Dynamics of bacterial community composition and activity during a mesocosm diatom bloom

Applied and Environmental Microbiology

Volumn 66, Issue 2, 2000, Pages 578-587

  Riemann, Lasse ^a,b   Steward, Grieg F ^a,c   Azam, Farooq ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c MONTEREY BAY AQUARIUM RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHLOROPHYLL A; SEA WATER;

CARBON; COMMUNITY COMPOSITION; COMMUNITY DYNAMICS; DIATOM; ENZYME ACTIVITY; LABORATORY METHOD; MESOCOSM; MICROBIAL COMMUNITY; NUTRIENT DYNAMICS;

ARTICLE; BACTERIAL COLONIZATION; BACTERIAL GROWTH; BACTERIUM COLONY; DIATOM; ENZYME ACTIVITY; FLEXIBACTERACEAE; METAZOON; MICROORGANISM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYTOPLANKTON; SEA;

ALPHAPROTEOBACTERIA; BACTERIA; BACTEROIDETES; CHLOROPHYLL; CLONING, MOLECULAR; DIATOMS; DNA, BACTERIAL; ECOSYSTEM; ELECTROPHORESIS; ENZYMES; EUTROPHICATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; WATER MICROBIOLOGY;

ALPHAPROTEOBACTERIA; BACILLARIOPHYTA; BACTERIA (MICROORGANISMS); FLEXIBACTERACEAE; MASTIGOPHORA (FLAGELLATES); METAZOA; SPHINGOBACTERIALES; THALASSIOSIRA;

EID: 0033951021     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.66.2.578-587.2000     Document Type: Article

References (77)

1. Acinas, S. G., J. Antón, and F. Rodríguez-Valera. 1999. Diversity of free-living and attached bacteria in offshore Western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA. Appl. Environ. Microbiol. 65:514-522.
2. Alldredge, A. L., U. Passow, and B. E. Logan. 1993. The abundance of a class of large, transparent organic particles in the ocean. Deep-Sea Res. 40: 1131-1140.
3. Altschul, S. F., T. L. Madden, A. A. Schaler, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
4. Azam, F. 1998. Microbial control of oceanic carbon flux: the plot thickens. Science 280:694-696.
5. Bidle, K., and M. Fletcher. 1995. Comparison of free-living and particle-associated bacterial communities in the Chesapeake Bay by stable low-molecular-weight RNA analysis. Appl. Environ. Microhiol. 61:944-952.
6. Bowman, J. P., S. A. McCammon, M. V. Brown, D. S. Nichols, and T. McMeekin. 1997. Diversity and association of psychrophilic bacteria in Antarctic Sea ice. Appl. Environ. Microbiol. 63:3068-3078.
7. Bratbak, G., M. Heldal, S. Norland, and T. F. Thingstad. 1990. Viruses as partners in spring bloom microbial trophodynamics. Appl. Environ. Microbiol. 56:1400-1405.
8. Caron, D. A. 1987. Grazing of attached bacteria by heterotrophic microflagellates. Microb. Ecol. 13:203-218.
9. Chróst, R. J., and J. Overbeck. 1987. Kinetics of alkaline phosphatase activity and phosphorus availability for phytoplankton and bacterioplankton in Lake Plußsee (north German eutrophic lake). Microb. Ecol. 13:229-248.
10. DeLong, E. F., D. G. Franks, and A. L. Alldredge. 1993. Phylogenetic diversity of aggregate-attached vs free-living marine bacterial assemblages. Limnol. Oceanogr. 38:924-934.
11. Don, R. H., P. T. Cox, B. J. Wainwright, K. Baker, and J. S. Mattick. 1991. "Touchdown" PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res. 19:4008.
12. Fandino, L. B., L. Riemann, G. F. Steward, R. A. Long, and F. Azam. 1998. Bacterial succession during a dinoflagellate bloom analyzed by DGGE and rDNA sequencing. Suppl. EOS Trans. Am. Geophys. Union 79:OS63.
13. Fernandez, E., T. Bienvenu, F. D. Arramond, K. Beldjord, J. C. Kaplan, and C. Beldjord. 1993. Use of chemical clamps in denaturing gradient gel electrophoresis: application in the detection of the most frequent Mediterranean β-thalassemic mutations. PCR Methods Applic. 3:122-124.
14. Field, K. G., D. Gordon, T. Wright, M. Rappé, E. Lrbach, K. Vergin, and S. J. Giovannoni. 1997. Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Appl. Environ. Microbiol. 63:63-70.
15. Fuhrman, J. A. 1999. Marine viruses and their biogeochemical and ecological effects. Nature 399:541-548.
16. Fuhrman, J. A., and L. Campbell. 1998. Microbial microdiversity. Nature 393:410-411.
17. Fuhrman, J. A., K. McCallum, and A. A. Davis. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl. Environ. Microbiol. 59:1294-1302.
18. Gajewski, A. J., R. J. Chróst, and W. Siuda. 1993. Bacterial lipolytic activity in a eutrophic lake. Arch. Hydrobiol. 128:107-126.
19. Glöckner, F. O., B. M. Fuchs, and R. Amann. 1999. Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl. Environ. Microbiol. 65:3721-3726.
20. González, J. M., and M. A. Moran. 1997. Numerical dominance of a group of marine bacteria in the α-subclass of Proteobacteria in coastal seawater. Appl. Environ. Microbiol. 63:4237-4242.
21. Gonzalez, J. M., J. Iriberri, L. Egea, and A. Barcina. 1990. Differential rates and digestion of bacteria by freshwater and marine phagotrophic protozoa. Appl. Environ. Microbiol. 56:1851-1857.
22. González, J. M., E. B. Sherr, and B. F. Sherr. 1993. Differential feeding by marine flagellates on growing versus starving, and on motile versus nonmotile, bacterial prey. Mar. Ecol. Prog. Ser. 102:257-267.
23. González, J. M., R. P. Kiene, and M. A. Moran. 1999. Transformations of sulfur compounds by an abundant lineage of marine bacteria in the α-sub-class of the class Proteobacteria. Appl. Environ. Microbiol. 65:3810-3819.
24. Griffith, P., F.-K. Shiah, K. Gloersen, H. W. Ducklow, and M. Fletcher. 1994. Activity and distribution of attached bacteria in Chesapeake Bay. Mar. Ecol. Prog. Ser. 108:1-10.
25. Grossart, H.-P., and M. Simon. 1998. Bacterial colonization and microbial decomposition of limnetic organic aggregates (lake snow). Aquat. Microb. Ecol. 15:127-140.
26. Hahn, M. W., E. R. B. Moore, and M. G. Höfle. 1999. Bacterial filament formation, a defense against flagellate grazing, is growth rate controlled in bacteria of different phyla. Appl. Environ. Microbiol. 65:25-35.
27. Hennes, K. P., C. A. Suttle, and A. M. Chan. 1995. Fluorescently labeled virus probes show that natural virus populations can control the structure of marine microbial communities. Appl. Environ. Microbiol. 61:3623-3627.
28. Höfle, M. G. 1992. Bacterioplankton community structure and dynamics after large-scale release of nonindigenous bacteria as revealed by low-molecular-weight analysis. Appl. Environ. Microbiol. 58:3387-3394.
29. Hoppe, H.-G. 1983. Significance of exoenzymatic activities in the ecology of brackish water: measurements by means of methylumbelliferyl-substrates. Mar. Ecol. Prog. Ser. 11:299-308.
30. Jespersen, A.-M., and K. Christoffersen. 1987. Measurements of chlorophyll-a from phytoplankton using ethanol as extraction solvent. Arch. Hydrobiol. 109:445-454.
31. Jürgens, K., and H. Güde. 1994. The potential importance of grazing-resistant bacteria in planktonic systems. Mar. Ecol. Prog. Ser. 112:169-188.
32. Karner, M., C. Ferrier-Pagés, and F. Rassoulzadegan. 1994. Phagotrophic nanoflagellates contribute to occurrence of α-glucosidase and aminopeptidase in marine environments. Mar. Ecol. Prog. Ser. 114:237-244.
33. Kirchman, D., E. K. Nees, and R. Hodson. 1985. Leucine incorporation and its potential as a measure of protein synthesis by bacteria in natural aquatic systems. Appl. Environ. Microbiol. 49:599-607.
34. Kirchman, D. L., Y. Suzuki, C. Garside, and H. W. Ducklow. 1991. High turnover rates of dissolved organic carbon during a spring phytoplankton bloom. Nature 352:612-614.
35. Koike, I., S. Hara, K. Terauchi, and K. Kogure. 1990. Role of sub-micrometre particles in the ocean. Nature 345:242-244.
36. Lafay, B., R. Ruimy, C. R. Trauenberg, V. Breittmayer, M. J. Gauthier, and R. Christen. 1995. Roseobacter algicola sp nov, a new marine bacterium isolated from the phycosphere of the toxin-producing dinoflagellate Prorocentrum lima. Int. J. Syst. Bacteriol. 45:290-296.
37. Lee, S., and J. A. Fuhrman. 1987. Relationships between biovolume and biomass of naturally derived marine bacterioplankton. Appl. Environ. Microbiol. 53:1298-1303.
38. Long, R. A., and F. Azam. 1996. Abundant protein-containing particles in the sea. Aquat. Microb. Ecol. 10:213-221.
39. Maidak, B. L., J. R. Cole, C. T. Parker, Jr., G. M. Garrity, N. Larsen, B. Li, T. G. Lilburn, M. J. McCaughey, G. J. Olsen, R. Overbeek, S. Pramanik, T. M. Schmidt, J. M. Tiedje, and C. R. Woese. 1999. A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27:171-173.
40. Manz, W., R. Amann, W. Ludwig, M. Vancanney, and K.-H. Schleifer. 1996. Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum Cytophaga-Flavobacter-Bacteroides in the natural environment. Microbiology 142:1097-1106.
41. Martinez, J., D. C. Smith, G. F. Steward, and F. Azam. 1996. Variability in ectohydrolytic enzyme activities of pelagic marine bacteria and its significance for substrate processing in the sea. Aquat. Microb. Ecol. 10:223-230.
42. McClung, C. R., D. G. Patriquin, and R. E. Davis. 1983. Campylobacter nitrofigilis sp nov, a nitrogen-fixing bacterium associated with roots of Spartina alterniflora Loisel. Int. J. Syst. Bacteriol. 33:605-612.
43. Middelboe, M., M. Søndergaard, Y. Letarte, and N. H. Borch. 1995. Attached and free-living bacteria: production and polymer hydrolysis during a diatom bloom. Microb. Ecol. 29:231-248.
44. Murray, A. E., C. M. Preston, R. Massana, L. T. Taylor, A. Blakis, K. Wu, and E. F. DeLong. 1998. Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl. Environ. Microbiol. 64:2585-2595.
45. 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.
46. Nagata, T., and D. L. Kirchman. 1992. Release of macromolecular organic complexes by heterotrophic marine flagellates. Mar. Ecol. Prog. Ser. 83: 233-240.
47. Noble, R. T., and J. A. Fuhrman. 1998. Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat. Microb. Ecol. 14:113-118.
48. Palumbo, A. V., R. L. Ferguson, and P. A. Rublee. 1984. Size of suspended bacterial cells and association of heterotrophic activity with size fractions of particles in estuarine and coastal waters. Appl. Environ. Microbiol. 48:157-164.
49. Parsons, T. R., Y. Maita, and C. M. Lalli. 1984. A manual of chemical and biological methods for seawater analysis. Pergamon Press, Elmsford, N.Y.
50. Peters, F. 1994. Prediction of planktonic protistan grazing rates. Limnol. Oceanogr. 39:195-206.
51. Pinhassi, J., F. Azam, J. Hempälä, R. A. Long, J. Martinez, U. L. Zweifel, and Å. Hagström. 1999. Coupling between bacterioplankton species composition, population dynamics, and organic matter degradation. Aquat. Microb. Ecol. 17:13-26.
52. Prokic, I., F. Bruemer, T. Brigge, H. D. Goertz, G. Gerdts, C. Schuett, M. Elbraechter, and W. E. G. Mueller. 1999. Bacteria of the genus Roseobacter associated with the toxic dinoflagellate Prorocentrum lima. Protist 149:347-357.
53. Raguenes, G., P. Pignet, G. Gauthier, A. Peres, R. Christen, H. Rougeaux, G. Barbier, and J. Guezennec. 1996. Description of a new polymer-secreting bacterium from a deep-sea hydrothermal vent, Alteromonas mucleodii subsp. fijiensi, and preliminary characterization of the polymer. Appl. Environ. Microbiol. 62:67-73.
54. Rappé, M. S., P. F. Kemp, and S. J. Giovannoni. 1997. Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina. Limnol. Oceanogr. 42:811-826.
55. Rath, J., K. Y. Wu, G. J. Herndl, and E. F. DeLong. 1998. High phylogenetic diversity in a marine-snow-associated bacterial assemblage. Aquat. Microb. Ecol. 14:262-269.
56. Reynolds, C. S. 1984. The ecology of freshwater phytoplankton. Cambridge University Press, Cambridge, United Kingdom.
57. Riemann, L., G. F. Steward, L. B. Fandino, L. Campbell, M. R. Landry, and F. Azam. 1999. Bacterial community composition during two consecutive NE monsoon periods in the Arabian Sea studied by denaturing gradient gel electrophoresis (DGGE) of rRNA genes. Deep Sea Res. II 46:1791-1811.
58. Robison-Cox, J. F., M. M. Bateson, and D. M. Ward. 1995. Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences. Appl. Environ. Microbiol. 61:1240-1245.
59. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
60. Shewan, J. M., and T. A. McMeekin. 1983. Taxonomy (and ecology) of Flavobacterium and related genera. Annu. Rev. Microbiol. 37:233-252.
61. Šimek, K., and T. H. Chrzanowski. 1992. Direct and indirect evidence of size-selective grazing on pelagic bacteria by freshwater nanoflagellates. Appl. Environ. Microbiol. 58:3715-3720.
62. Šimek, K., J. Vrba, J. Pernthaler, T. Posch, P. Hartman, J. Nedoma, and R. Psenner. 1997. Morphological and compositional shifts in an experimental bacterial community influenced by protists with contrasting feeding modes. Appl. Environ. Microbiol. 63:587-595.
63. Simon, M. 1987. Biomass and production of small and large free-living and attached bacteria in Lake Constance. Limnol. Oceanogr. 32:591-607.
64. Simon, M., and F. Azam. 1989. Protein content and protein synthesis rates of planktonic marine bacteria. Mar. Ecol. Prog. Ser. 51:201-213.
65. Simon, M., A. L. Alldredge, and F. Azam. 1990. Bacterial carbon dynamics on marine snow. Mar. Ecol. Prog. Ser. 65:205-211.
66. 3H-leucine. Mar. Microb. Food Webs 6:107-114.
67. Smith, D. C., M. Simon, A. L. Alldredge, and F. Azam. 1992 Intense hydrolytic enzyme activity on marine aggregates and implications for rapid particle dissolution. Nature 359:139-142.
68. Smith, D. C., G. F. Steward, R. A. Long, and F. Azam. 1995. Bacterial mediation of carbon fluxes during a diatom bloom in a mesocosm. Deep Sea Res. II 42:75-97.
69. Somerville, C. C., I. T. Knight, W. L. Straube, and R. T. Colwell. 1989. Simple, rapid method for direct isolation of nucleic acids from aquatic-environments. Appl. Environ. Microbiol. 55:548-554.
70. Suzuki, M. T., M. S. Rappé. Z. W. Haimberger, H. Winfield, N. Adair, J. Strobel, and S. J. Giovannoni. 1997. Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample. Appl. Environ. Microbiol. 63:983-989.
71. Turley, C. M., and P. J. Mackie. 1994. Biogeochemical significance of attached and free-living bacteria and the flux of particles in the NE Atlantic Ocean. Mar. Ecol. Prog. Ser. 115:191-203.
72. Unanue, M., B. Ayo, I. Azúa, I. Barcina, and J. Iriberri. 1992. Temporal variability of attached and free-living bacteria in coastal waters. Microb. Ecol. 23:27-39.
73. van Hannen, E. J., G. Zwart, M. P. van Aglerveld, H. J. Gons, J. Ebert, and H. J. Laanbroek. 1999. Changes in bacterial and eukaryotic community structure after mass lysis of filamentous Cyanobacteria associated with viruses. Appl. Environ. Microbiol. 65:795-801.
74. van Hannen, E. J., W. Mooij, M. P. van Agterveld, H. J. Gons, and H. J. Laanbroek. 1999. Detritus-dependent development of the microbial community in an experimental system: qualitative analysis by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 65:2478-2484.
75. Ward, D. M., M J. Ferris, S. C. Nold, and M. M. Bateson. 1998. A natural view of microbial hiodiversity within hot spring Cyanobacterial mat communities. Microbiol. Mol. Biol. Rev. 62:1353-1370.
76. Wells, M. L., and E. D. Goldberg. 1991. Occurrence of small colloids in sea water. Nature 353:342-344.
77. Yoon, W. B., and R. A. Rosson. 1990. Improved method for enumeration of attached bacteria for study of fluctuation in the abundance of attached and free-living bacteria in response to diel variation in seawater turbidity. Appl. Environ. Microhiol. 56:595-600.