The diversity of bacterial communities associated with Atlantic cod Gadus morhua

Microbial Ecology

Volumn 55, Issue 3, 2008, Pages 425-434

  Wilson, Bryan ^a   Danilowicz, Bret S ^a,b   Meijer, Wim G ^a  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

^b GEORGIA SOUTHERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RIBOSOME DNA; RNA 16S; SEA WATER;

ANIMAL; ARTICLE; ATLANTIC COD; ATLANTIC OCEAN; BACTERIUM; BIODIVERSITY; CLASSIFICATION; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MUCOSA; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEASON;

ANIMALS; ATLANTIC OCEAN; BACTERIA; BIODIVERSITY; DNA, BACTERIAL; DNA, RIBOSOMAL; GADUS MORHUA; MUCOUS MEMBRANE; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; SEASONS; SEAWATER; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); BACTEROIDES; BACTEROIDES (CLASS); BACTEROIDES SP.; CYTOPHAGA; FLAVOBACTER; GADUS MORHUA; GAMMAPROTEOBACTERIA; OTUS; PHOTOBACTERIUM; PHOTOBACTERIUM SP.; PSYCHROBACTER; PSYCHROBACTER SP.;

EID: 41049108077     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-007-9288-0     Document Type: Article

References (55)

1. Acinas, SG, Anton, J, Rodriguez-Valera, F (1999) Diversity of free-living and attached bacteria in offshore western Mediterranean waters as depicted by analysis of genes encoding16S rRNA. Appl Environ Microbiol 65:514-522
2. Al Harbi, AH, Naim Uddin, M (2004) Seasonal variation in the intestinal bacterial flora of hybrid tilapia (Oreochromis niloticus × Oreochromis aureus) cultured in earthern ponds in Saudi Arabia. Aquaculture 229:37-44
3. Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
4. Bano, N, Hollibaugh, JT (2002) Phylogenetic composition of bacterioplankton assemblages from the arctic ocean. Appl Environ Microbiol 68:505-518
5. Bjørkevoll, I, Olsen, RL, Skjerdal, OT (2003) Origin and spoilage potential of the microbiota dominating genus Psychrobacter in sterile rehydrated salt-cured and dried salt-cured cod (Gadus morhua). Int J Food Microbiol 84:175-187
6. Budsberg, KJ, Wimpee, CF, Braddock, JF (2003) Isolation and identification of Photobacterium phosphoreum from an unexpected niche: migrating salmon. Appl Environ Microbiol 69:6938-6942
7. Cooksey, KE, Wigglesworth-Cooksey, B (1995) Adhesion of bacteria and diatoms to surfaces in the sea. Aquat Microb Ecol 9:87-96
8. Cottrell, MT, Kirchman, DL (2000) Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Appl Environ Microbiol 66:5116-5122
9. Crouse-Eisnor, RA, Cone, DK, Odense, PH (1985) Studies on relations of bacteria with skin surface of Carassius auratus L. and Poecilia reticulata. J Fish Biol 27:395-402
10. Crump, BC, Armbrust, EV, Baross, JA (1999) Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia river, its estuary, and the adjacent coastal ocean. Appl Environ Microbiol 65:3192-3204
11. Dalgaard, P, Mejlholm, TJ, Christiansen, TJ, Huss, HH (1997) Importance of Photobacterium phosphoreum in relation to spoilage of modified atmosphere-packed fish products. Lett Appl Microbiol 24:373-378
12. del Cerro, A, Marquez, I, Guijarro, JA (2002) Simultaneous Detection of Aeromonas salmonicida, Flavobacterium psychrophilum, and Yersinia ruckeri, three major fish pathogens, by multiplex PCR. Appl Environ Microbiol 68:5177-5180
13. DeLong, EF, Franks, DG, Alldredge, AL (1993) Phylogenetic diversity of aggregate-attached vs. free-living marine bacteria assemblages. Limnol Oceanogr 38:924-934
14. Dunlap, PV (1985) Osmotic control of luminescence and growth in Photobacterium leiognathi from ponyfish light organs. Arch Microbiol 141:44-50
15. Dunlap, PV, Kita-Tsukamoto, K, Waterbury, JB, Callahan, SM (1995) Isolation and characterization of a visibly luminous variant of Vibrio fischeri strain ES114 from the sepiolid squid Euprymna scolopes. Arch Microbiol 164:194-202
16. Flemming, HC (2002) Biofouling in water systems-cases, causes and countermeasures. Appl Microbiol Biotechnol 59:629-640
17. Georgala, DL (1958) The bacterial flora of the skin of North Sea cod. J Gen Microbiol 18:84-91
18. Gillan, DC, Speksnijder, AGCL, Zwart, G, De Ridder, C (1998) Genetic diversity of the biofilm covering Montacuta ferruginosa (Mollusca, Bivalvia) as evaluated by denaturing gradient gel electrophoresis analysis and cloning of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 64:3464-3472
19. Giovannoni, SJ, Rappe, M (2000) Evolution, diversity and molecular ecology of marine prokaryotes. In: Kirchman DL (Ed.) Microbial ecology of the oceans. Wiley-Liss, New York, pp 47-84
20. Glöckner, FO, Fuchs, BM, Amann, R (1999) Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridisation. Appl Environ Microbiol 65:3721-3726
21. Gonzalez, JM, Moran, MA (1997) Numerical dominance of a group of marine bacteria in the alpha-subclass of the class Proteobacteria in coastal seawater. Appl Environ Microbiol 63:4237-4242
22. Hagi, T, Tanaka, D, Iwamura, Y, Hoshino, T (2004) Diversity and seasonal changes in lactic acid bacteria in the intestinal tract of cultured freshwater fish. Aquaculture 234:335-346
23. Hagström, Å, Pommier, T, Rohwer, F, Simu, K, Stolte, W, Svensson, D, Zweifel, UL (2002) Use of ribosomal DNA for delineation of marine bacterioplankton species. Appl Environ Microbiol 68:3628-3633
24. Hansen, GH, Olafsen, JA (1999) Bacterial interactions in early life stages of marine cold water fish. Microb Ecol 38:1-26
25. Hentschel, U, Hopke, J, Horn, M, Friedrich, AB, Wagner, M, Hacker, J, Moore, BS (2002) Molecular evidence for a uniform microbial community in sponges from different oceans. Appl Environ Microbiol 68:4431-4440
26. Holben, WE, Williams, P, Saarinen, M, Särkilahti, LK, Apajalahti, JHA (2002) Phylogenetic analysis of intestinal microflora indicates a novel mycoplasma phylotype in farmed and wild salmon. Microb Ecol 44:175-185
27. Horsley, RW (1973) The bacterial flora of the Atlantic salmon (Salmo salar L.) in relations to its environment. J Appl Bacteriol 36:377-386
28. Kirchman, DL (2002) The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol 39:91-100
29. Kreader, CA (1996) Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl Environ Microbiol 62:1102-1106
30. Lipp, EK, Jarrell, JL, Griffin, DW, Lukasik, J, Jacukiewicz, J, Rose, JB (2002) Preliminary evidence for fecal contamination on corals of the Florida Keys. Mar Pollut Bull 44:666-670
31. Liston, J (1957) The occurrence and distribution of bacterial types on flatfish. J Gen Microbiol 16:205-216
32. Lock, MA (1994) Dynamics of particulate and dissolved organic matter over the substratum of water bodies. In: Wotton, RS (Ed.) Particulate and dissolved matter in aquatic systems. Lewis, Chelsea, MI, pp 137-160
33. Lyons, MM, Aas, P, Pakulski, JD, Van Waasbergen, L, Miller, RV, Mitchell, DL, Jeffrey, WH (1998) DNA damage induced by ultraviolet radiation in coral-reef communities. Mar Biol 130:161-182
34. Maidak, BL, Olsen, GJ, Larsen, N, Overbeek, MJ, McCaughey, MJ, Woese, CR (1997) The RDP (Ribosomal Database Project). Nucleic Acids Res 25:109-111
35. Marchesi, JR, Sato, T, Weightman, AJ, Martin, TA, Fry, JC, Hiom, SJ, Dymock, D, Wade, WG (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64:795-799
36. Mudarris, M, Austin, B (1988) Quantitative and qualitative studies of the bacterial microflora of turbot, Scophthalmus maximus L., gills. J Fish Biol 32:223-229
37. Mullins, TD, Britschgi, TB, Krest, RL, Giovannoni, SJ (1995) Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol Oceanogr 40:148-158
38. Nieto, TP, Toranzo, AE, Barja, JL (1984) Comparison between the bacterial flora associated with fingerling rainbow trout cultured in two different hatcheries in the northwest of Spain. Aquaculture 42:193-206
39. Nocker, A, Lepo, JE, Snyder, RA (2004) Influence of an oyster reef on development of the microbial heterotrophic community of an estuarine biofilm. Appl Environ Microbiol 70:6834-6845
40. O'Toole, R, Lundberg, S, Fredriksson, S, Jansson, A, Nilsson, B, Wolf-Watz, H (1999) The chemotactic response of Vibrio anguillarum to fish intestinal mucus is mediated by a combination of multiple mucus components. J Bacteriol 181:4308-4317
41. Osborn, AM, Moore, ERB, Timmis, KN (2000) An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ Microbiol 2:39-50
42. Pinhassi, J, Hagström, A (2000) Seasonal succession in marine bacterioplankton. Aquat Microb Ecol 21:245-256
43. Polz, MF, Harbison, C, Cavanaugh, CM (1999) Diversity and heterogeneity of epibiotic bacterial communities on the marine nematode Eubostrichus dianae. Appl Environ Microbiol 65:4271-4275
44. Rehnstam, AS, Backman, S, Smith, DC, Azam, F, Hagström, A (1993) Blooms of sequence-specific culturable bacteria in the sea. FEMS Microbiol Lett 102:161-166
45. Ruby, EG, Lee, KH (1998) The Vibrio fischeri-Euprymna scolopes light organ association: current ecological paradigms. Appl Environ Microbiol 64:805-812
46. Sambrook, J, Manniatis, T, Fritsch, EF (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA
47. Smith, CJ, Danilowicz, BS, Clear, AK, Costello, FJ, Wilson, B, Meijer, WG (2005) T-Align, a web based tool for comparison of multiple terminal restriction fragment length polymorphism profiles. FEMS Microbiol Ecol 54:375-380
48. Sugita, H, Shibuya, K, Shimooka, H, Deguchi, Y (1996) Antibacterial abilities of intestinal bacteria in freshwater cultured fish. Aquaculture 145:195-203
49. Thompson, JD, Gibson, TJ, Plewniak, F, Jeanmougin, F, Higgins, DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 22:4673-4680
50. Van de Peer, Y, De Wachter, R (1994) TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10:569-570
51. Van Der Maarel, MJEC, Artz, RRE, Haanstra, R, Forney, LJ (1998) Association of marine Archaea with the digestive tracts of two marine fish species. Appl Environ Microbiol 64:2894-2898
52. Webster, NS, Wilson, KJ, Blackall, LL, Hill, RT (2001) Phylogenetic diversity of bacteria associated with the marine sponge Rhopaloeides odorabile. Appl Environ Microbiol 67:434-444
53. Wotton, RS (2004) The essential role of exopolymers (EPS) in aquatic systems. In: Gibson, RN, Atkinson, RJA, Gordon, JDM (Eds.) Oceanography and marine biology: an annual review, vol. 42, pp 57-94
54. Wotton, RS (2004) The ubiquity and many roles of exopolymers (EPS) in aquatic systems. Sci Mar 68:13-21
55. Yager, PL, Connelly, TL, Mortazavi, BB, Wommack, KE, Bano, N, Bauer, J, Opsahl, S, Hollibaugh, JT (2001) Dynamic microbial response to an Arctic algal bloom at sub-zero temperatures. Limnol Oceanogr 44:1882-1893