Global patterns of diversity and community structure in marine bacterioplankton

Molecular Ecology

Volumn 16, Issue 4, 2007, Pages 867-880

  Pommier, T ^a   Canback B ^b   Riemann, L ^a   Bostrom K H ^a   Simu, K ^a   Lundberg, P ^b   Tunlid, A ^b   Hagström, Åke ^a  

^a LINNAEUS UNIVERSITY   (Sweden)

^b LUND UNIVERSITY   (Sweden)

Author keywords

Bacterioplankton; Cosmopolitanism; Distribution; Diversity; Latitudinal gradient; Marine

Indexed keywords

PRIMER DNA; RNA 16S;

ARTICLE; BACTERIUM; BIOLOGICAL MODEL; BIOLOGY; CLASSIFICATION; DEMOGRAPHY; DNA SEQUENCE; ECOSYSTEM; GENE LIBRARY; GENETIC VARIABILITY; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANKTON; SEA; STATISTICAL MODEL;

BACTERIA; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DEMOGRAPHY; DNA PRIMERS; ECOSYSTEM; GENE LIBRARY; GENETIC VARIATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; OCEANS AND SEAS; PHYLOGENY; PLANKTON; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

OTUS;

EID: 33846914243     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2006.03189.x     Document Type: Article

References (68)

1. Acinas SG, Marcelino LA, Klepac-Ceraj V, Polz MF (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. Journal of Bacteriology, 186, 2629-2635.
2. Altschul SF, Madden TL, Schaffer AA et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 3389-3402.
3. Baas-Becking LGM (1934) Geobiologie of Inleiding Tot de Milieukunde. W.P. Van Stockum & Zoon N.V., den Haag.
4. Blackburn TM, Gaston KJ (2003) Macroecology: Concepts and Consequences, 1st edn. Blackwell Science Ltd, Oxford, UK.
5. Boström KH, Simu K, Hagström Å, Riemann L (2004) Optimization of DNA extraction for quantitative marine bacterioplankton community analysis. Limnology and Oceanography: Methods, 2, 374-386.
6. Bouman HA, Ulloa O, Scanlan DJ et al. (2006) Oceanographic basis of the global surface distribution of Prochlorococcus ecotypes. Science, 312, 918-921.
7. Bouvier TC, Del Giorgio PA (2002) Compositional changes in free-living bacterial communities along a salinity gradient in two temperate studies. Limnology and Oceanography, 47, 453-470.
8. Brown MV, Schwalbach MS, Hewson I, Fuhrman JA (2005) Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series. Environmental Microbiology, 7, 1466-1479.
9. Carr NG, Mann NH (1994) The oceanic cyanobacterial picoplankton. In: The Molecular Biology of Cyanobacteria (ed. Bryant DA), pp. 27-48. Kluwer Academic Publishers, Dordrecht.
10. Chao A, Ma M-C, Yang M (1993) Stopping rules and estimation for recapture debugging with unequal failure rates. Biometrika, 80, 193-201.
11. Chenna R, Sugawara H, Koike T et al. (2003) Multiple sequence alignment with the CLUSTAL series of programs. Nucleic Acids Research, 31, 3497-3500.
12. Cho JC, Tiedje JM (2000) Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Applied Environmental Microbiology, 66, 5448-5456.
13. Cohan FM (2001) Bacterial species and speciation. Systematic Biology, 50, 513-524.
14. Collins A (2001) Ocean circulation. In: Ocean Circulation (ed. Heineman B), pp. 208-209, Boston, MA.
15. Crump BC, Hopkinson CS, Sogin ML, Hobbie JE (2004) Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time. Applied Environmental Microbiology, 70, 1494-1505.
16. Dufresne A, Garczarek L, Partensky F (2005) Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biology, 6, R14.
17. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Research, 8, 186-194.
18. Fenchel T, Finlay BJ (2004) The ubiquity of small species: patterns of local and global diversity. Bioscience, 54, 777-784.
19. Finlay BJ (2002) Global dispersal of free-living microbial eukaryote species. Science, 296, 1061-1063.
20. Finlay BJ, Clarke KJ (1999) Ubiquitous dispersal of microbial species. Nature, 400, 828-828.
21. Fuhrman J, Comeau DE, Hagström Å, Chan AM (1988) Extraction from natural planktonic microorganisms of DNA suitable for molecular biological studies. Applied and Environmental Microbiology, 54, 1426-1429.
22. García-Martínez J, Rodríguez-Valera F (2000) Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archae of Group I. Molecular Ecology, 9, 935-948.
23. Gevers D, Cohan FM, Lawrence JG et al. (2005) Re-evaluating prokaryotic species. Nature Review Microbiology, 3, 733-739.
24. Giovannoni SJ, Rappé MS (2000) Evolution, diversity and molecular ecology of marine prokaryotes. In: Microbial Ecology of the Oceans (ed. Kirchman DL), pp. 47-84. Wiley-Liss, Inc., New York, N.Y.
25. Giovannoni SJ, Stingl U (2005) Molecular diversity and ecology of microbial plankton. Nature, 437, 343-348.
26. Giovannoni SJ, Rappe MS, Vergin KL, Adair NL (1996) 16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the green non-sulfur bacteria. Proceedings of the National Academy of Sciences of the USA, 93, 7979-7984.
27. Giovannoni SJ, Tripp HJ, Givan S et al. (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science, 309, 1242-1245.
28. Good IL (1953) The population frequencies of species and the estimation of population parameters. Biometrika, 80, 193-201.
29. Gordon DA, Giovannoni SJ (1996) Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific Oceans. Applied Environmental Microbiology, 62, 1171-1177.
30. Hagström Å, Pinhassi J, Zweifel UL (2000) Biogeographical diversity among marine bacterioplankton. Aquatic Microbial Ecology, 21, 231-244.
31. Hillebrand H (2004) On the generality of the latitudinal diversity gradient. American Naturalist, 163, 192-211.
32. Holt RD, Lawton JH, Gaston KJ (1997) On the relationship between range size and local abundance: back to basics. OIKOS, 78, 183-190.
33. Horner-Devine MC, Carney KM, Bohannan BJ (2004a) An ecological perspective on bacterial biodiversity. Proceedings of the Royal Society of London B Biological Science, 271, 113-122.
34. Horner-Devine MC, Lage M, Hughes JB, Bohannan BJ (2004b) A taxa-area relationship for bacteria. Nature, 432, 750-753.
35. Huang X, Chao KM (2003) A generalized global alignment algorithm. Bioinformatics, 19, 228-233.
36. Kemp PF, Aller JY (2004) Estimating prokaryotic diversity: when are 16S rDNA libraries large enough? Limnology and Oceanography: Methods, 2, 114-125.
37. Krebs C (1999) Ecological Methodology, 2nd edn. Benjamin/Cummings, Menlo Park, California.
38. Lane DJ (1991) 16S/23S rRNA Sequencing. In: Nucleic Acid Techniques in Bacterial Systematics (eds Stackebrandt E, Goodfellow M), pp. 115-147. John Wiley & Sons Ltd, Chichester.
39. Lee S-M, Chao A (1994) Estimating population size via sample coverage for closed capture-recapture models. Biometrics, 50, 88-97.
40. Lunn M, Sloan WT, Curtis TP (2004) Estimating bacterial diversity from clone libraries with flat rank abundance distributions. Environmental Microbiology, 6, 1081-1085.
41. Magurran AE (2004) Measuring Biological Diversity, 1st edn. Blackwell Publishing, Oxford.
42. Maguran AE, Henderson PA (2003) Explaining the excess of rare species abundance distributions. Nature, 422, 714-716.
43. Maidak BL, Cole JR, Parker CT Jr. et al. (1999) A new version of the RDP (Ribosomal Database Project). Nucleic Acids Research, 27, 171-173.
44. Martiny JB, Bohannan BJ, Brown JH et al. (2006) Microbial biogeography: putting microorganisms on the map. Nature Review Microbiology, 4, 102-112.
45. Massana R, DeLong EF, Pedros-Alio C (2000) A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Applied and Environmental Microbiology, 66, 1777-1787.
46. Morris RM, Rappé MS, Connon SA et al. (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature, 420, 806-810.
47. Oda Y, Star B, Huisman LA, Gottschal JC, Forney LJ (2003) Biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris. Applied Environmental Microbiology, 69, 5186-5191.
48. Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science, 276, 734-740.
49. Papke RT, Ramsing NB, Bateson MM, Ward DM (2003) Geographical isolation in hot spring cyanobacteria. Environmental Microbiology, 5, 650-659.
50. Pinhassi J, Winding A, Binnerup S et al. (2003) Spatial variability in bacterioplankton community composition at the Skagerrak-Kattegat front. Marine Ecology Progress Series, 255, 1-13.
51. Pommier T, Pinhassi J, Hagström Å (2005) Biogeography analysis of ribosomal RNA clusters from marine bacterioplankton. Aquatic Microbial Ecology, 41, 79-89.
52. Porter KG, Feig YS (1980) The use of DAPI for identifying and counting aquatic microflora. Limnology and Oceanography, 25, 943-948.
53. Rappé MS, Vergin K, Giovannoni SJ (2000) Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems. FEMS Microbiology Ecology, 33, 219-232.
54. Reche I, Pulido-Villena E, Morales-Baquero R, Casamayor EO (2005) Does ecosystem size determine bacterial richness? Ecology, 86, 1715-1722.
55. Riemann L, Steward GF, Fandino LB et al. (1999) Bacterial community composition during two consecutive NE monsoon periods in the Arabian Sea studied by denaturing gradient gel electrophoresis (DGGE). Deep Sea Research, II (46), 1791-1811.
56. Rocap G, Larimer FW, Lamerdin J et al. (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature, 424, 1042-1047.
57. Selje N, Simon M, Brinkhoff T (2004) A newly discovered Roseobacter cluster in temperate and polar oceans. Nature, 427, 445-448.
58. Stackebrandt E, Göbel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. International Journal of Systematic and Evolutionary Microbiology, 44, 846-849.
59. Staley JT, Gosink JJ (1999) Poles apart: biodiversity and biogeography of sea ice bacteria. Annual Review of Microbiology, 53, 189-215.
60. Swofford DL (2002) PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer Associates, Sunderland, Massachusetts.
61. Taylor MW, Schupp PJ, de Nys R, Kjelleberg S, Steinberg PD (2005) Biogeography of bacteria associated with the marine sponge Cymbastela concentrica. Environmental Microbiology, 7, 419-433.
62. Thingstad F (2000) Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnology and Oceanography, 45, 1320-1328.
63. Venter JC, Remington K, Heidelberg JF et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304, 66-74.
64. Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science, 301, 976-978.
65. Wilson WG, Lundberg P (2004) Biodiversity and the Lotka-Volterra theory of species interactions: open systems and the distribution of logarithmic densities. Proceeding of the Royal Society Series B, 271, 1977-1984.
66. Wintzingerode F, Göbel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples pitfalls of PCR-based RNA analysis. FEMS Microbiological Review, 21, 213-221.
67. Woese CR (1987) Bacterial evolution. Microbiology Reviews, 51, 221-271.
68. Zubkov MV, Fuchs BM, Archer SD et al. (2002) Rapid turnover of dissolved DMS and DMSP by defined bacterioplankton communities in the stratified euphotic zone of the North Sea. Deep Sea Research Part II: Topical Studies in Oceanography, 49, 3017-3038.