegen. ISBN 90-9010578-6 (1997).
40. Torsvik, V., Øvreås, L., Thingstad, T. F.: Prokaryotic diversity - magnitude, dynamics, and controlling factors. Science 296, 1064-1066 (2002).
41. Verner-Jeffreys, D. W., Shields, R. J., Birkbeck, T. H.: Bacterial influences on Atlantic halibut Hippoglossus hippoglossus yolk-sac larval survival and start-feed response. Dis. Aquat. Org. 56, 105-113 (2003a).
42. Verner-Jeffreys, D. W., Shields, R. J., Bricknell, I. R., Birkbeck, T. H.: Changes in the gut-associated microflora during the development of Atlantic halibut (Hippoglossus hippoglossus L.) larvae in three British hatcheries. Aquaculture 219, 21-42 (2003b).
43. Ward, D. M., Bateson, M. M., Weller, R., Ruff-Roberts, A. L.: Ribosomal RNA analysis of microorganisms as they occur in nature. Adv. Microb. Ecol. 12, 219-286 (1992).
44. Westerdahl, A., Olsson, J. C., Kjelleberg, S., Conway, P. L.: Isolation and characterization of turbot (Scophthalmus maximus) associated bacteria with inhibitory effects against Vibrio anguillarum. Appl. Environ. Microbiol. 57, 2223-2228 (1991).