Community structures of actively growing bacteria shift along a north-south transect in the western North Pacific

Environmental Microbiology

Volumn 10, Issue 4, 2008, Pages 1007-1017

  Taniguchi, Akito ^a   Hamasaki, Koji ^b  

^a HIROSHIMA UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BROXURIDINE; SEA WATER;

ARTICLE; BACTERIAL COUNT; BACTERIUM; COMPARATIVE STUDY; ENVIRONMENTAL MONITORING; ENZYME SPECIFICITY; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; OCEANOGRAPHY; PACIFIC OCEAN; POLYMERASE CHAIN REACTION; SPECIES DIFFERENCE;

BACTERIA; BROMODEOXYURIDINE; COLONY COUNT, MICROBIAL; ENVIRONMENTAL MONITORING; OCEANOGRAPHY; PACIFIC OCEAN; POLYMERASE CHAIN REACTION; SEAWATER; SPECIES SPECIFICITY; SUBSTRATE SPECIFICITY; WATER MICROBIOLOGY;

ALPHAPROTEOBACTERIA; ALTEROMONADALES; BACTERIA (MICROORGANISMS); BACTEROIDES; BACTEROIDES (CLASS); BACTEROIDETES; BETAPROTEOBACTERIA; CYANOBACTERIA; CYTOPHAGA; FLAVOBACTERIUM; GAMMAPROTEOBACTERIA; POSIBACTERIA; ROSEOBACTER; VIBRIONALES;

EID: 40949087773     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2007.01521.x     Document Type: Article

References (58)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389 3402.
2. Artursson, V. Jansson, J.K. (2003) Use of bromodeoxyuridine immunocapture to identify active bacteria associated with arbuscular mycorrhizal hyphage. Appl Environ Microbiol 69: 6208 6215.
3. Artursson, V., Finlay, R.D. Jansson, J.K. (2005) Combined bromodeoxyuridine immunocapture and terminal-restriction fragment length polymorphism analysis highlights differences in the active soil bacterial metagenome due to Glomus mosseae inoculation or plant species. Environ Microbiol 7: 1952 1966.
4. Azam, F. (1998) Microbial control of oceanic carbon flux: the plot thickens. Science 280: 694 696.
5. Barraquio, W.L., Pader, B.C., Jr, Watanabe, I. Knowles, R. (1986) Nitrogen fixation by Pseudomonas saccharophila Doudoroff ATCC 15946. J Gen Microbiol 132: 237 241.
6. Borneman, J. (1999) Culture-independent identification of microorganisms that respond to specified stimuli. Appl Environ Microbiol 65: 3398 3400.
7. Bouvier, T. del Giorgio, P.A. (2007) Key role of selective viral-induced mortality in determining marine bacterial community composition. Environ Microbiol 9: 287 297.
8. Capone, D.G., Zehr, J.P., Paerl, H.W., Bergman, B. Carpenter, E.J. (1997) Trichodesmium, a globally significant marine cyanobacterium. Science 276: 1221 1229.
9. Cole, J.J., Findlay, S. Pace, M.L. (1998) Bacterial production in fresh and saltwater ecosystem: a cross-system overview. Mar Ecol Prog Ser 43: 1 10.
10. Cottrell, M.T. Kirchman, D.L. (2000) Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high- molecular-weight dissolved organic matter. Appl Environ Microbiol 66: 1692 1697.
11. Cottrell, M.T. Kirchman, D.L. (2003) Contribution of major bacterial groups to bacterial biomass production (thymidine and leucine incorporation) in the Delaware estuary. Limnol Oceanogr 48: 168 178.
12. DeLong, E.F. (2005) Microbial community genomics in the ocean. Nat Rev Microbiol 3: 459 469.
13. DeLong, E.F. Karl, D.M. (2005) Genomic perspectives in microbial oceanography. Nature 437: 336 342.
14. Elifantz, H., Malmstrom, R.R., Cottrell, M.T. Kirchman, D.L. (2005) Assimilation of polysaccharides and glucose by major bacterial groups in the Delaware estuary. Appl Environ Microbiol 71: 7799 7805.
15. Fuhrman, J.A. Azam, F. (1980) Bacterioplankton secondary production estimates for coastal waters of British Columbia, Antarctica, and California. Appl Environ Microbiol 39: 1085 1095.
16. Giovannoni, S.J. Rappe, M.S. (2000) Evolution, diversity, and molecular ecology of marine prokaryotes. In Microbial Ecology of the Oceans. Kirchman, D.L. (ed). New York, USA: Wiley-Liss, pp. 47 84.
17. Giovannoni, S.J. Stingl, U. (2005) Molecular diversity and ecology of microbial plankton. Nature 437: 343 348.
18. Giovannoni, S.J., Britschgi, T.B., Moyer, C.L. Field, K.G. (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345: 60 63.
19. Gonzalez, J.M., Simo, R., Massana, R., Covert, J.S., Casamayor, E.O., Pedoros-Alio, C. Moran, M.A. (2000) Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom. Appl Environ Microbiol 66: 4237 4246.
20. Grossart, H.P., Levold, F., Allgaler, M., Simon, M. Brinkhoff, T. (2005) Marine diatom species harbour distinct bacterial communities. Environ Microbiol 7: 860 873.
21. Hamasaki, K. (2006) Comparison of bromodeoxyuridine immunoassay with tritiated thymidine radioassay for measuring bacterial productivity in oceanic waters. J Oceanogr 62: 793 799.
22. Hamasaki, K., Long, R.A. Azam, F. (2004) Individual cell growth rates of marine bacteria, measured by bromodeoxyuridine incorporation. Aquat Microb Ecol 35: 217 227.
23. Hamasaki, K., Taniguchi, A., Tada, Y., Long, R.A. Azam, F. (2007) Actively growing bacteria in the Inland Sea of Japan, identified by combined bromodeoxyuridine immunocapture and denaturing gradient gel electrophoresis. Appl Environ Microbiol 73: 2787 2798.
24. Hugenholtz, P., Goebel, B.M. Pace, N.R. (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180: 4765 4774.
25. Karl, D.M. (2002) Hidden in a sea of microbes. Nature 415: 590 591.
26. Kirchman, D.L., K'nees, E. Hodson, R.E. (1985) Leucine incorporation and its potential as a measure of protein synthesis by bacteria in natural aquatic systems. Appl Environ Microbiol 49: 599 607.
27. Kolber, Z.S., Van Dover, C.L., Niederman, R.A. Falkowski, P.G. (2000) Bacterial photosynthesis in surface waters of the open ocean. Nature 407: 177 179.
28. Kumar, S., Tamura, K. Nei, M. (2004) MEGA3: an integrated software for Molecular Evolutionary Genetics Analysis and Sequence alignment. Brief Bioinform 5: 150 163.
29. Maidak, B.L., Cole, J.R., Liburn, T.G., Parker, C.T. Saxman, P.R., Farris, R.J., et al. (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res 29: 173 174.
30. Malmstrom, R.R., Kiene, R.P. Kirchman, D.L. (2004) Identification and enumeration of bacterial assimilating dimethylsulfoniopropionate (DMSP) in the North Atlantic and Gulf of Mexico. Limnol Oceanogr 49: 597 606.
31. Moesender, M.M., Winter, C. Herndl, G.J. (2001) Horizontal and vertical complexity of attached and free-living bacteria of the eastern Mediterranean Sea, determined by 16S rDNA and 16S rRNA fingerprints. Limnol Oceanogr 46: 95 107.
32. Moran, M.A., Buchan, A., Gonzalez, J.M., Heidelberg, J.F., Whitman, W.B., Kiene, R.P., et al. (2004) Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432: 910 913.
33. Nelson, C.E. Carlson, C.A. (2005) A nonradioactive assay of bacterial productivity optimized for oligotrophic pelagic environments. Limnol Oceanogr Methods 3: 211 220.
34. Ogawa, H. Tanoue, E. (2003) Dissolved organic matter in the oceanic waters. J Oceanogr 59: 129 147.
35. Pernthaler, A. Pernthaler, J. (2005) Diurnal variation of cell proliferation in three bacterial taxa from coastal North Sea waters. Appl Environ Microbiol 71: 4638 4644.
36. Pernthaler, A., Pernthaler, J., Schattenhofer, M. Amann, R. (2002) Identification of DNA-synthesizing bacterial cells in coastal North Sea plankton. Appl Environ Microbiol 68: 5728 5736.
37. Porter, K.G. Feig, Y.S. (1980) The use of DAPI for identifying and counting aquatic microflora. Limnol Oceanogr 25: 943 948.
38. Riemann, L., Steward, G.F. Azam, F. (2000) Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl Environ Microbiol 66: 578 587.
39. Rusch, D.B., Halpern, A.L., Sutton, G., Heidelberg, K.B., Williamson, S., Yooseph, S., et al. (2007) The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific. PLoS Biol 5: 398 431.
40. Schafer, H. Muyzer, G. (2001) Denaturing gradient gel electrophoresis in marine microbial ecology. In Methods in Microbiology. Paul, J.H. (ed). New York, USA: Academic Press, 30: 425 468.
41. Schafer, H., Bernard, L., Courties, C., Lebaron, P., Servais, P., Pukall, R., et al. (2001) Microbial community dynamics in Mediterranean nutrient-enriched seawater mesocosms: changes in the genetic diversity of bacterial populations. FEMS Microbiol Ecol 34: 243 253.
42. Schmidt, T.M., DeLong, E.F. Pace, N.R. (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. Appl Environ Microbiol 173: 4371 4378.
43. Schwalbach, M.S., Brown, M. Fuhrman, J.A. (2005) Impact of light on marine bacterioplankton community structure. Aquat Microb Ecol 39: 235 245.
44. Sieracki, M.E., Gilg, I.C., Their, E.C. Poulton, N.J. (2006) Distribution of planktonic aerobic anoxygenic photoheterotrophic bacteria in the northwest Atlantic. Limnol Oceanogr 51: 38 46.
45. 3H-thymidine for measuring bacterial productivity in aquatic samples. Aquat Microb Ecol 19: 57 66.
46. Suzuki, R. Ishimaru, T. (1990) An improved method for the determination of phytoplankton chlorophyll using N,N-dimethylformamide. J Oceanogr 46: 190 194.
47. Thompson, J.D., Higgins, D.G. Gibson, T.J. (1994) 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.
48. Troussellier, M., Schafer, H., Batailler, N., Bernard, L., Courties, C., Lebaron, P., et al. (2002) Bacterial activity and genetic richness along an estuarine gradient (Rhone River plume, France). Aquat Microb Ecol 28: 13 24.
49. Tyson, G.W., Chapman, J., Hugenholtz, P., Allen, E.E., Ram, R.J., Richardson, P.M., et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37 43.
50. Urbach, E., Vergin, K.L. Giovannoni, S.J. (1999) Immunological detection and isolation of DNA from metabolically active and bacteria. Appl Environ Microbiol 65: 1207 1213.
51. Vaulot, D., Marie, D., Olson, R.J. Chisholm, S.W. (1995) Growth of Prochlorococcus, a photosynthetic prokaryote, in the Equatorial Pacific Ocean. Science 268: 1480 1482.
52. Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., et al. (2004) Environmental genomes shotgun sequencing of the Sargasso Sea. Science 304: 66 74.
53. Walters, S.P. Field, K.G. (2006) Persistence and growth of fecal Bacteroidetes assessed by bromodeoxyuridine immunocapture. Appl Environ Microbiol 72: 4532 4539.
54. Warnecke, F., Sommaruge, R., Sekar, R., Hofer, J.S. Pernthaler, J. (2005) Abundance, identify, and growth state of Actinobacteria in mountain lakes of different UV transparency. Appl Environ Microbiol 71: 5551 5559.
55. Welschmeyer, N.A. (1994) Fluorometric analysis of chlorophyll a in the presence of chlorophyll b and pheopigments. Limnol Oceanogr 39: 1985 1992.
56. T and IAM 12664 and Pseudomonas sacchatophila as Azohydromonas lata General nov., comb. nov., Azohydromonas australica sp. nov. and Pelomonas saccharophila General nov., comb., respectively. Int J Syst Evol Microbiol 55: 2419 2425.
57. Yin, B., Crowley, D., Sparovek, G., De Melo, W.J. Borneman, J. (2000) Bacterial functional redundancy along a soil reclamation gradient. Appl Environ Microbiol 66: 4361 4365.
58. Zubkov, M.V., Fuchs, B.M., Archer, S.D., Kiene, R.P., Amann, R. Burkill, P.H. (2001) Linking the composition of bacterioplankton to rapid turnover of dissolved dimethylsulphoniopropionate in an algal bloom in the North Sea. Environ Microbiol 3: 304 311.