Relationships between bacterial diversity and environmental variables in a tropical marine environment, Rio de Janeiro

Environmental Microbiology

Volumn 10, Issue 1, 2008, Pages 189-199

  Vieira, Ricardo P ^a   Gonzalez, Alessandra M ^a   Cardoso, Alexander M ^a   Oliveira, Denise N ^b   Albano, Rodolpho M ^b   Clementino, Maysa M ^c   Martins, Orlando B ^a   Paranhos, Rodolfo ^a  

^a FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^b STATE UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^c INSTITUTO OSWALDO CRUZ   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

FRESH WATER; RNA 16S; SEA WATER;

ARTICLE; BACTERIUM; BIODIVERSITY; BRAZIL; ECOSYSTEM; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; GROWTH, DEVELOPMENT AND AGING; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANKTON; RIVER; SALINITY; TROPIC CLIMATE;

BACTERIA; BASE SEQUENCE; BIODIVERSITY; BRAZIL; ECOSYSTEM; FRESH WATER; GEOGRAPHY; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANKTON; RIVERS; RNA, RIBOSOMAL, 16S; SALINITY; SEAWATER; TROPICAL CLIMATE; VARIATION (GENETICS); WATER MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 38149037021     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2007.01443.x     Document Type: Article

References (71)

1. Acinas, S.G., Klepac-Ceraj, V., Hunt, D.E., Pharino, C., Ceraj, I., Distel, D.L. Polz, M.F. (2004) Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430 : 551 554.
2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. Lipman, D.J. (1990) Basic local alignment search tool. J Mol Biol 5 : 403 410.
3. Andrade, L., Gonzalez, A.M., Araújo, F.V. Paranhos, R. (2003) Flow cytometry assessment of bacterioplankton in tropical marine environments. J Microbiol Methods 55 : 841 850.
4. Azam, F. Long, R.A. (2001) Sea snow microcosms. Nature 29 : 497 498.
5. Azam, F., Fenchel, T., Field, J.G., Gray, J.S., Meyer-Reil, L.A. Thingstad, F. (1983) The ecological role of water-column microbes in the sea. Mar Ecol Prog Ser 10 : 257 263.
6. Baldwin, A.J., Catala, P., Costas, B., Dolan, J.R., Fenchel, T., Foissner, W., et al. (2005) Biogeography of aquatic microbes. Aquat Microb Ecol 41 : 39 48.
7. Clementino, M.M., Fernandes, C.C., Vieira, R.P., Cardoso, A.M., Polycarpo, C.R. Martins, O.B. (2007) Archaeal diversity in naturally occurring and impacted environments from a tropical region. J Appl Microbiol 103 : 141 151.
8. Cnexo (1983) Manuel des analyses chimiques au milieu marin. In Cnexo - BNDO Documentation. Aminot, A. Chassieupied, M. (eds). Brest, France : Centre National Pour L'Exploration des Oceans, p. 397.
9. Cole, J.J., Findlay, S. Pace, M.L. (1988) Bacterial production in fresh and saltwater ecosystems: a cross-system overview. Mar Ecol Prog Ser 43 : 1 10.
10. Cole, J.R., Chai, B., Marsh, T.L., Farris, R.J., Wang, Q., Kulam, S.A., et al. (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31 : 442 443.
11. Cottrel, M.T., Waidner, L.A., Yu, L. Kirchman, D.L. (2005) Bacterial diversity of metagenomic and PCR libraries from the Delaware River. Environ Microbiol 7 : 1883 1895.
12. Crump, C.B., Hopkinson, C.S., Sogin, M.L. Hobbie, J.E. (2004) Microbial biogeography along an estuarine salinity gradient: combined influence of bacterial growth and residence time. Appl Environ Microbiol 70 : 1494 1505.
13. Del Giorgio, P.A., Bird, D.F., Prairie, Y.T. Planas, D. (1996) Flow cytometric determination of bacterial abundance in lake plankton with the green nucleic acid stain syto 13. Limnol Oceanogr 41 : 783 789.
14. DeLong, E.F. (2004) Microbial population genomics and ecology: the road ahead. Environ Microbiol 6 : 875 878.
15. DeLong, E.F. Karl, D.M. (2005) Genomic perspectives in microbial oceanography. Nature 15 : 336 342.
16. Edwing, B., Hillier, L., Wendl, M. Green, P. (1998) Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Gen Res 8 : 175 185.
17. Feema (1990) Projeto de Recuperação Gradual do Ecossistema da Baía de Guanabara. Rio de Janeiro. Fundação Estadual Engenharia do Meio Ambiente 2 : 203.
18. Fuhrman, J.A. (2002) Community structure and function in prokaryotic marine plankton. Antonie Van Leeuwenhoek 81 : 521 527.
19. Fuhrman, J.A., Hewson, I., Schwalbach, M.S., Steele, J.A., Brown, M.V. Naeem, S. (2006) Annually reoccurring bacterial communities are predictable from ocean conditions. Proc Natl Acad Sci USA 103 : 13104 13109.
20. Gasol, J.M. del Giorgio, P.A. (2000) Using flow cytometry for counting natural planktonic bacteria and understanding the structure of planktonic bacterial communities. Sci Mar 64 : 197 224.
21. Giovannoni, S.J. Stingl, U. (2005) Molecular diversity and ecology of microbial plankton. Nature 15 : 343 348.
22. Giovannoni, S.J., Britschgi, T.B., Moyer, C. Field, K.G. (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345 : 60 63.
23. Giovannoni, S.J., Tripp, H.J., Givan, S., Podar, M., Vergin, K.L., Baptista, D., et al. (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309 : 1242 1245.
24. 3H-leucine incorporation. Braz Arch Biol Technol 43 : 493 500.
25. Gonzalez, J.M., Sherr, E.B. Sherr, B.F. (1990) Size-selective grazing on bacteria by natural assemblages of estuarine flagellates and ciliates. Appl Environ Microbiol 56 : 583 589.
26. Grasshoff, K., Kremling, K. Erhardt, M. (1999) Methods of Seawater Analysis, 3rd edn. Weinheim, Germany : Wiley-VCH-Verlag.
27. Guixa-Boixereu, N., Vaqué, D., Gasol, J.M. Pedrós- Alió, C. (1999) Distribution of viruses and their potential effect on bacterioplankton in an oligotrophic marine system. Aquat Microb Ecol 19 : 205 213.
28. Hagler, A.N. Mendonça-Hagler, L.C. (1981) Yeast from marine and estuarine waters with different levels of pollution in the state of Rio de Janeiro, Brazil. Appl Environ Microbiol 41 : 173 178.
29. Heck, J.K.L., van Belle, G. Simberloff, D. (1975) Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology 56 : 1459 1461.
30. Hewson, I. Fuhrman, J.A. (2004) Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia. Appl Environ Microbiol 70 : 3425 3433.
31. Horner-Devine, M.C., Lage, M., Hughes, J.B. Bohannan, B.J. (2004) A taxa-area relationship for bacteria. Nature 432 : 750 753.
32. Hurlbert, S.H. (1971) The nonconcept of species diversity: a critique and alternative parameters. Ecology 52 : 577 586.
33. Kan, J.J., Crump, B.C., Wang, K. Chen, F. (2006) Bacterioplankton community in Chesapeake Bay: predictable or random assemblages. Limnol Oceanogr 51 : 2157 2169.
34. Karl, D.M. (2002) Microbiological oceanography - hidden in a sea of microbes. Nature 415 : 590 591.
35. Kemp, P.F. Aller, J.Y. (2004) Estimating prokaryotic diversity: when are 16S rDNA libraries large enough? Limnol Oceanogr 2 : 114 125.
36. Kimura, M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16 : 11 20.
37. Kirchman, D.L., K'nees, E. Hodson, R. (1985) Leucine incorporation and its potential as a measure of protein synthesis by bacteria in natural aquatic systems. Appl Environ Microbiol 49 : 599 607.
38. Kumar, S., Tamura, K., Jakobsen, I.B. Nei, M. (2001) mega2: molecular evolutionary genetics analysis software. Bioinformatics 17 : 1244 1245.
39. Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics. Stackebrandt, E. Goodfellow, M. (eds). New York, USA : Wiley, pp. 115 175.
40. Lebaron, P. Joux, F. (1994) Flow cytometric analysis of the cellular DNA content of Salmonella typhimurium and Alteromonas haloplanktis during starvation and recovery in seawater. Appl Environ Microbiol 60 : 4345 4350.
41. Legendre, L. Legendre, P. (1998) Numerical Ecology. New York, USA : Elsevier Science.
42. Mayr, L.M., Tenenbaum, D.R., Villac, M.C., Paranhos, R., Nogueira, C.R., Bonecker, S.L.C. Bonecker, A.C. (1989) Hydrobiological characterization of Guanabara Bay. In Coastlines of Brazil. Maggon, O.T. Neves, C. (eds). New York, USA : American Society of Civil Engineers, pp. 124 139.
43. Olsen, G.J., Lane, D.J., Giovannoni, S.J., Pace, N.R. Stahl, D.A. (1986) Microbial ecology and evolution: a ribosomal RNA approach. Ann Rev Microbiol 40 : 337 365.
44. Pace, N.R., Stahl, D.A., Lane, D.J. Olsen, G.J. (1986) The analysis of natural microbial populations by ribosomal RNA sequences. Adv Microb Ecol 9 : 1 55.
45. Paranhos, R., Pereira, A.P. Mayr, L.M. (1998) Diel variability of water quality in a tropical polluted bay. Environ Monit Assessm 50 : 131 141.
46. Paranhos, R., Andrade, L., Mendonça-Hagler, L.C. Pfeiffer, W.C. (2001) Coupling bacterial density with activity in a tropical polluted coastal bay. Serie Oecologia Brasiliensis 9 : 117 132.
47. Parsons, T.R., Maita, Y. Lalli, C.M. (1984) A Manual of Chemical and Biological Methods for Seawater Analysis. Oxford, UK : Pergamon Press.
48. Pedrós-Alió, C. (2006) Marine microbial diversity: can it be determined? Trends Microbiol 14 : 257 263.
49. Pommier, T., Pinhassi, J. Hangstrom, A. (2005) Biogeographic analysis of ribosomal RNA cluster from marine bacterioplankton. Aquat Microb Ecol 41 : 79 89.
50. Ranchou-Peyruse, A., Herbert, R., Caumette, P. Guyoneaud, R. (2006) Comparison of cultivation-dependent and molecular methods for studying the diversity of anoxygenic purple phototrophs in sediments of an eutrophic brackish lagoon. Environ Microbiol 8 : 1590 1599.
51. Rappe, M.S. Giovannoni, S.J. (2003) The uncultured microbial majority. Ann Rev Microbiol 57 : 369 394.
52. Rocap, G., Larimer, F.W., Lamerdin, J., Malfatti, S., Chain, P., Ahlgren, N.A., et al. (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 28 : 1042 1047.
53. Rossello-Mora, R. Amann, R. (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25 : 39 67.
54. 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 13 : 398 431.
55. Saitou, N. Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 : 406 425.
56. Schloss, P.D. Handelsman, J. (2005) Introducing dotur, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71 : 1501 1506.
57. Schloss, P.D., Larget, B.R. Handelsman, J. (2004) Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol 70 : 5485 5492.
58. Servais, P., Casamayor, E.O., Courties, C., Catala, P., Parthuisot, N. Lebaron, P. (2003) Activity and diversity of bacterial cells with high and low nucleic acid content. Aquat Microb Ecol 33 : 41 51.
59. 3H-leucine. Mar Microb Food Webs 6 : 107 114.
60. Sogin, M.L., Morrison, H.G., Huber, J.A., Welch, D.M., Huse, S.M., Neal, P.R., et al. (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere'. Proc Natl Acad Sci USA 103 : 12115 12120.
61. Somerville, C.C., Knight, I.T., Straube, W.L. Colwell, R.R. (1989) Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Appl Environ Microbiol 55 : 548 554.
62. Stepanaukas, R., Moran, M.A., Bergamachi, B.A. Hollibaugh, J.T. (2003) Covariance of bacterioplankton composition and environmental variables in a temperate delta system. Aquat Microb Ecol 31 : 85 98.
63. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. Higgins, D.G. (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24 : 4876 4882.
64. Urbach, E., Kevin, L.V., Young, L., Morse, A., Larson, G.L. Giovannoni, S.J. (2001) Unusual bacterioplankton community structure in ultra-oligotrophic Crater Lake. Limnol Oceanogr 46 : 557 572.
65. Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304 : 66 74.
66. Vieira, R.P., Clementino, M.M., Cardoso, A.M., Oliveira, D.N., Albano, R.M., Gonzalez, A.M., et al. (2007) Archaeal communities in a tropical estuarine ecosystem: Guanabara Bay, Brazil. Microb Ecol (in press). doi:10.1007/s00248- 007-9261-y.
67. Weisburg, W.G., Barns, S.M., Pelletier, D.A. Lane, D.J. (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173 : 697 703.
68. Yokokawa, T. Nagata, T. (2005) Growth and grazing mortality rates of phylogenetic groups of bacterioplankton in coastal marine environments. Appl Environ Microbiol 71 : 6799 6807.
69. Zar, J.H. (1999) Biostatistical Analysis, 4th edn. New Jersey, USA : Prentice-Hall.
70. Zehr, J.P. Ward, B.B. (2002) Nitrogen cycling in the ocean: new perspectives on processes and paradigms. Appl Environ Microbiol 68 : 1015 1024.
71. Zubkov, M.V., Fuchs, B.M., Archer, S.D., Kiene, R., 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.